TRP channels in calcium homeostasis: from hormonal control to structure-function relationship of TRPV5 and TRPV6.

PubMed

van Goor, Mark K C; Hoenderop, Joost G J; van der Wijst, Jenny

2017-06-01

Maintaining plasma calcium levels within a narrow range is of vital importance for many physiological functions. Therefore, calcium transport processes in the intestine, bone and kidney are tightly regulated to fine-tune the rate of absorption, storage and excretion. The TRPV5 and TRPV6 calcium channels are viewed as the gatekeepers of epithelial calcium transport. Several calciotropic hormones control the channels at the level of transcription, membrane expression, and function. Recent technological advances have provided the first near-atomic resolution structural models of several TRPV channels, allowing insight into their architecture. While this field is still in its infancy, it has increased our understanding of molecular channel regulation and holds great promise for future structure-function studies of these ion channels. This review will summarize the mechanisms that control the systemic calcium balance, as well as extrapolate structural views to the molecular functioning of TRPV5/6 channels in epithelial calcium transport. Copyright © 2016. Published by Elsevier B.V.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

43 CFR 6303.1 - How does BLM carry out administrative and emergency functions?

Code of Federal Regulations, 2011 CFR

2011-10-01

..., motorized equipment, mechanical transport, structures or installations, and land aircraft, in designated... conditions for use of motorized equipment, mechanical transport, aircraft, installations, structures, rock...

43 CFR 6303.1 - How does BLM carry out administrative and emergency functions?

Code of Federal Regulations, 2014 CFR

2014-10-01

..., motorized equipment, mechanical transport, structures or installations, and land aircraft, in designated... conditions for use of motorized equipment, mechanical transport, aircraft, installations, structures, rock...

43 CFR 6303.1 - How does BLM carry out administrative and emergency functions?

Code of Federal Regulations, 2012 CFR

2012-10-01

..., motorized equipment, mechanical transport, structures or installations, and land aircraft, in designated... conditions for use of motorized equipment, mechanical transport, aircraft, installations, structures, rock...

43 CFR 6303.1 - How does BLM carry out administrative and emergency functions?

Code of Federal Regulations, 2013 CFR

2013-10-01

..., motorized equipment, mechanical transport, structures or installations, and land aircraft, in designated... conditions for use of motorized equipment, mechanical transport, aircraft, installations, structures, rock...

CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

PubMed

Huynh, Kevin W; Jiang, Jiansen; Abuladze, Natalia; Tsirulnikov, Kirill; Kao, Liyo; Shao, Xuesi; Newman, Debra; Azimov, Rustam; Pushkin, Alexander; Zhou, Z Hong; Kurtz, Ira

2018-03-02

Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.

Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhongshan; College of Life Sciences, Sichuan University, Chengdu 610065; Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST

2014-09-26

Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane bymore » seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.« less

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System

PubMed Central

Clémençon, Benjamin; Lüscher, Benjamin P.; Fine, Michael; Baumann, Marc U.; Surbek, Daniel V.; Bonny, Olivier; Hediger, Matthias A.

2014-01-01

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies. PMID:25286413

Characterization of Carrier Transport Properties in Strained Crystalline Si Wall-Like Structures as a Function of Scaling into the Quasi-Quantum Regime

DTIC Science & Technology

2017-05-03

AS A FUNCTION OF SCALING INTO THE QUASI -QUANTUM REGIME Naz Islam University of Missouri Electrical and Computer Engineering 319 Engineering...Carrier Transport Properties in Strained Crystalline Si Wall-Like Structures as a Function of Scaling into the Quasi -Quantum Regime 5b. GRANT NUMBER...curves) and their comparisons with experimental data (black dots in both panels......................................... 16 Approved for public

Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure.

PubMed

Bracher, Susanne; Guérin, Kamila; Polyhach, Yevhen; Jeschke, Gunnar; Dittmer, Sophie; Frey, Sabine; Böhm, Maret; Jung, Heinrich

2016-03-04

The available structural information on LeuT and structurally related transporters suggests that external loop 4 (eL4) and the outer end of transmembrane domain (TM) 10' participate in the reversible occlusion of the outer pathway to the solute binding sites. Here, the functional significance of eL4 and the outer region of TM10' are explored using the sodium/proline symporter PutP as a model. Glu-311 at the tip of eL4, and various amino acids around the outer end of TM10' are identified as particularly crucial for function. Substitutions at these sites inhibit the transport cycle, and affect in part ligand binding. In addition, changes at selected sites induce a global structural alteration in the direction of an outward-open conformation. It is suggested that interactions between the tip of eL4 and the peptide backbone at the end of TM10' participate in coordinating conformational alterations underlying the alternating access mechanism of transport. Together with the structural information on LeuT-like transporters, the results further specify the idea that common design and functional principles are maintained across different transport families. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure*

PubMed Central

Bracher, Susanne; Guérin, Kamila; Polyhach, Yevhen; Jeschke, Gunnar; Dittmer, Sophie; Frey, Sabine; Böhm, Maret; Jung, Heinrich

2016-01-01

The available structural information on LeuT and structurally related transporters suggests that external loop 4 (eL4) and the outer end of transmembrane domain (TM) 10′ participate in the reversible occlusion of the outer pathway to the solute binding sites. Here, the functional significance of eL4 and the outer region of TM10′ are explored using the sodium/proline symporter PutP as a model. Glu-311 at the tip of eL4, and various amino acids around the outer end of TM10′ are identified as particularly crucial for function. Substitutions at these sites inhibit the transport cycle, and affect in part ligand binding. In addition, changes at selected sites induce a global structural alteration in the direction of an outward-open conformation. It is suggested that interactions between the tip of eL4 and the peptide backbone at the end of TM10′ participate in coordinating conformational alterations underlying the alternating access mechanism of transport. Together with the structural information on LeuT-like transporters, the results further specify the idea that common design and functional principles are maintained across different transport families. PMID:26728461

Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors*

PubMed Central

Nascimento, Andrey F. Z.; Trindade, Daniel M.; Tonoli, Celisa C. C.; de Giuseppe, Priscila O.; Assis, Leandro H. P.; Honorato, Rodrigo V.; de Oliveira, Paulo S. L.; Mahajan, Pravin; Burgess-Brown, Nicola A.; von Delft, Frank; Larson, Roy E.; Murakami, Mario T.

2013-01-01

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors. PMID:24097982

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.

PubMed

Thomas, James R; Gedeon, Patrick C; Grant, Barry J; Madura, Jeffry D

2012-07-03

Monoamine transporters (MATs) function by coupling ion gradients to the transport of dopamine, norepinephrine, or serotonin. Despite their importance in regulating neurotransmission, the exact conformational mechanism by which MATs function remains elusive. To this end, we have performed seven 250 ns accelerated molecular dynamics simulations of the leucine transporter, a model for neurotransmitter MATs. By varying the presence of binding-pocket leucine substrate and sodium ions, we have sampled plausible conformational states representative of the substrate transport cycle. The resulting trajectories were analyzed using principal component analysis of transmembrane helices 1b and 6a. This analysis revealed seven unique structures: two of the obtained conformations are similar to the currently published crystallographic structures, one conformation is similar to a proposed open inward structure, and four conformations represent novel structures of potential importance to the transport cycle. Further analysis reveals that the presence of binding-pocket sodium ions is necessary to stabilize the locked-occluded and open-inward conformations. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Atomistic full-quantum transport model for zigzag graphene nanoribbon-based structures: Complex energy-band method

NASA Astrophysics Data System (ADS)

Chen, Chun-Nan; Luo, Win-Jet; Shyu, Feng-Lin; Chung, Hsien-Ching; Lin, Chiun-Yan; Wu, Jhao-Ying

2018-01-01

Using a non-equilibrium Green’s function framework in combination with the complex energy-band method, an atomistic full-quantum model for solving quantum transport problems for a zigzag-edge graphene nanoribbon (zGNR) structure is proposed. For transport calculations, the mathematical expressions from the theory for zGNR-based device structures are derived in detail. The transport properties of zGNR-based devices are calculated and studied in detail using the proposed method.

Structural basis of transport function in major facilitator superfamily protein from Trichoderma harzianum.

PubMed

Chaudhary, Nitika; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-02-01

Trichothecenes are the sesquiterpenes secreted by Trichoderma spp. residing in the rhizosphere. These compounds have been reported to act as plant growth promoters and bio-control agents. The structural knowledge for the transporter proteins of their efflux remained limited. In this study, three-dimensional structure of Thmfs1 protein, a trichothecene transporter from Trichoderma harzianum, was homology modelled and further Molecular Dynamics (MD) simulations were used to decipher its mechanism. Fourteen transmembrane helices of Thmfs1 protein are observed contributing to an inward-open conformation. The transport channel and ligand binding sites in Thmfs1 are identified based on heuristic, iterative algorithm and structural alignment with homologous proteins. MD simulations were performed to reveal the differential structural behaviour occurring in the ligand free and ligand bound forms. We found that two discrete trichothecene binding sites are located on either side of the central transport tunnel running from the cytoplasmic side to the extracellular side across the Thmfs1 protein. Detailed analysis of the MD trajectories showed an alternative access mechanism between N and C-terminal domains contributing to its function. These results also demonstrate that the transport of trichodermin occurs via hopping mechanism in which the substrate molecule jumps from one binding site to another lining the transport tunnel. Copyright © 2016 Elsevier B.V. All rights reserved.

The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal

PubMed Central

2017-01-01

Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron–siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron–siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron–siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 Å resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2–3 Å shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs. PMID:29095164

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4;#8201;Å

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Zachary Lee; Cheong, Cheom-Gil; Lee, Seok-Yong

2012-07-11

Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes. A wide range of nucleoside-derived drugs, including anticancer drugsmore » (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 {angstrom}. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.« less

Membrane transporters for the special amino acid glutamine: Structure/function relationships and relevance to human health.

NASA Astrophysics Data System (ADS)

Pochini, Lorena; Scalise, Mariafrancesca; Galluccio, Michele; Indiveri, Cesare

2014-08-01

Glutamine together with glucose is essential for body’s homeostasis. It is the most abundant amino acid and is involved in many biosynthetic, regulatory and energy production processes. Several membrane transporters which differ in transport modes, ensure glutamine homeostasis by coordinating its absorption, reabsorption and delivery to tissues. These transporters belong to different protein families, are redundant and ubiquitous. Their classification, originally based on functional properties, has recently been associated with the SLC nomenclature. Function of glutamine transporters is studied in cells over-expressing the transporters or, more recently in proteoliposomes harboring the proteins extracted from animal tissues or over-expressed in microorganisms. The role of the glutamine transporters is linked to their transport modes and coupling with Na+ and H+. Most transporters share specificity for other neutral or cationic amino acids. Na+-dependent co-transporters efficiently accumulate glutamine while antiporters regulate the pools of glutamine and other amino acids. The most acknowledged glutamine transporters belong to the SLC1, 6, 7 and 38 families. The members involved in the homeostasis are the co-transporters B0AT1 and the SNAT members 1, 2, 3, 5 and 7; the antiporters ASCT2, LAT1 and 2. The last two are associated to the ancillary CD98 protein. Some information on regulation of the glutamine transporters exist, which, however, need to be deepened. No information at all is available on structures, besides some homology models obtained using similar bacterial transporters as templates. Some models of rat and human glutamine transporters highlight very similar structures between the orthologues. Moreover the presence of glycosylation and/or phosphorylation sites located at the extracellular or intracellular faces has been predicted. ASCT2 and LAT1 are over-expressed in several cancers, thus representing potential targets for pharmacological intervention.

Functional, structural and phylogenetic analysis of domains underlying the Al sensitivity of the aluminum-activated malate/anion transporter, TaALMT1.

PubMed

Ligaba, Ayalew; Dreyer, Ingo; Margaryan, Armine; Schneider, David J; Kochian, Leon; Piñeros, Miguel

2013-12-01

Triticum aestivum aluminum-activated malate transporter (TaALMT1) is the founding member of a unique gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small sub-group of root-localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (Al) resistance. TaALMT1 exhibits significant enhancement of transport activity in response to extracellular Al. In this study, we integrated structure-function analyses of structurally altered TaALMT1 proteins expressed in Xenopus oocytes with phylogenic analyses of the ALMT family. Our aim is to re-examine the role of protein domains in terms of their potential involvement in the Al-dependent enhancement (i.e. Al-responsiveness) of TaALMT1 transport activity, as well as the roles of all its 43 negatively charged amino acid residues. Our results indicate that the N-domain, which is predicted to form the conductive pathway, mediates ion transport even in the absence of the C-domain. However, segments in both domains are involved in Al(3+) sensing. We identified two regions, one at the N-terminus and a hydrophobic region at the C-terminus, that jointly contribute to the Al-response phenotype. Interestingly, the characteristic motif at the N-terminus appears to be specific for Al-responsive ALMTs. Our study highlights the need to include a comprehensive phylogenetic analysis when drawing inferences from structure-function analyses, as a significant proportion of the functional changes observed for TaALMT1 are most likely the result of alterations in the overall structural integrity of ALMT family proteins rather than modifications of specific sites involved in Al(3+) sensing. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Electronic and transport properties of Cobalt-based valence tautomeric molecules and polymers

NASA Astrophysics Data System (ADS)

Chen, Yifeng; Calzolari, Arrigo; Buongiorno Nardelli, Marco

2011-03-01

The advancement of molecular spintronics requires further understandings of the fundamental electronic structures and transport properties of prototypical spintronics molecules and polymers. Here we present a density functional based theoretical study of the electronic structures of Cobalt-based valence tautomeric molecules Co III (SQ)(Cat)L Co II (SQ)2 L and their polymers, where SQ refers to the semiquinone ligand, and Cat the catecholate ligand, while L is a redox innocent backbone ligand. The conversion from low-spin Co III ground state to high-spin Co II excited state is realized by imposing an on-site potential U on the Co atom and elongating the Co-N bond. Transport properties are subsequently calculated by extracting electronic Wannier functions from these systems and computing the charge transport in the ballistic regime using a Non-Equilibrium Green's Function (NEGF) approach. Our transport results show distinct charge transport properties between low-spin ground state and high-spin excited state, hence suggesting potential spintronics devices from these molecules and polymers such as spin valves.

Common folds and transport mechanisms of secondary active transporters.

PubMed

Shi, Yigong

2013-01-01

Secondary active transporters exploit the electrochemical potential of solutes to shuttle specific substrate molecules across biological membranes, usually against their concentration gradient. Transporters of different functional families with little sequence similarity have repeatedly been found to exhibit similar folds, exemplified by the MFS, LeuT, and NhaA folds. Observations of multiple conformational states of the same transporter, represented by the LeuT superfamily members Mhp1, AdiC, vSGLT, and LeuT, led to proposals that structural changes are associated with substrate binding and transport. Despite recent biochemical and structural advances, our understanding of substrate recognition and energy coupling is rather preliminary. This review focuses on the common folds and shared transport mechanisms of secondary active transporters. Available structural information generally supports the alternating access model for substrate transport, with variations and extensions made by emerging structural, biochemical, and computational evidence.

Transire, a Program for Generating Solid-State Interface Structures

DTIC Science & Technology

2017-09-14

function-based electron transport property calculator. Three test cases are presented to demonstrate the usage of Transire: the misorientation of the...graphene bilayer, the interface energy as a function of misorientation of copper grain boundaries, and electron transport transmission across the...gallium nitride/silicon carbide interface. 15. SUBJECT TERMS crystalline interface, electron transport, python, computational chemistry, grain boundary

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

Gating Topology of the Proton-Coupled Oligopeptide Symporters

PubMed Central

Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

2015-01-01

Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

Photovoltaic devices based on quantum dot functionalized nanowire arrays embedded in an organic matrix

NASA Astrophysics Data System (ADS)

Kung, Patrick; Harris, Nicholas; Shen, Gang; Wilbert, David S.; Baughman, William; Balci, Soner; Dawahre, Nabil; Butler, Lee; Rivera, Elmer; Nikles, David; Kim, Seongsin M.

2012-01-01

Quantum dot (QD) functionalized nanowire arrays are attractive structures for low cost high efficiency solar cells. QDs have the potential for higher quantum efficiency, increased stability and lifetime compared to traditional dyes, as well as the potential for multiple electron generation per photon. Nanowire array scaffolds constitute efficient, low resistance electron transport pathways which minimize the hopping mechanism in the charge transport process of quantum dot solar cells. However, the use of liquid electrolytes as a hole transport medium within such scaffold device structures have led to significant degradation of the QDs. In this work, we first present the synthesis uniform single crystalline ZnO nanowire arrays and their functionalization with InP/ZnS core-shell quantum dots. The structures are characterized using electron microscopy, optical absorption, photoluminescence and Raman spectroscopy. Complementing photoluminescence, transmission electron microanalysis is used to reveal the successful QD attachment process and the atomistic interface between the ZnO and the QD. Energy dispersive spectroscopy reveals the co-localized presence of indium, phosphorus, and sulphur, suggestive of the core-shell nature of the QDs. The functionalized nanowire arrays are subsequently embedded in a poly-3(hexylthiophene) hole transport matrix with a high degree of polymer infiltration to complete the device structure prior to measurement.

Transportation Safety Analysis

DOT National Transportation Integrated Search

1976-11-01

A conceptual structure was developed for a model expressing transportation accident deaths as a function of transportation activity levels. The literature and data bases were reviewed. A first-level model was developed for the following modes: highwa...

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.

PubMed

Venko, Katja; Roy Choudhury, A; Novič, Marjana

2017-01-01

The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix-helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.

Discovery of CLC transport proteins: cloning, structure, function and pathophysiology

PubMed Central

Jentsch, Thomas J

2015-01-01

Abstract After providing a personal description of the convoluted path leading 25 years ago to the molecular identification of the Torpedo Cl− channel ClC-0 and the discovery of the CLC gene family, I succinctly describe the general structural and functional features of these ion transporters before giving a short overview of mammalian CLCs. These can be categorized into plasma membrane Cl− channels and vesicular Cl−/H+-exchangers. They are involved in the regulation of membrane excitability, transepithelial transport, extracellular ion homeostasis, endocytosis and lysosomal function. Diseases caused by CLC dysfunction include myotonia, neurodegeneration, deafness, blindness, leukodystrophy, male infertility, renal salt loss, kidney stones and osteopetrosis, revealing a surprisingly broad spectrum of biological roles for chloride transport that was unsuspected when I set out to clone the first voltage-gated chloride channel. PMID:25590607

Electronic structure and transport properties of quasi-one-dimensional carbon nanomaterials

NASA Astrophysics Data System (ADS)

Wu, Y. N.; Cheng, P.; Wu, M. J.; Zhu, H.; Xiang, Q.; Ni, J.

2017-09-01

Based on the density functional theory combined with the nonequilibrium Green's function, the influence of the wrinkle on the electronic structures and transport properties of quasi-one-dimensional carbon nanomaterials have been investigated, in which the wrinkled armchair graphene nanoribbons (wAGNRs) and the composite of AGNRs and single walled carbon nanotubes (SWCNTs) were considered with different connection of ripples. The wrinkle adjusts the electronic structures and transport properties of AGNRs. With the change of the strain, the wAGNRs for three width families reveal different electrical behavior. The band gap of AGNR(6) increases in the presence of the wrinkle, which is opposite to that of AGNR(5) and AGNR(7). The transport of AGNRs with the widths 6 or 7 has been modified by the wrinkle, especially by the number of isolated ripples, but it is insensitive to the strain. The nanojunctions constructed by AGNRs and SWCNTs can form the quantum wells, and some specific states are confined in wAGNRs. Although these nanojunctions exhibit the metallic, they have poor conductance due to the wrinkle. The filling of C20 into SWCNT has less influence on the electronic structure and transport of the junctions. The width and connection type of ripples have greatly influenced on the electronic structures and transport properties of quasi-one-dimensional nanomaterials.

Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics.

PubMed

Mullen, Anna; Hall, Jenny; Diegel, Janika; Hassan, Isa; Fey, Adam; MacMillan, Fraser

2016-06-15

During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Transport rates of a glutamate transporter homologue are influenced by the lipid bilayer.

PubMed

McIlwain, Benjamin C; Vandenberg, Robert J; Ryan, Renae M

2015-04-10

The aspartate transporter from Pyrococcus horikoshii (GltPh) is a model for the structure of the SLC1 family of amino acid transporters. Crystal structures of GltPh provide insight into mechanisms of ion coupling and substrate transport; however, structures have been solved in the absence of a lipid bilayer so they provide limited information regarding interactions that occur between the protein and lipids of the membrane. Here, we investigated the effect of the lipid environment on aspartate transport by reconstituting GltPh into liposomes of defined lipid composition where the primary lipid is phosphatidylethanolamine (PE) or its methyl derivatives. We showed that the rate of aspartate transport and the transmembrane orientation of GltPh were influenced by the primary lipid in the liposomes. In PE liposomes, we observed the highest transport rate and showed that 85% of the transporters were orientated right-side out, whereas in trimethyl PE liposomes, 50% of transporters were right-side out, and we observed a 4-fold reduction in transport rate. Differences in orientation can only partially explain the lipid composition effect on transport rate. Crystal structures of GltPh revealed a tyrosine residue (Tyr-33) that we propose interacts with lipid headgroups during the transport cycle. Based on site-directed mutagenesis, we propose that a cation-π interaction between Tyr-33 and the lipid headgroups can influence conformational flexibility of the trimerization domain and thus the rate of transport. These results provide a specific example of how interactions between membrane lipids and membrane-bound proteins can influence function and highlight the importance of the role of the membrane in transporter function. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Transport Rates of a Glutamate Transporter Homologue Are Influenced by the Lipid Bilayer*

PubMed Central

McIlwain, Benjamin C.; Vandenberg, Robert J.; Ryan, Renae M.

2015-01-01

The aspartate transporter from Pyrococcus horikoshii (GltPh) is a model for the structure of the SLC1 family of amino acid transporters. Crystal structures of GltPh provide insight into mechanisms of ion coupling and substrate transport; however, structures have been solved in the absence of a lipid bilayer so they provide limited information regarding interactions that occur between the protein and lipids of the membrane. Here, we investigated the effect of the lipid environment on aspartate transport by reconstituting GltPh into liposomes of defined lipid composition where the primary lipid is phosphatidylethanolamine (PE) or its methyl derivatives. We showed that the rate of aspartate transport and the transmembrane orientation of GltPh were influenced by the primary lipid in the liposomes. In PE liposomes, we observed the highest transport rate and showed that 85% of the transporters were orientated right-side out, whereas in trimethyl PE liposomes, 50% of transporters were right-side out, and we observed a 4-fold reduction in transport rate. Differences in orientation can only partially explain the lipid composition effect on transport rate. Crystal structures of GltPh revealed a tyrosine residue (Tyr-33) that we propose interacts with lipid headgroups during the transport cycle. Based on site-directed mutagenesis, we propose that a cation-π interaction between Tyr-33 and the lipid headgroups can influence conformational flexibility of the trimerization domain and thus the rate of transport. These results provide a specific example of how interactions between membrane lipids and membrane-bound proteins can influence function and highlight the importance of the role of the membrane in transporter function. PMID:25713135

The structural basis of secondary active transport mechanisms.

PubMed

Forrest, Lucy R; Krämer, Reinhard; Ziegler, Christine

2011-02-01

Secondary active transporters couple the free energy of the electrochemical potential of one solute to the transmembrane movement of another. As a basic mechanistic explanation for their transport function the model of alternating access was put forward more than 40 years ago, and has been supported by numerous kinetic, biochemical and biophysical studies. According to this model, the transporter exposes its substrate binding site(s) to one side of the membrane or the other during transport catalysis, requiring a substantial conformational change of the carrier protein. In the light of recent structural data for a number of secondary transport proteins, we analyze the model of alternating access in more detail, and correlate it with specific structural and chemical properties of the transporters, such as their assignment to different functional states in the catalytic cycle of the respective transporter, the definition of substrate binding sites, the type of movement of the central part of the carrier harboring the substrate binding site, as well as the impact of symmetry on fold-specific conformational changes. Besides mediating the transmembrane movement of solutes, the mechanism of secondary carriers inherently involves a mechanistic coupling of substrate flux to the electrochemical potential of co-substrate ions or solutes. Mainly because of limitations in resolution of available transporter structures, this important aspect of secondary transport cannot yet be substantiated by structural data to the same extent as the conformational change aspect. We summarize the concepts of coupling in secondary transport and discuss them in the context of the available evidence for ion binding to specific sites and the impact of the ions on the conformational state of the carrier protein, which together lead to mechanistic models for coupling. Copyright © 2010 Elsevier B.V. All rights reserved.

Monitoring the function of membrane transport proteins in detergent-solubilized form

PubMed Central

Quick, Matthias; Javitch, Jonathan A.

2007-01-01

Transport proteins constitute ≈10% of most proteomes and play vital roles in the translocation of solutes across membranes of all organisms. Their (dys)function is implicated in many disorders, making them frequent targets for pharmacotherapy. The identification of substrates for members of this large protein family, still replete with many orphans of unknown function, has proven difficult, in part because high-throughput screening is greatly complicated by endogenous transporters present in many expression systems. In addition, direct structural studies require that transporters be extracted from the membrane with detergent, thereby precluding transport measurements because of the lack of a vectorial environment and necessitating reconstitution into proteoliposomes for activity measurements. Here, we describe a direct scintillation proximity-based radioligand-binding assay for determining transport protein function in crude cell extracts and in purified form. This rapid and universally applicable assay with advantages over cell-based platforms will greatly facilitate the identification of substrates for many orphan transporters and allows monitoring the function of transport proteins in a nonmembranous environment. PMID:17360689

Structure and function of Neisseria gonorrhoeae MtrF illuminates a class of antimetabolite efflux pumps

DOE PAGES

Su, Chih -Chia; Bolla, Jani  Reddy; Kumar, Nitin; ...

2015-04-01

Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein that belongs to the AbgT family of transporters for which no structural information is available. Here, we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm tomore » halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins, posing a plausible pathway for substrate transport. A combination of the crystal structure and biochemical functional assays suggests that MtrF is an antibiotic efflux pump mediating bacterial resistance to sulfonamide antimetabolite drugs.« less

Structure and function of Neisseria gonorrhoeae MtrF illuminates a class of antimetabolite efflux pumps

PubMed Central

Su, Chih-Chia; Bolla, Jani Reddy; Kumar, Nitin; Radhakrishnan, Abhijith; Long, Feng; Delmar, Jared A.; Chou, Tsung-Han; Rajashankar, Kanagalaghatta R.; Shafer, William M.; Yu, Edward W.

2015-01-01

SUMMARY Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually-transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein, which belongs to the AbgT family of transporters for which no structural information is available. Here we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins, posing a plausible pathway for substrate transport. A combination of the crystal structure and biochemical functional assays suggests that MtrF is an antibiotic efflux pump, mediating bacterial resistance to sulfonamide antimetabolite drugs. PMID:25818299

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

PubMed Central

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-01-01

The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective.

PubMed

Greene, Nicholas P; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.

Structure of a CLC chloride ion channel by cryo-electron microscopy

PubMed Central

Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

2017-01-01

CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

PubMed Central

Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

2014-01-01

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

Stochastic steps in secondary active sugar transport

PubMed Central

Adelman, Joshua L.; Ghezzi, Chiara; Bisignano, Paola; Loo, Donald D. F.; Choe, Seungho; Abramson, Jeff; Rosenberg, John M.; Wright, Ernest M.; Grabe, Michael

2016-01-01

Secondary active transporters, such as those that adopt the leucine-transporter fold, are found in all domains of life, and they have the unique capability of harnessing the energy stored in ion gradients to accumulate small molecules essential for life as well as expel toxic and harmful compounds. How these proteins couple ion binding and transport to the concomitant flow of substrates is a fundamental structural and biophysical question that is beginning to be answered at the atomistic level with the advent of high-resolution structures of transporters in different structural states. Nonetheless, the dynamic character of the transporters, such as ion/substrate binding order and how binding triggers conformational change, is not revealed from static structures, yet it is critical to understanding their function. Here, we report a series of molecular simulations carried out on the sugar transporter vSGLT that lend insight into how substrate and ions are released from the inward-facing state of the transporter. Our simulations reveal that the order of release is stochastic. Functional experiments were designed to test this prediction on the human homolog, hSGLT1, and we also found that cytoplasmic release is not ordered, but we confirmed that substrate and ion binding from the extracellular space is ordered. Our findings unify conflicting published results concerning cytoplasmic release of ions and substrate and hint at the possibility that other transporters in the superfamily may lack coordination between ions and substrate in the inward-facing state. PMID:27325773

Stochastic steps in secondary active sugar transport.

PubMed

Adelman, Joshua L; Ghezzi, Chiara; Bisignano, Paola; Loo, Donald D F; Choe, Seungho; Abramson, Jeff; Rosenberg, John M; Wright, Ernest M; Grabe, Michael

2016-07-05

Secondary active transporters, such as those that adopt the leucine-transporter fold, are found in all domains of life, and they have the unique capability of harnessing the energy stored in ion gradients to accumulate small molecules essential for life as well as expel toxic and harmful compounds. How these proteins couple ion binding and transport to the concomitant flow of substrates is a fundamental structural and biophysical question that is beginning to be answered at the atomistic level with the advent of high-resolution structures of transporters in different structural states. Nonetheless, the dynamic character of the transporters, such as ion/substrate binding order and how binding triggers conformational change, is not revealed from static structures, yet it is critical to understanding their function. Here, we report a series of molecular simulations carried out on the sugar transporter vSGLT that lend insight into how substrate and ions are released from the inward-facing state of the transporter. Our simulations reveal that the order of release is stochastic. Functional experiments were designed to test this prediction on the human homolog, hSGLT1, and we also found that cytoplasmic release is not ordered, but we confirmed that substrate and ion binding from the extracellular space is ordered. Our findings unify conflicting published results concerning cytoplasmic release of ions and substrate and hint at the possibility that other transporters in the superfamily may lack coordination between ions and substrate in the inward-facing state.

Molecular Aspects of Structure, Gating, and Physiology of pH-Sensitive Background K2P and Kir K+-Transport Channels

PubMed Central

Sepúlveda, Francisco V.; Pablo Cid, L.; Teulon, Jacques; Niemeyer, María Isabel

2015-01-01

K+ channels fulfill roles spanning from the control of excitability to the regulation of transepithelial transport. Here we review two groups of K+ channels, pH-regulated K2P channels and the transport group of Kir channels. After considering advances in the molecular aspects of their gating based on structural and functional studies, we examine their participation in certain chosen physiological and pathophysiological scenarios. Crystal structures of K2P and Kir channels reveal rather unique features with important consequences for the gating mechanisms. Important tasks of these channels are discussed in kidney physiology and disease, K+ homeostasis in the brain by Kir channel-equipped glia, and central functions in the hearing mechanism in the inner ear and in acid secretion by parietal cells in the stomach. K2P channels fulfill a crucial part in central chemoreception probably by virtue of their pH sensitivity and are central to adrenal secretion of aldosterone. Finally, some unorthodox behaviors of the selectivity filters of K2P channels might explain their normal and pathological functions. Although a great deal has been learned about structure, molecular details of gating, and physiological functions of K2P and Kir K+-transport channels, this has been only scratching at the surface. More molecular and animal studies are clearly needed to deepen our knowledge. PMID:25540142

Comparison of mechanistic transport cycle models of ABC exporters.

PubMed

Szöllősi, Dániel; Rose-Sperling, Dania; Hellmich, Ute A; Stockner, Thomas

2018-04-01

ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. "This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain." Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Transport characteristics of mammalian Rh and Rh glycoproteins expressed in heterologous systems.

PubMed

Westhoff, C M; Wylie, D E

2006-01-01

The development and use of heterologous expression systems is critical for deciphering the function of mammalian Rh and Rh-glycoproteins. The studies here use Xenopus oocytes, well known for their ability to readily traffic and express difficult membrane proteins, and S. cerevisiae wild-type strains and mutants that are defective in ammonium transport. Data obtained in both of these expression systems revealed that mammalian Rh-glycoprotein-mediated transport (RhAG, RhBG, and RhCG) is an electroneutral process that is driven by the NH4+ concentration and the transmembrane H+ gradient, effectively exchanging NH4+ for H+ in a process that results in transport of net NH3. Homology modeling and functional studies suggest that the more recently evolved erythrocyte blood group proteins, RhCE and RhD, may not function directly in ammonia transport and may be evolving a new function in the RBC membrane. The relationship of Rh and Rh-glycoproteins to the Amt/Mep ammonium transporters is substantiated with functional transport data and structural modeling.

Structural rearrangements at the translocation pore of the human glutamate transporter, EAAT1.

PubMed

Leighton, Barbara H; Seal, Rebecca P; Watts, Spencer D; Skyba, Mary O; Amara, Susan G

2006-10-06

Structure-function studies of mammalian and bacterial excitatory amino acid transporters (EAATs), as well as the crystal structure of a related archaeal glutamate transporter, support a model in which TM7, TM8, and the re-entrant loops HP1 and HP2 participate in forming a substrate translocation pathway within each subunit of a trimer. However, the transport mechanism, including precise binding sites for substrates and co-transported ions and changes in the tertiary structure underlying transport, is still not known. In this study, we used chemical cross-linking of introduced cysteine pairs in a cysteine-less version of EAAT1 to examine the dynamics of key domains associated with the translocation pore. Here we show that cysteine substitution at Ala-395, Ala-367, and Ala-440 results in functional single and double cysteine transporters and that in the absence of glutamate or dl-threo-beta-benzyloxyaspartate (dl-TBOA), A395C in the highly conserved TM7 can be cross-linked to A367C in HP1 and to A440C in HP2. The formation of these disulfide bonds is reversible and occurs intra-molecularly. Interestingly, cross-linking A395C to A367C appears to abolish transport, whereas cross-linking A395C to A440C lowers the affinities for glutamate and dl-TBOA but does not change the maximal transport rate. Additionally, glutamate and dl-TBOA binding prevent cross-linking in both double cysteine transporters, whereas sodium binding facilitates cross-linking in the A395C/A367C transporter. These data provide evidence that within each subunit of EAAT1, Ala-395 in TM7 resides close to a residue at the tip of each re-entrant loop (HP1 and HP2) and that these residues are repositioned relative to one another at different steps in the transport cycle. Such behavior likely reflects rearrangements in the tertiary structure of the translocation pore during transport and thus provides constraints for modeling the structural dynamics associated with transport.

Study on the Electronic Transport Properties of Zigzag GaN Nanotubes

NASA Astrophysics Data System (ADS)

Li, Enling; Wang, Xiqiang; Hou, Liping; Zhao, Danna; Dai, Yuanbin; Wang, Xuewen

2011-02-01

The electronic transport properties of zigzag GaN nanotubes (n, 0) (4 <= n <= 9) have been calculated using the density functional theory and non-equilibrium Green's functions method. Firstly, the density functional theory (DFT) is used to optimize and calculate the electronic structure of GaNNTs (n, 0) (4<=n<=9). Secondly, DFT and non-equilibrium Green function (NEGF) method are also used to predict the electronic transport properties of GaNNTs two-probe system. The results showed: there is a corresponding relation between the electronic transport properties and the valley of state density of each GaNNT. In addition, the volt-ampere curve of GaNNT is approximately linear.

Cys Site-Directed Mutagenesis of the Human SLC1A5 (ASCT2) Transporter: Structure/Function Relationships and Crucial Role of Cys467 for Redox Sensing and Glutamine Transport

PubMed Central

Scalise, Mariafrancesca; Pochini, Lorena; Console, Lara; Pappacoda, Gilda; Pingitore, Piero; Hedfalk, Kristina; Indiveri, Cesare

2018-01-01

The human plasma membrane transporter ASCT2 is responsible for mediating Na- dependent antiport of neutral amino acids. New insights into structure/function relationships were unveiled by a combined approach of recombinant over-expression, site-directed mutagenesis, transport assays in proteoliposomes and bioinformatics. WT and Cys mutants of hASCT2 were produced in P. pastoris and purified for functional assay. The reactivity towards SH reducing and oxidizing agents of WT protein was investigated and opposite effects were revealed; transport activity increased upon treatment with the Cys reducing agent DTE, i.e., when Cys residues were in thiol (reduced) state. Methyl-Hg, which binds to SH groups, was able to inhibit WT and seven out of eight Cys to Ala mutants. On the contrary, C467A loses the sensitivity to both DTE activation and Methyl-Hg inhibition. The C467A mutant showed a Km for Gln one order of magnitude higher than that of WT. Moreover, the C467 residue is localized in the substrate binding region of the protein, as suggested by bioinformatics on the basis of the EAAT1 structure comparison. Taken together, the experimental data allowed identifying C467 residue as crucial for substrate binding and for transport activity modulation of hASCT2. PMID:29495336

Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.

PubMed

Tanaka, Yoshiki; Iwaki, Shigehiro; Tsukazaki, Tomoya

2017-09-05

The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.

The FapF amyloid secretion transporter possesses an atypical asymmetric coiled coil.

PubMed

Rouse, Sarah L; Stylianou, Fisentzos; Grace Wu, H Y; Berry, Jamie-Lee; Sewell, Lee; Morgan, R Marc L; Sauerwein, Andrea C; Matthews, Steve

2018-06-07

Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits, the fibres of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialised outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8 Å resolution. This domain forms a novel asymmetric trimeric coiled-coil that possesses a single buried tyrosine residue as well as a extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail. Copyright © 2018. Published by Elsevier Ltd.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

PubMed

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

EHD proteins: Key conductors of endocytic transport

PubMed Central

Naslavsky, Naava; Caplan, Steve

2010-01-01

Regulation of endocytic transport is controlled by an elaborate network of proteins. Rab GTP-binding proteins and their effectors have well-defined roles in mediating specific endocytic transport steps, but until recently, less was known about the four mammalian dynamin-like C-terminal Eps15 Homology Domain (EHD) proteins that also regulate endocytic events. In recent years, however, great strides have been made in understanding the structure and function of these unique proteins. Indeed, a growing body of literature addresses EHD protein structure, interactions with binding partners, functions in mammalian cells, and the generation of various new model systems. Accordingly, this is now an opportune time to pause and review the function and mechanisms of action of EHD proteins, and to highlight some of the challenges and future directions for the field. PMID:21067929

Mapping of the minimal inorganic phosphate transporting unit of human PiT2 suggests a structure universal to PiT-related proteins from all kingdoms of life

PubMed Central

2011-01-01

Background The inorganic (Pi) phosphate transporter (PiT) family comprises known and putative Na+- or H+-dependent Pi-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with Pi to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na+-dependent Pi (NaPi) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins. Results We show that the human PiT2 histidine, H502, and the human PiT1 glutamate, E70, - both conserved in eukaryotic PiT family members - are critical for Pi transport function. Noticeably, human PiT2 H502 is located in the C-terminal PiT family signature sequence, and human PiT1 E70 is located in ProDom domains characteristic for all PiT family members. A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR254-V483), was found to be a fully functional Pi transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL183-V483) did also support Pi transport albeit at very low levels. Conclusions The results suggest that the overall structure of the Pi-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship. PMID:21586110

Mapping of the minimal inorganic phosphate transporting unit of human PiT2 suggests a structure universal to PiT-related proteins from all kingdoms of life.

PubMed

Bøttger, Pernille; Pedersen, Lene

2011-05-17

The inorganic (Pi) phosphate transporter (PiT) family comprises known and putative Na(+)- or H(+)-dependent Pi-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with Pi to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na(+)-dependent P(i) (NaP(i)) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins. We show that the human PiT2 histidine, H(502), and the human PiT1 glutamate, E(70),--both conserved in eukaryotic PiT family members--are critical for P(i) transport function. Noticeably, human PiT2 H(502) is located in the C-terminal PiT family signature sequence, and human PiT1 E(70) is located in ProDom domains characteristic for all PiT family members.A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR(254)-V(483)), was found to be a fully functional P(i) transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL(183)-V(483)) did also support P(i) transport albeit at very low levels. The results suggest that the overall structure of the P(i)-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship. © 2011 Bøttger and Pedersen; licensee BioMed Central Ltd.

Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family

PubMed Central

Ehrnstorfer, Ines A.; Manatschal, Cristina; Arnold, Fabian M.; Laederach, Juerg; Dutzler, Raimund

2017-01-01

Secondary active transporters of the SLC11/NRAMP family catalyse the uptake of iron and manganese into cells. These proteins are highly conserved across all kingdoms of life and thus likely share a common transport mechanism. Here we describe the structural and functional properties of the prokaryotic SLC11 transporter EcoDMT. Its crystal structure reveals a previously unknown outward-facing state of the protein family. In proteoliposomes EcoDMT mediates proton-coupled uptake of manganese at low micromolar concentrations. Mutants of residues in the transition-metal ion-binding site severely affect transport, whereas a mutation of a conserved histidine located near this site results in metal ion transport that appears uncoupled to proton transport. Combined with previous results, our study defines the conformational changes underlying transition-metal ion transport in the SLC11 family and it provides molecular insight to its coupling to protons. PMID:28059071

Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1.

PubMed

Singh, Natesh; Ecker, Gerhard F

2018-04-24

The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood⁻Brain Barrier (BBB) where it facilitates the transport of thyroid hormones, pharmaceuticals (e.g., l-DOPA, gabapentin), and metabolites into the brain. Moreover, its expression is highly upregulated in various types of human cancer that are characterized by an intense demand for amino acids for growth and proliferation. Therefore, LAT1 is believed to be an important drug target for cancer treatment. With the crystallization of the arginine/agmatine antiporter (AdiC) from Escherichia Coli , numerous homology models of LAT1 have been built to elucidate the substrate binding site, ligand⁻transporter interaction, and structure⁻function relationship. The use of these models in combination with molecular docking and experimental testing has identified novel chemotypes of ligands of LAT1. Here, we highlight the structure, function, transport mechanism, and homology modeling of LAT1. Additionally, results from structure⁻function studies performed on LAT1 are addressed, which have enhanced our knowledge of the mechanism of substrate binding and translocation. This is followed by a discussion on ligand- and structure-based approaches, with an emphasis on elucidating the molecular basis of LAT1 inhibition. Finally, we provide an exhaustive summary of different LAT1 inhibitors that have been identified so far, including the recently discovered irreversible covalent inhibitors.

Transport According to GARP: Receiving Retrograde Cargo at the Trans-Golgi Network

PubMed Central

Bonifacino, Juan S.; Hierro, Aitor

2010-01-01

Tethering factors are large protein complexes that capture transport vesicles and enable their fusion with acceptor organelles at different stages of the endomembrane system. Recent studies have shed new light on the structure and function of a heterotetrameric tethering factor named Golgi-associated retrograde protein (GARP), which promotes fusion of endosome-derived, retrograde transport carriers to the trans-Golgi network (TGN). X-ray crystallography of the Vps53 and Vps54 subunits of GARP has revealed that this complex is structurally related to other tethering factors such as the exocyst, COG and Dsl1, indicating that they all might work by a similar mechanism. Loss of GARP function compromises the growth, fertility and/or viability of the defective organisms, underscoring the essential nature of GARP-mediated retrograde transport. PMID:21183348

Structural basis for the blockade of MATE multidrug efflux pumps

DOE PAGES

Radchenko, Martha; Symersky, Jindrich; Nie, Rongxin; ...

2015-08-06

Multidrug and toxic compound extrusion (MATE) transporters underpin multidrug resistance by using the H + or Na + electrochemical gradient to extrude different drugs across cell membranes. MATE transporters can be further parsed into the DinF, NorM and eukaryotic subfamilies based on their amino-acid sequence similarity. Here we report the 3.0 Å resolution X-ray structures of a protonation-mimetic mutant of an H +-coupled DinF transporter, as well as of an H +-coupled DinF and a Na +-coupled NorM transporters in complexes with verapamil, a small-molecule pharmaceutical that inhibits MATE-mediated multidrug extrusion. Combining structure-inspired mutational and functional studies, we confirm themore » biological relevance of our crystal structures, reveal the mechanistic differences among MATE transporters, and suggest how verapamil inhibits MATE-mediated multidrug efflux. Our findings offer insights into how MATE transporters extrude chemically and structurally dissimilar drugs and could inform the design of new strategies for tackling multidrug resistance.« less

Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

NASA Astrophysics Data System (ADS)

Zhang, Tuo; Sui, Dexin; Hu, Jian

2016-06-01

The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins.

Tripartite ATP-independent Periplasmic (TRAP) Transporters Use an Arginine-mediated Selectivity Filter for High Affinity Substrate Binding*

PubMed Central

Fischer, Marcus; Hopkins, Adam P.; Severi, Emmanuele; Hawkhead, Judith; Bawdon, Daniel; Watts, Andrew G.; Hubbard, Roderick E.; Thomas, Gavin H.

2015-01-01

Tripartite ATP-independent periplasmic (TRAP) transporters are secondary transporters that have evolved an obligate dependence on a substrate-binding protein (SBP) to confer unidirectional transport. Different members of the DctP family of TRAP SBPs have binding sites that recognize a diverse range of organic acid ligands but appear to only share a common electrostatic interaction between a conserved arginine and a carboxylate group in the ligand. We investigated the significance of this interaction using the sialic acid-specific SBP, SiaP, from the Haemophilus influenzae virulence-related SiaPQM TRAP transporter. Using in vitro, in vivo, and structural methods applied to SiaP, we demonstrate that the coordination of the acidic ligand moiety of sialic acid by the conserved arginine (Arg-147) is essential for the function of the transporter as a high affinity scavenging system. However, at high substrate concentrations, the transporter can function in the absence of Arg-147 suggesting that this bi-molecular interaction is not involved in further stages of the transport cycle. As well as being required for high affinity binding, we also demonstrate that the Arg-147 is a strong selectivity filter for carboxylate-containing substrates in TRAP transporters by engineering the SBP to recognize a non-carboxylate-containing substrate, sialylamide, through water-mediated interactions. Together, these data provide biochemical and structural support that TRAP transporters function predominantly as high affinity transporters for carboxylate-containing substrates. PMID:26342690

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective

PubMed Central

Greene, Nicholas P.; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking. PMID:29892271

Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations.

PubMed

Yamane, Tsutomu; Murakami, Satoshi; Ikeguchi, Mitsunori

2013-10-29

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

A structure-function analysis of ion transport in crustacean gills and excretory organs.

PubMed

Freire, Carolina A; Onken, Horst; McNamara, John C

2008-11-01

Osmotic and ionic regulation in the Crustacea is mostly accomplished by the multifunctional gills, together with the excretory organs. In addition to their role in gas exchange, the gills constitute organs of active, transepithelial, ion transport, an activity of major importance that underlies many essential physiological functions like osmoregulation, calcium homeostasis, ammonium excretion and extracellular pH regulation. This review focuses on structure-function relationships in crustacean gills and excretory effectors, from the organ to molecular levels of organization. We address the diversity of structural architectures encountered in different crustacean gill types, and in constituent cell types, before examining the physiological mechanisms of Na(+), Cl(-), Ca(2+) and NH(4)(+) transport, and of acid-base equivalents, based on findings obtained over the last two decades employing advanced techniques. The antennal and maxillary glands constitute the principal crustacean excretory organs, which have received less attention in functional studies. We examine the diversity present in antennal and maxillary gland architecture, highlighting the structural similarities between both organ types, and we analyze the functions ascribed to each glandular segment. Emphasis is given to volume and osmoregulatory functions, capacity to produce dilute urine in freshwater crustaceans, and the effect of acclimation salinity on urine volume and composition. The microanatomy and diversity of function ascribed to gills and excretory organs are appraised from an evolutionary perspective, and suggestions made as to future avenues of investigation that may elucidate evolutionary and adaptive trends underpinning the invasion and exploitation of novel habitats.

Electronic Structure and Transport in Solids from First Principles

NASA Astrophysics Data System (ADS)

Mustafa, Jamal Ibrahim

The focus of this dissertation is the determination of the electronic structure and trans- port properties of solids. We first review some of the theory and computational methodology used in the calculation of electronic structure and materials properties. Throughout the dissertation, we make extensive use of state-of-the-art software packages that implement density functional theory, density functional perturbation theory, and the GW approximation, in addition to specialized methods for interpolating matrix elements for extremely accurate results. The first application of the computational framework introduced is the determination of band offsets in semiconductor heterojunctions using a theory of quantum dipoles at the interface. This method is applied to the case of heterojunction formed between a new metastable phase of silicon, with a rhombohedral structure, and cubic silicon. Next, we introduce a novel method for the construction of localized Wannier functions, which we have named the optimized projection functions method (OPFM). We illustrate the method on a variety of systems and find that it can reliably construct localized Wannier functions with minimal user intervention. We further develop the OPFM to investigate a class of materials called topological insulators, which are insulating in the bulk but have conductive surface states. These properties are a result of a nontrivial topology in their band structure, which has interesting effects on the character of the Wannier functions. In the last sections of the main text, the noble metals are studied in great detail, including their electronic properties and carrier dynamics. In particular, we investigate, the Fermi surface properties of the noble metals, specifically electron-phonon scattering lifetimes, and subsequently the transport properties determined by carriers on the Fermi surface. To achieve this, a novel sampling technique is developed, with wide applicability to transport calculations. Additionally, the generation and transport of hot carriers is studied extensively. The distribution of hot carriers generated from the decay of plasmons is explored over a range of energy, and the transport properties, particularly the lifetimes and mean-free-paths, of the hot carriers are determined. Lastly, appendices detailing the implementation of the algorithms developed in the work is presented, along with a useful derivation of the electron-plasmon matrix elements.

Probing plasmodesmata function with biochemical inhibitors.

PubMed

White, Rosemary G

2015-01-01

To investigate plasmodesmata (PD) function, a useful technique is to monitor the effect on cell-to-cell transport of applying an inhibitor of a physiological process, protein, or other cell component of interest. Changes in PD transport can then be monitored in one of several ways, most commonly by measuring the cell-to-cell movement of fluorescent tracer dyes or of free fluorescent proteins. Effects on PD structure can be detected in thin sections of embedded tissue observed using an electron microscope, most commonly a Transmission Electron Microscope (TEM). This chapter outlines commonly used inhibitors, methods for treating different tissues, how to detect altered cell-to-cell transport and PD structure, and important caveats.

Comparative physiology and architecture associated with the mammalian urine concentrating mechanism: role of inner medullary water and urea transport pathways in the rodent medulla.

PubMed

Pannabecker, Thomas L

2013-04-01

Comparative studies of renal structure and function have potential to provide insights into the urine-concentrating mechanism of the mammalian kidney. This review focuses on the tubular transport pathways for water and urea that play key roles in fluid and solute movements between various compartments of the rodent renal inner medulla. Information on aquaporin water channel and urea transporter expression has increased our understanding of functional segmentation of medullary thin limbs of Henle's loops, collecting ducts, and vasa recta. A more complete understanding of membrane transporters and medullary architecture has identified new and potentially significant interactions between these structures and the interstitium. These interactions are now being introduced into our concept of how the inner medullary urine-concentrating mechanism works. A variety of regulatory pathways lead directly or indirectly to variable patterns of fluid and solute movements among the interstitial and tissue compartments. Animals with the ability to produce highly concentrated urine, such as desert species, are considered to exemplify tubular structure and function that optimize urine concentration. These species may provide unique insights into the urine-concentrating process.(1)

Comparative physiology and architecture associated with the mammalian urine concentrating mechanism: role of inner medullary water and urea transport pathways in the rodent medulla

PubMed Central

2013-01-01

Comparative studies of renal structure and function have potential to provide insights into the urine-concentrating mechanism of the mammalian kidney. This review focuses on the tubular transport pathways for water and urea that play key roles in fluid and solute movements between various compartments of the rodent renal inner medulla. Information on aquaporin water channel and urea transporter expression has increased our understanding of functional segmentation of medullary thin limbs of Henle's loops, collecting ducts, and vasa recta. A more complete understanding of membrane transporters and medullary architecture has identified new and potentially significant interactions between these structures and the interstitium. These interactions are now being introduced into our concept of how the inner medullary urine-concentrating mechanism works. A variety of regulatory pathways lead directly or indirectly to variable patterns of fluid and solute movements among the interstitial and tissue compartments. Animals with the ability to produce highly concentrated urine, such as desert species, are considered to exemplify tubular structure and function that optimize urine concentration. These species may provide unique insights into the urine-concentrating process.1 PMID:23364530

Structural and electronic properties of copper-doped chalcogenide glasses

NASA Astrophysics Data System (ADS)

Guzman, David M.; Strachan, Alejandro

2017-10-01

Using ab initio molecular dynamics based on density functional theory, we study the atomic and electronic structure, and transport properties of copper-doped germanium-based chalcogenide glasses. These mixed ionic-electronic conductor materials exhibit resistance or threshold switching under external electric field depending on slight variations of chemical composition. Understanding the origin of the transport character is essential for the functionalization of glassy chalcogenides for nanoelectronics applications. To this end, we generated atomic structures for GeX3 and GeX6 (X = S, Se, Te) at different copper concentrations and characterized the atomic origin of electronic states responsible for transport and the tendency of copper clustering as a function of metal concentration. Our results show that copper dissolution energies explain the tendency of copper to agglomerate in telluride glasses, consistent with filamentary conduction. In contrast, copper is less prone to cluster in sulfides and selenides leading to hysteresisless threshold switching where the nature of transport is dominated by electronic midgap defects derived from polar chalcogen bonds and copper atoms. Simulated I -V curves show that at least 35% by weight of copper is required to achieve the current demands of threshold-based devices for memory applications.

Use of a Molecular Decoy to Segregate Transport from Antigenicity in the FrpB Iron Transporter from Neisseria meningitidis

PubMed Central

Saleem, Muhammad; Prince, Stephen M.; Rigby, Stephen E. J.; Imran, Muhammad; Patel, Hema; Chan, Hannah; Sanders, Holly; Maiden, Martin C. J.; Feavers, Ian M.; Derrick, Jeremy P.

2013-01-01

FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT) family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe3+ with high affinity. EPR spectra of the bound Fe3+ ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe3+ binding was reduced or abolished on mutation of the Fe3+-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe3+. The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a ‘molecular decoy’ to distract immune surveillance. PMID:23457610

Use of a molecular decoy to segregate transport from antigenicity in the FrpB iron transporter from Neisseria meningitidis.

PubMed

Saleem, Muhammad; Prince, Stephen M; Rigby, Stephen E J; Imran, Muhammad; Patel, Hema; Chan, Hannah; Sanders, Holly; Maiden, Martin C J; Feavers, Ian M; Derrick, Jeremy P

2013-01-01

FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT) family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe(3+) with high affinity. EPR spectra of the bound Fe(3+) ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe(3+) binding was reduced or abolished on mutation of the Fe(3+)-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe(3+). The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a 'molecular decoy' to distract immune surveillance.

The best thermoelectric.

PubMed Central

Mahan, G D; Sofo, J O

1996-01-01

What electronic structure provides the largest figure of merit for thermoelectric materials? To answer that question, we write the electrical conductivity, thermopower, and thermal conductivity as integrals of a single function, the transport distribution. Then we derive the mathematical function for the transport distribution, which gives the largest figure of merit. A delta-shaped transport distribution is found to maximize the thermoelectric properties. This result indicates that a narrow distribution of the energy of the electrons participating in the transport process is needed for maximum thermoelectric efficiency. Some possible realizations of this idea are discussed. PMID:11607692

The structure and function of the dopamine transporter and its role in CNS diseases.

PubMed

McHugh, Patrick C; Buckley, David A

2015-01-01

In this chapter, we explore the basic science of the dopamine transporter (DAT), an integral component of a system that regulates dopamine homeostasis. Dopamine is a key neurotransmitter for several brain functions including locomotor control and reward systems. The transporter structure, function, mechanism of action, localization, and distribution, in addition to gene regulation, are discussed. Over many years, a wealth of information concerning the DAT has been accrued and has led to increased interest in the role of the DAT in a plethora of central nervous system diseases. These DAT characteristics are explored in relation to a range of neurological and neuropsychiatric diseases, with a particular focus on the genetics of the DAT. In addition, we discuss the pharmacology of the DAT and how this relates to disease and addiction. © 2015 Elsevier Inc. All rights reserved.

4-D crustal structure of the conterminous U.S.: Continental assembly, crustal growth, and deformation history from receiver functions, xenoliths, and structural mapping

NASA Astrophysics Data System (ADS)

Schulte-Pelkum, V.; Mahan, K. H.

2015-12-01

We investigate seismic and geological features related to the tectonic evolution of the crust on a continent-wide scale. We present continent-wide features using Transportable Array data receiver function analysis, followed by regional comparisons to tie to ground truth from xenolith studies and structural mapping. We stress that the Transportable Array, at ~75 km station spacing, only offers a collection of point measurements of the crust due to the lack of crossing raypaths. 7.x layers (lower crust with high seismic velocities) can be created during crustal growth processes such as magmatic or mechanical underplating and during crustal modification such as large-scale melting. We present receiver function results and a compilation of previous regional studies using refraction data or receiver functions from regional dense networks. 7.x layers appear predominantly in parts of the northern U.S. Cordillera and across the southeastern U.S. We compare the seismic results with a xenolith study in Montana that details incremental growth of the 7.x layer from the Archean on. Hydration of a granulitic lower crust can destroy the 7.x layer and has the potential to cause epirogenic uplift. We interpret the pattern seen across the Transportable Array in the light of this hypothesis. Ductile deformation of the deep crust generates shear fabrics that can be detected seismically. Receiver functions detect shear zones via contrasts in foliation to the surrounding material. We map foliation strikes and depths in the crust across the Transportable Array using azimuthal analysis of receiver functions. Strikes from receiver functions typically align with surface fault traces in tectonically active regions, with depths of the converters exceeding the brittle zone. We discuss continent-wide strikes mapped with receiver functions. Contrasting orientations of Proterozoic shear zones and pervasive surrounding foliations in basement exposures in Colorado are reflected in seismic results from the Transportable Array and CREST experiment.

The versatility of a truss mounted mobile transporter for in-space construction

NASA Technical Reports Server (NTRS)

Bush, Harold G.; Lake, Mark S.; Watson, Judith J.; Heard, Walter L., Jr.

1988-01-01

The Mobile Transporter (MT) evolution from early erectable structures assembly activities is detailed. The MT operational features which are required to support astronauts performing on-orbit structure construction or spacecraft assembly functions are presented and discussed. Use of the MT to perform a variety of assembly functions is presented. Estimated EVA assembly times for a precision segmented reflector approximately 20 m in diameter are presented. The EVA/MT technique under study for construction of the reflector (and the entire spacecraft) is illustrated. Finally, the current status of development activities and test results involving the MT and Space Station structural assembly are presented.

The influence of sediment transport rate on the development of structure in gravel bed rivers

NASA Astrophysics Data System (ADS)

Ockelford, Annie; Rice, Steve; Powell, Mark; Reid, Ian; Nguyen, Thao; Tate, Nick; Wood, Jo

2013-04-01

Although adjustments of surface grain size are known to be strongly influenced by sediment transport rate little work has systematically explored how different transport rates can affect the development of surface structure in gravel bed rivers. Specifically, it has been well established that the transport of mixed sized sediments leads to the development of a coarser surface or armour layer which occurs over larger areas of the gravel bed. Armour layer development is known to moderate overall sediment transport rate as well as being extremely sensitive to changes in applied shear stress. However, during this armouring process a bed is created where, smaller gain scale changes, to the bed surface are also apparent such as the development of pebble clusters and imbricate structures. Although these smaller scale changes affect the overall surface grain size distribution very little their presence has the ability to significantly increase the surface stability and hence alter overall sediment transport rates. Consequently, the interplay between the moderation of transport rate as a function of surface coarsening at a larger scale and moderation of transport rate as a function of the development of structure on the bed surface at the smaller scale is complicated and warrants further investigation. During experiments a unimodal grain size distribution (σg = 1.30, D50 = 8.8mm) was exposed to 3 different levels of constant discharge that produced sediment transport conditions ranging from marginal transport to conditions approaching full mobility of all size fractions. Sediment was re-circulated during the experiments surface grain size distribution bed load and fractional transport rates were measured at a high temporal resolution such that the time evolution of the beds could be fully described. Discussion concentrates on analysing the effects of the evolving bed condition sediment transport rate (capacity) and transported grain size (competence). The outcome of this research is pertinent to developing new methods of linking the development of bed surface organisation with near bed flow characteristics and bed load transport in gravel bed rivers. Keywords: Graded, Sediment, Structure

Transportation and handling loads

NASA Technical Reports Server (NTRS)

Ostrem, F. E.

1971-01-01

Criteria and recommended practices are presented for the prediction and verification of transportation and handling loads for the space vehicle structure and for monitoring these loads during transportation and handling of the vehicle or major vehicle segments. Elements of the transportation and handling systems, and the forcing functions and associated loads are described. The forcing functions for common carriers and typical handling devices are assessed, and emphasis is given to the assessment of loads at the points where the space vehicle is supported during transportation and handling. Factors which must be considered when predicting the loads include the transportation and handling medium; type of handling fixture; transport vehicle speed; types of terrain; weather (changes in pressure of temperature, wind, etc.); and dynamics of the transportation modes or handling devices (acceleration, deceleration, and rotations of the transporter or handling device).

Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria.

PubMed

Herrou, Julien; Willett, Jonathan W; Czyż, Daniel M; Babnigg, Gyorgy; Kim, Youngchang; Crosson, Sean

2017-03-01

Brucella abortus σ E1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226 , is among the most highly activated gene sets in the σ E1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σ S in Enterobacteriaceae , which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1 -null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li + ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCE Brucella abortus σ E1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1 Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs. Copyright © 2017 American Society for Microbiology.

Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herrou, Julien; Willett, Jonathan W.; Czyż, Daniel M.

ABSTRACT Brucella abortusσ E1is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon,bab1_0223-bab1_0226, is among the most highly activated gene sets in the σ E1regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription ofyehZYXWis activated by the general stress sigma factor σ SinEnterobacteriaceae, which suggests a functional role for this transport systemmore » in bacterial stress response across the classesAlphaproteobacteriaandGammaproteobacteria. We present evidence thatB. abortusYehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1-null strain. The solein vitrophenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li +ion concentrations. A crystal structure ofB. abortusYehZ revealed a class II periplasmic binding protein fold with significant structural homology toArchaeoglobus fulgidusProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCEBrucella abortusσ E1regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1. Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure ofB. abortusYehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.« less

Structure and function of the interphotoreceptor matrix surrounding retinal photoreceptor cells.

PubMed

Ishikawa, Makoto; Sawada, Yu; Yoshitomi, Takeshi

2015-04-01

The interphotoreceptor matrix (IPM) is a highly organized structure with interconnected domains surrounding cone and rod photoreceptor cells and extends throughout the subretinal space. Based on known roles of the extracellular matrix in other tissues, the IPM is thought to have several prominent functions including serving as a receptor for growth factors, regulating retinoid transport, participating in cytoskeletal organization in surrounding cells, and regulation of oxygen and nutrient transport. In addition, a number of studies suggest that the IPM also may play a significant role in the etiology of retinal degenerative disorders. In this review, we describe the present knowledge concerning the structure and function of the IPM under physiological and pathological conditions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG.

PubMed

Dong, Haohao; Zhang, Zhengyu; Tang, Xiaodi; Paterson, Neil G; Dong, Changjiang

2017-08-09

The cell surface of most Gram-negative bacteria contains lipopolysaccharide that is essential for their viability and drug resistance. A 134-kDa protein complex LptB 2 FG is unique among ATP-binding cassette transporters because it extracts lipopolysaccharide from the external leaflet of the inner membrane and propels it along a filament that extends across the periplasm to directly deliver lipopolysaccharide into the external leaflet of the outer membrane. Here we report the crystal structure of the lipopolysaccharide transporter LptB 2 FG from Klebsiella pneumoniae, in which both LptF and LptG are composed of a β-jellyroll-like periplasmic domain and six α-helical segments in the transmembrane domain. LptF and LptG form a central cavity containing highly conserved hydrophobic residues. Structural and functional studies suggest that LptB 2 FG uses an alternating lateral access mechanism to extract lipopolysaccharide and traffic it along the hydrophobic cavity toward the transporter's periplasmic domains.Lipopolysaccharides (LPS) are synthesized at the periplasmic side of the inner membrane of Gram-negative bacteria and are then extracted by the LptB 2 FG complex during the first step of LPS transport to the outer membrane. Here the authors present the LptB 2 FG structure, which supports an alternating lateral access mechanism for LPS extraction.

Expression, purification and functional characterization of human equilibrative nucleoside transporter subtype-1 (hENT1) protein from Sf9 insect cells.

PubMed

Rehan, Shahid; Jaakola, Veli-Pekka

2015-10-01

Human equilibrative nucleoside transporter-1 (hENT1) is the major plasma membrane transporter involved in transportation of natural nucleosides as well as nucleoside analog drugs, used in anti-cancer and anti-viral therapies. Despite extensive biochemical and pharmacological studies, little is known about the structure-function relationship of this protein. The major obstacles to purification include a low endogenous expression level, the lack of an efficient expression and purification protocol, and the hydrophobic nature of the protein. Here, we report protein expression, purification and functional characterization of hENT1 from Sf9 insect cells. hENT1 expressed by Sf9 cells is functionally active as demonstrated by saturation binding with a Kd of 1.2±0.2nM and Bmax of 110±5pmol/mg for [(3)H]nitrobenzylmercaptopurine ribonucleoside ([(3)H]NBMPR). We also demonstrate purification of hENT1 using FLAG antibody affinity resin in lauryl maltose neopentyl glycol detergent with a Kd of 4.3±0.7nM. The yield of hENT1 from Sf9 cells was ∼0.5mg active transporter per liter of culture. The purified protein is functionally active, stable, homogenous and appropriate for further biophysical and structural studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Electronic transport properties of nano-scale Si films: an ab initio study

NASA Astrophysics Data System (ADS)

Maassen, Jesse; Ke, Youqi; Zahid, Ferdows; Guo, Hong

2010-03-01

Using a recently developed first principles transport package, we study the electronic transport properties of Si films contacted to heavily doped n-type Si leads. The quantum transport analysis is carried out using density functional theory (DFT) combined with nonequilibrium Green's functions (NEGF). This particular combination of NEGF-DFT allows the investigation of Si films with thicknesses in the range of a few nanometers and lengths up to tens of nanometers. We calculate the conductance, the momentum resolved transmission, the potential profile and the screening length as a function of length, thickness, orientation and surface structure. Moreover, we compare the properties of Si films with and without a top surface passivation by hydrogen.

Structural basis for amino acid export by DMT superfamily transporter YddG.

PubMed

Tsuchiya, Hirotoshi; Doki, Shintaro; Takemoto, Mizuki; Ikuta, Tatsuya; Higuchi, Takashi; Fukui, Keita; Usuda, Yoshihiro; Tabuchi, Eri; Nagatoishi, Satoru; Tsumoto, Kouhei; Nishizawa, Tomohiro; Ito, Koichi; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

2016-06-16

The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.

Substituted cysteine accessibility method (SCAM) analysis of the transport domain of human concentrative nucleoside transporter 3 (hCNT3) and other family members reveals features of structural and functional importance

PubMed Central

Mulinta, Ras; Yao, Sylvia Y. M.; Ng, Amy M. L.; Cass, Carol E.; Young, James D.

2017-01-01

The human SLC28 family of concentrative nucleoside transporter (CNT) proteins has three members: hCNT1, hCNT2, and hCNT3. Na+-coupled hCNT1 and hCNT2 transport pyrimidine and purine nucleosides, respectively, whereas hCNT3 transports both pyrimidine and purine nucleosides utilizing Na+ and/or H+ electrochemical gradients. Escherichia coli CNT family member NupC resembles hCNT1 in permeant selectivity but is H+-coupled. Using heterologous expression in Xenopus oocytes and the engineered cysteine-less hCNT3 protein hCNT3(C−), substituted cysteine accessibility method analysis with the membrane-impermeant thiol reactive reagent p-chloromercuribenzene sulfonate was performed on the transport domain (interfacial helix 2, hairpin 1, putative transmembrane domain (TM) 7, and TM8), as well as TM9 of the scaffold domain of the protein. This systematic scan of the entire C-terminal half of hCNT3(C−) together with parallel studies of the transport domain of wild-type hCNT1 and the corresponding TMs of cysteine-less NupC(C−) yielded results that validate the newly developed structural homology model of CNT membrane architecture for human CNTs, revealed extended conformationally mobile regions within transport-domain TMs, identified pore-lining residues of functional importance, and provided evidence of an emerging novel elevator-type mechanism of transporter function. PMID:28385889

Correlating electronic transport to atomic structures in self-assembled quantum wires.

PubMed

Qin, Shengyong; Kim, Tae-Hwan; Zhang, Yanning; Ouyang, Wenjie; Weitering, Hanno H; Shih, Chih-Kang; Baddorf, Arthur P; Wu, Ruqian; Li, An-Ping

2012-02-08

Quantum wires, as a smallest electronic conductor, are expected to be a fundamental component in all quantum architectures. The electronic conductance in quantum wires, however, is often dictated by structural instabilities and electron localization at the atomic scale. Here we report on the evolutions of electronic transport as a function of temperature and interwire coupling as the quantum wires of GdSi(2) are self-assembled on Si(100) wire-by-wire. The correlation between structure, electronic properties, and electronic transport are examined by combining nanotransport measurements, scanning tunneling microscopy, and density functional theory calculations. A metal-insulator transition is revealed in isolated nanowires, while a robust metallic state is obtained in wire bundles at low temperature. The atomic defects lead to electron localizations in isolated nanowire, and interwire coupling stabilizes the structure and promotes the metallic states in wire bundles. This illustrates how the conductance nature of a one-dimensional system can be dramatically modified by the environmental change on the atomic scale. © 2012 American Chemical Society

Unique magnetic and thermoelectric properties of chemically functionalized narrow carbon polymers.

PubMed

Zberecki, K; Wierzbicki, M; Swirkowicz, R; Barnaś, J

2017-02-01

We analyze magnetic, transport and thermoelectric properties of narrow carbon polymers, which are chemically functionalized with nitroxide groups. Numerical calculations of the electronic band structure and the corresponding transmission function are based on density functional theory. Transport and thermoelectric parameters are calculated in the linear response regime, with particular interest in charge and spin thermopowers (charge and spin Seebeck effects). Such nanoribbons are shown to have thermoelectric properties described by large thermoelectric efficiency, which makes these materials promising from the application point of view.

Electron transport in gated InGaAs and InAsP quantum well wires in selectively grown InP ridge structures

NASA Astrophysics Data System (ADS)

Granger, G.; Kam, A.; Studenikin, S. A.; Sachrajda, A. S.; Aers, G. C.; Williams, R. L.; Poole, P. J.

2010-09-01

The purpose of this work is to fabricate ribbon-like InGaAs and InAsP wires embedded in InP ridge structures and investigate their transport properties. The InP ridge structures that contain the wires are selectively grown by chemical beam epitaxy (CBE) on pre-patterned InP substrates. To optimize the growth and micro-fabrication processes for electronic transport, we explore the Ohmic contact resistance, the electron density, and the mobility as a function of the wire width using standard transport and Shubnikov-de Haas measurements. At low temperatures the ridge structures reveal reproducible mesoscopic conductance fluctuations. We also fabricate ridge structures with submicron gate electrodes that exhibit non-leaky gating and good pinch-off characteristics acceptable for device operation. Using such wrap gate electrodes, we demonstrate that the wires can be split to form quantum dots evidenced by Coulomb blockade oscillations in transport measurements.

Structure-Function Relationship of Transporters in the Glutamate-Glutamine Cycle of the Central Nervous System.

PubMed

Hayashi, Mariko Kato

2018-04-12

Many kinds of transporters contribute to glutamatergic excitatory synaptic transmission. Glutamate is loaded into synaptic vesicles by vesicular glutamate transporters to be released from presynaptic terminals. After synaptic vesicle release, glutamate is taken up by neurons or astrocytes to terminate the signal and to prepare for the next signal. Glutamate transporters on the plasma membrane are responsible for transporting glutamate from extracellular fluid to cytoplasm. Glutamate taken up by astrocyte is converted to glutamine by glutamine synthetase and transported back to neurons through glutamine transporters on the plasma membranes of the astrocytes and then on neurons. Glutamine is converted back to glutamate by glutaminase in the neuronal cytoplasm and then loaded into synaptic vesicles again. Here, the structures of glutamate transporters and glutamine transporters, their conformational changes, and how they use electrochemical gradients of various ions for substrate transport are summarized. Pharmacological regulations of these transporters are also discussed.

Structures and construction of nuclear power plants on lunar surface

NASA Astrophysics Data System (ADS)

Shimizu, Katsunori; Kobatake, Masuhiko; Ogawa, Sachio; Kanamori, Hiroshi; Okada, Yasuhiko; Mano, Hideyuki; Takagi, Kenji

1991-07-01

The best structure and construction techniques of nuclear power plants in the severe environments on the lunar surface are studied. Facility construction types (functional conditions such as stable structure, shield thickness, maintainability, safety distances, and service life), construction conditions (such as construction methods, construction equipment, number of personnel, time required for construction, external power supply, and required transportation) and construction feasibility (construction method, reactor transportation between the moon and the earth, ground excavation for installation, loading and unloading, transportation, and installation, filling up the ground, electric power supply of plant S (300 kW class) and plant L (3000 kW class)) are outlined. Items to pay attention to in construction are (1) automation and robotization of construction; (2) cost reduction by multi functional robots; and (3) methods of supplying power to robots. A precast concrete block manufacturing plant is also outlined.

Plant Ion Channels: Gene Families, Physiology, and Functional Genomics Analyses

PubMed Central

Ward, John M.; Mäser, Pascal; Schroeder, Julian I.

2016-01-01

Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization-and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide–gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport. PMID:18842100

Plant ion channels: gene families, physiology, and functional genomics analyses.

PubMed

Ward, John M; Mäser, Pascal; Schroeder, Julian I

2009-01-01

Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization- and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide-gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport.

Nonlinear and Nonequilibrium Spin Injection in Magnetic Tunneling Junctions

NASA Astrophysics Data System (ADS)

Guo, Hong

2007-03-01

Quantitative analysis of charge and spin quantum transport in spintronic devices requires an atomistic first principles approach that can handle nonlinear and nonequilibrium transport conditions. We have developed an approach for this purpose based on real space density functional theory (DFT) carried out within the Keldysh nonequilibrium Green's function formalism (NEGF). We report theoretical analysis of nonlinear and nonequilibrium spin injection and quantum transport in Fe/MgO/Fe trilayer structures as a function of external bias voltage. Devices with well relaxed atomic structures and with FeO oxidization layers are investigated as a function of external bias voltage. We also report calculations of nonequilibrium spin injection into molecular layers and graphene. Comparisons to experimental data will be presented. Work in collaborations with: Derek Waldron, Vladimir Timochevski (McGill University); Ke Xia (Institute of Physics, Chinese Academy of Science, Beijing, China); Eric Zhu, Jian Wang (University of Hong Kong); Paul Haney, and Allan MacDonald (University of Texas at Austin).

Structure and function of bordered pits: new discoveries and impacts on whole-plant hydraulic function.

PubMed

Choat, Brendan; Cobb, Alexander R; Jansen, Steven

2008-01-01

Bordered pits are cavities in the lignified cell walls of xylem conduits (vessels and tracheids) that are essential components in the water-transport system of higher plants. The pit membrane, which lies in the center of each pit, allows water to pass between xylem conduits but limits the spread of embolism and vascular pathogens in the xylem. Averaged across a wide range of species, pits account for > 50% of total xylem hydraulic resistance, indicating that they are an important factor in the overall hydraulic efficiency of plants. The structure of pits varies dramatically across species, with large differences evident in the porosity and thickness of pit membranes. Because greater porosity reduces hydraulic resistance but increases vulnerability to embolism, differences in pit structure are expected to correlate with trade-offs between efficiency and safety of water transport. However, trade-offs in hydraulic function are influenced both by pit-level differences in structure (e.g. average porosity of pit membranes) and by tissue-level changes in conduit allometry (average length, diameter) and the total surface area of pit membranes that connects vessels. In this review we address the impact of variation in pit structure on water transport in plants from the level of individual pits to the whole plant.

Thermoelectric properties of AgSbTe₂ from first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezaei, Nafiseh; Akbarzadeh, Hadi; Hashemifar, S. Javad, E-mail: hashemifar@cc.iut.ac.ir

2014-09-14

The structural, electronic, and transport properties of AgSbTe₂ are studied by using full-relativistic first-principles electronic structure calculation and semiclassical description of transport parameters. The results indicate that, within various exchange-correlation functionals, the cubic Fd3⁻m and trigonal R3⁻m structures of AgSbTe₂ are more stable than two other considered structures. The computed Seebeck coefficients at different values of the band gap and carrier concentration are accurately compared with the available experimental data to speculate a band gap of about 0.1–0.35 eV for AgSbTe₂ compound, in agreement with our calculated electronic structure within the hybrid HSE (Heyd-Scuseria-Ernzerhof) functional. By calculating the semiclassical Seebeckmore » coefficient, electrical conductivity, and electronic part of thermal conductivity, we present the theoretical upper limit of the thermoelectric figure of merit of AgSbTe₂ as a function of temperature and carrier concentration.« less

Structure-function relationships in sapwood water transport and storage.

Treesearch

Barbara L. Gartner; Frederick C. Meinzer

2005-01-01

Primary production by plants requires the loss of substantial quantities of water when the stomata are open for carbon assimilation. The delivery of that water to the leaves occurs through the xylem. The structure, condition, and quantity of the xylem control not only the transport efficiency but also the release of water from storage. For example, if there is high...

The Split Personality of Glutamate Transporters: A Chloride Channel and a Transporter.

PubMed

Cater, Rosemary J; Ryan, Renae M; Vandenberg, Robert J

2016-03-01

Transporters and ion channels are conventionally categorised into distinct classes of membrane proteins. However, some membrane proteins have a split personality and can function as both transporters and ion channels. The excitatory amino acid transporters (EAATs) in particular, function as both glutamate transporters and chloride (Cl(-)) channels. The EAATs couple the transport of glutamate to the co-transport of three Na(+) ions and one H(+) ion into the cell, and the counter-transport of one K(+) ion out of the cell. The EAAT Cl(-) channel is activated by the binding of glutamate and Na(+), but is thermodynamically uncoupled from glutamate transport and involves molecular determinants distinct from those responsible for glutamate transport. Several crystal structures of an EAAT archaeal homologue, GltPh, at different stages of the transport cycle, alongside numerous functional studies and molecular dynamics simulations, have provided extensive insights into the mechanism of substrate transport via these transporters. However, the molecular determinants involved in Cl(-) permeation, and the mechanism by which this channel is activated are not entirely understood. Here we will discuss what is currently known about the molecular determinants involved in EAAT-mediated Cl(-) permeation and the mechanisms that underlie their split personality.

Hormones and the blood-brain barrier.

PubMed

Hampl, Richard; Bičíková, Marie; Sosvorová, Lucie

2015-03-01

Hormones exert many actions in the brain, and brain cells are also hormonally active. To reach their targets in brain structures, hormones must overcome the blood-brain barrier (BBB). The BBB is a unique device selecting desired/undesired molecules to reach or leave the brain, and it is composed of endothelial cells forming the brain vasculature. These cells differ from other endothelial cells in their almost impermeable tight junctions and in possessing several membrane structures such as receptors, transporters, and metabolically active molecules, ensuring their selection function. The main ways how compounds pass through the BBB are briefly outlined in this review. The main part concerns the transport of major classes of hormones: steroids, including neurosteroids, thyroid hormones, insulin, and other peptide hormones regulating energy homeostasis, growth hormone, and also various cytokines. Peptide transporters mediating the saturable transport of individual classes of hormones are reviewed. The last paragraph provides examples of how hormones affect the permeability and function of the BBB either at the level of tight junctions or by various transporters.

Structure-Function Studies of the SLC17 Transporter Sialin Identify Crucial Residues and Substrate-induced Conformational Changes*

PubMed Central

Courville, Pascal; Quick, Matthias; Reimer, Richard J.

2010-01-01

Salla disease and infantile sialic acid storage disorder are human diseases caused by loss of function of sialin, a lysosomal transporter that mediates H+-coupled symport of acidic sugars N-acetylneuraminic acid and glucuronic acid out of lysosomes. Along with the closely related vesicular glutamate transporters, sialin belongs to the SLC17 transporter family. Despite their critical role in health and disease, these proteins remain poorly understood both structurally and mechanistically. Here, we use substituted cysteine accessibility screening and radiotracer flux assays to evaluate experimentally a computationally generated three-dimensional structure model of sialin. According to this model, sialin consists of 12 transmembrane helices (TMs) with an overall architecture similar to that of the distantly related glycerol 3-phosphate transporter GlpT. We show that TM4 in sialin lines a large aqueous cavity that forms a part of the substrate permeation pathway and demonstrate substrate-induced alterations in accessibility of substituted cysteine residues in TM4. In addition, we demonstrate that one mutant, F179C, has a dramatically different effect on the apparent affinity and transport rate for N-acetylneuraminic acid and glucuronic acid, suggesting that it may be directly involved in substrate recognition and/or translocation. These findings offer a basis for further defining the transport mechanism of sialin and other SLC17 family members. PMID:20424173

Identification of Transport-critical Residues in a Folate Transporter from the Folate-Biopterin Transporter (FBT) Family*

PubMed Central

Eudes, Aymerick; Kunji, Edmund R. S.; Noiriel, Alexandre; Klaus, Sebastian M. J.; Vickers, Tim J.; Beverley, Stephen M.; Gregory, Jesse F.; Hanson, Andrew D.

2010-01-01

The Synechocystis Slr0642 protein and its plastidial Arabidopsis (Arabidopsis thaliana) ortholog At2g32040 belong to the folate-biopterin transporter (FBT) family within the major facilitator superfamily. Both proteins transport folates when expressed in Escherichia coli. Because the structural requirements for transport activity are not known for any FBT protein, we applied mutational analysis to identify residues that are critical to transport and interpreted the results using a comparative structural model based on E. coli lactose permease. Folate transport was assessed via the growth of an E. coli pabA abgT strain, which cannot synthesize or take up folates or p-aminobenzoylglutamate. In total, 47 residues were replaced with Cys or Ala. Mutations at 22 positions abolished folate uptake without affecting Slr0642 expression in membranes, whereas other mutations had no effect. Residues important for function mostly line the predicted central cavity and are concentrated in the core α-helices H1, H4, H7, and H10. The essential residue locations are consistent with a folate-binding site lying roughly equidistant from both faces of the transporter. Arabidopsis has eight FBT proteins besides At2g32040, often lacking conserved critical residues. When six of these proteins were expressed in E. coli or in Leishmania folate or pterin transporter mutants, none showed evidence of folate or pterin transport activity, and only At2g32040 was isolated by functional screening of Arabidopsis cDNA libraries in E. coli. Such negative data could reflect roles in transport of other substrates. These studies provide the first insights into the native structure and catalytic mechanism of FBT family carriers. PMID:19923217

Electronic Transport Properties of Carbon-Nanotube Networks: The Effect of Nitrate Doping on Intratube and Intertube Conductances

NASA Astrophysics Data System (ADS)

Ketolainen, T.; Havu, V.; Jónsson, E. Ö.; Puska, M. J.

2018-03-01

The conductivity of carbon-nanotube (CNT) networks can be improved markedly by doping with nitric acid. In the present work, CNTs and junctions of CNTs functionalized with NO3 molecules are investigated to understand the microscopic mechanism of nitric acid doping. According to our density-functional-theory band-structure calculations, there is charge transfer from the CNT to adsorbed molecules indicating p -type doping. The average doping efficiency of the NO3 molecules is higher if the NO3 molecules form complexes with water molecules. In addition to electron transport along individual CNTs, we also study electron transport between different types (metallic, semiconducting) of CNTs. Reflecting the differences in the electronic structures of semiconducting and metallic CNTs, we find that in addition to turning semiconducting CNTs metallic, doping further increases electron transport most efficiently along semiconducting CNTs as well as through the junctions between them.

Structure and function of the mannitol permease of the Escherichia coli phosphotransferase sugar transport system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephan, M.M.

1988-01-01

The mannitol permease, or mannitol enzyme II, is responsible for the phosphorylation and transmembrane transport of the hexitol mannitol via the phosphotransferase sugar transport system (PTS) in Escherichia coli. Neither the detailed molecular mechanisms by which this protein carries out these functions nor its three dimensional structure in the membrane are known. An in vivo selective radiolabeling system was used to study the enzyme's subunits interactions as they related to function, as well as its membrane topography, by polyacrylamide gel electrophoresis. The intramembrane topography of the mannitol enzyme II was investigated using proteases as probes of enzyme structure in themore » membrane. The enzyme was found to have two distinct domains, a very hydrophobic, membrane-bound, N-terminal domain, and a relatively hyprophilic C-terminal domain which protrudes into the cytoplasm. The membrane-bound domain was further dissected, and an extra-membrane loop region was identified using peptide-specific antibodies. The cytoplasmic domain was found to contain a site of covalent phosphorylation using (/sup 32/p)-labeled PEP, as well as the binding site for the phosphodonor HPr.« less

Electron crystallography reveals that substrate release from the PTS IIC glucose transporter is coupled to a subtle conformational change.

PubMed

Kalbermatter, David; Chiu, Po-Lin; Jeckelmann, Jean-Marc; Ucurum, Zöhre; Walz, Thomas; Fotiadis, Dimitrios

2017-07-01

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIIC glc ) to visualize the structure of the transporter in the presence and absence of its substrate. Using an in vivo transport assay and binding competition experiments, we first established that, while it transports d-glucose, ecIIC glc does not bind l-glucose. We then determined the projection structure of ecIIC glc from tubular crystals embedded in d- and l-glucose and found a subtle conformational change. From comparison of the ecIIC glc projection maps with crystal structures of other IIC transporters, we can deduce that the transporter adopts an inward-facing conformation, and that the maps in the presence and absence of the substrate reflect the transporter before and after release of the transported glucose into the cytoplasm. The transition associated with substrate release appears to require a subtle structural rearrangement in the region that includes hairpin 1. Copyright © 2017 Elsevier Inc. All rights reserved.

Development of a structural health monitoring (SHM) guidebook for critical bridge structures.

DOT National Transportation Integrated Search

2013-07-01

A recently completed study suggests that approximately 25% of them are either structurally deficient : or functionally obsolete (FHWA, 2007). Therefore, the Federal Highway Administration (FHWA) : and the Oklahoma Transportation Center (OTC) have mad...

Snapshots of the maltose transporter during ATP hydrolysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oldham, Michael L.; Chen, Jue

2011-12-05

ATP-binding cassette transporters are powered by ATP, but the mechanism by which these transporters hydrolyze ATP is unclear. In this study, four crystal structures of the full-length wild-type maltose transporter, stabilized by adenosine 5{prime}-({beta},{gamma}-imido)triphosphate or ADP in conjunction with phosphate analogs BeF{sub 3}{sup -}, VO{sub 4}{sup 3-}, or AlF{sub 4}{sup -}, were determined to 2.2- to 2.4-{angstrom} resolution. These structures led to the assignment of two enzymatic states during ATP hydrolysis and demonstrate specific functional roles of highly conserved residues in the nucleotide-binding domain, suggesting that ATP-binding cassette transporters catalyze ATP hydrolysis via a general base mechanism.

CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease.

PubMed

Jentsch, Thomas J; Pusch, Michael

2018-07-01

CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl - channels, whereas ClC-3 through ClC-7 are 2Cl - /H + -exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl - channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.

Ion transport in complex layered graphene-based membranes with tuneable interlayer spacing.

PubMed

Cheng, Chi; Jiang, Gengping; Garvey, Christopher J; Wang, Yuanyuan; Simon, George P; Liu, Jefferson Z; Li, Dan

2016-02-01

Investigation of the transport properties of ions confined in nanoporous carbon is generally difficult because of the stochastic nature and distribution of multiscale complex and imperfect pore structures within the bulk material. We demonstrate a combined approach of experiment and simulation to describe the structure of complex layered graphene-based membranes, which allows their use as a unique porous platform to gain unprecedented insights into nanoconfined transport phenomena across the entire sub-10-nm scales. By correlation of experimental results with simulation of concentration-driven ion diffusion through the cascading layered graphene structure with sub-10-nm tuneable interlayer spacing, we are able to construct a robust, representative structural model that allows the establishment of a quantitative relationship among the nanoconfined ion transport properties in relation to the complex nanoporous structure of the layered membrane. This correlation reveals the remarkable effect of the structural imperfections of the membranes on ion transport and particularly the scaling behaviors of both diffusive and electrokinetic ion transport in graphene-based cascading nanochannels as a function of channel size from 10 nm down to subnanometer. Our analysis shows that the range of ion transport effects previously observed in simple one-dimensional nanofluidic systems will translate themselves into bulk, complex nanoslit porous systems in a very different manner, and the complex cascading porous circuities can enable new transport phenomena that are unattainable in simple fluidic systems.

Ion transport in complex layered graphene-based membranes with tuneable interlayer spacing

PubMed Central

Cheng, Chi; Jiang, Gengping; Garvey, Christopher J.; Wang, Yuanyuan; Simon, George P.; Liu, Jefferson Z.; Li, Dan

2016-01-01

Investigation of the transport properties of ions confined in nanoporous carbon is generally difficult because of the stochastic nature and distribution of multiscale complex and imperfect pore structures within the bulk material. We demonstrate a combined approach of experiment and simulation to describe the structure of complex layered graphene-based membranes, which allows their use as a unique porous platform to gain unprecedented insights into nanoconfined transport phenomena across the entire sub–10-nm scales. By correlation of experimental results with simulation of concentration-driven ion diffusion through the cascading layered graphene structure with sub–10-nm tuneable interlayer spacing, we are able to construct a robust, representative structural model that allows the establishment of a quantitative relationship among the nanoconfined ion transport properties in relation to the complex nanoporous structure of the layered membrane. This correlation reveals the remarkable effect of the structural imperfections of the membranes on ion transport and particularly the scaling behaviors of both diffusive and electrokinetic ion transport in graphene-based cascading nanochannels as a function of channel size from 10 nm down to subnanometer. Our analysis shows that the range of ion transport effects previously observed in simple one-dimensional nanofluidic systems will translate themselves into bulk, complex nanoslit porous systems in a very different manner, and the complex cascading porous circuities can enable new transport phenomena that are unattainable in simple fluidic systems. PMID:26933689

Disulfide Cross-linking of a Multidrug and Toxic Compound Extrusion Transporter Impacts Multidrug Efflux*

PubMed Central

Radchenko, Martha; Nie, Rongxin; Lu, Min

2016-01-01

Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance by extruding different drugs across cell membranes. The MATE transporters alternate between their extracellular and intracellular facing conformations to propel drug export, but how these structural changes occur is unclear. Here we combine site-specific cross-linking and functional studies to probe the movement of transmembrane helices in NorM from Neiserria gonorrheae (NorM-NG), a MATE transporter with known extracellular facing structure. We generated an active, cysteine-less NorM-NG and conducted pairwise cysteine mutagenesis on this variant. We found that copper phenanthroline catalyzed disulfide bond formation within five cysteine pairs and increased the electrophoretic mobility of the corresponding mutants. Furthermore, copper phenanthroline abolished the activity of the five paired cysteine mutants, suggesting that these substituted amino acids come in spatial proximity during transport, and the proximity changes are functionally indispensable. Our data also implied that the substrate-binding transmembrane helices move up to 10 Å in NorM-NG during transport and afforded distance restraints for modeling the intracellular facing transporter, thereby casting new light on the underlying mechanism. PMID:26975373

An example of requirements for Advanced Subsonic Civil Transport (ASCT) flight control system using structured techniques

NASA Technical Reports Server (NTRS)

Mclees, Robert E.; Cohen, Gerald C.

1991-01-01

The requirements are presented for an Advanced Subsonic Civil Transport (ASCT) flight control system generated using structured techniques. The requirements definition starts from initially performing a mission analysis to identify the high level control system requirements and functions necessary to satisfy the mission flight. The result of the study is an example set of control system requirements partially represented using a derivative of Yourdon's structured techniques. Also provided is a research focus for studying structured design methodologies and in particular design-for-validation philosophies.

Implications of Mycobacterium Major Facilitator Superfamily for Novel Measures against Tuberculosis.

PubMed

Wang, Rui; Zhang, Zhen; Xie, Longxiang; Xie, Jianping

2015-01-01

Major facilitator superfamily (MFS) is an important secondary membrane transport protein superfamily conserved from prokaryotes to eukaryotes. The MFS proteins are widespread among bacteria and are responsible for the transfer of substrates. Pathogenic Mycobacterium MFS transporters, their distribution, function, phylogeny, and predicted crystal structures were studied to better understand the function of MFS and to discover specific inhibitors of MFS for better tuberculosis control.

Overcoming the heterologous bias: An in vivo functional analysis of multidrug efflux transporter, CgCdr1p in matched pair clinical isolates of Candida glabrata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puri, Nidhi; Manoharlal, Raman; Sharma, Monika

2011-01-07

Research highlights: {yields} First report to demonstrate an in vivo expression system of an ABC multidrug transporter CgCdr1p of C. glabrata. {yields} First report on the structure and functional characterization of CgCdr1p. {yields} Functional conservation of divergent but typical residues of CgCdr1p. {yields} CgCdr1p elicits promiscuity towards substrates and has a large drug binding pocket with overlapping specificities. -- Abstract: We have taken advantage of the natural milieu of matched pair of azole sensitive (AS) and azole resistant (AR) clinical isolates of Candida glabrata for expressing its major ABC multidrug transporter, CgCdr1p for structure and functional analysis. This was accomplishedmore » by tagging a green fluorescent protein (GFP) downstream of ORF of CgCDR1 and integrating the resultant fusion protein at its native chromosomal locus in AS and AR backgrounds. The characterization confirmed that in comparison to AS isolate, CgCdr1p-GFP was over-expressed in AR isolates due to its hyperactive native promoter and the GFP tag did not affect its functionality in either construct. We observed that in addition to Rhodamine 6 G (R6G) and Fluconazole (FLC), a recently identified fluorescent substrate of multidrug transporters Nile Red (NR) could also be expelled by CgCdr1p. Competition assays with these substrates revealed the presence of overlapping multiple drug binding sites in CgCdr1p. Point mutations employing site directed mutagenesis confirmed that the role played by unique amino acid residues critical to ATP catalysis and localization of ABC drug transporter proteins are well conserved in C. glabrata as in other yeasts. This study demonstrates a first in vivo novel system where over-expression of GFP tagged MDR transporter protein can be driven by its own hyperactive promoter of AR isolates. Taken together, this in vivo system can be exploited for the structure and functional analysis of CgCdr1p and similar proteins wherein the arte-factual concerns encountered in using heterologous systems are totally excluded.« less

Neurological Organization and Reading.

ERIC Educational Resources Information Center

Consilia, Sister Mary

The structure and function of the nervous system as it puts us into contact with our environment is described. Section 1 presents a detailed discussion of the structure of the brain, drawing an analogy to a computer, and discusses the sensory input function. The transport system is then explained in a description of the transmission of sensory…

[Hemoglobin oxygen transport capacity in surgical endotoxicosis ].

PubMed

Poryadin, G V; Vlasov, A P; Trofimov, V A; Vlasova, T I; Kamkina, O V; Grigoryev, A G; Vlasov, P A

2016-01-01

In surgical endointoxication hemoglobin oxygen transport capacity of red blood cells (hemoglobin affinity ligands: the ability to bind and release ligands) is reduced and is associated with the severity of endogenous intoxication. Violation of oxygen transport function of hemoglobin at endogenous intoxication is associated with conformational changes of a biomolecule, and its possible influence on reactive oxygen species, which confirmed in experiments in vitro: under the influence of oxygen-iron ascorbate ability of hemoglobin deteriorates. Largely similar structural and functional changes in hemoglobin occur in patients with surgical endotoxicosis.

Membrane Transporters: Structure, Function and Targets for Drug Design

NASA Astrophysics Data System (ADS)

Ravna, Aina W.; Sager, Georg; Dahl, Svein G.; Sylte, Ingebrigt

Current therapeutic drugs act on four main types of molecular targets: enzymes, receptors, ion channels and transporters, among which a major part (60-70%) are membrane proteins. This review discusses the molecular structures and potential impact of membrane transporter proteins on new drug discovery. The three-dimensional (3D) molecular structure of a protein contains information about the active site and possible ligand binding, and about evolutionary relationships within the protein family. Transporters have a recognition site for a particular substrate, which may be used as a target for drugs inhibiting the transporter or acting as a false substrate. Three groups of transporters have particular interest as drug targets: the major facilitator superfamily, which includes almost 4000 different proteins transporting sugars, polyols, drugs, neurotransmitters, metabolites, amino acids, peptides, organic and inorganic anions and many other substrates; the ATP-binding cassette superfamily, which plays an important role in multidrug resistance in cancer chemotherapy; and the neurotransmitter:sodium symporter family, which includes the molecular targets for some of the most widely used psychotropic drugs. Recent technical advances have increased the number of known 3D structures of membrane transporters, and demonstrated that they form a divergent group of proteins with large conformational flexibility which facilitates transport of the substrate.

The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis

PubMed Central

King, Steven C

2004-01-01

Background In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR) analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant) for comparison to other transporters. Results Using the Escherichia coli GABA (4-aminobutyrate) permease (GabP) as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i) indifference to the particular substrate concentrations used, (ii) indifference to extreme changes (40-fold) in transporter expression level, and within broad limits (iii) indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i) applicability in the analysis of membrane transport, and (ii) particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations). The TSR was used to identify gab permease (GabP) variants that exhibit relative changes in catalytic specificity (kcat/Km) for [14C]GABA (4-aminobutyrate) versus [3H]NA (nipecotic acid). Conclusions The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR), represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb) that translocation catalysts rely upon to decrease activation energy (). TSR analysis is therefore a structure-function tool that enables parsimonious scanning for positions in the protein fold that couple to the transition state, creating stability and thereby serving as functional determinants of catalytic power (efficiency, or specificity). PMID:15548327

Structural Insights into the Transport Mechanism of the Human Sodium-dependent Lysophosphatidylcholine Transporter MFSD2A*♦

PubMed Central

Quek, Debra Q. Y.; Nguyen, Long N.; Fan, Hao; Silver, David L.

2016-01-01

Major facilitator superfamily domain containing 2A (MFSD2A) was recently characterized as a sodium-dependent lysophosphatidylcholine transporter expressed at the blood-brain barrier endothelium. It is the primary route for importation of docosohexaenoic acid and other long-chain fatty acids into fetal and adult brain and is essential for mouse and human brain growth and function. Remarkably, MFSD2A is the first identified major facilitator superfamily member that uniquely transports lipids, implying that MFSD2A harbors unique structural features and transport mechanism. Here, we present three three-dimensional structural models of human MFSD2A derived by homology modeling using MelB- and LacY-based crystal structures and refined by biochemical analysis. All models revealed 12 transmembrane helices and connecting loops and represented the partially outward-open, outward-partially occluded, and inward-open states of the transport cycle. In addition to a conserved sodium-binding site, three unique structural features were identified as follows: a phosphate headgroup binding site, a hydrophobic cleft to accommodate a hydrophobic hydrocarbon tail, and three sets of ionic locks that stabilize the outward-open conformation. Ligand docking studies and biochemical assays identified Lys-436 as a key residue for transport. It is seen forming a salt bridge with the negative charge on the phosphate headgroup. Importantly, MFSD2A transported structurally related acylcarnitines but not a lysolipid without a negative charge, demonstrating the necessity of a negatively charged headgroup interaction with Lys-436 for transport. These findings support a novel transport mechanism by which lysophosphatidylcholines are “flipped” within the transporter cavity by pivoting about Lys-436 leading to net transport from the outer to the inner leaflet of the plasma membrane. PMID:26945070

Heteromeric amino acid transporters. In search of the molecular bases of transport cycle mechanisms.

PubMed

Palacín, Manuel; Errasti-Murugarren, Ekaitz; Rosell, Albert

2016-06-15

Heteromeric amino acid transporters (HATs) are relevant targets for structural studies. On the one hand, HATs are involved in inherited and acquired human pathologies. On the other hand, these molecules are the only known examples of solute transporters composed of two subunits (heavy and light) linked by a disulfide bridge. Unfortunately, structural knowledge of HATs is scarce and limited to the atomic structure of the ectodomain of a heavy subunit (human 4F2hc-ED) and distant prokaryotic homologues of the light subunits that share a LeuT-fold. Recent data on human 4F2hc/LAT2 at nanometer resolution revealed 4F2hc-ED positioned on top of the external loops of the light subunit LAT2. Improved resolution of the structure of HATs, combined with conformational studies, is essential to establish the structural bases for light subunit recognition and to evaluate the functional relevance of heavy and light subunit interactions for the amino acid transport cycle. © 2016 Authors; published by Portland Press Limited.

Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex.

PubMed

Yu, Fang; He, Fangyuan; Yao, Hongyan; Wang, Chengyuan; Wang, Jianchuan; Li, Jianxu; Qi, Xiaofeng; Xue, Hongwei; Ding, Jianping; Zhang, Peng

2015-07-01

Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins. © 2015 The Authors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herrou, Julien; Willett, Jonathan W.; Czyż, Daniel M.

ABSTRACT Brucella abortusσ E1is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon,bab1_0223-bab1_0226, is among the most highly activated gene sets in the σ E1regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription ofyehZYXWis activated by the general stress sigma factor σ SinEnterobacteriaceae, which suggests a functional role for this transport systemmore » in bacterial stress response across the classesAlphaproteobacteriaandGammaproteobacteria. We present evidence thatB. abortusYehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1-null strain. The solein vitrophenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li +ion concentrations. A crystal structure ofB. abortusYehZ revealed a class II periplasmic binding protein fold with significant structural homology toArchaeoglobus fulgidusProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCEBrucella abortusσ E1regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1. Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure ofB. abortusYehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.« less

Diffusion and viscosity of liquid tin: Green-Kubo relationship-based calculations from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mouas, Mohamed; Gasser, Jean-Georges; Hellal, Slimane; Grosdidier, Benoît; Makradi, Ahmed; Belouettar, Salim

2012-03-01

Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.

Functional Characterization of Pneumocystis carinii Inositol Transporter 1

PubMed Central

Collins, Margaret S.; Sesterhenn, Thomas; Porollo, Aleksey; Vadukoot, Anish Kizhakkekkara; Merino, Edward J.

2016-01-01

ABSTRACT Fungi in the genus Pneumocystis live in the lungs of mammals, where they can cause a fatal pneumonia (PCP [Pneumocystis pneumonia]) in hosts with compromised immune systems. The absence of a continuous in vitro culture system for any species of Pneumocystis has led to limited understanding of these fungi, especially for the discovery of new therapies. We recently reported that Pneumocystis carinii, Pneumocystis murina, and most significantly, Pneumocystis jirovecii lack both enzymes necessary for myo-inositol biosynthesis but contain genes with homologies to fungal myo-inositol transporters. Since myo-inositol is essential for eukaryotic viability, the primary transporter, ITR1, was functionally and structurally characterized in P. carinii. The predicted structure of P. carinii ITR1 (PcITR1) contained 12 transmembrane alpha-helices with intracellular C and N termini, consistent with other inositol transporters. The apparent Km was 0.94 ± 0.08 (mean ± standard deviation), suggesting that myo-inositol transport in P. carinii is likely through a low-affinity, highly selective transport system, as no other sugars or inositol stereoisomers were significant competitive inhibitors. Glucose transport was shown to use a different transport system. The myo-inositol transport was distinct from mammalian transporters, as it was not sodium dependent and was cytochalasin B resistant. Inositol transport in these fungi offers an attractive new drug target because of the reliance of the fungi on its transport, clear differences between the mammalian and fungal transporters, and the ability of the host to both synthesize and transport this critical nutrient, predicting low toxicity of potential inhibitors to the fungal transporter. PMID:27965450

Study of transmission function and electronic transport in one dimensional silver nanowire: Ab-initio method using density functional theory (DFT)

NASA Astrophysics Data System (ADS)

Thakur, Anil; Kashyap, Rajinder

2018-05-01

Single nanowire electrode devices have their application in variety of fields which vary from information technology to solar energy. Silver nanowires, made in an aqueous chemical reduction process, can be reacted with gold salt to create bimetallic nanowires. Silver nanowire can be used as electrodes in batteries and have many other applications. In this paper we investigated structural and electronic transport properties of Ag nanowire using density functional theory (DFT) with SIESTA code. Electronic transport properties of Ag nanowire have been studied theoretically. First of all an optimized geometry for Ag nanowire is obtained using DFT calculations, and then the transport relations are obtained using NEGF approach. SIESTA and TranSIESTA simulation codes are used in the calculations respectively. The electrodes are chosen to be the same as the central region where transport is studied, eliminating current quantization effects due to contacts and focusing the electronic transport study to the intrinsic structure of the material. By varying chemical potential in the electrode regions, an I-V curve is traced which is in agreement with the predicted behavior. Bulk properties of Ag are in agreement with experimental values which make the study of electronic and transport properties in silver nanowires interesting because they are promising materials as bridging pieces in nanoelectronics. Transmission coefficient and V-I characteristic of Ag nano wire reveals that silver nanowire can be used as an electrode device.

Modeling of Glycerol-3-Phosphate Transporter Suggests a Potential ‘Tilt’ Mechanism involved in its Function

PubMed Central

Tsigelny, Igor F.; Greenberg, Jerry; Kouznetsova, Valentina; Nigam, Sanjay K.

2009-01-01

Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical topologies with two six-helix halves connected by a long loop. In humans, these transporters participate in key physiological processes and are also, as in the case of members of the organic anion transporter (OAT) family, of pharmaceutical interest. Recently, crystal structures of two bacterial representatives of the MFS family — the glycerol-3-phosphate transporter (GlpT) and lac-permease (LacY) — have been solved and, because of assumptions regarding the high structural conservation of this family, there is hope that the results can be applied to mammalian transporters as well. Based on crystallography, it has been suggested that a major conformational “switching” mechanism accounts for ligand transport by MFS proteins. This conformational switch would then allow periodic changes in the overall transporter configuration, resulting in its cyclic opening to the periplasm or cytoplasm. Following this lead, we have modeled a possible “switch” mechanism in GlpT, using the concept of rotation of protein domains as in the DynDom program17 and membranephilic constraints predicted by the MAPAS program.23 We found that the minima of energies of intersubunit interactions support two alternate positions consistent with their transport properties. Thus, for GlpT, a “tilt” of 9°–10° rotation had the most favorable energetics of electrostatic interaction between the two halves of the transporter; moreover, this confirmation was sufficient to suggest transport of the ligand across the membrane. We conducted steered molecular dynamics simulations of the GlpT-ligand system to explore how glycerol-3-phosphate would be handled by the “tilted” structure, and obtained results generally consistent with experimental mutagenesis data. While biochemical data remain most consistent with a single-site alternating access model, our results raise the possibility that, while the “rocker switch” may apply to certain MFS transporters, intermediate “tilted” states may exist under certain circumstances or as transitional structures. While wet lab experimental confirmation is required, our results suggest that transport mechanisms in this transporter family should probably not be assumed to be conserved simply based on standard structural homology considerations. Furthermore, steered molecular dynamics elucidating energetic interactions of ligands with amino acid residues in an appropriately modeled transporter may have predictive value in understanding the impact of mutations and/or polymorphisms on transporter function. PMID:18942157

Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters

PubMed Central

Diallinas, George

2014-01-01

Transporters are ubiquitous proteins mediating the translocation of solutes across cell membranes, a biological process involved in nutrition, signaling, neurotransmission, cell communication and drug uptake or efflux. Similarly to enzymes, most transporters have a single substrate binding-site and thus their activity follows Michaelis-Menten kinetics. Substrate binding elicits a series of structural changes, which produce a transporter conformer open toward the side opposite to the one from where the substrate was originally bound. This mechanism, involving alternate outward- and inward-facing transporter conformers, has gained significant support from structural, genetic, biochemical and biophysical approaches. Most transporters are specific for a given substrate or a group of substrates with similar chemical structure, but substrate specificity and/or affinity can vary dramatically, even among members of a transporter family that show high overall amino acid sequence and structural similarity. The current view is that transporter substrate affinity or specificity is determined by a small number of interactions a given solute can make within a specific binding site. However, genetic, biochemical and in silico modeling studies with the purine transporter UapA of the filamentous ascomycete Aspergillus nidulans have challenged this dogma. This review highlights results leading to a novel concept, stating that substrate specificity, but also transport kinetics and transporter turnover, are determined by subtle intramolecular interactions between a major substrate binding site and independent outward- or cytoplasmically-facing gating domains, analogous to those present in channels. This concept is supported by recent structural evidence from several, phylogenetically and functionally distinct transporter families. The significance of this concept is discussed in relationship to the role and potential exploitation of transporters in drug action. PMID:25309439

Applications of the microdosimetric function implemented in the macroscopic particle transport simulation code PHITS.

PubMed

Sato, Tatsuhiko; Watanabe, Ritsuko; Sihver, Lembit; Niita, Koji

2012-01-01

Microdosimetric quantities such as lineal energy are generally considered to be better indices than linear energy transfer (LET) for expressing the relative biological effectiveness (RBE) of high charge and energy particles. To calculate their probability densities (PD) in macroscopic matter, it is necessary to integrate microdosimetric tools such as track-structure simulation codes with macroscopic particle transport simulation codes. As an integration approach, the mathematical model for calculating the PD of microdosimetric quantities developed based on track-structure simulations was incorporated into the macroscopic particle transport simulation code PHITS (Particle and Heavy Ion Transport code System). The improved PHITS enables the PD in macroscopic matter to be calculated within a reasonable computation time, while taking their stochastic nature into account. The microdosimetric function of PHITS was applied to biological dose estimation for charged-particle therapy and risk estimation for astronauts. The former application was performed in combination with the microdosimetric kinetic model, while the latter employed the radiation quality factor expressed as a function of lineal energy. Owing to the unique features of the microdosimetric function, the improved PHITS has the potential to establish more sophisticated systems for radiological protection in space as well as for the treatment planning of charged-particle therapy.

Polaronic transport in Ag-based quaternary chalcogenides

NASA Astrophysics Data System (ADS)

Wei, Kaya; Khabibullin, Artem R.; Stedman, Troy; Woods, Lilia M.; Nolas, George S.

2017-09-01

Low temperature resistivity measurements on dense polycrystalline quaternary chalcogenides Ag2+xZn1-xSnSe4, with x = 0, 0.1, and 0.3, indicate polaronic type transport which we analyze employing a two-component Holstein model based on itinerant and localized polaron contributions. Electronic structure property calculations via density functional theory simulations on Ag2ZnSnSe4 for both energetically similar kesterite and stannite structure types were also performed in order to compare our results to those of the compositionally similar but well known Cu2ZnSnSe4. This theoretical comparison is crucial in understanding the bonding that results in polaronic type transport for Ag2ZnSnSe4, as well as the structural and electronic properties of both crystal structure types. In addition to possessing this unique electronic transport, the thermal conductivity of Ag2ZnSnSe4 is low and decreases with increasing silver content. This work reveals unique structure-property relationships in materials that continue to be of interest for thermoelectric and photovoltaic applications.

Genuine functions of P-glycoprotein (ABCB1).

PubMed

Mizutani, Takaharu; Masuda, Masatoshi; Nakai, Emi; Furumiya, Kenji; Togawa, Hiroshi; Nakamura, Yutaka; Kawai, Yuko; Nakahira, Keiko; Shinkai, Shigeko; Takahashi, Kazuhiko

2008-02-01

P-glycoprotein (P-gp, ABCB1, MDR1) was recognized as a drug-exporting protein from cancer cells three decade ago. Apart from the multidrug transporter side effects of P-gp, normal physiological functions of P-gp have been reported. P-gp could be responsible for translocating platelet-activating factor (PAF) across the plasma membrane and PAF inhibited drug transport mediated by P-gp in cancer cells. P-gp regulated the translocation of sphingomyelin (SM) and GlcCer, and short chain C(6)-NBD-GlcCer was found in the apical medium of P-gp cells exclusively and not in the basolateral membrane. SM plays an important role in the esterification of cholesterol. High expression of P-gp prevents stem-cell differentiation, leading to the proliferation and amplification of this cell repertoire, and functional P-gp plays a fundamental role in regulating programmed cell death, apoptosis. The transporter function of P-gp is therefore necessary to protect cells from death. P-gp can translocate both C(6)-NBD-PC and C(6)-NBD-PE across the apical membrane. This PC translocation was also confirmed with [(3)H]choline radioactivity. Progesterone is not transported by P-gp, but blocks P-gp-mediated efflux of other drugs and P-gp can mediate the transport of a variety of steroids. Cells transfected with human P-gp esterified more cholesterol. P-gp might also be involved in the transport of cytokines, particularly IL-1beta, IL-2, IL-4 and IFNgamma, out of activated normal lymphocytes into the surrounding medium. P-gp expression is also associated with a volume-activated chloride channel, thus P-gp is bifunctional with both transport and channel regulators. We also present information about P-gp polymorphism and new structural concepts, "gate" and "twist", of the P-gp structure.

Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters

PubMed Central

Cheng, Mary Hongying; Torres-Salazar, Delany; Gonzalez-Suarez, Aneysis D; Amara, Susan G; Bahar, Ivet

2017-01-01

Advances in structure-function analyses and computational biology have enabled a deeper understanding of how excitatory amino acid transporters (EAATs) mediate chloride permeation and substrate transport. However, the mechanism of structural coupling between these functions remains to be established. Using a combination of molecular modeling, substituted cysteine accessibility, electrophysiology and glutamate uptake assays, we identified a chloride-channeling conformer, iChS, transiently accessible as EAAT1 reconfigures from substrate/ion-loaded into a substrate-releasing conformer. Opening of the anion permeation path in this iChS is controlled by the elevator-like movement of the substrate-binding core, along with its wall that simultaneously lines the anion permeation path (global); and repacking of a cluster of hydrophobic residues near the extracellular vestibule (local). Moreover, our results demonstrate that stabilization of iChS by chemical modifications favors anion channeling at the expense of substrate transport, suggesting a mutually exclusive regulation mediated by the movement of the flexible wall lining the two regions. DOI: http://dx.doi.org/10.7554/eLife.25850.001 PMID:28569666

Applying Alkyl-Chain Surface Functionalizations in Mesoporous Inorganic Structures: Their Impact on Gas Flow and Selectivity Depending on Temperature.

PubMed

Besser, Benjamin; Ahmed, Atiq; Baune, Michael; Kroll, Stephen; Thöming, Jorg; Rezwan, Kurosch

2016-10-12

Porous inorganic capillary membranes are prepared to serve as model structures for the experimental investigation of the gas transport in functionalized mesopores. The porous structures possess a mean pore diameter of 23 nm which is slightly reduced to 20 nm after immobilizing C 16 -alkyl chains on the surface. Gas permeation measurements are performed at temperatures ranging from 0 to 80 °C using Ar, N 2 , and CO 2 . Nonfunctionalized structures feature a gas transport according to Knudsen diffusion with regard to gas flow and selectivity. After C 16 -functionalization, the gas flow is reduced by a factor of 10, and the ideal selectivities deviate from the Knudsen theory. CO 2 adsorption measurements show a decrease in total amount of adsorbed gas and isosteric heat of adsorption. It is hypothesized that the immobilized C 16 -chains sterically influence the gas transport behavior without a contribution from adsorption effects. The reduced gas flow derives from an additional surface resistance caused by the C 16 -chains spacially limiting the adsorption and desorption directions for gas molecules propagating through the structure, resulting in longer diffusion paths. In agreement, the gas flow is found to correlate with the molecular diameter of the gas species (CO 2 < Ar < N 2 ) increasing the resistance for larger molecules. This affects the ideal selectivities with the relation [Formula: see text]. The influence on selectivity increases with increasing temperature which leads to the conclusion that the temperature induced movement of the C 16 -chains is responsible for the stronger interaction between gas molecules and surface functional groups.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

PubMed

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

2013-10-01

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids

PubMed Central

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

2013-01-01

Lignin comprises 15.25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP.binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute.binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. PMID:23606130

Functional, structural and phylogenetic analysis of domains underlying the Al-sensitivity of the aluminium-activated malate/anion transporter, TaALMT1

USDA-ARS?s Scientific Manuscript database

TaALMT1 (Triticum aestivum Aluminum Activated Malate Transporter) is the founding member of a novel gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small subgroup of root-localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (...

Molecular Dynamical Simulation of Thermal Conductivity in Amorphous Structures

NASA Astrophysics Data System (ADS)

Deangelis, Freddy; Henry, Asegun

While current descriptions of thermal transport exists for well-ordered materials such as crystal latices, new methods are needed to describe thermal transport in disordered materials, including amorphous solids. Because such structures lack periodic, long-range order, a group velocity cannot be defined for thermal modes of vibration; thus, the phonon gas model cannot be applied to these structures. Instead, a new framework must be applied to analyze such materials. Using a combination of density functional theory and molecular dynamics, we have analyzed thermal transport in amorphous structures, chiefly amorphous germanium. The analysis allows us to categorize vibrational modes as propagons, diffusons, or locons, and to determine how they contribute to thermal conductivity within amorphous structures. This method is also being extended to other disordered structures such as amorphous polymers. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1148903.

Active transport of vesicles in neurons is modulated by mechanical tension.

PubMed

Ahmed, Wylie W; Saif, Taher A

2014-03-27

Effective intracellular transport of proteins and organelles is critical in cells, and is especially important for ensuring proper neuron functionality. In neurons, most proteins are synthesized in the cell body and must be transported through thin structures over long distances where normal diffusion is insufficient. Neurons transport subcellular cargo along axons and neurites through a stochastic interplay of active and passive transport. Mechanical tension is critical in maintaining proper function in neurons, but its role in transport is not well understood. To this end, we investigate the active and passive transport of vesicles in Aplysia neurons while changing neurite tension via applied strain, and quantify the resulting dynamics. We found that tension in neurons modulates active transport of vesicles by increasing the probability of active motion, effective diffusivity, and induces a retrograde bias. We show that mechanical tension modulates active transport processes in neurons and that external forces can couple to internal (subcellular) forces and change the overall transport dynamics.

Active transport of vesicles in neurons is modulated by mechanical tension

PubMed Central

Ahmed, Wylie W.; Saif, Taher A.

2014-01-01

Effective intracellular transport of proteins and organelles is critical in cells, and is especially important for ensuring proper neuron functionality. In neurons, most proteins are synthesized in the cell body and must be transported through thin structures over long distances where normal diffusion is insufficient. Neurons transport subcellular cargo along axons and neurites through a stochastic interplay of active and passive transport. Mechanical tension is critical in maintaining proper function in neurons, but its role in transport is not well understood. To this end, we investigate the active and passive transport of vesicles in Aplysia neurons while changing neurite tension via applied strain, and quantify the resulting dynamics. We found that tension in neurons modulates active transport of vesicles by increasing the probability of active motion, effective diffusivity, and induces a retrograde bias. We show that mechanical tension modulates active transport processes in neurons and that external forces can couple to internal (subcellular) forces and change the overall transport dynamics. PMID:24670781

Chemical Transport Knockout for Oxidized Vitamin C, Dehydroascorbic Acid, Reveals Its Functions in vivo.

PubMed

Tu, Hongbin; Wang, Yu; Li, Hongyan; Brinster, Lauren R; Levine, Mark

2017-09-01

Despite its transport by glucose transporters (GLUTs) in vitro, it is unknown whether dehydroascorbic acid (oxidized vitamin C, DHA) has any in vivo function. To investigate, we created a chemical transport knockout model using the vitamin C analog 6-bromo-ascorbate. This analog is transported on sodium-dependent vitamin C transporters but its oxidized form, 6-bromo-dehydroascorbic acid, is not transported by GLUTs. Mice (gulo -/- ) unable to synthesize ascorbate (vitamin C) were raised on 6-bromo-ascorbate. Despite normal survival, centrifugation of blood produced hemolysis secondary to near absence of red blood cell (RBC) ascorbate/6-bromo-ascorbate. Key findings with clinical implications were that RBCs in vitro transported dehydroascorbic acid but not bromo-dehydroascorbic acid; RBC ascorbate in vivo was obtained only via DHA transport; ascorbate via DHA transport in vivo was necessary for RBC structural integrity; and internal RBC ascorbate was essential to maintain ascorbate plasma concentrations in vitro/in vivo. Published by Elsevier B.V.

Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.

PubMed

Merkle, Patrick S; Gotfryd, Kamil; Cuendet, Michel A; Leth-Espensen, Katrine Z; Gether, Ulrik; Loland, Claus J; Rand, Kasper D

2018-05-01

LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na + - and K + -dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.

Structures and transport dynamics of a Campylobacter jejuni multidrug efflux pump

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Chih-Chia; Yin, Linxiang; Kumar, Nitin

2017-08-01

Resistance-nodulation-cell division efflux pumps are integral membrane proteins that catalyze the export of substrates across cell membranes. Within the hydrophobe-amphiphile efflux subfamily, these resistance-nodulation-cell division proteins largely form trimeric efflux pumps. The drug efflux process has been proposed to entail a synchronized motion between subunits of the trimer to advance the transport cycle, leading to the extrusion of drug molecules. Here we use X-ray crystallography and single-molecule fluorescence resonance energy transfer imaging to elucidate the structures and functional dynamics of the Campylobacter jejuni CmeB multidrug efflux pump. We find that the CmeB trimer displays a very unique conformation. A directmore » observation of transport dynamics in individual CmeB trimers embedded in membrane vesicles indicates that each CmeB subunit undergoes conformational transitions uncoordinated and independent of each other. On the basis of our findings and analyses, we propose a model for transport mechanism where CmeB protomers function independently within the trimer.« less

The Texas horned lizard as model for robust capillary structures for passive directional transport of cooling lubricants

NASA Astrophysics Data System (ADS)

Comanns, Philipp; Winands, Kai; Pothen, Mario; Bott, Raya A.; Wagner, Hermann; Baumgartner, Werner

2016-04-01

Moisture-harvesting lizards, such as the Texas horned lizard Phrynosoma cornutum, have remarkable adaptations for inhabiting arid regions. Special skin structures, in particular capillary channels in between imbricate overlapping scales, enable the lizard to collect water by capillarity and to transport it to the snout for ingestion. This fluid transport is passive and directional towards the lizard's snout. The directionality is based on geometric principles, namely on a periodic pattern of interconnected half-open capillary channels that narrow and widen. Following a biomimetic approach, these principles were transferred to technical prototype design and manufacturing. Capillary structures, 50 μm to 300 μm wide and approx. 70 μm deep, were realized by use of a pulsed picosecond laser in hot working tool steel, hardened to 52 HRC. In order to achieve highest functionality, strategies were developed to minimize potential structural inaccuracies, which can occur at the bottom of the capillary structures caused by the laser process. Such inaccuracies are in the range of 10 μm to 15 μm and form sub-capillary structures with greater capillary forces than the main channels. Hence, an Acceleration Compensation Algorithm was developed for the laser process to minimize or even avoid these inaccuracies. The capillary design was also identified to have substantial influence; by a hexagonal capillary network of non-parallel capillaries potential influences of sub-capillaries on the functionality were reduced to realize a robust passive directional capillary transport. Such smart surface structures can lead to improvements of technical systems by decreasing energy consumption and increasing the resource efficiency.

Molecular mechanism of substrate recognition and transport by the AtSWEET13 sugar transporter.

PubMed

Han, Lei; Zhu, Yongping; Liu, Min; Zhou, Ye; Lu, Guangyuan; Lan, Lan; Wang, Xianping; Zhao, Yongfang; Zhang, Xuejun C

2017-09-19

Sugar Will Eventually be Exported Transporters (SWEETs) are recently identified sugar transporters that can discriminate and transport di- or monosaccharides across a membrane following the concentration gradient. SWEETs play key roles in plant biological processes, such as pollen nutrition, nectar secretion, seed filling, and phloem loading. SWEET13 from Arabidopsis thaliana (AtSWEET13) is an important sucrose transporter in pollen development. Here, we report the 2.8-Å resolution crystal structure of AtSWEET13 in the inward-facing conformation with a substrate analog, 2'-deoxycytidine 5'-monophosphate, bound in the central cavity. In addition, based on the results of an in-cell transport activity assay and single-molecule Förster resonance energy transfer analysis, we suggest a mechanism for substrate selectivity based on the size of the substrate-binding pocket. Furthermore, AtSWEET13 appears to form a higher order structure presumably related to its function.

Connectingthe puzzle pieces between cytoskeleton andsecretory pathway

PubMed Central

Gurel, Pinar S.; Hatch, Anna L.; Higgs, Henry N.

2014-01-01

A tendency in cell biology is to divide and conquer. For example, decades of painstaking work have led to an understanding of endoplasmic reticulum (ER) and Golgi structure, dynamics, and transport. In parallel, cytoskeletal researchers have revealed a fantastic diversity of structure and cellular function in both actin and microtubules. Increasingly, these areas overlap, necessitating an understanding of both organelle and cytoskeletal biology. This review addressesconnections between the actin/microtubule cytoskeletons and organelles in animal cells, focusing on threetopics: ER structure/function, ER-to-Golgi transport; and Golgi structure/function. Making these connections has been challenging, due to 1) the small sizes and dynamic characteristics of some components, 2) the fact that organelle-specific cytoskeleton can easily be obscured by more abundant cytoskeletal structures, and 3) the difficulties in imaging membranes and cytoskeleton simultaneously, especially at the ultra-structural level. One major concept is that the cytoskeleton is frequently used to generate force for membrane movement, with two potential consequences: translocation of the organelle, or deformation of the organelle membrane. While initially discussing issues common to metazoan cells in general, we subsequently highlight specific features of neurons, since these highly polarized cells present unique challenges for organellar distribution and dynamics. PMID:25050967

Asp133 Residue in NhaA Na+/H+ Antiporter Is Required for Stability Cation Binding and Transport.

PubMed

Rimon, Abraham; Dwivedi, Manish; Friedler, Assaf; Padan, Etana

2018-03-16

Na + /H + antiporters have a crucial role in pH and Na + homeostasis in cells. The crystal structure of NhaA, the main antiporter of Escherichia coli, has provided general insights into antiporter mechanisms and revealed a previously unknown structural fold, which has since been identified in several secondary active transporters. This unique structural fold is very delicately electrostatically balanced. Asp133 and Lys 300 have been ascribed essential roles in this balance and, more generally, in the structure and function of the antiporter. In this work, we show the multiple roles of Asp133 in NhaA: (i) The residue's negative charge is critical for the stability of the NhaA structure. (ii) Its main chain is part of the active site. (iii) Its side chain functions as an alkaline-pH-dependent gate, changing the protein's conformation from an inward-facing conformation at acidic pH to an outward-open conformation at alkaline pH, opening the periplasm funnel. On the basis of the experimental data, we propose a tentative mechanism integrating the structural and functional roles of Asp133. Copyright © 2018 Elsevier Ltd. All rights reserved.

Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport

PubMed Central

Sherman, David J.; Lazarus, Michael B.; Murphy, Lea; Liu, Charles; Walker, Suzanne; Ruiz, Natividad; Kahne, Daniel

2014-01-01

The cell surface of Gram-negative bacteria contains lipopolysaccharides (LPS), which provide a barrier against the entry of many antibiotics. LPS assembly involves a multiprotein LPS transport (Lpt) complex that spans from the cytoplasm to the outer membrane. In this complex, an unusual ATP-binding cassette transporter is thought to power the extraction of LPS from the outer leaflet of the cytoplasmic membrane and its transport across the cell envelope. We introduce changes into the nucleotide-binding domain, LptB, that inactivate transporter function in vivo. We characterize these residues using biochemical experiments combined with high-resolution crystal structures of LptB pre- and post-ATP hydrolysis and suggest a role for an active site residue in phosphate exit. We also identify a conserved residue that is not required for ATPase activity but is essential for interaction with the transmembrane components. Our studies establish the essentiality of ATP hydrolysis by LptB to power LPS transport in cells and suggest strategies to inhibit transporter function away from the LptB active site. PMID:24639492

Exact Thermal Transport Properties of Gray-Arsenic using Electon-Phonon Coupling

NASA Astrophysics Data System (ADS)

Kang, Seoung-Hun; Kwon, Young-Kyun

Using various theoretical methods, we investigate the thermoelectric property of gray arsenic. Thermoelectric devices that utilize the Seebeck effect convert heat flow into electrical energy. The conversion efficiency of such a device is determined by its figure of merit or ZT value, which is related to various transport coefficients, such as Seebeck coefficient and the ratio of its electrical conductivity to its thermal counterpart for given temperature. To calculate various transport coefficients and thus the ZT values of gray arsenic, we apply the Boltzmann transport theory to its electronic and phononic structures obtained by density functional theory and density functional perturbation theory together with maximally locallized Wannier functions. During this procedure, we evaluate its relaxation time accurately by explicitly considering electron-phonon coupling. Our result reveals that gray arsenic may be used for a good p-type thermoelectric devices.

Investigation of thermoelectricity in KScSn half-Heusler compound

NASA Astrophysics Data System (ADS)

Shrivastava, Deepika; Acharya, Nikita; Sanyal, Sankar P.

2018-05-01

The electronic and transport properties of KScSn half-Heusler (HH) compound have been investigated using first-principles density functional theory and semi classical Boltzmann transport theory. The electronic band structure and density of states (total and partial) show semiconducting nature of KScSn with band gap 0.48 eV which agree well with previously reported results. The transport coefficient such as electrical conductivity, Seebeck coefficient, electronic thermal conductivity and power factor as a function of chemical potential are evaluated. KScSn has high power factor for p-type doping and is a potential candidate for thermoelectric applications.

Proceedings of the Workshop on Transportation/Urban Form Interactions held at Cambridge, MA. on August 14-15, 1978

DOT National Transportation Integrated Search

1979-06-01

Contents: A form of utility function for the UMOT model; An analysis of transportation/land use interactions; Toward a methodology to shape urban structure; Approaches for improving urban travel forecasts; Quasi-dynamic urban location models with end...

Structures manual

DOT National Transportation Integrated Search

2001-01-01

This manual was written as a guide for use by design personnel in the Vermont Agency of Transportation Structures Section. This manual covers the design responsibilities of the Section. It does not cover other functions that are a part of the Structu...

Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications.

PubMed

Stockner, Thomas; Mullen, Anna; MacMillan, Fraser

2015-10-01

ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented. © 2015 Authors; published by Portland Press Limited.

Structure-Function Relationship of a Plant NCS1 Member – Homology Modeling and Mutagenesis Identified Residues Critical for Substrate Specificity of PLUTO, a Nucleobase Transporter from Arabidopsis

PubMed Central

Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M. Joanne; Möhlmann, Torsten

2014-01-01

Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. PMID:24621654

Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis.

PubMed

Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M Joanne; Möhlmann, Torsten

2014-01-01

Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.

Functional interactions between arginine-133 and aspartate-88 in the human reduced folate carrier: evidence for a charge-pair association.

PubMed Central

Liu, X Y; Matherly, L H

2001-01-01

The human reduced folate carrier (hRFC) is an integral membrane protein that mediates cellular uptake of reduced folates and antifolates. hRFC contains several highly conserved charged residues predicted to lie in the transmembrane domains (TMDs). To explore the possible roles of the conserved arginine-133, located in TMD 4, in hRFC structure and function, this residue was systematically mutagenized to histidine, leucine, lysine and glutamate. When transfected into transport-impaired K562 cells, the mutant hRFC constructs were expressed at high levels; however, only lysine-133 hRFC was able to transport methotrexate and (6S)-5-formyl tetrahydrofolate. Substitution of aspartate-453 (in hRFC TMD 12) by valine largely preserved transport activity for both substrates. Although mutagenesis of aspartate-88 (in TMD 2) to leucine completely abolished transport activity in transfected cells, substitution with a glutamate preserved low levels ( approximately 12%) of transport. To assess the possibility that arginine-133 and aspartate-88 may form a charge-pair to stabilize hRFC tertiary structure, both charges were neutralized (by substituting leucine and valine, respectively) in the same construct. In contrast to the singly mutated hRFCs, the double mutant exhibited high levels of transport with both methotrexate and 5-formyl tetrahydrofolate. These results strongly suggest that arginine-133 and aspartate-88 form a charge-pair and that TMD 4 lies next to TMD 2 in the hRFC tertiary structure. PMID:11513752

Discrete and continuum links to a nonlinear coupled transport problem of interacting populations

NASA Astrophysics Data System (ADS)

Duong, M. H.; Muntean, A.; Richardson, O. M.

2017-07-01

We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind are inspired by the dynamics of pedestrian flows in open spaces and are intimately connected to cross-diffusion and thermo-diffusion problems holding a variational structure. The tools we use include a suitable structure of the relative entropy controlling TV-norms, the construction of Lyapunov functionals and particular closed-form solutions to nonlinear transport equations, a hydrodynamics limiting procedure due to Philipowski, as well as the construction of numerical approximates to both the continuum limit problem in 2D and to the original interacting particle systems.

Anatomical features associated with water transport in imperforate tracheary elements of vessel-bearing angiosperms

PubMed Central

Sano, Yuzou; Morris, Hugh; Shimada, Hiroshi; Ronse De Craene, Louis P.; Jansen, Steven

2011-01-01

Background and Aims Imperforate tracheary elements (ITEs) in wood of vessel-bearing angiosperms may or may not transport water. Despite the significance of hydraulic transport for defining ITE types, the combination of cell structure with water transport visualization in planta has received little attention. This study provides a quantitative analysis of structural features associated with the conductive vs. non-conductive nature of ITEs. Methods Visualization of water transport was studied in 15 angiosperm species by dye injection and cryo-scanning electron microscopy. Structural features of ITEs were examined using light and electron microscopy. Key Results ITEs connected to each other by pit pairs with complete pit membranes contributed to water transport, while cells showing pit membranes with perforations up to 2 µm were hydraulically not functional. A close relationship was found between pit diameter and pit density, with both characters significantly higher in conductive than in non-conductive cells. In species with both conductive and non-conductive ITEs, a larger diameter was characteristic of the conductive cells. Water transport showed no apparent relationship with the length of ITEs and vessel grouping. Conclusions The structure and density of pits between ITEs represent the main anatomical characters determining water transport. The pit membrane structure of ITEs provides a reliable, but practically challenging, criterion to determine their conductive status. It is suggested that the term tracheids should strictly be used for conductive ITEs, while fibre-tracheids and libriform fibres are non-conductive. PMID:21385773

Molecular Spintronics: Theory of Spin-Dependent Electron Transport in Fe/BDT/Fe Molecular Wire Systems

NASA Astrophysics Data System (ADS)

Dalgleish, Hugh; Kirczenow, George

2004-03-01

Metal/Molecule/Metal junction systems forming molecular wires are currently the focus of intense study. Recently, spin-dependent electron transport in molecular wires with magnetic Ni electrodes has been studied theoretically, and spin-valve effects have been predicted.* Here we explore theoretically another magnetic molecular wire system, namely, ferromagnetic Fe nano-contacts bridged with 1,4-benzene-dithiolate (BDT). We estimate the essential structural and electronic parameters for this system based on ab initio density functional calculations (DFT) for some simple model systems involving thiol groups and Fe clusters as well as semi-empirical considerations and the known electronic structure of bulk Fe. We then use Lippmann-Schwinger and Green's function techniques together with the Landauer formalism to study spin-dependent transport. *E. G. Emberly and G. Kirczenow, Chem. Phys. 281, 311 (2002); R. Pati, L. Senapati, P.M. Ajayan and S.K. Nayak, Phys. Rev. B68, 100407 (2003).

Transport characteristics of a ZnMgO/ZnO hetero junction and the effect of temperature and Mg content

NASA Astrophysics Data System (ADS)

Uslu, Salih; Yarar, Zeki

2017-02-01

The Ensemble Monte Carlo method is used to calculate the transport characteristics of two dimensional electron gas (2DEG) at a ZnMgO/ZnO hetero structure. The spontaneous and piezoelectric polarizations are considered and there is no intentional doping in either material. Numerical Schrödinger and Poisson equations are solved self consistently to obtain the scattering rates of various scattering mechanisms. The density of carriers, each energy sub bands, potential profile and corresponding wave functions are obtained from the self consistent calculations. The self consistent sub band wave functions of acoustic and optic phonon scattering and interface roughness scattering are used in Monte Carlo method to obtain transport characteristics at ZnMgO/ZnO junction. Two dimensional electron gas confined to ZnMgO/ZnO hetero structure is studied and the effect of temperature and Mg content are investigated.

Diazonium functionalized graphene: microstructure, electric, and magnetic properties.

PubMed

Huang, Ping; Jing, Long; Zhu, Huarui; Gao, Xueyun

2013-01-15

The unique honeycomb lattice structure of graphene gives rise to its outstanding electronic properties such as ultrahigh carrier mobility, ballistic transport, and more. However, a crucial obstacle to its use in the electronics industry is its lack of an energy bandgap. A covalent chemistry strategy could overcome this problem, and would have the benefits of being highly controllable and stable in the ambient environment. One possible approach is aryl diazonium functionalization. In this Account, we investigate the micromolecular/lattice structure, electronic structure, and electron-transport properties of nitrophenyl-diazonium-functionalized graphene. We find that nitrophenyl groups mainly adopt random and inhomogeneous configurations on the graphene basal plane, and that their bonding with graphene carbon atoms leads to slight elongation of the graphene lattice spacing. By contrast, hydrogenated graphene has a compressed lattice. Low levels of functionalization suppressed the electric conductivity of the resulting functionalized graphene, while highly functionalized graphene showed the opposite effect. This difference arises from the competition between the charge transfer effect and the scattering enhancement effect introduced by nitrophenyl groups bonding with graphene carbon atoms. Detailed electron transport measurements revealed that the nitrophenyl diazonium functionalization locally breaks the symmetry of graphene lattice, which leads to an increase in the density of state near the Fermi level, thus increasing the carrier density. On the other hand, the bonded nitrophenyl groups act as scattering centers, lowering the mean free path of the charge carriers and suppressing the carrier mobility. In rare cases, we observed ordered configurations of nitrophenyl groups in local domains on graphene flakes due to fluctuations in the reaction processes. We describe one example of such a superlattice, with a lattice constant nearly twice of that of pristine graphene. We performed comprehensive theoretical calculations to investigate the lattice and the electronic structure of the superlattice structure. Our results reveal that it is a thermodynamically stable, spin-polarized semiconductor with a bandgap of ∼0.5 eV. Our results demonstrate the possibility of controlling graphene's electronic properties using aryl diazonium functionalization. Asymmetric addition of aryl groups to different sublattices of graphene is a promising approach for producing ferromagnetic, semiconductive graphene, which will have broad applications in the electronic industry.

Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics

NASA Astrophysics Data System (ADS)

Hirokawa, N.; Takemura, R.

Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.

Transport, Structural and Mechanical Properties of Quaternary FeVTiAl Alloy

NASA Astrophysics Data System (ADS)

Bhat, Tahir Mohiuddin; Gupta, Dinesh C.

2016-11-01

The electronic, structural, magnetic and transport properties of FeVTiAl quaternary alloy have been investigated within the framework of density functional theory. The material is a completely spin-polarized half-metallic ferromagnet in its ground state with F-43m structure. The structural stability was further confirmed by elastic constants in the cubic phase with high Young's modulus and brittle nature. The present study predicts an energy band gap of 0.72 eV in a localized minority spin channel at equilibrium lattice parameter of 6.00 Å. The transport properties of the material are discussed based on the Seebeck coefficient, and electrical and thermal conductivity coefficients. The alloy presents large values of Seebeck coefficients, ~39 μV K-1 at room temperature (300 K), and has an excellent thermoelectric performance with ZT = ~0.8.

A tonoplast intrinsic protein in Gardenia jasminoides

NASA Astrophysics Data System (ADS)

Gao, Lan; Li, Hao-Ming

2017-08-01

Physiological and molecular studies proved that plasma membrane intrinsic proteins (PIPs) and tonoplast intrinsic proteins (TIPs) subfamily of aquaporins play key functions in plant water homeostasis. Five specialized subgroups (TIP1-5) of TIPs have been found in higher plants, in which the TIP1 and TIP2 isoforms are the largest arbitrary groups. TIPs have high water-transport activity than PIPs, some TIPs can transport other small molecule such as urea, ammonia, hydrogen peroxide, and carbon dioxide. In this work, the structure of the putative tonoplast aquaporin from Gardenia jasminoides (GjTIP) was analyzed. Its transcript level has increased during fruit maturation. A phylogenetic analysis indicates that the protein belongs to TIP1 subfamily. A three-dimensional model structure of GjTIP was built based on crystal structure of an ammonia-permeable AtTIP2-1 from Arabidopsis thaliana. The model structure displayed as a homo-tetramer, each monomer has six trans-membrane and two half-membrane-spanning α helices. The data suggests that the GjTIP has tendency to be a mixed function aquaporin, might involve in water, urea and hydrogen peroxide transport, and the gating machanism founded in some AQPs involving pH and phosphorylation response have not been proved in GjTIP.

Overexpression of neurofilament H disrupts normal cell structure and function

NASA Technical Reports Server (NTRS)

Szebenyi, Gyorgyi; Smith, George M.; Li, Ping; Brady, Scott T.

2002-01-01

Studying exogenously expressed tagged proteins in live cells has become a standard technique for evaluating protein distribution and function. Typically, expression levels of experimentally introduced proteins are not regulated, and high levels are often preferred to facilitate detection. However, overexpression of many proteins leads to mislocalization and pathologies. Therefore, for normative studies, moderate levels of expression may be more suitable. To understand better the dynamics of intermediate filament formation, transport, and stability in a healthy, living cell, we inserted neurofilament heavy chain (NFH)-green fluorescent protein (GFP) fusion constructs in adenoviral vectors with tetracycline (tet)-regulated promoters. This system allows for turning on or off the synthesis of NFH-GFP at a selected time, for a defined period, in a dose-dependent manner. We used this inducible system for live cell imaging of changes in filament structure and cell shape, motility, and transport associated with increasing NFH-GFP expression. Cells with low to intermediate levels of NFH-GFP were structurally and functionally similar to neighboring, nonexpressing cells. In contrast, overexpression led to pathological alterations in both filament organization and cell function. Copyright 2002 Wiley-Liss, Inc.

Relationship Between Nutrient Enrichment and Benthic Function: Local Effects and Spatial Patterns

EPA Science Inventory

Eutrophication-induced changes to benthic structure and function are problems of enormous ecological and economic significance. Understanding the relationships between nutrient enrichment and effects, modifying factors such as localized transport time, and symptoms of eutrophica...

Correlation Function Analysis of Fiber Networks: Implications for Thermal Conductivity

NASA Technical Reports Server (NTRS)

Martinez-Garcia, Jorge; Braginsky, Leonid; Shklover, Valery; Lawson, John W.

2011-01-01

The heat transport in highly porous fiber structures is investigated. The fibers are supposed to be thin, but long, so that the number of the inter-fiber connections along each fiber is large. We show that the effective conductivity of such structures can be found from the correlation length of the two-point correlation function of the local conductivities. Estimation of the parameters, determining the conductivity, from the 2D images of the structures is analyzed.

Ion Binding Energies Determining Functional Transport of ClC Proteins

NASA Astrophysics Data System (ADS)

Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

2014-06-01

The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

The Functions of Metallothionein and ZIP and ZnT Transporters: An Overview and Perspective

PubMed Central

Kimura, Tomoki; Kambe, Taiho

2016-01-01

Around 3000 proteins are thought to bind zinc in vivo, which corresponds to ~10% of the human proteome. Zinc plays a pivotal role as a structural, catalytic, and signaling component that functions in numerous physiological processes. It is more widely used as a structural element in proteins than any other transition metal ion, is a catalytic component of many enzymes, and acts as a cellular signaling mediator. Thus, it is expected that zinc metabolism and homeostasis have sophisticated regulation, and elucidating the underlying molecular basis of this is essential to understanding zinc functions in cellular physiology and pathogenesis. In recent decades, an increasing amount of evidence has uncovered critical roles of a number of proteins in zinc metabolism and homeostasis through influxing, chelating, sequestrating, coordinating, releasing, and effluxing zinc. Metallothioneins (MT) and Zrt- and Irt-like proteins (ZIP) and Zn transporters (ZnT) are the proteins primarily involved in these processes, and their malfunction has been implicated in a number of inherited diseases such as acrodermatitis enteropathica. The present review updates our current understanding of the biological functions of MTs and ZIP and ZnT transporters from several new perspectives. PMID:26959009

Crystal structure of the plasma membrane proton pump.

PubMed

Pedersen, Bjørn P; Buch-Pedersen, Morten J; Morth, J Preben; Palmgren, Michael G; Nissen, Poul

2007-12-13

A prerequisite for life is the ability to maintain electrochemical imbalances across biomembranes. In all eukaryotes the plasma membrane potential and secondary transport systems are energized by the activity of P-type ATPase membrane proteins: H+-ATPase (the proton pump) in plants and fungi, and Na+,K+-ATPase (the sodium-potassium pump) in animals. The name P-type derives from the fact that these proteins exploit a phosphorylated reaction cycle intermediate of ATP hydrolysis. The plasma membrane proton pumps belong to the type III P-type ATPase subfamily, whereas Na+,K+-ATPase and Ca2+-ATPase are type II. Electron microscopy has revealed the overall shape of proton pumps, however, an atomic structure has been lacking. Here we present the first structure of a P-type proton pump determined by X-ray crystallography. Ten transmembrane helices and three cytoplasmic domains define the functional unit of ATP-coupled proton transport across the plasma membrane, and the structure is locked in a functional state not previously observed in P-type ATPases. The transmembrane domain reveals a large cavity, which is likely to be filled with water, located near the middle of the membrane plane where it is lined by conserved hydrophilic and charged residues. Proton transport against a high membrane potential is readily explained by this structural arrangement.

The effects of electron and hole transport layer with the electrode work function on perovskite solar cells

NASA Astrophysics Data System (ADS)

Deng, Quanrong; Li, Yiqi; Chen, Lian; Wang, Shenggao; Wang, Geming; Sheng, Yonglong; Shao, Guosheng

2016-09-01

The effects of electron and hole transport layer with the electrode work function on perovskite solar cells with the interface defects were simulated by using analysis of microelectronic and photonic structures-one-dimensional (AMPS-1D) software. The simulation results suggest that TiO2 electron transport layer provides best device performance with conversion efficiency of 25.9% compared with ZnO and CdS. The threshold value of back electrode work function for Spiro-OMeTAD, NiO, CuI and Cu2O hole transport layer are calculated to be 4.9, 4.8, 4.7 and 4.9 eV, respectively, to reach the highest conversion efficiency. The mechanisms of device physics with various electron and hole transport materials are discussed in details. The device performance deteriorates gradually as the increased density of interface defects located at ETM/absorber or absorber/HTM. This research results can provide helpful guidance for materials and metal electrode choice for perovskite solar cells.

The Transporter Classification Database: recent advances.

PubMed

Saier, Milton H; Yen, Ming Ren; Noto, Keith; Tamang, Dorjee G; Elkan, Charles

2009-01-01

The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.

[Lipoproteins as a specific circulatory transport system].

PubMed

Titov, V N

1998-01-01

In accordance with the systemic approach, each circulatory transport system is highly specific and transports an elementary substance from cell to cell in the hydrated medium. In the author's opinion, the lipoprotein system has also a functional specificity and carries the elementary substance fatty acid in the blood stream. A great variety of fatty acids, the individuality of their physicochemical properties, great stereochemic differences of saturated and polyenic fatty acids make their transport virtually impossible. The steric individuality of fatty acids can be reduced if the acids are covalently bonded by a matrix as complex lipids. For formation of complex lipids, nature prefers esterification of fatty acids with alcohols which have a varying hydrophoby, such as glycerol, sphingosine, cholesterol, cetyl alcohol. The steric differences of saturated and polyenic fatty acids form a basis for their being structurized in different lipids. Triacyl glycerides are a transport form of saturated, monounsaturated fatty acids and their transforms and give rise to a crystalline phase. Phospholipids and cholesterol esters are a transport form of mainly polyunsaturated fatty acids in the polar phase in the former case and in the crystalline phase in the latter one. The individual apolipoproteins structure complex lipids into individual lipoprotein particles and transport them in the hydrated medium of blood flow. Saturated fatty acids chiefly transport lipoprotein particles formed by apoB-48- and apoB-100-isoproteins. Polyenic acids transport mainly high-density apoA-1-lipoprotein particles, which makes up a main physiological function of the latter. Cholesterol is nothing more than a matrix; it reesterifies polyenic fatty acids from the polar transport form of phospholipids into the unpolar transport form of cholesterol esters. Cholesterol esterification of polyenic fatty acids may structure complex lipid in the unpolar phase and transport it to the cells via apoB-100-ligand-receptor interaction, which is considered to be a key stage in the multistage process of active transport to the cells of polyenic fatty acids. However, the significant differences of active and inactive transport of polyenic fatty acids in the blood stream await a separate consideration.

Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter

PubMed Central

2014-01-01

Uptake of neurotransmitters by sodium-coupled monoamine transporters of the NSS family is required for termination of synaptic transmission. Transport is tightly regulated by protein–protein interactions involving the small cytoplasmic segments at the amino- and carboxy-terminal ends of the transporter. Although structures of homologues provide information about the transmembrane regions of these transporters, the structural arrangement of the terminal domains remains largely unknown. Here, we combined molecular modeling, biochemical, and biophysical approaches in an iterative manner to investigate the structure of the 82-residue N-terminal and 30-residue C-terminal domains of human serotonin transporter (SERT). Several secondary structures were predicted in these domains, and structural models were built using the Rosetta fragment-based methodology. One-dimensional 1H nuclear magnetic resonance and circular dichroism spectroscopy supported the presence of helical elements in the isolated SERT N-terminal domain. Moreover, introducing helix-breaking residues within those elements altered the fluorescence resonance energy transfer signal between terminal cyan fluorescent protein and yellow fluorescent protein tags attached to full-length SERT, consistent with the notion that the fold of the terminal domains is relatively well-defined. Full-length models of SERT that are consistent with these and published experimental data were generated. The resultant models predict confined loci for the terminal domains and predict that they move apart during the transport-related conformational cycle, as predicted by structures of homologues and by the “rocking bundle” hypothesis, which is consistent with spectroscopic measurements. The models also suggest the nature of binding to regulatory interaction partners. This study provides a structural context for functional and regulatory mechanisms involving SERT terminal domains. PMID:25093911

Simulation of electron transport in quantum well devices

NASA Technical Reports Server (NTRS)

Miller, D. R.; Gullapalli, K. K.; Reddy, V. R.; Neikirk, D. P.

1992-01-01

Double barrier resonant tunneling diodes (DBRTD) have received much attention as possible terahertz devices. Despite impressive experimental results, the specifics of the device physics (i.e., how the electrons propagate through the structure) are only qualitatively understood. Therefore, better transport models are warranted if this technology is to mature. In this paper, the Lattice Wigner function is used to explain the important transport issues associated with DBRTD device behavior.

Plasma membrane dynamics and tetrameric organisation of ABCG2 transporters in mammalian cells revealed by single particle imaging techniques.

PubMed

Wong, Kelvin; Briddon, Stephen J; Holliday, Nicholas D; Kerr, Ian D

2016-01-01

ABCG2 is one of three human ATP binding cassette (ABC) transporters involved in the export from cells of a chemically and structurally diverse range of compounds. This multidrug efflux capability, together with a broad tissue distribution in the body, means that ABCG2 exerts a range of effects on normal physiology such as kidney urate transport, as well as contributing towards the pharmacokinetic profiles of many exogenous drugs. The primary sequence of ABCG2 contains only half the number of domains required for a functioning ABC transporter and so it must oligomerise in order to function, yet its oligomeric state in intact cell membranes remains uncharacterized. We have analysed ABCG2 in living cell membranes using a combination of fluorescence correlation spectroscopy, photon counting histogram analysis, and stepwise photobleaching to demonstrate a predominantly tetrameric structure for ABCG2 in the presence or absence of transport substrates. These results provide the essential basis for exploring pharmacological manipulation of oligomeric state as a strategy to modulate ABCG2 activity in future selective therapeutics. Copyright © 2015 Elsevier B.V. All rights reserved.

Spin transport properties of n-polyacene molecules (n = 1–15) connected to Ni surface electrodes: Theoretical analysis

PubMed Central

Caliskan, S.; Laref, A.

2014-01-01

Using non-equilibrium Green function formalism in conjunction with density functional theory, we explore the spin-polarized transport characteristics of several planar n-acene molecules suspended between two semi-infinite Ni electrodes via the thiol group. We examine the spin-dependence transport on Ni-n-acenes-Ni junctions, while the number of fused benzene rings varies between 1 and 15. Intriguingly, the induced magnetic moments of small acene molecules are higher than that of longer acene rings. The augmentation of fused benzene rings affects both the magnetic and transport features, such as the transmission function and conductance owing to their coupling to the Ni surface contacts via the anchoring group. The interplay between the spin-polarized transport properties, structural configuration and molecular electronic is a fortiori essential in these attractive molecular devices. Thus, this can conduct to the engineering of the electron spin transport in atomistic and molecular junctions. These prominent molecules convincingly infer that the molecular spin valves can conduct to thriving molecular devices. PMID:25482076

In vivo Visuotopic Brain Mapping with Manganese-Enhanced MRI and Resting-State Functional Connectivity MRI

PubMed Central

Chan, Kevin C.; Fan, Shu-Juan; Chan, Russell W.; Cheng, Joe S.; Zhou, Iris Y.; Wu, Ed X.

2014-01-01

The rodents are an increasingly important model for understanding the mechanisms of development, plasticity, functional specialization and disease in the visual system. However, limited tools have been available for assessing the structural and functional connectivity of the visual brain network globally, in vivo and longitudinally. There are also ongoing debates on whether functional brain connectivity directly reflects structural brain connectivity. In this study, we explored the feasibility of manganese-enhanced MRI (MEMRI) via 3 different routes of Mn2+ administration for visuotopic brain mapping and understanding of physiological transport in normal and visually deprived adult rats. In addition, resting-state functional connectivity MRI (RSfcMRI) was performed to evaluate the intrinsic functional network and structural-functional relationships in the corresponding anatomical visual brain connections traced by MEMRI. Upon intravitreal, subcortical, and intracortical Mn2+ injection, different topographic and layer-specific Mn enhancement patterns could be revealed in the visual cortex and subcortical visual nuclei along retinal, callosal, cortico-subcortical, transsynaptic and intracortical horizontal connections. Loss of visual input upon monocular enucleation to adult rats appeared to reduce interhemispheric polysynaptic Mn2+ transfer but not intra- or inter-hemispheric monosynaptic Mn2+ transport after Mn2+ injection into visual cortex. In normal adults, both structural and functional connectivity by MEMRI and RSfcMRI was stronger interhemispherically between bilateral primary/secondary visual cortex (V1/V2) transition zones (TZ) than between V1/V2 TZ and other cortical nuclei. Intrahemispherically, structural and functional connectivity was stronger between visual cortex and subcortical visual nuclei than between visual cortex and other subcortical nuclei. The current results demonstrated the sensitivity of MEMRI and RSfcMRI for assessing the neuroarchitecture, neurophysiology and structural-functional relationships of the visual brains in vivo. These may possess great potentials for effective monitoring and understanding of the basic anatomical and functional connections in the visual system during development, plasticity, disease, pharmacological interventions and genetic modifications in future studies. PMID:24394694

Effects of pressure and electrical charge on macromolecular transport across bovine lens basement membrane.

PubMed

Ferrell, Nicholas; Cameron, Kathleen O; Groszek, Joseph J; Hofmann, Christina L; Li, Lingyan; Smith, Ross A; Bian, Aihua; Shintani, Ayumi; Zydney, Andrew L; Fissell, William H

2013-04-02

Molecular transport through the basement membrane is important for a number of physiological functions, and dysregulation of basement membrane architecture can have serious pathological consequences. The structure-function relationships that govern molecular transport in basement membranes are not fully understood. The basement membrane from the lens capsule of the eye is a collagen IV-rich matrix that can easily be extracted and manipulated in vitro. As such, it provides a convenient model for studying the functional relationships that govern molecular transport in basement membranes. Here we investigate the effects of increased transmembrane pressure and solute electrical charge on the transport properties of the lens basement membrane (LBM) from the bovine eye. Pressure-permeability relationships in LBM transport were governed primarily by changes in diffusive and convective contributions to solute flux and not by pressure-dependent changes in intrinsic membrane properties. The solute electrical charge had a minimal but statistically significant effect on solute transport through the LBM that was opposite of the expected electrokinetic behavior. The observed transport characteristics of the LBM are discussed in the context of established membrane transport modeling and previous work on the effects of pressure and electrical charge in other basement membrane systems. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

System data communication structures for active-control transport aircraft, volume 2

NASA Technical Reports Server (NTRS)

Hopkins, A. L.; Martin, J. H.; Brock, L. D.; Jansson, D. G.; Serben, S.; Smith, T. B.; Hanley, L. D.

1981-01-01

The application of communication structures to advanced transport aircraft are addressed. First, a set of avionic functional requirements is established, and a baseline set of avionics equipment is defined that will meet the requirements. Three alternative configurations for this equipment are then identified that represent the evolution toward more dispersed systems. Candidate communication structures are proposed for each system configuration, and these are compared using trade off analyses; these analyses emphasize reliability but also address complexity. Multiplex buses are recognized as the likely near term choice with mesh networks being desirable for advanced, highly dispersed systems.

Structural basis of Na(+)-independent and cooperative substrate/product antiport in CaiT.

PubMed

Schulze, Sabrina; Köster, Stefan; Geldmacher, Ulrike; Terwisscha van Scheltinga, Anke C; Kühlbrandt, Werner

2010-09-09

Transport of solutes across biological membranes is performed by specialized secondary transport proteins in the lipid bilayer, and is essential for life. Here we report the structures of the sodium-independent carnitine/butyrobetaine antiporter CaiT from Proteus mirabilis (PmCaiT) at 2.3-A and from Escherichia coli (EcCaiT) at 3.5-A resolution. CaiT belongs to the family of betaine/carnitine/choline transporters (BCCT), which are mostly Na(+) or H(+) dependent, whereas EcCaiT is Na(+) and H(+) independent. The three-dimensional architecture of CaiT resembles that of the Na(+)-dependent transporters LeuT and BetP, but in CaiT a methionine sulphur takes the place of the Na(+) ion to coordinate the substrate in the central transport site, accounting for Na(+)-independent transport. Both CaiT structures show the fully open, inward-facing conformation, and thus complete the set of functional states that describe the alternating access mechanism. EcCaiT contains two bound butyrobetaine substrate molecules, one in the central transport site, the other in an extracellular binding pocket. In the structure of PmCaiT, a tryptophan side chain occupies the transport site, and access to the extracellular site is blocked. Binding of both substrates to CaiT reconstituted into proteoliposomes is cooperative, with Hill coefficients up to 1.7, indicating that the extracellular site is regulatory. We propose a mechanism whereby the occupied regulatory site increases the binding affinity of the transport site and initiates substrate translocation.

Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of Cryptococcus humicola response to aluminum stress.

PubMed

Zhang, Jingjing; Zhang, Lei; Qiu, Jinkui; Nian, Hongjuan

2015-10-01

Cryptococcus humicola is a highly aluminum (Al) tolerant yeast strain isolated from a tea field. Here the relative changes of protein expression in C. humicola undergoing aluminum stress were analyzed to understand the genetic basis of aluminum tolerance. In this work, iTRAQ-based (isobaric tags for relative and absolute quantification) quantitative proteomic technology was used to detect statistically significant proteins associated with the response to aluminum stress. A total of 625 proteins were identified and were mainly involved in translation/ribosomal structure and biogenesis, posttranslational modification/protein turnover/chaperones, energy production and conversion, and amino acid transport and metabolism. Of these proteins, 59 exhibited differential expression during aluminum stress. Twenty-nine proteins up-regulated by aluminum were mainly involved in translation/ribosomal structure and biogenesis, posttranslational modification/protein turnover and chaperones, and lipid transport and metabolism. Thirty proteins down-regulated by aluminum were mainly associated with energy transport and metabolism, translation/ribosomal structure and biogenesis, posttranslational modification/protein turnover/chaperones, and lipid transport and metabolism. The potential functions of some proteins in aluminum tolerance are discussed. These functional changes may be beneficial for cells to protect themselves from aluminum toxic conditions. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Investigation of evolution-related aspects of bacterial rhodopsins

NASA Technical Reports Server (NTRS)

1994-01-01

We have investigated evolution-related aspects of bacterial rhodopsins, the unique retinal-based energy transducing systems of halophilic archae. The approach was to describe both structural and functional aspects: the structure by sequencing genes to explore which regions are conserved, and the function by comparing proton and chloride transport in the closely related systems, bacteriorhodopsin and halorhodopsin, respectively. In the latter, we have made a good start toward the ultimate goal of separating the attributes of the general principles of retinal-based ionic pumps from those of the specific ion specificities, by determining the thermodynamics of the internal steps of the protein-mediated active transport process, as well as some of the intraprotein ion-transfer steps. Our present emphasis is on continuing to acquire the tools for studying what distinguishes proton transport from chloride transport. We consider it important, therefore, that we have been able to provide firm mathematical grounds for the kinetics analyses which underlies these studies. Our molecular biological studies have received a great boost from the expression vector for the bop gene based on a halobacterial plasmid, that we recently developed.

The axonal transport of mitochondria

PubMed Central

Saxton, William M.; Hollenbeck, Peter J.

2012-01-01

Vigorous transport of cytoplasmic components along axons over substantial distances is crucial for the maintenance of neuron structure and function. The transport of mitochondria, which serves to distribute mitochondrial functions in a dynamic and non-uniform fashion, has attracted special interest in recent years following the discovery of functional connections among microtubules, motor proteins and mitochondria, and their influences on neurodegenerative diseases. Although the motor proteins that drive mitochondrial movement are now well characterized, the mechanisms by which anterograde and retrograde movement are coordinated with one another and with stationary axonal mitochondria are not yet understood. In this Commentary, we review why mitochondria move and how they move, focusing particularly on recent studies of transport regulation, which implicate control of motor activity by specific cell-signaling pathways, regulation of motor access to transport tracks and static microtubule–mitochondrion linkers. A detailed mechanism for modulating anterograde mitochondrial transport has been identified that involves Miro, a mitochondrial Ca2+-binding GTPase, which with associated proteins, can bind and control kinesin-1. Elements of the Miro complex also have important roles in mitochondrial fission–fusion dynamics, highlighting questions about the interdependence of biogenesis, transport, dynamics, maintenance and degradation. PMID:22619228

Molecular Determinants for Functional Differences between Alanine-Serine-Cysteine Transporter 1 and Other Glutamate Transporter Family Members*

PubMed Central

Scopelliti, Amanda J.; Ryan, Renae M.; Vandenberg, Robert J.

2013-01-01

The ASCTs (alanine, serine, and cysteine transporters) belong to the solute carrier family 1 (SLC1), which also includes the human glutamate transporters (excitatory amino acid transporters, EAATs) and the prokaryotic aspartate transporter GltPh. Despite the high degree of amino acid sequence identity between family members, ASCTs function quite differently from the EAATs and GltPh. The aim of this study was to mutate ASCT1 to generate a transporter with functional properties of the EAATs and GltPh, to further our understanding of the structural basis for the different transport mechanisms of the SLC1 family. We have identified three key residues involved in determining differences between ASCT1, the EAATs and GltPh. ASCT1 transporters containing the mutations A382T, T459R, and Q386E were expressed in Xenopus laevis oocytes, and their transport and anion channel functions were investigated. A382T and T459R altered the substrate selectivity of ASCT1 to allow the transport of acidic amino acids, particularly l-aspartate. The combination of A382T and T459R within ASCT1 generates a transporter with a similar profile to that of GltPh, with preference for l-aspartate over l-glutamate. Interestingly, the amplitude of the anion conductance activated by the acidic amino acids does not correlate with rates of transport, highlighting the distinction between these two processes. Q386E impaired the ability of ASCT1 to bind acidic amino acids at pH 5.5; however, this was reversed by the additional mutation A382T. We propose that these residues differences in TM7 and TM8 combine to determine differences in substrate selectivity between members of the SLC1 family. PMID:23393130

A Conserved Aspartate Residue Located at the Extracellular End of the Binding Pocket Controls Cation Interactions in Brain Glutamate Transporters*

PubMed Central

Rosental, Noa; Gameiro, Armanda; Grewer, Christof; Kanner, Baruch I.

2011-01-01

In the brain, transporters of the major excitatory neurotransmitter glutamate remove their substrate from the synaptic cleft to allow optimal glutamatergic neurotransmission. Their transport cycle consists of two sequential translocation steps, namely cotransport of glutamic acid with three Na+ ions, followed by countertransport of K+. Recent studies, based on several crystal structures of the archeal homologue GltPh, indicate that glutamate translocation occurs by an elevator-like mechanism. The resolution of these structures was not sufficiently high to unambiguously identify the sites of Na+ binding, but functional and computational studies suggest some candidate sites. In the GltPh structure, a conserved aspartate residue (Asp-390) is located adjacent to a conserved tyrosine residue, previously shown to be a molecular determinant of ion selectivity in the brain glutamate transporter GLT-1. In this study, we characterize mutants of Asp-440 of the neuronal transporter EAAC1, which is the counterpart of Asp-390 of GltPh. Except for substitution by glutamate, this residue is functionally irreplaceable. Using biochemical and electrophysiological approaches, we conclude that although D440E is intrinsically capable of net flux, this mutant behaves as an exchanger under physiological conditions, due to increased and decreased apparent affinities for Na+ and K+, respectively. Our present and previous data are compatible with the idea that the conserved tyrosine and aspartate residues, located at the external end of the binding pocket, may serve as a transient or stable cation binding site in the glutamate transporters. PMID:21984827

A conserved aspartate residue located at the extracellular end of the binding pocket controls cation interactions in brain glutamate transporters.

PubMed

Rosental, Noa; Gameiro, Armanda; Grewer, Christof; Kanner, Baruch I

2011-12-02

In the brain, transporters of the major excitatory neurotransmitter glutamate remove their substrate from the synaptic cleft to allow optimal glutamatergic neurotransmission. Their transport cycle consists of two sequential translocation steps, namely cotransport of glutamic acid with three Na(+) ions, followed by countertransport of K(+). Recent studies, based on several crystal structures of the archeal homologue Glt(Ph), indicate that glutamate translocation occurs by an elevator-like mechanism. The resolution of these structures was not sufficiently high to unambiguously identify the sites of Na(+) binding, but functional and computational studies suggest some candidate sites. In the Glt(Ph) structure, a conserved aspartate residue (Asp-390) is located adjacent to a conserved tyrosine residue, previously shown to be a molecular determinant of ion selectivity in the brain glutamate transporter GLT-1. In this study, we characterize mutants of Asp-440 of the neuronal transporter EAAC1, which is the counterpart of Asp-390 of Glt(Ph). Except for substitution by glutamate, this residue is functionally irreplaceable. Using biochemical and electrophysiological approaches, we conclude that although D440E is intrinsically capable of net flux, this mutant behaves as an exchanger under physiological conditions, due to increased and decreased apparent affinities for Na(+) and K(+), respectively. Our present and previous data are compatible with the idea that the conserved tyrosine and aspartate residues, located at the external end of the binding pocket, may serve as a transient or stable cation binding site in the glutamate transporters.

Structures of a Na+-coupled, substrate-bound MATE multidrug transporter

PubMed Central

Lu, Min; Symersky, Jindrich; Radchenko, Martha; Koide, Akiko; Guo, Yi; Nie, Rongxin; Koide, Shohei

2013-01-01

Multidrug transporters belonging to the multidrug and toxic compound extrusion (MATE) family expel dissimilar lipophilic and cationic drugs across cell membranes by dissipating a preexisting Na+ or H+ gradient. Despite its clinical relevance, the transport mechanism of MATE proteins remains poorly understood, largely owing to a lack of structural information on the substrate-bound transporter. Here we report crystal structures of a Na+-coupled MATE transporter NorM from Neisseria gonorrheae in complexes with three distinct translocation substrates (ethidium, rhodamine 6G, and tetraphenylphosphonium), as well as Cs+ (a Na+ congener), all captured in extracellular-facing and drug-bound states. The structures revealed a multidrug-binding cavity festooned with four negatively charged amino acids and surprisingly limited hydrophobic moieties, in stark contrast to the general belief that aromatic amino acids play a prominent role in multidrug recognition. Furthermore, we discovered an uncommon cation–π interaction in the Na+-binding site located outside the drug-binding cavity and validated the biological relevance of both the substrate- and cation-binding sites by conducting drug resistance and transport assays. Additionally, we uncovered potential rearrangement of at least two transmembrane helices upon Na+-induced drug export. Based on our structural and functional analyses, we suggest that Na+ triggers multidrug extrusion by inducing protein conformational changes rather than by directly competing for the substrate-binding amino acids. This scenario is distinct from the canonical antiport mechanism, in which both substrate and counterion compete for a shared binding site in the transporter. Collectively, our findings provide an important step toward a detailed and mechanistic understanding of multidrug transport. PMID:23341609

Atomic resolution structure of the E. coli YajR transporter YAM domain.

PubMed

Jiang, Daohua; Zhao, Yan; Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei; Zhang, Xuejun C

2014-07-25

YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration. Copyright © 2014 Elsevier Inc. All rights reserved.

Detergent-free purification of ABC (ATP-binding-cassette) transporters.

PubMed

Gulati, Sonali; Jamshad, Mohammed; Knowles, Timothy J; Morrison, Kerrie A; Downing, Rebecca; Cant, Natasha; Collins, Richard; Koenderink, Jan B; Ford, Robert C; Overduin, Michael; Kerr, Ian D; Dafforn, Timothy R; Rothnie, Alice J

2014-07-15

ABC (ATP-binding-cassette) transporters carry out many vital functions and are involved in numerous diseases, but study of the structure and function of these proteins is often hampered by their large size and membrane location. Membrane protein purification usually utilizes detergents to solubilize the protein from the membrane, effectively removing it from its native lipid environment. Subsequently, lipids have to be added back and detergent removed to reconstitute the protein into a lipid bilayer. In the present study, we present the application of a new methodology for the extraction and purification of ABC transporters without the use of detergent, instead, using a copolymer, SMA (polystyrene-co-maleic acid). SMA inserts into a bilayer and assembles into discrete particles, essentially solubilizing the membrane into small discs of bilayer encircled by a polymer, termed SMALPs (SMA lipid particles). We show that this polymer can extract several eukaryotic ABC transporters, P-glycoprotein (ABCB1), MRP1 (multidrug-resistance protein 1; ABCC1), MRP4 (ABCC4), ABCG2 and CFTR (cystic fibrosis transmembrane conductance regulator; ABCC7), from a range of different expression systems. The SMALP-encapsulated ABC transporters can be purified by affinity chromatography, and are able to bind ligands comparably with those in native membranes or detergent micelles. A greater degree of purity and enhanced stability is seen compared with detergent solubilization. The present study demonstrates that eukaryotic ABC transporters can be extracted and purified without ever being removed from their lipid bilayer environment, opening up a wide range of possibilities for the future study of their structure and function.

Lysine 300 is essential for stability but not for electrogenic transport of the Escherichia coli NhaA Na+/H+ antiporter

PubMed Central

Călinescu, Octavian; Dwivedi, Manish; Patiño-Ruiz, Miyer; Padan, Etana; Fendler, Klaus

2017-01-01

Na+/H+ antiporters are located in the cytoplasmic and intracellular membranes and play crucial roles in regulating intracellular pH, Na+, and volume. The NhaA antiporter of Escherichia coli is the best studied member of the Na+/H+ exchanger family and a model system for all related Na+/H+ exchangers, including eukaryotic representatives. Several amino acid residues are important for the transport activity of NhaA, including Lys-300, a residue that has recently been proposed to carry one of the two H+ ions that NhaA exchanges for one Na+ ion during one transport cycle. Here, we sought to characterize the effects of mutating Lys-300 of NhaA to amino acid residues containing side chains of different polarity and length (i.e. Ala, Arg, Cys, His, Glu, and Leu) on transporter stability and function. Salt resistance assays, acridine-orange fluorescence dequenching, solid supported membrane-based electrophysiology, and differential scanning fluorometry were used to characterize Na+ and H+ transport, charge translocation, and thermal stability of the different variants. These studies revealed that NhaA could still perform electrogenic Na+/H+ exchange even in the absence of a protonatable residue at the Lys-300 position. However, all mutants displayed lower thermal stability and reduced ion transport activity compared with the wild-type enzyme, indicating the critical importance of Lys-300 for optimal NhaA structural stability and function. On the basis of these experimental data, we propose a tentative mechanism integrating the functional and structural role of Lys-300. PMID:28330875

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine.

PubMed

Wong, Darren Chern Jan; Zhang, Li; Merlin, Isabelle; Castellarin, Simone D; Gambetta, Gregory A

2018-04-11

The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family's tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation. A total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs. Combining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation.

Multiscale image-based modeling and simulation of gas flow and particle transport in the human lungs

PubMed Central

Tawhai, Merryn H; Hoffman, Eric A

2013-01-01

Improved understanding of structure and function relationships in the human lungs in individuals and sub-populations is fundamentally important to the future of pulmonary medicine. Image-based measures of the lungs can provide sensitive indicators of localized features, however to provide a better prediction of lung response to disease, treatment and environment, it is desirable to integrate quantifiable regional features from imaging with associated value-added high-level modeling. With this objective in mind, recent advances in computational fluid dynamics (CFD) of the bronchial airways - from a single bifurcation symmetric model to a multiscale image-based subject-specific lung model - will be reviewed. The interaction of CFD models with local parenchymal tissue expansion - assessed by image registration - allows new understanding of the interplay between environment, hot spots where inhaled aerosols could accumulate, and inflammation. To bridge ventilation function with image-derived central airway structure in CFD, an airway geometrical modeling method that spans from the model ‘entrance’ to the terminal bronchioles will be introduced. Finally, the effects of turbulent flows and CFD turbulence models on aerosol transport and deposition will be discussed. CFD simulation of airflow and particle transport in the human lung has been pursued by a number of research groups, whose interest has been in studying flow physics and airways resistance, improving drug delivery, or investigating which populations are most susceptible to inhaled pollutants. The three most important factors that need to be considered in airway CFD studies are lung structure, regional lung function, and flow characteristics. Their correct treatment is important because the transport of therapeutic or pollutant particles is dependent on the characteristics of the flow by which they are transported; and the airflow in the lungs is dependent on the geometry of the airways and how ventilation is distributed to the peripheral tissue. The human airway structure spans more than 20 generations, beginning with the extra-thoracic airways (oral or nasal cavity, and through the pharynx and larynx to the trachea), then the conducting airways, the respiratory airways, and to the alveoli. The airways in individuals and sub-populations (by gender, age, ethnicity, and normal vs. diseased states) may exhibit different dimensions, branching patterns and angles, and thickness and rigidity. At the local level, one would like to capture detailed flow characteristics, e.g. local velocity profiles, shear stress, and pressure, for prediction of particle transport in an airway (lung structure) model that is specific to the geometry of an individual, to understand how inter-subject variation in airway geometry (normal or pathological) influences the transport and deposition of particles. In a systems biology – or multiscale modeling – approach, these local flow characteristics can be further integrated with epithelial cell models for the study of mechanotransduction. At the global (organ) level, one would like to match regional ventilation (lung function) that is specific to the individual, thus ensuring that the flow that transports inhaled particles is appropriately distributed throughout the lung model. Computational models that do not account for realistic distribution of ventilation are not capable of predicting realistic particle distribution or targeted drug deposition. Furthermore, the flow in the human lung can be transitional or turbulent in the upper and proximal airways, and becomes laminar in the distal airways. The flows in the laminar, transitional and turbulent regimes have different temporal and spatial scales. Therefore, modeling airway structure and predicting gas flow and particle transport at both local and global levels require image-guided multiscale modeling strategies. In this article, we will review the aforementioned three key aspects of CFD studies of the human lungs: airway structure (conducting airways), lung function (regional ventilation and boundary conditions), and flow characteristics (modeling of turbulent flow and its effect on particle transport). For modeling airway structure, we will focus on the conducting airways, and review both symmetric vs. asymmetric airway models, idealized vs. CT-based airway models, and multiscale subject-specific airway models. Imposition of physiological subject-specific boundary conditions (BCs) in CFD is essential to match regional ventilation in individuals, which is also critical in studying preferential deposition of inhaled aerosols in sub-populations, e.g. normals vs. asthmatics that may exhibit different ventilation patterns. Subject-specific regional ventilation defines flow distributions and characteristics in airway segments and bifurcations, which subsequently determines the transport and deposition of aerosols in the entire lungs. Turbulence models are needed to capture the transient and turbulent nature of the gas flow in the human lungs. Thus, the advantages and disadvantages of different turbulence models as well as their effects on particle transport will be discussed. The ultimate goal of the development is to identify sensitive structural and functional variables in sub-populations of normal and diseased lungs for potential clinical applications. PMID:23843310

Mutations in SLC2A2 Gene Reveal hGLUT2 Function in Pancreatic β Cell Development*

PubMed Central

Michau, Aurélien; Guillemain, Ghislaine; Grosfeld, Alexandra; Vuillaumier-Barrot, Sandrine; Grand, Teddy; Keck, Mathilde; L'Hoste, Sébastien; Chateau, Danielle; Serradas, Patricia; Teulon, Jacques; De Lonlay, Pascale; Scharfmann, Raphaël; Brot-Laroche, Edith; Leturque, Armelle; Le Gall, Maude

2013-01-01

The structure-function relationships of sugar transporter-receptor hGLUT2 coded by SLC2A2 and their impact on insulin secretion and β cell differentiation were investigated through the detailed characterization of a panel of mutations along the protein. We studied naturally occurring SLC2A2 variants or mutants: two single-nucleotide polymorphisms and four proposed inactivating mutations associated to Fanconi-Bickel syndrome. We also engineered mutations based on sequence alignment and conserved amino acids in selected domains. The single-nucleotide polymorphisms P68L and T110I did not impact on sugar transport as assayed in Xenopus oocytes. All the Fanconi-Bickel syndrome-associated mutations invalidated glucose transport by hGLUT2 either through absence of protein at the plasma membrane (G20D and S242R) or through loss of transport capacity despite membrane targeting (P417L and W444R), pointing out crucial amino acids for hGLUT2 transport function. In contrast, engineered mutants were located at the plasma membrane and able to transport sugar, albeit with modified kinetic parameters. Notably, these mutations resulted in gain of function. G20S and L368P mutations increased insulin secretion in the absence of glucose. In addition, these mutants increased insulin-positive cell differentiation when expressed in cultured rat embryonic pancreas. F295Y mutation induced β cell differentiation even in the absence of glucose, suggesting that mutated GLUT2, as a sugar receptor, triggers a signaling pathway independently of glucose transport and metabolism. Our results describe the first gain of function mutations for hGLUT2, revealing the importance of its receptor versus transporter function in pancreatic β cell development and insulin secretion. PMID:23986439

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17

DOE PAGES

Czerny, Daniel D.; Padmanaban, Senthilkumar; Anishkin, Andriy; ...

2016-05-11

Using Arabidopsis thaliana AtCHX17 as an example, we combine structural modeling and mutagenesis to provide insights on its protein architecture and transport function which is poorly characterized. This approach is based on the observation that protein structures are significantly more conserved in evolution than linear sequences, and mechanistic similarities among diverse transporters are emerging. Two homology models of AtCHX17 were obtained that show a protein fold similar to known structures of bacterial Na +/H + antiporters, EcNhaA and TtNapA. The distinct secondary and tertiary structure models highlighted residues at positions potentially important for CHX17 activity. Mutagenesis showed that asparagine-N200 andmore » aspartate-D201 inside transmembrane5 (TM5), and lysine-K355 inside TM10 are critical for AtCHX17 activity. We reveal previously unrecognized threonine-T170 and lysine-K383 as key residues at unwound regions in the middle of TM4 and TM11 α-helices, respectively. Mutation of glutamate-E111 located near the membrane surface inhibited AtCHX17 activity, suggesting a role in pH sensing. The long carboxylic tail of unknown purpose has an alternating β-sheet and α-helix secondary structure that is conserved in prokaryote universal stress proteins. Here, these results support the overall architecture of AtCHX17 and identify D201, N200 and novel residues T170 and K383 at the functional core which likely participates in ion recognition, coordination and/or translocation, similar to characterized cation/H + exchangers. The core of AtCHX17 models according to EcNhaA and TtNapA templates faces inward and outward, respectively, which may reflect two conformational states of the alternating access transport mode for proteins belonging to the plant CHX family.« less

Modeling of flux, binding and substitution of urea molecules in the urea transporter dvUT.

PubMed

Zhang, Hai-Tian; Wang, Zhe; Yu, Tao; Sang, Jian-Ping; Zou, Xian-Wu; Zou, Xiaoqin

2017-09-01

Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model. To model the substitution of urea by the urea analogue N,N'-dimethylurea (DMU) in dvUT, we calculated the occupation probability of DMU along the urea pore and the ratio of the occupation probabilities of DMU at the external (S ext ) and internal (S int ) binding sites, and we established the mutual substitution rule for binding and substitution of urea and DMU. Based on these calculations and modelings, together with the use of the Monte Carlo (MC) method, we further modeled the urea flux in dvUT, equilibrium urea binding to dvUT, and the substitution of urea by DMU in the dvUT. Our modeling results are in good agreement with the existing experimental functional data. Furthermore, the modelings have discovered the microscopic process and mechanisms of those functional characteristics. The methods and the results would help our future understanding of the underlying mechanisms of the diseases associated with impaired UT functions and rational drug design for the treatment of these diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

The role of Monosaccharide Transport Proteins in carbohydrate assimilation, distribution, metabolism and homeostasis

PubMed Central

Cura, Anthony J.; Carruthers, Anthony

2012-01-01

The facilitated diffusion of glucose, galactose, fructose, urate, myoinositol and dehydroascorbic acid in mammals is catalyzed by a family of 14 monosaccharide transport proteins called GLUTs. These transporters may be divided into 3 classes according to sequence similarity and function/substrate specificity. GLUT1 appears to be highly expressed in glycolytically active cells and has been co-opted in vitamin C auxotrophs to maintain the redox state of the blood through transport of dehydroascorbate. Several GLUTs are definitive glucose/galactose transporters, GLUT2 and GLUT5 are physiologically important fructose transporters, GLUT9 appears to be a urate transporter while GLUT13 (HMIT1) is a proton/myoinositol co-transporter. The physiologic substrates of some GLUTs remain to be established. The GLUTs are expressed in a tissue specific manner where affinity, specificity and capacity for substrate transport are paramount for tissue function. Although great strides have been made in characterizing GLUT-catalyzed monosaccharide transport and mapping GLUT membrane topography and determinants of substrate specificity, a unifying model for GLUT structure and function remains elusive. The GLUTs play a major role in carbohydrate homeostasis and the redistribution of sugar-derived carbons among the various organ systems. This is accomplished through a multiplicity of GLUT-dependent glucose sensing and effector mechanisms that regulate monosaccharide ingestion, absorption, distribution, cellular transport and metabolism and recovery/retention. Glucose transport and metabolism have co-evolved in mammals to support cerebral glucose utilization. PMID:22943001

A domain-based approach for analyzing the function of aluminum-activated malate transporters from wheat (Triticum aestivum) and Arabidopsis thaliana in Xenopus oocytes.

PubMed

Sasaki, Takayuki; Tsuchiya, Yoshiyuki; Ariyoshi, Michiyo; Ryan, Peter R; Furuichi, Takuya; Yamamoto, Yoko

2014-12-01

Wheat and Arabidopsis plants respond to aluminum (Al) ions by releasing malate from their root apices via Al-activated malate transporter. Malate anions bind with the toxic Al ions and contribute to the Al tolerance of these species. The genes encoding the transporters in wheat and Arabidopsis, TaALMT1 and AtALMT1, respectively, were expressed in Xenopus laevis oocytes and characterized electrophysiologically using the two-electrode voltage clamp system. The Al-activated currents generated by malate efflux were detected for TaALMT1 but not for AtALMT1. Chimeric proteins were generated by swapping the N- and C-terminal halves of TaALMT1 and AtALMT1 (Ta::At and At::Ta). When these chimeras were characterized in oocytes, Al-activated malate efflux was detected for the Ta::At chimera but not for At::Ta, suggesting that the N-terminal half of TaALMT1 is necessary for function in oocytes. An additional chimera, Ta(48)::At, generated by swapping 17 residues from the N-terminus of AtALMT1 with the equivalent 48 residues from TaALMT1, was sufficient to support transport activity. This 48 residue region includes a helical region with a putative transmembrane domain which is absent in AtALMT1. The deletion of this domain from Ta(48)::At led to the complete loss of transport activity. Furthermore, truncations and a deletion at the C-terminal end of TaALMT1 indicated that a putative helical structure in this region was also required for transport function. This study provides insights into the structure-function relationships of Al-activated ALMT proteins by identifying specific domains on the N- and C-termini of TaALMT1 that are critical for basal transport function and Al responsiveness in oocytes. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

On-wire lithography: synthesis, encoding and biological applications

PubMed Central

Banholzer, Matthew J; Qin, Lidong; Millstone, Jill E; Osberg, Kyle D; Mirkin, Chad A

2014-01-01

The next step in the maturing field of nanotechnology is to develop ways to introduce unusual architectural changes to simple building blocks. For nanowires, on-wire lithography (OWL) has emerged as a powerful way of synthesizing a segmented structure and subsequently introducing architectural changes through post-chemical treatment. In the OWL protocol presented here, multisegmented nanowires are grown and a support layer is deposited on one side of each nanostructure. After selective chemical etching of sacrificial segments, structures with gaps as small as 2 nm and disks as thin as 20 nm can be created. These nanostructures are highly tailorable and can be used in electrical transport, Raman enhancement and energy conversion. Such nanostructures can be functionalized with many types of adsorbates, enabling the use of OWL-generated structures as bioactive probes for diagnostic assays and molecular transport junctions. The process takes 13–36 h depending on the type of adsorbate used to functionalize the nanostructures. PMID:19444241

Theoretical investigation of the electronic structure and quantum transport in the graphene-C(111) diamond surface system.

PubMed

Selli, Daniele; Baburin, Igor; Leoni, Stefano; Zhu, Zhen; Tománek, David; Seifert, Gotthard

2013-10-30

We investigate the interaction of a graphene monolayer with the C(111) diamond surface using ab initio density functional theory. To accommodate the lattice mismatch between graphene and diamond, the overlayer deforms into a wavy structure that binds strongly to the diamond substrate. The detached ridges of the wavy graphene overlayer behave electronically as free-standing polyacetylene chains with delocalized π electrons, separated by regions containing only sp(3) carbon atoms covalently bonded to the (111) diamond surface. We performed quantum transport calculations for different geometries of the system to study how the buckling of the graphene layer and the associated bonding to the diamond substrate affect the transport properties. The system displays high carrier mobility along the ridges and a wide transport gap in the direction normal to the ridges. These intriguing, strongly anisotropic transport properties qualify the hybrid graphene-diamond system as a viable candidate for electronic nanodevices.

Innovative polymer nanocomposite electrolytes: nanoscale manipulation of ion channels by functionalized graphenes.

PubMed

Choi, Bong Gill; Hong, Jinkee; Park, Young Chul; Jung, Doo Hwan; Hong, Won Hi; Hammond, Paula T; Park, Hoseok

2011-06-28

The chemistry and structure of ion channels within the polymer electrolytes are of prime importance for studying the transport properties of electrolytes as well as for developing high-performance electrochemical devices. Despite intensive efforts on the synthesis of polymer electrolytes, few studies have demonstrated enhanced target ion conduction while suppressing unfavorable ion or mass transport because the undesirable transport occurs through an identical pathway. Herein, we report an innovative, chemical strategy for the synthesis of polymer electrolytes whose ion-conducting channels are physically and chemically modulated by the ionic (not electronic) conductive, functionalized graphenes and for a fundamental understanding of ion and mass transport occurring in nanoscale ionic clusters. The functionalized graphenes controlled the state of water by means of nanoscale manipulation of the physical geometry and chemical functionality of ionic channels. Furthermore, the confinement of bound water within the reorganized nanochannels of composite membranes was confirmed by the enhanced proton conductivity at high temperature and the low activation energy for ionic conduction through a Grotthus-type mechanism. The selectively facilitated transport behavior of composite membranes such as high proton conductivity and low methanol crossover was attributed to the confined bound water, resulting in high-performance fuel cells.

Directed assembly of bio-inspired hierarchical materials with controlled nanofibrillar architectures

NASA Astrophysics Data System (ADS)

Tseng, Peter; Napier, Bradley; Zhao, Siwei; Mitropoulos, Alexander N.; Applegate, Matthew B.; Marelli, Benedetto; Kaplan, David L.; Omenetto, Fiorenzo G.

2017-05-01

In natural systems, directed self-assembly of structural proteins produces complex, hierarchical materials that exhibit a unique combination of mechanical, chemical and transport properties. This controlled process covers dimensions ranging from the nano- to the macroscale. Such materials are desirable to synthesize integrated and adaptive materials and systems. We describe a bio-inspired process to generate hierarchically defined structures with multiscale morphology by using regenerated silk fibroin. The combination of protein self-assembly and microscale mechanical constraints is used to form oriented, porous nanofibrillar networks within predesigned macroscopic structures. This approach allows us to predefine the mechanical and physical properties of these materials, achieved by the definition of gradients in nano- to macroscale order. We fabricate centimetre-scale material geometries including anchors, cables, lattices and webs, as well as functional materials with structure-dependent strength and anisotropic thermal transport. Finally, multiple three-dimensional geometries and doped nanofibrillar constructs are presented to illustrate the facile integration of synthetic and natural additives to form functional, interactive, hierarchical networks.

Equations of state and transport properties of mixtures in the warm dense regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Yong; Dai, Jiayu; Kang, Dongdong

2015-02-15

We have performed average-atom molecular dynamics to simulate the CH and LiH mixtures in the warm dense regime, and obtained equations of state and the ionic transport properties. The electronic structures are calculated by using the modified average-atom model, which have included the broadening of energy levels, and the ion-ion pair potentials of mixtures are constructed based on the temperature-dependent density functional theory. The ionic transport properties, such as ionic diffusion and shear viscosity, are obtained through the ionic velocity correlation functions. The equations of state and transport properties for carbon, hydrogen and lithium, hydrogen mixtures in a wide regionmore » of density and temperature are calculated. Through our computing the average ionization degree, average ion-sphere diameter and transition properties in the mixture, it is shown that transport properties depend not only on the ionic mass but also on the average ionization degree.« less

RNA folding: structure prediction, folding kinetics and ion electrostatics.

PubMed

Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

2015-01-01

Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

Functional diversity of the superfamily of K⁺ transporters to meet various requirements.

PubMed

Diskowski, Marina; Mikusevic, Vedrana; Stock, Charlott; Hänelt, Inga

2015-09-01

The superfamily of K+ transporters unites proteins from plants, fungi, bacteria, and archaea that translocate K+ and/or Na+ across membranes. These proteins are key components in osmotic regulation, pH homeostasis, and resistance to high salinity and dryness. The members of the superfamily are closely related to K+ channels such as KcsA but also show several striking differences that are attributed to their altered functions. This review highlights these functional differences, focusing on the bacterial superfamily members KtrB, TrkH, and KdpA. The functional variations within the family and comparison to MPM-type K+ channels are discussed in light of the recently solved structures of the Ktr and Trk systems.

Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2.

PubMed

Logeman, Brandon L; Wood, L Kent; Lee, Jaekwon; Thiele, Dennis J

2017-07-07

Copper is an essential element for proper organismal development and is involved in a range of processes, including oxidative phosphorylation, neuropeptide biogenesis, and connective tissue maturation. The copper transporter (Ctr) family of integral membrane proteins is ubiquitously found in eukaryotes and mediates the high-affinity transport of Cu + across both the plasma membrane and endomembranes. Although mammalian Ctr1 functions as a Cu + transporter for Cu acquisition and is essential for embryonic development, a homologous protein, Ctr2, has been proposed to function as a low-affinity Cu transporter, a lysosomal Cu exporter, or a regulator of Ctr1 activity, but its functional and evolutionary relationship to Ctr1 is unclear. Here we report a biochemical, genetic, and phylogenetic comparison of metazoan Ctr1 and Ctr2, suggesting that Ctr2 arose over 550 million years ago as a result of a gene duplication event followed by loss of Cu + transport activity. Using a random mutagenesis and growth selection approach, we identified amino acid substitutions in human and mouse Ctr2 proteins that support copper-dependent growth in yeast and enhance copper accumulation in Ctr1 -/- mouse embryonic fibroblasts. These mutations revert Ctr2 to a more ancestral Ctr1-like state while maintaining endogenous functions, such as stimulating Ctr1 cleavage. We suggest key structural aspects of metazoan Ctr1 and Ctr2 that discriminate between their biological roles, providing mechanistic insights into the evolutionary, biochemical, and functional relationships between these two related proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.

PubMed

Bozzi, Aaron T; Bane, Lukas B; Weihofen, Wilhelm A; Singharoy, Abhishek; Guillen, Eduardo R; Ploegh, Hidde L; Schulten, Klaus; Gaudet, Rachelle

2016-12-06

The widely conserved natural resistance-associated macrophage protein (Nramp) family of divalent metal transporters enables manganese import in bacteria and dietary iron uptake in mammals. We determined the crystal structure of the Deinococcus radiodurans Nramp homolog (DraNramp) in an inward-facing apo state, including the complete transmembrane (TM) segment 1a (absent from a previous Nramp structure). Mapping our cysteine accessibility scanning results onto this structure, we identified the metal-permeation pathway in the alternate outward-open conformation. We investigated the functional impact of two natural anemia-causing glycine-to-arginine mutations that impaired transition metal transport in both human Nramp2 and DraNramp. The TM4 G153R mutation perturbs the closing of the outward metal-permeation pathway and alters the selectivity of the conserved metal-binding site. In contrast, the TM1a G45R mutation prevents conformational change by sterically blocking the essential movement of that helix, thus locking the transporter in an inward-facing state. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nuclear quantum effects on structure and transport properties of dense liquid helium

NASA Astrophysics Data System (ADS)

Kang, Dongdong; Dai, Jiayu; Yuan, Jianmin

2015-11-01

Transport properties of dense liquid helium under the conditions of planet's core and cool atmosphere of white dwarfs are important for determining the structure and evolution of these astrophysical objects. We have investigated these properties of dense liquid helium by using the improved centroid path-integral simulations combined with density functional theory. The results show that with the inclusion of nuclear quantum effects (NQEs), the self-diffusion is largely higher while the shear viscosity is notably lower than the results of without the inclusion of NQEs due to the lower collision cross sections even when the NQEs have little effects on the static structures. The potential surface of helium atom along the simulation trajectory is quite different between MD and PIMD simulations. We have shown that the quantum nuclear character induces complex behaviors for ionic transport properties of dense liquid helium. NQEs bring more fluctuations of local electronic density of states than the classical treatment. Therefore, in order to construct more reasonable structure and evolution model for the planets and WDs, NQEs must be reconsidered when calculating the transport properties at certain temperature and density conditions.

Glutamine Transporters in Mammalian Cells and Their Functions in Physiology and Cancer

PubMed Central

Bhutia, Yangzom D.; Ganapathy, Vadivel

2016-01-01

The SLC (solute carrier)-type transporters (∼400 in number) in mammalian cells consist of 52 distinct gene families, grouped solely based on the amino acid sequence (primary structure) of the transporter proteins and not on their transport function. Among them are the transporters for amino acids. Fourteen of them, capable of transporting glutamine across the plasma membrane, are found in four families: SLC1, SLC6, SLC7, and SLC38. However, it is generally thought that the members of the SLC38 family are the principal transporters for glutamine. Some of the glutamine transporters are obligatory exchangers whereas some function as active transporters in one direction. While most glutamine transporters mediate the influx of the amino acid into cells, some actually mediate the efflux of the amino acid out of the cells. Glutamine transporters play important roles in a variety of tissues, including the liver, brain, kidney, and placenta, as clearly evident from the biological and biochemical phenotypes resulting from the deletion of specific glutamine transporters in mice. Owing to the obligatory role of glutamine in growth and proliferation of tumor cells, there is increasing attention on glutamine transporters in cancer biology as potential drug targets for cancer treatment. Selective blockers of certain glutamine transporters might be effective in preventing the entry of glutamine and other important amino acids into tumor cells, thus essentially starving these cells to death. This could represent the beginning of a new era in the discovery of novel anticancer drugs with a previously unexplored mode of action. PMID:26724577

The origin of anomalous transport in porous media - is it possible to make a priori predictions?

NASA Astrophysics Data System (ADS)

Bijeljic, Branko; Blunt, Martin

2013-04-01

Despite the range of significant applications of flow and solute transport in porous rock, including contaminant migration in subsurface hydrology, geological storage of carbon-dioxide and tracer studies and miscible displacement in oil recovery, even the qualitative behavior in the subsurface is uncertain. The non-Fickian nature of dispersive processes in heterogeneous porous media has been demonstrated experimentally from pore to field scales. However, the exact relationship between structure, velocity field and transport has not been fully understood. Advances in X ray imaging techniques made it possible to accurately describe structure of the pore space, helping predict flow and anomalous transport behaviour using direct simulation. This is demonstrated by simulating solute transport through 3D images of rock samples, with resolutions of a few microns, representing geological media of increasing pore-scale complexity: a sandpack, a sandstone, and a carbonate. A novel methodology is developed that predicts solute transport at the pore scale by using probability density functions of displacement (propagators) and probability density function of transit time between the image voxels, and relates it to probability density function of normalized local velocity. A key advantage is that full information on velocity and solute concentration is retained in the models. The methodology includes solving for Stokes flow by Open Foam, solving for advective transport by the novel streamline simulation method, and superimposing diffusive transport diffusion by the random walk method. It is shown how computed propagators for beadpack, sandstone and carbonate depend on the spread in the velocity distribution. A narrow velocity distribution in the beadpack leads to the least anomalous behaviour where the propagators rapidly become Gaussian; the wider velocity distribution in the sandstone gives rise to a small immobile concentration peak, and a large secondary mobile peak moving at approximately the average flow speed; in the carbonate with the widest velocity distribution the stagnant concentration peak is persistent, while the emergence of a smaller secondary mobile peak is observed, leading to a highly anomalous behavior. This defines different generic nature of non-Fickian transport in the three media and quantifies the effect of pore structure on transport. Moreover, the propagators obtained by the model are in a very good agreement with the propagators measured on beadpack, Bentheimer sandstone and Portland carbonate cores in nuclear magnetic resonance experiments. These findings demonstrate that it is possible to make a priori predictions of anomalous transport in porous media. The importance of these findings for transport in complex carbonate rock micro-CT images is discussed, classifying them in terms of degree of anomalous transport that can have an impact at the field scale. Extensions to reactive transport will be discussed.

Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea.

PubMed

Mulligan, Christopher; Fischer, Marcus; Thomas, Gavin H

2011-01-01

The tripartite ATP-independent periplasmic (TRAP) transporters are the best-studied family of substrate-binding protein (SBP)-dependent secondary transporters and are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP of the DctP or TAXI families and two integral membrane proteins of unequal sizes that form the DctQ and DctM protein families, respectively. The SBP component has a structure comprised of two domains connected by a hinge that closes upon substrate binding. In DctP-TRAP transporters, substrate binding is mediated through a conserved and specific arginine/carboxylate interaction in the SBP. While the SBP component has now been relatively well characterized, the membrane components of TRAP transporters are still poorly understood both in terms of their structure and function. We review the expanding repertoire of substrates and physiological roles for experimentally characterized TRAP transporters in bacteria and discuss mechanistic aspects of these transporters using data primarily from the sialic acid-specific TRAP transporter SiaPQM from Haemophilus influenzae, which suggest that TRAP transporters are high-affinity, Na(+)-dependent unidirectional secondary transporters. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Functional characterization of putative cilia genes by high-content analysis

PubMed Central

Lai, Cary K.; Gupta, Nidhi; Wen, Xiaohui; Rangell, Linda; Chih, Ben; Peterson, Andrew S.; Bazan, J. Fernando; Li, Li; Scales, Suzie J.

2011-01-01

Cilia are microtubule-based protrusions from the cell surface that are involved in a number of essential signaling pathways, yet little is known about many of the proteins that regulate their structure and function. A number of putative cilia genes have been identified by proteomics and comparative sequence analyses, but functional data are lacking for the vast majority. We therefore monitored the effects in three cell lines of small interfering RNA (siRNA) knockdown of 40 of these genes by high-content analysis. We assayed cilia number, length, and transport of two different cargoes (membranous serotonin receptor 6-green fluorescent protein [HTR6-GFP] and the endogenous Hedgehog [Hh] pathway transcription factor Gli3) by immunofluorescence microscopy; and cilia function using a Gli-luciferase Hh signaling assay. Hh signaling was most sensitive to perturbations, with or without visible structural cilia defects. Validated hits include Ssa2 and mC21orf2 with ciliation defects; Ift46 with short cilia; Ptpdc1 and Iqub with elongated cilia; and Arl3, Nme7, and Ssna1 with distinct ciliary transport but not length defects. Our data confirm various ciliary roles for several ciliome proteins and show it is possible to uncouple ciliary cargo transport from cilia formation in vertebrates. PMID:21289087

Overcoming the heterologous bias: an in vivo functional analysis of multidrug efflux transporter, CgCdr1p in matched pair clinical isolates of Candida glabrata.

PubMed

Puri, Nidhi; Manoharlal, Raman; Sharma, Monika; Sanglard, Dominique; Prasad, Rajendra

2011-01-07

We have taken advantage of the natural milieu of matched pair of azole sensitive (AS) and azole resistant (AR) clinical isolates of Candida glabrata for expressing its major ABC multidrug transporter, CgCdr1p for structure and functional analysis. This was accomplished by tagging a green fluorescent protein (GFP) downstream of ORF of CgCDR1 and integrating the resultant fusion protein at its native chromosomal locus in AS and AR backgrounds. The characterization confirmed that in comparison to AS isolate, CgCdr1p-GFP was over-expressed in AR isolates due to its hyperactive native promoter and the GFP tag did not affect its functionality in either construct. We observed that in addition to Rhodamine 6 G (R6G) and Fluconazole (FLC), a recently identified fluorescent substrate of multidrug transporters Nile Red (NR) could also be expelled by CgCdr1p. Competition assays with these substrates revealed the presence of overlapping multiple drug binding sites in CgCdr1p. Point mutations employing site directed mutagenesis confirmed that the role played by unique amino acid residues critical to ATP catalysis and localization of ABC drug transporter proteins are well conserved in C. glabrata as in other yeasts. This study demonstrates a first in vivo novel system where over-expression of GFP tagged MDR transporter protein can be driven by its own hyperactive promoter of AR isolates. Taken together, this in vivo system can be exploited for the structure and functional analysis of CgCdr1p and similar proteins wherein the artefactual concerns encountered in using heterologous systems are totally excluded. Copyright © 2010 Elsevier Inc. All rights reserved.

Histidine residues in the Na+-coupled ascorbic acid transporter-2 (SVCT2) are central regulators of SVCT2 function, modulating pH sensitivity, transporter kinetics, Na+ cooperativity, conformational stability, and subcellular localization.

PubMed

Ormazabal, Valeska; Zuñiga, Felipe A; Escobar, Elizabeth; Aylwin, Carlos; Salas-Burgos, Alexis; Godoy, Alejandro; Reyes, Alejandro M; Vera, Juan Carlos; Rivas, Coralia I

2010-11-19

Na(+)-coupled ascorbic acid transporter-2 (SVCT2) activity is impaired at acid pH, but little is known about the molecular determinants that define the transporter pH sensitivity. SVCT2 contains six histidine residues in its primary sequence, three of which are exofacial in the transporter secondary structure model. We used site-directed mutagenesis and treatment with diethylpyrocarbonate to identify histidine residues responsible for SVCT2 pH sensitivity. We conclude that five histidine residues, His(109), His(203), His(206), His(269), and His(413), are central regulators of SVCT2 function, participating to different degrees in modulating pH sensitivity, transporter kinetics, Na(+) cooperativity, conformational stability, and subcellular localization. Our results are compatible with a model in which (i) a single exofacial histidine residue, His(413), localized in the exofacial loop IV that connects transmembrane helices VII-VIII defines the pH sensitivity of SVCT2 through a mechanism involving a marked attenuation of the activation by Na(+) and loss of Na(+) cooperativity, which leads to a decreased V(max) without altering the transport K(m); (ii) exofacial histidine residues His(203), His(206), and His(413) may be involved in maintaining a functional interaction between exofacial loops II and IV and influence the general folding of the transporter; (iii) histidines 203, 206, 269, and 413 affect the transporter kinetics by modulating the apparent transport K(m); and (iv) histidine 109, localized at the center of transmembrane helix I, might be fundamental for the interaction of SVCT2 with the transported substrate ascorbic acid. Thus, histidine residues are central regulators of SVCT2 function.

Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

NASA Astrophysics Data System (ADS)

Flechsig, Holger

2016-02-01

ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter. Possible explanations are discussed in the light of currently debated transport scenarios of ABC transporters.

Structural correlates of the creatine transporter function regulation: the undiscovered country.

PubMed

Santacruz, Lucia; Jacobs, Danny O

2016-08-01

Creatine (Cr) and phosphocreatine constitute an energy shuttle that links ATP production in mitochondria to subcellular locations of ATP consumption. Cells in tissues that are reliant on this energy shuttle, such as myocytes and neurons, appear to have very limited ability to synthesize creatine. Therefore, these cells depend on Cr uptake across the cell membrane by a specialized creatine transporter (CrT solute carrier SLC6A8) in order to maintain intracellular creatine levels. Cr supplementation has been shown to have a beneficial effect in numerous in vitro and in vivo models, particularly in cases of oxidative stress, and is also widely used by athletes as a performance enhancement nutraceutical. Intracellular creatine content is maintained within narrow limits. However, the physiological and cellular mechanisms that mediate Cr transport during health and disease (such as cardiac failure) are not understood. In this narrative mini-review, we summarize the last three decades of research on CrT structure, function and regulation.

ATP-binding cassette exporters: structure and mechanism with a focus on P-glycoprotein and MRP1.

PubMed

Arana, Maite Rocío; Altenberg, Guillermo

2017-10-12

The majority of proteins that belong to the ATP-binding cassette (ABC) superfamily are transporters that mediate the efflux of substrates from cells. These exporters include multidrug resistance proteins of the ABCB and ABCC subfamilies, such as P-glycoprotein (Pgp) and MRP1, respectively. These proteins are not only involved in the resistance of cancer to cytotoxic agents, but also in the protection from endo and xenobiotics, and the determination of drug pharmacokinetics, as well as in the pathophysiology of a variety of disorders. Here, we present a review of the information available on ABC exporters, with a focus on Pgp, MRP1 and related proteins. We describe tissue localization and function of these transporters in health and disease, and discuss the mechanisms of substrate transport. We also correlate recent structural information with the function of the exporters, and discuss details of their molecular mechanism with a focus on the nucleotide-binding domains. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Revealing an outward-facing open conformational state in a CLC Cl –/H + exchange transporter

DOE PAGES

Khantwal, Chandra M.; Abraham, Sherwin J.; Han, Wei; ...

2016-01-22

CLC secondary active transporters exchange Cl - for H + . Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Glu ex ) upon its protonation. Using 19 F NMR, we show that as [H + ] is increased to protonate Glu ex and enrich the outward-facing state, a residue ~20 Å away from Glu ex , near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that themore » cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function.« less

Review. The mammalian proton-coupled peptide cotransporter PepT1: sitting on the transporter-channel fence?

PubMed

Meredith, David

2009-01-27

The proton-coupled di- and tripeptide transporter PepT1 (SLC15a1) is the major route by which dietary nitrogen is taken up from the small intestine, as well as being the route of entry for important therapeutic (pro)drugs such as the beta-lactam antibiotics, angiotensin-converting enzyme inhibitors and antiviral and anti-cancer agents. PepT1 is a member of the major facilitator superfamily of 12 transmembrane domain transporter proteins. Expression studies in Xenopus laevis on rabbit PepT1 that had undergone site-directed mutagenesis of a conserved arginine residue (arginine282 in transmembrane domain 7) to a glutamate revealed that this residue played a role in the coupling of proton and peptide transport and prevented the movement of non-coupled ions during the transporter cycle. Mutations of arginine282 to other non-positive residues did not uncouple proton-peptide cotransport, but did allow additional ion movements when substrate was added. By contrast, mutations to positive residues appeared to function the same as wild-type. These findings are discussed in relation to the functional role that arginine282 may play in the way PepT1 operates, together with structural information from the homology model of PepT1 based on the Escherichia coli lactose permease crystal structure.

Molecular and ionic mimicry and the transport of toxic metals

PubMed Central

Bridges, Christy C.; Zalups, Rudolfs K.

2008-01-01

Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport of selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues. PMID:15845419

Molecular and ionic mimicry and the transport of toxic metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bridges, Christy C.; Zalups, Rudolfs K.

Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport ofmore » selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues.« less

Surface Plasmon Polariton-Assisted Long-Range Exciton Transport in Monolayer Semiconductor Lateral Heterostructure

NASA Astrophysics Data System (ADS)

Shi, Jinwei; Lin, Meng-Hsien; Chen, Yi-Tong; Estakhri, Nasim Mohammadi; Tseng, Guo-Wei; Wang, Yanrong; Chen, Hung-Ying; Chen, Chun-An; Shih, Chih-Kang; Alã¹, Andrea; Li, Xiaoqin; Lee, Yi-Hsien; Gwo, Shangjr

Recently, two-dimensional (2D) semiconductor heterostructures, i.e., atomically thin lateral heterostructures (LHSs) based on transition metal dichalcogenides (TMDs) have been demonstrated. In an optically excited LHS, exciton transport is typically limited to a rather short spatial range ( 1 micron). Furthermore, additional losses may occur at the lateral interfacial regions. Here, to overcome these challenges, we experimentally implement a planar metal-oxide-semiconductor (MOS) structure by placing a monolayer of WS2/MoS2 LHS on top of an Al2O3 capped Ag single-crystalline plate. We found that the exciton transport range can be extended to tens of microns. The process of long-range exciton transport in the MOS structure is confirmed to be mediated by an exciton-surface plasmon polariton-exciton conversion mechanism, which allows a cascaded energy transfer process. Thus, the planar MOS structure provides a platform seamlessly combining 2D light-emitting materials with plasmonic planar waveguides, offering great potential for developing integrated photonic/plasmonic functionalities.

Analysis of Tryptophan Residues in the Staphylococcal Multidrug Transporter QacA Reveals Long-Distance Functional Associations of Residues on Opposite Sides of the Membrane▿

PubMed Central

Hassan, Karl A.; Souhani, Talal; Skurray, Ronald A.; Brown, Melissa H.

2008-01-01

Tryptophan residues can possess a multitude of functions within a multidrug transport protein, e.g., mediating interactions with substrates or distal parts of the protein, or fulfilling a structural requirement, such as guiding the depth of membrane insertion. In this study, the nine tryptophan residues of the staphylococcal QacA multidrug efflux protein were individually mutated to alanine and phenylalanine, and the functional consequences of these changes were determined. Phenylalanine substitutions for each tryptophan residue were functionally tolerated. However, alanine modifications revealed an important functional role for three tryptophan residues, W58, W149, and W173, each of which is well conserved among QacA-related transport proteins in the major facilitator superfamily. The most functionally compromising mutation, an alanine substitution for W58, likely to be located at the extracellular interface of transmembrane segment 2, abolished all detectable QacA-mediated resistance and transport function. Second-site suppressor analyses identified several mutations that rescued the function of the W58A QacA mutant. Remarkably, all of these suppressor mutations were shown to be located in cytoplasmic loops between transmembrane helices 2 and 3 or 12 and 13, demonstrating novel functional associations between amino acid positions on opposite sides of the membrane and in distal N- and C-terminal regions of the QacA protein. PMID:18223078

Structural basis of the alternating-access mechanism in a bile acid transporter

NASA Astrophysics Data System (ADS)

Zhou, Xiaoming; Levin, Elena J.; Pan, Yaping; McCoy, Jason G.; Sharma, Ruchika; Kloss, Brian; Bruni, Renato; Quick, Matthias; Zhou, Ming

2014-01-01

Bile acids are synthesized from cholesterol in hepatocytes and secreted through the biliary tract into the small intestine, where they aid in absorption of lipids and fat-soluble vitamins. Through a process known as enterohepatic recirculation, more than 90% of secreted bile acids are then retrieved from the intestine and returned to the liver for resecretion. In humans, there are two Na+-dependent bile acid transporters involved in enterohepatic recirculation, the Na+-taurocholate co-transporting polypeptide (NTCP; also known as SLC10A1) expressed in hepatocytes, and the apical sodium-dependent bile acid transporter (ASBT; also known as SLC10A2) expressed on enterocytes in the terminal ileum. In recent years, ASBT has attracted much interest as a potential drug target for treatment of hypercholesterolaemia, because inhibition of ASBT reduces reabsorption of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption. However, a lack of three-dimensional structures of bile acid transporters hampers our ability to understand the molecular mechanisms of substrate selectivity and transport, and to interpret the wealth of existing functional data. The crystal structure of an ASBT homologue from Neisseria meningitidis (ASBTNM) in detergent was reported recently, showing the protein in an inward-open conformation bound to two Na+ and a taurocholic acid. However, the structural changes that bring bile acid and Na+ across the membrane are difficult to infer from a single structure. To understand the structural changes associated with the coupled transport of Na+ and bile acids, here we solved two structures of an ASBT homologue from Yersinia frederiksenii (ASBTYf) in a lipid environment, which reveal that a large rigid-body rotation of a substrate-binding domain gives the conserved `crossover' region, where two discontinuous helices cross each other, alternating accessibility from either side of the cell membrane. This result has implications for the location and orientation of the bile acid during transport, as well as for the translocation pathway for Na+.

Structural basis of the alternating-access mechanism in a bile acid transporter

PubMed Central

Zhou, Xiaoming; Levin, Elena J.; Pan, Yaping; McCoy, Jason G.; Sharma, Ruchika; Kloss, Brian; Bruni, Renato; Quick, Matthias; Zhou, Ming

2014-01-01

Bile acids are synthesized from cholesterol in hepatocytes and secreted via the biliary tract into the small intestine, where they aid in absorption of lipids and fat-soluble vitamins. Through a process known as enterohepatic recirculation, more than 90% of secreted bile acids are then retrieved from the intestine and returned to the liver for re-secretion1. In humans, there are two Na+-dependent bile acid transporters involved in enterohepatic recirculation, the Na+-taurocholate co-transporting polypeptide (NTCP or SLC10A1) expressed in hepatocytes, and the apical sodium-dependent bile acid transporter (ASBT or SLC10A2) expressed on enterocytes in the terminal ileum2. In recent years, ASBT has attracted much interest as a potential drug target for treatment of hypercholesterolemia, because inhibition of ASBT reduces reabsorption of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption3,4. However, a lack of 3-dimensional structures of bile acid transporters hampers our ability to understand the molecular mechanisms of substrate selectivity and transport, and to interpret the wealth of existing functional data2,5-8. The crystal structure of an ASBT homolog from Neisseria meningitidis (ASBTNM) in detergent was reported recently9, showing the protein in an inward-open conformation bound to two Na+ and a taurocholic acid. However, the structural changes that bring bile acid and Na+ across the membrane are difficult to infer from a single structure. To understand better the structural changes associated with the coupled transport of Na+ and bile acids, we crystallized and solved two structures of a ASBT homolog from Yersinia frederiksenii (ASBTYf) in a lipid environment, which reveal that a large rigid-body rotation of a substrate-binding domain gives alternate accessibility to the highly conserved “crossover” region, where two discontinuous transmembrane helices cross each other. This result has implications for the location and orientation of the bile acid during transport, as well as for the translocation pathway for Na+. PMID:24317697

Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations

PubMed Central

Hayashi, Shigehiko

2017-01-01

The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown. Here, we report an atomic structure of the IF form predicted by atomic-level molecular dynamics (MD) simulations of the alternating access transition with a recently developed accelerating technique. We successfully obtained a significantly stable IF structure characterized by newly formed well-packed and -organized inter-domain interactions through the accelerated simulations of unprecedentedly large conformational changes of the alternating access without a prior knowledge of the target protein structure. The simulation also shed light on an atomistic mechanism of the strict transport selectivity of adenosine nucleotides over guanosine and inosine ones. Furthermore, the IF structure was shown to bind ATP and BA, and thus revealed their binding mechanisms. The present study proposes a qualitatively novel view of the alternating access of transporters having the unique three-fold symmetry in atomic details and opens the way for rational drug design targeting the transporter in the dynamic functional cycle. PMID:28727843

Role of oxygen functionality on the band structure evolution and conductance of reduced graphene oxide

NASA Astrophysics Data System (ADS)

Roy, Rajarshi; Thapa, Ranjit; Chakrabarty, Soubhik; Jha, Arunava; Midya, Priyanka R.; Kumar, E. Mathan; Chattopadhyay, Kalyan K.

2017-06-01

Here we report, structural and electrical transport properties of reduced graphene oxide as a function of oxygen bonding configuration. We find that mainly epoxy (Csbnd Osbnd C) and carbonyl (Cdbnd O) functional groups remain as major residual components after reduction using three different reducing agents. We calculate the band structure in the presence of epoxy and carbonyl groups and defects. Finally, we calculate the theoretical band mobility and find that it is less for the carbonyl with epoxy system. We correlate the distortion of linear dispersion and opening of bandgap at K-point with conductance for different graphene system in presence of oxygen moieties.

Electronic, thermoelectric and transport properties of cesium cadmium trifluoride: A DFT study

NASA Astrophysics Data System (ADS)

Abraham, Jisha Annie; Pagare, G.; Sanyal, Sankar P.

2018-04-01

The full potential linearized augmented plane wave method based on density functional theory is employed to investigate the electronic structure of CsCdF3. The electronic properties of this compound have been studied from the band structure plot and density of states. The presence of indirect energy gap reveals its insulating nature. Using constant relaxation time, the electrical conductivity, electronic thermal conductivity, Seebeck coefficient and figure of merit are calculated by using Boltzmann transport theory. We have also studied the temperature dependence of thermoelectric properties of this compound.

New Computational Approach to Electron Transport in Irregular Graphene Nanostructures

NASA Astrophysics Data System (ADS)

Mason, Douglas; Heller, Eric; Prendergast, David; Neaton, Jeffrey

2009-03-01

For novel graphene devices of nanoscale-to-macroscopic scale, many aspects of their transport properties are not easily understood due to difficulties in fabricating devices with regular edges. Here we develop a framework to efficiently calculate and potentially screen electronic transport properties of arbitrary nanoscale graphene device structures. A generalization of the established recursive Green's function method is presented, providing access to arbitrary device and lead geometries with substantial computer-time savings. Using single-orbital nearest-neighbor tight-binding models and the Green's function-Landauer scattering formalism, we will explore the transmission function of irregular two-dimensional graphene-based nanostructures with arbitrary lead orientation. Prepared by LBNL under contract DE-AC02-05CH11231 and supported by the U.S. Dept. of Energy Computer Science Graduate Fellowship under grant DE-FG02-97ER25308.

Structure-activity relationships for xenobiotic transport substrates and inhibitory ligands of P-glycoprotein.

PubMed Central

Bain, L J; McLachlan, J B; LeBlanc, G A

1997-01-01

The multixenobiotic resistance phenotype is characterized by the reduced accumulation of xenobiotics by cells or organisms due to increased efflux of the compounds by P-glycoprotein (P-gp) or related transporters. An extensive xenobiotic database, consisting primarily of pesticides, was utilized in this study to identify molecular characteristics that render a xenobiotic susceptible to transport by or inhibition of P-gp. Transport substrates were differentiated by several molecular size/shape parameters, lipophilicity, and hydrogen bonding potential. Electrostatic features differentiated inhibitory ligands from compounds not catagorized as transport substrates and that did no interact with P-gp. A two-tiered system was developed using the derived structure-activity relationships to identify P-gp transport substrates and inhibitory ligands. Prediction accuracy of the approach was 82%. We then validated the system using six additional pesticides of which tow were predicted to be P-gp inhibitors and four were predicted to be noninteractors, based upon the structure-activity analyses. Experimental determinations using cells transfected with the human MDR1 gene demonstrated that five of the six pesticides were properly catagorized by the structure-activity analyses (83% accuracy). Finally, structure-activity analyses revealed that among P-gp inhibitors, relative inhibitory potency can be predicted based upon the surface area or volume of the compound. These results demonstrate that P-gp transport substrates and inhibitory ligands can be distinguished using molecular characteristics. Molecular characteristics of transport substrates suggest that P-gp may function in the elimination of hydroxylated metabolites of xenobiotics. Images Figure 1. A Figure 1. B Figure 1. C Figure 1. D Figure 1. E Figure 1. F Figure 1. G Figure 1. H Figure 2. Figure 2. Figure 2. Figure 2. Figure 2. Figure 2. Figure 3. A Figure 3. B PMID:9347896

Structural Studies on Cytosolic Domain of Magnesium Transporter MgtE from Enterococcus faecalis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ragumani, S.; Sauder, J; Burley, S

2009-01-01

Magnesium (Mg{sup 2+}) is an essential element for growth and maintenance of living cells. It acts as a cofactor for many enzymes and is also essential for stability of the plasma membrane. There are two distinct classes of magnesium transporters identified in bacteria that convey Mg{sup 2+} from periplasm to cytoplasm [ATPase-dependent (MgtA and MgtB) and constitutively active (CorA and MgtE)]. Previously published work on Mg{sup 2+} transporters yielded structures of full length MgtE from Thermus thermophilus, determined at 3.5 {angstrom} resolution, and its cytoplasmic domain with and without bond Mg{sup 2+} determined at 2.3 and 3.9 {angstrom} resolution, respectively.more » Here, they report the crystal structure of the Mg{sup 2+} bound form of the cytosolic portion of MgtE (residues 6-262) from Enterococcus faecalis at 2.2 {angstrom} resolution. The present structure and magnesium bound cytosolic domain structure from T. thermophilus (PDB ID: 2YVY) are structurally similar. Three magnesium binding sites are common to both MgtE full length and the present structure. Their work revealed an additional Mg{sup 2+} binding site in the E. faecalis structure. In this report, they discuss the functional significance of Mg{sup 2+} binding sites in the cytosolic domains of MgtE transporters.« less

Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function

PubMed Central

Ungar, Daniel; Oka, Toshihiko; Brittle, Elizabeth E.; Vasile, Eliza; Lupashin, Vladimir V.; Chatterton, Jon E.; Heuser, John E.; Krieger, Monty; Waters, M. Gerard

2002-01-01

Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Three complexes that have previously been partially characterized include (a) the Golgi transport complex (GTC), identified in an in vitro membrane transport assay, (b) the ldlCp complex, identified in analyses of CHO cell mutants with defects in Golgi-associated glycosylation reactions, and (c) the mammalian Sec34 complex, identified by homology to yeast Sec34p, implicated in vesicular transport. We show that these three complexes are identical and rename them the conserved oligomeric Golgi (COG) complex. The COG complex comprises four previously characterized proteins (Cog1/ldlBp, Cog2/ldlCp, Cog3/Sec34, and Cog5/GTC-90), three homologues of yeast Sec34/35 complex subunits (Cog4, -6, and -8), and a previously unidentified Golgi-associated protein (Cog7). EM of ldlB and ldlC mutants established that COG is required for normal Golgi morphology. “Deep etch” EM of purified COG revealed an ∼37-nm-long structure comprised of two similarly sized globular domains connected by smaller extensions. Consideration of biochemical and genetic data for mammalian COG and its yeast homologue suggests a model for the subunit distribution within this complex, which plays critical roles in Golgi structure and function. PMID:11980916

High performance, durable polymers including poly(phenylene)

DOEpatents

Fujimoto, Cy; Pratt, Harry; Anderson, Travis Mark

2017-02-28

The present invention relates to functionalized polymers including a poly(phenylene) structure. In some embodiments, the polymers and copolymers of the invention include a highly localized concentration of acidic moieties, which facilitate proton transport and conduction through networks formed from these polymers. In addition, the polymers can include functional moieties, such as electron-withdrawing moieties, to protect the polymeric backbone, thereby extending its durability. Such enhanced proton transport and durability can be beneficial for any high performance platform that employs proton exchange polymeric membranes, such as in fuel cells or flow batteries.

Tunnel magnetoresistance of ferrocene molecules

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2018-01-01

The spin transport in ferrocene molecules has been examined by using the nonequilibrium Green's function formalism with density functional theory. The ferrocene molecules were sandwiched between the two nickel electrodes in a parallel magnetic configuration, which enhanced the current in comparison with that in an antiparallel spin state and resulting in tunnel magnetoresistance (TMR). The current, having an opposite spin state to that of the ferromagnetic electrode, was the main channel for electron transport. In addition, it became clear that ferrocenylene molecules, having a fulvalene structure with an extended π-conjugation, enhanced the TMR effect.

The naphthoquinones, vitamin K3 and its structural analogue plumbagin, are substrates of the multidrug resistance linked ATP binding cassette drug transporter ABCG2.

PubMed

Shukla, Suneet; Wu, Chung-Pu; Nandigama, Krishnamachary; Ambudkar, Suresh V

2007-12-01

Vitamin K3 (menadione; 2-methyl-1,4-naphthoquinone) is a structural precursor of vitamins K1 and K2, which are essential for blood clotting. The naturally occurring structural analogue of this vitamin, plumbagin (5-hydroxy-menadione), is known to modulate cellular proliferation, apoptosis, carcinogenesis, and radioresistance. We here report that both vitamin K3 and plumbagin are substrates of the multidrug resistance-linked ATP binding cassette drug transporter, ABCG2. Vitamin K3 and plumbagin specifically inhibited the ABCG2-mediated efflux of mitoxantrone but did not have any effect on the ABCB1-mediated efflux of rhodamine 123. This inhibition of ABCG2 function was due to their interaction at the substrate-binding site(s). Vitamin K3 and plumbagin inhibited the binding of [(125)I]iodoarylazidoprazosin, a substrate of ABCG2, to this transporter in a concentration-dependent manner with IC(50) values of 7.3 and 22.6 micromol/L, respectively, but had no effect on the binding of the photoaffinity analogue to ABCB1. Both compounds stimulated ABCG2-mediated ATP hydrolysis and also inhibited the mitoxantrone-stimulated ATPase activity of the ABCG2 transporter, but did not have any significant effect on the ATPase activity of ABCB1. In a cytotoxicity assay, ABCG2-expressing HEK cells were 2.8- and 2.3-fold resistant to plumbagin and vitamin K3, respectively, compared with the control cells, suggesting that they are substrates of this transporter. Collectively, these data show for the first time that vitamin K3 is a substrate of the ABCG2 transporter. Thus, ABCG2 may have a role in the regulation of vitamin K3 levels in the body. In addition, vitamin K3 and its structural derivative, plumbagin, could potentially be used to modulate ABCG2 function.

The naphthoquinones, vitamin K3 and its structural analog plumbagin, are substrates of the multidrug resistance-linked ABC drug transporter ABCG2

PubMed Central

Shukla, Suneet; Wu, Chung-Pu; Nandigama, Krishnamachary; Ambudkar, Suresh V.

2008-01-01

Vitamin K3 (Menadione; 2-methyl-1,4-naphthoquinone) is a structural precursor of vitamins K1 and K2 which are essential for blood clotting. The naturally occurring structural analog of this vitamin, plumbagin (5-hydroxy-menadione), is known to modulate cellular proliferation, apoptosis, carcinogenesis, and radioresistance. We, here, report that both vitamin K3 and plumbagin are substrates of the multidrug resistance-linked ATP binding cassette (ABC) drug transporter, ABCG2. Vitamin K3 and plumbagin specifically inhibited the ABCG2-mediated efflux of mitoxantrone, but did not have any effect on the ABCB1-mediated efflux of rhodamine 123. This inhibition of ABCG2 function was due to their interaction at the substrate-binding site(s). They inhibited the binding of [125I]-Iodoarylazidoprazosin (IAAP), a substrate of ABCG2, to this transporter in a concentration-dependent manner with IC50 values of 7.3 and 22.6 μM, respectively, but had no effect on the binding of this photoaffinity analog to ABCB1. Both compounds stimulated ABCG2-mediated ATP hydrolysis and also inhibited the mitoxantrone-stimulated ATPase activity of this transporter, but did not have any significant effect on the ATPase activity of ABCB1. In a cytotoxicity assay, ABCG2-expressing HEK cells were 2.8- and 2.3-fold resistant to plumbagin and vitamin K3, respectively, compared to the control cells, suggesting that they are substrates of this transporter. Collectively, these data demonstrate for the first time that vitamin K3 is a substrate of the ABCG2 transporter. Thus, ABCG2 may have a role in the regulation of vitamin K3 levels in the body. In addition, vitamin K3 and its structural derivative, plumbagin, could potentially be used to modulate ABCG2 function. PMID:18065489

Lysine 300 is essential for stability but not for electrogenic transport of the Escherichia coli NhaA Na+/H+ antiporter.

PubMed

Călinescu, Octavian; Dwivedi, Manish; Patiño-Ruiz, Miyer; Padan, Etana; Fendler, Klaus

2017-05-12

Na + /H + antiporters are located in the cytoplasmic and intracellular membranes and play crucial roles in regulating intracellular pH, Na + , and volume. The NhaA antiporter of Escherichia coli is the best studied member of the Na + /H + exchanger family and a model system for all related Na + /H + exchangers, including eukaryotic representatives. Several amino acid residues are important for the transport activity of NhaA, including Lys-300, a residue that has recently been proposed to carry one of the two H + ions that NhaA exchanges for one Na + ion during one transport cycle. Here, we sought to characterize the effects of mutating Lys-300 of NhaA to amino acid residues containing side chains of different polarity and length ( i.e. Ala, Arg, Cys, His, Glu, and Leu) on transporter stability and function. Salt resistance assays, acridine-orange fluorescence dequenching, solid supported membrane-based electrophysiology, and differential scanning fluorometry were used to characterize Na + and H + transport, charge translocation, and thermal stability of the different variants. These studies revealed that NhaA could still perform electrogenic Na + /H + exchange even in the absence of a protonatable residue at the Lys-300 position. However, all mutants displayed lower thermal stability and reduced ion transport activity compared with the wild-type enzyme, indicating the critical importance of Lys-300 for optimal NhaA structural stability and function. On the basis of these experimental data, we propose a tentative mechanism integrating the functional and structural role of Lys-300. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

45 CFR 144.103 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... amounts paid for the purpose of affecting any structure or function of the body; (2) Transportation... period. Product means a discrete package of health insurance coverage benefits that a health insurance...

Development of truck equivalent single-axle load (ESAL) factors based on weigh-in-motion data for pavement design in Virginia.

DOT National Transportation Integrated Search

2009-01-01

The Virginia Department of Transportation's (VDOT's) current pavement design procedure is based on the 1993 AASHTO Guide for Design of Pavement Structures. In this procedure, a required structural capacity is calculated as a function of the anticipat...

Cation-Coupled Bicarbonate Transporters

PubMed Central

Aalkjaer, Christian; Boedtkjer, Ebbe; Choi, Inyeong; Lee, Soojung

2016-01-01

Cation-coupled HCO3− transport was initially identified in the mid-1970s when pioneering studies showed that acid extrusion from cells is stimulated by CO2/HCO3− and associated with Na+ and Cl− movement. The first Na+-coupled bicarbonate transporter (NCBT) was expression-cloned in the late 1990s. There are currently five mammalian NCBTs in the SLC4-family: the electrogenic Na,HCO3-cotransporters NBCe1 and NBCe2 (SLC4A4 and SLC4A5 gene products); the electroneutral Na,HCO3-cotransporter NBCn1 (SLC4A7 gene product); the Na+-driven Cl,HCO3-exchanger NDCBE (SLC4A8 gene product); and NBCn2/NCBE (SLC4A10 gene product), which has been characterized as an electroneutral Na,HCO3-cotransporter or a Na+-driven Cl,HCO3-exchanger. Despite the similarity in amino acid sequence and predicted structure among the NCBTs of the SLC4-family, they exhibit distinct differences in ion dependency, transport function, pharmacological properties, and interactions with other proteins. In epithelia, NCBTs are involved in transcellular movement of acid-base equivalents and intracellular pH control. In nonepithelial tissues, NCBTs contribute to intracellular pH regulation; and hence, they are crucial for diverse tissue functions including neuronal discharge, sensory neuron development, performance of the heart, and vascular tone regulation. The function and expression levels of the NCBTs are generally sensitive to intracellular and systemic pH. Animal models have revealed pathophysiological roles of the transporters in disease states including metabolic acidosis, hypertension, visual defects, and epileptic seizures. Studies are being conducted to understand the physiological consequences of genetic polymorphisms in the SLC4-members, which are associated with cancer, hypertension, and drug addiction. Here, we describe the current knowledge regarding the function, structure, and regulation of the mammalian cation-coupled HCO3− transporters of the SLC4-family. PMID:25428855

Assessment of the Requirements for Magnesium Transporters in Bacillus subtilis

PubMed Central

Wakeman, Catherine A.; Goodson, Jonathan R.; Zacharia, Vineetha M.

2014-01-01

Magnesium is the most abundant divalent metal in cells and is required for many structural and enzymatic functions. For bacteria, at least three families of proteins function as magnesium transporters. In recent years, it has been shown that a subset of these transport proteins is regulated by magnesium-responsive genetic control elements. In this study, we investigated the cellular requirements for magnesium homeostasis in the model microorganism Bacillus subtilis. Putative magnesium transporter genes were mutationally disrupted, singly and in combination, in order to assess their general importance. Mutation of only one of these genes resulted in strong dependency on supplemental extracellular magnesium. Notably, this transporter gene, mgtE, is known to be under magnesium-responsive genetic regulatory control. This suggests that the identification of magnesium-responsive genetic mechanisms may generally denote primary transport proteins for bacteria. To investigate whether B. subtilis encodes yet additional classes of transport mechanisms, suppressor strains that permitted the growth of a transporter-defective mutant were identified. Several of these strains were sequenced to determine the genetic basis of the suppressor phenotypes. None of these mutations occurred in transport protein homologues; instead, they affected housekeeping functions, such as signal recognition particle components and ATP synthase machinery. From these aggregate data, we speculate that the mgtE protein provides the primary route of magnesium import in B. subtilis and that the other putative transport proteins are likely to be utilized for more-specialized growth conditions. PMID:24415722

Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding

PubMed Central

Cheng, Mary Hongying; Block, Ethan; Hu, Feizhuo; Cobanoglu, Murat Can; Sorkin, Alexander; Bahar, Ivet

2015-01-01

Human dopamine (DA) transporter (hDAT) regulates dopaminergic signaling in the central nervous system by maintaining the synaptic concentration of DA at physiological levels, upon reuptake of DA into presynaptic terminals. DA translocation involves the co-transport of two sodium ions and the channeling of a chloride ion, and it is achieved via alternating access between outward-facing (OF) and inward-facing states of DAT. hDAT is a target for addictive drugs, such as cocaine, amphetamine (AMPH), and therapeutic antidepressants. Our recent quantitative systems pharmacology study suggested that orphenadrine (ORPH), an anticholinergic agent and anti-Parkinson drug, might be repurposable as a DAT drug. Previous studies have shown that DAT-substrates like AMPH or -blockers like cocaine modulate the function of DAT in different ways. However, the molecular mechanisms of modulation remained elusive due to the lack of structural data on DAT. The newly resolved DAT structure from Drosophila melanogaster opens the way to a deeper understanding of the mechanism and time evolution of DAT–drug/ligand interactions. Using a combination of homology modeling, docking analysis, molecular dynamics simulations, and molecular biology experiments, we performed a comparative study of the binding properties of DA, AMPH, ORPH, and cocaine and their modulation of hDAT function. Simulations demonstrate that binding DA or AMPH drives a structural transition toward a functional form predisposed to translocate the ligand. In contrast, ORPH appears to inhibit DAT function by arresting it in the OF open conformation. The analysis shows that cocaine and ORPH competitively bind DAT, with the binding pose and affinity dependent on the conformational state of DAT. Further assays show that the effect of ORPH on DAT uptake and endocytosis is comparable to that of cocaine. PMID:26106364

Spin Transport in Nondegenerate Si with a Spin MOSFET Structure at Room Temperature

NASA Astrophysics Data System (ADS)

Sasaki, Tomoyuki; Ando, Yuichiro; Kameno, Makoto; Tahara, Takayuki; Koike, Hayato; Oikawa, Tohru; Suzuki, Toshio; Shiraishi, Masashi

2014-09-01

Spin transport in nondegenerate semiconductors is expected to pave the way to the creation of spin transistors, spin logic devices, and reconfigurable logic circuits, because room-temperature (RT) spin transport in Si has already been achieved. However, RT spin transport has been limited to degenerate Si, which makes it difficult to produce spin-based signals because a gate electric field cannot be used to manipulate such signals. Here, we report the experimental demonstration of spin transport in nondegenerate Si with a spin metal-oxide-semiconductor field-effect transistor (MOSFET) structure. We successfully observe the modulation of the Hanle-type spin-precession signals, which is a characteristic spin dynamics in nondegenerate semiconductors. We obtain long spin transport of more than 20 μm and spin rotation greater than 4π at RT. We also observe gate-induced modulation of spin-transport signals at RT. The modulation of the spin diffusion length as a function of a gate voltage is successfully observed, which we attribute to the Elliott-Yafet spin relaxation mechanism. These achievements are expected to lead to the creation of practical Si-based spin MOSFETs.

Investigation of cross-linking characteristics of novel hole-transporting materials for solution-processed phosphorescent OLEDs

NASA Astrophysics Data System (ADS)

Lee, Jaemin; Ameen, Shahid; Lee, Changjin

2016-04-01

After the success of commercialization of the vacuum-evaporated organic light-emitting diodes (OLEDs), solutionprocessing or printing of OLEDs are currently attracting much research interests. However, contrary to various kinds of readily available vacuum-evaporable OLED materials, the solution-processable OLED materials are still relatively rare. Hole-transporting layer (HTL) materials for solution-processed OLEDs are especially limited, because they need additional characteristics such as cross-linking to realize multilayer structures in solution-processed OLEDs, as well as their own electrically hole-transporting characteristics. The presence of such cross-linking characteristics of solutionprocessable HTL materials therefore makes them more challenging in the development stage, and also makes them essence of solution-processable OLED materials. In this work, the structure-property relationships of thermally crosslinkable HTL materials were systematically investigated by changing styrene-based cross-linking functionalities and modifying the carbazole-based hole-transporting core structures. The temperature dependency of the cross-linking characteristics of the HTL materials was systematically investigated by the UV-vis. absorption spectroscopy. The new HTL materials were also applied to green phosphorescent OLEDs, and their device characteristics were also investigated based on the chemical structures of the HTL materials. The device configuration was [ITO / PEDOT:PSS / HTL / EML / ETL / CsF / Al]. We found out that the chemical structures of the cross-linking functionalities greatly affect not only the cross-linking characteristics of the resultant HTL materials, but also the resultant OLED device characteristics. The increase of the maximum luminance and efficiency of OLEDs was evident as the cross-linking temperature decreases from higher than 200°C to at around 150°C.

The impacts of water stress on phloem transport in Douglas-fir trees

Treesearch

David Woodruff

2014-01-01

Despite the critical role that phloem plays in a number of plant functional processes and the potential impact of water stress on phloem structural and phloem sap compositional characteristics, little research has been done to examine how water stress influences phloem transport. The objectives of this study were to develop a more accurate understanding of how water...

Electronic and transport properties of fluorite structure of La2Ce2O7

NASA Astrophysics Data System (ADS)

Mahida, H. R.; Singh, Deobrat; Gupta, Sanjeev K.; Sonvane, Yogesh; Thakor, P. B.

2017-05-01

In this paper, we have symmetrically investigated the structural, electronic and transport properties of fluorite structure of lanthanum cerate oxide (La2Ce2O7) using density functional theory (DFT). The electronic band structure of La2Ce2O7 show semiconducting in nature with band gap of 1.54 eV (indirect at R-X points) and 1.71 eV (direct at R points). We have also calculated the susceptibility, hall resistance, electrical, and thermal conductivity by using Boltztrap equation. The electrical conductivity decreases where as thermal conductivity increases with increase in the temperature. Our result shows that La2Ce2O7 has application in Proton exchange membrane (PEM) fuel cells applications.

Electromechanical and Chemical Sensing at the Nanoscale: DFT and Transport Modeling

NASA Astrophysics Data System (ADS)

Maiti, Amitesh

Of the many nanoelectronic applications proposed for near to medium-term commercial deployment, sensors based on carbon nanotubes (CNT) and metal-oxide nanowires are receiving significant attention from researchers. Such devices typically operate on the basis of the changes of electrical response characteristics of the active component (CNT or nanowire) when subjected to an externally applied mechanical stress or the adsorption of a chemical or bio-molecule. Practical development of such technologies can greatly benefit from quantum chemical modeling based on density functional theory (DFT), and from electronic transport modeling based on non-equilibrium Green's function (NEGF). DFT can compute useful quantities like possible bond-rearrangements, binding energy, charge transfer, and changes to the electronic structure, while NEGF can predict changes in electronic transport behavior and contact resistance. Effects of surrounding medium and intrinsic structural defects can also be taken into account. In this work we review some recent DFT and transport investigations on (1) CNT-based nano-electromechanical sensors (NEMS) and (2) gas-sensing properties of CNTs and metal-oxide nanowires. We also briefly discuss our current understanding of CNT-metal contacts which, depending upon the metal, the deposition technique, and the masking method can have a significant effect on device performance.

Impaired organic ion transport in proximal tubules of rats with Heymann nephritis.

PubMed

Park, E K; Hong, S K; Goldinger, J; Andres, G; Noble, B

1985-10-01

Organic ion transport across the basolateral membrane of proximal tubules was measured by means of the tissue slice technique in each of the four different stages of Heymann nephritis. Impairment of both organic anion and cation transport was detected early in Stage 2, and became more severe in Stage 3 of Heymann nephritis. The decreased transport function was associated with extensive damage to proximal tubule cells, including loss of brush border microvilli and basal infoldings. Despite these abnormalities of structure and function, oxygen consumption of proximal tubule cells remained essentially normal. Partial recovery of organic cation transport was noted late in Heymann nephritis (Stage 4). Recovery of the cation transport function was associated with a partial restoration of brush border microvilli and basal infoldings to proximal tubule cells. However, organic anion transport remained depressed throughout the entire course of disease. Impairment of organic ion transport in rats with Heymann nephritis appeared to result from damage to basolateral membrane transport elements rather than general deterioration of the metabolic machinery of proximal tubule cells. Decreased organic cation transport appeared to be the consequence of a reduction in the number of carrier sites, a phenomenon that could have resulted from decreased membrane surface area. However, the depression of organic anion transport was associated with decreased substrate affinity of the anion carrier, indicating that qualitative, rather than quantitative changes, were primarily responsible for that defect. Specific antibody-mediated damage to the anion transport elements in basolateral membranes of proximal tubules is postulated to occur in Heymann nephritis.

Ballistic transport in nanowires through non-magnetic or magnetic cavity

NASA Astrophysics Data System (ADS)

Nonoyama, Shinji; Honma, Yukari; Ono, Miyuki; Nakamura, Atsunobu

2015-07-01

Ballistic transport phenomena through a region containing a cavity in a quasi-one-dimensional quantum nanowire are investigated. Conductance curves calculated as a function of a structural parameter show quantum interference effects on transport clearly. In a special geometry, very narrow periodic dips, which are attributable to the anti-resonance, appear on the conductance curve. The nature of the virtual bound state resulting in the anti-resonance is studied in detail. Electron conductions through a small dilute magnetic semiconductor are also investigated.

Effect of sulfur doping on thermoelectric properties of Sodium Tantalate - A first principles study

NASA Astrophysics Data System (ADS)

Chowdary, Bharadwaj; Jayaraman, Kaushik; Molli, Muralikrishna

2018-05-01

In this work, we report the thermoelectric (TE) transport properties of perovskite-like Sodium Tantalate and studied the effect of Sulfur doping on TE properties of Sodium Tantalate. The band structures are calculated in the purview of density functional theory using the mBJ exchange correlation potential. The transport properties are evaluated using the Boltzmann transport theory in the constant relaxation time approximation. Our results suggest that Sulfur doped Sodium Tantalate is better n-type thermoelectric compared to Sodium Tantalate.

Urea uptake enhances barrier function and antimicrobial defense in humans by regulating epidermal gene expression

PubMed Central

Grether-Beck, Susanne; Felsner, Ingo; Brenden, Heidi; Kohne, Zippora; Majora, Marc; Marini, Alessandra; Jaenicke, Thomas; Rodriguez-Martin, Marina; Trullas, Carles; Hupe, Melanie; Elias, Peter M.; Krutmann, Jean

2012-01-01

Urea is an endogenous metabolite, known to enhance stratum corneum hydration. Yet, topical urea anecdotally also improves permeability barrier function, and it appears to exhibit antimicrobial activity. Hence, we hypothesized that urea is not merely a passive metabolite, but a small-molecule regulator of epidermal structure and function. In 21 human volunteers, topical urea improved barrier function in parallel with enhanced antimicrobial peptide (LL-37 and β-defensin-2) expression. Urea both stimulates expression of, and is transported into keratinocytes by two urea transporters, UT-A1 and UT-A2, and by aquaporin 3, 7 and 9. Inhibitors of these urea transporters block the downstream biological effects of urea, which include increased mRNA and protein levels for: (i) transglutaminase-1, involucrin, loricrin and filaggrin; (ii) epidermal lipid synthetic enzymes, and (iii) cathelicidin/LL-37 and β-defensin-2. Finally, we explored the potential clinical utility of urea, showing that topical urea applications normalized both barrier function and antimicrobial peptide expression in a murine model of atopic dermatitis (AD). Together, these results show that urea is a small-molecule regulator of epidermal permeability barrier function and antimicrobial peptide expression after transporter uptake, followed by gene regulatory activity in normal epidermis, with potential therapeutic applications in diseased skin. PMID:22418868

Temperature Dependent Electrical Transport Properties of Ni-Cr and Co-Cr Binary Alloys

NASA Astrophysics Data System (ADS)

Thakore, B. Y.; Suthar, P. H.; Khambholja, S. G.; Gajjar, P. N.; Bhatt, N. K.; Jani, A. R.

2011-12-01

The temperature dependent electrical transport properties viz. electrical resistivity and thermal conductivity of Ni10Cr90 and Co20Cr80 alloys are computed at various temperatures. The electrical resistivity has been calculated according to Faber-Ziman model combined with Ashcroft-Langreth partial structure factors. In the present work, to include the ion-electron interaction, we have used a well tested local model potential. For exchange-correlation effects, five different forms of local field correction functions due to Hartree (H), Taylor (T), Ichimaru and Utsumi (IU), Farid et al (F) and Sarkar et al (S) are used. The present results due to S function are in good agreement with the experimental data as compared to results obtained using other four functions. The S functions satisfy compressibility sum rule in long wave length limit more accurately as compared to T, IU and F functions, which may be responsible for better agreement of results, obtained using S function. Also, present result confirms the validity of present approach in determining the transport properties of alloys like Ni-Cr and Co-Cr.

Structure of a eukaryotic SWEET transporter in a homotrimeric complex.

PubMed

Tao, Yuyong; Cheung, Lily S; Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B; Feng, Liang

2015-11-12

Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as the dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter family (SSF; only in the animal kingdom), and SWEETs. SWEETs carry mono- and disaccharides across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion, phloem loading for long distance translocation, pollen nutrition, and seed filling. Plant SWEETs cause pathogen susceptibility possibly by sugar leakage from infected cells. The vacuolar Arabidopsis thaliana AtSWEET2 sequesters sugars in root vacuoles; loss-of-function mutants show increased susceptibility to Pythium infection. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice (Oryza sativa), consists of an asymmetrical pair of triple-helix bundles, connected by an inversion linker transmembrane helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first triple-helix bundle within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs are valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux.

Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1

PubMed Central

Park, Min-Sun

2015-01-01

Glucose transporters (GLUTs) provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and caner. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE), a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM) domains and the intracellular helices (ICH) domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states. PMID:25919356

Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics

PubMed Central

Ando, David; Korabel, Nickolay; Huang, Kerwyn Casey; Gopinathan, Ajay

2015-01-01

Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design. PMID:26488648

Understanding the Contribution of Zinc Transporters in the Function of the Early Secretory Pathway

PubMed Central

Matsunaga, Mayu; Takeda, Taka-aki

2017-01-01

More than one-third of newly synthesized proteins are targeted to the early secretory pathway, which is comprised of the endoplasmic reticulum (ER), Golgi apparatus, and other intermediate compartments. The early secretory pathway plays a key role in controlling the folding, assembly, maturation, modification, trafficking, and degradation of such proteins. A considerable proportion of the secretome requires zinc as an essential factor for its structural and catalytic functions, and recent findings reveal that zinc plays a pivotal role in the function of the early secretory pathway. Hence, a disruption of zinc homeostasis and metabolism involving the early secretory pathway will lead to pathway dysregulation, resulting in various defects, including an exacerbation of homeostatic ER stress. The accumulated evidence indicates that specific members of the family of Zn transporters (ZNTs) and Zrt- and Irt-like proteins (ZIPs), which operate in the early secretory pathway, play indispensable roles in maintaining zinc homeostasis by regulating the influx and efflux of zinc. In this review, the biological functions of these transporters are discussed, focusing on recent aspects of their roles. In particular, we discuss in depth how specific ZNT transporters are employed in the activation of zinc-requiring ectoenzymes. The means by which early secretory pathway functions are controlled by zinc, mediated by specific ZNT and ZIP transporters, are also subjects of this review. PMID:29048339

Understanding the Contribution of Zinc Transporters in the Function of the Early Secretory Pathway.

PubMed

Kambe, Taiho; Matsunaga, Mayu; Takeda, Taka-Aki

2017-10-19

More than one-third of newly synthesized proteins are targeted to the early secretory pathway, which is comprised of the endoplasmic reticulum (ER), Golgi apparatus, and other intermediate compartments. The early secretory pathway plays a key role in controlling the folding, assembly, maturation, modification, trafficking, and degradation of such proteins. A considerable proportion of the secretome requires zinc as an essential factor for its structural and catalytic functions, and recent findings reveal that zinc plays a pivotal role in the function of the early secretory pathway. Hence, a disruption of zinc homeostasis and metabolism involving the early secretory pathway will lead to pathway dysregulation, resulting in various defects, including an exacerbation of homeostatic ER stress. The accumulated evidence indicates that specific members of the family of Zn transporters (ZNTs) and Zrt- and Irt-like proteins (ZIPs), which operate in the early secretory pathway, play indispensable roles in maintaining zinc homeostasis by regulating the influx and efflux of zinc. In this review, the biological functions of these transporters are discussed, focusing on recent aspects of their roles. In particular, we discuss in depth how specific ZNT transporters are employed in the activation of zinc-requiring ectoenzymes. The means by which early secretory pathway functions are controlled by zinc, mediated by specific ZNT and ZIP transporters, are also subjects of this review.

Transport mechanism and regulatory properties of the human amino acid transporter ASCT2 (SLC1A5).

PubMed

Scalise, Mariafrancesca; Pochini, Lorena; Panni, Simona; Pingitore, Piero; Hedfalk, Kristina; Indiveri, Cesare

2014-11-01

The kinetic mechanism of the transport catalyzed by the human glutamine/neutral amino acid transporter hASCT2 over-expressed in P. pastoris was determined in proteoliposomes by pseudo-bi-substrate kinetic analysis of the Na(+)-glutamineex/glutaminein transport reaction. A random simultaneous mechanism resulted from the experimental analysis. Purified functional hASCT2 was chemically cross-linked to a stable dimeric form. The oligomeric structure correlated well with the kinetic mechanism of transport. Half-saturation constants (Km) of the transporter for the other substrates Ala, Ser, Asn and Thr were measured both on the external and internal side. External Km were much lower than the internal ones confirming the asymmetry of the transporter. The electric nature of the transport reaction was determined imposing a negative inside membrane potential generated by K(+) gradients in the presence of valinomycin. The transport reaction resulted to be electrogenic and the electrogenicity originated from external Na(+). Internal Na(+) exerted a stimulatory effect on the transport activity which could be explained by a regulatory, not a counter-transport, effect. Native and deglycosylated hASCT2 extracted from HeLa showed the same transport features demonstrating that the glycosyl moiety has no role in transport function. Both in vitro and in vivo interactions of hASCT2 with the scaffold protein PDZK1 were revealed.

Functional Analysis of Arabidopsis Sucrose Transporters

DOE Office of Scientific and Technical Information (OSTI.GOV)

John M. Ward

2009-03-31

Sucrose is the main photosynthetic product that is transported in the vasculature of plants. The long-distance transport of carbohydrates is required to support the growth and development of net-importing (sink) tissues such as fruit, seeds and roots. This project is focused on understanding the transport mechanism sucrose transporters (SUTs). These are proton-coupled sucrose uptake transporters (membrane proteins) that are required for transport of sucrose in the vasculature and uptake into sink tissues. The accomplishments of this project included: 1) the first analysis of substrate specificity for any SUT. This was accomplished using electrophysiology to analyze AtSUC2, a sucrose transporter frommore » companion cells in Arabidopsis. 2) the first analysis of the transport activity for a monocot SUT. The transport kinetics and substrate specificity of HvSUT1 from barley were studied. 3) the first analysis of a sucrose transporter from sugarcane. and 4) the first analysis of transport activity of a sugar alcohol transporter homolog from plants, AtPLT5. During this period four primary research papers, funded directly by the project, were published in refereed journals. The characterization of several sucrose transporters was essential for the current effort in the analysis of structure/function for this gene family. In particular, the demonstration of strong differences in substrate specificity between type I and II SUTs was important to identify targets for site-directed mutagenesis.« less

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

PubMed Central

Hoffmann, Federico G.; Opazo, Juan C.; Storz, Jay F.

2010-01-01

Natural selection often promotes evolutionary innovation by coopting preexisting genes for new functions, and this process may be greatly facilitated by gene duplication. Here we report an example of cooptive convergence where paralogous members of the globin gene superfamily independently evolved a specialized O2 transport function in the two deepest branches of the vertebrate family tree. Specifically, phylogenetic evidence demonstrates that erythroid-specific O2 transport hemoglobins evolved independently from different ancestral precursor proteins in jawed vertebrates (gnathostomes) and jawless fish (cyclostomes, represented by lamprey and hagfish). A comprehensive phylogenetic analysis of the vertebrate globin gene superfamily revealed that the erythroid hemoglobins of cyclostomes are orthologous to the cytoglobin protein of gnathostome vertebrates, a hexacoordinate globin that has no O2 transport function and that is predominantly expressed in fibroblasts and related cell types. The phylogeny reconstruction also revealed that vertebrate-specific globins are grouped into four main clades: (i) cyclostome hemoglobin + cytoglobin, (ii) myoglobin + globin E, (iii) globin Y, and (iv) the α- and β-chain hemoglobins of gnathostomes. In the hemoglobins of gnathostomes and cyclostomes, multisubunit quaternary structures provide the basis for cooperative O2 binding and allosteric regulation by coupling the effects of ligand binding at individual subunits with interactions between subunits. However, differences in numerous structural details belie their independent origins. This example of convergent evolution of protein function provides an impressive demonstration of the ability of natural selection to cobble together complex design solutions by tinkering with different variations of the same basic protein scaffold. PMID:20660759

Electrical Transport Properties of Liquid Al-Cu Alloys

NASA Astrophysics Data System (ADS)

Thakore, B. Y.; Khambholja, S. G.; Suthar, P. H.; Jani, A. R.

2010-06-01

Electrical transport properties viz. electrical resistivity, thermoelectric power and thermal conductivity of liquid Al-Cu alloys as a function of Cu concentration have been studied in the present paper. Ashcroft empty core model potential has been used to incorporate the ion-electron interaction. To incorporate the exchange and correlation effects, five different forms of local field correction functions viz. Hartree, Taylor, Ichimaru et al., Farid et al. and Sarkar et al. have been used. The transport properties of binary system have been studied using Faber-Ziman formulation combined with Ashcroft-Langreth (AL) partial structure factor. The computed values of electrical resistivity are compared with experimental data and for low Cu concentration, good agreement has been observed. Further, thermoelectric power and thermal conductivity have also been predicted.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Toward Optimal Transport Networks

NASA Technical Reports Server (NTRS)

Alexandrov, Natalia; Kincaid, Rex K.; Vargo, Erik P.

2008-01-01

Strictly evolutionary approaches to improving the air transport system a highly complex network of interacting systems no longer suffice in the face of demand that is projected to double or triple in the near future. Thus evolutionary approaches should be augmented with active design methods. The ability to actively design, optimize and control a system presupposes the existence of predictive modeling and reasonably well-defined functional dependences between the controllable variables of the system and objective and constraint functions for optimization. Following recent advances in the studies of the effects of network topology structure on dynamics, we investigate the performance of dynamic processes on transport networks as a function of the first nontrivial eigenvalue of the network's Laplacian, which, in turn, is a function of the network s connectivity and modularity. The last two characteristics can be controlled and tuned via optimization. We consider design optimization problem formulations. We have developed a flexible simulation of network topology coupled with flows on the network for use as a platform for computational experiments.

Flow and Transport in Highly Heterogeneous Porous Formations: Numerical Experiments Performed Using the Analytic Element Method

NASA Astrophysics Data System (ADS)

Jankovic, I.

2002-05-01

Flow and transport in porous formations are analyzed using numerical simulations. Hydraulic conductivity is treated as a spatial random function characterized by a probability density function and a two-point covariance function. Simulations are performed for a multi-indicator conductivity structure developed by Gedeon Dagan (personal communication). This conductivity structure contains inhomogeneities (inclusions) of elliptical and ellipsoidal geometry that are embedded in a homogeneous background. By varying the distribution of sizes and conductivities of inclusions, any probability density function and two-point covariance may be reproduced. The multi-indicator structure is selected since it yields simple approximate transport solutions (Aldo Fiori, personal communication) and accurate numerical solutions (based on the Analytic Element Method). The dispersion is examined for two conceptual models. Both models are based on the multi-indicator conductivity structure. The first model is designed to examine dispersion in aquifers with continuously varying conductivity. The inclusions in this model cover as much area/volume of the porous formation as possible. The second model is designed for aquifers that contain clay/sand/gravel lenses embedded in otherwise homogeneous background. The dispersion in both aquifer types is simulated numerically. Simulation results are compared to those obtained using simple approximate solutions. In order to infer transport statistics that are representative of an infinite domain using the numerical experiments, the inclusions are placed in a domain that was shaped as a large ellipse (2D) and a large spheroid (3D) that were submerged in an unbounded homogeneous medium. On a large scale, the large body of inclusions behaves like a single large inhomogeneity. The analytic solution for a uniform flow past the single inhomogeneity of such geometry yields uniform velocity inside the domain. The velocity differs from that at infinity and can be used to infer the effective conductivity of the medium. As many as 100,000 inhomogeneities are placed inside the domain for 2D simulations. Simulations in 3D were limited to 50,000 inclusions. A large number of simulations was conducted on a massively parallel supercomputer cluster at the Center for Computational Research, University at Buffalo. Simulations range from mildly heterogeneous formations to highly heterogeneous formations (variance of the logarithm of conductivity equal to 10) and from sparsely populated systems to systems where inhomogeneities cover 95% of the volume. Particles are released and tracked inside the core of constant mean velocity. Following the particle tracking, various medium, flow, and transport statistics are computed. These include: spatial moments of particle positions, probability density function of hydraulic conductivity and each component of velocity, their two-point covariance function in the direction of flow and normal to it, covariance of Lagrangean velocities, and probability density function of travel times to various break-through locations. Following the analytic nature of the flow solution, all the results are presented in dimensionless forms. For example, the dispersion coefficients are made dimensionless with respect to the mean velocity and size of inhomogeneities. Detailed results will be presented and compared to well known first-order results and the results that are based on simple approximate transport solutions of Aldo Fiori.

Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation.

PubMed

Bera, Krishnendu; Rani, Priyanka; Kishor, Gaurav; Agarwal, Shikha; Kumar, Antresh; Singh, Durg Vijay

2017-09-20

ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.

Water and solute transport across the peritoneal membrane.

PubMed

Morelle, Johann; Devuyst, Olivier

2015-09-01

We review the molecular mechanisms of peritoneal transport and discuss how a better understanding of these mechanisms is relevant for dialysis therapy. Peritoneal dialysis involves diffusion and osmosis through the highly vascularized peritoneal membrane. Computer simulations, expression studies and functional analyses in Aqp1 knockout mice demonstrated the critical role of the water channel aquaporin-1 (AQP1) in water removal during peritoneal dialysis. Pharmacologic regulation of AQP1, either through increased expression or gating, is associated with increased water transport in rodent models of peritoneal dialysis. Water transport is impaired during acute peritonitis, despite unchanged expression of AQP1, resulting from the increased microvascular area that dissipates the osmotic gradient across the membrane. In long-term peritoneal dialysis patients, the fibrotic interstitium also impairs water transport, resulting in ultrafiltration failure. Recent data suggest that stroke and drug intoxications might benefit from peritoneal dialysis and could represent novel applications of peritoneal transport in the future. A better understanding of the regulation of osmotic water transport across the peritoneum offers novel insights into the role of water channels in microvascular endothelia, the functional importance of structural changes in the peritoneal interstitium and the transport of water and solutes across biological membranes in general.

Direct observation of electrogenic NH4(+) transport in ammonium transport (Amt) proteins.

PubMed

Wacker, Tobias; Garcia-Celma, Juan J; Lewe, Philipp; Andrade, Susana L A

2014-07-08

Ammonium transport (Amt) proteins form a ubiquitous family of integral membrane proteins that specifically shuttle ammonium across membranes. In prokaryotes, archaea, and plants, Amts are used as environmental NH4(+) scavengers for uptake and assimilation of nitrogen. In the eukaryotic homologs, the Rhesus proteins, NH4(+)/NH3 transport is used instead in acid-base and pH homeostasis in kidney or NH4(+)/NH3 (and eventually CO2) detoxification in erythrocytes. Crystal structures and variant proteins are available, but the inherent challenges associated with the unambiguous identification of substrate and monitoring of transport events severely inhibit further progress in the field. Here we report a reliable in vitro assay that allows us to quantify the electrogenic capacity of Amt proteins. Using solid-supported membrane (SSM)-based electrophysiology, we have investigated the three Amt orthologs from the euryarchaeon Archaeoglobus fulgidus. Af-Amt1 and Af-Amt3 are electrogenic and transport the ammonium and methylammonium cation with high specificity. Transport is pH-dependent, with a steep decline at pH values of ∼5.0. Despite significant sequence homologies, functional differences between the three proteins became apparent. SSM electrophysiology provides a long-sought-after functional assay for the ubiquitous ammonium transporters.

Quantum currents and pair correlation of electrons in a chain of localized dots

NASA Astrophysics Data System (ADS)

Morawetz, Klaus

2017-03-01

The quantum transport of electrons in a wire of localized dots by hopping, interaction and dissipation is calculated and a representation by an equivalent RCL circuit is found. The exact solution for the electric-field induced currents allows to discuss the role of virtual currents to decay initial correlations and Bloch oscillations. The dynamical response function in random phase approximation (RPA) is calculated analytically with the help of which the static structure function and pair correlation function are determined. The pair correlation function contains a form factor from the Brillouin zone and a structure factor caused by the localized dots in the wire.

Uniform structure of eukaryotic plasma membrane: lateral domains in plants.

PubMed

Malínská, Kateŕina; Zažímalová, Eva

2011-03-01

Current models of the plasma membrane (PM) organization focus on the lateral heterogeneity of the membrane and its relation to the cell function. Increasing evidence in mammals and yeast supports the direct relationship between PM lateral microdomains and specific cell processes and functions (nutrient transport, signaling, protein and lipid sorting, endocytosis, pathogen entry etc.). However, for the present the functional significance of an enrichment of specific proteins and possibly lipids in plant PM domains as well as the underlying molecular mechanism driving the lateral PM segregation remain unaddressed. Here we summarize recent findings on the plant PM organization and its role in signaling pathways, with the special emphasis on auxin transport.

A Comparison of Geographic Information Systems, Complex Networks, and Other Models for Analyzing Transportation Network Topologies

NASA Technical Reports Server (NTRS)

Alexandrov, Natalia (Technical Monitor); Kuby, Michael; Tierney, Sean; Roberts, Tyler; Upchurch, Christopher

2005-01-01

This report reviews six classes of models that are used for studying transportation network topologies. The report is motivated by two main questions. First, what can the "new science" of complex networks (scale-free, small-world networks) contribute to our understanding of transport network structure, compared to more traditional methods? Second, how can geographic information systems (GIS) contribute to studying transport networks? The report defines terms that can be used to classify different kinds of models by their function, composition, mechanism, spatial and temporal dimensions, certainty, linearity, and resolution. Six broad classes of models for analyzing transport network topologies are then explored: GIS; static graph theory; complex networks; mathematical programming; simulation; and agent-based modeling. Each class of models is defined and classified according to the attributes introduced earlier. The paper identifies some typical types of research questions about network structure that have been addressed by each class of model in the literature.

Mechanistic logic underlying the axonal transport of cytosolic proteins

PubMed Central

Scott, David A.; Das, Utpal; Tang, Yong; Roy, Subhojit

2011-01-01

Proteins vital to presynaptic function are synthesized in the neuronal perikarya and delivered into synapses via two modes of axonal transport. While membrane-anchoring proteins are conveyed in fast axonal transport via motor-driven vesicles, cytosolic proteins travel in slow axonal transport; via mechanisms that are poorly understood. We found that in cultured axons, populations of cytosolic proteins tagged to photoactivable-GFP (PA-GFP) move with a slow motor-dependent anterograde bias; distinct from vesicular-trafficking or diffusion of untagged PA-GFP. The overall bias is likely generated by an intricate particle-kinetics involving transient assembly and short-range vectorial spurts. In-vivo biochemical studies reveal that cytosolic proteins are organized into higher-order structures within axon-enriched fractions that are largely segregated from vesicles. Data-driven biophysical modeling best predicts a scenario where soluble molecules dynamically assemble into mobile supra-molecular structures. We propose a model where cytosolic proteins are transported by dynamically assembling into multi-protein complexes that are directly/indirectly conveyed by motors. PMID:21555071

TMEM16 proteins: unknown structure and confusing functions.

PubMed

Picollo, Alessandra; Malvezzi, Mattia; Accardi, Alessio

2015-01-16

The TMEM16 family of membrane proteins, also known as anoctamins, plays key roles in a variety of physiological functions that range from ion transport to phospholipid scrambling and to regulating other ion channels. The first two family members to be functionally characterized, TMEM16A (ANO1) and TMEM16B (ANO2), form Ca(2+)-activated Cl(-) channels and are important for transepithelial ion transport, olfaction, phototransduction, smooth muscle contraction, nociception, cell proliferation and control of neuronal excitability. The roles of other family members, such as TMEM16C (ANO3), TMEM16D (ANO4), TMEM16F (ANO6), TMEM16G (ANO7) and TMEM16J (ANO9), remain poorly understood and controversial. These homologues were reported to be phospholipid scramblases, ion channels, to have both functions or to be regulatory subunits of other channels. Mutations in TMEM16F cause Scott syndrome, a bleeding disorder caused by impaired Ca(2+)-dependent externalization of phosphatidylserine in activated platelets, suggesting that this homologue might be a scramblase. However, overexpression of TMEM16F has also been associated with a remarkable number of different ion channel types, raising the possibility that this protein might be involved in both ion and lipid transports. The recent identification of an ancestral TMEM16 homologue with intrinsic channel and scramblase activities supports this hypothesis. Thus, the TMEM16 family might have diverged in two or three different subclasses, channels, scramblases and dual-function channel/scramblases. The structural bases and functional implication of such a functional diversity within a single protein family remain to be elucidated and the links between TMEM16 functions and human physiology and pathologies need to be investigated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit.

PubMed

Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

2016-01-08

One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ∼3  nm. Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.

First principles study of the structural, electronic, and transport properties of triarylamine-based nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akande, Akinlolu, E-mail: akandea@tcd.ie; Bhattacharya, Sandip; Cathcart, Thomas

2014-02-21

We investigate with state of the art density functional theory the structural, electronic, and transport properties of a class of recently synthesized nanostructures based on triarylamine derivatives. First, we consider the single molecule precursors in the gas phase and calculate their static properties, namely (i) the geometrical structure of the neutral and cationic ions, (ii) the electronic structure of the frontier molecular orbitals, and (iii) the ionization potential, hole extraction potential, and internal reorganization energy. This initial study does not evidence any direct correlation between the properties of the individual molecules and their tendency to self-assembly. Subsequently, we investigate themore » charge transport characteristics of the triarylamine derivatives nanowires, by using Marcus theory. For one derivative we further construct an effective Hamiltonian including intermolecular vibrations and evaluate the mobility from the Kubo formula implemented with Monte Carlo sampling. These two methods, valid respectively in the sequential hopping and polaronic band limit, give us values for the room-temperature mobility in the range 0.1–12 cm{sup 2}/Vs. Such estimate confirms the superior transport properties of triarylamine-based nanowires, and make them an attracting materials platform for organic electronics.« less

Structure of Yeast OSBP-Related Protein Osh1 Reveals Key Determinants for Lipid Transport and Protein Targeting at the Nucleus-Vacuole Junction.

PubMed

Manik, Mohammad Kawsar; Yang, Huiseon; Tong, Junsen; Im, Young Jun

2017-04-04

Yeast Osh1 belongs to the oxysterol-binding protein (OSBP) family of proteins and contains multiple targeting modules optimized for lipid transport at the nucleus-vacuole junction (NVJ). The key determinants for NVJ targeting and the role of Osh1 at NVJs have remained elusive because of unknown lipid specificities. In this study, we determined the structures of the ankyrin repeat domain (ANK), and OSBP-related domain (ORD) of Osh1, in complex with Nvj1 and ergosterol, respectively. The Osh1 ANK forms a unique bi-lobed structure that recognizes a cytosolic helical segment of Nvj1. We discovered that Osh1 ORD binds ergosterol and phosphatidylinositol 4-phosphate PI(4)P in a competitive manner, suggesting counter-transport function of the two lipids. Ergosterol is bound to the hydrophobic pocket in a head-down orientation, and the structure of the PI(4)P-binding site in Osh1 is well conserved. Our results suggest that Osh1 performs non-vesicular transport of ergosterol and PI(4)P at the NVJ. Copyright © 2017 Elsevier Ltd. All rights reserved.

Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit

NASA Astrophysics Data System (ADS)

Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

2016-01-01

One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ˜3 nm . Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.

Tuning transport properties on graphene multiterminal structures by mechanical deformations

NASA Astrophysics Data System (ADS)

Latge, Andrea; Torres, Vanessa; Faria, Daiara

The realization of mechanical strain on graphene structures is viewed as a promise route to tune electronic and transport properties such as changing energy band-gaps and promoting localization of states. Using continuum models, mechanical deformations are described by effective gauge fields, mirrored as pseudomagnetic fields that may reach quite high values. Interesting symmetry features are developed due to out of plane deformations on graphene; lift sublattice symmetry was predicted and observed in centrosymmetric bumps and strained nanobubbles. Here we discuss the effects of Gaussian-like strain on a hexagonal graphene flake connected to three leads, modeled as perfect graphene nanoribbons. The Green function formalism is used within a tight-binding approximation. For this particular deformation sharp resonant states are achieved depending on the strained structure details. We also study a fold-strained structure in which the three leads are deformed extending up to the very center of the hexagonal flake. We show that conductance suppressions can be controlled by the strain intensity and important transport features are modeled by the electronic band structure of the leads.

Protein–Protein Interactions between Sucrose Transporters of Different Affinities Colocalized in the Same Enucleate Sieve Element

PubMed Central

Reinders, Anke; Schulze, Waltraud; Kühn, Christina; Barker, Laurence; Schulz, Alexander; Ward, John M.; Frommer, Wolf B.

2002-01-01

Suc represents the major transport form for carbohydrates in plants. Suc is loaded actively against a concentration gradient into sieve elements, which constitute the conduit for assimilate export out of leaves. Three members of the Suc transporter family with different properties were identified: SUT1, a high-affinity Suc proton cotransporter; SUT4, a low-affinity transporter; and SUT2, which in yeast is only weakly active and shows features similar to those of the yeast sugar sensors RGT2 and SNF3. Immunolocalization demonstrated that all three SUT proteins are localized in the same enucleate sieve element. Thus, the potential of Suc transporters to form homooligomers was tested by the yeast-based split-ubiquitin system. The results show that both SUT1 and SUT2 have the potential to form homooligomers. Moreover, all three Suc transporters have the potential to interact with each other. As controls, a potassium channel and a monosaccharide transporter, expressed in the plasma membrane, did not interact with the SUTs. The in vivo interaction between the functionally different Suc transporters indicates that the membrane proteins are capable of forming oligomeric structures that, like mammalian Glc transporter complexes, might be of functional significance for the regulation of transport. PMID:12119375

Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling

PubMed Central

Diaz, Maira; Sanchez-Barrena, Maria Jose; Gonzalez-Rubio, Juana Maria; Rodriguez, Lesia; Fernandez, Daniel; Antoni, Regina; Yunta, Cristina; Belda-Palazon, Borja; Gonzalez-Guzman, Miguel; Peirats-Llobet, Marta; Menendez, Margarita; Boskovic, Jasminka; Marquez, Jose A.; Rodriguez, Pedro L.; Albert, Armando

2016-01-01

Regulation of ion transport in plants is essential for cell function. Abiotic stress unbalances cell ion homeostasis, and plants tend to readjust it, regulating membrane transporters and channels. The plant hormone abscisic acid (ABA) and the second messenger Ca2+ are central in such processes, as they are involved in the regulation of protein kinases and phosphatases that control ion transport activity in response to environmental stimuli. The identification and characterization of the molecular mechanisms underlying the effect of ABA and Ca2+ signaling pathways on membrane function are central and could provide opportunities for crop improvement. The C2-domain ABA-related (CAR) family of small proteins is involved in the Ca2+-dependent recruitment of the pyrabactin resistance 1/PYR1-like (PYR/PYL) ABA receptors to the membrane. However, to fully understand CAR function, it is necessary to define a molecular mechanism that integrates Ca2+ sensing, membrane interaction, and the recognition of the PYR/PYL interacting partners. We present structural and biochemical data showing that CARs are peripheral membrane proteins that functionally cluster on the membrane and generate strong positive membrane curvature in a Ca2+-dependent manner. These features represent a mechanism for the generation, stabilization, and/or specific recognition of membrane discontinuities. Such structures may act as signaling platforms involved in the recruitment of PYR/PYL receptors and other signaling components involved in cell responses to stress. PMID:26719420

Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.

PubMed

Diaz, Maira; Sanchez-Barrena, Maria Jose; Gonzalez-Rubio, Juana Maria; Rodriguez, Lesia; Fernandez, Daniel; Antoni, Regina; Yunta, Cristina; Belda-Palazon, Borja; Gonzalez-Guzman, Miguel; Peirats-Llobet, Marta; Menendez, Margarita; Boskovic, Jasminka; Marquez, Jose A; Rodriguez, Pedro L; Albert, Armando

2016-01-19

Regulation of ion transport in plants is essential for cell function. Abiotic stress unbalances cell ion homeostasis, and plants tend to readjust it, regulating membrane transporters and channels. The plant hormone abscisic acid (ABA) and the second messenger Ca(2+) are central in such processes, as they are involved in the regulation of protein kinases and phosphatases that control ion transport activity in response to environmental stimuli. The identification and characterization of the molecular mechanisms underlying the effect of ABA and Ca(2+) signaling pathways on membrane function are central and could provide opportunities for crop improvement. The C2-domain ABA-related (CAR) family of small proteins is involved in the Ca(2+)-dependent recruitment of the pyrabactin resistance 1/PYR1-like (PYR/PYL) ABA receptors to the membrane. However, to fully understand CAR function, it is necessary to define a molecular mechanism that integrates Ca(2+) sensing, membrane interaction, and the recognition of the PYR/PYL interacting partners. We present structural and biochemical data showing that CARs are peripheral membrane proteins that functionally cluster on the membrane and generate strong positive membrane curvature in a Ca(2+)-dependent manner. These features represent a mechanism for the generation, stabilization, and/or specific recognition of membrane discontinuities. Such structures may act as signaling platforms involved in the recruitment of PYR/PYL receptors and other signaling components involved in cell responses to stress.

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.

PubMed

Hohl, Michael; Hürlimann, Lea M; Böhm, Simon; Schöppe, Jendrik; Grütter, Markus G; Bordignon, Enrica; Seeger, Markus A

2014-07-29

ATP binding cassette (ABC) transporters mediate vital transport processes in every living cell. ATP hydrolysis, which fuels transport, displays positive cooperativity in numerous ABC transporters. In particular, heterodimeric ABC exporters exhibit pronounced allosteric coupling between a catalytically impaired degenerate site, where nucleotides bind tightly, and a consensus site, at which ATP is hydrolyzed in every transport cycle. Whereas the functional phenomenon of cooperativity is well described, its structural basis remains poorly understood. Here, we present the apo structure of the heterodimeric ABC exporter TM287/288 and compare it to the previously solved structure with adenosine 5'-(β,γ-imido)triphosphate (AMP-PNP) bound at the degenerate site. In contrast to other ABC exporter structures, the nucleotide binding domains (NBDs) of TM287/288 remain in molecular contact even in the absence of nucleotides, and the arrangement of the transmembrane domains (TMDs) is not influenced by AMP-PNP binding, a notion confirmed by double electron-electron resonance (DEER) measurements. Nucleotide binding at the degenerate site results in structural rearrangements, which are transmitted to the consensus site via two D-loops located at the NBD interface. These loops owe their name from a highly conserved aspartate and are directly connected to the catalytically important Walker B motif. The D-loop at the degenerate site ties the NBDs together even in the absence of nucleotides and substitution of its aspartate by alanine is well-tolerated. By contrast, the D-loop of the consensus site is flexible and the aspartate to alanine mutation and conformational restriction by cross-linking strongly reduces ATP hydrolysis and substrate transport.

A Comparison of Hyporheic Transport at a Cross-Vane Structure and Natural Riffle.

PubMed

Smidt, Samuel J; Cullin, Joseph A; Ward, Adam S; Robinson, Jesse; Zimmer, Margaret A; Lautz, Laura K; Endreny, Theodore A

2015-01-01

While restoring hyporheic flowpaths has been cited as a benefit to stream restoration structures, little documentation exists confirming that constructed restoration structures induce comparable hyporheic exchange to natural stream features. This study compares a stream restoration structure (cross-vane) to a natural feature (riffle) concurrently in the same stream reach using time-lapsed electrical resistivity (ER) tomography. Using this hydrogeophysical approach, we were able to quantify hyporheic extent and transport beneath the cross-vane structure and the riffle. We interpret from the geophysical data that the cross-vane and the natural riffle induced spatially and temporally unique hyporheic extent and transport, and the cross-vane created both spatially larger and temporally longer hyporheic flowpaths than the natural riffle. Tracer from the 4.67-h injection was detected along flowpaths for 4.6 h at the cross-vane and 4.2 h at the riffle. The spatial extent of the hyporheic zone at the cross-vane was 12% larger than that at the riffle. We compare ER results of this study to vertical fluxes calculated from temperature profiles and conclude significant differences in the interpretation of hyporheic transport from these different field techniques. Results of this study demonstrate a high degree of heterogeneity in transport metrics at both the cross-vane and the riffle and differences between the hyporheic flowpath networks at the two different features. Our results suggest that restoration structures may be capable of creating sufficient exchange flux and timescales of transport to achieve the same ecological functions as natural features, but engineering of the physical and biogeochemical environment may be necessary to realize these benefits. © 2014, National Ground Water Association.

Structural insight into lipopolysaccharide transport from the Gram-negative bacterial inner membrane to the outer membrane.

PubMed

Dong, Haohao; Tang, Xiaodi; Zhang, Zhengyu; Dong, Changjiang

2017-11-01

Lipopolysaccharide (LPS) is an important component of the outer membrane (OM) of Gram-negative bacteria, playing essential roles in protecting bacteria from harsh environments, in drug resistance and in pathogenesis. LPS is synthesized in the cytoplasm and translocated to the periplasmic side of the inner membrane (IM), where it matures. Seven lipopolysaccharide transport proteins, LptA-G, form a trans‑envelope complex that is responsible for LPS extraction from the IM and transporting it across the periplasm to the OM. The LptD/E of the complex transports LPS across the OM and inserts it into the outer leaflet of the OM. In this review we focus upon structural and mechanistic studies of LPS transport proteins, with a particular focus upon the LPS ABC transporter LptB 2 FG. This ATP binding cassette transporter complex consists of twelve transmembrane segments and has a unique mechanism whereby it extracts LPS from the periplasmic face of the IM through a pair of lateral gates and then powers trans‑periplasmic transport to the OM through a slide formed by either of the periplasmic domains of LptF or LptG, LptC, LptA and the N-terminal domain of LptD. The structural and functional studies of the seven lipopolysaccharide transport proteins provide a platform to explore the unusual mechanisms of LPS extraction, transport and insertion from the inner membrane to the outer membrane. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2017 Elsevier B.V. All rights reserved.

A Simple Question to Think about When Considering the Hemoglobin Function

ERIC Educational Resources Information Center

Ruiz-Larrea, M. Begona

2002-01-01

Hemoglobin is a complex protein formed by various subunits interacting with each other. These noncovalent interactions, quaternary structure, are responsible for hemoglobin functioning as an excellent oxygen transporter, loading up with oxygen in the lungs and delivering it to tissues, where the oxygen pressure is lower. The communications between…

Structural Efficiency of Percolated Landscapes in Flow Networks

PubMed Central

Serrano, M. Ángeles; De Los Rios, Paolo

2008-01-01

The large-scale structure of complex systems is intimately related to their functionality and evolution. In particular, global transport processes in flow networks rely on the presence of directed pathways from input to output nodes and edges, which organize in macroscopic connected components. However, the precise relation between such structures and functional or evolutionary aspects remains to be understood. Here, we investigate which are the constraints that the global structure of directed networks imposes on transport phenomena. We define quantitatively under minimal assumptions the structural efficiency of networks to determine how robust communication between the core and the peripheral components through interface edges could be. Furthermore, we assess that optimal topologies in terms of access to the core should look like “hairy balls” so to minimize bottleneck effects and the sensitivity to failures. We illustrate our investigation with the analysis of three real networks with very different purposes and shaped by very different dynamics and time-scales–the Internet customer-provider set of relationships, the nervous system of the worm Caenorhabditis elegans, and the metabolism of the bacterium Escherichia coli. Our findings prove that different global connectivity structures result in different levels of structural efficiency. In particular, biological networks seem to be close to the optimal layout. PMID:18985157

Natively Unfolded FG Repeats Stabilize the Structure of the Nuclear Pore Complex.

PubMed

Onischenko, Evgeny; Tang, Jeffrey H; Andersen, Kasper R; Knockenhauer, Kevin E; Vallotton, Pascal; Derrer, Carina P; Kralt, Annemarie; Mugler, Christopher F; Chan, Leon Y; Schwartz, Thomas U; Weis, Karsten

2017-11-02

Nuclear pore complexes (NPCs) are ∼100 MDa transport channels assembled from multiple copies of ∼30 nucleoporins (Nups). One-third of these Nups contain phenylalanine-glycine (FG)-rich repeats, forming a diffusion barrier, which is selectively permeable for nuclear transport receptors that interact with these repeats. Here, we identify an additional function of FG repeats in the structure and biogenesis of the yeast NPC. We demonstrate that GLFG-containing FG repeats directly bind to multiple scaffold Nups in vitro and act as NPC-targeting determinants in vivo. Furthermore, we show that the GLFG repeats of Nup116 function in a redundant manner with Nup188, a nonessential scaffold Nup, to stabilize critical interactions within the NPC scaffold needed for late steps of NPC assembly. Our results reveal a previously unanticipated structural role for natively unfolded GLFG repeats as Velcro to link NPC subcomplexes and thus add a new layer of connections to current models of the NPC architecture. Copyright © 2017 Elsevier Inc. All rights reserved.

The influence of Coulomb correlations on nonequilibrium quantum transport in quadruple quantum-dot structure

NASA Astrophysics Data System (ADS)

Kagan, M. Yu.; Aksenov, S. V.

2018-04-01

The description of quantum transport in a quadruple quantum-dot structure (QQD) is proposed taking into account the Coulomb correlations and nonzero bias voltages. To achieve this goal the combination of nonequilibrium Green's functions and equation-of-motion technique is used. It is shown that the anisotropy of kinetic processes in the QQD leads to negative differential conductance (NDC). The reason of the effect is an interplay of the Fano resonances which are induced by the interdot Coulomb correlations. Different ways to increase the peak-to-valley ratio related to the observed NDC are discussed.

Trim and Structural Optimization of Subsonic Transport Wings Using Nonconventional Aeroelastic Tailoring

NASA Technical Reports Server (NTRS)

Stanford, Bret K.; Jutte, Christine V.

2014-01-01

Several minimum-mass aeroelastic optimization problems are solved to evaluate the effectiveness of a variety of novel tailoring schemes for subsonic transport wings. Aeroelastic strength and panel buckling constraints are imposed across a variety of trimmed maneuver loads. Tailoring with metallic thickness variations, functionally graded materials, composite laminates, tow steering, and distributed trailing edge control effectors are all found to provide reductions in structural wing mass with varying degrees of success. The question as to whether this wing mass reduction will offset the increased manufacturing cost is left unresolved for each case.

Approach to an Affordable and Sustainable Space Transportation System

NASA Technical Reports Server (NTRS)

McCleskey, Caey M.; Rhodes, R. E.; Robinson, J. W.; Henderson, E. M.

2012-01-01

This paper describes an approach and a general procedure for creating space transportation architectural concepts that are at once affordable and sustainable. Previous papers by the authors and other members of the Space Propulsion Synergy Team (SPST) focused on a functional system breakdown structure for an architecture and definition of high-payoff design techniques with a technology integration strategy. This paper follows up by using a structured process that derives architectural solutions focused on achieving life cycle affordability and sustainability. Further, the paper includes an example concept that integrates key design techniques discussed in previous papers. !

Functional Characterization of the Small Regulatory Subunit PetP from the Cytochrome b6f Complex in Thermosynechococcus elongatus[C][W

PubMed Central

Rexroth, Sascha; Rexroth, Dorothea; Veit, Sebastian; Plohnke, Nicole; Cormann, Kai U.; Nowaczyk, Marc M.; Rögner, Matthias

2014-01-01

The cyanobacterial cytochrome b6f complex is central for the coordination of photosynthetic and respiratory electron transport and also for the balance between linear and cyclic electron transport. The development of a purification strategy for a highly active dimeric b6f complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled characterization of the structural and functional role of the small subunit PetP in this complex. Moreover, the efficient transformability of this strain allowed the generation of a ΔpetP mutant. Analysis on the whole-cell level by growth curves, photosystem II light saturation curves, and P700+ reduction kinetics indicate a strong decrease in the linear electron transport in the mutant strain versus the wild type, while the cyclic electron transport via photosystem I and cytochrome b6f is largely unaffected. This reduction in linear electron transport is accompanied by a strongly decreased stability and activity of the isolated ΔpetP complex in comparison with the dimeric wild-type complex, which binds two PetP subunits. The distinct behavior of linear and cyclic electron transport may suggest the presence of two distinguishable pools of cytochrome b6f complexes with different functions that might be correlated with supercomplex formation. PMID:25139006

Acclimation of mechanical and hydraulic functions in trees: impact of the thigmomorphogenetic process

PubMed Central

Badel, Eric; Ewers, Frank W.; Cochard, Hervé; Telewski, Frank W.

2015-01-01

The secondary xylem (wood) of trees mediates several functions including water transport and storage, mechanical support and storage of photosynthates. The optimal structures for each of these functions will most likely differ. The complex structure and function of xylem could lead to trade-offs between conductive efficiency, resistance to embolism, and mechanical strength needed to count for mechanical loading due to gravity and wind. This has been referred to as the trade-off triangle, with the different optimal solutions to the structure/function problems depending on the environmental constraints as well as taxonomic histories. Thus, the optimisation of each function will lead to drastically different anatomical structures. Trees are able to acclimate the internal structure of their trunk and branches according to the stress they experience. These acclimations lead to specific structures that favor the efficiency or the safety of one function but can be antagonistic with other functions. Currently, there are no means to predict the way a tree will acclimate or optimize its internal structure in support of its various functions under differing environmental conditions. In this review, we will focus on the acclimation of xylem anatomy and its resulting mechanical and hydraulic functions to recurrent mechanical strain that usually result from wind-induced thigmomorphogenesis with a special focus on the construction cost and the possible trade-off between wood functions. PMID:25954292

Probing the conformation of a conserved glutamic acid within the Cl− pathway of a CLC H+/Cl− exchanger

PubMed Central

Vien, Malvin

2017-01-01

The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H+/Cl− exchange. One of these states, in which Gluex occupies the central binding site (Scen) while Cl− ions fill the internal and external sites (Sint and Sext), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Gluex trapped in Scen between two Cl− ions. Transport by CLC-ec1 is reduced when [Cl−] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Gluex in Scen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl−] is abolished in the E148A mutant, in which the Gluex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Gluex can occupy Scen as well as the Sext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to Scen play a role in determining the equilibrium between these two conformations. PMID:28246117

The Combined Action of Duplicated Boron Transporters Is Required for Maize Growth in Boron-Deficient Conditions.

PubMed

Chatterjee, Mithu; Liu, Qiujie; Menello, Caitlin; Galli, Mary; Gallavotti, Andrea

2017-08-01

The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members ( RTE2 - RTE6 ) that show tissue-specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells surrounding the vasculature. Despite sharing a similar function with RTE , mutations in the RTE2 gene do not cause growth defects in the shoot, even in boron-deficient conditions. However, rte2 mutants strongly enhance the rte phenotype in soils with low boron content, producing shorter plants that fail to form all reproductive structures. The joint action of RTE and RTE2 is also required in root development. These defects can be fully complemented by supplying boric acid, suggesting that diffusion or additional transport mechanisms overcome active boron transport deficiencies in the presence of an excess of boron. Overall, these results suggest that RTE2 and RTE function are essential for maize shoot and root growth in boron-deficient conditions. Copyright © 2017 by the Genetics Society of America.

Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2.

PubMed

Subramanian, Nandhitha; Scopelitti, Amanda J; Carland, Jane E; Ryan, Renae M; O'Mara, Megan L; Vandenberg, Robert J

2016-01-01

The Na+/Cl- dependent glycine transporters GlyT1 and GlyT2 regulate synaptic glycine concentrations. Glycine transport by GlyT2 is coupled to the co-transport of three Na+ ions, whereas transport by GlyT1 is coupled to the co-transport of only two Na+ ions. These differences in ion-flux coupling determine their respective concentrating capacities and have a direct bearing on their functional roles in synaptic transmission. The crystal structures of the closely related bacterial Na+-dependent leucine transporter, LeuTAa, and the Drosophila dopamine transporter, dDAT, have allowed prediction of two Na+ binding sites in GlyT2, but the physical location of the third Na+ site in GlyT2 is unknown. A bacterial betaine transporter, BetP, has also been crystallized and shows structural similarity to LeuTAa. Although betaine transport by BetP is coupled to the co-transport of two Na+ ions, the first Na+ site is not conserved between BetP and LeuTAa, the so called Na1' site. We hypothesized that the third Na+ binding site (Na3 site) of GlyT2 corresponds to the BetP Na1' binding site. To identify the Na3 binding site of GlyT2, we performed molecular dynamics (MD) simulations. Surprisingly, a Na+ placed at the location consistent with the Na1' site of BetP spontaneously dissociated from its initial location and bound instead to a novel Na3 site. Using a combination of MD simulations of a comparative model of GlyT2 together with an analysis of the functional properties of wild type and mutant GlyTs we have identified an electrostatically favorable novel third Na+ binding site in GlyT2 formed by Trp263 and Met276 in TM3, Ala481 in TM6 and Glu648 in TM10.

Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2

PubMed Central

Subramanian, Nandhitha; Scopelitti, Amanda J.; Carland, Jane E.; Ryan, Renae M.; O’Mara, Megan L.; Vandenberg, Robert J.

2016-01-01

The Na+/Cl- dependent glycine transporters GlyT1 and GlyT2 regulate synaptic glycine concentrations. Glycine transport by GlyT2 is coupled to the co-transport of three Na+ ions, whereas transport by GlyT1 is coupled to the co-transport of only two Na+ ions. These differences in ion-flux coupling determine their respective concentrating capacities and have a direct bearing on their functional roles in synaptic transmission. The crystal structures of the closely related bacterial Na+-dependent leucine transporter, LeuTAa, and the Drosophila dopamine transporter, dDAT, have allowed prediction of two Na+ binding sites in GlyT2, but the physical location of the third Na+ site in GlyT2 is unknown. A bacterial betaine transporter, BetP, has also been crystallized and shows structural similarity to LeuTAa. Although betaine transport by BetP is coupled to the co-transport of two Na+ ions, the first Na+ site is not conserved between BetP and LeuTAa, the so called Na1' site. We hypothesized that the third Na+ binding site (Na3 site) of GlyT2 corresponds to the BetP Na1' binding site. To identify the Na3 binding site of GlyT2, we performed molecular dynamics (MD) simulations. Surprisingly, a Na+ placed at the location consistent with the Na1' site of BetP spontaneously dissociated from its initial location and bound instead to a novel Na3 site. Using a combination of MD simulations of a comparative model of GlyT2 together with an analysis of the functional properties of wild type and mutant GlyTs we have identified an electrostatically favorable novel third Na+ binding site in GlyT2 formed by Trp263 and Met276 in TM3, Ala481 in TM6 and Glu648 in TM10. PMID:27337045

SH3-like motif-containing C-terminal domain of staphylococcal teichoic acid transporter suggests possible function.

PubMed

Ko, Tzu-Ping; Tseng, Shih-Ting; Lai, Shu-Jung; Chen, Sheng-Chia; Guan, Hong-Hsiang; Shin Yang, Chia; Jung Chen, Chun; Chen, Yeh

2016-09-01

The negatively charged bacterial polysaccharides-wall teichoic acids (WTAs) are synthesized intracellularly and exported by a two-component transporter, TagGH, comprising a transmembrane subunit TagG and an ATPase subunit TagH. We determined the crystal structure of the C-terminal domain of TagH (TagH-C) to investigate its function. The structure shows an N-terminal SH3-like subdomain wrapped by a C-terminal subdomain with an anti-parallel β-sheet and an outer shell of α-helices. A stretch of positively charged surface across the subdomain interface is flanked by two negatively charged regions, suggesting a potential binding site for negatively charged polymers, such as WTAs or acidic peptide chains. Proteins 2016; 84:1328-1332. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Core Transmembrane Domain 6 Plays a Pivotal Role in the Transport Cycle of the Sodium/Proline Symporter PutP*

PubMed Central

Bracher, Susanne; Schmidt, Claudia C.; Dittmer, Sophie I.; Jung, Heinrich

2016-01-01

Crystal structures of transporters with a LeuT-type structural fold assign core transmembrane domain 6 (TM6′) a central role in substrate binding and translocation. Here, the function of TM6′ in the sodium/proline symporter PutP, a member of the solute/sodium symporter family, was investigated. A complete scan of TM6′ identified eight amino acids as particularly important for PutP function. Of these residues, Tyr-248, His-253, and Arg-257 impact sodium binding, whereas Arg-257 and Ala-260 may participate in interactions leading to closure of the inner gate. Furthermore, the previous suggestion of an involvement of Trp-244, Tyr-248, and Pro-252 in proline binding is further supported. In addition, substitution of Gly-245, Gly-247, and Gly-250 affects the amount of PutP in the membrane. A Cys accessibility analysis suggests an involvement of the inner half of TM6′ in the formation of a hydrophilic pathway that is open to the inside in the absence of ligands and closed in the presence of sodium and proline. In conclusion, the results demonstrate that TM6′ plays a central role in substrate binding and release on the inner side of the membrane also in PutP and extend the knowledge on functionally relevant amino acids in transporters with a LeuT-type structural fold. PMID:27793991

Catalytic and transport cycles of ABC exporters.

PubMed

Al-Shawi, Marwan K

2011-09-07

ABC (ATP-binding cassette) transporters are arguably the most important family of ATP-driven transporters in biology. Despite considerable effort and advances in determining the structures and physiology of these transporters, their fundamental molecular mechanisms remain elusive and highly controversial. How does ATP hydrolysis by ABC transporters drive their transport function? Part of the problem in answering this question appears to be a perceived need to formulate a universal mechanism. Although it has been generally hoped and assumed that the whole superfamily of ABC transporters would exhibit similar conserved mechanisms, this is proving not to be the case. Structural considerations alone suggest that there are three overall types of coupling mechanisms related to ABC exporters, small ABC importers and large ABC importers. Biochemical and biophysical characterization leads us to the conclusion that, even within these three classes, the catalytic and transport mechanisms are not fully conserved, but continue to evolve. ABC transporters also exhibit unusual characteristics not observed in other primary transporters, such as uncoupled basal ATPase activity, that severely complicate mechanistic studies by established methods. In this chapter, I review these issues as related to ABC exporters in particular. A consensus view has emerged that ABC exporters follow alternating-access switch transport mechanisms. However, some biochemical data suggest that alternating catalytic site transport mechanisms are more appropriate for fully symmetrical ABC exporters. Heterodimeric and asymmetrical ABC exporters appear to conform to simple alternating-access-type mechanisms.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

[Cognitive Function and Calcium. Structures and functions of Ca2+-permeable channels].

PubMed

Kaneko, Shuji

2015-02-01

Calcium is essential for living organisms where the increase in intracellular Ca2+ concentration functions as a second messenger for many cellular processes including synaptic transmission and neural plasticity. The cytosolic concentration of Ca2+ is finely controlled by many Ca2+-permeable ion channels and transporters. The comprehensive view of their expression, function, and regulation will advance our understanding of neural and cognitive functions of Ca2+, which leads to the future drug discovery.

Structure, function and regulation of plant photosystem I.

PubMed

Jensen, Poul Erik; Bassi, Roberto; Boekema, Egbert J; Dekker, Jan P; Jansson, Stefan; Leister, Dario; Robinson, Colin; Scheller, Henrik Vibe

2007-05-01

Photosystem I (PSI) is a multisubunit protein complex located in the thylakoid membranes of green plants and algae, where it initiates one of the first steps of solar energy conversion by light-driven electron transport. In this review, we discuss recent progress on several topics related to the functioning of the PSI complex, like the protein composition of the complex in the plant Arabidopsis thaliana, the function of these subunits and the mechanism by which nuclear-encoded subunits can be inserted into or transported through the thylakoid membrane. Furthermore, the structure of the native PSI complex in several oxygenic photosynthetic organisms and the role of the chlorophylls and carotenoids in the antenna complexes in light harvesting and photoprotection are reviewed. The special role of the 'red' chlorophylls (chlorophyll molecules that absorb at longer wavelength than the primary electron donor P700) is assessed. The physiology and mechanism of the association of the major light-harvesting complex of photosystem II (LHCII) with PSI during short term adaptation to changes in light quality and quantity is discussed in functional and structural terms. The mechanism of excitation energy transfer between the chlorophylls and the mechanism of primary charge separation is outlined and discussed. Finally, a number of regulatory processes like acclimatory responses and retrograde signalling is reviewed with respect to function of the thylakoid membrane. We finish this review by shortly discussing the perspectives for future research on PSI.

Giant oscillating magnetoresistance in silicene-based structures

NASA Astrophysics Data System (ADS)

Oubram, O.; Navarro, O.; Rodríguez-Vargas, I.; Guzman, E. J.; Cisneros-Villalobos, L.; Velásquez-Aguilar, J. G.

2018-02-01

Ballistic electron transport in a silicene structure, composed of a pair of magnetic gates, in the ferromagnetic and an-tiferromagnetic configuration is studied. This theoretical study has been done using the matrix transfer method to calculate the transmission, the conductance for parallel and antiparallel magnetic alignment and the magnetoresistance. Results show that conductance and magnetoresistance oscillate as a function of the length between the two magnetic domains. The forbidden transmission region also increases as a function of the barrier separation distance.

Conformational Transitions in Molecular Systems

NASA Astrophysics Data System (ADS)

Bachmann, M.; Janke, W.

2008-11-01

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

Electronic Transport Through Carbon Nanotubes: Effects of Structural Deformation and the Tube Chirality

NASA Technical Reports Server (NTRS)

Maiti, Amitesh; Svizhenko, Alexei; Anantram, M. P.; Biegel, Bryan (Technical Monitor)

2001-01-01

Atomistic simulations using a combination of classical force field and Density-Functional-Theory (DFT) show that carbon atoms remain essentially sp2 coordinated in either bent tubes or tubes pushed by an atomically sharp AFM tip. Subsequent Green's-function-based transport calculations reveal that for armchair tubes there is no significant drop in conductance, while for zigzag tubes the conductance can drop by several orders of magnitude in AFM-pushed tubes. The effect can be attributed to simple stretching of the tube under tip deformation, which opens up an energy gap at the Fermi surface.

Electron transport in all-Heusler Co2CrSi/Cu2CrAl/Co2CrSi device, based on ab-initio NEGF calculations

NASA Astrophysics Data System (ADS)

Mikaeilzadeh, L.; Pirgholi, M.; Tavana, A.

2018-05-01

Based on the ab-initio non-equilibrium Green's function (NEGF) formalism based on the density functional theory (DFT), we have studied the electron transport in the all-Heusler device Co2CrSi/Cu2CrAl/Co2CrSi. Results show that the calculated transmission spectra is very sensitive to the structural parameters and the interface. Also, we obtain a range for the thickness of the spacer layer for which the MR effect is optimum. Calculations also show a perfect GMR effect in this device.

Structural, magnetic and transport studies of Mn0.8Cr0.2CoGe alloy

NASA Astrophysics Data System (ADS)

Das, S. C.; Dutta, P.; Pramanick, S.; Chatterjee, S.

2018-04-01

Different physical and functional properties of Mn0.8Cr0.2CoGe alloy has been investigated through structural, magnetic and electrical transport measurements. Substitution of Cr for Mn results significant decrease in both structural and magnetic transition temperature and brings them well below the room temperature. A reasonable amount of conventional magnetocaloric effect (ΔS˜ - 2.22 J/kg-K for magnetic field (H) changing from 0 to 50 kOe) with large relative cooling power (251.7 J/kg for H changing from 0 to 50 kOe) has also been observed around the region of transition. On thermal cycling through the structural transition, noticeable training effect is found to be associated with the resistivity of the alloy.

Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters

PubMed Central

Zhang, Minhua; Bao, Zhihao; Zhao, Qin; Guo, Hui; Xu, Ke; Wang, Chengcheng

2014-01-01

Energy-coupling factor (ECF) transporters are a unique group of ATP-binding cassette (ABC) transporters responsible for micronutrient uptake from the environment. Each ECF transporter is composed of an S component (or EcfS protein) and T/A/A′ components (or EcfT/A/A′ proteins; ECF module). Among the group II ECF transporters, several EcfS proteins share one ECF module; however, the underlying mechanism remains unknown. Here we report the structure of a group II ECF transporter–pantothenate transporter from Lactobacillus brevis (LbECF-PanT), which shares the ECF module with the folate and hydroxymethylpyrimidine transporters (LbECF-FolT and LbECF-HmpT). Structural and mutational analyses revealed the residues constituting the pantothenate-binding pocket. We found that although the three EcfS proteins PanT, FolT, and HmpT are dissimilar in sequence, they share a common surface area composed of the transmembrane helices 1/2/6 (SM1/2/6) to interact with the coupling helices 2/3 (CH2/3) of the same EcfT. CH2 interacts mainly with SM1 via hydrophobic interactions, which may modulate the sliding movement of EcfS. CH3 binds to a hydrophobic surface groove formed by SM1, SM2, and SM6, which may transmit the conformational changes from EcfA/A′ to EcfS. We also found that the residues at the intermolecular surfaces in LbECF-PanT are essential for transporter activity, and that these residues may mediate intermolecular conformational transmission and/or affect transporter complex stability. In addition, we found that the structure of EcfT is conformationally dynamic, which supports its function as a scaffold to mediate the interaction of the ECF module with various EcfS proteins to form different transporter complexes. PMID:25512487

Functional significance of the E loop, a novel motif conserved in the lantibiotic immunity ATP-binding cassette transport systems.

PubMed

Okuda, Ken-ichi; Yanagihara, Sae; Sugayama, Tomomichi; Zendo, Takeshi; Nakayama, Jiro; Sonomoto, Kenji

2010-06-01

Lantibiotics are peptide-derived antibacterial substances produced by some Gram-positive bacteria and characterized by the presence of unusual amino acids, like lanthionines and dehydrated amino acids. Because lantibiotic producers may be attacked by self-produced lantibiotics, they express immunity proteins on the cytoplasmic membrane. An ATP-binding cassette (ABC) transport system mediated by the LanFEG protein complex is a major system in lantibiotic immunity. Multiple-sequence alignment analysis revealed that LanF proteins contain the E loop, a variant of the Q loop, which is a well-conserved motif in the nucleotide-binding domains (NBDs) of general ABC transporters. To elucidate E loop function, we introduced a mutation in the NukF protein, which is involved in the nukacin-ISK-1 immunity system. Amino acid replacement of glutamic acid in the E loop with glutamine (E85Q) resulted in slight decreases in the immunity level and transport activity. Additionally, the E85A mutation severely impaired the immunity level and transport activity. On the other hand, ATPase activities of purified E85Q and E85A mutants were almost similar to that of the wild type. These results suggested that the E loop found in ABC transporters involved in lantibiotic immunity plays a significant role in the function of these transporters, especially in the structural change of transmembrane domains.

A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform[OPEN

PubMed Central

Nagarajan, Yagnesh; Rongala, Jay; Luang, Sukanya; Shadiac, Nadim; Sutton, Tim; Tyerman, Stephen D.; McPhee, Gordon; Voelcker, Nicolas H.; Lee, Jung-Goo

2016-01-01

Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na+ ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na+-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na+ ion binding site. Our data enhance the understanding of the permeation functions of Bot1. PMID:26672067

Chlorite dismutases, DyPs, and EfeB: 3 microbial heme enzyme families comprise the CDE structural superfamily

PubMed Central

Goblirsch, Brandon; Kurker, Richard C.; Streit, Bennett R.; Wilmot, Carrie M.; DuBois, Jennifer L.

2011-01-01

Heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. The chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic ClO2−, a function believed to have evolved only in the last few decades. Family members have since been found in fifteen bacterial and archaeal genera, suggesting ancient roots. A structure- and sequence-based examination of the family is presented, in which key sequence and structural motifs are identified and possible functions for family proteins are proposed. Newly identified structural homologies moreover demonstrate clear connections to two other large, ancient, and functionally mysterious protein families. We propose calling them collectively the CDE superfamily of heme proteins. PMID:21354424

Inhibition of the norepinephrine transporter by χ-conotoxin dendrimers.

PubMed

Wan, Jingjing; Brust, Andreas; Bhola, Rebecca F; Jha, Prerna; Mobli, Mehdi; Lewis, Richard J; Christie, Macdonald J; Alewood, Paul F

2016-05-01

Peptide dendrimers are a novel class of macromolecules of emerging interest with the potential of delayed renal clearance due to their molecular size and enhanced activity due to the multivalency effect. In this work, an active analogue of the disulfide-rich χ-conotoxin χ-MrIA (χ-MrIA), a norepinephrine reuptake (norepinephrine transporter) inhibitor, was grafted onto a polylysine dendron. Dendron decoration was achieved by employing copper-catalyzed alkyne-azide cycloaddition with azido-PEG chain-modified χ-MrIA analogues, leading to homogenous 4-mer and 8-mer χ-MrIA dendrimers with molecular weights ranging from 8 to 22 kDa. These dendrimers were investigated for their impact on peptide secondary structure, in vitro functional activity, and potential anti-allodynia in vivo. NMR studies showed that the χ-MrIA tertiary structure was maintained in the χ-MrIA dendrimers. In a functional norepinephrine transporter reuptake assay, χ-MrIA dendrimers showed slightly increased potency relative to the azido-PEGylated χ-MrIA analogues with similar potency to the parent peptide. In contrast to χ-MrIA, no anti-allodynic action was observed when the χ-MrIA dendrimers were administered intrathecally in a rat model of neuropathic pain, suggesting that the larger dendrimer structures are unable to diffuse through the spinal column tissue and reach the norepinephrine transporter. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Calcium binding and transport by coenzyme Q.

PubMed

Bogeski, Ivan; Gulaboski, Rubin; Kappl, Reinhard; Mirceski, Valentin; Stefova, Marina; Petreska, Jasmina; Hoth, Markus

2011-06-22

Coenzyme Q10 (CoQ10) is one of the essential components of the mitochondrial electron-transport chain (ETC) with the primary function to transfer electrons along and protons across the inner mitochondrial membrane (IMM). The concomitant proton gradient across the IMM is essential for the process of oxidative phosphorylation and consequently ATP production. Cytochrome P450 (CYP450) monoxygenase enzymes are known to induce structural changes in a variety of compounds and are expressed in the IMM. However, it is unknown if CYP450 interacts with CoQ10 and how such an interaction would affect mitochondrial function. Using voltammetry, UV-vis spectrometry, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), fluorescence microscopy and high performance liquid chromatography-mass spectrometry (HPLC-MS), we show that both CoQ10 and its analogue CoQ1, when exposed to CYP450 or alkaline media, undergo structural changes through a complex reaction pathway and form quinone structures with distinct properties. Hereby, one or both methoxy groups at positions 2 and 3 on the quinone ring are replaced by hydroxyl groups in a time-dependent manner. In comparison with the native forms, the electrochemically reduced forms of the new hydroxylated CoQs have higher antioxidative potential and are also now able to bind and transport Ca(2+) across artificial biomimetic membranes. Our results open new perspectives on the physiological importance of CoQ10 and its analogues, not only as electron and proton transporters, but also as potential regulators of mitochondrial Ca(2+) and redox homeostasis.

Switch loop flexibility affects substrate transport of the AcrB efflux pump

DOE PAGES

Muller, Reinke T.; Travers, Timothy; Cha, Hi-jea; ...

2017-10-05

The functionally important switch-loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11 amino acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutionsmore » on the PC1 proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway towards the deep binding pocket. Here, two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.« less

Switch loop flexibility affects substrate transport of the AcrB efflux pump

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muller, Reinke T.; Travers, Timothy; Cha, Hi-jea

The functionally important switch-loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11 amino acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutionsmore » on the PC1 proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway towards the deep binding pocket. Here, two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.« less

Revealing an outward-facing open conformational state in a CLC Cl–/H+ exchange transporter

PubMed Central

Khantwal, Chandra M; Abraham, Sherwin J; Han, Wei; Jiang, Tao; Chavan, Tanmay S; Cheng, Ricky C; Elvington, Shelley M; Liu, Corey W; Mathews, Irimpan I; Stein, Richard A; Mchaourab, Hassane S; Tajkhorshid, Emad; Maduke, Merritt

2016-01-01

CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20 Å away from Gluex, near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that the cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function. DOI: http://dx.doi.org/10.7554/eLife.11189.001 PMID:26799336

Eukaryotic and Prokaryotic Cytoskeletons: Structure and Mechanics

NASA Astrophysics Data System (ADS)

Gopinathan, Ajay

2013-03-01

The eukaryotic cytoskeleton is an assembly of filamentous proteins and a host of associated proteins that collectively serve functional needs ranging from spatial organization and transport to the production and transmission of forces. These systems can exhibit a wide variety of non-equilibrium, self-assembled phases depending on context and function. While much recent progress has been made in understanding the self-organization, rheology and nonlinear mechanical properties of such active systems, in this talk, we will concentrate on some emerging aspects of cytoskeletal physics that are promising. One such aspect is the influence of cytoskeletal network topology and its dynamics on both active and passive intracellular transport. Another aspect we will highlight is the interplay between chirality of filaments, their elasticity and their interactions with the membrane that can lead to novel conformational states with functional implications. Finally we will consider homologs of cytoskeletal proteins in bacteria, which are involved in templating cell growth, segregating genetic material and force production, which we will discuss with particular reference to contractile forces during cell division. These prokaryotic structures function in remarkably similar yet fascinatingly different ways from their eukaryotic counterparts and can enrich our understanding of cytoskeletal functioning as a whole.

A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.

PubMed

Zaman, Aubhishek; Fancy, Nurun Nahar

2012-12-01

Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.

Developing Hypothetical Inhibition Mechanism of Novel Urea Transporter B Inhibitor

NASA Astrophysics Data System (ADS)

Li, Min; Tou, Weng Ieong; Zhou, Hong; Li, Fei; Ren, Huiwen; Chen, Calvin Yu-Chian; Yang, Baoxue

2014-07-01

Urea transporter B (UT-B) is a membrane channel protein that specifically transports urea. UT-B null mouse exhibited urea selective urine concentrating ability deficiency, which suggests the potential clinical applications of the UT-B inhibitors as novel diuretics. Primary high-throughput virtual screening (HTVS) of 50000 small-molecular drug-like compounds identified 2319 hit compounds. These 2319 compounds were screened by high-throughput screening using an erythrocyte osmotic lysis assay. Based on the pharmacological data, putative UT-B binding sites were identified by structure-based drug design and validated by ligand-based and QSAR model. Additionally, UT-B structural and functional characteristics under inhibitors treated and untreated conditions were simulated by molecular dynamics (MD). As the result, we identified four classes of compounds with UT-B inhibitory activity and predicted a human UT-B model, based on which computative binding sites were identified and validated. A novel potential mechanism of UT-B inhibitory activity was discovered by comparing UT-B from different species. Results suggest residue PHE198 in rat and mouse UT-B might block the inhibitor migration pathway. Inhibitory mechanisms of UT-B inhibitors and the functions of key residues in UT-B were proposed. The binding site analysis provides a structural basis for lead identification and optimization of UT-B inhibitors.

First principles study on the electronic structures and transport properties of armchair/zigzag edge hybridized graphene nanoribbons

NASA Astrophysics Data System (ADS)

Yi, Xiuying; Long, Mengqiu; Liu, Anhua; Li, Mingjun; Xu, Hui

2018-05-01

Graphene nanoribbons (GNRs) can be mainly classified into armchair graphene nanoribbons (aGNRs) and zigzag graphene nanoribbons (zGNRs) by different edge chiral directions. In this work, by introducing Stone-Wales defects on the edges of the V-shaped aGNRs, we propose a kind of armchair/zigzag edge hybridized GNRs (a/zHGNRs) and using the density functional theory and the nonequilibrium Green's function method, the band structures and electronic transport properties of the a/zHGNRs have been calculated. Our results show that an indirect bandgap appears in the band structures of the a/zHGNRs, which is very different from the direct bandgap of aGNRs and gapless of zGNRs. We also find that the valance band is mainly derived from the armchair partial atoms on the hybridized edge, while the conduction band comes mainly from the zigzag partial atoms of the hybridized edge. Meanwhile, the bandgap also oscillates with a period of three when the ribbon width increases. In addition, our quantum transport calculations show that there is a remarkable transition between the semiconductor and the metal with different ribbon widths in the a/zHGNRs devices, and the corresponding physical analysis is given.

Similarity of Turbulent Energy Scale Budget Equation of a Round Turbulent Jet

NASA Astrophysics Data System (ADS)

Sadeghi, Hamed; Lavoie, Philippe; Pollard, Andrew

2014-11-01

A novel extension to the similarity-based form of the transport equation for the second-order velocity structure function of <(δq) 2 > along the jet centreline (see Danaila et al., 2004) has been obtained. This new self-similar equation has the desirable benefit of requiring less extensive measurements to calculate the inhomogeneous (decay and production) terms of the transport equation. According to this equation, the normalized third-order structure function can be uniquely determined when the normalized second-order structure function, the power-law exponent of and the decay rate constants of and are available. In addition, on the basis of the current similarity analysis, the similarity assumptions in combination with power-law decay of mean velocity (U ~(x -x0) - 1) are strong enough to imply power-law decay of fluctuations ( ~(x -x0) m). The similarity solutions are then tested against new experimental data, which were taken along the centreline of a round jet at ReD = 50 , 000 . For the present set of initial conditions, exhibits a power-law behaviour with m = - 1 . 83 . This work was supported by grants from NSERC (Canada).

Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance

PubMed Central

Barber-Zucker, Shiran; Uebe, René; Davidov, Geula; Navon, Yotam; Sherf, Dror; Chill, Jordan H.; Kass, Itamar; Bitton, Ronit; Schüler, Dirk; Zarivach, Raz

2016-01-01

Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human. PMID:27550551

Biochemical characterization of the selenoproteome in Gallus gallus via bioinformatics analysis: structure-function relationships and interactions of binding molecules.

PubMed

Zhu, Shi-Yong; Li, Xue-Nan; Sun, Xiao-Chen; Lin, Jia; Li, Wei; Zhang, Cong; Li, Jin-Long

2017-02-22

Knowledge about mammalian selenoproteins is increasing. However, the selenoproteome of birds remains considerably less understood, especially concerning its biochemical characterization, structure-function relationships and the interactions of binding molecules. In this work, the SECIS elements, subcellular localization, protein domains and interactions of binding molecules of the selenoproteome in Gallus gallus were analyzed using bioinformatics tools. We carried out comprehensive analyses of the structure-function relationships and interactions of the binding molecules of selenoproteins, to provide biochemical characterization of the selenoproteome in Gallus gallus. Our data provided a wealth of information on the biochemical functions of bird selenoproteins. Members of the selenoproteome were found to be involved in various biological processes in chickens, such as in antioxidants, maintenance of the redox balance, Se transport, and interactions with metals. Six membrane-bound selenoproteins (SelI, SelK, SelS, SelT, DIO1 and DIO3) played important roles in maintaining the membrane integrity. Chicken selenoproteins were classified according to their ligand binding sites as zinc-containing matrix metalloselenoproteins (Sep15, MsrB1, SelW and SelM), POP-containing selenoproteins (GPx1-4), FAD-interacting selenoproteins (TrxR1-3), secretory transport selenoproteins (GPx3 and SelPa) and other selenoproteins. The results of our study provided new evidence for the unknown biological functions of the selenoproteome in birds. Future research is required to confirm the novel biochemical functions of bird selenoproteins.

Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

PubMed Central

Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Razafsky, David S.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

2012-01-01

Cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. However, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. Here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus Neurospora crassa, in which dynein is nonessential. Interestingly, our studies show that these mutations segregate into five different classes based on the in vivo localization of the mutated dynein motors. Furthermore, we have determined that the different classes of dynein mutations alter vesicle trafficking, microtubule organization, and nuclear distribution in distinct ways and require dynactin to different extents. In addition, biochemical analyses of dynein from one mutant strain show a strong correlation between its in vitro biochemical properties and the aberrant intracellular function of that altered dynein. When the mutations were mapped to the published dynein crystal structure, we found that the three-dimensional structural locations of the heavy chain mutations were linked to particular classes of altered dynein functions observed in cells. Together, our data indicate that the five classes of dynein mutations represent the entrapment of dynein at five separate points in the dynein mechanochemical and transport cycles. We have developed N. crassa as a model system where we can dissect the complexities of dynein structure, function, and interaction with other proteins with genetic, biochemical, and cell biological studies. PMID:22649085

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

Ion transport and selectivity in biomimetic nanopores with pH-tunable zwitterionic polyelectrolyte brushes.

PubMed

Zeng, Zhenping; Yeh, Li-Hsien; Zhang, Mingkan; Qian, Shizhi

2015-10-28

Inspired by nature, functionalized nanopores with biomimetic structures have attracted growing interests in using them as novel platforms for applications of regulating ion and nanoparticle transport. To improve these emerging applications, we study theoretically for the first time the ion transport and selectivity in short nanopores functionalized with pH tunable, zwitterionic polyelectrolyte (PE) brushes. In addition to background salt ions, the study takes into account the presence of H(+) and OH(-) ions along with the chemistry reactions between functional groups on PE chains and protons. Due to ion concentration polarization, the charge density of PE layers is not homogeneously distributed and depends significantly on the background salt concentration, pH, grafting density of PE chains, and applied voltage bias, thereby resulting in many interesting and unexpected ion transport phenomena in the nanopore. For example, the ion selectivity of the biomimetic nanopore can be regulated from anion-selective (cation-selective) to cation-selective (anion-selective) by diminishing (raising) the solution pH when a sufficiently small grafting density of PE chains, large voltage bias, and low background salt concentration are applied.

Asymmetric transmission and optical low-pass filtering in a stack of random media with graded transport mean free path

NASA Astrophysics Data System (ADS)

Bingi, J.; Hemalatha, M.; Anita, R. W.; Vijayan, C.; Murukeshan, V. M.

2015-11-01

Light transport and the physical phenomena related to light propagation in random media are very intriguing, they also provide scope for new paradigms of device functionality, most of which remain unexplored. Here we demonstrate, experimentally and by simulation, a novel kind of asymmetric light transmission (diffusion) in a stack of random media (SRM) with graded transport mean free path. The structure is studied in terms of transmission, of photons propagated through and photons generated within the SRM. It is observed that the SRM exhibits asymmetric transmission property with a transmission contrast of 0.25. In addition, it is shown that the SRM works as a perfect optical low-pass filter with a well-defined cutoff wavelength at 580 nm. Further, the photons generated within the SRM found to exhibit functionality similar to an optical diode with a transmission contrast of 0.62. The basis of this functionality is explained in terms of wavelength dependent photon randomization and the graded transport mean free path of SRM.

Restraint of presynaptic protein levels by Wnd/DLK signaling mediates synaptic defects associated with the kinesin-3 motor Unc-104

PubMed Central

Asghari Adib, Elham; Stanchev, Doychin T; Xiong, Xin; Klinedinst, Susan; Soppina, Pushpanjali; Jahn, Thomas Robert; Hume, Richard I

2017-01-01

The kinesin-3 family member Unc-104/KIF1A is required for axonal transport of many presynaptic components to synapses, and mutation of this gene results in synaptic dysfunction in mice, flies and worms. Our studies at the Drosophila neuromuscular junction indicate that many synaptic defects in unc-104-null mutants are mediated independently of Unc-104’s transport function, via the Wallenda (Wnd)/DLK MAP kinase axonal damage signaling pathway. Wnd signaling becomes activated when Unc-104’s function is disrupted, and leads to impairment of synaptic structure and function by restraining the expression level of active zone (AZ) and synaptic vesicle (SV) components. This action concomitantly suppresses the buildup of synaptic proteins in neuronal cell bodies, hence may play an adaptive role to stresses that impair axonal transport. Wnd signaling also becomes activated when pre-synaptic proteins are over-expressed, suggesting the existence of a feedback circuit to match synaptic protein levels to the transport capacity of the axon. PMID:28925357

Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall.

PubMed

Jonsson, Ing-Marie; Juuti, Jarmo T; François, Patrice; AlMajidi, Rana; Pietiäinen, Milla; Girard, Myriam; Lindholm, Catharina; Saller, Manfred J; Driessen, Arnold J M; Kuusela, Pentti; Bokarewa, Maria; Schrenzel, Jacques; Kontinen, Vesa P

2010-12-02

Ecs is an ATP-binding cassette (ABC) transporter present in aerobic and facultative anaerobic gram-positive Firmicutes. Inactivation of Bacillus subtilis Ecs causes pleiotropic changes in the bacterial phenotype including inhibition of intramembrane proteolysis. The molecule(s) transported by Ecs is (are) still unknown. In this study we mutated the ecsAB operon in two Staphylococcus aureus strains, Newman and LS-1. Phenotypic and functional characterization of these Ecs deficient mutants revealed a defect in growth, increased autolysis and lysostaphin sensitivity, altered composition of cell wall proteins including the precursor form of staphylokinase and an altered bacterial surface texture. DNA microarray analysis indicated that the Ecs deficiency changed expression of the virulence factor regulator protein Rot accompanied by differential expression of membrane transport proteins, particularly ABC transporters and phosphate-specific transport systems, protein A, adhesins and capsular polysaccharide biosynthesis proteins. Virulence of the ecs mutants was studied in a mouse model of hematogenous S. aureus infection. Mice inoculated with the ecs mutant strains developed markedly milder infections than those inoculated with the wild-type strains and had consequently lower mortality, less weight loss, milder arthritis and decreased persistence of staphylococci in the kidneys. The ecs mutants had higher susceptibility to ribosomal antibiotics and plant alkaloids chelerythrine and sanguinarine. Our results show that Ecs is essential for staphylococcal virulence and antimicrobial resistance probably since the transport function of Ecs is essential for the normal structure and function of the cell wall. Thus targeting Ecs may be a new approach in combating staphylococcal infection.

Retrograde transport from the yeast Golgi is mediated by two ARF GAP proteins with overlapping function.

PubMed Central

Poon, P P; Cassel, D; Spang, A; Rotman, M; Pick, E; Singer, R A; Johnston, G C

1999-01-01

ARF proteins, which mediate vesicular transport, have little or no intrinsic GTPase activity. They rely on the actions of GTPase-activating proteins (GAPs) for their function. The in vitro GTPase activity of the Saccharomyces cerevisiae ARF proteins Arf1 and Arf2 is stimulated by the yeast Gcs1 protein, and in vivo genetic interactions between arf and gcs1 mutations implicate Gcs1 in vesicular transport. However, the Gcs1 protein is dispensable, indicating that additional ARF GAP proteins exist. We show that the structurally related protein Glo3, which is also dispensable, also exhibits ARF GAP activity. Genetic and in vitro approaches reveal that Glo3 and Gcs1 have an overlapping essential function at the endoplasmic reticulum (ER)-Golgi stage of vesicular transport. Mutant cells deficient for both ARF GAPs cannot proliferate, undergo a dramatic accumulation of ER and are defective for protein transport between ER and Golgi. The glo3Delta and gcs1Delta single mutations each interact with a sec21 mutation that affects a component of COPI, which mediates vesicular transport within the ER-Golgi shuttle, while increased dosage of the BET1, BOS1 and SEC22 genes encoding members of a v-SNARE family that functions within the ER-Golgi alleviates the effects of a glo3Delta mutation. An in vitro assay indicates that efficient retrieval from the Golgi to the ER requires these two proteins. These findings suggest that Glo3 and Gcs1 ARF GAPs mediate retrograde vesicular transport from the Golgi to the ER. PMID:9927415

Concepts for Life Cycle Cost Control Required to Achieve Space Transportation Affordability and Sustainability

NASA Technical Reports Server (NTRS)

Rhodes, Russel E.; Zapata, Edgar; Levack, Daniel J. H.; Robinson, John W.; Donahue, Benjamin B.

2009-01-01

Cost control must be implemented through the establishment of requirements and controlled continually by managing to these requirements. Cost control of the non-recurring side of life cycle cost has traditionally been implemented in both commercial and government programs. The government uses the budget process to implement this control. The commercial approach is to use a similar process of allocating the non-recurring cost to major elements of the program. This type of control generally manages through a work breakdown structure (WBS) by defining the major elements of the program. If the cost control is to be applied across the entire program life cycle cost (LCC), the approach must be addressed very differently. A functional breakdown structure (FBS) is defined and recommended. Use of a FBS provides the visibifity to allow the choice of an integrated solution reducing the cost of providing many different elements of like function. The different functional solutions that drive the hardware logistics, quantity of documentation, operational labor, reliability and maintainability balance, and total integration of the entire system from DDT&E through the life of the program must be fully defined, compared, and final decisions made among these competing solutions. The major drivers of recurring cost have been identified and are presented and discussed. The LCC requirements must be established and flowed down to provide control of LCC. This LCC control will require a structured rigid process similar to the one traditionally used to control weight/performance for space transportation systems throughout the entire program. It has been demonstrated over the last 30 years that without a firm requirement and methodically structured cost control, it is unlikely that affordable and sustainable space transportation system LCC will be achieved.

Electron and thermal transport via variable range hopping in MoSe2 single crystals

NASA Astrophysics Data System (ADS)

Suri, Dhavala; Patel, R. S.

2017-06-01

Bulk single crystal molybdenum diselenide has been studied for its electronic and thermal transport properties. We perform resistivity measurements with current in-plane (CIP) and current perpendicular to plane (CPP) as a function of temperature. The CIP measurements exhibit metal to semiconductor transition at ≃31 K. In the semiconducting phase (T > 31 K), the transport is best explained by the variable range hopping (VRH) model. Large magnitude of resistivity in the CPP mode indicates strong structural anisotropy. The Seebeck coefficient as a function of temperature measured in the range of 90-300 K also agrees well with the VRH model. The room temperature Seebeck coefficient is found to be 139 μV/K. VRH fittings of the resistivity and the Seebeck coefficient data indicate high degree of localization.

Quantum transport of the single metallocene molecule

NASA Astrophysics Data System (ADS)

Yu, Jing-Xin; Chang, Jing; Wei, Rong-Kai; Liu, Xiu-Ying; Li, Xiao-Dong

2016-10-01

The Quantum transport of three single metallocene molecule is investigated by performing theoretical calculations using the non-equilibrium Green's function method combined with density functional theory. We find that the three metallocen molecules structure become stretched along the transport direction, the distance between two Cp rings longer than the other theory and experiment results. The lager conductance is found in nickelocene molecule, the main transmission channel is the electron coupling between molecule and the electrodes is through the Ni dxz and dyz orbitals and the s, dxz, dyz of gold. This is also confirmed by the highest occupied molecular orbital resonance at Fermi level. In addition, negative differential resistance effect is found in the ferrocene, cobaltocene molecules, this is also closely related with the evolution of the transmission spectrum under applied bias.

Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics.

PubMed

Ando, David; Korabel, Nickolay; Huang, Kerwyn Casey; Gopinathan, Ajay

2015-10-20

Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Structure of a eukaryotic SWEET transporter in a homo-trimeric complex

PubMed Central

Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B.; Feng, Liang

2016-01-01

Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use related proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter Family (SSF; only animal kingdom), and SWEETs1-5. SWEETs carry mono- and disaccharides6 across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion7, phloem loading for long distance translocation8, pollen nutrition9, and seed filling10. Plant SWEETs cause pathogen susceptibility by sugar leakage from infected cells3,11,12. The vacuolar AtSWEET2 sequesters sugars in root vacuoles; loss-of-function increases susceptibility to Pythium infection13. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice, consists of an asymmetrical pair of triple-helix-bundles (THBs), connected by an inversion linker helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first THB within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs is valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux. PMID:26479032

[Structure-functional organization of eukaryotic high-affinity copper importer CTR1 determines its ability to transport copper, silver and cisplatin].

PubMed

Skvortsov, A N; Zatulovskiĭ, E A; Puchkova, L V

2012-01-01

It was shown recently, that high affinity Cu(I) importer eukaryotic protein CTR1 can also transport in vitro abiogenic Ag(I) ions and anticancer drug cisplatin. At present there is no rational explanation how CTR1 can transfer platinum group, which is different by coordination properties from highly similar Cu(I) and Ag(I). To understand this phenomenon we analyzed 25 sequences of chordate CTR1 proteins, and found out conserved patterns of organization of N-terminal extracellular part of CTR1 which correspond to initial metal binding. Extracellular copper-binding motifs were qualified by their coordination properties. It was shown that relative position of Met- and His-rich copper-binding motifs in CTR1 predisposes the extracellular CTR1 part to binding of copper, silver and cisplatin. Relation between tissue-specific expression of CTR1 gene, steady-state copper concentration, and silver and platinum accumulation in organs of mice in vivo was analyzed. Significant positive but incomplete correlation exists between these variables. Basing on structural and functional peculiarities of N-terminal part of CTR1 a hypothesis of coupled transport of copper and cisplatin has been suggested, which avoids the disagreement between CTR1-mediated cisplatin transport in vitro, and irreversible binding of platinum to Met-rich peptides.

Structural and functional engineering of one-dimensional nanostructures for device applications

NASA Astrophysics Data System (ADS)

Singh, Krishna Veer

Fabrication of 1-D nanostructures has been an area of keen interest due to their application in nanodevices. Carbon nanotubes (CNTs) and semiconducting nanorods are 1-D nanostructures of great importance. There are various challenges related to structural and functional aspects of these materials, which need to be addressed for their adaptation in devices. To this end, two approaches have been developed: (1) structural engineering of the nanorods and (2) functionalization of CNTs for device applications. In first approach, a new technique to produce single crystal semiconducting nanorods was developed. Single crystalline structure of nanorods is essential to obtain reproducible performance. The novel synthesis technique 'template assisted sonoelectrochemical deposition' was utilized to develop 'copper sulfide' and 'copper indium sulfide' nanorods. The use of sonoelectrochemical method resulted in the best deposition rate as compared to stirring-assisted and regular electrochemical deposition, respectively. Observed increase in the bulk electrolyte temperature, high acoustic pressure and shock waves generated from the collapse of bubbles could explain improved mass transport and reaction rate, which results in the formation of single crystal nanorods. Nanorods in the range of 50-200nm in diameter were synthesized and electrically characterized as p-type semiconductors. Excellent structural and repeatable electrical properties of the various nanorods developed by this technique make it suitable for developing nanorods for device applications. In addition, detailed statistical analysis of the polycarbonate templates (50-200 nm nominal pore size) used in electrodeposition provided a better understanding of template's as well as nanorods' structure. In the second approach, we functionally engineered single walled carbon nanotubes (SWNTs) with peptide nucleic acid (PNA) to form functional conjugates for molecular electronics. SWNT-PNA-SWNT conjugates were synthesized using carbodiimide chemistry. Also in this work, the electric transport measurements of SWNT-PNA conjugates are reported for the first time. Corresponding analysis reveals that these conjugates exhibit diodic behaviour and in some devices negative differential resistance (NDR) was also observed. The unique electrical and structural properties of these conjugates make them a potential candidate for application in CNT based nanodevices. Hence, this work demonstrates novel techniques to functionally and structurally engineer 1-D nanomaterials for device applications.

Temperature Dependent Electrical Transport Properties of Ni-Cr and Co-Cr Binary Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thakore, B. Y.; Khambholja, S. G.; Bhatt, N. K.

2011-12-12

The temperature dependent electrical transport properties viz. electrical resistivity and thermal conductivity of Ni{sub 10}Cr{sub 90} and Co{sub 20}Cr{sub 80} alloys are computed at various temperatures. The electrical resistivity has been calculated according to Faber-Ziman model combined with Ashcroft-Langreth partial structure factors. In the present work, to include the ion-electron interaction, we have used a well tested local model potential. For exchange-correlation effects, five different forms of local field correction functions due to Hartree (H), Taylor (T), Ichimaru and Utsumi (IU), Farid et al (F) and Sarkar et al (S) are used. The present results due to S function aremore » in good agreement with the experimental data as compared to results obtained using other four functions. The S functions satisfy compressibility sum rule in long wave length limit more accurately as compared to T, IU and F functions, which may be responsible for better agreement of results, obtained using S function. Also, present result confirms the validity of present approach in determining the transport properties of alloys like Ni-Cr and Co-Cr.« less

Structural model of FeoB, the iron transporter from Pseudomonas aeruginosa, predicts a cysteine lined, GTP-gated pore

PubMed Central

Seyedmohammad, Saeed; Fuentealba, Natalia Alveal; Marriott, Robert A.J.; Goetze, Tom A.; Edwardson, J. Michael; Barrera, Nelson P.; Venter, Henrietta

2016-01-01

Iron is essential for the survival and virulence of pathogenic bacteria. The FeoB transporter allows the bacterial cell to acquire ferrous iron from its environment, making it an excellent drug target in intractable pathogens. The protein consists of an N-terminal GTP-binding domain and a C-terminal membrane domain. Despite the availability of X-ray crystal structures of the N-terminal domain, many aspects of the structure and function of FeoB remain unclear, such as the structure of the membrane domain, the oligomeric state of the protein, the molecular mechanism of iron transport, and how this is coupled to GTP hydrolysis at the N-terminal domain. In the present study, we describe the first homology model of FeoB. Due to the lack of sequence homology between FeoB and other transporters, the structures of four different proteins were used as templates to generate the homology model of full-length FeoB, which predicts a trimeric structure. We confirmed this trimeric structure by both blue-native-PAGE (BN-PAGE) and AFM. According to our model, the membrane domain of the trimeric protein forms a central pore lined by highly conserved cysteine residues. This pore aligns with a central pore in the N-terminal GTPase domain (G-domain) lined by aspartate residues. Biochemical analysis of FeoB from Pseudomonas aeruginosa further reveals a putative iron sensor domain that could connect GTP binding/hydrolysis to the opening of the pore. These results indicate that FeoB might not act as a transporter, but rather as a GTP-gated channel. PMID:26934982

Structure of the human transcobalamin beta domain in four distinct states

PubMed Central

Bloch, Joël S.; Ruetz, Markus; Kräutler, Bernhard

2017-01-01

Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states. These include the apo and CNCbl-bound states, providing insight into the early steps of holo-TC assembly. We found that in vitro assembly of TC-alpha and TC-beta to a complex was Cbl-dependent. We also determined the structure of TC-beta in complex with cobinamide (Cbi), an alternative substrate, shedding light on the specificity of TC. We finally determined the structure of TC-beta in complex with an inhibitory antivitamin B12 (anti-B12). We used this structure to model the binding of anti-B12 into full-length holo-TC and could rule out that the inhibitory function of anti-B12 was based on an inability to form a functional complex with TC. PMID:28910388

Differential Internalization Rates and Postendocytic Sorting of the Norepinephrine and Dopamine Transporters Are Controlled by Structural Elements in the N Termini*

PubMed Central

Vuorenpää, Anne; Jørgensen, Trine N.; Newman, Amy H.; Madsen, Kenneth L.; Scheinin, Mika

2016-01-01

The norepinephrine transporter (NET) mediates reuptake of synaptically released norepinephrine in central and peripheral noradrenergic neurons. The molecular processes governing availability of NET in the plasma membrane are poorly understood. Here we use the fluorescent cocaine analogue JHC 1-64, as well as several other approaches, to investigate the trafficking itinerary of NET in live noradrenergic neurons. Confocal imaging revealed extensive constitutive internalization of JHC 1-64-labeled NET in the neuronal somata, proximal extensions and presynaptic boutons. Phorbol 12-myristate 13-acetate increased intracellular accumulation of JHC 1-64-labeled NET and caused a parallel reduction in uptake capacity. Internalized NET strongly colocalized with the “long loop” recycling marker Rab11, whereas less overlap was seen with the “short loop” recycling marker Rab4 and the late endosomal marker Rab7. Moreover, mitigating Rab11 function by overexpression of dominant negative Rab11 impaired NET function. Sorting of NET to the Rab11 recycling compartment was further supported by confocal imaging and reversible biotinylation experiments in transfected differentiated CATH.a cells. In contrast to NET, the dopamine transporter displayed markedly less constitutive internalization and limited sorting to the Rab11 recycling compartment in the differentiated CATH.a cells. Exchange of domains between the two homologous transporters revealed that this difference was determined by non-conserved structural elements in the intracellular N terminus. We conclude that NET displays a distinct trafficking itinerary characterized by continuous shuffling between the plasma membrane and the Rab11 recycling compartment and that the functional integrity of the Rab11 compartment is critical for maintaining proper presynaptic NET function. PMID:26786096

Membrane Assembly and Ion Transport Ability of a Fluorinated Nanopore

PubMed Central

Godbout, Raphaël; Légaré, Sébastien; Auger, Maud; Carpentier, Claudia; Otis, François; Auger, Michèle; Lagüe, Patrick; Voyer, Normand

2016-01-01

A novel 21-residue peptide incorporating six fluorinated amino acids was prepared. It was designed to fold into an amphiphilic alpha helical structure of nanoscale length with one hydrophobic face and one fluorinated face. The formation of a fluorous interface serves as the main vector for the formation of a superstructure in a bilayer membrane. Fluorescence assays showed this ion channel's ability to facilitate the translocation of alkali metal ions through a phospholipid membrane, with selectivity for sodium ions. Computational studies showed that a tetramer structure is the most probable and stable supramolecular assembly for the active ion channel structure. The results illustrate the possibility of exploiting multiple Fδ-:M+ interactions for ion transport and using fluorous interfaces to create functional nanostructures. PMID:27835700

Membrane Assembly and Ion Transport Ability of a Fluorinated Nanopore.

PubMed

Godbout, Raphaël; Légaré, Sébastien; Auger, Maud; Carpentier, Claudia; Otis, François; Auger, Michèle; Lagüe, Patrick; Voyer, Normand

2016-01-01

A novel 21-residue peptide incorporating six fluorinated amino acids was prepared. It was designed to fold into an amphiphilic alpha helical structure of nanoscale length with one hydrophobic face and one fluorinated face. The formation of a fluorous interface serves as the main vector for the formation of a superstructure in a bilayer membrane. Fluorescence assays showed this ion channel's ability to facilitate the translocation of alkali metal ions through a phospholipid membrane, with selectivity for sodium ions. Computational studies showed that a tetramer structure is the most probable and stable supramolecular assembly for the active ion channel structure. The results illustrate the possibility of exploiting multiple Fδ-:M+ interactions for ion transport and using fluorous interfaces to create functional nanostructures.

Aeroelastic Tailoring of Transport Aircraft Wings: State-of-the-Art and Potential Enabling Technologies

NASA Technical Reports Server (NTRS)

Jutte, Christine; Stanford, Bret K.

2014-01-01

This paper provides a brief overview of the state-of-the-art for aeroelastic tailoring of subsonic transport aircraft and offers additional resources on related research efforts. Emphasis is placed on aircraft having straight or aft swept wings. The literature covers computational synthesis tools developed for aeroelastic tailoring and numerous design studies focused on discovering new methods for passive aeroelastic control. Several new structural and material technologies are presented as potential enablers of aeroelastic tailoring, including selectively reinforced materials, functionally graded materials, fiber tow steered composite laminates, and various nonconventional structural designs. In addition, smart materials and structures whose properties or configurations change in response to external stimuli are presented as potential active approaches to aeroelastic tailoring.

Personnel controlling system principles and structural goals of the industrial companies

NASA Astrophysics Data System (ADS)

Pimenova, Anna; Kuzmina, Svetlana; Zavialov, Kirill; Ushakova, Elena

2017-10-01

This article peruses the basics of the controlling system, its functions and structural phases of the industrial companies. The personnel controlling of the industrial companies (for examples transportation or energy company) is examined in detail. Controlling system occurs applicable within various activity fields of an enterprise. Modern approaches of the domestic scholars are inspected. Goals and focuses of the personnel controlling system of the industrial companies have been analyzed. Foremost it occurs crucial to analyze and define the entire labor process to figure out primary requirements issued to the labor and employees. In article is offered the road map to follow to structure the purposes of all management system of personnel in the specific organization - in the transportation or energy company or other enterprises.

A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations

PubMed Central

Charles, Hubert; Balmand, Séverine; Lamelas, Araceli; Cottret, Ludovic; Pérez-Brocal, Vicente; Burdin, Béatrice; Latorre, Amparo; Febvay, Gérard; Colella, Stefano; Calevro, Federica; Rahbé, Yvan

2011-01-01

Buchnera aphidicola is an obligate symbiotic bacterium that sustains the physiology of aphids by complementing their exclusive phloem sap diet. In this study, we reappraised the transport function of different Buchnera strains, from the aphids Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistaciae and Cinara cedri, using the re-annotation of their transmembrane proteins coupled with an exploration of their metabolic networks. Although metabolic analyses revealed high interdependencies between the host and the bacteria, we demonstrate here that transport in Buchnera is assured by low transporter diversity, when compared to free-living bacteria, being mostly based on a few general transporters, some of which probably have lost their substrate specificity. Moreover, in the four strains studied, an astonishing lack of inner-membrane importers was observed. In Buchnera, the transport function has been shaped by the distinct selective constraints occurring in the Aphididae lineages. Buchnera from A. pisum and S. graminum have a three-membraned system and similar sets of transporters corresponding to most compound classes. Transmission electronic microscopic observations and confocal microscopic analysis of intracellular pH fields revealed that Buchnera does not show any of the typical structures and properties observed in integrated organelles. Buchnera from B. pistaciae seem to possess a unique double membrane system and has, accordingly, lost all of its outer-membrane integral proteins. Lastly, Buchnera from C. cedri revealed an extremely poor repertoire of transporters, with almost no ATP-driven active transport left, despite the clear persistence of the ancestral three-membraned system. PMID:22229056

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

Molecular Characterization of Zebrafish Oatp1d1 (Slco1d1), a Novel Organic Anion-transporting Polypeptide*

PubMed Central

Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko

2013-01-01

The organic anion-transporting polypeptide (OATP/Oatp) superfamily includes a group of polyspecific transporters that mediate transport of large amphipathic, mostly anionic molecules across cell membranes of eukaryotes. OATPs/Oatps are involved in the disposition and elimination of numerous physiological and foreign compounds. However, in non-mammalian species, the functional properties of Oatps remain unknown. We aimed to elucidate the role of Oatp1d1 in zebrafish to gain insights into the functional and structural evolution of the OATP1/Oatp1 superfamily. We show that diversification of the OATP1/Oatp1 family occurs after the emergence of jawed fish and that the OATP1A/Oatp1a and OATP1B/Oatp1b subfamilies appeared at the root of tetrapods. The Oatp1d subfamily emerged in teleosts and is absent in tetrapods. The zebrafish Oatp1d1 is similar to mammalian OATP1A/Oatp1a and OATP1B/Oatp1b members, with the main physiological role in transport and balance of steroid hormones. Oatp1d1 activity is dependent upon pH gradient, which could indicate bicarbonate exchange as a mode of transport. Our analysis of evolutionary conservation and structural properties revealed that (i) His-79 in intracellular loop 3 is conserved within OATP1/Oatp1 family and is crucial for the transport activity; (ii) N-glycosylation impacts membrane targeting and is conserved within the OATP1/Oatp1 family with Asn-122, Asn-133, Asn-499, and Asn-512 residues involved; (iii) the evolutionarily conserved cholesterol recognition interaction amino acid consensus motif is important for membrane localization; and (iv) Oatp1d1 is present in dimeric and possibly oligomeric form in the cell membrane. In conclusion, we describe the first detailed characterization of a new Oatp transporter in zebrafish, offering important insights into the functional evolution of the OATP1/Oatp1 family and the physiological role of Oatp1d1. PMID:24126916

Structure and function of enzymes in heme biosynthesis.

PubMed

Layer, Gunhild; Reichelt, Joachim; Jahn, Dieter; Heinz, Dirk W

2010-06-01

Tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. Heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors. Heme is synthesized in most organisms via a highly conserved biosynthetic route. In humans, defects in heme biosynthesis lead to severe metabolic disorders called porphyrias. The elucidation of the 3D structures for all heme biosynthetic enzymes over the last decade provided new insights into their function and elucidated the structural basis of many known diseases. In terms of structure and function several rather unique proteins were revealed such as the V-shaped glutamyl-tRNA reductase, the dipyrromethane cofactor containing porphobilinogen deaminase, or the "Radical SAM enzyme" coproporphyrinogen III dehydrogenase. This review summarizes the current understanding of the structure-function relationship for all heme biosynthetic enzymes and their potential interactions in the cell.

Functional analysis of tight junction organization.

PubMed

DiBona, D R

1985-01-01

The functional basis of tight junction design has been examined from the point of view that this rate-limiting barrier to paracellular transport is a multicompartment system. Review of the osmotic sensitivity of these structures points to the need for this sort of analysis for meaningful correlation of structure and function under a range of conditions. A similar conclusion is drawn with respect to results from voltage-clamping protocols where reversal of spontaneous transmural potential difference elicits parallel changes in both structure and function in much the same way as does reversal of naturally occurring osmotic gradients. In each case, it becomes necessary to regard the junction as a functionally polarized structure to account for observations of its rectifying properties. Lastly, the details of experimentally-induced junction deformation are examined in light of current theories of its organization; arguments are presented in favor of the view that the primary components of intramembranous organization (as viewed with freeze-fracture techniques) are lipidic rather than proteinaceous.

Inducing injection barrier by covalent functionalization of multiwall carbon nanotubes acting as Moiré crystals

NASA Astrophysics Data System (ADS)

Bonnet, Roméo; Barraud, Clément; Martin, Pascal; Della Rocca, Maria Luisa; Lafarge, Philippe

2016-10-01

Covalent functionalization of multiwall carbon nanotubes is a direct method to suppress the conduction of the outermost shell, subject to interactions with the environment. The rehybridized sp3 external shell of the functionalized multiwall carbon nanotubes becomes naturally a hybrid injection barrier allowing the control of the contact resistances and the study of quantum transport in the more protected inner shells. Charge transport measurements performed on isolated multiwall carbon nanotubes of large diameter show an increase of the contact resistance and stabilization in the MΩ range. Electronic quantum properties of the inner shells are highlighted by the observation of superlattice structures in the conductance, recently attributed to the formation of a one-dimensional Moiré pattern.

Molecular and functional characterization of riboflavin specific transport system in rat brain capillary endothelial cells.

PubMed

Patel, Mitesh; Vadlapatla, Ramya Krishna; Pal, Dhananjay; Mitra, Ashim K

2012-08-15

Riboflavin is an important water soluble vitamin (B2) required for metabolic reactions, normal cellular growth, differentiation and function. Mammalian brain cells cannot synthesize riboflavin and must import from systemic circulation. However, the uptake mechanism, cellular translocation and intracellular trafficking of riboflavin in brain capillary endothelial cells are poorly understood. The primary objective of this study is to investigate the existence of a riboflavin-specific transport system and delineate the uptake and intracellular regulation of riboflavin in immortalized rat brain capillary endothelial cells (RBE4). The uptake of [3H]-riboflavin is sodium, temperature and energy dependent but pH independent. [3H]-Riboflavin uptake is saturable with K(m) and V(max) values of 19 ± 3 μM and 0.235 ± 0.012 pmol/min/mg protein, respectively. The uptake process is inhibited by unlabelled structural analogs (lumiflavin, lumichrome) but not by structurally unrelated vitamins. Ca(++)/calmodulin and protein kinase A (PKA) pathways are found to play an important role in the intracellular regulation of [3H]-riboflavin. Apical and baso-lateral uptake of [3H]-riboflavin clearly indicates that a riboflavin specific transport system is predominantly localized on the apical side of RBE4 cells. A 628 bp band corresponding to a riboflavin transporter is revealed in RT-PCR analysis. These findings, for the first time report the existence of a specialized and high affinity transport system for riboflavin in RBE4 cells. The blood-brain barrier (BBB) is a major obstacle limiting drug transport inside the brain as it regulates drug permeation from systemic circulation. This transporter can be utilized for targeted delivery in enhancing brain permeation of highly potent drugs on systemic administration. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural controls on anomalous transport in fractured porous rock

NASA Astrophysics Data System (ADS)

Edery, Yaniv; Geiger, Sebastian; Berkowitz, Brian

2016-07-01

Anomalous transport is ubiquitous in a wide range of disordered systems, notably in fractured porous formations. We quantitatively identify the structural controls on anomalous tracer transport in a model of a real fractured geological formation that was mapped in an outcrop. The transport, determined by a continuum scale mathematical model, is characterized by breakthrough curves (BTCs) that document anomalous (or "non-Fickian") transport, which is accounted for by a power law distribution of local transition times ψ>(t>) within the framework of a continuous time random walk (CTRW). We show that the determination of ψ>(t>) is related to fractures aligned approximately with the macroscopic direction of flow. We establish the dominant role of fracture alignment and assess the statistics of these fractures by determining a concentration-visitation weighted residence time histogram. We then convert the histogram to a probability density function (pdf) that coincides with the CTRW ψ>(t>) and hence anomalous transport. We show that the permeability of the geological formation hosting the fracture network has a limited effect on the anomalous nature of the transport; rather, it is the fractures transverse to the flow direction that play the major role in forming the long BTC tail associated with anomalous transport. This is a remarkable result, given the complexity of the flow field statistics as captured by concentration transitions.

Implementation and local calibration of the MEPDG transfer functions in Wyoming.

DOT National Transportation Integrated Search

2015-11-01

The Wyoming Department of Transportation (WYDOT) currently uses the empirical AASHTO Design for Design of : Pavement Structures as their standard pavement design procedure. WYDOT plans to transition to the Mechanistic : Empirical Pavement Design Guid...

Quasi-likelihood generalized linear regression analysis of fatality risk data

DOT National Transportation Integrated Search

2009-01-01

Transportation-related fatality risks is a function of many interacting human, vehicle, and environmental factors. Statisitcally valid analysis of such data is challenged both by the complexity of plausable structural models relating fatality rates t...

Structure and Function of Caltrin (Calcium Transport Inhibitor) Proteins

PubMed Central

Grasso, Ernesto Javier; Coronel, Carlos Enrique

2017-01-01

Caltrin (calcium transport inhibitor) is a family of small and basic proteins of the mammalian seminal plasma which bind to sperm cells during ejaculation and inhibit the extracellular Ca2+ uptake, preventing the premature acrosomal exocytosis and hyperactivation when sperm cells ascend through the female reproductive tract. The binding of caltrin proteins to specific areas of the sperm surface suggests the existence of caltrin receptors, or precise protein-phospholipid arrangements in the sperm membrane, distributed in the regions where Ca2+ influx may take place. However, the molecular mechanisms of recognition and interaction between caltrin and spermatozoa have not been elucidated. Therefore, the aim of this article is to describe in depth the known structural features and functional properties of caltrin proteins, to find out how they may possibly interact with the sperm membranes to control the intracellular signaling that trigger physiological events required for fertilization. PMID:29308010

Proposed structure of putative glucose channel in GLUT1 facilitative glucose transporter.

PubMed Central

Zeng, H; Parthasarathy, R; Rampal, A L; Jung, C Y

1996-01-01

A family of structurally related intrinsic membrane proteins (facilitative glucose transporters) catalyzes the movement of glucose across the plasma membrane of animal cells. Evidence indicates that these proteins show a common structural motif where approximately 50% of the mass is embedded in lipid bilayer (transmembrane domain) in 12 alpha-helices (transmembrane helices; TMHs) and accommodates a water-filled channel for substrate passage (glucose channel) whose tertiary structure is currently unknown. Using recent advances in protein structure prediction algorithms we proposed here two three-dimensional structural models for the transmembrane glucose channel of GLUT1 glucose transporter. Our models emphasize the physical dimension and water accessibility of the channel, loop lengths between TMHs, the macrodipole orientation in four-helix bundle motif, and helix packing energy. Our models predict that five TMHs, either TMHs 3, 4, 7, 8, 11 (Model 1) or TMHs 2, 5, 11, 8, 7 (Model 2), line the channel, and the remaining TMHs surround these channel-lining TMHs. We discuss how our models are compatible with the experimental data obtained with this protein, and how they can be used in designing new biochemical and molecular biological experiments in elucidation of the structural basis of this important protein function. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 PMID:8770183

Charge delocalization characteristics of regioregular high mobility polymers

DOE PAGES

Coughlin, J. E.; Zhugayevych, A.; Wang, M.; ...

2017-01-01

Controlling the regioregularity among the structural units of narrow bandgap conjugated polymer backbones has led to improvements in optoelectronic properties, for example in the mobilities observed in field effect transistor devices. To investigate how the regioregularity affects quantities relevant to hole transport, regioregular and regiorandom oligomers representative of polymeric structures were studied using density functional theory. Several structural and electronic characteristics of the oligomers were compared, including chain planarity, cation spin density, excess charges on molecular units and internal reorganizational energy. The main difference between the regioregular and regiorandom oligomers is found to be the conjugated backbone planarity, while themore » reorganizational energies calculated are quite similar across the molecular family. Lastly, this work constitutes the first step on understanding the complex interplay of atomistic changes and an oligomer backbone structure toward modeling the charge transport properties.« less

HKT transporters mediate salt stress resistance in plants: from structure and function to the field

DOE PAGES

Hamamoto, Shin; Horie, Tomoaki; Hauser, Felix; ...

2014-12-18

Plant cells are sensitive to salinity stress and do not require sodium as an essential element for their growth and development. Saline soils reduce crop yields and limit available land. The research shows that HKT transporters provide a potent mechanism for mediating salt tolerance in plants. Knowledge of the molecular ion transport and regulation mechanisms and the control of HKT gene expression are crucial for understanding the mechanisms by which HKT transporters enhance crop performance under salinity stress. Our review focuses on HKT transporters in monocot plants and in Arabidopsis as a dicot plant, as a guide to efforts towardmore » improving salt tolerance of plants for increasing the production of crops and bioenergy feedstocks.« less

Insulated Conducting Cantilevered Nanotips and Two-Chamber Recording System for High Resolution Ion Sensing AFM

PubMed Central

Meckes, Brian; Arce, Fernando Teran; Connelly, Laura S.; Lal, Ratnesh

2014-01-01

Biological membranes contain ion channels, which are nanoscale pores allowing controlled ionic transport and mediating key biological functions underlying normal/abnormal living. Synthetic membranes with defined pores are being developed to control various processes, including filtration of pollutants, charge transport for energy storage, and separation of fluids and molecules. Although ionic transport (currents) can be measured with single channel resolution, imaging their structure and ionic currents simultaneously is difficult. Atomic force microscopy enables high resolution imaging of nanoscale structures and can be modified to measure ionic currents simultaneously. Moreover, the ionic currents can also be used to image structures. A simple method for fabricating conducting AFM cantilevers to image pore structures at high resolution is reported. Tungsten microwires with nanoscale tips are insulated except at the apex. This allows simultaneous imaging via cantilever deflections in normal AFM force feedback mode as well as measuring localized ionic currents. These novel probes measure ionic currents as small as picoampere while providing nanoscale spatial resolution surface topography and is suitable for measuring ionic currents and conductance of biological ion channels. PMID:24663394

Effect of spin-orbit interactions on the structural stability, thermodynamic properties, and transport properties of lead under pressure

NASA Astrophysics Data System (ADS)

Smirnov, N. A.

2018-03-01

The paper investigates the role of spin-orbit interaction in the prediction of structural stability, lattice dynamics, elasticity, thermodynamic and transport properties (electrical resistivity and thermal conductivity) of lead under pressure with the FP-LMTO (full-potential linear-muffin-tin orbital) method for the first-principles band structure calculations. Our calculations were carried out for three polymorphous lead modifications (fcc, hcp, and bcc) in generalized gradient approximation with the exchange-correlation functional PBEsol. They suggest that compared to the scalar-relativistic calculation, the account for the SO effects insignificantly influences the compressibility of Pb. At the same time, in the calculation of phonon spectra and transport properties, the role of SO interaction is important, at least, for P ≲150 GPa. At higher pressures, the contribution from SO interaction reduces but not vanishes. As for the relative structural stability, our studies show that SO effects influence weakly the pressure of the fcc →hcp transition and much higher the pressure of the hcp →bcc transition.

Direct observation of electrogenic NH4+ transport in ammonium transport (Amt) proteins

PubMed Central

Wacker, Tobias; Garcia-Celma, Juan J.; Lewe, Philipp; Andrade, Susana L. A.

2014-01-01

Ammonium transport (Amt) proteins form a ubiquitous family of integral membrane proteins that specifically shuttle ammonium across membranes. In prokaryotes, archaea, and plants, Amts are used as environmental NH4+ scavengers for uptake and assimilation of nitrogen. In the eukaryotic homologs, the Rhesus proteins, NH4+/NH3 transport is used instead in acid–base and pH homeostasis in kidney or NH4+/NH3 (and eventually CO2) detoxification in erythrocytes. Crystal structures and variant proteins are available, but the inherent challenges associated with the unambiguous identification of substrate and monitoring of transport events severely inhibit further progress in the field. Here we report a reliable in vitro assay that allows us to quantify the electrogenic capacity of Amt proteins. Using solid-supported membrane (SSM)-based electrophysiology, we have investigated the three Amt orthologs from the euryarchaeon Archaeoglobus fulgidus. Af-Amt1 and Af-Amt3 are electrogenic and transport the ammonium and methylammonium cation with high specificity. Transport is pH-dependent, with a steep decline at pH values of ∼5.0. Despite significant sequence homologies, functional differences between the three proteins became apparent. SSM electrophysiology provides a long-sought-after functional assay for the ubiquitous ammonium transporters. PMID:24958855

Structural determinants of NH3 and NH4+ transport by mouse Rhbg, a renal Rh glycoprotein.

PubMed

Abdulnour-Nakhoul, Solange; Le, Trang; Rabon, Edd; Hamm, L Lee; Nakhoul, Nazih L

2016-12-01

Renal Rhbg is localized to the basolateral membrane of intercalated cells and is involved in NH 3 /NH 4 + transport. The structure of Rhbg is not yet resolved; however, a high-resolution crystal structure of AmtB, a bacterial homolog of Rh, has been determined. We aligned the sequence of Rhbg to that of AmtB and identified important sites of Rhbg that may affect transport. Our analysis positioned three conserved amino acids, histidine 183 (H183), histidine 342 (H342), and tryptophan 230 (W230), within the hydrophobic pore where they presumably serve to control NH 3 transport. A fourth residue, phenylalanine 128 (F128) was positioned at the upper vestibule, presumably contributing to recruitment of NH 4 + We generated three mutations each of H183, H342, W230, and F128 and expressed them in frog oocytes. Immunolabeling showed that W230 and F128 mutants were localized to the cell membrane, whereas H183 and H342 staining was diffuse and mostly intracellular. To determine function, we compared measurements of NH 3 /NH 4 + and methyl amine (MA)/methyl ammonium (MA + )-induced currents, intracellular pH, and surface pH (pHs) among oocytes expressing the mutants, Rhbg, or injected with H 2 O. In H183 and W230 mutants, NH 4 + -induced current and intracellular acidification were inhibited compared with that of Rhbg, and MA-induced intracellular alkalinization was completely absent. Expression of H183A or W230A mutants inhibited NH 3 /NH 4 + - and MA/MA + -induced decrease in pHs to the level observed in H 2 O-injected oocytes. Mutations of F128 did not significantly affect transport of NH 3 or NH 4 + These data demonstrated that mutating H183 or W230 caused loss of function but not F128. H183 and H342 may affect membrane expression of the transporter.

Structural determinants of NH3 and NH4+ transport by mouse Rhbg, a renal Rh glycoprotein

PubMed Central

Abdulnour-Nakhoul, Solange; Le, Trang; Rabon, Edd; Hamm, L. Lee

2016-01-01

Renal Rhbg is localized to the basolateral membrane of intercalated cells and is involved in NH3/NH4+ transport. The structure of Rhbg is not yet resolved; however, a high-resolution crystal structure of AmtB, a bacterial homolog of Rh, has been determined. We aligned the sequence of Rhbg to that of AmtB and identified important sites of Rhbg that may affect transport. Our analysis positioned three conserved amino acids, histidine 183 (H183), histidine 342 (H342), and tryptophan 230 (W230), within the hydrophobic pore where they presumably serve to control NH3 transport. A fourth residue, phenylalanine 128 (F128) was positioned at the upper vestibule, presumably contributing to recruitment of NH4+. We generated three mutations each of H183, H342, W230, and F128 and expressed them in frog oocytes. Immunolabeling showed that W230 and F128 mutants were localized to the cell membrane, whereas H183 and H342 staining was diffuse and mostly intracellular. To determine function, we compared measurements of NH3/NH4+ and methyl amine (MA)/methyl ammonium (MA+)-induced currents, intracellular pH, and surface pH (pHs) among oocytes expressing the mutants, Rhbg, or injected with H2O. In H183 and W230 mutants, NH4+-induced current and intracellular acidification were inhibited compared with that of Rhbg, and MA-induced intracellular alkalinization was completely absent. Expression of H183A or W230A mutants inhibited NH3/NH4+- and MA/MA+-induced decrease in pHs to the level observed in H2O-injected oocytes. Mutations of F128 did not significantly affect transport of NH3 or NH4+. These data demonstrated that mutating H183 or W230 caused loss of function but not F128. H183 and H342 may affect membrane expression of the transporter. PMID:27681563

Characterization of a novel domain ‘GATE’ in the ABC protein DrrA and its role in drug efflux by the DrrAB complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Han; Rahman, Sadia; Li, Wen

2015-03-27

A novel domain, GATE (Glycine-loop And Transducer Element), is identified in the ABC protein DrrA. This domain shows sequence and structural conservation among close homologs of DrrA as well as distantly-related ABC proteins. Among the highly conserved residues in this domain are three glycines, G215, G221 and G231, of which G215 was found to be critical for stable expression of the DrrAB complex. Other conserved residues, including E201, G221, K227 and G231, were found to be critical for the catalytic and transport functions of the DrrAB transporter. Structural analysis of both the previously published crystal structure of the DrrA homologmore » MalK and the modeled structure of DrrA showed that G215 makes close contacts with residues in and around the Walker A motif, suggesting that these interactions may be critical for maintaining the integrity of the ATP binding pocket as well as the complex. It is also shown that G215A or K227R mutation diminishes some of the atomic interactions essential for ATP catalysis and overall transport function. Therefore, based on both the biochemical and structural analyses, it is proposed that the GATE domain, located outside of the previously identified ATP binding and hydrolysis motifs, is an additional element involved in ATP catalysis. - Highlights: • A novel domain ‘GATE’ is identified in the ABC protein DrrA. • GATE shows high sequence and structural conservation among diverse ABC proteins. • GATE is located outside of the previously studied ATP binding and hydrolysis motifs. • Conserved GATE residues are critical for stability of DrrAB and for ATP catalysis.« less

Viscosity, conductivity, and electrochemical property of dicyanamide ionic liquids

NASA Astrophysics Data System (ADS)

Yuan, Wen-Li; Yang, Xiao; He, Ling; Xue, Ying; Qin, Song; Tao, Guo-Hong

2018-03-01

The instructive structure-property relationships of ionic liquids (ILs) can be put to task-specific design of new functionalized ILs. The dicyanamide (DCA) ILs are typical CHN type ILs which are halogen free, chemical stable, low-viscous and fuel-rich. The transport properties of DCA ionic liquids are significant for their applications as solvents, electrolytes and hypergolic propellants. This work systematically investigates several important transport properties of four DCA ILs ([C4mim][N(CN)2], [C4m2im][N(CN)2], N4442[N(CN)2], and N8444[N(CN)2]) including viscosity, conductivity, and electrochemical property at different temperatures. The melting points, temperature-dependent viscosities and conductivities reveal the structure-activity relationship of four DCA ILs. From the Walden plots, the imidazolium cations exhibit stronger cation–anion attraction than the ammonium cations. DCA ILs have relatively high values of electrochemical windows (EWs), which indicates that the DCA ILs are potential candidates for electrolytes in electrochemical applications. The cyclic voltammograms of Eu(III) in these DCA ILs at GC working electrode at various temperatures 303–333 K consists of quasi-reversible waves. The electrochemical properties of the DCA ILs are also dominated by the cationic structures. The current intensity (ip), the diffusion coefficients (Do), the charge transfer rate constants (ks) of Eu(III) in DCA ILs all increased with the molar conductivities increased. The cationic structure-transport property relationships of DCA ILs were constructed for designing novel functionalized ILs to fulfill specific demands.

Viscosity, Conductivity, and Electrochemical Property of Dicyanamide Ionic Liquids

PubMed Central

Yuan, Wen-Li; Yang, Xiao; He, Ling; Xue, Ying; Qin, Song; Tao, Guo-Hong

2018-01-01

The instructive structure-property relationships of ionic liquids (ILs) can be put to task-specific design of new functionalized ILs. The dicyanamide (DCA) ILs are typical CHN type ILs which are halogen free, chemical stable, low-viscous, and fuel-rich. The transport properties of DCA ionic liquids are significant for their applications as solvents, electrolytes, and hypergolic propellants. This work systematically investigates several important transport properties of four DCA ILs ([C4mim][N(CN)2], [C4m2im][N(CN)2], N4442[N(CN)2], and N8444[N(CN)2]) including viscosity, conductivity, and electrochemical property at different temperatures. The melting points, temperature-dependent viscosities and conductivities reveal the structure-activity relationship of four DCA ILs. From the Walden plots, the imidazolium cations exhibit stronger cation–anion attraction than the ammonium cations. DCA ILs have relatively high values of electrochemical windows (EWs), which indicates that the DCA ILs are potential candidates for electrolytes in electrochemical applications. The cyclic voltammograms of Eu(III) in these DCA ILs at GC working electrode at various temperatures 303–333 K consists of quasi-reversible waves. The electrochemical properties of the DCA ILs are also dominated by the cationic structures. The current intensity (ip), the diffusion coefficients (Do), the charge transfer rate constants (ks) of Eu(III) in DCA ILs all increased with the molar conductivities increased. The cationic structure-transport property relationships of DCA ILs were constructed for designing novel functionalized ILs to fulfill specific demands. PMID:29600245

Expression, purification, and functional characterization of the insulin-responsive facilitative glucose transporter GLUT4.

PubMed

Kraft, Thomas E; Hresko, Richard C; Hruz, Paul W

2015-12-01

The insulin-responsive facilitative glucose transporter GLUT4 is of fundamental importance for maintenance of glucose homeostasis. Despite intensive effort, the ability to express and purify sufficient quantities of structurally and functionally intact protein for biophysical analysis has previously been exceedingly difficult. We report here the development of novel methods to express, purify, and functionally reconstitute GLUT4 into detergent micelles and proteoliposomes. Rat GLUT4 containing FLAG and His tags at the amino and carboxy termini, respectively, was engineered and stably transfected into HEK-293 cells. Overexpression in suspension culture yielded over 1.5 mg of protein per liter of culture. Systematic screening of detergent solubilized GLUT4-GFP fusion protein via fluorescent-detection size exclusion chromatography identified lauryl maltose neopentyl glycol (LMNG) as highly effective for isolating monomeric GLUT4 micelles. Preservation of structural integrity and ligand binding was demonstrated via quenching of tryptophan fluorescence and competition of ATB-BMPA photolabeling by cytochalasin B. GLUT4 was reconstituted into lipid nanodiscs and proper folding was confirmed. Reconstitution of purified GLUT4 with amphipol A8-35 stabilized the transporter at elevated temperatures for extended periods of time. Functional activity of purified GLUT4 was confirmed by reconstitution of LMNG-purified GLUT4 into proteoliposomes and measurement of saturable uptake of D-glucose over L-glucose. Taken together, these data validate the development of an efficient means to generate milligram quantities of stable and functionally intact GLUT4 that is suitable for a wide array of biochemical and biophysical analyses. © 2015 The Protein Society.

Effects of cytoskeletal disruption on transport, structure, and rheology within mammalian cells

PubMed Central

Weihs, Daphne; Mason, Thomas G.; Teitell, Michael A.

2009-01-01

Quantification of cellular responses to stimuli is challenging. Cells respond to changing external conditions through internal structural and compositional and functional modifications, thereby altering their transport and mechanical properties. By properly interpreting particle-tracking microrheology, we evaluate the response of live cells to cytoskeletal disruption mediated by the drug nocodazole. Prior to administering the drug, the particles exhibit an apparently diffusive behavior that is actually a combination of temporally heterogeneous ballistic and caged motion. Selectively depolymerizing microtubules with the drug causes actively crawling cells to halt, providing a means for assessing drug efficacy, and making the caged motion of the probes readily apparent. PMID:19816550

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily.

PubMed

Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

2015-01-01

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

ABC Transporters Involved in Export of Cell Surface Glycoconjugates

PubMed Central

Cuthbertson, Leslie; Kos, Veronica; Whitfield, Chris

2010-01-01

Summary: Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles. PMID:20805402

De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder.

PubMed

Hamilton, P J; Campbell, N G; Sharma, S; Erreger, K; Herborg Hansen, F; Saunders, C; Belovich, A N; Sahai, M A; Cook, E H; Gether, U; McHaourab, H S; Matthies, H J G; Sutcliffe, J S; Galli, A

2013-12-01

De novo genetic variation is an important class of risk factors for autism spectrum disorder (ASD). Recently, whole-exome sequencing of ASD families has identified a novel de novo missense mutation in the human dopamine (DA) transporter (hDAT) gene, which results in a Thr to Met substitution at site 356 (hDAT T356M). The dopamine transporter (DAT) is a presynaptic membrane protein that regulates dopaminergic tone in the central nervous system by mediating the high-affinity reuptake of synaptically released DA, making it a crucial regulator of DA homeostasis. Here, we report the first functional, structural and behavioral characterization of an ASD-associated de novo mutation in the hDAT. We demonstrate that the hDAT T356M displays anomalous function, characterized as a persistent reverse transport of DA (substrate efflux). Importantly, in the bacterial homolog leucine transporter, substitution of A289 (the homologous site to T356) with a Met promotes an outward-facing conformation upon substrate binding. In the substrate-bound state, an outward-facing transporter conformation is required for substrate efflux. In Drosophila melanogaster, the expression of hDAT T356M in DA neurons-lacking Drosophila DAT leads to hyperlocomotion, a trait associated with DA dysfunction and ASD. Taken together, our findings demonstrate that alterations in DA homeostasis, mediated by aberrant DAT function, may confer risk for ASD and related neuropsychiatric conditions.

Structures of the tRNA export factor in the nuclear and cytosolic states.

PubMed

Cook, Atlanta G; Fukuhara, Noemi; Jinek, Martin; Conti, Elena

2009-09-03

Transfer RNAs are among the most ubiquitous molecules in cells, central to decoding information from messenger RNAs on translating ribosomes. In eukaryotic cells, tRNAs are actively transported from their site of synthesis in the nucleus to their site of function in the cytosol. This is mediated by a dedicated nucleo-cytoplasmic transport factor of the karyopherin-beta family (Xpot, also known as Los1 in Saccharomyces cerevisiae). Here we report the 3.2 A resolution structure of Schizosaccharomyces pombe Xpot in complex with tRNA and RanGTP, and the 3.1 A structure of unbound Xpot, revealing both nuclear and cytosolic snapshots of this transport factor. Xpot undergoes a large conformational change on binding cargo, wrapping around the tRNA and, in particular, binding to the tRNA 5' and 3' ends. The binding mode explains how Xpot can recognize all mature tRNAs in the cell and yet distinguish them from those that have not been properly processed, thus coupling tRNA export to quality control.

Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media

NASA Astrophysics Data System (ADS)

Ray, Nadja; Rupp, Andreas; Prechtel, Alexander

2017-09-01

Upscaling transport in porous media including both biomass development and simultaneous structural changes in the solid matrix is extremely challenging. This is because both affect the medium's porosity as well as mass transport parameters and flow paths. We address this challenge by means of a multiscale model. At the pore scale, the local discontinuous Galerkin (LDG) method is used to solve differential equations describing particularly the bacteria's and the nutrient's development. Likewise, a sticky agent tightening together solid or bio cells is considered. This is combined with a cellular automaton method (CAM) capturing structural changes of the underlying computational domain stemming from biomass development and solid restructuring. Findings from standard homogenization theory are applied to determine the medium's characteristic time- and space-dependent properties. Investigating these results enhances our understanding of the strong interplay between a medium's functional properties and its geometric structure. Finally, integrating such properties as model parameters into models defined on a larger scale enables reflecting the impact of pore scale processes on the larger scale.

Influence of Hydrogen Sulfide Exposure on the Transport and Structural Properties of the Metal–Organic Framework ZIF-8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, Akshita; Tymi?ska, Nina; Zhu, Guanghui

In this paper, the interaction between hydrogen sulfide and ZIF-8 was studied via structural characterizations and guest molecule diffusion measurements. It was found that hydrogen sulfide reacts with the ZIF-8 external particle surface to form a surface barrier that excludes the uptake of larger molecules (ethanol) and slows down the uptake of smaller molecules (carbon dioxide). Nonetheless, bulk transport properties were unaltered, as supported by pulsed field gradient nuclear magnetic resonance studies. Dispersion-corrected density functional theory calculations revealed that H 2S is consumed by reactions occurring at the ZIF external surface. These reactions result in water and defect formation, bothmore » of which were found to be exothermic and independent of both crystallographic facets ({001} and {110}) and surface termination. Finally, we concluded that these surface reactions lead to structural and chemical changes to the ZIF-8 external surface that generate surface barriers to molecular transport.« less

Influence of Hydrogen Sulfide Exposure on the Transport and Structural Properties of the Metal–Organic Framework ZIF-8

DOE PAGES

Dutta, Akshita; Tymi?ska, Nina; Zhu, Guanghui; ...

2018-03-09

In this paper, the interaction between hydrogen sulfide and ZIF-8 was studied via structural characterizations and guest molecule diffusion measurements. It was found that hydrogen sulfide reacts with the ZIF-8 external particle surface to form a surface barrier that excludes the uptake of larger molecules (ethanol) and slows down the uptake of smaller molecules (carbon dioxide). Nonetheless, bulk transport properties were unaltered, as supported by pulsed field gradient nuclear magnetic resonance studies. Dispersion-corrected density functional theory calculations revealed that H 2S is consumed by reactions occurring at the ZIF external surface. These reactions result in water and defect formation, bothmore » of which were found to be exothermic and independent of both crystallographic facets ({001} and {110}) and surface termination. Finally, we concluded that these surface reactions lead to structural and chemical changes to the ZIF-8 external surface that generate surface barriers to molecular transport.« less

Photothermal heating in metal-embedded microtools for material transport

NASA Astrophysics Data System (ADS)

Villangca, Mark; Palima, Darwin; Bañas, Andrew; Glückstad, Jesper

2016-03-01

Material transport is an important mechanism in microfluidics and drug delivery. The methods and solutions found in literature involve passively diffusing structures, microneedles and chemically fueled structures. In this work, we make use of optically actuated microtools with embedded metal layer as heating element for controlled loading and release. The new microtools take advantage of the photothermal-induced convection current to load and unload cargo. We also discuss some challenges encountered in realizing a self-contained polymerized microtool. Microfluidic mixing, fluid flow control and convection currents have been demonstrated both experimentally and numerically for static metal thin films or passively floating nanoparticles. Here we show an integration of aforementioned functionalities in an optically fabricated and actuated microtool. As proof of concept, we demonstrate loading and unloading of beads. This can be extended to controlled transport and release of genetic material, bio-molecules, fluorescent dyes. We envisioned these microtools to be an important addition to the portfolio of structure-mediated contemporary biophotonics.

Role of transmembrane domain 10 for the function of organic anion transporting polypeptide 1B1

PubMed Central

Gui, Chunshan; Hagenbuch, Bruno

2009-01-01

The liver-specific organic anion transporting polypeptides OATP1B1 and OATP1B3 are highly homologous and share numerous substrates. However, at low concentrations OATP1B1 shows substrate selectivity for estrone-3-sulfate. In this study, we investigated the molecular mechanism for this substrate selectivity of OATP1B1 by constructing OATP1B1/1B3 chimeric transporters and by site-directed mutagenesis. Functional studies of chimeras showed that transmembrane domain 10 is critical for the function of OATP1B1. We further identified four amino acid residues, namely L545, F546, L550, and S554 in TM10, whose simultaneous mutation caused almost complete loss of OATP1B1-mediated estrone-3-sulfate transport. Comparison of the kinetics of estrone-3-sulfate transport confirmed a biphasic pattern for OATP1B1, but showed a monophasic pattern for the quadruple mutant L545S/F546L/L550T/S554T. This mutant also showed reduced transport for other OATP1B1 substrates such as bromosulfophthalein and [d-penicillamine2,5]enkephalin. Helical wheel analysis and molecular modeling suggest that L545 is facing the substrate translocation pathway, whereas F546, L550, and S554 are located inside the protein. These results indicate that L545 might contribute to OATP1B1 function by interacting with substrates, whereas F546, L550, and S554 seem important for protein structure. In conclusion, our results show that TM10 is critical for the function of OATP1B1. PMID:19760661

Kinetic Adaptations of Myosins for their Diverse Cellular Functions

PubMed Central

Heissler, Sarah M.; Sellers, James R.

2016-01-01

Members of the myosin superfamily are involved in all aspects of eukaryotic life. Their function ranges from the transport of organelles and cargos to the generation of membrane tension, and the contraction of muscle. The diversity of physiological functions is remarkable, given that all enzymatically active myosins follow a conserved mechanoenzymatic cycle in which the hydrolysis of ATP to ADP and inorganic phosphate is coupled to either actin-based transport or tethering of actin to defined cellular compartments. Kinetic capacities and limitations of a myosin are determined by the extent to with actin can accelerate the hydrolysis of ATP and the release of the hydrolysis products and are indispensably linked to its physiological tasks. This review focuses on kinetic competencies that – together with structural adaptations – result in myosins with unique mechanoenzymatic properties targeted to their diverse cellular function. PMID:26929436

Asymmetric ion transport through ion-channel-mimetic solid-state nanopores.

PubMed

Guo, Wei; Tian, Ye; Jiang, Lei

2013-12-17

Both scientists and engineers are interested in the design and fabrication of synthetic nanofluidic architectures that mimic the gating functions of biological ion channels. The effort to build such structures requires interdisciplinary efforts at the intersection of chemistry, materials science, and nanotechnology. Biological ion channels and synthetic nanofluidic devices have some structural and chemical similarities, and therefore, they share some common features in regulating the traverse ionic flow. In the past decade, researchers have identified two asymmetric ion transport phenomena in synthetic nanofluidic structures, the rectified ionic current and the net diffusion current. The rectified ionic current is a diode-like current-voltage response that occurs when switching the voltage bias. This phenomenon indicates a preferential direction of transport in the nanofluidic system. The net diffusion current occurs as a direct product of charge selectivity and is generated from the asymmetric diffusion through charged nanofluidic channels. These new ion transport phenomena and the elaborate structures that occur in biology have inspired us to build functional nanofluidic devices for both fundamental research and practical applications. In this Account, we review our recent progress in the design and fabrication of biomimetic solid-state nanofluidic devices with asymmetric ion transport behavior. We demonstrate the origin of the rectified ionic current and the net diffusion current. We also identify several influential factors and discuss how to build these asymmetric features into nanofluidic systems by controlling (1) nanopore geometry, (2) surface charge distribution, (3) chemical composition, (4) channel wall wettability, (5) environmental pH, (6) electrolyte concentration gradient, and (7) ion mobility. In the case of the first four features, we build these asymmetric features directly into the nanofluidic structures. With the final three, we construct different environmental conditions in the electrolyte solutions on either side of the nanochannel. The novel and well-controlled nanofluidic phenomena have become the foundation for many promising applications, and we have highlighted several representative examples. Inspired by the electrogenic cell of the electric eel, we have demonstrated a proof-of-concept nanofluidic reverse electrodialysis system (NREDS) that converts salinity gradient energy into electricity by means of net diffusion current. We have also constructed chirality analysis systems into nanofluidic architectures and monitored these sensing events as the change in the degree of ionic current rectification. Moreover, we have developed a biohybrid nanosystem, in which we reconstituted the F0F1-ATPase on a liposome-coated, solid-state nanoporous membrane. By applying a transmembrane proton concentration gradient, the biohybrid nanodevice can synthesize ATP in vitro. These findings have improved our understanding of the asymmetric ion transport phenomena in synthetic nanofluidic systems and offer innovative insights into the design of functional nanofluidic devices.

Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

PubMed

Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

2016-01-01

Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

Correlation Function Approach for Estimating Thermal Conductivity in Highly Porous Fibrous Materials

NASA Technical Reports Server (NTRS)

Martinez-Garcia, Jorge; Braginsky, Leonid; Shklover, Valery; Lawson, John W.

2011-01-01

Heat transport in highly porous fiber networks is analyzed via two-point correlation functions. Fibers are assumed to be long and thin to allow a large number of crossing points per fiber. The network is characterized by three parameters: the fiber aspect ratio, the porosity and the anisotropy of the structure. We show that the effective thermal conductivity of the system can be estimated from knowledge of the porosity and the correlation lengths of the correlation functions obtained from a fiber structure image. As an application, the effects of the fiber aspect ratio and the network anisotropy on the thermal conductivity is studied.

Molecular cloning and biochemical characterization of two cation chloride cotransporter subfamily members of Hydra vulgaris.

PubMed

Hartmann, Anna-Maria; Pisella, Lucie I; Medina, Igor; Nothwang, Hans Gerd

2017-01-01

Cation Chloride Cotransporters (CCCs) comprise secondary active membrane proteins mainly mediating the symport of cations (Na+, K+) coupled with chloride (Cl-). They are divided into K+-Cl- outward transporters (KCCs), the Na+-K+-Cl- (NKCCs) and Na+-Cl- (NCCs) inward transporters, the cation chloride cotransporter interacting protein CIP1, and the polyamine transporter CCC9. KCCs and N(K)CCs are established in the genome since eukaryotes and metazoans, respectively. Most of the physiological and functional data were obtained from vertebrate species. To get insights into the basal functional properties of KCCs and N(K)CCs in the metazoan lineage, we cloned and characterized KCC and N(K)CC from the cnidarian Hydra vulgaris. HvKCC is composed of 1,032 amino-acid residues. Functional analyses revealed that hvKCC mediates a Na+-independent, Cl- and K+ (Tl+)-dependent cotransport. The classification of hvKCC as a functional K-Cl cotransporter is furthermore supported by phylogenetic analyses and a similar structural organization. Interestingly, recently obtained physiological analyses indicate a role of cnidarian KCCs in hyposmotic volume regulation of nematocytes. HvN(K)CC is composed of 965 amino-acid residues. Phylogenetic analyses and structural organization suggest that hvN(K)CC is a member of the N(K)CC subfamily. However, no inorganic ion cotransport function could be detected using different buffer conditions. Thus, hvN(K)CC is a N(K)CC subfamily member without a detectable inorganic ion cotransporter function. Taken together, the data identify two non-bilaterian solute carrier 12 (SLC12) gene family members, thereby paving the way for a better understanding of the evolutionary paths of this important cotransporter family.

Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120.

PubMed

Nieves-Morión, Mercedes; Lechno-Yossef, Sigal; López-Igual, Rocío; Frías, José E; Mariscal, Vicente; Nürnberg, Dennis J; Mullineaux, Conrad W; Wolk, C Peter; Flores, Enrique

2017-04-01

When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO 2 through oxygenic photosynthesis and heterocysts that are specialized in N 2 fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of Anabaena mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of Anabaena was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in Anabaena , glucoside transporters influence the structure and function of septal junctions. IMPORTANCE Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO 2 and N 2 These organisms grow as filaments that fix these gases specifically in vegetative cells and heterocysts, respectively. For the filaments to grow, these types of cells exchange nutrients, including sucrose, which serves as a source of reducing power and of carbon skeletons for the heterocysts. Movement of sucrose between cells in the filament takes place through septal junctions and has been traced with a fluorescent sucrose analog, esculin, that can be taken up by the cells. Here, we identified α-glucoside transporters of Anabaena that mediate uptake of esculin and, notably, influence septal structure and the function of septal junctions. Copyright © 2017 American Society for Microbiology.

Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120

PubMed Central

Nieves-Morión, Mercedes; Lechno-Yossef, Sigal; López-Igual, Rocío; Frías, José E.; Mariscal, Vicente; Nürnberg, Dennis J.; Mullineaux, Conrad W.; Wolk, C. Peter

2017-01-01

ABSTRACT When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO2 through oxygenic photosynthesis and heterocysts that are specialized in N2 fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of Anabaena mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of Anabaena was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in Anabaena, glucoside transporters influence the structure and function of septal junctions. IMPORTANCE Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO2 and N2. These organisms grow as filaments that fix these gases specifically in vegetative cells and heterocysts, respectively. For the filaments to grow, these types of cells exchange nutrients, including sucrose, which serves as a source of reducing power and of carbon skeletons for the heterocysts. Movement of sucrose between cells in the filament takes place through septal junctions and has been traced with a fluorescent sucrose analog, esculin, that can be taken up by the cells. Here, we identified α-glucoside transporters of Anabaena that mediate uptake of esculin and, notably, influence septal structure and the function of septal junctions. PMID:28096449

Functional and cytometric examination of different human lung epithelial cell types as drug transport barriers.

PubMed

Min, Kyoung Ah; Rosania, Gus R; Kim, Chong-Kook; Shin, Meong Cheol

2016-03-01

To develop inhaled medications, various cell culture models have been used to examine the transcellular transport or cellular uptake properties of small molecules. For the reproducible high throughput screening of the inhaled drug candidates, a further verification of cell architectures as drug transport barriers can contribute to establishing appropriate in vitro cell models. In the present study, side-by-side experiments were performed to compare the structure and transport function of three lung epithelial cells (Calu-3, normal human bronchial primary cells (NHBE), and NL-20). The cells were cultured on the nucleopore membranes in the air-liquid interface (ALI) culture conditions, with cell culture medium in the basolateral side only, starting from day 1. In transport assays, paracellular transport across all three types of cells appeared to be markedly different with the NHBE or Calu-3 cells, showing low paracellular permeability and high TEER values, while the NL-20 cells showed high paracellular permeability and low TEER. Quantitative image analysis of the confocal microscope sections further confirmed that the Calu-3 cells formed intact cell monolayers in contrast to the NHBE and NL-20 cells with multilayers. Among three lung epithelial cell types, the Calu-3 cell cultures under the ALI condition showed optimal cytometric features for mimicking the biophysical characteristics of in vivo airway epithelium. Therefore, the Calu-3 cell monolayers could be used as functional cell barriers for the lung-targeted drug transport studies.

Functional and cytometric examination of different human lung epithelial cell types as drug transport barriers

PubMed Central

Min, Kyoung Ah; Rosania, Gus R.; Kim, Chong-Kook; Shin, Meong Cheol

2016-01-01

To develop inhaled medications, various cell culture models have been used to examine the transcellular transport or cellular uptake properties of small molecules. For the reproducible high throughput screening of the inhaled drug candidates, a further verification of cell architectures as drug transport barriers can contribute to establishing appropriate in vitro cell models. In the present study, side-by-side experiments were performed to compare the structure and transport function of three lung epithelial cells (Calu-3, normal human bronchial primary cells (NHBE), and NL-20). The cells were cultured on the nucleopore membranes in the air-liquid interface (ALI) culture conditions, with cell culture medium in the basolateral side only, starting from day 1. In transport assays, paracellular transport across all three types of cells appeared to be markedly different with the NHBE or Calu-3 cells, showing low paracellular permeability and high TEER values, while the NL-20 cells showed high paracellular permeability and low TEER. Quantitative image analysis of the confocal microscope sections further confirmed that the Calu-3 cells formed intact cell monolayers in contrast to the NHBE and NL-20 cells with multilayers. Among three lung epithelial cell types, the Calu-3 cell cultures under the ALI condition showed optimal cytometric features for mimicking the biophysical characteristics of in vivo airway epithelium. Therefore, the Calu-3 cell monolayers could be used as functional cell barriers for the lung-targeted drug transport studies. PMID:26746641

A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5

DOE PAGES

Vild, Cody J.; Li, Yan; Guo, Emily Z.; ...

2015-01-30

Disassembly of the endosomal sorting complex required for transport (ESCRT) machinery from biological membranes is a critical final step in cellular processes that require the ESCRT function. This reaction is catalyzed by VPS4, an AAA-ATPase whose activity is tightly regulated by a host of proteins, including LIP5 and the ESCRT-III proteins. In this paper, we present structural and functional analyses of molecular interactions between human VPS4, LIP5, and the ESCRT-III proteins. The N-terminal domain of LIP5 (LIP5NTD) is required for LIP5-mediated stimulation of VPS4, and the ESCRT-III protein CHMP5 strongly inhibits the stimulation. Both of these observations are distinct frommore » what was previously described for homologous yeast proteins. The crystal structure of LIP5NTD in complex with the MIT (microtubule-interacting and transport)-interacting motifs of CHMP5 and a second ESCRT-III protein, CHMP1B, was determined at 1 Å resolution. It reveals an ESCRT-III binding induced moderate conformational change in LIP5NTD, which results from insertion of a conserved CHMP5 tyrosine residue (Tyr 182) at the core of LIP5NTD structure. Finally, mutation of Tyr 182 partially relieves the inhibition displayed by CHMP5. Together, these results suggest a novel mechanism of VPS4 regulation in metazoans, where CHMP5 functions as a negative allosteric switch to control LIP5-mediated stimulation of VPS4.« less

Density Functional Study of Stacking Structures and Electronic Behaviors of AnE-PV Copolymer.

PubMed

Dong, Chuan-Ding; Beenken, Wichard J D

2016-10-10

In this work, we report an in-depth investigation on the π-stacking and interdigitating structures of poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene) copolymer with octyl and ethyl-hexyl side chains and the resulting electronic band structures using density functional theory calculations. We found that in the π-stacking direction, the preferred stacking structure, determined by the steric effect of the branched ethyl-hexyl side chains, is featured by the anthracene-ethynylene units stacking on the phenylene-vinylene units of the neighboring chains and vice versa. This stacking structure, combined with the interdigitating structure where the branched side chains of the laterally neighboring chains are isolated, defines the energetically favorable structure of the ordered copolymer phase, which provides a good compromise between light absorption and charge-carrier transport.

Controllable molecular motors engineered from myosin and RNA

NASA Astrophysics Data System (ADS)

Omabegho, Tosan; Gurel, Pinar S.; Cheng, Clarence Y.; Kim, Laura Y.; Ruijgrok, Paul V.; Das, Rhiju; Alushin, Gregory M.; Bryant, Zev

2018-01-01

Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems1 or in living cells2. Previously, synthetic nucleic acid motors3-5 and modified natural protein motors6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors11-15. Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure7,9. We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing16. Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement17 reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.

Structure, transport and photoconductance of PbS quantum dot monolayers functionalized with a copper phthalocyanine derivative.

PubMed

André, A; Theurer, C; Lauth, J; Maiti, S; Hodas, M; Samadi Khoshkhoo, M; Kinge, S; Meixner, A J; Schreiber, F; Siebbeles, L D A; Braun, K; Scheele, M

2017-01-31

We simultaneously surface-functionalize PbS nanocrystals with Cu 4,4',4'',4'''-tetraaminophthalocyanine and assemble this hybrid material into macroscopic monolayers. Electron microscopy and X-ray scattering reveal a granular mesocrystalline structure with strong coherence between the atomic lattice and the superlattice of nanocrystals within each domain. Terahertz spectroscopy and field-effect transistor measurements indicate efficient coupling of holes throughout the hybrid thin film, in conjunction with a pronounced photoresponse. We demonstrate the potential of this material for optoelectronic applications by fabricating a light-effect transistor.

Thermally Cross-Linkable Hole Transport Materials for Solution Processed Phosphorescent OLEDs

NASA Astrophysics Data System (ADS)

Kim, Beom Seok; Kim, Ohyoung; Chin, Byung Doo; Lee, Chil Won

2018-04-01

Materials for unique fabrication of a solution-processed, multi-layered organic light-emitting diode (OLED) were developed. Preparation of a hole transport layer with a thermally cross-linkable chemical structure, which can be processed to form a thin film and then transformed into an insoluble film by using an amine-alcohol condensation reaction with heat treatment, was investigated. Functional groups, such as triplenylamine linked with phenylcarbazole or biphenyl, were employed in the chemical structure of the hole transport layer in order to maintain high triplet energy properties. When phenylcarbazole or biphenyl compounds continuously react with triphenylamine under acid catalysis, a chemically stable thin film material with desirable energy-level properties for a blue OLED could be obtained. The prepared hole transport materials showed excellent surface roughness and thermal stability in comparison with the commercial reference material. On the solution-processed model hole transport layer, we fabricated a device with a blue phosphorescent OLED by using sequential vacuum deposition. The maximum external quantum, 19.3%, was improved by more than 40% over devices with the commercial reference material (11.4%).

Money circulation networks reveal emerging geographical communities

NASA Astrophysics Data System (ADS)

Brockmann, D.; Theis, F.; David, V.

2008-03-01

Geographical communities and their boundaries are key determinants of various spatially extended dynamical phenomena. Examples are migration dynamics of species, the spread of infectious diseases, bioinvasive processes, and the spatial evolution of language. We address the question to what extend multiscale human transportation networks encode geographical community structures, how they differ from geopolitical classifications, whether they are spatially coherent, and analyse their structure as a function of length scale. Our analysis is based on a proxy network for human transportation obtained from the geographic circulation of more than 10 million dollar bills in the United States recorded at the bill tracking website www.wheresgeorge.com. The data extends that of a previous study (Brockmann et al., Nature 2006) on the discovery of scaling laws of human travel by an order of magnitude and permits an approach to multiscale human transportation from a network perspective.

A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases.

PubMed

Tuckerman, Mark E; Chandra, Amalendu; Marx, Dominik

2010-09-28

Extraction of relaxation times, lifetimes, and rates associated with the transport of topological charge defects in hydrogen-bonded networks from molecular dynamics simulations is a challenge because proton transfer reactions continually change the identity of the defect core. In this paper, we present a statistical mechanical theory that allows these quantities to be computed in an unbiased manner. The theory employs a set of suitably defined indicator or population functions for locating a defect structure and their associated correlation functions. These functions are then used to develop a chemical master equation framework from which the rates and lifetimes can be determined. Furthermore, we develop an integral equation formalism for connecting various types of population correlation functions and derive an iterative solution to the equation, which is given a graphical interpretation. The chemical master equation framework is applied to the problems of both hydronium and hydroxide transport in bulk water. For each case it is shown that the theory establishes direct links between the defect's dominant solvation structures, the kinetics of charge transfer, and the mechanism of structural diffusion. A detailed analysis is presented for aqueous hydroxide, examining both reorientational time scales and relaxation of the rotational anisotropy, which is correlated with recent experimental results for these quantities. Finally, for OH(-)(aq) it is demonstrated that the "dynamical hypercoordination mechanism" is consistent with available experimental data while other mechanistic proposals are shown to fail. As a means of going beyond the linear rate theory valid from short up to intermediate time scales, a fractional kinetic model is introduced in the Appendix in order to describe the nonexponential long-time behavior of time-correlation functions. Within the mathematical framework of fractional calculus the power law decay ∼t(-σ), where σ is a parameter of the model and depends on the dimensionality of the system, is obtained from Mittag-Leffler functions due to their long-time asymptotics, whereas (stretched) exponential behavior is found for short times.

Cytoplasm localization of aminopeptidase M1 and its functional activity in root hair cells and BY-2 cells.

PubMed

Lee, Ok Ran; Cho, Hyung-Taeg

2012-12-01

Aminopeptidase M1 (APM1) was the first M1 metallopeptidase family member identified in Arabidopsis, isolated by its affinity for the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). A loss-of-function mutation showed various developmental defects in cell division and auxin transport. APM1 was shown to be localized in endomembrane structures, the cytoplasm, and the plasma membrane. These previous results suggested that APM1 has diverse functional roles in different cell and tissue types. Here we report that APM1 localized to the cytoplasm, and its over-expression in the root hair cell caused longer root hair phenotypes. Treatment of aminopeptidase inhibitors caused internalization of auxin efflux PIN-FORMED proteins in root hair cells and suppressed short root hair phenotype of PIN3 overexpression line (PIN3ox). APM1 also localized to the cytoplasm in tobacco BY-2 cells, its over-expression had little effect on auxin transport in these cells.

CELLULAR MULTITASKING: THE DUAL ROLE OF HUMAN CU-ATPASES IN COFACTOR DELIVERY AND INTRACELLULAR COPPER BALANCE

PubMed Central

Lutsenko, Svetlana; Gupta, Arnab; Burkhead, Jason L.; Zuzel, Vesna

2008-01-01

Summary The human copper-transporting ATPases (Cu-ATPases) are essential for dietary copper uptake, normal development and function of the CNS, and regulation of copper homeostasis in the body. In a cell, Cu-ATPases maintain the intracellular concentration of copper by transporting copper into intracellular exocytic vesicles. In addition, these P-type ATPases mediate delivery of copper to copper-dependent enzymes in the secretory pathway and in specialized cell compartments such as secretory granules or melanosomes. The multiple functions of human Cu-ATPase necessitate complex regulation of these transporters that is mediated through the presence of regulatory domains in their structure, posttranslational modification and intracellular trafficking, as well as interactions with the copper chaperone Atox1 and other regulatory molecules. In this review, we summarize the current information on the function and regulatory mechanisms acting on human Cu-ATPases ATP7A and ATP7B. Brief comparison with the Cu-ATPase orthologues from other species is included. PMID:18534184

Perfluoroalkyl Acids Shift Microbial Community Structure Across Experimental Scales

NASA Astrophysics Data System (ADS)

Weathers, T. S.; Sharp, J.

2016-12-01

Perfluoroalkyl acids (PFAAs) are contaminants of emerging concern that have increasingly been found in groundwater and drinking water systems. Previously, we demonstrated that PFAAs significantly alter the abundance of specific microbial clades in batch reductive dechlorinating systems, resulting in decreased chlorinated solvent attenuation capabilities. To further understand the impacts of PFAA exposure on subsurface microbial processes and PFAA transport, we investigated changes in microbial community structure as a function of PFAA presence in flow-through columns simulating aquifer transport. Phylogenetic analysis using high throughput, next generation sequencing performed after exposure to 250 pore volumes of source zone concentrations of PFAAs (10 mg/L each of 11 analytes including PFOS and PFOA) resulted in patterns that mirrored those observed in batch systems, demonstrating a conservation of community dynamics across experimental scales. Of the nine clades observed in both batch and flow-through systems, six were similarly impacted as a function of PFAA exposure, regardless of the experimental differences in transport and redox state. Specifically, the presence of PFAAs enhanced the relative abundance of Archaea, Bacteroidetes (phylum), and the family Veillonellaceae in both systems. Repressed clades include the genus Sedimentibacter, Ruminococcaceae (family), and the Anaerolineales, which contains Dehalococcoides, a genus known for its ability to fully dechlorinate TCE. As PFAAs are often co-located with TCE and BTEX, changes in microbial community structure can result in hindered bioremediation of these co-contaminants. Consideration of community shifts and corresponding changes in behavior, such as repressed reductive dechlorination or increased biofilm formation, will aid in the development of conceptual site models that account for co-contaminant bioremediation potential and PFAA transport.

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires. Using quantum-based calculations, we modeled 'p-type' polaron transport through oligophenylenethiophene (OPTI) wires and assigned transport activation energies to specific modes of nuclear motion. We also show control over 'n-type', LUMO-mediated transport in short ( 2 nm) redox-active perylenediimide (PDI) SAMs bound to contacts through isocyano linkers. By changing the contact work function (φ) and temperature, we were able to verify thermally-assisted LUMO transport. Transition voltage spectroscopy and the single level model was employed to fit the experimental I-V curves and extract the electronic coupling (epsilon) and the EF-LUMO offset (epsilonl). It was found that epsilonl does not change with φ (LUMO pinning), while Gamma changes with both φ and temperature. Further, the PDI SAMs could be reversibly chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

1997 Economic Census : transportation : 1997 Commodity Flow Survey : exports

DOT National Transportation Integrated Search

2000-04-01

The Commodity Flow Survey comprises one section of the 1997 Economic Census. The economic census is the major source of facts about the structure and functioning of the Nation's economy. It provides essential information for government, business, ind...

Calibration of the MEPDG transfer functions in Georgia : task order 2 report.

DOT National Transportation Integrated Search

2015-03-28

The Georgia Department of Transportation (GDOT) currently uses the empirical 1972 AASHTO Interim Guide for : Design of Pavement Structures as their standard pavement design procedure. However, GDOT plans to transition to the : Mechanistic Empirical P...

Model for the role of auxin polar transport in patterning of the leaf adaxial-abaxial axis.

PubMed

Shi, Jianmin; Dong, Jiaqiang; Xue, Jingshi; Wang, Hua; Yang, Zhongnan; Jiao, Yuling; Xu, Lin; Huang, Hai

2017-11-01

Leaf adaxial-abaxial polarity refers to the two leaf faces, which have different types of cells performing distinct biological functions. In 1951, Ian Sussex reported that when an incipient leaf primordium was surgically isolated by an incision across the vegetative shoot apical meristem (SAM), a radialized structure without an adaxial domain would form. This led to the proposal that a signal, now called the Sussex signal, is transported from the SAM to emerging primordia to direct leaf adaxial-abaxial patterning. It was recently proposed that instead of the Sussex signal, polar transport of the plant hormone auxin is critical in leaf polarity formation. However, how auxin polar transport functions in the process is unknown. Through live imaging, we established a profile of auxin polar transport in and around young leaf primordia. Here we show that auxin polar transport in lateral regions of an incipient primordium forms auxin convergence points. We demonstrated that blocking auxin polar transport in the lateral regions of the incipient primordium by incisions abolished the auxin convergence points and caused abaxialized leaves to form. The lateral incisions also blocked the formation of leaf middle domain and margins and disrupted expression of the middle domain/margin-associated marker gene WUSCHEL-RELATED HOMEOBOX 1 (SlWOX1). Based on these results we propose that the auxin convergence points are required for the formation of leaf middle domain and margins, and the functional middle domain and margins ensure leaf adaxial-abaxial polarity. How middle domain and margins function in the process is discussed. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

PubMed Central

Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. PMID:23093919

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

PubMed

Chovancova, Eva; Pavelka, Antonin; Benes, Petr; Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

ClC Channels and Transporters: Structure, Physiological Functions, and Implications in Human Chloride Channelopathies

PubMed Central

Poroca, Diogo R.; Pelis, Ryan M.; Chappe, Valérie M.

2017-01-01

The discovery of ClC proteins at the beginning of the 1990s was important for the development of the Cl- transport research field. ClCs form a large family of proteins that mediate voltage-dependent transport of Cl- ions across cell membranes. They are expressed in both plasma and intracellular membranes of cells from almost all living organisms. ClC proteins form transmembrane dimers, in which each monomer displays independent ion conductance. Eukaryotic members also possess a large cytoplasmic domain containing two CBS domains, which are involved in transport modulation. ClC proteins function as either Cl- channels or Cl-/H+ exchangers, although all ClC proteins share the same basic architecture. ClC channels have two gating mechanisms: a relatively well-studied fast gating mechanism, and a slow gating mechanism, which is poorly defined. ClCs are involved in a wide range of physiological processes, including regulation of resting membrane potential in skeletal muscle, facilitation of transepithelial Cl- reabsorption in kidneys, and control of pH and Cl- concentration in intracellular compartments through coupled Cl-/H+ exchange mechanisms. Several inherited diseases result from C1C gene mutations, including myotonia congenita, Bartter’s syndrome (types 3 and 4), Dent’s disease, osteopetrosis, retinal degeneration, and lysosomal storage diseases. This review summarizes general features, known or suspected, of ClC structure, gating and physiological functions. We also discuss biophysical properties of mammalian ClCs that are directly involved in the pathophysiology of several human inherited disorders, or that induce interesting phenotypes in animal models. PMID:28386229

Interaction of the P-Glycoprotein Multidrug Transporter with Sterols.

PubMed

Clay, Adam T; Lu, Peihua; Sharom, Frances J

2015-11-03

The ABC transporter P-glycoprotein (Pgp, ABCB1) actively exports structurally diverse substrates from within the lipid bilayer, leading to multidrug resistance. Many aspects of Pgp function are altered by the phospholipid environment, but its interactions with sterols remain enigmatic. In this work, the functional interaction between purified Pgp and various sterols was investigated in detergent solution and proteoliposomes. Fluorescence studies showed that dehydroergosterol, cholestatrienol, and NBD-cholesterol interact intimately with Pgp, resulting in both quenching of protein Trp fluorescence and enhancement of sterol fluorescence. Kd values indicated binding affinities in the range of 3-9 μM. Collisional quenching experiments showed that Pgp-bound NBD-cholesterol was protected from the external milieu, resonance energy transfer was observed between Pgp Trp residues and the sterol, and the fluorescence emission of bound sterol was enhanced. These observations suggested an intimate interaction of bound sterols with the transporter at a protected nonpolar site. Cholesterol hemisuccinate altered the thermal unfolding of Pgp and greatly stabilized its basal ATPase activity in both a detergent solution and reconstituted proteoliposomes of certain phospholipids. Other sterols, including dehydroergosterol, did not stabilize the basal ATPase activity of detergent-solubilized Pgp, which suggests that this is not a generalized sterol effect. The phospholipid composition and cholesterol hemisuccinate content of Pgp proteoliposomes altered the basal ATPase and drug transport cycles differently. Sterols may interact with Pgp and modulate its structure and function by occupying part of the drug-binding pocket or by binding to putative consensus cholesterol-binding (CRAC/CARC) motifs located within the transmembrane domains.

Physical modeling of geometrically confined disordered protein assemblies

NASA Astrophysics Data System (ADS)

Ando, David

2015-08-01

The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature and uncertainty regarding the properties of individual nucleoporins. We first study the defining characteristics of the amino acid sequences of nucleoporins through bioinformatics techniques, although bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of FG motif containing nucleoporins (FG nups). The biophysical mechanism by which the critical FG nups regulate nucleocytoplasmic transport has remained elusive, yet our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These sequence features are likely conserved due to a common functionality between species regarding how FG nups functionally regulate traffic, therefore these results constrain current models and eliminate proposed biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC which would not result in such a conserved amino acid sequence structure. Additionally, this method allows us to identify potentially functionally analogous disordered proteins across distantly related species. To understand the physical implications of the sequence features on structure and dynamics of the nucleoporins, we performed coarse-grained simulations of nucleoporins to understand their individual polymer properties. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature, consistent with the results of our physical bioinformatic analysis. Further simulations of grafted rings of FG nups mimicking the in vivo geometry of the NPC were performed and supplemented with polymer brush modeling to understand how aggregates of FG nups regulate transport in vivo. We found that the block structure at the individual protein level in terms of polymer properties is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies that correspond to open and closed states could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability in our Diblock Copolymer Brush Gate model. Previous experimental research has concluded that FG nups from S. cerevisiae are present in a bimodal distribution, with the "Forest Model" classifying FG nups as either diblock polymer like "trees" or single block polymer like "shrubs." Our simulation and polymer brush modeling results indicated that the function of the tree FG nups in the Diblock Copolymer Brush Gate (DCBG) model is to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. Here we perform coarse grained simulations of the shrub FG nups which confirm that they have a single block polymer structure rather than the diblock structure of tree nups. Our molecular simulations also demonstrate that these single block FG nups are likely compact collapsed coil polymers, implying that shrubs are generally localized to their grafting location within the NPC. We find that adding a layer of shrub FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving shrub and tree nups. This effect can explain the puzzling connection between shrub FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single block and diblock FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability. In summary, this dissertation presents a cohesive body of research that uses a combination of techniques including bioinformatics, coarse grained molecular modeling, and polymer brush theory to understand the properties of individual FG nups and how they behave in aggregate, strongly constraining possible biophysical mechanisms which may play a role in regulating traffic through the NPC. Our results are observed across different species and are consistent with many experimental observations which have been reported. Finally, our DCBG model for NPC function provides testable predictions for future experimental investigation and provides a foundation for the design and commercialization of biomimetic pores for filtering applications in vitro and industrial use.

ABC transporters and immunity: mechanism of self-defense.

PubMed

Hinz, Andreas; Tampé, Robert

2012-06-26

The transporter associated with antigen processing (TAP) is a prototype of an asymmetric ATP-binding cassette (ABC) transporter, which uses ATP binding and hydrolysis to translocate peptides from the cytosol to the lumen of the endoplasmic reticulum (ER). Here, we review molecular details of peptide binding and ATP binding and hydrolysis as well as the resulting allosteric cross-talk between the nucleotide-binding domains and the transmembrane domains that drive translocation of the solute across the ER membrane. We also discuss the general molecular architecture of ABC transporters and demonstrate the importance of structural and functional studies for a better understanding of the role of the noncanonical site of asymmetric ABC transporters. Several aspects of peptide binding and specificity illustrate details of peptide translocation by TAP. Furthermore, this ABC transporter forms the central part of the major histocompatibility complex class I (MHC I) peptide-loading machinery. Hence, TAP is confronted with a number of viral factors, which prevent antigen translocation and MHC I loading in virally infected cells. We review how these viral factors have been used as molecular tools to decipher mechanistic aspects of solute translocation and discuss how they can help in the structural analysis of TAP.

Structural imaging of nanoscale phonon transport in ferroelectrics excited by metamaterial-enhanced terahertz fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Yi; Chen, Frank; Park, Joonkyu

Nanoscale phonon transport is a key process that governs thermal conduction in a wide range of materials and devices. Creating controlled phonon populations by resonant excitation at terahertz (THz) frequencies can drastically change the characteristics of nanoscale thermal transport and allow a direct real-space characterization of phonon mean-free paths. Using metamaterial-enhanced terahertz excitation, we tailored a phononic excitation by selectively populating low-frequency phonons within a nanoscale volume in a ferroelectric BaTiO3 thin film. Real-space time-resolved x-ray diffraction microscopy following THz excitation reveals ballistic phonon transport over a distance of hundreds of nm, two orders of magnitude longer than the averagedmore » phonon mean-free path in BaTiO3. On longer length scales, diffusive phonon transport dominates the recovery of the transient strain response, largely due to heat conduction into the substrate. The measured real-space phonon transport can be directly compared with the phonon mean-free path as predicted by molecular dynamics modeling. This time-resolved real-space visualization of THz-matter interactions opens up opportunities to engineer and image nanoscale transient structural states with new functionalities.« less

Structural imaging of nanoscale phonon transport in ferroelectrics excited by metamaterial-enhanced terahertz fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Yi; Chen, Frank; Park, Joonkyu

Nanoscale phonon transport is a key process that governs thermal conduction in a wide range of materials and devices. Creating controlled phonon populations by resonant excitation at terahertz (THz) frequencies can drastically change the characteristics of nanoscale thermal transport and allow a direct real-space characterization of phonon mean-free paths. Using metamaterial-enhanced terahertz excitation, we tailored a phononic excitation by selectively populating low-frequency phonons within a nanoscale volume in a ferroelectric BaTiO 3 thin film. Real-space time-resolved x-ray diffraction microscopy following THz excitation reveals ballistic phonon transport over a distance of hundreds of nm, two orders of magnitude longer than themore » averaged phonon mean-free path in BaTiO 3. On longer length scales, diffusive phonon transport dominates the recovery of the transient strain response, largely due to heat conduction into the substrate. The measured real-space phonon transport can be directly compared with the phonon mean-free path as predicted by molecular dynamics modeling. In conclusion, this time-resolved real-space visualization of THz-matter interactions opens up opportunities to engineer and image nanoscale transient structural states with new functionalities.« less

Structural imaging of nanoscale phonon transport in ferroelectrics excited by metamaterial-enhanced terahertz fields

DOE PAGES

Zhu, Yi; Chen, Frank; Park, Joonkyu; ...

2017-11-16

Nanoscale phonon transport is a key process that governs thermal conduction in a wide range of materials and devices. Creating controlled phonon populations by resonant excitation at terahertz (THz) frequencies can drastically change the characteristics of nanoscale thermal transport and allow a direct real-space characterization of phonon mean-free paths. Using metamaterial-enhanced terahertz excitation, we tailored a phononic excitation by selectively populating low-frequency phonons within a nanoscale volume in a ferroelectric BaTiO 3 thin film. Real-space time-resolved x-ray diffraction microscopy following THz excitation reveals ballistic phonon transport over a distance of hundreds of nm, two orders of magnitude longer than themore » averaged phonon mean-free path in BaTiO 3. On longer length scales, diffusive phonon transport dominates the recovery of the transient strain response, largely due to heat conduction into the substrate. The measured real-space phonon transport can be directly compared with the phonon mean-free path as predicted by molecular dynamics modeling. In conclusion, this time-resolved real-space visualization of THz-matter interactions opens up opportunities to engineer and image nanoscale transient structural states with new functionalities.« less

Computational design of intrinsic molecular rectifiers based on asymmetric functionalization of N-phenylbenzamide

DOE PAGES

Ding, Wendu; Koepf, Matthieu; Koenigsmann, Christopher; ...

2015-11-03

Here, we report a systematic computational search of molecular frameworks for intrinsic rectification of electron transport. The screening of molecular rectifiers includes 52 molecules and conformers spanning over 9 series of structural motifs. N-Phenylbenzamide is found to be a promising framework with both suitable conductance and rectification properties. A targeted screening performed on 30 additional derivatives and conformers of N-phenylbenzamide yielded enhanced rectification based on asymmetric functionalization. We demonstrate that electron-donating substituent groups that maintain an asymmetric distribution of charge in the dominant transport channel (e.g., HOMO) enhance rectification by raising the channel closer to the Fermi level. These findingsmore » are particularly valuable for the design of molecular assemblies that could ensure directionality of electron transport in a wide range of applications, from molecular electronics to catalytic reactions.« less

Thermal transport in binary colloidal glasses: Composition dependence and percolation assessment

NASA Astrophysics Data System (ADS)

Ruckdeschel, Pia; Philipp, Alexandra; Kopera, Bernd A. F.; Bitterlich, Flora; Dulle, Martin; Pech-May, Nelson W.; Retsch, Markus

2018-02-01

The combination of various types of materials is often used to create superior composites that outperform the pure phase components. For any rational design, the thermal conductivity of the composite as a function of the volume fraction of the filler component needs to be known. When approaching the nanoscale, the homogeneous mixture of various components poses an additional challenge. Here, we investigate binary nanocomposite materials based on polymer latex beads and hollow silica nanoparticles. These form randomly mixed colloidal glasses on a sub-μ m scale. We focus on the heat transport properties through such binary assembly structures. The thermal conductivity can be well described by the effective medium theory. However, film formation of the soft polymer component leads to phase segregation and a mismatch between existing mixing models. We confirm our experimental data by finite element modeling. This additionally allowed us to assess the onset of thermal transport percolation in such random particulate structures. Our study contributes to a better understanding of thermal transport through heterostructured particulate assemblies.

Be together, not the same: Spatiotemporal organization of different cilia types generates distinct transport functions

NASA Astrophysics Data System (ADS)

Nawroth, Janna; Guo, Hanliang; Ruby, Edward; Dabiri, John; McFall-Ngai, Margaret; Kanso, Eva

2016-11-01

Motile cilia are microscopic, hair-like structures on the cell surface that can sense and propel the extracellular fluid environment. Cilia are often thought to be limited to stereotypic morphologies, beat kinematics and non-discriminatory clearance functions, but we find that the spatiotemporal organization of different cilia types and beat behaviors can generate complex flow patterns and transport functions. Here, we present a case study in the Hawaiian bobtail squid where collective ciliary activity and resulting flow fields help recruit symbiont bacteria to the animal host. In particular, we demonstrate empirically and computationally how the squid's internal cilia act like a microfluidic device that actively filters the water for potential bacterial candidates and also provides a sheltered zone allowing for accumulation of mucus and bacteria into a biofilm. Moreover, in this sheltered zone, different cilia-driven flows enhance diffusion of biochemical signals, which could accelerate specific bacteria-host recognition. These results suggest that studying cilia activity on the population level might reveal a diverse range of biological transport and sensing functions. Moreover, understanding cilia as functional building blocks could inspire the design of ciliated robots and devices.

Comparative Study of Exchange-Correlation Functional and Potential for Evaluating Thermoelectric Transport Properties in d0 Perovskite Oxides

NASA Astrophysics Data System (ADS)

Ohkubo, Isao; Mori, Takao

2017-07-01

The influence of two different types of exchange-correlation functional/potential, namely, the generalized gradient approximation Perdew-Burke-Ernzerhof (GGA-PBE) functional and the modified Becke-Johnson (mBJ) potential, on the thermoelectric transport properties of d0 perovskite oxides (SrTiO3 and KTaO3) was investigated. The reduction of band dispersion induced by the mBJ scheme allows the improved prediction of band gap values by thelocal density approximation (LDA) and GGA, which increases the resolution of the increases in the density of states (DOS), carrier concentration, and effective mass near the conduction band edge. A comparison of the experimental effective mass values of d0 perovskite oxides shows that the effective mass values provided by the mBJ potential are similar to those provided by the GGA-PBE functional. Comparative analysis of the data obtained from Boltzmann theory calculations using the electronic structures determined with the GGA-PBE functional and the mBJ potential shows a difference in the transport coefficients owing to the increases in the DOS, carrier concentration, and effective mass induced by the mBJ scheme.

Intracellular transport and compartmentation of phosphate in plants.

PubMed

Versaw, Wayne K; Garcia, L Rene

2017-10-01

Phosphate (Pi) is an essential macronutrient with structural and metabolic roles within every compartment of the plant cell. Intracellular Pi transporters direct Pi to each organelle and also control its exchange between subcellular compartments thereby providing the means to coordinate compartmented metabolic processes, including glycolysis, photosynthesis, and respiration. In this review we summarize recent advances in the identification and functional analysis of Pi transporters that localize to vacuoles, chloroplasts, non-photosynthetic plastids, mitochondria, and the Golgi apparatus. Electrical potentials across intracellular membranes and the pH of subcellular environments will also be highlighted as key factors influencing the energetics of Pi transport, and therefore pose limits for Pi compartmentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Zn(2+) site engineering at the oligomeric interface of the dopamine transporter.

PubMed

Norgaard-Nielsen, Kristine; Norregaard, Lene; Hastrup, Hanne; Javitch, Jonathan A; Gether, Ulrik

2002-07-31

Increasing evidence suggests that Na(+)/Cl(-)-dependent neurotransmitter transporters exist as homo-oligomeric proteins. However, the functional implication of this oligomerization remains unclear. Here we demonstrate the engineering of a Zn(2+) binding site at the predicted dimeric interface of the dopamine transporter (DAT) corresponding to the external end of transmembrane segment 6. Upon binding to this site, which involves a histidine inserted in position 310 (V310H) and the endogenous Cys306 within the same DAT molecule, Zn(2+) potently inhibits [(3)H]dopamine uptake. These data provide indirect evidence that conformational changes critical for the translocation process may occur at the interface between two transporter molecules in the oligomeric structure.

Tuning the conductivity along atomic chains by selective chemisorption

NASA Astrophysics Data System (ADS)

Edler, F.; Miccoli, I.; Stöckmann, J. P.; Pfnür, H.; Braun, C.; Neufeld, S.; Sanna, S.; Schmidt, W. G.; Tegenkamp, C.

2017-03-01

Adsorption of Au on vicinal Si(111) surfaces results in growth of long-range ordered metallic quantum wires. In this paper, we utilized site-specific and selective adsorption of oxygen to modify chemically the transport via different channels in the systems Si(553)-Au and Si(557)-Au. They were analyzed by electron diffraction and four-tip STM-based transport experiments. Modeling of the adsorption process by density functional theory shows that the adatoms and rest atoms on Si(557)-Au provide energetically favored adsorption sites, which predominantly alter the transport along the wire direction. Since this structural motif is missing on Si(553)-Au, the transport channels remain almost unaffected by oxidation.

Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs.

PubMed

Nies, Anne T; Damme, Katja; Schaeffeler, Elke; Schwab, Matthias

2012-12-01

Antimicrobial drugs are essential in the treatment of infectious diseases. A better understanding of transport processes involved in drug disposition will improve the predictability of drug-drug interactions with consequences for drug response. Multidrug And Toxin Extrusion (MATE; SLC47A) proteins are efflux transporters mediating the excretion of several antimicrobial drugs as well as other organic compounds into bile and urine, thereby contributing to drug disposition. This review summarizes current knowledge of the structural and molecular features of human MATE transporters including their functional role in drug transport with a specific focus on antimicrobial drugs. The PubMed database was searched using the terms "MATE1," "MATE-2K," "MATE2," "SLC47A1," "SLC47A2," and "toxin extrusion protein" (up to June 2012). MATE proteins have been recognized as important transporters mediating the final excretion step of cationic drugs into bile and urine. These include the antiviral drugs acyclovir, amprenavir, and ganciclovir, the antibiotics cephalexin, cephradine and levofloxacin, as well as the antimalarial agents chloroquine and quinine. It is therefore important to enhance our understanding of the role of MATEs in drug extrusion with particular emphasis on the functional consequences of genetic variants on disposition of these antimicrobial drugs.

CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication.

PubMed

Dettmer, Jan; Ursache, Robertas; Campilho, Ana; Miyashima, Shunsuke; Belevich, Ilya; O'Regan, Seana; Mullendore, Daniel Leroy; Yadav, Shri Ram; Lanz, Christa; Beverina, Luca; Papagni, Antonio; Schneeberger, Korbinian; Weigel, Detlef; Stierhof, York-Dieter; Moritz, Thomas; Knoblauch, Michael; Jokitalo, Eija; Helariutta, Ykä

2014-07-10

Phloem, a plant tissue responsible for long-distance molecular transport, harbours specific junctions, sieve areas, between the conducting cells. To date, little is known about the molecular framework related to the biogenesis of these sieve areas. Here we identify mutations at the CHER1/AtCTL1 locus of Arabidopsis thaliana. The mutations cause several phenotypic abnormalities, including reduced pore density and altered pore structure in the sieve areas associated with impaired phloem function. CHER1 encodes a member of a poorly characterized choline transporter-like protein family in plants and animals. We show that CHER1 facilitates choline transport, localizes to the trans-Golgi network, and during cytokinesis is associated with the phragmoplast. Consistent with its function in the elaboration of the sieve areas, CHER1 has a sustained, polar localization in the forming sieve plates. Our results indicate that the regulation of choline levels is crucial for phloem development and conductivity in plants.

Multiple functions of the crustacean gill: osmotic/ionic regulation, acid-base balance, ammonia excretion, and bioaccumulation of toxic metals

PubMed Central

Henry, Raymond P.; Lucu, Čedomil; Onken, Horst; Weihrauch, Dirk

2012-01-01

The crustacean gill is a multi-functional organ, and it is the site of a number of physiological processes, including ion transport, which is the basis for hemolymph osmoregulation; acid-base balance; and ammonia excretion. The gill is also the site by which many toxic metals are taken up by aquatic crustaceans, and thus it plays an important role in the toxicology of these species. This review provides a comprehensive overview of the ecology, physiology, biochemistry, and molecular biology of the mechanisms of osmotic and ionic regulation performed by the gill. The current concepts of the mechanisms of ion transport, the structural, biochemical, and molecular bases of systemic physiology, and the history of their development are discussed. The relationship between branchial ion transport and hemolymph acid-base regulation is also treated. In addition, the mechanisms of ammonia transport and excretion across the gill are discussed. And finally, the toxicology of heavy metal accumulation via the gill is reviewed in detail. PMID:23162474

Surface Connectivity and Interocean Exchanges From Drifter-Based Transition Matrices

NASA Astrophysics Data System (ADS)

McAdam, Ronan; van Sebille, Erik

2018-01-01

Global surface transport in the ocean can be represented by using the observed trajectories of drifters to calculate probability distribution functions. The oceanographic applications of the Markov Chain approach to modeling include tracking of floating debris and water masses, globally and on yearly-to-centennial time scales. Here we analyze the error inherent with mapping trajectories onto a grid and the consequences for ocean transport modeling and detection of accumulation structures. A sensitivity analysis of Markov Chain parameters is performed in an idealized Stommel gyre and western boundary current as well as with observed ocean drifters, complementing previous studies on widespread floating debris accumulation. Focusing on two key areas of interocean exchange—the Agulhas system and the North Atlantic intergyre transport barrier—we assess the capacity of the Markov Chain methodology to detect surface connectivity and dynamic transport barriers. Finally, we extend the methodology's functionality to separate the geostrophic and nongeostrophic contributions to interocean exchange in these key regions.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Calculation of effective transport properties of partially saturated gas diffusion layers

NASA Astrophysics Data System (ADS)

Bednarek, Tomasz; Tsotridis, Georgios

2017-02-01

A large number of currently available Computational Fluid Dynamics numerical models of Polymer Electrolyte Membrane Fuel Cells (PEMFC) are based on the assumption that porous structures are mainly considered as thin and homogenous layers, hence the mass transport equations in structures such as Gas Diffusion Layers (GDL) are usually modelled according to the Darcy assumptions. Application of homogenous models implies that the effects of porous structures are taken into consideration via the effective transport properties of porosity, tortuosity, permeability (or flow resistance), diffusivity, electric and thermal conductivity. Therefore, reliable values of those effective properties of GDL play a significant role for PEMFC modelling when employing Computational Fluid Dynamics, since these parameters are required as input values for performing the numerical calculations. The objective of the current study is to calculate the effective transport properties of GDL, namely gas permeability, diffusivity and thermal conductivity, as a function of liquid water saturation by using the Lattice-Boltzmann approach. The study proposes a method of uniform water impregnation of the GDL based on the "Fine-Mist" assumption by taking into account the surface tension of water droplets and the actual shape of GDL pores.

Spatially and temporally resolved exciton dynamics and transport in single nanostructures and assemblies

NASA Astrophysics Data System (ADS)

Huang, Libai

2015-03-01

The frontier in solar energy conversion now lies in learning how to integrate functional entities across multiple length scales to create optimal devices. To address this new frontier, I will discuss our recent efforts on elucidating multi-scale energy transfer, migration, and dissipation processes with simultaneous femtosecond temporal resolution and nanometer spatial resolution. We have developed ultrafast microscopy that combines ultrafast spectroscopy with optical microscopy to map exciton dynamics and transport with simultaneous ultrafast time resolution and diffraction-limited spatial resolution. We have employed pump-probe transient absorption microscopy to elucidate morphology and structure dependent exciton dynamics and transport in single nanostructures and molecular assemblies. More specifically, (1) We have applied transient absorption microscopy (TAM) to probe environmental and structure dependent exciton relaxation pathways in sing-walled carbon nanotubes (SWNTs) by mapping dynamics in individual pristine SWNTs with known structures. (2) We have systematically measured and modeled the optical properties of the Frenkel excitons in self-assembled porphyrin tubular aggregates that represent an analog to natural photosynthetic antennae. Using a combination of ultrafast optical microscopy and stochastic exciton modeling, we address exciton transport and relaxation pathways, especially those related to disorder.

Simulating the Effect of Contact Atomic Structure on the Spin-Dependent Transport Properties of Gold Nanowires

NASA Astrophysics Data System (ADS)

Ansarino, Masoud; Ravan, Bahram Abedi

Some experimental research works report on the superb magnetoresistance properties of magnetically contacted gold nanowires. With the intention of trying to understand the spin-dependent transport mechanism of these structures, in this work we have used first-principles density functional theory methods to investigate effects of interface structure on the spintronic characteristics of Au nanowires. Monatomic chains of gold are sandwiched between two ferromagnetic electrodes of Fe and by substituting the interfacial Fe atoms with some other transition metal elements (including Cr, Mn, Co and Ni) the occurrence of possible enhancement in the electronic conductance and magnetoresistance characteristics of the device are investigated. It is observed that replacing the interfacial atoms with Ni raises the junction’s magnetoresistance ratio to as high as 2000%.

Disorder-assisted quantum transport in suboptimal decoherence regimes

PubMed Central

Novo, Leonardo; Mohseni, Masoud; Omar, Yasser

2016-01-01

We investigate quantum transport in binary tree structures and in hypercubes for the disordered Frenkel-exciton Hamiltonian under pure dephasing noise. We compute the energy transport efficiency as a function of disorder and dephasing rates. We demonstrate that dephasing improves transport efficiency not only in the disordered case, but also in the ordered one. The maximal transport efficiency is obtained when the dephasing timescale matches the hopping timescale, which represent new examples of the Goldilocks principle at the quantum scale. Remarkably, we find that in weak dephasing regimes, away from optimal levels of environmental fluctuations, the average effect of increasing disorder is to improve the transport efficiency until an optimal value for disorder is reached. Our results suggest that rational design of the site energies statistical distributions could lead to better performances in transport systems at nanoscale when their natural environments are far from the optimal dephasing regime. PMID:26726133

A Sponge-like Structure Involved in the Association and Transport of Maternal Products during Drosophila Oogenesis

PubMed Central

Wilsch-Bräuninger, Michaela; Schwarz, Heinz; Nüsslein-Volhard, Christiane

1997-01-01

Localization of maternally provided RNAs during oogenesis is required for formation of the antero–posterior axis of the Drosophila embryo. Here we describe a subcellular structure in nurse cells and oocytes which may function as an intracellular compartment for assembly and transport of maternal products involved in RNA localization. This structure, which we have termed “sponge body,” consists of ER-like cisternae, embedded in an amorphous electron-dense mass. It lacks a surrounding membrane and is frequently associated with mitochondria. The sponge bodies are not identical to the Golgi complexes. We suggest that the sponge bodies are homologous to the mitochondrial cloud in Xenopus oocytes, a granulo-fibrillar structure that contains RNAs involved in patterning of the embryo. Exuperantia protein, the earliest factor known to be required for the localization of bicoid mRNA to the anterior pole of the Drosophila oocyte, is highly enriched in the sponge bodies but not an essential structural component of these. RNA staining indicates that sponge bodies contain RNA. However, neither the intensity of this staining nor the accumulation of Exuperantia in the sponge bodies is dependent on the amount of bicoid mRNA present in the ovaries. Sponge bodies surround nuage, a possible polar granule precursor. Microtubules and microfilaments are not present in sponge bodies, although transport of the sponge bodies through the cells is implied by their presence in cytoplasmic bridges. We propose that the sponge bodies are structures that, by assembly and transport of included molecules or associated structures, are involved in localization of mRNAs in Drosophila oocytes. PMID:9348297

Complex band structure and electronic transmission eigenchannels

NASA Astrophysics Data System (ADS)

Jensen, Anders; Strange, Mikkel; Smidstrup, Søren; Stokbro, Kurt; Solomon, Gemma C.; Reuter, Matthew G.

2017-12-01

It is natural to characterize materials in transport junctions by their conductance length dependence, β. Theoretical estimations of β are made employing two primary theories: complex band structure and density functional theory (DFT) Landauer transport. It has previously been shown that the β value derived from total Landauer transmission can be related to the β value from the smallest |ki| complex band; however, it is an open question whether there is a deeper relationship between the two. Here we probe the details of the relationship between transmission and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two molecular junctions. The molecular junctions show that both the length dependence of the total transmission and the individual transmission eigenvalues can be, almost always, found through the complex band structure. The complex band structure of the semi-conducting material, however, does not predict the length dependence of the total transmission but only of the individual channels, at some k-points, due to multiple channels contributing to transmission. We also observe instances of vertical bands, some of which are the smallest |ki| complex bands, that do not contribute to transport. By understanding the deeper relationship between complex bands and individual transmission eigenchannels, we can make a general statement about when the previously accepted wisdom linking transmission and complex band structure will fail, namely, when multiple channels contribute significantly to the transmission.

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

PubMed Central

Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel; McMahon, Katherine D; Stepanauskas, Ramunas; Andersson, Siv G E; Bertilsson, Stefan

2014-01-01

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. PMID:24118837

The BCCT family of carriers: from physiology to crystal structure.

PubMed

Ziegler, Christine; Bremer, Erhard; Krämer, Reinhard

2010-10-01

Increases in the environmental osmolarity are key determinants for the growth of microorganisms. To ensure a physiologically acceptable level of cellular hydration and turgor at high osmolarity, many bacteria accumulate compatible solutes. Osmotically controlled uptake systems allow the scavenging of these compounds from scarce environmental sources as effective osmoprotectants. A number of these systems belong to the BCCT family (betaine-choline-carnitine-transporter), sodium- or proton-coupled transporters (e.g. BetP and BetT respectively) that are ubiquitous in microorganisms. The BCCT family also contains CaiT, an L-carnitine/γ-butyrobetaine antiporter that is not involved in osmotic stress responses. The glycine betaine transporter BetP from Corynebacterium glutamicum is a representative for osmoregulated symporters of the BCCT family and functions both as an osmosensor and osmoregulator. The crystal structure of BetP in an occluded conformation in complex with its substrate glycine betaine and two crystal structures of CaiT in an inward-facing open conformation in complex with L-carnitine and γ-butyrobetaine were reported recently. These structures and the wealth of biochemical data on the activity control of BetP in response to osmotic stress enable a correlation between the sensing of osmotic stress by a transporter protein with the ensuing regulation of transport activity. Molecular determinants governing the high-affinity binding of the compatible solutes by BetP and CaiT, the coupling in symporters and antiporters, and the osmoregulatory properties are discussed in detail for BetP and various BCCT carriers. © 2010 Blackwell Publishing Ltd.

Structure-Function of the Cytochrome b 6f Complex of Oxygenic Photosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cramer, W. A.; Yamashita, E.; Baniulis, D.

2014-03-20

Structure–function of the major integral membrane cytochrome b 6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH 2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groupsmore » embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (c n) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes b p, b n, c n) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H + to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme c n and the connection of the n-side of the membrane and b 6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc 1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH 2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.« less

[The ABC transporters of Saccharomyces cerevisiae].

PubMed

Wawrzycka, Donata

2011-01-01

The ABC transporters (ATP Binding Cassette) compose one of the bigest protein family with the great medical, industrial and economical impact. They are found in all organism from bacteria to man. ABC proteins are responsible for resistance of microorganism to antibiotics and fungicides and multidrug resistance of cancer cells. Mutations in ABC transporters genes cause seriuos deseases like cystic fibrosis, adrenoleucodystrophy or ataxia. Transport catalized by ABC proteins is charged with energy from the ATP hydrolysis. The ABC superfamily contains transporters, canals, receptors. Analysis of the Saccharomyces cerevisiae genome allowed to distinguish 30 potential ABC proteins which are classified into 6 subfamilies. The structural and functional similarity of the yeast and human ABC proteins allowes to use the S. cerevisiae as a model organism for ABC transporters characterisation. In this work the present state of knowleadge on yeast S. cerevisiae ABC proteins was summarised.

Seasonal trends in photosynthesis and electron transport during the Mediterranean summer drought in leaves of deciduous oaks.

PubMed

Osuna, Jessica L; Baldocchi, Dennis D; Kobayashi, Hideki; Dawson, Todd E

2015-05-01

The California Mediterranean savanna has harsh summer conditions with minimal soil moisture, high temperature, high incoming solar radiation and little or no precipitation. Deciduous blue oaks, Quercus douglasii Hook. and Arn., are winter-deciduous obligate phreatophytes, transpiring mostly groundwater throughout the summer drought. The objective of this work is to fully characterize the seasonal trends of photosynthesis in blue oaks as well as the mechanistic relationships between leaf structure and function. We estimate radiative load of the leaves via the FLiES model and perform in situ measurements of leaf water potential, leaf nitrogen content, an index of chlorophyll content (SPAD readings), photosynthetic and electron transport capacity, and instantaneous rates of CO2 assimilation and electron transport. We measured multiple trees over 3 years providing data from a range of conditions. Our study included one individual that demonstrated strong drought stress as indicated by changes in SPAD readings, leaf nitrogen and all measures of leaf functioning. In the year following severe environmental stress, one individual altered foliation patterns on the crown but did not die. In all other individuals, we found that net carbon assimilation and photosynthetic capacity decreased during the summer drought. SPAD values, electron transport rate (ETR) and quantum yield of photosystem II (PSII) did not show a strong decrease during the summer drought. In most individuals, PSII activity and SPAD readings did not indicate leaf structural or functional damage throughout the season. While net carbon assimilation was tightly coupled to stomatal conductance, the coupling was not as tight with ETR possibly due to contributions from photorespiration or other protective processes. Our work demonstrates that the blue oaks avoid structural damage by maintaining the capacity to convert and dissipate incoming solar radiation during the hot summer drought and are effective at fixing carbon by maximizing rates during the mild spring conditions. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Diverse carrier mobility of monolayer BNC_x: A combined density functional theory and Boltzmann transport theory study.

PubMed

Wu, Tao; Deng, Kaiming; Deng, Wei-Qiao; Lu, Ruifeng

2017-09-19

BNCX monolayer as a kind of two-dimensional material has numerous chemical atomic ratios and arrangements with different electronic structures. Via calculations on the basis of density functional theory and Boltzmann transport theory under deformation potential approximation, the band structures and carrier mobilities of BNCX (x=1,2,3,4) nanosheets are systematically investigated. The calculated results show that BNC2-1 is a material with very small band gap (0.02 eV) among all the structures while other BNCX monolayers are semiconductors with band gap ranging from 0.51 to 1.32 eV. The carrier mobility of BNCX varies considerably from tens to millions of cm2 V-1 s-1. For BNC2-1, the hole mobility and electron mobility along both x and y directions can reach 105 orders of magnitude, which is similar to the carrier mobility of graphene. Besides, all studied BNCX monolayers obviously have anisotropic hole mobility and electron mobility. In particular, for semiconductor BNC4, its hole mobility along y direction and electron mobility along x direction unexpectedly reach 106 orders of magnitude, even higher than that of graphene. Our findings suggest that BNCX layered materials with proper ratio and arrangement of carbon atoms will possess desirable charge transport properties, exhibiting potential applications in nanoelectronic devices. © 2017 IOP Publishing Ltd.

Evolutionary Descent of Prion Genes from the ZIP Family of Metal Ion Transporters

PubMed Central

Schmitt-Ulms, Gerold; Ehsani, Sepehr; Watts, Joel C.; Westaway, David; Wille, Holger

2009-01-01

In the more than twenty years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into a possible function of PrP may be obtained through the characterization of its molecular neighborhood in cells. Quantitative interactome data demonstrated the spatial proximity of two metal ion transporters of the ZIP family, ZIP6 and ZIP10, to mammalian prion proteins in vivo. A subsequent bioinformatic analysis revealed the unexpected presence of a PrP-like amino acid sequence within the N-terminal, extracellular domain of a distinct sub-branch of the ZIP protein family that includes ZIP5, ZIP6 and ZIP10. Additional structural threading and orthologous sequence alignment analyses argued that the prion gene family is phylogenetically derived from a ZIP-like ancestral molecule. The level of sequence homology and the presence of prion protein genes in most chordate species place the split from the ZIP-like ancestor gene at the base of the chordate lineage. This relationship explains structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The phylogenetic and spatial connection to ZIP proteins is expected to open new avenues of research to elucidate the biology of the prion protein in health and disease. PMID:19784368

Generalisation and specialisation in hoverfly (Syrphidae) grassland pollen transport networks revealed by DNA metabarcoding.

PubMed

Lucas, Andrew; Bodger, Owen; Brosi, Berry J; Ford, Col R; Forman, Dan W; Greig, Carolyn; Hegarty, Matthew; Neyland, Penelope J; de Vere, Natasha

2018-04-16

Pollination by insects is a key ecosystem service and important to wider ecosystem function. Most species-level pollination networks studied have a generalised structure, with plants having several potential pollinators, and pollinators in turn visiting a number of different plant species. This is in apparent contrast to a plant's need for efficient conspecific pollen transfer. The aim of this study was to investigate the structure of pollen transport networks at three levels of biological hierarchy: community, species and individual. We did this using hoverflies in the genus Eristalis, a key group of non-Hymenopteran pollinators. We constructed pollen transport networks using DNA metabarcoding to identify pollen. We captured hoverflies in conservation grasslands in west Wales, UK, removed external pollen loads, sequenced the pollen DNA on the Illumina MiSeq platform using the standard plant barcode rbcL, and matched sequences using a pre-existing plant DNA barcode reference library. We found that Eristalis hoverflies transport pollen from 65 plant taxa, more than previously appreciated. Networks were generalised at the site and species level, suggesting some degree of functional redundancy, and were more generalised in late summer compared to early summer. In contrast, pollen transport at the individual level showed some degree of specialisation. Hoverflies defined as "single-plant visitors" varied from 40% of those captured in early summer to 24% in late summer. Individual hoverflies became more generalised in late summer, possibly in response to an increase in floral resources. Rubus fruticosus agg. and Succisa pratensis were key plant species for hoverflies at our sites Our results contribute to resolving the apparent paradox of how generalised pollinator networks can provide efficient pollination to plant species. Generalised hoverfly pollen transport networks may result from a varied range of short-term specialised feeding bouts by individual insects. The generalisation and functional redundancy of Eristalis pollen transport networks may increase the stability of the pollination service they deliver. © 2018 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

1995-01-01

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

Electrophysiological characterization of the archaeal transporter NCX_Mj using solid supported membrane technology

PubMed Central

Barthmes, Maria; Liao, Jun; Jiang, Youxing; Brüggemann, Andrea

2016-01-01

Sodium–calcium exchangers (NCXs) are membrane transporters that play an important role in Ca2+ homeostasis and Ca2+ signaling. The recent crystal structure of NCX_Mj, a member of the NCX family from the archaebacterium Methanococcus jannaschii, provided insight into the atomistic details of sodium–calcium exchange. Here, we extend these findings by providing detailed functional data on purified NCX_Mj using solid supported membrane (SSM)–based electrophysiology, a powerful but unexploited tool for functional studies of electrogenic transporter proteins. We show that NCX_Mj is highly selective for Na+, whereas Ca2+ can be replaced by Mg2+ and Sr2+ and that NCX_Mj can be inhibited by divalent ions, particularly Cd2+. By directly comparing the apparent affinities of Na+ and Ca2+ for NCX_Mj with those for human NCX1, we show excellent agreement, indicating a strong functional similarity between NCX_Mj and its eukaryotic isoforms. We also provide detailed instructions to facilitate the adaption of this method to other electrogenic transporter proteins. Our findings demonstrate that NCX_Mj can serve as a model for the NCX family and highlight several possible applications for SSM-based electrophysiology. PMID:27241699

Transport activity and presence of ClC-7/Ostm1 complex account for different cellular functions.

PubMed

Weinert, Stefanie; Jabs, Sabrina; Hohensee, Svea; Chan, Wing Lee; Kornak, Uwe; Jentsch, Thomas J

2014-07-01

Loss of the lysosomal ClC-7/Ostm1 2Cl(-)/H(+) exchanger causes lysosomal storage disease and osteopetrosis in humans and additionally changes fur colour in mice. Its conversion into a Cl(-) conductance in Clcn7(unc/unc) mice entails similarly severe lysosomal storage, but less severe osteopetrosis and no change in fur colour. To elucidate the basis for these phenotypical differences, we generated Clcn7(td/td) mice expressing an ion transport-deficient mutant. Their osteopetrosis was as severe as in Clcn7(-/-) mice, suggesting that the electric shunt provided by ClC-7(unc) can partially rescue osteoclast function. The normal coat colour of Clcn7(td/td) mice and their less severe neurodegeneration suggested that the ClC-7 protein, even when lacking measurable ion transport activity, is sufficient for hair pigmentation and that the conductance of ClC-7(unc) is harmful for neurons. Our in vivo structure-function analysis of ClC-7 reveals that both protein-protein interactions and ion transport must be considered in the pathogenesis of ClC-7-related diseases. © 2014 The Authors.

Zinc transporters and dysregulated channels in cancers

PubMed Central

Pan, Zui; Choi, Sangyong; Ouadid-Ahidouch, Halima; Yang, Jin-Ming; Beattie, John H.; Korichneva, Irina

2016-01-01

As a nutritionally essential metal ion, zinc (Zn) not only constitutes a structural element for more than 3000 proteins but also plays important regulatory functions in cellular signal transduction. Zn homeostasis is tightly controlled by regulating the flux of Zn across cell membranes through specific transporters, i.e. ZnT and ZIP family proteins. Zn deficiency and malfunction of Zn transporters have been associated with many chronic diseases including cancer. However, the mechanisms underlying Zn regulatory functions in cellular signaling and their impact on the pathogenesis and progression of cancers remain largely unknown. In addition to these acknowledged multifunctions, Zn modulates a wide range of ion channels that in turn may also play an important role in cancer biology. The goal of this review is to propose how zinc deficiency, through modified Zn homeostasis, transporter activity and the putative regulatory function of Zn can influence ion channel activity, and thereby contribute to carcinogenesis and tumorigenesis. This review intends to stimulate interest in, and support for research into the understanding of Zn-modulated channels in cancers, and to search for novel biomarkers facilitating effective clinical stratification of high risk cancer patients as well as improved prevention and therapy in this emerging field. PMID:27814637

1997 economic census : transportation 1997 commodity flow survey : United States

DOT National Transportation Integrated Search

1999-12-01

The 1997 Commodity Flow Survey is part of the 1997 Economic Census. The economic census is the major source of facts about the structure and functioning of the Nation's economy. It provides essential information for government, business, industry, an...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

21 CFR 99.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the purpose of affecting any structure or function of the body; (2) Amounts paid for transportation... AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL DISSEMINATION OF INFORMATION... clinical investigation is an investigation in humans that tests a specific clinical hypothesis. (c) Group...

Structuring Education for Business Management.

ERIC Educational Resources Information Center

Whitt, Robert L.

Studies of school district organization generally include an examination of enrollments, average daily attendance, assessed valuation, potential and predicted growth rate, bonded indebtedness, school district boundaries, transportation, special services, and other factors, but little concern or attention is given to the business functions because…

Phloem unloading follows an extensive apoplasmic pathway in cucumber (Cucumis sativus L.) fruit from anthesis to marketable maturing stage.

PubMed

Hu, Liping; Sun, Huihui; Li, Ruifu; Zhang, Lingyun; Wang, Shaohui; Sui, Xiaolei; Zhang, Zhenxian

2011-11-01

The phloem unloading pathway remains unclear in fruits of Cucurbitaceae, a classical stachyose-transporting species with bicollateral phloem. Using a combination of electron microscopy, transport of phloem-mobile symplasmic tracer carboxyfluorescein, assays of acid invertase and sucrose transporter, and [(14)C]sugar uptake, the phloem unloading pathway was studied in cucumber (Cucumis sativus) fruit from anthesis to the marketable maturing stage. Structural investigations showed that the sieve element-companion cell (SE-CC) complex of the vascular bundles feeding fruit flesh is apparently symplasmically restricted. Imaging of carboxyfluorescein unloading showed that the dye remained confined to the phloem strands of the vascular bundles in the whole fruit throughout the stages examined. A 37 kDa acid invertase was located predominantly in the cell walls of SE-CC complexes and parenchyma cells. Studies of [(14)C]sugar uptake suggested that energy-driven transporters may be functional in sugar trans-membrane transport within symplasmically restricted SE-CC complex, which was further confirmed by the existence of a functional plasma membrane sucrose transporter (CsSUT4) in cucumber fruit. These data provide a clear evidence for an apoplasmic phloem unloading pathway in cucumber fruit. A presumption that putative raffinose or stachyose transporters may be involved in soluble sugars unloading was discussed. © 2011 Blackwell Publishing Ltd.

Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK

NASA Astrophysics Data System (ADS)

Fukuda, Masahiro; Takeda, Hironori; Kato, Hideaki E.; Doki, Shintaro; Ito, Koichi; Maturana, Andrés D.; Ishitani, Ryuichiro; Nureki, Osamu

2015-05-01

NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous studies provided insight into the overall structure and the substrate recognition of NarK, its molecular mechanism, including the driving force for nitrate transport, remained elusive. Here we demonstrate that NarK is a nitrate/nitrite antiporter, using an in vitro reconstituted system. Furthermore, we present the high-resolution crystal structures of NarK from Escherichia coli in the nitrate-bound occluded, nitrate-bound inward-open and apo inward-open states. The integrated structural, functional and computational analyses reveal the nitrate/nitrite antiport mechanism of NarK, in which substrate recognition is coupled to the transport cycle by the concomitant movement of the transmembrane helices and the key tyrosine and arginine residues in the substrate-binding site.

Overview and introduction: The blood–brain barrier in health and disease

PubMed Central

Abbott, N. Joan; Friedman, Alon

2013-01-01

Summary This article introduces the special issue on “Blood–Brain Barrier and Epilepsy.” We review briefly current understanding of the structure and function of the blood–brain barrier (BBB), including its development and normal physiology, and ways in which it can be affected in pathology. The BBB formed by the endothelium of cerebral blood vessels is one of three main barrier sites protecting the central nervous system (CNS). The barrier is not a rigid structure, but a dynamic interface with a range of interrelated functions, resulting from extremely effective tight junctions, transendothelial transport systems, enzymes, and regulation of leukocyte permeation, which thereby generates the physical, transport, enzymatic, and immune regulatory functions of the BBB. The brain endothelial cells are important components of a “modular” structure, the neurovascular unit (NVU), with several associated cell types and extracellular matrix components. Modern methods have helped in identifying a range of proteins involved in barrier structure and function, and recent studies have revealed important stages, cell types, and signaling pathways important in BBB development. There is a growing list of CNS pathologies showing BBB dysfunction, with strong evidence that this can play a major role in certain disease etiologies. The articles that follow in this issue summarize in more detail reports and discussions of the recent international meeting on “BBB in Neurological Dysfunctions,” which took place recently at Ben-Gurion University of the Negev Desert Campus (Beer-Sheva, Israel), focusing on the link between experimental and clinical studies, and the ways in which these lead to improved drug treatments. PMID:23134489

Breast cancer cell cyclooxygenase-2 expression alters extracellular matrix structure and function and numbers of cancer associated fibroblasts.

PubMed

Krishnamachary, Balaji; Stasinopoulos, Ioannis; Kakkad, Samata; Penet, Marie-France; Jacob, Desmond; Wildes, Flonne; Mironchik, Yelena; Pathak, Arvind P; Solaiyappan, Meiyappan; Bhujwalla, Zaver M

2017-03-14

Cyclooxygenase-2 (COX-2) is a critically important mediator of inflammation that significantly influences tumor angiogenesis, invasion, and metastasis. We investigated the role of COX-2 expressed by triple negative breast cancer cells in altering the structure and function of the extracellular matrix (ECM). COX-2 downregulation effects on ECM structure and function were investigated using magnetic resonance imaging (MRI) and second harmonic generation (SHG) microscopy of tumors derived from triple negative MDA-MB-231 breast cancer cells, and a derived clone stably expressing a short hairpin (shRNA) molecule downregulating COX-2. MRI of albumin-GdDTPA was used to characterize macromolecular fluid transport in vivo and SHG microscopy was used to quantify collagen 1 (Col1) fiber morphology. COX-2 downregulation decreased Col1 fiber density and altered macromolecular fluid transport. Immunohistochemistry identified significantly fewer activated cancer associated fibroblasts (CAFs) in low COX-2 expressing tumors. Metastatic lung nodules established by COX-2 downregulated cells were infrequent, smaller, and contained fewer Col1 fibers.COX-2 overexpression studies were performed with tumors derived from triple negative SUM-149 breast cancer cells lentivirally transduced to overexpress COX-2. SHG microscopy identified significantly higher Col1 fiber density in COX-2 overexpressing tumors with an increase of CAFs. These data expand upon the roles of COX-2 in shaping the structure and function of the ECM in primary and metastatic tumors, and identify the potential role of COX-2 in modifying the number of CAFs in tumors that may have contributed to the altered ECM.

HKT transporters mediate salt stress resistance in plants: from structure and function to the field.

PubMed

Hamamoto, Shin; Horie, Tomoaki; Hauser, Felix; Deinlein, Ulrich; Schroeder, Julian I; Uozumi, Nobuyuki

2015-04-01

Plant cells are sensitive to salinity stress and do not require sodium as an essential element for their growth and development. Saline soils reduce crop yields and limit available land. Research shows that HKT transporters provide a potent mechanism for mediating salt tolerance in plants. Knowledge of the molecular ion transport and regulation mechanisms and the control of HKT gene expression are crucial for understanding the mechanisms by which HKT transporters enhance crop performance under salinity stress. This review focuses on HKT transporters in monocot plants and in Arabidopsis as a dicot plant, as a guide to efforts toward improving salt tolerance of plants for increasing the production of crops and bioenergy feedstocks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Impact of the Topological Surface State on the Thermoelectric Transport in Sb2Te3 Thin Films.

PubMed

Hinsche, Nicki F; Zastrow, Sebastian; Gooth, Johannes; Pudewill, Laurens; Zierold, Robert; Rittweger, Florian; Rauch, Tomáš; Henk, Jürgen; Nielsch, Kornelius; Mertig, Ingrid

2015-04-28

Ab initio electronic structure calculations based on density functional theory and tight-binding methods for the thermoelectric properties of p-type Sb2Te3 films are presented. The thickness-dependent electrical conductivity and the thermopower are computed in the diffusive limit of transport based on the Boltzmann equation. Contributions of the bulk and the surface to the transport coefficients are separated, which enables to identify a clear impact of the topological surface state on the thermoelectric properties. When the charge carrier concentration is tuned, a crossover between a surface-state-dominant and a Fuchs-Sondheimer transport regime is achieved. The calculations are corroborated by thermoelectric transport measurements on Sb2Te3 films grown by atomic layer deposition.

Digestion and digestive-transport surfaces in cestodes and their fish hosts.

PubMed

Izvekova, G I; Kuperman, B I; Kuz'mina, V V

1997-12-01

The structural and functional organization of digestive-transport surfaces in some lower cestodes and their fish hosts was studied. It has been shown that the ultrastructure of cestode microtriches and fish enterocyte microvilli being the basis of membrane-linked digestion is quite similar. These organelles increase the digestive-transport surfaces both in helminths and fishes. However, the hydrolytic enzyme activity in helminths is usually 2-4 times lower than that of the fishes. Desorption (adsorption) characteristics of various hydrolases in helminths and fishes are also different. In helminths the easily desorbed fraction of each enzyme is always more abundant than in fishes. In contrast, the intensity of transport processes in helminths is higher when compared with fishes. The adaptation of digestive-transport surfaces and enzyme systems to feeding conditions is discussed.

Aquaporin structure-function relationships: water flow through plant living cells.

PubMed

Zhao, Chang-Xing; Shao, Hong-Bo; Chu, Li-Ye

2008-04-01

Plant aquaporins play an important role in water uptake and movement-an aquaporin that opens and closes a gate that regulates water movement in and out of cells. Some plant aquaporins also play an important role in response to water stress. Since their discovery, advancing knowledge of their structures and properties led to an understanding of the basic features of the water transport mechanism and increased illumination to water relations. Meanwhile, molecular and functional characterization of aquaporins has revealed the significance of their regulation in response to the adverse environments such as salinity and drought. This paper reviews the structure, species diversity, physiology function, regulation of plant aquaporins, and the relations between environmental factors and plant aquaporins. Complete understanding of aquaporin function and regulation is to integrate those mechanisms in time and space and to well regulate the permeation of water across biological membranes under changing environmental and developmental conditions.

Probing the conformation of a conserved glutamic acid within the Cl- pathway of a CLC H+/Cl- exchanger.

PubMed

Vien, Malvin; Basilio, Daniel; Leisle, Lilia; Accardi, Alessio

2017-04-03

The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Glu ex , can adopt three conformations and that the interconversion of its side chain between these states underlies H + /Cl - exchange. One of these states, in which Glu ex occupies the central binding site (S cen ) while Cl - ions fill the internal and external sites (S int and S ext ), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Glu ex trapped in S cen between two Cl - ions. Transport by CLC-ec1 is reduced when [Cl - ] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Glu ex in S cen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl - ] is abolished in the E148A mutant, in which the Glu ex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Glu ex can occupy S cen as well as the S ext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to S cen play a role in determining the equilibrium between these two conformations. © 2017 Vien et al.

Computational models for predicting interactions with membrane transporters.

PubMed

Xu, Y; Shen, Q; Liu, X; Lu, J; Li, S; Luo, C; Gong, L; Luo, X; Zheng, M; Jiang, H

2013-01-01

Membrane transporters, including two members: ATP-binding cassette (ABC) transporters and solute carrier (SLC) transporters are proteins that play important roles to facilitate molecules into and out of cells. Consequently, these transporters can be major determinants of the therapeutic efficacy, toxicity and pharmacokinetics of a variety of drugs. Considering the time and expense of bio-experiments taking, research should be driven by evaluation of efficacy and safety. Computational methods arise to be a complementary choice. In this article, we provide an overview of the contribution that computational methods made in transporters field in the past decades. At the beginning, we present a brief introduction about the structure and function of major members of two families in transporters. In the second part, we focus on widely used computational methods in different aspects of transporters research. In the absence of a high-resolution structure of most of transporters, homology modeling is a useful tool to interpret experimental data and potentially guide experimental studies. We summarize reported homology modeling in this review. Researches in computational methods cover major members of transporters and a variety of topics including the classification of substrates and/or inhibitors, prediction of protein-ligand interactions, constitution of binding pocket, phenotype of non-synonymous single-nucleotide polymorphisms, and the conformation analysis that try to explain the mechanism of action. As an example, one of the most important transporters P-gp is elaborated to explain the differences and advantages of various computational models. In the third part, the challenges of developing computational methods to get reliable prediction, as well as the potential future directions in transporter related modeling are discussed.

Mechanisms of sterol uptake and transport in yeast.

PubMed

Jacquier, Nicolas; Schneiter, Roger

2012-03-01

Sterols are essential lipid components of eukaryotic membranes. Here we summarize recent advances in understanding how sterols are transported between different membranes. Baker's yeast is a particularly attractive organism to dissect this lipid transport pathway, because cells can synthesize their own major sterol, ergosterol, in the membrane of the endoplasmic reticulum from where it is then transported to the plasma membrane. However, Saccharomyces cerevisiae is also a facultative anaerobic organism, which becomes sterol auxotroph in the absence of oxygen. Under these conditions, cells take up sterol from the environment and transport the lipid back into the membrane of the endoplasmic reticulum, where the free sterol becomes esterified and is then stored in lipid droplets. Steryl ester formation is thus a reliable readout to assess the back-transport of exogenously provided sterols from the plasma membrane to the endoplasmic reticulum. Structure/function analysis has revealed that the bulk membrane function of the fungal ergosterol can be provided by structurally related sterols, including the mammalian cholesterol. Foreign sterols, however, are subject to a lipid quality control cycle in which the sterol is reversibly acetylated. Because acetylated sterols are efficiently excreted from cells, the substrate specificity of the deacetylating enzymes determines which sterols are retained. Membrane-bound acetylated sterols are excreted by the secretory pathway, more soluble acetylated sterol derivatives such as the steroid precursor pregnenolone, on the other hand, are excreted by a pathway that is independent of vesicle formation and fusion. Further analysis of this lipid quality control cycle is likely to reveal novel insight into the mechanisms that ensure sterol homeostasis in eukaryotic cells. Article from a special issue on Steroids and Microorganisms. Copyright © 2010. Published by Elsevier Ltd.

Identification of a Disulfide Bridge in Sodium-Coupled Neutral Amino Acid Transporter 2(SNAT2) by Chemical Modification.

PubMed

Chen, Chen; Wang, Jiahong; Cai, Ruiping; Yuan, Yanmeng; Guo, Zhanyun; Grewer, Christof; Zhang, Zhou

2016-01-01

Sodium-coupled neutral amino acid transporter 2 (SNAT2) belongs to solute carrier 38 (SLC38) family of transporters, which is ubiquitously expressed in mammalian tissues and mediates transport of small, neutral amino acids, exemplified by alanine(Ala, A). Yet structural data on SNAT2, including the relevance of intrinsic cysteine residues on structure and function, is scarce, in spite of its essential roles in many tissues. To better define the potential of intrinsic cysteines to form disulfide bonds in SNAT2, mutagenesis experiments and thiol-specific chemical modifications by N-ethylmaleimide (NEM) and methoxy-polyethylene glycol maleimide (mPEG-Mal, MW 5000) were performed, with or without the reducing regent dithiothreitol (DTT) treatment. Seven single mutant transporters with various cysteine (Cys, C) to alanine (Ala, A) substitutions, and a C245,279A double mutant were introduced to SNAT2 with a hemagglutinin (HA) tag at the C-terminus. The results showed that the cells expressing C245A or C279A were labeled by one equivalent of mPEG-Mal in the presence of DTT, while wild-type or all the other single Cys to Ala mutants were modified by two equivalents of mPEG-Mal. Furthermore, the molecular weight of C245,279A was not changed in the presence or absence of DTT treatment. The results suggest a disulfide bond between Cys245 and Cys279 in SNAT2 which has no effect on cell surface trafficking, as well as transporter function. The proposed disulfide bond may be important to delineate proximity in the extracellular domain of SNAT2 and related proteins.

Structural assurance testing for post-shipping satellite inspection

NASA Astrophysics Data System (ADS)

Reynolds, Whitney D.; Doyle, Derek; Arritt, Brandon

2012-04-01

Current satellite transportation sensors can provide a binary indication of the acceleration or shock that a satellite has experienced during the shipping process but do little to identify if significant structural change has occurred in the satellite and where it may be located. When a sensor indicates that the satellite has experienced shock during transit, an extensive testing process begins to evaluate the satellite functionality. If errors occur during the functional checkout, extensive physical inspection of the structure follows. In this work an alternate method for inspecting satellites for structural defects after shipping is presented. Electro- Mechanical Impedance measurements are used as an indication of the structural state. In partnership with the Air Force Research Laboratory University Nanosatellite Program, Cornell's CUSat mass model was instrumented with piezoelectric transducers and tested under several structural damage scenarios. A method for detecting and locating changes in the structure using EMI data is presented.

The Origin and Early Evolution of Membrane Proteins

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Schweighofer, Karl; Wilson, Michael A.

2005-01-01

Membrane proteins mediate functions that are essential to all cells. These functions include transport of ions, nutrients and waste products across cell walls, capture of energy and its transduction into the form usable in chemical reactions, transmission of environmental signals to the interior of the cell, cellular growth and cell volume regulation. In the absence of membrane proteins, ancestors of cell (protocells), would have had only very limited capabilities to communicate with their environment. Thus, it is not surprising that membrane proteins are quite common even in simplest prokaryotic cells. Considering that contemporary membrane channels are large and complex, both structurally and functionally, a question arises how their presumably much simpler ancestors could have emerged, perform functions and diversify in early protobiological evolution. Remarkably, despite their overall complexity, structural motifs in membrane proteins are quite simple, with a-helices being most common. This suggests that these proteins might have evolved from simple building blocks. To explain how these blocks could have organized into functional structures, we performed large-scale, accurate computer simulations of folding peptides at a water-membrane interface, their insertion into the membrane, self-assembly into higher-order structures and function. The results of these simulations, combined with analysis of structural and functional experimental data led to the first integrated view of the origin and early evolution of membrane proteins.

Phononic heat transport in nanomechanical structures: steady-state and pumping

NASA Astrophysics Data System (ADS)

Sena-Junior, Marcone I.; Lima, Leandro R. F.; Lewenkopf, Caio H.

2017-10-01

We study the heat transport due to phonons in nanomechanical structures using a phase space representation of non-equilibrium Green’s functions. This representation accounts for the atomic degrees of freedom making it particularly suited for the description of small (molecular) junctions systems. We rigorously show that for the steady state limit our formalism correctly recovers the heuristic Landauer-like heat conductance for a quantum coherent molecular system coupled to thermal reservoirs. We find general expressions for the non-stationary heat current due to an external periodic drive. In both cases we discuss the quantum thermodynamic properties of the systems. We apply our formalism to the case of a diatomic molecular junction.

Functional Properties and Genomics of Glucose Transporters

PubMed Central

Zhao, Feng-Qi; Keating, Aileen F

2007-01-01

Glucose is the major energy source for mammalian cells as well as an important substrate for protein and lipid synthesis. Mammalian cells take up glucose from extracellular fluid into the cell through two families of structurallyrelated glucose transporters. The facilitative glucose transporter family (solute carriers SLC2A, protein symbol GLUT) mediates a bidirectional and energy-independent process of glucose transport in most tissues and cells, while the NaM+/glucose cotransporter family (solute carriers SLC5A, protein symbol SGLT) mediates an active, Na+-linked transport process against an electrochemical gradient. The GLUT family consists of thirteen members (GLUT1-12 and HMIT). Phylogenetically, the members of the GLUT family are split into three classes based on protein similarities. Up to now, at least six members of the SGLT family have been cloned (SGLT1-6). In this review, we report both the genomic structure and function of each transporter as well as intra-species comparative genomic analysis of some of these transporters. The affinity for glucose and transport kinetics of each transporter differs and ranges from 0.2 to 17mM. The ability of each protein to transport alternative substrates also differs and includes substrates such as fructose and galactose. In addition, the tissue distribution pattern varies between species. There are different regulation mechanisms of these transporters. Characterization of transcriptional control of some of the gene promoters has been investigated and alternative promoter usage to generate different protein isoforms has been demonstrated. We also introduce some pathophysiological roles of these transporters in human. PMID:18660845

Coiled Coils - A Model System for the 21st Century.

PubMed

Lupas, Andrei N; Bassler, Jens

2017-02-01

α-Helical coiled coils were described more than 60 years ago as simple, repetitive structures mediating oligomerization and mechanical stability. Over the past 20 years, however, they have emerged as one of the most diverse protein folds in nature, enabling many biological functions beyond mechanical rigidity, such as membrane fusion, signal transduction, and solute transport. Despite this great diversity, their structures can be described by parametric equations, making them uniquely suited for rational protein design. Far from having been exhausted as a source of structural insight and a basis for functional engineering, coiled coils are poised to become even more important for protein science in the coming decades. Copyright © 2016 Elsevier Ltd. All rights reserved.

Opposite temperature effect on transport activity of KCC2/KCC4 and N(K)CCs in HEK-293 cells.

PubMed

Hartmann, Anna-Maria; Nothwang, Hans Gerd

2011-12-09

Cation chloride cotransporters play essential roles in many physiological processes such as volume regulation, transepithelial salt transport and setting the intracellular chloride concentration in neurons. They consist mainly of the inward transporters NCC, NKCC1, and NKCC2, and the outward transporters KCC1 to KCC4. To gain insight into regulatory and structure-function relationships, precise determination of their activity is required. Frequently, these analyses are performed in HEK-293 cells. Recently the activity of the inward transporters NKCC1 and NCC was shown to increase with temperature in these cells. However, the temperature effect on KCCs remains largely unknown. Here, we determined the temperature effect on KCC2 and KCC4 transport activity in HEK-293 cells. Both transporters demonstrated significantly higher transport activity (2.5 fold for KCC2 and 3.3 fold for KCC4) after pre-incubation at room temperature compared to 37°C. These data identify a reciprocal temperature dependence of cation chloride inward and outward cotransporters in HEK-293 cells. Thus, lower temperature should be used for functional characterization of KCC2 and KCC4 and higher temperatures for N(K)CCs in heterologous mammalian expression systems. Furthermore, if this reciprocal effect also applies to neurons, the action of inhibitory neurotransmitters might be more affected by changes in temperature than previously thought.

Mdr65 decreases toxicity of multiple insecticides in Drosophila melanogaster.

PubMed

Sun, Haina; Buchon, Nicolas; Scott, Jeffrey G

2017-10-01

ABC transporters are ubiquitous membrane-bound proteins, present in both prokaryotes and eukaryotes. The major function of eukaryotic ABC transporters is to mediate the efflux of a variety of substrates (including xenobiotics) out of cells. ABC transporters have been widely investigated in humans, particularly for their involvement in multidrug resistance (MDR). Considerably less is known about their roles in transport and/or excretion in insects. ABC transporters are only known to function as exporters in insects. Drosophila melanogaster has 56 ABC transporter genes, including eight which are phylogenetically most similar to the human Mdr genes (ABCB1 clade). We investigated the role of ABC transporters in the ABCB1 clade in modulating the susceptibility to insecticides. We took advantage of the GAL4/UAS system in D. melanogaster to knockdown the expression levels of Mdr65, Mdr50, Mdr49 and ABCB6 using transgenic UAS-RNAi lines and conditional driver lines. The most notable effects were increased sensitivities to nine different insecticides by silencing of Mdr65. Furthermore, a null mutation of Mdr65 decreased the malathion, malaoxon and fipronil LC 50 values by a factor of 1.9, 2.1 and 3.9, respectively. Altogether, this data demonstrates the critical role of ABC transporters, particularly Mdr65, in altering the toxicity of specific, structurally diverse, insecticides in D. melanogaster. Copyright © 2017 Elsevier Ltd. All rights reserved.

Low levels of graphene and graphene oxide inhibit cellular xenobiotic defense system mediated by efflux transporters.

PubMed

Liu, Su; Jiang, Wei; Wu, Bing; Yu, Jing; Yu, Haiyan; Zhang, Xu-Xiang; Torres-Duarte, Cristina; Cherr, Gary N

2016-01-01

Low levels of graphene and graphene oxide (GO) are considered to be environmentally safe. In this study, we analyzed the potential effects of graphene and GO at relatively low concentrations on cellular xenobiotic defense system mediated by efflux transporters. The results showed that graphene (<0.5 μg/mL) and GO (<20 μg/mL) did not decrease cell viability, generate reactive oxygen species, or disrupt mitochondrial function. However, graphene and GO at the nontoxic concentrations could increase calcein-AM (CAM, an indicator of membrane ATP-binding cassette (ABC) transporter) activity) accumulation, indicating inhibition of ABC transporters' efflux capabilities. This inhibition was observed even at 0.005 μg/mL graphene and 0.05 μg/mL GO, which are 100 times and 400 times lower than their lowest toxic concentration from cytotoxicity experiments, respectively. The inhibition of ABC transporters significantly increased the toxicity of paraquat and arsenic, known substrates of ABC transporters. The inhibition of ABC transporters was found to be based on graphene and GO damaging the plasma membrane structure and fluidity, thus altering functions of transmembrane ABC transporters. This study demonstrates that low levels of graphene and GO are not environmentally safe since they can significantly make cell more susceptible to other xenobiotics, and this chemosensitizing activity should be considered in the risk assessment of graphene and GO.

Nucleocytoplasmic transport in cells with progerin-induced defective nuclear lamina.

PubMed

Ferri, Gianmarco; Storti, Barbara; Bizzarri, Ranieri

2017-10-01

Recent data indicate that nuclear lamina (NL) plays a relevant role in many fundamental cellular functions. The peculiar role of NL in cells is dramatically demonstrated by the Hutchinson-Gilford progeria syndrome (HGPS), an inherited laminopathy that causes premature, rapid aging shortly after birth. In HGPS, a mutant form of Lamin A (progeria) leads to a dysmorphic NL structure, but how this perturbation is transduced into cellular changes is still largely unknown. Owing to the close structural relationship between NL and the Nuclear Pore Complex (NPC), in this work we test whether HGPS affects passive and active nucleo-cytoplasmic shuttling of cargoes by means of an established model based of fluorescence recovery after photobleaching. Our findings clearly demonstrate that dysmorphic NL is decoupled from the dynamic characteristics of passive and active transport towards and from the nucleus, as well as from the binding affinity of transport protein mediators. Copyright © 2017 Elsevier B.V. All rights reserved.

Multidrug Transport Protein NorM from Vibrio cholerae Simultaneously Couples to Sodium- and Proton-Motive Force*

PubMed Central

Jin, Yoonhee; Nair, Asha; van Veen, Hendrik W.

2014-01-01

Membrane transporters belonging to the multidrug and toxic compound extrusion family mediate the efflux of unrelated pharmaceuticals from the interior of the cell in organisms ranging from bacteria to human. These proteins are thought to fall into two classes that couple substrate efflux to the influx of either Na+ or H+. We studied the energetics of drug extrusion by NorM from Vibrio cholerae in proteoliposomes in which purified NorM protein was functionally reconstituted in an inside-out orientation. We establish that NorM simultaneously couples to the sodium-motive force and proton-motive force, and biochemically identify protein regions and residues that play important roles in Na+ or H+ binding. As the positions of protons are not available in current medium and high-resolution crystal structures of multidrug and toxic compound extrusion transporters, our findings add a previously unrecognized parameter to mechanistic models based of these structures. PMID:24711447

Zinc and Zinc Transporters: Novel Regulators of Ventricular Myocardial Development.

PubMed

Lin, Wen; Li, Deqiang

2018-06-01

Ventricular myocardial development is a well-orchestrated process involving different cardiac structures, multiple signal pathways, and myriad proteins. Dysregulation of this important developmental event can result in cardiomyopathies, such as left ventricle non-compaction, which affect the pediatric population and the adults. Human and mouse studies have shed light upon the etiology of some cardiomyopathy cases and highlighted the contribution of both genetic and environmental factors. However, the regulation of ventricular myocardial development remains incompletely understood. Zinc is an essential trace metal with structural, enzymatic, and signaling function. Perturbation of zinc homeostasis has resulted in developmental and physiological defects including cardiomyopathy. In this review, we summarize several mechanisms by which zinc and zinc transporters can impact the regulation of ventricular myocardial development. Based on our review, we propose that zinc deficiency and mutations of zinc transporters may underlie some cardiomyopathy cases especially those involving ventricular myocardial development defects.

Dynamics of leaf gas exchange, xylem and phloem transport, water potential and carbohydrate concentration in a realistic 3-D model tree crown.

PubMed

Nikinmaa, Eero; Sievänen, Risto; Hölttä, Teemu

2014-09-01

Tree models simulate productivity using general gas exchange responses and structural relationships, but they rarely check whether leaf gas exchange and resulting water and assimilate transport and driving pressure gradients remain within acceptable physical boundaries. This study presents an implementation of the cohesion-tension theory of xylem transport and the Münch hypothesis of phloem transport in a realistic 3-D tree structure and assesses the gas exchange and transport dynamics. A mechanistic model of xylem and phloem transport was used, together with a tested leaf assimilation and transpiration model in a realistic tree architecture to simulate leaf gas exchange and water and carbohydrate transport within an 8-year-old Scots pine tree. The model solved the dynamics of the amounts of water and sucrose solute in the xylem, cambium and phloem using a fine-grained mesh with a system of coupled ordinary differential equations. The simulations predicted the observed patterns of pressure gradients and sugar concentration. Diurnal variation of environmental conditions influenced tree-level gradients in turgor pressure and sugar concentration, which are important drivers of carbon allocation. The results and between-shoot variation were sensitive to structural and functional parameters such as tree-level scaling of conduit size and phloem unloading. Linking whole-tree-level water and assimilate transport, gas exchange and sink activity opens a new avenue for plant studies, as features that are difficult to measure can be studied dynamically with the model. Tree-level responses to local and external conditions can be tested, thus making the approach described here a good test-bench for studies of whole-tree physiology.

Hai Long | NREL

Science.gov Websites

research interests are broadly in computational modeling for renewable energy generation and energy ions transport in fuel cell and bioenergetics enzymes, and functional membrane structure modeling and University Featured Publications Hydroxide Degradation Pathways for Imidazolium Cations: A DFT Study, J. Phys

Response of plain concrete to a state of biaxial fatigue loading : equipment and technique.

DOT National Transportation Integrated Search

1974-01-01

The fatigue strength of concrete is an important factor in the design of certain structures, particularly those associated with transportation functions. A considerable body of research has been developed on fatigue using specimens subjected to uniax...

Repairing/strengthening of bridges with post-tensioned FRP materials and performance evaluation.

DOT National Transportation Integrated Search

2015-09-01

One of the challenges that transportation agencies are facing is to keep bridges in good condition during their service life. : Numerous bridges are classified as structurally and/or functionally deficient in the country. In the state of Louisiana, 4...

New insight in expression, transport, and secretion of brain-derived neurotrophic factor: Implications in brain-related diseases

PubMed Central

Adachi, Naoki; Numakawa, Tadahiro; Richards, Misty; Nakajima, Shingo; Kunugi, Hiroshi

2014-01-01

Brain-derived neurotrophic factor (BDNF) attracts increasing attention from both research and clinical fields because of its important functions in the central nervous system. An adequate amount of BDNF is critical to develop and maintain normal neuronal circuits in the brain. Given that loss of BDNF function has been reported in the brains of patients with neurodegenerative or psychiatric diseases, understanding basic properties of BDNF and associated intracellular processes is imperative. In this review, we revisit the gene structure, transcription, translation, transport and secretion mechanisms of BDNF. We also introduce implications of BDNF in several brain-related diseases including Alzheimer’s disease, Huntington’s disease, depression and schizophrenia. PMID:25426265

Aeroelastic Tailoring Study of N+2 Low-Boom Supersonic Commercial Transport Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2015-01-01

The Lockheed Martins N+2 Low-boom Supersonic Commercial Transport (LSCT) aircraft is optimized in this study through the use of a multidisciplinary design optimization tool developed at the NASA Armstrong Flight Research Center. A total of 111 design variables are used in the first optimization run. Total structural weight is the objective function in this optimization run. Design requirements for strength, buckling, and flutter are selected as constraint functions during the first optimization run. The MSC Nastran code is used to obtain the modal, strength, and buckling characteristics. Flutter and trim analyses are based on ZAERO code and landing and ground control loads are computed using an in-house code.

Some methods to regulate low-bias negative differential resistance in σ barrier separating nanoscale molecular transport systems

NASA Astrophysics Data System (ADS)

Shen, Ji-Mei; Liu, Jing; Min, Yi; Zhou, Li-Ping

2016-12-01

Using the first-principles method which combines the nonequilibrium Green’s function (NEGF) with density functional theory (DFT), the role of defect, dopant, barrier length and geometric deformation for low-bias negative differential resistance (NDR) in two capped armchair carbon nanotubes (CNTs) sandwiching σ barrier are systematically analyzed. We found that this method can regulate the negative differential resistance (NDR) effects such as current peak and peak position. The adjusting mechanism may originate from orbital interaction and orbital reconstruction. Our calculations try to manipulate the transport characteristics in energy space by simply manipulating the structure in real space, which may promise the potential applications in nanomolecular-electronics in the future.

Mutations in the Na+/Citrate Cotransporter NaCT (SLC13A5) in Pediatric Patients with Epilepsy and Developmental Delay

PubMed Central

Klotz, Jenna; Porter, Brenda E; Colas, Claire; Schlessinger, Avner; Pajor, Ana M

2016-01-01

Mutations in the SLC13A5 gene that codes for the Na+/citrate cotransporter, NaCT, are associated with early onset epilepsy, developmental delay and tooth dysplasia in children. In this study, we identify additional SLC13A5 mutations in nine epilepsy patients from six families. To better characterize the syndrome, families with affected children answered questions about the scope of illness and the treatment strategies. Currently, there are no effective treatments, but some antiepileptic drugs targeting the γ-aminobutyric acid system reduce seizure frequency. Acetazolamide, a carbonic anhydrase inhibitor and atypical antiseizure medication, decreases seizures in four patients. In contrast to previous reports, the ketogenic diet and fasting resulted in worsening of symptoms. The effects of the mutations on NaCT transport function and protein expression were examined by transient transfections of COS-7 cells. There was no transport activity from any of the mutant transporters, although some of the mutant transporter proteins were present on the plasma membrane. The structural model of NaCT suggests that these mutations can affect helix packing or substrate binding. We tested various treatments, including chemical chaperones and low temperatures, but none improved transport function in the NaCT mutants. Interestingly, coexpression of NaCT and the mutants results in decreased protein expression and activity of the wild-type transporter, indicating functional interaction. In conclusion, this study has identified additional SLC13A5 mutations in patients with chronic epilepsy starting in the neonatal period, with the mutations producing inactive Na+/citrate transporters. PMID:27261973

Targeting the brain--surmounting or bypassing the blood-brain barrier.

PubMed

Potschka, Heidrun

2010-01-01

The constituents of the blood-brain barrier, including its efflux transporter system, can efficiently limit brain penetration of potential CNS therapeutics. Effective extrusion from the brain by transporters is a frequent reason for the pharmaceutical industry to exclude novel compounds from further development for CNS therapeutics. Moreover, high transporter expression levels that are present in individual patients or may be generally associated with the pathophysiology seem to be a major cause of therapeutic failure in a variety of CNS diseases including brain tumors, epilepsy, brain HIV infection, and psychiatric disorders. Increasing knowledge of the structure and function of the blood-brain barrier creates a basis for the development of strategies which aim to enhance brain uptake of beneficial pharmaceutical compounds. The different strategies discussed in this review aim to modulate blood-brain barrier function or to bypass constituents of the blood-brain barrier.

Leptin regulates glutamate and glucose transporters in hypothalamic astrocytes

PubMed Central

Fuente-Martín, Esther; García-Cáceres, Cristina; Granado, Miriam; de Ceballos, María L.; Sánchez-Garrido, Miguel Ángel; Sarman, Beatrix; Liu, Zhong-Wu; Dietrich, Marcelo O.; Tena-Sempere, Manuel; Argente-Arizón, Pilar; Díaz, Francisca; Argente, Jesús; Horvath, Tamas L.; Chowen, Julie A.

2012-01-01

Glial cells perform critical functions that alter the metabolism and activity of neurons, and there is increasing interest in their role in appetite and energy balance. Leptin, a key regulator of appetite and metabolism, has previously been reported to influence glial structural proteins and morphology. Here, we demonstrate that metabolic status and leptin also modify astrocyte-specific glutamate and glucose transporters, indicating that metabolic signals influence synaptic efficacy and glucose uptake and, ultimately, neuronal function. We found that basal and glucose-stimulated electrical activity of hypothalamic proopiomelanocortin (POMC) neurons in mice were altered in the offspring of mothers fed a high-fat diet. In adulthood, increased body weight and fasting also altered the expression of glucose and glutamate transporters. These results demonstrate that whole-organism metabolism alters hypothalamic glial cell activity and suggest that these cells play an important role in the pathology of obesity. PMID:23064363

Probability and Cumulative Density Function Methods for the Stochastic Advection-Reaction Equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barajas-Solano, David A.; Tartakovsky, Alexandre M.

We present a cumulative density function (CDF) method for the probabilistic analysis of $d$-dimensional advection-dominated reactive transport in heterogeneous media. We employ a probabilistic approach in which epistemic uncertainty on the spatial heterogeneity of Darcy-scale transport coefficients is modeled in terms of random fields with given correlation structures. Our proposed CDF method employs a modified Large-Eddy-Diffusivity (LED) approach to close and localize the nonlocal equations governing the one-point PDF and CDF of the concentration field, resulting in a $(d + 1)$ dimensional PDE. Compared to the classsical LED localization, the proposed modified LED localization explicitly accounts for the mean-field advectivemore » dynamics over the phase space of the PDF and CDF. To illustrate the accuracy of the proposed closure, we apply our CDF method to one-dimensional single-species reactive transport with uncertain, heterogeneous advection velocities and reaction rates modeled as random fields.« less