Science.gov

Sample records for conserved folding mechanisms

  1. Kinetic partitioning mechanism of HDV ribozyme folding

    SciTech Connect

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  2. Kinetic partitioning mechanism of HDV ribozyme folding

    NASA Astrophysics Data System (ADS)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  3. Protein Folding and Mechanisms of Proteostasis

    PubMed Central

    Díaz-Villanueva, José Fernando; Díaz-Molina, Raúl; García-González, Victor

    2015-01-01

    Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis. PMID:26225966

  4. Mechanical Models of Fault-Related Folding

    SciTech Connect

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  5. Folded membrane dialyzer with mechanically sealed edges

    DOEpatents

    Markley, Finley W.

    1976-01-01

    A semipermeable membrane is folded in accordion fashion to form a stack of pleats and the edges are sealed so as to isolate the opposite surfaces of the membrane. The stack is contained within a case that provides ports for flow of blood in contact with one surface of the membrane through channels formed by the pleats and also provides ports for flow of a dialysate through channels formed by the pleats in contact with the other surface of the membrane. The serpentine side edges of the membrane are sealed by a solidified plastic material, whereas effective mechanical means are provided to seal the end edges of the folded membrane. The mechanical means include a clamping strip which biases case sealing flanges into a sealed relationship with end portions of the membrane near the end edges, which portions extend from the stack and between the sealing flanges.

  6. Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis

    SciTech Connect

    Ramanathan, Arvind; Agarwal, Pratul K

    2011-01-01

    Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme substrate interactions, thereby impacting

  7. Cellular Mechanisms of Membrane Protein Folding

    PubMed Central

    Skach, William R.

    2010-01-01

    The membrane protein folding problem can be articulated by two central questions. How is protein topology established by selective peptide transport to opposite sides of the cellular membrane? And how are transmembrane segments inserted, integrated and folded within the lipid bilayer? In eukaryotes, this process usually takes place in the endoplasmic reticulum (ER) coincident with protein synthesis, and is facilitated by the translating Ribosome and the Sec61 Translocon Complex (RTC). At its core, the RTC forms a dynamic pathway through which the elongating nascent polypeptide moves as it is delivered into cytosolic, lumenal and lipid compartments. This perspective will focus on emerging evidence that the RTC functions as a protein folding machine that restricts conformational space by establishing transmembrane topology and yet provides a permissive environment that enables nascent transmembrane domains to efficiently progress down their folding energy landscape. PMID:19491932

  8. Mechanics of large folds in thin interfacial films

    NASA Astrophysics Data System (ADS)

    Démery, Vincent; Davidovitch, Benny; Santangelo, Christian D.

    2014-10-01

    A thin film confined to a liquid interface responds to uniaxial compression by wrinkling, and then by folding, that has been solved exactly before self-contact. Here, we address the mechanics of large folds, i.e., folds that absorb a length much larger than the wrinkle wavelength. With scaling arguments and numerical simulations, we show that the antisymmetric fold is energetically favorable and can absorb any excess length at zero pressure. Then, motivated by puzzles arising in the comparison of this simple model to experiments on lipid monolayers or capillary rafts, we discuss how to incorporate film weight, self-adhesion, or energy dissipation.

  9. Role of phylogenetically conserved amino acids in folding of Na,K-ATPase.

    PubMed

    Jørgensen, J R; Pedersen, P A

    2001-06-19

    This paper focuses on the amino acid sequence 708-TGDGVNDSPALKK in pig kidney Na,K-ATPase as one of the best conserved among P-type ATPases. In Ca-ATPase this sequence forms a strand-loop-helix structure as part of a Rossman fold next to the phosphorylation site. Substitution of polar residues in the investigated sequence interfered with high-level accumulation of mutant protein. Mutant alpha1-subunit protein only accumulated in membranes from yeast cells grown at 15 degrees C whereas wild-type protein accumulated at both 15 and 35 degrees C. A systematic screen for the molecular mechanism behind lack of accumulation of mutant protein at 35 degrees C showed that transcription and translation were unaffected by the mutations. To demonstrate in vivo protein folding problems, an unfolded protein response reporter system was constructed in yeast. In this strain, only expression of mutant Na,K-ATPase alpha1-subunit caused induction of the unfolded protein response at 35 degrees C, indicating folding problems in the ER. Lowering the expression temperature to 15 degrees C prevented induction of the unfolded protein response after mutant protein expression, indicating correct folding at this temperature. At the permissive temperature mutant proteins were able to escape the endoplasmic reticulum quality control, reach the plasma membrane, and bind ouabain with high affinity. Since mutants in the 708-TGDGVNDSPALKK segment had a thermo inactivation profile identical to that of wild type, they were classified as temperature-sensitive synthesis mutants. The results indicate that this segment contributes side chains of importance for overall folding and maturation of Na,K-ATPase and all other P-type ATPases.

  10. $\\cN$-FOLD SUPERSYMMETRY IN QUANTUM MECHANICAL MATRIX MODELS

    NASA Astrophysics Data System (ADS)

    Tanaka, Toshiaki

    2012-03-01

    We formulate Ņ-fold supersymmetry in quantum mechanical matrix models. As an example, we construct general two-by-two Hermitian matrix two-fold supersymmetric quantum mechanical systems. We find that there are two inequivalent such systems, both of which are characterized by two arbitrary scalar functions, and one of which does not reduce to the scalar system. The obtained systems are all weakly quasi-solvable.

  11. Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

    SciTech Connect

    Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei; Forouhar, Farhad; Mesyanzhinov, Vadim V.; Tong, Liang; Rossmann, Michael G.

    2012-02-21

    Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.

  12. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

    PubMed

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

  13. Fold of the conserved DTC domain in deltex proteins

    SciTech Connect

    Obiero, Josiah; Walker, John R.; Dhe-Paganon, Sirano

    2012-04-30

    Human Deltex 3-like (DTX3L) is a member of the Deltex family of proteins. Initially identified as a B-lymphoma and BAL-associated protein, DTX3L is an E3 ligase that regulates subcellular localization of its partner protein, BAL, by a dynamic nucleocytoplasmic trafficking mechanism. Unlike other members of the Deltex family of proteins, DTX3L lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex proteins, and instead contains other unique N-terminal domains. The C-terminal domains are, however, homologous with other members of the Deltex family of proteins; these include a RING domain and a previously unidentified C-terminal domain. In this study, we report the high-resolution crystal structure of this previously uncharacterized C-terminal domain of human DTX3L, which we term the Deltex C-terminal domain.

  14. The X-38 V-201 Fin Fold Actuation Mechanism

    NASA Technical Reports Server (NTRS)

    Lupo, Christian; Robertson, Brandan; Gafka, George

    2004-01-01

    The X-38 Vehicle 201 (V-201) is a space flight prototype lifting body vehicle that was designed to launch to orbit in the Space Shuttle orbiter payload bay. Although the project was cancelled in May 2003, many of the systems were nearly complete. This paper will describe the fin folding actuation mechanism flight subsystems and development units as well as lessons learned in the design, assembly, development testing, and qualification testing. The two vertical tail fins must be stowed (folded inboard) to allow the orbiter payload bay doors to close. The fin folding actuation mechanism is a remotely or extravehicular activity (EVA) actuated single fault tolerant system consisting of seven subsystems capable of repeatedly deploying or stowing the fins.

  15. Mechanics, Structure and Dynamics of Metaphase Chromosome Folding

    NASA Astrophysics Data System (ADS)

    Marko, John F.

    2014-03-01

    During cell division, eukaryote chromosomes are restructured from a relatively dispersed interphase form, into a relatively compact folded metaphase form. I will discuss experiments aimed at analyzing the folding scheme of metaphase chromosomes, where mechanical response and biochemical perturbation are used as tools for diagnosing structure. Experiments with nucleases reveal that the continuity of the metaphase chromosome depends on DNA, i.e., that the metaphase chromosome can be considered to be a ``chromatin gel.'' Experiments with topoisomerases indicate that chromatin entanglements play an appreciable role in determining chromosome mechanical properties, suggesting that they may play a structural role. We further show that perturbation of condensin complexes dramatically changes metaphase chromosome mechanics. Finally we report results of fluorescence visualization of distributions of condensin I and II along metaphase chromosomes. Supported by NSF Grants MCB-1022117 and DMR-1206868, and by NIH Grants 1U54CA143869-01, 1U54HD076188 and 1R01GM105847-01.

  16. Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

    SciTech Connect

    Chandonia, John-Marc; Kim, Sung-Hou

    2006-03-15

    Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

  17. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.

    PubMed

    Pechmann, Sebastian; Frydman, Judith

    2013-02-01

    The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear. Here, we derive a revised translational efficiency scale that incorporates the competition between tRNA supply and demand. Applying this scale to ten closely related yeast species, we uncover the evolutionary conservation of codon optimality in eukaryotes. This analysis reveals universal patterns of conserved optimal and nonoptimal codons, often in clusters, which associate with the secondary structure of the translated polypeptides independent of the levels of expression. Our analysis suggests an evolved function for codon optimality in regulating the rhythm of elongation to facilitate cotranslational polypeptide folding, beyond its previously proposed role of adapting to the cost of expression. These findings establish how mRNA sequences are generally under selection to optimize the cotranslational folding of corresponding polypeptides.

  18. Statistical mechanics of simple models of protein folding and design.

    PubMed Central

    Pande, V S; Grosberg, A Y; Tanaka, T

    1997-01-01

    It is now believed that the primary equilibrium aspects of simple models of protein folding are understood theoretically. However, current theories often resort to rather heavy mathematics to overcome some technical difficulties inherent in the problem or start from a phenomenological model. To this end, we take a new approach in this pedagogical review of the statistical mechanics of protein folding. The benefit of our approach is a drastic mathematical simplification of the theory, without resort to any new approximations or phenomenological prescriptions. Indeed, the results we obtain agree precisely with previous calculations. Because of this simplification, we are able to present here a thorough and self contained treatment of the problem. Topics discussed include the statistical mechanics of the random energy model (REM), tests of the validity of REM as a model for heteropolymer freezing, freezing transition of random sequences, phase diagram of designed ("minimally frustrated") sequences, and the degree to which errors in the interactions employed in simulations of either folding and design can still lead to correct folding behavior. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 6 PMID:9414231

  19. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    PubMed

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-01

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels.

  20. Role of mechanical factors in cortical folding development

    NASA Astrophysics Data System (ADS)

    Razavi, Mir Jalil; Zhang, Tuo; Li, Xiao; Liu, Tianming; Wang, Xianqiao

    2015-09-01

    Deciphering mysteries of the structure-function relationship in cortical folding has emerged as the cynosure of recent research on brain. Understanding the mechanism of convolution patterns can provide useful insight into the normal and pathological brain function. However, despite decades of speculation and endeavors the underlying mechanism of the brain folding process remains poorly understood. This paper focuses on the three-dimensional morphological patterns of a developing brain under different tissue specification assumptions via theoretical analyses, computational modeling, and experiment verifications. The living human brain is modeled with a soft structure having outer cortex and inner core to investigate the brain development. Analytical interpretations of differential growth of the brain model provide preliminary insight into the critical growth ratio for instability and crease formation of the developing brain followed by computational modeling as a way to offer clues for brain's postbuckling morphology. Especially, tissue geometry, growth ratio, and material properties of the cortex are explored as the most determinant parameters to control the morphogenesis of a growing brain model. As indicated in results, compressive residual stresses caused by the sufficient growth trigger instability and the brain forms highly convoluted patterns wherein its gyrification degree is specified with the cortex thickness. Morphological patterns of the developing brain predicted from the computational modeling are consistent with our neuroimaging observations, thereby clarifying, in part, the reason of some classical malformation in a developing brain.

  1. The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold

    PubMed Central

    Zhang, Hua; Zhu, Fan; Yang, Tiandi; Ding, Lei; Zhou, Meixian; Li, Jingzhi; Haslam, Stuart M; Dell, Anne; Erlandsen, Heidi; Wu, Hui

    2014-01-01

    More than 33,000 glycosyltransferases have been identified. Structural studies, however, have only revealed two distinct glycosyltransferase (GT) folds, GT-A and GT-B. Here we report a 1.34 Å resolution X-ray crystallographic structure of a previously uncharacterized “domain of unknown function” 1792 (DUF1792) and show that the domain adopts a new fold and is required for glycosylation of a family of serine-rich repeat streptococcal adhesins. Biochemical studies reveal that the domain is a glucosyltransferase, and it catalyzes the transfer of glucose to the branch point of the hexasaccharide O-linked to the serine-rich repeat of the bacterial adhesin, Fap1 of Streptococcus parasanguinis. DUF1792 homologs from both Gram-positive and Gram-negative bacteria also exhibit the activity. Thus DUF1792 represents a new family of glycosyltransferases, so we designate it as a GT-D glycosyltransferase fold. As the domain is highly conserved in bacteria and not found in eukaryotes, it can be explored as a new antibacterial target. PMID:25023666

  2. Conservation of Fold and Topology of Functional Elements in Thiamin Pyrophosphate Enzymes

    NASA Technical Reports Server (NTRS)

    Dominiak, P.; Ciszak, E. M.

    2005-01-01

    Thiamin pyrophosphate (TPP)-dependent enzymes are a highly divergent family of proteins binding both TPP and metal ions. They perform decarboxylation-hydroxyaldehydes. Prior -ketoacids and of a common - (O=)C-C(OH)- fragment of to knowledge of three-dimensional structures of these enzmes, the GDGY25-30NN sequence was used to identify these enzymes. Subsequently, a number of structural studies on those enzymes revealed multi-subunit organization and the features of the two duplicate cofactor binding sites. Analyzing the structures of 44 structurally known enzymes, we found that the common structure of these enzymes is reduced to 180-220 amino acid long fragments of two PP and two PYR domains that form the [PP:PYR]2 binding center of two cofactor molecules. The structures of PP and PYR are arranged in a similar fold-sheet with triplets of helices on both sides.Dconsisting of a six-stranded Residues surrounding the cofactors are not strictly conserved, but they provide the same interatomic contacts required for the catalytic functions that these enzymes perform while maintaining interactive structural integrity. These structural and functional amino acids are topological counterparts located in the same positions of the conserved fold of sets of PP and PYR domains. Additional parallels include short fragments of sequences that link these amino acids to the fold and function. This report on the structural commonalities amongst TPP dependent enzymes is thought to contribute new approaches to annotation that may assist in advancing the functional proteomics of TPP dependent enzymes, and trace their complexity within evolutionary context.

  3. Statistical mechanics of kinetic proofreading in protein folding in vivo.

    PubMed Central

    Gulukota, K; Wolynes, P G

    1994-01-01

    The statistical energy landscape picture of protein folding has led to the understanding that the energy landscape must have guiding forces leading to a protein folding funnel in order to avoid the Levinthal paradox in vitro. Since folding in vivo often requires the action of chaperone molecules and ATP hydrolysis, we must ask whether folding in a system maintained away from equilibrium can avoid the Levinthal paradox in other ways. We describe a model of the action of chaperone molecules in protein folding in vivo on the basis of a repetitive cycle of binding and unbinding, allowing the possibility of kinetic proofreading. We also study models in which chaperone binding is locally biased, depending on the similarity of the conformation to the native one. We show that while kinetic proofreading can modestly facilitate folding, it is insufficient by itself to overcome the Levinthal paradox. On the other hand, such kinetic proofreading with biasing can provide the nonequilibrium analog of a folding funnel and greatly enhance folding yields and speed up folding. PMID:7937758

  4. Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms.

    PubMed

    Holmquist, M

    2000-09-01

    The alpha/beta-hydrolase fold family of enzymes is rapidly becoming one of the largest group of structurally related enzymes with diverse catalytic functions. Members in this family include acetylcholinesterase, dienelactone hydrolase, lipase, thioesterase, serine carboxypeptidase, proline iminopeptidase, proline oligopeptidase, haloalkane dehalogenase, haloperoxidase, epoxide hydrolase, hydroxynitrile lyase and others. The enzymes all have a Nucleophile-His-Acid catalytic triad evolved to efficiently operate on substrates with different chemical composition or physicochemical properties and in various biological contexts. For example, acetylcholine esterase catalyzes the cleavage of the neurotransmitter acetylcholine, at a rate close to the limits of diffusion of substrate to the active site of the enzyme. Dienelactone hydrolase uses substrate-assisted catalysis to degrade aromatic compounds. Lipases act adsorbed at the water/lipid interface of their neutral water-insoluble ester substrates. Most lipases have their active site buried under secondary structure elements, a flap, which must change conformation to allow substrate to access the active site. Thioesterases are involved in a multitude of biochemical processes including bioluminiscence, fatty acid- and polyketide biosynthesis and metabolism. Serine carboxypeptidases recognize the negatively charged carboxylate terminus of their peptide substrates. Haloalkane dehalogenase is a detoxifying enzyme that converts halogenated aliphatics to the corresponding alcohols, while haloperoxidase catalyzes the halogenation of organic compounds. Hydroxynitrile lyase cleaves carbon-carbon bonds in cyanohydrins with concomitant hydrogen cyanide formation as a defense mechanism in plants. This paper gives an overview of catalytic activities reported for this family of enzymes by discussing selected examples. The current state of knowledge of the molecular basis for catalysis and substrate specificity is outlined

  5. Molecular mechanism of a hotdog-fold acyl-CoA thioesterase.

    PubMed

    Cantu, David C; Ardèvol, Albert; Rovira, Carme; Reilly, Peter J

    2014-07-14

    Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and metabolism, as well as polyketide biosynthesis. The reaction molecular mechanism of most hotdog-fold acyl-CoA thioesterases remains unknown, but several hypotheses have been put forward in structural and biochemical investigations. The reaction of a human thioesterase (hTHEM2), representing a thioesterase family with a hotdog fold where a coenzyme A moiety is cleaved, was simulated by quantum mechanics/molecular mechanics metadynamics techniques to elucidate atomic and electronic details of its mechanism, its transition-state conformation, and the free energy landscape of the process. A single-displacement acid-base-like mechanism, in which a nucleophilic water molecule is activated by an aspartate residue acting as a base, was found, confirming previous experimental proposals. The results provide unambiguous evidence of the formation of a tetrahedral-like transition state. They also explain the roles of other conserved active-site residues during the reaction, especially that of a nearby histidine/serine pair that protonates the thioester sulfur atom, the participation of which could not be elucidated from mutation analyses alone. PMID:24894958

  6. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

    PubMed Central

    Muñoz, Victor; Cerminara, Michele

    2016-01-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. PMID:27574021

  7. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

    PubMed

    Muñoz, Victor; Cerminara, Michele

    2016-09-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. PMID:27574021

  8. Mechanisms for folding of high-grade rocks in extensional tectonic settings

    NASA Astrophysics Data System (ADS)

    Harris, Lyal B.; Koyi, Hemin A.; Fossen, Haakon

    2002-11-01

    This review of structures developed in extensional high-grade terrains, combined with results of centrifuge analogue modelling, illustrates the range of fold styles and mechanisms for folding of amphibolite to granulite facies rocks during rifting or the collapse of a thrust-thickened orogen. Several extensional fold mechanisms (such as folding within detachment shear zones) are similar to those in contractional settings. The metamorphic P- T- t path, and not fold style or mode of formation, is therefore required to determine the tectonic setting in which some folds developed. Other mechanisms such as rollover above and folding between listric normal shear zones, and folding due to isostatic adjustments during crustal thinning, are unique to extensional tectonic settings. Several mechanisms for folding during crustal extension produce structures that could easily be misinterpreted as implying regional contraction and hence lead to errors in their tectonic interpretation. It is shown that isoclinal recumbent folds refolded by open, upright folds may develop during regional extension in the deep crust. Folds with a thrust sense of asymmetry can develop due to high shear strains within an extensional detachment, or from enhanced back-rotation of layers between normal shear zones. During back-rotation folding, layers rotated into the shortening field undergo further buckle folding, and all may rotate towards orthogonality to the maximum shortening direction. This mechanism explains the presence of many transposed folds, folds with axial planar pegmatites and folds with opposite vergence in extensional terrains. Examples of folds in high-grade rocks interpreted as forming during regional extension included in this paper are from the Grenville Province of Canada, Norwegian Caledonides, Albany Mobile Belt and Leeuwin Complex of Western Australia, Ruby Mountains in the Basin and Range Province of Nevada, the Atâ Sund area of Greenland, the Napier Complex of Enderby Land

  9. The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing.

    PubMed

    Harada, Ryuhei; Kitao, Akio

    2012-01-10

    The fast-folding mechanism of a 35-residue mini-protein, villin headpiece subdomain (HP35), was investigated using folding free energy landscape analysis with the multiscale free energy landscape calculation method (MSFEL). A major and a minor folding pathway were deduced from the folding free energy landscape. In the major folding pathway, the formation of helices II and III was the rate-limiting step in the transition to an intermediate state, triggered by the folding of the PLWK motif. HP35 then folds into the native structure through the formation of the hydrophobic core located at the center of the three-helix bundle. Mutations in the motif and hydrophobic core that suppressed folding into the native state drastically changed the folding free energy landscape compared to the wild type protein. In the minor folding pathway, nucleation of the hydrophobic core preceded formation of the motif.

  10. Mechanisms of protein-folding diseases at a glance

    PubMed Central

    Valastyan, Julie S.; Lindquist, Susan

    2014-01-01

    For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In addition, degradation pathways participate by destroying improperly folded proteins. The intricacy of this multisystem process provides many opportunities for error. Furthermore, mutations cause misfolded, nonfunctional forms of proteins to accumulate. As a result, many pathological conditions are fundamentally rooted in the protein-folding problem that all cells must solve to maintain their function and integrity. Here, to illustrate the breadth of this phenomenon, we describe five examples of protein-misfolding events that can lead to disease: improper degradation, mislocalization, dominant-negative mutations, structural alterations that establish novel toxic functions, and amyloid accumulation. In each case, we will highlight current therapeutic options for battling such diseases. PMID:24396149

  11. Statistical mechanics of RNA folding: Importance of alphabet size

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Ranjan; Emberly, Eldon; Tang, Chao; Wingreen, Ned S.

    2003-10-01

    We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

  12. Mechanical Modeling and Computer Simulation of Protein Folding

    ERIC Educational Resources Information Center

    Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

    2014-01-01

    In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

  13. Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond

    PubMed Central

    Hsu, Shang-Te D.; van Anken, Eelco; Liscaljet, I. Marije; Dankers, Martijn; Bontjer, Ilja; Land, Aafke; Braakman, Ineke; Bonvin, Alexandre M.J.J.; Berkhout, Ben

    2008-01-01

    The majority of eukaryotic secretory and membrane proteins contain disulfide bonds, which are strongly conserved within protein families because of their crucial role in folding or function. The exact role of these disulfide bonds during folding is unclear. Using virus-driven evolution we generated a viral glycoprotein variant, which is functional despite the lack of an absolutely conserved disulfide bond that links two antiparallel β-strands in a six-stranded β-barrel. Molecular dynamics simulations revealed that improved hydrogen bonding and side chain packing led to stabilization of the β-barrel fold, implying that β-sheet preference codirects glycoprotein folding in vivo. Our results show that the interactions between two β-strands that are important for the formation and/or integrity of the β-barrel can be supported by either a disulfide bond or β-sheet favoring residues. PMID:18753405

  14. Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach.

    PubMed

    Goyal, Amit; Sokalingam, Sriram; Hwang, Kyu-Suk; Lee, Sun-Gu

    2014-07-10

    Design of an efficient fingerprint that detects homologous proteins at distant sequence identity has been a great challenge. This paper proposes a strategy to extract an ideal-like fingerprint with high specificity and sensitivity from a group of sequences related to a fold. The approach is devised based on the assumptions that the critical residues for a protein fold may be conserved in three aspects, i.e. sequence, structure, and intramolecular interaction, and embedded in secondary structures. We hypothesized that the residues satisfying such conditions simultaneously may work as an efficient fingerprint. This idea was tested on protein folds of various classes, such as beta-strand rich, alpha + beta proteins and alpha/beta proteins with discrete sequence similarities. The fingerprint for each fold was generated by selecting the overlapped conserved residues (OCR) from the conserved residues obtained using independent three alignment methods, i.e. multiple sequence alignment, structure-based alignment, and alignment based on the interstrand hydrogen-bonds. The OCR fingerprints showed more than 90% detection efficiency for all the folds tested and were identified to be almost the minimal fingerprints composed of only critical residues. This study is expected to provide an important conceptual improvement in the identification or design of ideal fingerprints for a protein fold.

  15. Evolution of ribonuclease in relation to polypeptide folding mechanisms.

    NASA Technical Reports Server (NTRS)

    Barnard, E. A.; Cohen, M. S.; Gold, M. H.; Kim, J.-K.

    1972-01-01

    Comparisons of the N-terminal region of pancreatic RNAase in seven species are presented, taking into account cow, bison, deer, rat, pig, kangaroo, and turtle. The available limited evidence on hypervariable regions indicates that there is still an evolutionary constraint on them. It is proposed that there is a selection pressure acting on all regions of a protein sequence in evolution. Mutations that tend to obstruct the folding process can lead to various intensities of selection pressure.

  16. From mechanical folding trajectories to intrinsic energy landscapes of biopolymers

    PubMed Central

    Hinczewski, Michael; Gebhardt, J. Christof M.; Rief, Matthias; Thirumalai, D.

    2013-01-01

    In single-molecule laser optical tweezer (LOT) pulling experiments, a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent changes in the distance between the beads. How to construct the full intrinsic folding landscape (without the handles and beads) from the measured time series is a major unsolved problem. By using rigorous theoretical methods—which account for fluctuations of the DNA handles, rotation of the optical beads, variations in applied tension due to finite trap stiffness, as well as environmental noise and limited bandwidth of the apparatus—we provide a tractable method to derive intrinsic free-energy profiles. We validate the method by showing that the exactly calculable intrinsic free-energy profile for a generalized Rouse model, which mimics the two-state behavior in nucleic acid hairpins, can be accurately extracted from simulated time series in a LOT setup regardless of the stiffness of the handles. We next apply the approach to trajectories from coarse-grained LOT molecular simulations of a coiled-coil protein based on the GCN4 leucine zipper and obtain a free-energy landscape that is in quantitative agreement with simulations performed without the beads and handles. Finally, we extract the intrinsic free-energy landscape from experimental LOT measurements for the leucine zipper. PMID:23487746

  17. Critical taper wedge mechanics of fold-and-thrust belts on Venus - Initial results from Magellan

    NASA Technical Reports Server (NTRS)

    Suppe, John; Connors, Chris

    1992-01-01

    Examples of fold-and-thrust belts from a variety of tectonic settings on Venus are introduced. Predictions for the mechanics of fold-and-thrust belts on Venus are examined on the basis of wedge theory, rock mechanics data, and currently known conditions on Venus. The theoretical predictions are then compared with new Magellan data.

  18. Decoupling mechanisms-paying for conservation

    SciTech Connect

    Cross, P.S.

    1993-07-15

    In 1988, the National Association of Regulatory Utility Commissioners issued a policy statement that said [open quotes]ratemaking practices should align utilities' pursuit of profit with least-cost planning.[close quotes] This policy coincided with then-current thinkingg at a number of state commissions about the much-touted goal of encouraging utilities to invest in conservation, or demand-side management (DSM) programs, rather than in generating resources to meet system load requirements. Besides utility concerns about recovering conservation program investments, regulators also notices a built-in [open quotes]disincentive[close quotes] to investment in the traditional ratemaking format: If profit is tied to sales, then utilities will always shy away from aggressively promoting conservation. Or so the thinkin went. [open quotes]Decoupling mechanisms[close quotes] were born to remove this disincentive. A number of states have implemented these mechanisms, while several others are investigating the issue. One chief drawback of the mechanisms is that if sales go down, rates go up to cover the shortfall. (Of course, rates go down if sales exceed forecasted levels.) A major problem has been that rate increases have occurred at exactly the wrong time, during economic slowdowns when utilities are struggling to retain price-sensitive customers and residential ratepayers are least likely to bear with quiet stoicism the burden placed on family budgets. Decoupling is seen by some as a step backwards in the move to competitive regulatory reforms that seek to encourage utilities to behave like free-market companies. Indeed, the newest decoupling mechanisms face serious challenge.

  19. Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin

    PubMed Central

    Garcia-Manyes, Sergi; Dougan, Lorna; Badilla, Carmen L.; Brujić, Jasna; Fernández, Julio M.

    2009-01-01

    Statistical theories of protein folding have long predicted plausible mechanisms for reducing the vast conformational space through distinct ensembles of structures. However, these predictions have remained untested by bulk techniques, because the conformational diversity of folding molecules has been experimentally unapproachable. Owing to recent advances in single molecule force-clamp spectroscopy, we are now able to probe the structure and dynamics of the small protein ubiquitin by measuring its length and mechanical stability during each stage of folding. Here, we discover that upon hydrophobic collapse, the protein rapidly selects a subset of minimum energy structures that are mechanically weak and essential precursors of the native fold. From this much reduced ensemble, the native state is acquired through a barrier-limited transition. Our results support the validity of statistical mechanics models in describing the folding of a small protein on biological timescales. PMID:19541635

  20. Connecting thermal and mechanical protein (un)folding landscapes.

    PubMed

    Sun, Li; Noel, Jeffrey K; Sulkowska, Joanna I; Levine, Herbert; Onuchic, José N

    2014-12-16

    Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying force at both termini. The unfolding time-force relation τ(F) indicates that the force-induced unfolding behavior of filamin can be characterized into three regimes: barrier-limited low- and intermediate-force regimes, and a barrierless high-force regime. Slope changes of τ(F) separate the three regimes. We show that the behavior of τ(F) can be understood from a two-dimensional free energy landscape projected onto the extension X and the fraction of native contacts Q. In the low-force regime, the unfolding rate is roughly force-independent due to the small (even negative) separation in X between the native ensemble and transition state ensemble (TSE). In the intermediate-force regime, force sufficiently separates the TSE from the native ensemble such that τ(F) roughly follows an exponential relation. This regime is typically explored by pulling experiments. While X may fail to resolve the TSE due to overlap with the unfolded ensemble just below the folding temperature, the overlap is minimal at lower temperatures where experiments are likely to be conducted. The TSE becomes increasingly structured with force, whereas the average order of structural events during unfolding remains roughly unchanged. The high-force regime is characterized by barrierless unfolding, and the unfolding time approaches a limit of ∼10 μs for the highest forces we studied. Finally, a combination of X and Q is shown to be a good reaction coordinate for almost the entire force range. PMID:25517160

  1. Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms.

    PubMed

    Netzer, W J; Hartl, F U

    1998-02-01

    Recent findings suggest that a combination of chaperonin-assisted and unassisted mechanisms operate in protein folding in the cytosol. While nascent chain-binding chaperones, such as Hsp70, could have a general role in maintaining the folding competence of translating polypeptide chains, the contribution of the cylindrical chaperonin complexes to overall folding is limited to a subset of aggregation-sensitive polypeptides. The majority of bacterial proteins are relatively small and they are synthesized rapidly and folded independently of the chaperonin GroEL in a posttranslational manner. Eukaryotes have a proportionally larger number of multi-domain proteins than bacteria. The individual domains of these proteins can be folded cotranslationally and sequentially. The use of this mechanism explains how large proteins fold independently of a chaperonin and could have been crucial in the evolution of a wide array of modular polypeptides in eukaryotes.

  2. Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism.

    PubMed

    Espah Borujeni, Amin; Salis, Howard M

    2016-06-01

    RNA folding plays an important role in controlling protein synthesis as well as other cellular processes. Existing models have focused on how RNA folding energetics control translation initiation rate under equilibrium conditions but have largely ignored the effects of nonequilibrium RNA folding. We introduce a new mechanism, called "ribosome drafting", that explains how a mRNA's folding kinetics and the ribosome's binding rate collectively control its translation initiation rate. During cycles of translation, ribosome drafting emerges whenever successive ribosomes bind to a mRNA faster than the mRNA can refold, maintaining it in a nonequilibrium state with an acceleration of protein synthesis. Using computational design, time-correlated single photon counting, and expression measurements, we demonstrate that slow-folding and fast-folding RNA structures with equivalent folding energetics can vary protein synthesis rates by 1000-fold. We determine the necessary conditions for ribosome drafting by characterizing mRNAs with rationally designed ribosome binding rates, folding kinetics, and folding energetics, confirming the predictions of a nonequilibrium Markov model of translation. Our results have widespread implications, illustrating how competitive folding and assembly kinetics can shape the gene expression machinery's sequence-structure-function relationship inside cells. PMID:27199273

  3. Statistical Mechanical Model for pH-Induced Protein Folding: Application to Apomyoglobin.

    PubMed

    Mizukami, Takuya; Sakuma, Yosuke; Maki, Kosuke

    2016-09-01

    Despite the major role of pH in protein folding and stability, a quantitative understanding of the pH-induced protein folding mechanism remains elusive. Two conventional models, the Monod-Wyman-Changeux and Linderstrøm-Lang smeared charge models, respectively, have been used to analyze the formation/disruption of specific native structures and fluctuating non-native states. However, there are only a few models that can represent the overall kinetic events of folding/unfolding independent of the properties of relevant molecular species, which has hampered the efforts to systematically analyze pH-induced folding. Here, we constructed a statistical mechanical model that incorporates the protonation mechanism of conventional models along with a combined manual search and least-squares fitting procedure, which was used to investigate the folding of horse apomyoglobin over a wide pH range (2.2-6.7), with a time window ranging from ∼40 μs to ∼100 s, using continuous-/stopped-flow fluorescence at 8 °C. Quantitative analysis assuming a five-state sequential scheme indicated that (1) pH-induced folding/unfolding is represented by both specific binding and Coulombic interactions; (2) kinetic folding/unfolding intermediates share kinetic mechanisms with the equilibrium intermediate, indicating their equivalence; and (3) native-like properties are acquired successively during folding by intermediates and in transition states. This model could also be applied to a variety of association/dissociation processes. PMID:27491483

  4. A Two-step Mechanism for the Folding of Actin by the Yeast Cytosolic Chaperonin

    PubMed Central

    Stuart, Sarah F.; Leatherbarrow, Robin J.; Willison, Keith R.

    2011-01-01

    Actin requires the chaperonin containing TCP1 (CCT), a hexadecameric ATPase essential for cell viability in eukaryotes, to fold to its native state. Following binding of unfolded actin to CCT, the cavity of the chaperone closes and actin is folded and released in an ATP-dependent folding cycle. In yeast, CCT forms a ternary complex with the phosducin-like protein PLP2p to fold actin, and together they can return nascent or chemically denatured actin to its native state in a pure in vitro folding assay. The complexity of the CCT-actin system makes the study of the actin folding mechanism technically challenging. We have established a novel spectroscopic assay through selectively labeling the C terminus of yeast actin with acrylodan and observe significant changes in the acrylodan fluorescence emission spectrum as actin is chemically unfolded and then refolded by the chaperonin. The variation in the polarity of the environment surrounding the fluorescent probe during the unfolding/folding processes has allowed us to monitor actin as it folds on CCT. The rate of actin folding at a range of temperatures and ATP concentrations has been determined for both wild type CCT and a mutant CCT, CCT4anc2, defective in folding actin in vivo. Binding of the non-hydrolysable ATP analog adenosine 5′-(β,γ-imino)triphosphate to the ternary complex leads to 3-fold faster release of actin from CCT following addition of ATP, suggesting a two-step folding process with a conformational change occurring upon closure of the cavity and a subsequent final folding step involving packing of the C terminus to the native-like state. PMID:21056978

  5. Lithological Controls on 3D Fold Geometry in Mechanically Layered Rocks

    NASA Astrophysics Data System (ADS)

    Pearce, M. A.; Jones, R. R.; Rock, G.

    2010-12-01

    Folding and thrusting are key processes in accommodating shortening in evolving orogens. In the outer parts of mountain belts, the combination of tectonism and sedimentation often leads to viable petroleum systems where folds trap migrating hydrocarbons. A key aspect of the success of these traps is the 3D fold geometry, which must prevent up-plunge hydrocarbon escape. Fold shapes in a multilayered system are governed by the fold mechanism, and the rheology of the layers. In sedimentary environments where laterally heterogeneous thicknesses of interbedded carbonates, clastics, and evaporates may be present, predicting the sub-surface geometry of structures is challenging. We present field data combined with satellite and seismic interpretation from the Zagros fold and thrust belt of SE Turkey where Neogene shortening has affected an Ordovician to Miocene aged sedimentary pile comprising shales, sandstones, carbonates and minor evaporites. Miocene carbonates capping the sequence allow 3D fold geometries to be ascertained at surface with a high degree of confidence, whilst the underlying ~1km of shales and mudstones allows folds to develop that depart substantially from standard “text-book” geometries. Beneath these incompetent units a further 1.7km of carbonates and clastics overlie Ordovician shales up to 1.5km thick. In relatively low strain sections asymmetric, angular, kink-like folds form long wavelength structures and thrust faults rarely reach the surface. With increasing strain, the wavelength/amplitude ratio decreases and thrusts cut through the fold limbs. Folds are interpreted to detach above a thick sequence of Ordovician shales. They originate by buckling of the competent units within the two weaker horizons, with initial perturbations probably provided by sedimentary heterogeneities. As the folds amplify, thrusts form in the more competent units above the shale. These then propagate upwards with fold amplification dominated by fault-tip

  6. Understanding the Mechanism of Prosegment-catalyzed Folding by Solution NMR Spectroscopy*

    PubMed Central

    Wang, Shenlin; Horimoto, Yasumi; Dee, Derek R.; Yada, Rickey Y.

    2014-01-01

    Multidomain protein folding is often more complex than a two-state process, which leads to the spontaneous folding of the native state. Pepsin, a zymogen-derived enzyme, without its prosegment (PS), is irreversibly denatured and folds to a thermodynamically stable, non-native conformation, termed refolded pepsin, which is separated from native pepsin by a large activation barrier. While it is known that PS binds refolded pepsin and catalyzes its conversion to the native form, little structural details are known regarding this conversion. In this study, solution NMR was used to elucidate the PS-catalyzed folding mechanism by examining the key equilibrium states, e.g. native and refolded pepsin, both in the free and PS-bound states, and pepsinogen, the zymogen form of pepsin. Refolded pepsin was found to be partially structured and lacked the correct domain-domain structure and active-site cleft formed in the native state. Analysis of chemical shift data revealed that upon PS binding refolded pepsin folds into a state more similar to that of pepsinogen than to native pepsin. Comparison of pepsin folding by wild-type and mutant PSs, including a double mutant PS, indicated that hydrophobic interactions between residues of prosegment and refolded pepsin lower the folding activation barrier. A mechanism is proposed for the binding of PS to refolded pepsin and how the formation of the native structure is mediated. PMID:24265313

  7. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction

    PubMed Central

    CAO, Song; CHEN, Shi-Jie

    2016-01-01

    In spite of the success of computational methods for predicting RNA secondary structure, the problem of predicting RNA tertiary structure folding remains. Low-resolution structural models show promise as they allow for rigorous statistical mechanical computation for the conformational entropies, free energies, and the coarse-grained structures of tertiary folds. Molecular dynamics refinement of coarse-grained structures leads to all-atom 3D structures. Modeling based on statistical mechanics principles also has the unique advantage of predicting the full free energy landscape, including local minima and the global free energy minimum. The energy landscapes combined with the 3D structures form the basis for quantitative predictions of RNA functions. In this chapter, we present an overview of statistical mechanical models for RNA folding and then focus on a recently developed RNA statistical mechanical model -- the Vfold model. The main emphasis is placed on the physics underpinning the models, the computational strategies, and the connections to RNA biology. PMID:27293312

  8. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement.

    PubMed

    Le Coq, Johanne; Ghosh, Partho

    2011-08-30

    Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10(20) potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

  9. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

    SciTech Connect

    Le Coq, Johanne; Ghosh, Partho

    2012-06-19

    Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

  10. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

    PubMed Central

    Le Coq, Johanne; Ghosh, Partho

    2011-01-01

    Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd (∼16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 1020 potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation. PMID:21873231

  11. Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

    PubMed

    Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

    2016-06-01

    Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract.

  12. Mechanical Folding and Unfolding of Protein Barnase at the Single-Molecule Level.

    PubMed

    Alemany, Anna; Rey-Serra, Blanca; Frutos, Silvia; Cecconi, Ciro; Ritort, Felix

    2016-01-01

    The unfolding and folding of protein barnase has been extensively investigated in bulk conditions under the effect of denaturant and temperature. These experiments provided information about structural and kinetic features of both the native and the unfolded states of the protein, and debates about the possible existence of an intermediate state in the folding pathway have arisen. Here, we investigate the folding/unfolding reaction of protein barnase under the action of mechanical force at the single-molecule level using optical tweezers. We measure unfolding and folding force-dependent kinetic rates from pulling and passive experiments, respectively, and using Kramers-based theories (e.g., Bell-Evans and Dudko-Hummer-Szabo models), we extract the position of the transition state and the height of the kinetic barrier mediating unfolding and folding transitions, finding good agreement with previous bulk measurements. Measurements of the force-dependent kinetic barrier using the continuous effective barrier analysis show that protein barnase verifies the Leffler-Hammond postulate under applied force and allow us to extract its free energy of folding, ΔG0. The estimated value of ΔG0 is in agreement with our predictions obtained using fluctuation relations and previous bulk studies. To address the possible existence of an intermediate state on the folding pathway, we measure the power spectrum of force fluctuations at high temporal resolution (50 kHz) when the protein is either folded or unfolded and, additionally, we study the folding transition-path time at different forces. The finite bandwidth of our experimental setup sets the lifetime of potential intermediate states upon barnase folding/unfolding in the submillisecond timescale. PMID:26745410

  13. Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

    NASA Astrophysics Data System (ADS)

    Homouz, D.; Stagg, L.; Wittungstafshede, P.; Cheung, M.

    2009-01-01

    Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.

  14. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    EPA Science Inventory

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  15. Surface folding in metals: a mechanism for delamination wear in sliding

    PubMed Central

    Mahato, Anirban; Guo, Yang; Sundaram, Narayan K.; Chandrasekar, Srinivasan

    2014-01-01

    Using high-resolution, in situ imaging of a hard, wedge-shaped model asperity sliding against a metal surface, we demonstrate a new mechanism for particle formation and delamination wear. Damage to the residual surface is caused by the occurrence of folds on the free surface of the prow-shaped region ahead of the wedge. This damage manifests itself as shallow crack-like features and surface tears, which are inclined at very acute angles to the surface. The transformation of folds into cracks, tears and particles is directly captured. Notably, a single sliding pass is sufficient to damage the surface, and subsequent passes result in the generation of platelet-like wear particles. Tracking the folding process at every stage from surface bumps to folds to cracks/tears/particles ensures that there is no ambiguity in capturing the mechanism of wear. Because fold formation and consequent delamination are quite general, our findings have broad applicability beyond wear itself, including implications for design of surface generation and conditioning processes. PMID:25197251

  16. A Better 2-D Mechanical Energy Conservation Experiment

    ERIC Educational Resources Information Center

    Paesler, Michael

    2012-01-01

    A variety of simple classical mechanics energy conservation experiments are used in teaching laboratories. Typical one-dimensional (1-D) setups may involve falling balls or oscillating springs. Many of these can be quite satisfying in that students can confirm--within a few percent--that mechanical energy is conserved. Students generally have…

  17. Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates.

    PubMed

    Motlagh, Hesam N; Toptygin, Dmitri; Kaiser, Christian M; Hilser, Vincent J

    2016-03-29

    Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments. PMID:27028638

  18. Cyt toxins produced by Bacillus thuringiensis: a protein fold conserved in several pathogenic microorganisms.

    PubMed

    Soberón, Mario; López-Díaz, Jazmin A; Bravo, Alejandra

    2013-03-01

    Bacillus thuringiensis bacteria produce different insecticidal proteins known as Cry and Cyt toxins. Among them the Cyt toxins represent a special and interesting group of proteins. Cyt toxins are able to affect insect midgut cells but also are able to increase the insecticidal damage of certain Cry toxins. Furthermore, the Cyt toxins are able to overcome resistance to Cry toxins in mosquitoes. There is an increasing potential for the use of Cyt toxins in insect control. However, we still need to learn more about its mechanism of action in order to define it at the molecular level. In this review we summarize important aspects of Cyt toxins produced by Bacillus thuringiensis, including current knowledge of their mechanism of action against mosquitoes and also we will present a primary sequence and structural comparison with related proteins found in other pathogenic bacteria and fungus that may indicate that Cyt toxins have been selected by several pathogenic organisms to exert their virulence phenotypes.

  19. Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding

    PubMed Central

    Arai, Munehito; Sugase, Kenji; Dyson, H. Jane; Wright, Peter E.

    2015-01-01

    Intrinsically disordered proteins (IDPs) frequently function in protein interaction networks that regulate crucial cellular signaling pathways. Many IDPs undergo transitions from disordered conformational ensembles to folded structures upon binding to their cellular targets. Several possible binding mechanisms for coupled folding and binding have been identified: folding of the IDP after association with the target (“induced fit”), or binding of a prefolded state in the conformational ensemble of the IDP to the target protein (“conformational selection”), or some combination of these two extremes. The interaction of the intrinsically disordered phosphorylated kinase-inducible domain (pKID) of the cAMP-response element binding (CREB) protein with the KIX domain of a general transcriptional coactivator CREB-binding protein (CBP) provides an example of the induced-fit mechanism. Here we show by NMR relaxation dispersion experiments that a different intrinsically disordered ligand, the transactivation domain of the transcription factor c-Myb, interacts with KIX at the same site as pKID but via a different binding mechanism that involves elements of conformational selection and induced fit. In contrast to pKID, the c-Myb activation domain has a strong propensity for spontaneous helix formation in its N-terminal region, which binds to KIX in a predominantly folded conformation. The C-terminal region of c-Myb exhibits a much smaller helical propensity and likely folds via an induced-fit process after binding to KIX. We propose that the intrinsic secondary structure propensities of pKID and c-Myb determine their binding mechanisms, consistent with their functions as inducible and constitutive transcriptional activators. PMID:26195786

  20. Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding.

    PubMed

    Arai, Munehito; Sugase, Kenji; Dyson, H Jane; Wright, Peter E

    2015-08-01

    Intrinsically disordered proteins (IDPs) frequently function in protein interaction networks that regulate crucial cellular signaling pathways. Many IDPs undergo transitions from disordered conformational ensembles to folded structures upon binding to their cellular targets. Several possible binding mechanisms for coupled folding and binding have been identified: folding of the IDP after association with the target ("induced fit"), or binding of a prefolded state in the conformational ensemble of the IDP to the target protein ("conformational selection"), or some combination of these two extremes. The interaction of the intrinsically disordered phosphorylated kinase-inducible domain (pKID) of the cAMP-response element binding (CREB) protein with the KIX domain of a general transcriptional coactivator CREB-binding protein (CBP) provides an example of the induced-fit mechanism. Here we show by NMR relaxation dispersion experiments that a different intrinsically disordered ligand, the transactivation domain of the transcription factor c-Myb, interacts with KIX at the same site as pKID but via a different binding mechanism that involves elements of conformational selection and induced fit. In contrast to pKID, the c-Myb activation domain has a strong propensity for spontaneous helix formation in its N-terminal region, which binds to KIX in a predominantly folded conformation. The C-terminal region of c-Myb exhibits a much smaller helical propensity and likely folds via an induced-fit process after binding to KIX. We propose that the intrinsic secondary structure propensities of pKID and c-Myb determine their binding mechanisms, consistent with their functions as inducible and constitutive transcriptional activators.

  1. Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain

    PubMed Central

    Gruber, Tobias; Balbach, Jochen

    2015-01-01

    The human AmphyphisinII/Bin1 N-BAR domain belongs to the BAR domain superfamily, whose members sense and generate membrane curvatures. The N-BAR domain is a 57 kDa homodimeric protein comprising a six helix bundle. Here we report the protein folding mechanism of this protein as a representative of this protein superfamily. The concentration dependent thermodynamic stability was studied by urea equilibrium transition curves followed by fluorescence and far-UV CD spectroscopy. Kinetic unfolding and refolding experiments, including rapid double and triple mixing techniques, allowed to unravel the complex folding behavior of N-BAR. The equilibrium unfolding transition curve can be described by a two-state process, while the folding kinetics show four refolding phases, an additional burst reaction and two unfolding phases. All fast refolding phases show a rollover in the chevron plot but only one of these phases depends on the protein concentration reporting the dimerization step. Secondary structure formation occurs during the three fast refolding phases. The slowest phase can be assigned to a proline isomerization. All kinetic experiments were also followed by fluorescence anisotropy detection to verify the assignment of the dimerization step to the respective folding phase. Based on these experiments we propose for N-BAR two parallel folding pathways towards the homodimeric native state depending on the proline conformation in the unfolded state. PMID:26368922

  2. Universality and diversity of folding mechanics for three-helix bundle proteins

    PubMed Central

    Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I.

    2008-01-01

    In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous pfold analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Φ values is obtained for protein A. Φ values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins. PMID:18195374

  3. Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

    PubMed

    Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

    2004-05-01

    The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

  4. A conserved Glu-Arg salt bridge connects coevolved motifs that define the eukaryotic protein kinase fold.

    PubMed

    Yang, Jie; Wu, Jian; Steichen, Jon M; Kornev, Alexandr P; Deal, Michael S; Li, Sheng; Sankaran, Banumathi; Woods, Virgil L; Taylor, Susan S

    2012-01-27

    Eukaryotic protein kinases (EPKs) feature two coevolved structural segments, the Activation segment, which starts with the Asp-Phe-Gly (DFG) and ends with the Ala-Pro-Glu (APE) motifs, and the helical GHI subdomain that comprises αG-αH-αI helices. Eukaryotic-like kinases have a much shorter Activation segment and lack the GHI subdomain. They thus lack the conserved salt bridge interaction between the APE Glu and an Arg from the GHI subdomain, a hallmark signature of EPKs. Although the conservation of this salt bridge in EPKs is well known and its implication in diseases has been illustrated by polymorphism analysis, its function has not been carefully studied. In this work, we use murine cAMP-dependent protein kinase (protein kinase A) as the model enzyme (Glu208 and Arg280) to examine the role of these two residues. We showed that Ala replacement of either residue caused a 40- to 120-fold decrease in catalytic efficiency of the enzyme due to an increase in K(m)(ATP) and a decrease in k(cat). Crystal structures, as well as solution studies, also demonstrate that this ion pair contributes to the hydrophobic network and stability of the enzyme. We show that mutation of either Glu or Arg to Ala renders both mutant proteins less effective substrates for upstream kinase phosphoinositide-dependent kinase 1. We propose that the Glu208-Arg280 pair serves as a center hub of connectivity between these two structurally conserved elements in EPKs. Mutations of either residue disrupt communication not only between the two segments but also within the rest of the molecule, leading to altered catalytic activity and enzyme regulation.

  5. Conservation of Mechanical Energy Using Dry Ice Slider-Projectiles

    ERIC Educational Resources Information Center

    Gales, Jenna; Baker, Blane

    2008-01-01

    Energy concepts are fundamentally important for describing and analyzing systems ranging from subatomic particles to spiral galaxies. In general, students first encounter such concepts in introductory courses that typically focus on forms of energy, energy transfer, and conservation laws. Within these courses, conservation of mechanical energy is…

  6. Optical measurements of vocal fold tensile properties: implications for phonatory mechanics.

    PubMed

    Kelleher, Jordan E; Siegmund, Thomas; Chan, Roger W; Henslee, Erin A

    2011-06-01

    In voice research, in vitro tensile stretch experiments of vocal fold tissues are commonly employed to determine the tissue biomechanical properties. In the standard stretch-release protocol, tissue deformation is computed from displacements applied to sutures inserted through the thyroid and arytenoid cartilages, with the cartilages assumed to be rigid. Here, a non-contact optical method was employed to determine the actual tissue deformation of vocal fold lamina propria specimens from three excised human larynges in uniaxial tensile tests. Specimen deformation was found to consist not only of deformation of the tissue itself, but also deformation of the cartilages, as well as suture alignment and tightening. Stress-stretch curves of a representative load cycle were characterized by an incompressible Ogden model. The initial longitudinal elastic modulus was found to be considerably higher if determined based on optical displacement measurements than typical values reported in the literature. The present findings could change the understanding of the mechanics underlying vocal fold vibration. Given the high longitudinal elastic modulus the lamina propria appeared to demonstrate a substantial level of anisotropy. Consequently, transverse shear could play a significant role in vocal fold vibration, and fundamental frequencies of phonation should be predicted by beam theories accounting for such effects.

  7. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex.

    PubMed

    Chen, Hai-Feng

    2008-08-01

    The PAZ domain plays a key role in gene silencing pathway. The PAZ domain binds with siRNAs to form the multimeric RNA-induced silencing complex (RISC). RISC identifies mRNAs homologous to the siRNAs and promotes their degradation. It was found that binding with siRNA significantly enhances apo-PAZ folding. However, the mechanism by which folding is coupled to binding is poorly understood. Thus, the coupling relationship between binding and folding is very important for understanding the function of gene silencing. We have performed molecular dynamics (MD) of both bound and apo-PAZ to study the coupling mechanism between binding and folding in the siRNA-PAZ complex. Room-temperature MD simulations suggest that both PAZ and siRNA become more rigid and stable upon siRNA binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-PAZ unfold via a two-state process. The unfolding pathways are different between bound and apo-PAZ: the order of helix III and helices I & II unfolding is switched. Furthermore, transition probability was used to determine the transition state ensemble for both bound and apo-PAZ. It was found that the transition state of bound PAZ is more compact than that of apo-PAZ. The predicted Φ-values suggest that the Φ-values of helix III and sheets of β3-β7 for bound PAZ are more native-like than those of apo-PAZ upon the binding of siRNA. The results can help us to understand the mechanism of gene silencing.

  8. The development of a simplified Fin Folding Mechanism for a future space transportation vehicle

    NASA Astrophysics Data System (ADS)

    Wood, Brian; Heinrich, Beat; Sutter, Guido; Spycher, Peter; Urmston, Peter

    2005-07-01

    In the time when the Crew Return Vehicle (CRV) was being considered as a follow on joint venture between ESA and NASA, Contraves Space AG was being considered as the sub-contractor for the Fin Folding Mechanism. Although due to the lack of funding in the USA, the CRV programme was stopped, ESTEC decided to continue the development of the Fin Folding Mechanism (FFM) for a "future Space Transportation Vehicle" (STV) for launch and re-entry. Contraves Space was subsequently awarded with a contract to develop a simplified mechanism to replace the mechanism that was designed for CRV. The function of the FFM is to fold the Vehicle Fin inboard so that any future STV can be accommodated in today's launchers. The FFM must be able to support the fin during launch, deploy the fin and then support the fin in the deployed position during re-entry. Contraves Space reviewed the functionality of the old CRV design, with its' different mechanisms for each of the functions, and a synchronisation system, and established a novel design where one mechanism can be used to perform all three functions. The final design utilises a four bar link mechanism, driven over-centre in both of the end positions, driven by a high-torque drive unit comprising a Harmonic Drive, a conventional gearbox and a 3 Phase DC motor. To protect the high-torque drive system against stall, a clutch has been utilised based on spring and rotating ball technology. These devices are used seldom in space, but as surviving stall is often a problem for mechanisms, the results from the test programme will be interesting with respect to the use of such devices in future space mechanisms. The design of the mechanism consists of three almost identical nodes, one of which has been built and is undergoing "qualification" testing at Contraves Space. The mechanism will be subjected to the full range of tests including, functional tests, random vibration tests, thermal vacuum tests and a static load test. This paper will detail

  9. Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins.

    PubMed

    Maitip, Jakkrawut; Trueman, Holly E; Kaehler, Benjamin D; Huttley, Gavin A; Chantawannakul, Panuwan; Sutherland, Tara D

    2015-04-01

    Multiple gene duplication events in the precursor of the Aculeata (bees, ants, hornets) gave rise to four silk genes. Whilst these homologs encode proteins with similar amino acid composition and coiled coil structure, the retention of all four homologs implies they each are important. In this study we identified, produced and characterized the four silk proteins from Apis dorsata, the giant Asian honeybee. The proteins were readily purified, allowing us to investigate the folding behavior of solutions of individual proteins in comparison to mixtures of all four proteins at concentrations where they assemble into their native coiled coil structure. In contrast to solutions of any one protein type, solutions of a mixture of the four proteins formed coiled coils that were stable against dilution and detergent denaturation. The results are consistent with the formation of a heteromeric coiled coil protein complex. The mechanism of silk protein coiled coil formation and evolution is discussed in light of these results. PMID:25712559

  10. Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins.

    PubMed

    Maitip, Jakkrawut; Trueman, Holly E; Kaehler, Benjamin D; Huttley, Gavin A; Chantawannakul, Panuwan; Sutherland, Tara D

    2015-04-01

    Multiple gene duplication events in the precursor of the Aculeata (bees, ants, hornets) gave rise to four silk genes. Whilst these homologs encode proteins with similar amino acid composition and coiled coil structure, the retention of all four homologs implies they each are important. In this study we identified, produced and characterized the four silk proteins from Apis dorsata, the giant Asian honeybee. The proteins were readily purified, allowing us to investigate the folding behavior of solutions of individual proteins in comparison to mixtures of all four proteins at concentrations where they assemble into their native coiled coil structure. In contrast to solutions of any one protein type, solutions of a mixture of the four proteins formed coiled coils that were stable against dilution and detergent denaturation. The results are consistent with the formation of a heteromeric coiled coil protein complex. The mechanism of silk protein coiled coil formation and evolution is discussed in light of these results.

  11. A Better 2-D Mechanical Energy Conservation Experiment

    NASA Astrophysics Data System (ADS)

    Paesler, Michael

    2012-02-01

    A variety of simple classical mechanics energy conservation experiments are used in teaching laboratories. Typical one-dimensional (1-D) setups may involve falling balls or oscillating springs. Many of these can be quite satisfying in that students can confirm—within a few percent—that mechanical energy is conserved. Students generally have little trouble identifying discrepancies such as the loss of a few percent of the gravitational potential energy due to air friction encountered by a falling ball. Two-dimensional (2-D) systems can require more sophisticated analysis for higher level laboratories, but such systems often incorporate complicating components that can make the exercise academically incomplete and experimentally less accurate. The following describes a simple 2-D energy conservation experiment based on the popular "Newton's Cradle" toy that allows students to account for nearly all of the mechanical energy in the system in an academically complete analysis.

  12. A three-dimensional statistical mechanical model of folding double-stranded chain molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbing; Chen, Shi-Jie

    2001-05-01

    Based on a graphical representation of intrachain contacts, we have developed a new three-dimensional model for the statistical mechanics of double-stranded chain molecules. The theory has been tested and validated for the cubic lattice chain conformations. The statistical mechanical model can be applied to the equilibrium folding thermodynamics of a large class of chain molecules, including protein β-hairpin conformations and RNA secondary structures. The application of a previously developed two-dimensional model to RNA secondary structure folding thermodynamics generally overestimates the breadth of the melting curves [S-J. Chen and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 97, 646 (2000)], suggesting an underestimation for the sharpness of the conformational transitions. In this work, we show that the new three-dimensional model gives much sharper melting curves than the two-dimensional model. We believe that the new three-dimensional model may give much improved predictions for the thermodynamic properties of RNA conformational changes than the previous two-dimensional model.

  13. Origami mechanical metamaterials based on the Miura-derivative fold patterns

    NASA Astrophysics Data System (ADS)

    Zhou, Xiang; Zang, Shixi; You, Zhong

    2016-07-01

    This paper presents two new types of origami-inspired mechanical metamaterials based on the Miura-derivative fold patterns that consist of non-identical parallelogram facets. The analytical models to predict dimension changes and deformation kinematics of the proposed metamaterials are developed. Furthermore, by modelling the creases as revolute hinges with certain rotational spring constants, we derived analytical models for stretching and bulk moduli. The analytical models are validated through finite-element simulation results. Numerical examples reveal that the proposed metamaterials possess some intriguing properties, including negative Poisson's ratios and bulk modulus. The work presented in this paper can provide a highly flexible framework for the design of versatile tunable mechanical metamaterials.

  14. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    PubMed

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  15. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    PubMed Central

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  16. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-09-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  17. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    PubMed

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  18. Conservation laws in the quantum mechanics of closed systems

    SciTech Connect

    Hartle, J.B. ||; Laflamme, R. |; Marolf, D.

    1995-06-15

    We investigate conservation laws in the quantum mechanics of closed systems and begin by reviewing an argument that exact decoherence implies the exact conservation of quantities that commute with the Hamiltonian. However, we also show that decoherence limits the alternatives that can be included in sets of histories that assess the conservation of these quantities. In the case of charge and energy, these limitations would be severe were these quantities not coupled to a gauge field. However, for the realistic cases of electric charge coupled to the electromagnetic field and mass coupled to spacetime curvature, we show that when alternative values of charge and mass decohere they always decohere exactly and are exactly conserved. Further, while decohering histories that describe possible changes in time of the total charge and mass are also subject to the limitations mentioned above, we show that these do not, in fact, restrict {ital physical} alternatives and are therefore not really limitations at all.

  19. Role of five-fold twin boundary on the enhanced mechanical properties of fcc Fe nanowires.

    PubMed

    Wu, J Y; Nagao, S; He, J Y; Zhang, Z L

    2011-12-14

    The role of 5-fold twin boundary on the structural and mechanical properties of fcc Fe nanowire under tension is explored by classical molecular dynamics. Twin-stabilized fcc nanowire with various diameters (6-24 nm) are examined by tension tests at several temperatures ranging from 0.01 to 1100 K. Significant increase in the Young's modulus of the smaller nanowires is revealed to originate from the central area of quinquefoliolate-like stress-distribution over the 5-fold twin, rather than from the surface tension that is often considered as the main source of such size-effects found in nanostructures. Because of the excess compressive stress caused by crossing twin-boundaries, the atoms in the center behave stiffer than those in bulk and even expand laterally under axial tension, providing locally negative Poisson's ratio. The yield strength of nanowire is also enhanced by the twin boundary that suppresses dislocation nucleation within a fcc twin-domain; therefore, the plasticity of nanowire is initiated by strain-induced fcc→bcc phase transformation that destroys the twin structure. After the yield, the nucleated bcc phase immediately spreads to the entire area, and forms a multigrain structure to realize ductile deformation followed by necking. As temperature elevated close to the critical temperature between bcc and fcc phases, the increased stability of fcc phase competes with the phase transformation under tension, and hence dislocation nucleations in fcc phase are observed exclusively at the highest temperature in our study.

  20. The E. coli thioredoxin folding mechanism: the key role of the C-terminal helix.

    PubMed

    Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

    2015-02-01

    In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability.

  1. Conservation of Mechanical and Electric Energy: Simple Experimental Verification

    ERIC Educational Resources Information Center

    Ponikvar, D.; Planinsic, G.

    2009-01-01

    Two similar experiments on conservation of energy and transformation of mechanical into electrical energy are presented. Both can be used in classes, as they offer numerous possibilities for discussion with students and are simple to perform. Results are presented and are precise within 20% for the version of the experiment where measured values…

  2. Rule-Governed Approaches to Physics: Conservation of Mechanical Energy.

    ERIC Educational Resources Information Center

    Maloney, David P.

    1985-01-01

    Investigated methods science and nonscience majors use to make predictions about five situations involving the conservation of mechanical energy. Two findings, among others, show that subjects did not employ identifiable strategies in over 97 percent of the cases and show differences in the way majors and nonmajors worked the problems given.…

  3. Mechanics of fold-and-thrust belts and accretionary wedges Cohesive Coulomb theory

    NASA Technical Reports Server (NTRS)

    Dahlen, F. A.; Suppe, J.; Davis, D.

    1984-01-01

    A self-consistent theory for the mechanics of thin-skinned accretionary Coulomb wedges is developed and applied to the active fold-and-thrust belt of western Taiwan. The state of stress everywhere within a critical wedge is determined by solving the static equilibrium equations subject to the appropriate boundary conditions. The influence of wedge cohesion, which gives rise to a concave curvature of the critical topographic surface and affects the orientation of the principal stresses and Coulomb fracture within the wedge, is considered. The shape of the topographic surface and the angles at which thrust faults step up from the basal decollement in the Taiwanese belt is analyzed taking into account the extensive structural and fluid-pressure data available there. It is concluded that the gross geometry and structure of the Taiwan wedge are consistent with normal laboratory frictional and fracture strengths of sedimentary rocks.

  4. Constraints on bed scale fracture chronology with a FEM mechanical model of folding: The case of Split Mountain (Utah, USA)

    NASA Astrophysics Data System (ADS)

    Sassi, W.; Guiton, M. L. E.; Leroy, Y. M.; Daniel, J.-M.; Callot, J.-P.

    2012-11-01

    A technique is presented for improving the structural analysis of natural fractures development in large scale fold structures. A 3D restoration of a fold provides the external displacement loading conditions to solve, by the finite element method, the forward mechanical problem of an idealized rock material with a stress-strain relationship based on the activation of pervasive fracture sets. In this elasto-plasticity constitutive law, any activated fracture set contributes to the total plastic strain by either an opening or a sliding mode of rock failure. Inherited versus syn-folding fracture sets development can be studied using this mechanical model. The workflow of this methodology was applied to the Weber sandstone formation deformed by forced folding at Split Mountain Anticline, Utah for which the different fracture sets were created and developed successively during the Sevier and the syn-folding Laramide orogenic phases. The field observations at the top stratigraphic surface of the Weber sandstone lead to classify the fracture sets into a pre-fold WNW-ESE fracture set, and a NE-SW fracture set post-dating the former. The development and relative chronology of the fracture sets are discussed based on the geomechanical modeling results. Starting with a 3D restoration of the Split Mountain Anticline, three fold-fracture development models were generated, alternately assuming that the WNW-ESE fracture set is either present or absent prior to folding process. Depending on the initial fracture configuration, the calculated fracture patterns are markedly different, showing that assuming a WNW-ESE joint set to predate the fold best correlates with field observations. This study is a first step addressing the complex problem of identification of fold-related fracturing events using an elementary concept of rock mechanics. When tight to complementary field observations, including petrography, diagenesis and burial history, the approach can be used to better

  5. Metric space formulation of quantum mechanical conservation laws

    NASA Astrophysics Data System (ADS)

    Sharp, P. M.; D'Amico, I.

    2014-03-01

    We show that conservation laws in quantum mechanics naturally lead to metric spaces for the set of related physical quantities. All such metric spaces have an "onion-shell" geometry. We demonstrate the power of this approach by considering many-body systems immersed in a magnetic field, with a finite ground state current. In the associated metric spaces we find regions of allowed and forbidden distances, a "band structure" in metric space directly arising from the conservation of the z component of the angular momentum.

  6. Flux continuity and probability conservation in complexified Bohmian mechanics

    SciTech Connect

    Poirier, Bill

    2008-02-15

    Recent years have seen increased interest in complexified Bohmian mechanical trajectory calculations for quantum systems as both a pedagogical and computational tool. In the latter context, it is essential that trajectories satisfy probability conservation to ensure they are always guided to where they are most needed. We consider probability conservation for complexified Bohmian trajectories. The analysis relies on time-reversal symmetry considerations, leading to a generalized expression for the conjugation of wave functions of complexified variables. This in turn enables meaningful discussion of complexified flux continuity, which turns out not to be satisfied in general, though a related property is found to be true. The main conclusion, though, is that even under a weak interpretation, probability is not conserved along complex Bohmian trajectories.

  7. Effect of hydrogen bond networks on the nucleation mechanism of protein folding

    NASA Astrophysics Data System (ADS)

    Djikaev, Y. S.; Ruckenstein, Eli

    2009-12-01

    We have recently developed a kinetic model for the nucleation mechanism of protein folding (NMPF) in terms of ternary nucleation by using the first passage time analysis. A protein was considered as a random heteropolymer consisting of hydrophobic, hydrophilic (some of which are negatively or positively ionizable), and neutral beads. The main idea of the NMPF model consisted of averaging the dihedral potential in which a selected residue is involved over all possible configurations of all neighboring residues along the protein chain. The combination of the average dihedral, effective pairwise (due to Lennard-Jones-type and electrostatic interactions), and confining (due to the polymer connectivity constraint) potentials gives rise to an overall potential around the cluster that, as a function of the distance from the cluster center, has a double-well shape. This allows one to evaluate the protein folding time. In the original NMPF model hydrogen bonding was not taken into account explicitly. To improve the NMPF model and make it more realistic, in this paper we modify our (previously developed) probabilistic hydrogen bond model and combine it with the former. Thus, a contribution due to the disruption of hydrogen bond networks around the interacting particles (cluster of native residues and residue in the protein unfolded part) appears in the overall potential field around a cluster. The modified model is applied to the folding of the same model proteins that were examined in the original model: a short protein consisting of 124 residues (roughly mimicking bovine pancreatic ribonuclease) and a long one consisting of 2500 residues (as a representative of large proteins with superlong polypeptide chains), at pH=8.3 , 7.3, and 6.3. The hydrogen bond contribution now plays a dominant role in the total potential field around the cluster (except for very short distances thereto where the repulsive energy tends to infinity). It is by an order of magnitude stronger for

  8. Deep evolutionary conservation of an intramolecular protein kinase activation mechanism.

    PubMed

    Han, Jingfen; Miranda-Saavedra, Diego; Luebbering, Nathan; Singh, Aman; Sibbet, Gary; Ferguson, Michael A J; Cleghon, Vaughn

    2012-01-01

    DYRK-family kinases employ an intramolecular mechanism to autophosphorylate a critical tyrosine residue in the activation loop. Once phosphorylated, DYRKs lose tyrosine kinase activity and function as serine/threonine kinases. DYRKs have been characterized in organisms from yeast to human; however, all entities belong to the Unikont supergroup, only one of five eukaryotic supergroups. To assess the evolutionary age and conservation of the DYRK intramolecular kinase-activation mechanism, we surveyed 21 genomes representing four of the five eukaryotic supergroups for the presence of DYRKs. We also analyzed the activation mechanism of the sole DYRK (class 2 DYRK) present in Trypanosoma brucei (TbDYRK2), a member of the excavate supergroup and separated from Drosophila by ∼850 million years. Bioinformatics showed the DYRKs clustering into five known subfamilies, class 1, class 2, Yaks, HIPKs and Prp4s. Only class 2 DYRKs were present in all four supergroups. These diverse class 2 DYRKs also exhibited conservation of N-terminal NAPA regions located outside of the kinase domain, and were shown to have an essential role in activation loop autophosphorylation of Drosophila DmDYRK2. Class 2 TbDYRK2 required the activation loop tyrosine conserved in other DYRKs, the NAPA regions were critical for this autophosphorylation event, and the NAPA-regions of Trypanosoma and human DYRK2 complemented autophosphorylation by the kinase domain of DmDYRK2 in trans. Finally, sequential deletion analysis was used to further define the minimal region required for trans-complementation. Our analysis provides strong evidence that class 2 DYRKs were present in the primordial or root eukaryote, and suggest this subgroup may be the oldest, founding member of the DYRK family. The conservation of activation loop autophosphorylation demonstrates that kinase self-activation mechanisms are also primitive.

  9. Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

    PubMed Central

    Brás, Joana L. A.; Cartmell, Alan; Carvalho, Ana Luísa M.; Verzé, Genny; Bayer, Edward A.; Vazana, Yael; Correia, Márcia A. S.; Prates, José A. M.; Ratnaparkhe, Supriya; Boraston, Alisdair B.; Romão, Maria J.; Fontes, Carlos M. G. A.; Gilbert, Harry J.

    2011-01-01

    Clostridium thermocellum is a well-characterized cellulose-degrading microorganism. The genome sequence of C. thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose-degrading apparatus, but display no significant sequence similarity to known plant cell wall–degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel48S, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Å, displays a superhelical fold in which a constellation of α-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose. PMID:21393568

  10. Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity.

    PubMed

    Caniparoli, Luca; O'Brien, Edward P

    2015-04-14

    In a cell, the folding of a protein molecule into tertiary structure can begin while it is synthesized by the ribosome. The rate at which individual amino acids are incorporated into the elongating nascent chain has been shown to affect the likelihood that proteins will populate their folded state, indicating that co-translational protein folding is a far from equilibrium process. Developing a theoretical framework to accurately describe this process is, therefore, crucial for advancing our understanding of how proteins acquire their functional conformation in living cells. Current state-of-the-art computational approaches, such as molecular dynamics simulations, are very demanding in terms of the required computer resources, making the simulation of co-translational protein folding difficult. Here, we overcome this limitation by introducing an efficient approach that predicts the effects that variable codon translation rates have on co-translational folding pathways. Our approach is based on Markov chains. By using as an input a relatively small number of molecular dynamics simulations, it allows for the computation of the probability that a nascent protein is in any state as a function of the translation rate of individual codons along a mRNA's open reading frame. Due to its computational efficiency and favorable scalability with the complexity of the folding mechanism, this approach could enable proteome-wide computational studies of the influence of translation dynamics on co-translational folding. PMID:25877595

  11. Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity

    NASA Astrophysics Data System (ADS)

    Caniparoli, Luca; O'Brien, Edward P.

    2015-04-01

    In a cell, the folding of a protein molecule into tertiary structure can begin while it is synthesized by the ribosome. The rate at which individual amino acids are incorporated into the elongating nascent chain has been shown to affect the likelihood that proteins will populate their folded state, indicating that co-translational protein folding is a far from equilibrium process. Developing a theoretical framework to accurately describe this process is, therefore, crucial for advancing our understanding of how proteins acquire their functional conformation in living cells. Current state-of-the-art computational approaches, such as molecular dynamics simulations, are very demanding in terms of the required computer resources, making the simulation of co-translational protein folding difficult. Here, we overcome this limitation by introducing an efficient approach that predicts the effects that variable codon translation rates have on co-translational folding pathways. Our approach is based on Markov chains. By using as an input a relatively small number of molecular dynamics simulations, it allows for the computation of the probability that a nascent protein is in any state as a function of the translation rate of individual codons along a mRNA's open reading frame. Due to its computational efficiency and favorable scalability with the complexity of the folding mechanism, this approach could enable proteome-wide computational studies of the influence of translation dynamics on co-translational folding.

  12. Methods for detecting formation mechanisms and determining a final strain value for different scales of folded structures

    NASA Astrophysics Data System (ADS)

    Yakovlev, Fedor L.

    2012-03-01

    Linear folding, developing in fold and thrust belts, is treated as a hierarchic system, at each level of which objects are described by special kinematic models. Geometric parameters of natural folded structures are determined by a combination of various mechanisms incorporated in the model, and a value of finite strain. Several case studies demonstrate how such data enables one to solve structural and geodynamic problems for natural objects of different size. Shortening value of two morphological types of folds is determined based on the geometry of competent layers. Application of the method to analyze the folds of the Vorontsov nappe (Greater Caucasus) determines its gravitational origin. Structural cross-sections though several tectonic zones are subdivided into relatively small domains, the geometry of which, particularly in thin-bedded flysch deposits, making it possible to identify the mechanisms of formation of both local and large structures, and also to reconstruct the pre-folded state of each domain and of the entire cross-sections. By aggregation of tectonic domains into large modules and determination of the value of shortening, we have constructed for the first time a 3D model of the present-day structure of the northwestern Caucasus, which is balanced for the whole sedimentary cover. The geometry of large structures makes it possible to validate geodynamic models.

  13. A new mechanism for energy conservation technology services

    SciTech Connect

    Yan, Feng

    1996-12-31

    In the ninth-five year plan of China, the socialist market economy model will be developed. In the stage of transferring from planning economy to market economy, the energy conservation technology services industry in China has met new challenges. Over the past ten to fifteen years, there has developed a new mechanism for financing energy efficiency investments in market economies. The process is simple. After inspecting an enterprise or an entity for energy saving opportunities, an Energy Service Company (ESCO) which business aimed at making money will review the recommended energy conservation opportunities with the enterprise or the entity (user) and implement those measures acceptable to the user at no front end cost to the user. The ESCO then guarantees that the energy savings will cover the cost of the capital renovations using the Performance Contracting.

  14. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    SciTech Connect

    Hsu, P. J.; Lai, S. K.; Cheong, S. A.

    2014-05-28

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein

  15. Using D-amino acids to delineate the mechanism of protein folding: Application to Trp-cage

    NASA Astrophysics Data System (ADS)

    Culik, Robert M.; Annavarapu, Srinivas; Nanda, Vikas; Gai, Feng

    2013-08-01

    Using the miniprotein Trp-cage as a model, we show that D-amino acids can be used to facilitate the delineation of protein folding mechanism. Specifically, we study the folding-unfolding kinetics of three Trp-cage mutants where the native glycine residue near the C-terminus of the α-helix is replaced by a D-amino acid. A previous study showed that these mutations increase the Trp-cage stability, due to a terminal capping effect. Our results show that the stabilizing effect of D-asparagine and D-glutamine originates almost exclusively from a decrease in the unfolding rate, while the D-alanine mutation results in a similar decrease in the unfolding rate, but it also increases the folding rate. Together, these results support a folding mechanism wherein the α-helix formation in the transition state is nucleated at the N-terminus, whereas those long-range native interactions stabilizing this helix are developed at the downhill side of the folding free energy barrier.

  16. Significance of first-order faults in folding mechanically isotropic layers: evidence from the Sudbury Basin, Canada.

    NASA Astrophysics Data System (ADS)

    Clark, Martin; Riller, Ulrich

    2016-04-01

    The Sudbury Basin in Canada is a fold basin demarcated by the Sudbury Igneous Complex (SIC). Folding of the SIC is particularly notable due to its petrographically distinct but mechanically similar layers that are hardly strained when compared to folded strata in other deformed terranes. The Sudbury Basin has three ranges, the North Range, the South Range, and the East Range. The East Range differs from the other ranges by inclosing a remarkably shorter SIC segment with a strong concave curvature. Lacking significant mechanical anisotropy and solid-state strain within the SIC brings to question how the SIC in the East Range acquired its curvature. To address this question, we analyzed the orientation of prominent km-scale faults and their slip vectors. These faults transect the SIC at low angles and mimic its plan view curvature suggesting that the faults were folded along with the SIC. We have developed a G.I.S.-based workflow to address this problem that harnesses high-resolution LiDAR data to generate near surface fault geometries, and combines these geometries with local fault-slip inversions of slickensides to identify slip vectors of prominent curved faults. Analysis of slip vectors along curved faults yields clusters of slip vectors with normal and reverse slip motion in the northern and southern fault segments, respectively. The variation in slip vectors is interpreted to be non-primary and thus shows a temporal relationship between faulting and folding of the SIC. Therefore, prominent curved faults in the East Range must have occurred as a pre-folding brittle response to horizontal shortening. These faults later assumed the role of mechanical anisotropic elements necessary for folding of the SIC layers to occur. This interpretation is corroborated by two sets of principal strain axes inferred from fault-slip inversions. The first set is characterized by its principal axis of shortening oriented NW-SE, comparable in orientation to regional shortening as

  17. Statistical mechanics of a correlated energy landscape model for protein folding funnels

    NASA Astrophysics Data System (ADS)

    Plotkin, Steven S.; Wang, Jin; Wolynes, Peter G.

    1997-02-01

    In heteropolymers, energetic correlations exist due to polymeric constraints and the locality of interactions. Pair correlations in conjunction with the a priori specification of the existence of a particularly low energy state provide a method of introducing the aspect of minimal frustration to the energy landscapes of random heteropolymers. The resulting funneled landscape exhibits both a phase transition from a molten globule to a folded state, and the heteropolymeric glass transition in the globular state. We model the folding transition in the self-averaging regime, which together with a simple theory of collapse allows us to depict folding as a double-well free energy surface in terms of suitable reaction coordinates. Observed trends in barrier positions and heights with protein sequence length and thermodynamic conditions are discussed within the context of the model. We also discuss the new physics which arises from the introduction of explicitly cooperative many-body interactions, as might arise from sidechain packing and nonadditive hydrophobic forces.

  18. New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation

    PubMed Central

    Kieft, Jeffrey S; Rabe, Jennifer L; Chapman, Erich G

    2015-01-01

    Arthropod-borne flaviviruses (FVs) are a growing world-wide health threat whose incidence and range are increasing. The pathogenicity and cytopathicity of these single-stranded RNA viruses are influenced by viral subgenomic non-protein-coding RNAs (sfRNAs) that the viruses produce to high levels during infection. To generate sfRNAs the virus co-opts the action of the abundant cellular exonuclease Xrn1, which is part of the cell's normal RNA turnover machinery. This exploitation of the cellular machinery is enabled by discrete, highly structured, Xrn1-resistant RNA elements (xrRNAs) in the 3′UTR that interact with Xrn1 to halt processive 5′ to 3′ decay of the viral genomic RNA. We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance. Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested. However, there is some variability in the structures that correlates with unexplained patterns in the viral 3′ UTRs. Finally, examination of these structures and their behavior in the context of viral infection leads to a new hypothesis linking RNA tertiary structure, overall 3′ UTR architecture, sfRNA production, and host adaptation. PMID:26399159

  19. Architecture and Folding Mechanism of the Azoarcus Group I Pre-tRNA

    SciTech Connect

    Rangan,P.; Masquida, B.; Westhof, E.; Woodson, S.

    2004-01-01

    Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA{sup ile} from the bacterium Azoarcus was probed by ribonuclease T1 and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3{prime}-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg{sup 2+} and the concentration of urea, and RNase T1 experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5{prime} and 3{prime} ends of unspliced pre-tRNA.

  20. Three-dimensional geometry, strain rates and basement deformation mechanisms of thrust-bend folding

    NASA Astrophysics Data System (ADS)

    Wibberley, Christopher A. J.

    1997-03-01

    Models for thrust-bend folding of an isotropic medium are used to predict initial basement thrust sheet geometries and sub-surface thrust fault shapes from final basement thrust sheet structure. Predicted strains and strain rates from these models are compared with data on deformation fabrics in an example of a basement thrustbend fold in order to characterise the deformation response to thrust-bend folding. The Glencoul thrust sheet in the Moine Thrust Zone of north-west Scotland is restored to an initial thrust sheet geometry. Spatial and orientation distribution data of syn-emplacement fractures and cataclastic fault zones from within the Glencoul thrust sheet are then compared with the strain and strain rate histories predicted by thrust-bend folding models. A different set of cataclastic fault seams is demonstrated to have been generated at each frontal thrust bend. Cataclastic failure is restricted to portions of the thrust sheet that have moved over frontal bends with smaller radii of curvature. From model thrust-bend geometries and an assumed slip rate of 1 x 10 -10 ms -1, estimated minimum (critical) strain rates required for fracture failure of the Lewisian basement are 10 -11 to 10 -14 s -1 for shear strain rates and 10 -12 to 10 -15 s -1 for extensional strain rates.

  1. Modelling "reality" in tectonics: Simulation of the mechanical evolution of the Jura Mountains-Molasse Basin system, and routes to forward-inverse modelling of fold thrust belts.

    NASA Astrophysics Data System (ADS)

    Hindle, David; Kley, Jonas

    2016-04-01

    The ultimate validation of any numerical model of any geological process comes when it can accurately forward model a case study from the geological record. However, as the example of the Jura-Molasse fold thrust belt demonstrates, geological information on even the most basic aspects of the present day state of such systems is highly incomplete and usually known only with large uncertainties. Fold thrust-belts are studied and understood by geologists in an iterative process of constructing their subsurface geometries and structures (folds, faults, bedding etc) based on limited subsurface information from boreholes, tunnels or seismic data where available, and surface information on outcrops of different layers and their dips. This data is usually processed through geometric models which involve conservation of line length of different beds over the length of an entire cross section. Constructing such sections is the art of cross section balancing. A balanced cross section can be easily restored to its pre-deformation state, assuming (usually) originally horizontal bedding to remove the effects of folding and faulting. Such a pre-deformation state can then form an initial condition for a forward mechanical model of the section. A mechanical model introduces new parameters into the system such as rock elasticity, cohesion, and frictional properties. However, a forward mechanical model can also potentially show the continuous evolution of a fold thrust belt, including dynamic quantities like stress. Moreover, a forward mechanical model, if correct in most aspects, should match in its final state, the present day geological cross section it is simulating. However, when attempting to achieve a match between geometric and mechanical models, it becomes clear that many more aspects of the geodynamic history of a fold thrust belt have to be taken into account. Erosion of the uppermost layers of an evolving thrust belt is the most obvious one of these. This can potentially

  2. RNA under tension: Folding Landscapes, Kinetic partitioning Mechanism, and Molecular Tensegrity.

    PubMed

    Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D

    2012-11-19

    Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single molecule pulling when combined with with theory and simulations can be used to quantitatively explore the folding landscape of nucleic acid hairpins, and riboswitches with tertiary interactions. Applications to riboswitches, which are non-coding RNA elements that control gene expression by undergoing dynamical conformational changes in response to binding of metabolites, lead to an organization principle that assembly of RNA is determined by the stability of isolated helices. We also point out the limitations of single molecule pulling experiments, with molecular extension as the only accessible parameter, in extracting key parameters of the folding landscapes of RNA molecules. PMID:23336034

  3. Conservation of information and the foundations of quantum mechanics

    NASA Astrophysics Data System (ADS)

    Chiribella, Giulio; Scandolo, Carlo Maria

    2015-05-01

    We review a recent approach to the foundations of quantum mechanics inspired by quantum information theory [1, 2]. The approach is based on a general framework, which allows one to address a large class of physical theories which share basic information-theoretic features. We first illustrate two very primitive features, expressed by the axioms of causality and purity-preservation, which are satisfied by both classical and quantum theory. We then discuss the axiom of purification, which expresses a strong version of the Conservation of Information and captures the core of a vast number of protocols in quantum information. Purification is a highly non-classical feature and leads directly to the emergence of entanglement at the purely conceptual level, without any reference to the superposition principle. Supplemented by a few additional requirements, satisfied by classical and quantum theory, it provides a complete axiomatic characterization of quantum theory for finite dimensional systems.

  4. Molecular mechanism of energy conservation in polysulfide respiration

    PubMed Central

    Jormakka, Mika; Yokoyama, Ken; Yano, Takahiro; Tamakoshi, Masatada; Akimoto, Satoru; Shimamura, Tatsuro; Curmi, Paul; Iwata, So

    2010-01-01

    Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex responsible for quinone coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. We determined the structure of polysulfide reductase from Thermus thermophilus at 2.4 Å resolution, revealing how the PsrA subunit recognizes and reduces its unique poly anionic substrate. The integral membrane subunit PsrC was characterized using the natural substrate menaquinone-7 and inhibitors, providing a comprehensive representation of a quinone binding site and revealing the presence of a water filled cavity connecting the quinone binding site on the periplasmic side to the cytoplasm. These results suggest that polysulfide reductase could be a key energy-conserving enzyme of the T. thermophilus respiratory chain, utilizing polysulfide as the terminal electron acceptor and pumping protons across the membrane via a previously unknown mechanism. PMID:18536726

  5. Gauge transformations and conserved quantities in classical and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Berche, Bertrand; Malterre, Daniel; Medina, Ernesto

    2016-08-01

    We are taught that gauge transformations in classical and quantum mechanics do not change the physics of the problem. Nevertheless, here we discuss three broad scenarios where under gauge transformations: (i) conservation laws are not preserved in the usual manner; (ii) non-gauge-invariant quantities can be associated with physical observables; and (iii) there are changes in the physical boundary conditions of the wave function that render it non-single-valued. We give worked examples that illustrate these points, in contrast to general opinions from classic texts. We also give a historical perspective on the development of Abelian gauge theory in relation to our particular points. Our aim is to provide a discussion of these issues at the graduate level.

  6. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P).

    PubMed

    da Palma, Joel Ramos; Cendron, Laura; Seidah, Nabil Georges; Pasquato, Antonella; Kunz, Stefan

    2016-01-29

    The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process.

  7. NMR Structure of Conserved Eukaryotic Protein ZK652.3 from C. elegans: a Ubiquitin-like Fold

    SciTech Connect

    Cort, John R. ); Chiang, Yiwen; Zheng, Deyou; Kennedy, Michael A. ); Montelione, Gaetano

    2002-09-01

    Structural proteomics aims to provide one or more representative 3D structures for every structural domain family in nature. As part of an international effort in structural proteomics, the Northeast Structural Genomics Consortium has targeted clusters of strongly conserved eukaryotic protein families for structural and functional analysis. On this basis, protein ZK652.3 (nesg WR41 / YOY3{_}CAEEL / Swiss-Prot P34661 / gi|17557033) from Caenorhabditis elegans was selected for structure determination. Expression of the ZK652.3 gene has been observed in a transcriptional profile of C. elegans genes, where it was one of a cluster of 89 genes whose expression levels co-varied during development1. The biochemical function of this protein is presently unknown. Sequencing of cDNA libraries shows that homologues of ZK652.3 occur widely in vertebrates and plants (Fig. 1). However, ZK652.3 homologues are conspicuously absent from the yeast and Drosophila genomes. Here we describe the three-dimensional structure of ZK652.3 determined by NMR spectroscopy and discuss structural similarities with other proteins which provide clues to potential biochemical functions.

  8. Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB

    SciTech Connect

    Hung, Kuo-Wei; Chang, Yi-Wei; Eng, Edward T.; Chen, Jai-Hui; Chen, Yi-Chung; Sun, Yuh-Ju; Hsiao, Chwan-Deng; Dong, Gang; Spasov, Krasimir A.; Unger, Vinzenz M.; Huang, Tai-huang

    2010-09-17

    FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. Here, we report the crystal structures of the intracellular domain of FeoB (NFeoB) from Klebsiella pneumoniae (KpNFeoB) and Pyrococcus furiosus (PfNFeoB) with and without bound ligands. In the structures, a canonical G-protein domain (G domain) is followed by a helical bundle domain (S-domain), which despite its lack of sequence similarity between species is structurally conserved. In the nucleotide-free state, the G-domain's two switch regions point away from the binding site. This gives rise to an open binding pocket whose shallowness is likely to be responsible for the low nucleotide-binding affinity. Nucleotide binding induced significant conformational changes in the G5 motif which in the case of GMPPNP binding was accompanied by destabilization of the switch I region. In addition to the structural data, we demonstrate that Fe(II)-induced foot printing cleaves the protein close to a putative Fe(II)-binding site at the tip of switch I, and we identify functionally important regions within the S-domain. Moreover, we show that NFeoB exists as a monomer in solution, and that its two constituent domains can undergo large conformational changes. The data show that the S-domain plays important roles in FeoB function.

  9. Effect of hydrophobic interactions on the folding mechanism of β-hairpins.

    PubMed

    Popp, Alexander; Wu, Ling; Keiderling, Timothy A; Hauser, Karin

    2014-12-11

    Hydrophobic interactions are essential in stabilizing protein structures. How they affect the folding pathway and kinetics, however, is less clear. We used time-resolved infrared spectroscopy to study the dynamics of hydrophobic interactions of β-hairpin variants of the sequence Trpzip2 (SWTWENGKWTWK-NH2) that is stabilized by two cross-strand Trp-Trp pairs. The hydrophobicity strength was varied by substituting the tryptophans pairwise by either tyrosines or valines. Relaxation dynamics were induced by a laser-excited temperature jump, which separately probed for the loss of the cross-strand β-hairpin interaction and the rise of the disordered structure. All substitutions tested result in reduced thermal stability, lower transition temperatures, and faster dynamics compared to Trpzip2. However, the changes in folding dynamics depend on the amino acid substituted for Trp. The aromatic substitution of Tyr for Trp results in the same kinetics for the unfolding of sheet and growth of disorder, with similar activation energies, independent of the substitution position. Substitution of Trp with a solely hydrophobic Val results in even faster kinetics than substitution with Tyr but is additionally site-dependent. If the hairpin has a Val pair close to its termini, the rate constants for loss of sheet and gain of disorder are the same, but if the pair is close to the turn, the sheet and disorder components show different relaxation kinetics. The Trp → Val substitutions reveal that hydrophobic interactions alone weakly stabilize the hairpin structure, but adding edge-to-face aromatic interaction strengthens it, and both modify the complex folding process.

  10. Mechanisms for GroEL/GroES-mediated folding of a large 86-kDa fusion polypeptide in vitro.

    PubMed

    Huang, Y S; Chuang, D T

    1999-04-01

    Our understanding of mechanisms for GroEL/GroES-assisted protein folding to date has been derived mostly from studies with small proteins. Little is known concerning the interaction of these chaperonins with large multidomain polypeptides during folding. In the present study, we investigated chaperonin-dependent folding of a large 86-kDa fusion polypeptide, in which the mature maltose-binding protein (MBP) sequence was linked to the N terminus of the alpha subunit of the decarboxylase (E1) component of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex. The fusion polypeptide, MBP-alpha, when co-expressed with the beta subunit of E1, produced a chimeric protein MBP-E1 with an (MBP-alpha)2beta2 structure, similar to the alpha2 beta2 structure in native E1. Reactivation of MBP-E1 denatured in 8 M urea was absolutely dependent on GroEL/GroES and Mg2+-ATP, and exhibited strikingly slow kinetics with a rate constant of 376 M-1 s-1, analogous to denatured untagged E1. Chaperonin-mediated refolding of the MBP-alpha fusion polypeptide showed that the folding of the MBP moiety was about 7-fold faster than that of the alpha moiety on the same chain with rate constants of 1.9 x 10(-3) s-1 and 2.95 x 10(-4) s-1, respectively. This explained the occurrence of an MBP-alpha. GroEL binary complex that was isolated with amylose resin from the refolding mixture and transformed Escherichia coli lysates. The data support the thesis that distinct functional sequences in a large polypeptide exhibit different folding characteristics on the same GroEL scaffold. Moreover, we show that when the alpha.GroEL complex (molar ratio 1:1) was incubated with GroES, the latter was capable of capping either the very ring that harbored the 48-kDa (His)6-alpha polypeptide (in cis) or the opposite unoccupied cavity (in trans). In contrast, the MBP-alpha.GroEL (1:1) complex was capped by GroES exclusively in the trans configuration. These findings suggest that the productive

  11. Role of folded anisotropic fabric in the failure mode of gneiss: new insights from mechanical, microseismic and microstructural laboratory data

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Vinciguerra, Sergio; Dobbs, Marcus R.; Zanchetta, Stefano

    2015-04-01

    Fabric anisotropy is a key control of the mechanical behaviour of rocks in a variety of geological settings and on different timescales. However, the effects of inherited, tectonically folded anisotropic fabrics on the brittle strength and failure mode of foliated metamorphic rocks is yet to be fully understood. Data from laboratory uniaxial compression tests on folded gneiss (Agliardi et al., 2014, Tectonophysics) recently showed that the brittle failure mode of this rock type depends on the arrangement of two distinct anisotropies (i.e. foliation and fold axial plane anisotropy), and that rock strength correlates with failure mode. Here we investigate the effects of confining pressure on this behaviour by performing triaxial compression experiments with acoustic emission (AE) monitoring, and analyse resulting fracture mechanisms and their microfabric controls using high resolution microanalysis techniques. We tested the Monte Canale Gneiss (Austroalpine Bernina nappe, Central Italian Alps), characterized by low phyllosilicate content, compositional layering folded at the cm-scale, and absence of a well-developed axial plane foliation. We used a servo-controlled hydraulic loading system to test 19 air-dry cylindrical specimens (diameter: 54 mm) that were characterized both in terms of fold geometry and orientation of foliation and fold axial planes to the axial load direction. We instrumented the specimens with direct contact axial and circumferential strain gauges. We performed tests at confining pressures of 40 MPa and constant axial strain rates of 5*10-6 s-1, measuring acoustic emissions and P- and S-wave velocities by three wideband (350-1000 kHz) piezoelectric transceivers with 40 dB preamps, mounted in the compression platens. We carried out post-failure microscale observation of fracture mechanisms, microcrack patterns and related fabric controls on resin-impregnated samples, using X-ray MicroCT (resolution: 9 μm), optical microscopy and SEM. Samples

  12. Conservation of structure and mechanism by Trm5 enzymes

    PubMed Central

    Christian, Thomas; Gamper, Howard; Hou, Ya-Ming

    2013-01-01

    Enzymes of the Trm5 family catalyze methyl transfer from S-adenosyl methionine (AdoMet) to the N1 of G37 to synthesize m1G37-tRNA as a critical determinant to prevent ribosome frameshift errors. Trm5 is specific to eukaryotes and archaea, and it is unrelated in evolution from the bacterial counterpart TrmD, which is a leading anti-bacterial target. The successful targeting of TrmD requires detailed information on Trm5 to avoid cross-species inhibition. However, most information on Trm5 is derived from studies of the archaeal enzyme Methanococcus jannaschii (MjTrm5), whereas little information is available for eukaryotic enzymes. Here we use human Trm5 (Homo sapiens; HsTrm5) as an example of eukaryotic enzymes and demonstrate that it has retained key features of catalytic properties of the archaeal MjTrm5, including the involvement of a general base to mediate one proton transfer. We also address the protease sensitivity of the human enzyme upon expression in bacteria. Using the tRNA-bound crystal structure of the archaeal enzyme as a model, we have identified a single substitution in the human enzyme that improves resistance to proteolysis. These results establish conservation in both the catalytic mechanism and overall structure of Trm5 between evolutionarily distant eukaryotic and archaeal species and validate the crystal structure of the archaeal enzyme as a useful model for studies of the human enzyme. PMID:23887145

  13. Kinetic partitioning mechanism governs the folding of the third FnIII domain of tenascin-C: evidence at the single-molecule level.

    PubMed

    Peng, Qing; Fang, Jie; Wang, Meijia; Li, Hongbin

    2011-09-30

    Statistical mechanics and molecular dynamics simulations proposed that the folding of proteins can follow multiple parallel pathways on a rugged energy landscape from unfolded state en route to their folded native states. Kinetic partitioning mechanism is one of the possible mechanisms underlying such complex folding dynamics. Here, we use single-molecule atomic force microscopy technique to directly probe the multiplicity of the folding pathways of the third fibronectin type III domain from the extracellular matrix protein tenascin-C (TNfn3). By stretching individual (TNfn3)(8) molecules, we forced TNfn3 domains to undergo mechanical unfolding and refolding cycles, allowing us to directly observe the folding pathways of TNfn3. We found that, after being mechanically unraveled and then relaxed to zero force, TNfn3 follows multiple parallel pathways to fold into their native states. The majority of TNfn3 fold into the native state in a simple two-state fashion, while a small percentage of TNfn3 were found to be trapped into kinetically stable folding intermediate states with well-defined three-dimensional structures. Furthermore, the folding of TNfn3 was also influenced by its neighboring TNfn3 domains. Complex misfolded states of TNfn3 were observed, possibly due to the formation of domain-swapped dimeric structures. Our studies revealed the ruggedness of the folding energy landscape of TNfn3 and provided direct experimental evidence that the folding dynamics of TNfn3 are governed by the kinetic partitioning mechanism. Our results demonstrated the unique capability of single-molecule AFM to probe the folding dynamics of proteins at the single-molecule level.

  14. The 69 kDa Escherichia coli maltodextrin glucosidase does not get encapsulated underneath GroES and folds through trans mechanism during GroEL/GroES-assisted folding.

    PubMed

    Paul, Subhankar; Singh, Chanpreet; Mishra, Saroj; Chaudhuri, Tapan K

    2007-09-01

    Escherichia coli chaperonin GroEL and GroES assist in folding of a wide variety of substrate proteins in the molecular mass range of approximately 50 kDa, using cis mechanism, but limited information is available on how they assist in folding of larger proteins. Considering that the central cavity of GroEL can accommodate a non-native protein of approximately 60 kDa, it is important to study the GroEL-GroES-assisted folding of substrate proteins that are large enough for cis encapsulation. In this study, we have reported the mechanism of GroEL/GroES-assisted in vivo and in vitro folding of a 69 kDa monomeric E. coli protein maltodextrin glucosidase (MalZ). Coexpression of GroEL and GroES in E. coli causes a 2-fold enhancement of exogenous MalZ activity in vivo. In vitro, GroEL and GroES in the presence of ATP give rise to a 7-fold enhancement in MalZ refolding. Neither GroEL nor single ring GroEL (SR1) in the presence or absence of ATP could enhance the in vitro folding of MalZ. GroES could not encapsulate GroEL-bound MalZ. All these experimental findings suggested that GroEL/GroES-assisted folding of MalZ followed trans mechanism, whereas denatured MalZ and GroES bound to the opposite rings of a GroEL molecule.

  15. The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold

    PubMed Central

    Santini, Sébastien; Claverie, Jean-Michel; Mouz, Nicolas; Rousselle, Tristan; Maza, Caroline; Monchois, Vincent; Abergel, Chantal

    2011-01-01

    Nosocomial diseases due to Candida albicans infections are in constant rise in hospitals, where they cause serious complications to already fragile intensive care patients. Antifungal drug resistance is fast becoming a serious issue due to the emergence of strains resistant to currently available antifungal agents. Thus the urgency to identify new potential protein targets, the function and structure of which may guide the development of new antifungal drugs. In this context, we initiated a comparative genomics study in search of promising protein coding genes among the most conserved ones in reference fungal genomes. The CA3427 gene was selected on the basis of its presence among pathogenic fungi contrasting with its absence in the non pathogenic Saccharomyces cerevisiae. We report the crystal 3D-structure of the Candida albicans CA3427 protein at 2.1 Å resolution. The combined analysis of its sequence and structure reveals a structural fold originally associated with periplasmic binding proteins. The CA3427 structure highlights a binding site located between the two protein domains, corresponding to a sequence segment conserved among fungi. Two crystal forms of CA3427 were found, suggesting that the presence or absence of a ligand at the proposed binding site might trigger a “Venus flytrap” motion, coupled to the previously described activity of bacterial periplasmic binding proteins. The conserved binding site defines a new subfamily of periplasmic binding proteins also found in many bacteria of the bacteroidetes division, in a choanoflagellate (a free-living unicellular and colonial flagellate eukaryote) and in a placozoan (the closest multicellular relative of animals). A phylogenetic analysis suggests that this gene family originated in bacteria before its horizontal transfer to an ancestral eukaryote prior to the radiation of fungi. It was then lost by the Saccharomycetales which include Saccharomyces cerevisiae. PMID:21494601

  16. Self-oscillating Vocal Fold Model Mechanics: Healthy, Diseased, and Aging

    NASA Astrophysics Data System (ADS)

    Hiubler, Elizabeth P.; Pollok, Lucas F. E.; Apostoli, Adam G.; Hancock, Adrienne B.; Plesniak, Michael W.

    2014-11-01

    Voice disorders have been estimated to have a substantial economic impact of 2.5 billion annually. Approximately 30% of people will suffer from a voice disorder at some point in their lives. Life-sized, self-oscillating, synthetic vocal fold (VF) models are fabricated to exhibit material properties representative of human VFs. These models are created both with and without a polyp-like structure, a pathology that has been shown to produce rich viscous flow structures not normally observed for healthy VFs during normal phonation. Pressure measurements are acquired upstream of the VFs and high-speed images are captured at varying flow rates during VF oscillation to facilitate an understanding of the characteristics of healthy and diseased VFs. The images are analyzed using a videokymography line-scan technique. Clinically-relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to human data collected from two groups of males aged 18-30 and 60-80. This study extends the use of synthetic VF models by assessing their ability to replicate behaviors observed in human subject data to advance a means of investigating changes associated with normal, pathological, and the aging voice. Supported by the GWU Institute for Biomedical Engineering (GWIBE) and GWU Center for Biomimetics and Bioinspired Engineering (COBRE).

  17. Folding mechanism of reduced cytochrome c: Equilibrium and kinetic properties in the presence of carbon monoxide

    PubMed Central

    Latypov, Ramil F.; Maki, Kosuke; Cheng, Hong; Luck, Stanley D.; Roder, Heinrich

    2008-01-01

    Despite close structural similarity, the ferric and ferrous forms of cytochrome c (cyt c) differ greatly in terms of their ligand binding properties, stability, folding and dynamics. The reduced heme iron binds diatomic ligands such as CO only under destabilizing conditions that promote weakening or disruption of the native methionine-iron linkage. This makes CO a useful conformational probe for detecting partially structured states that cannot be observed in the absence of endogenous ligands. Heme absorbance, circular dichroism and NMR were used to characterize the denaturant-induced unfolding equilibrium of Fe2+ cyt c in the presence and absence of CO. In addition to the native state (N), which does not bind CO, and the unfolded CO-complex (U-CO), a structurally distinct CO-bound form (M-CO) accumulates to high levels (~75% of the population) at intermediate guanidine hydrochloride concentrations. Comparison of the unfolding transition for different conformational probes reveals that M-CO is a compact state containing a native-like helical core and regions of local disorder in the segment containing the native Met80 ligand and adjacent loops. Kinetic measurements of CO binding and dissociation under native, partially denaturing and fully unfolded conditions indicate that a state, M, that is structurally analogous to M-CO is populated even in the absence of CO. The binding energy of the CO ligand lowers the free energy of this high-energy state to such an extent that it accumulates even under mildly denaturing equilibrium conditions. The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO-binding equilibria of reduced cyt c. PMID:18761351

  18. Neuroendocrine aging in birds: comparing lifespan differences and conserved mechanisms.

    PubMed

    Ottinger, Mary Ann

    2007-05-01

    As more comparative data become available, it is clear that the process of aging has fundamental similarities across classes of vertebrates. Birds provide a fascinating collection of species because of the considerable range in reproductive lifespan and variation in reproductive strategies that often relate to lifespan. One fascinating aspect of the comparative biology of aging in different avian species is the conserved mechanisms that appear very similar to those observed in mammals. Despite marked differences in sexual differentiation and reproductive function, including a single functional ovary and the internal testes, there appears to be remarkable similarity in elements of neuroendocrine aging and their end results. Furthermore, although beyond the scope of this review, the intense endocrine and energetic demands on many species of temperate zone birds for long migration and the accompanying seasonal alterations in endocrine responses add an additional layer of complexity in understanding aging. It is the purpose of this review to focus on neuroendocrine changes that accompany aging in a short-lived bird, with mention of some of the available data in field birds and long-lived species. Unfortunately, few neuroendocrine data are available for these long-lived avian species. It would be very interesting to determine if these long-lived birds somehow manage to delay the cascade of changes that contribute to the demise of metabolic and reproductive endocrine function. This review will also attempt to integrate the time-related events that occur in the responses of the hypothalamus and the gonads, especially relative to the neuroregulatory systems that have been implicated in the age-related decline in reproductive function. Finally, emerging areas of interest will be considered in the context of future research areas. PMID:17452025

  19. Analyses of simulations of three-dimensional lattice proteins in comparison with a simplified statistical mechanical model of protein folding.

    PubMed

    Abe, H; Wako, H

    2006-07-01

    Folding and unfolding simulations of three-dimensional lattice proteins were analyzed using a simplified statistical mechanical model in which their amino acid sequences and native conformations were incorporated explicitly. Using this statistical mechanical model, under the assumption that only interactions between amino acid residues within a local structure in a native state are considered, the partition function of the system can be calculated for a given native conformation without any adjustable parameter. The simulations were carried out for two different native conformations, for each of which two foldable amino acid sequences were considered. The native and non-native contacts between amino acid residues occurring in the simulations were examined in detail and compared with the results derived from the theoretical model. The equilibrium thermodynamic quantities (free energy, enthalpy, entropy, and the probability of each amino acid residue being in the native state) at various temperatures obtained from the simulations and the theoretical model were also examined in order to characterize the folding processes that depend on the native conformations and the amino acid sequences. Finally, the free energy landscapes were discussed based on these analyses.

  20. Conservation.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  1. Folding Beauties

    ERIC Educational Resources Information Center

    Berman, Leah Wrenn

    2006-01-01

    This article has its genesis in an MAA mini-course on origami, where a way to get a parabola by folding paper was presented. This article discusses the methods and mathematics of other curves obtained by paper-folding.

  2. Malleability of the folding mechanism of the outer membrane protein PagP: parallel pathways and the effect of membrane elasticity.

    PubMed

    Huysmans, Gerard H M; Radford, Sheena E; Baldwin, Stephen A; Brockwell, David J

    2012-02-24

    Understanding the interactions between membrane proteins and the lipid bilayer is key to increasing our ability to predict and tailor the folding mechanism, structure and stability of membrane proteins. Here, we have investigated the effects of changing the membrane composition and the relative concentrations of protein and lipid on the folding mechanism of the bacterial outer membrane protein PagP. The folding pathway, monitored by tryptophan fluorescence, was found to be characterized by a burst phase, representing PagP adsorption to the liposome surface, followed by a time course that reflects the folding and insertion of the protein into the membrane. In 1,2-dilauroyl-sn-glycero-3-phosphocholine (diC(12:0)PC) liposomes, the post-adsorption time course fits well to a single exponential at high lipid-to-protein ratios (LPRs), but at low LPRs, a second exponential phase with a slower folding rate constant is observed. Interrupted refolding assays demonstrated that the two exponential phases reflect the presence of parallel folding pathways. Partitioning between these pathways was found to be modulated by the elastic properties of the membrane. Folding into mixed 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine:diC(12:0)PC liposomes resulted in a decrease in PagP adsorption to the liposomes and a switch to the slower folding pathway. By contrast, inclusion of 1,2-dilauroyl-sn-glycero-3-phosphoserine into diC(12:0)PC liposomes resulted in a decrease in the folding rate of the fast pathway. The results highlight the effect of lipid composition in tailoring the folding mechanism of a membrane protein, revealing that membrane proteins have access to multiple, competing folding routes to a unique native structure.

  3. Extreme Folding

    NASA Astrophysics Data System (ADS)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  4. GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding.

    PubMed

    Georgescauld, Florian; Popova, Kristina; Gupta, Amit J; Bracher, Andreas; Engen, John R; Hayer-Hartl, Manajit; Hartl, F Ulrich

    2014-05-01

    The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (βα)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. Here, we analyzed the folding of DapA at peptide resolution using hydrogen/deuterium exchange and mass spectrometry. During spontaneous folding, all elements of the DapA TIM barrel acquire structure simultaneously in a process associated with a long search time. In contrast, GroEL/ES accelerates folding more than 30-fold by catalyzing segmental structure formation in the TIM barrel. Segmental structure formation is also observed during the fast spontaneous folding of a structural homolog of DapA from a bacterium that lacks GroEL/ES. Thus, chaperonin independence correlates with folding properties otherwise enforced by protein confinement in the GroEL/ES cage. We suggest that folding catalysis by GroEL/ES is required by a set of proteins to reach native state at a biologically relevant timescale, avoiding aggregation or degradation.

  5. Conservative Diffusions: a Constructive Approach to Nelson's Stochastic Mechanics.

    NASA Astrophysics Data System (ADS)

    Carlen, Eric Anders

    In Nelson's stochastic mechanics, quantum phenomena are described in terms of diffusions instead of wave functions; this thesis is a study of that description. We emphasize that we are concerned here with the possibility of describing, as opposed to explaining, quantum phenomena in terms of diffusions. In this direction, the following questions arise: "Do the diffusions of stochastic mechanics--which are formally given by stochastic differential equations with extremely singular coefficients--really exist?" Given that they exist, one can ask, "Do these diffusions have physically reasonable sample path behavior, and can we use information about sample paths to study the behavior of physical systems?" These are the questions we treat in this thesis. In Chapter I we review stochastic mechanics and diffusion theory, using the Guerra-Morato variational principle to establish the connection with the Schroedinger equation. This chapter is largely expository; however, there are some novel features and proofs. In Chapter II we settle the first of the questions raised above. Using PDE methods, we construct the diffusions of stochastic mechanics. Our result is sufficiently general to be of independent mathematical interest. In Chapter III we treat potential scattering in stochastic mechanics and discuss direct probabilistic methods of studying quantum scattering problems. Our results provide a solid "Yes" in answer to the second question raised above.

  6. Independent recruitment of a conserved developmental mechanism during leaf evolution.

    PubMed

    Harrison, C Jill; Corley, Susie B; Moylan, Elizabeth C; Alexander, Debbie L; Scotland, Robert W; Langdale, Jane A

    2005-03-24

    Vascular plants evolved in the Middle to Late Silurian period, about 420 million years ago. The fossil record indicates that these primitive plants had branched stems with sporangia but no leaves. Leaf-like lateral outgrowths subsequently evolved on at least two independent occasions. In extant plants, these events are represented by microphyllous leaves in lycophytes (clubmosses, spikemosses and quillworts) and megaphyllous leaves in euphyllophytes (ferns, gymnosperms and angiosperms). Our current understanding of how leaves develop is restricted to processes that operate during megaphyll formation. Because microphylls and megaphylls evolved independently, different mechanisms might be required for leaf formation. Here we show that this is not so. Gene expression data from a microphyllous lycophyte, phylogenetic analyses, and a cross-species complementation experiment all show that a common developmental mechanism can underpin both microphyll and megaphyll formation. We propose that this mechanism might have operated originally in the context of primitive plant apices to facilitate bifurcation. Recruitment of this pathway to form leaves occurred independently and in parallel in different plant lineages.

  7. A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications

    PubMed Central

    Burroughs, A Maxwell; Aravind, L

    2014-01-01

    A protein family including mammalian NEMF, Drosophila caliban, yeast Tae2, and bacterial FpbA-like proteins was first defined over a decade ago and found to be universally distributed across the three domains/superkingdoms of life. Since its initial characterization, this family of proteins has been tantalizingly linked to a wide range of biochemical functions. Tapping the enormous wealth of genome information that has accumulated since the initial characterization of these proteins, we perform a detailed computational analysis of the family, identifying multiple conserved domains. Domains identified include an enzymatic domain related to the formamidopyrimidine (Fpg), MutM, and Nei/EndoVIII family of DNA glycosylases, a novel, predicted RNA-binding domain, and a domain potentially mediating protein–protein interactions. Through this characterization, we predict that the DNA glycosylase-like domain catalytically operates on double-stranded RNA, as part of a hitherto unknown base modification mechanism that probably targets rRNAs. At least in archaea, and possibly eukaryotes, this pathway might additionally include the AMMECR1 family of proteins. The predicted RNA-binding domain associated with this family is also observed in distinct architectural contexts in other proteins across phylogenetically diverse prokaryotes. Here it is predicted to play a key role in a new pathway for tRNA 4-thiouridylation along with TusA-like sulfur transfer proteins. PMID:24646681

  8. FERM-dependent E3 ligase recognition is a conserved mechanism for targeted degradation of lipoprotein receptors.

    PubMed

    Calkin, Anna C; Goult, Benjamin T; Zhang, Li; Fairall, Louise; Hong, Cynthia; Schwabe, John W R; Tontonoz, Peter

    2011-12-13

    The E3 ubiquitin ligase IDOL (inducible degrader of the LDL receptor) regulates LDL receptor (LDLR)-dependent cholesterol uptake, but its mechanism of action, including the molecular basis for its stringent specificity, is poorly understood. Here we show that IDOL uses a singular strategy among E3 ligases for target recognition. The IDOL FERM domain binds directly to a recognition sequence in the cytoplasmic tails of lipoprotein receptors. This physical interaction is independent of IDOL's really interesting new gene (RING) domain E3 ligase activity and its capacity for autoubiquitination. Furthermore, IDOL controls its own stability through autoubiquitination of a unique FERM subdomain fold not present in other FERM proteins. Key residues defining the IDOL-LDLR interaction and IDOL autoubiquitination are functionally conserved in their insect homologs. Finally, we demonstrate that target recognition by IDOL involves a tripartite interaction between the FERM domain, membrane phospholipids, and the lipoprotein receptor tail. Our data identify the IDOL-LDLR interaction as an evolutionarily conserved mechanism for the regulation of lipid uptake and suggest that this interaction could potentially be exploited for the pharmacologic modulation of lipid metabolism.

  9. FERM-dependent E3 ligase recognition is a conserved mechanism for targeted degradation of lipoprotein receptors

    PubMed Central

    Calkin, Anna C.; Goult, Benjamin T.; Zhang, Li; Fairall, Louise; Hong, Cynthia; Schwabe, John W. R.; Tontonoz, Peter

    2011-01-01

    The E3 ubiquitin ligase IDOL (inducible degrader of the LDL receptor) regulates LDL receptor (LDLR)-dependent cholesterol uptake, but its mechanism of action, including the molecular basis for its stringent specificity, is poorly understood. Here we show that IDOL uses a singular strategy among E3 ligases for target recognition. The IDOL FERM domain binds directly to a recognition sequence in the cytoplasmic tails of lipoprotein receptors. This physical interaction is independent of IDOL's really interesting new gene (RING) domain E3 ligase activity and its capacity for autoubiquitination. Furthermore, IDOL controls its own stability through autoubiquitination of a unique FERM subdomain fold not present in other FERM proteins. Key residues defining the IDOL–LDLR interaction and IDOL autoubiquitination are functionally conserved in their insect homologs. Finally, we demonstrate that target recognition by IDOL involves a tripartite interaction between the FERM domain, membrane phospholipids, and the lipoprotein receptor tail. Our data identify the IDOL–LDLR interaction as an evolutionarily conserved mechanism for the regulation of lipid uptake and suggest that this interaction could potentially be exploited for the pharmacologic modulation of lipid metabolism. PMID:22109552

  10. Influence of hydrogel mechanical properties and mesh size on vocal fold fibroblast extracellular matrix production and phenotype

    PubMed Central

    Hahn, Mariah S.; Liao, Huimin; Munoz-Pinto, Dany; Qu, Xin; Hou, Yaping; Grunlan, Melissa A.

    2008-01-01

    Current clinical management of vocal fold (VF) scarring produces inconsistent and often suboptimal results. Researchers are investigating a number of alternative treatments for VF lamina propria (LP) scarring, including designer implant materials for functional LP regeneration. In the present study, we investigate the effects of the initial scaffold elastic modulus and mesh size on encapsulated VF fibroblast (VFF) extracellular matrix (ECM) production toward rational scaffold design. Polyethylene glycol diacrylate (PEGDA) hydrogels were selected for this study since their material properties, including mechanical properties, mesh size, degradation rate and bioactivity, can be tightly controlled and systematically modified. Porcine VFF were encapsulated in four PEGDA hydrogels with degradation half lives of ~25 days and initial elastic compressive moduli ranging from ~30 to 100 kPa and initial mesh sizes ranging from ~9 to 27 nm. After 30 days of static culture, VFF ECM production and phenotype in each formulation was assessed biochemically and histologically. Sulfated glycosaminoglycan synthesis increased in similar degree with both increasing initial modulus and decreasing initial mesh size. In contrast, elastin production decreased with increasing initial modulus but increased with decreasing initial mesh size. Both collagen deposition and the induction of a myofibroblastic phenotype depended strongly on initial mesh size but appeared largely unaffected by variations in initial modulus. The present results indicate that scaffold mesh size warrants further investigation as a critical regulator of VFF ECM synthesis. Furthermore, this study validates a systematic and controlled approach for analyzing VFF response to scaffold properties, which should aid in rational scaffold selection/design. PMID:18515199

  11. NMR analysis of partially folded states and persistent structure in the alpha subunit of tryptophan synthase: implications for the equilibrium folding mechanism of a 29-kDa TIM barrel protein.

    PubMed

    Vadrevu, Ramakrishna; Wu, Ying; Matthews, C Robert

    2008-03-14

    Structural insights into the equilibrium folding mechanism of the alpha subunit of tryptophan synthase (alpha TS) from Escherichia coli, a (beta alpha)(8) TIM barrel protein, were obtained with a pair of complementary nuclear magnetic resonance (NMR) spectroscopic techniques. The secondary structures of rare high-energy partially folded states were probed by native-state hydrogen-exchange NMR analysis of main-chain amide hydrogens. 2D heteronuclear single quantum coherence NMR analysis of several (15)N-labeled nonpolar amino acids was used to probe the side chains involved in stabilizing a highly denatured intermediate that is devoid of secondary structure. The dynamic broadening of a subset of isoleucine and leucine side chains and the absence of protection against exchange showed that the highest energy folded state on the free-energy landscape is stabilized by a hydrophobic cluster lacking stable secondary structure. The core of this cluster, centered near the N-terminus of alpha TS, serves as a nucleus for the stabilization of what appears to be nonnative secondary structure in a marginally stable intermediate. The progressive decrease in protection against exchange from this nucleus toward both termini and from the N-termini to the C-termini of several beta-strands is best described by an ensemble of weakly coupled conformers. Comparison with previous data strongly suggests that this ensemble corresponds to a marginally stable off-pathway intermediate that arises in the first few milliseconds of folding and persists under equilibrium conditions. A second, more stable intermediate, which has an intact beta-barrel and a frayed alpha-helical shell, coexists with this marginally stable species. The conversion of the more stable intermediate to the native state of alpha TS entails the formation of a stable helical shell and completes the acquisition of the tertiary structure.

  12. Fast protein folding kinetics

    PubMed Central

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  13. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.

    PubMed

    Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

    2015-11-10

    To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

  14. Folding by Design

    NASA Astrophysics Data System (ADS)

    Dodd, Paul; Damasceno, Pablo; Glotzer, Sharon

    2014-03-01

    A form of self-assembly, ``self-folding'' presents an alternative approach to the creation of reconfigurable, responsive materials with applications ranging from robotics to drug design. However, the complexity of interactions present in biological and engineered systems that undergo folding makes it challenging to isolate the main factors controlling their assembly and dis-assembly. Here we use computer simulations of simple, minimalistic self-foldable structures and investigate their stochastic folding process. By dynamically accessing all the states that lead to, or inhibit, successful folding, we show that the mechanisms by which general stochastic systems can achieve their ``native'' structures can be identified and used to design rules for optimized folding propensity. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  15. The interplay of fold mechanisms and basement weaknesses at the transition between Laramide basement-involved arches, north-central Wyoming, USA

    NASA Astrophysics Data System (ADS)

    Neely, Thomas G.; Erslev, Eric A.

    2009-09-01

    Horizontally-shortened, basement-involved foreland orogens commonly exhibit anastomosing networks of bifurcating basement highs (here called arches) whose structural culminations are linked by complex transition zones of diversely-oriented faults and folds. The 3D geometry and kinematics of the southern Beartooth arch transition zone of north-central Wyoming were studied to understand the fold mechanisms and control on basement-involved arches. Data from 1581 slickensided minor faults are consistent with a single regional shortening direction of 065°. Evidence for oblique-slip, vertical axis rotations and stress refraction at anomalously-oriented folds suggests formation over reactivated pre-existing weaknesses. Restorable cross-sections and 3D surfaces, constrained by surface, well, and seismic data, document blind, ENE-directed basement thrusting and associated thin-skinned backthrusting and folding along the Beartooth and Oregon Basin fault systems. Between these systems, the basement-cored Rattlesnake Mountain backthrust followed basement weaknesses and rotated a basement chip toward the basin before the ENE-directed Line Creek fault system broke through and connected the Beartooth and Oregon Basin fault systems. Slip was transferred at the terminations of the Rattlesnake Mountain fault block by pivoting to the north and tear faulting to the south. In summary, unidirectional Laramide compression and pre-existing basement weaknesses combined with fault-propagation and rotational fault-bend folding to create an irregular yet continuous basement arch transition.

  16. Statistical mechanical foundation of the peridynamic nonlocal continuum theory: energy and momentum conservation laws.

    PubMed

    Lehoucq, R B; Sears, Mark P

    2011-09-01

    The purpose of this paper is to derive the energy and momentum conservation laws of the peridynamic nonlocal continuum theory using the principles of classical statistical mechanics. The peridynamic laws allow the consideration of discontinuous motion, or deformation, by relying on integral operators. These operators sum forces and power expenditures separated by a finite distance and so represent nonlocal interaction. The integral operators replace the differential divergence operators conventionally used, thereby obviating special treatment at points of discontinuity. The derivation presented employs a general multibody interatomic potential, avoiding the standard assumption of a pairwise decomposition. The integral operators are also expressed in terms of a stress tensor and heat flux vector under the assumption that these fields are differentiable, demonstrating that the classical continuum energy and momentum conservation laws are consequences of the more general peridynamic laws. An important conclusion is that nonlocal interaction is intrinsic to continuum conservation laws when derived using the principles of statistical mechanics.

  17. Folding of a Cyclin Box

    PubMed Central

    Chemes, Lucía B.; Noval, María G.; Sánchez, Ignacio E.; de Prat-Gay, Gonzalo

    2013-01-01

    The retinoblastoma tumor suppressor (Rb) controls the proliferation, differentiation, and survival of cells in most eukaryotes with a role in the fate of stem cells. Its inactivation by mutation or oncogenic viruses is required for cellular transformation and eventually carcinogenesis. The high conservation of the Rb cyclin fold prompted us to investigate the link between conformational stability and ligand binding properties of the RbAB pocket domain. RbAB unfolding presents a three-state transition involving cooperative secondary and tertiary structure changes and a partially folded intermediate that can oligomerize. The first transition corresponds to unfolding of the metastable B subdomain containing the binding site for the LXCXE motif present in cellular and viral targets, and the second transition corresponds to the stable A subdomain. The low thermodynamic stability of RbAB translates into a propensity to rapidly oligomerize and aggregate at 37 °C (T50 = 28 min) that is suppressed by human papillomavirus E7 and E2F peptide ligands, suggesting that Rb is likely stabilized in vivo through binding to target proteins. We propose that marginal stability and associated oligomerization may be conserved for function as a “hub” protein, allowing the formation of multiprotein complexes, which could constitute a robust mechanism to retain its cell cycle regulatory role throughout evolution. Decreased stability and oligomerization are shared with the p53 tumor suppressor, suggesting a link between folding and function in these two essential cell regulators that are inactivated in most cancers and operate within multitarget signaling pathways. PMID:23632018

  18. Single-Molecule Folding Mechanisms of the apo- and Mg2+-Bound States of Human Neuronal Calcium Sensor-1

    PubMed Central

    Naqvi, Mohsin M.; Heidarsson, Pétur O.; Otazo, Mariela R.; Mossa, Alessandro; Kragelund, Birthe B.; Cecconi, Ciro

    2015-01-01

    Neuronal calcium sensor-1 (NCS-1) is the primordial member of a family of proteins responsible primarily for sensing changes in neuronal Ca2+ concentration. NCS-1 is a multispecific protein interacting with a number of binding partners in both calcium-dependent and independent manners, and acting in a variety of cellular processes in which it has been linked to a number of disorders such as schizophrenia and autism. Despite extensive studies on the Ca2+-activated state of NCS proteins, little is known about the conformational dynamics of the Mg2+-bound and apo states, both of which are populated, at least transiently, at resting Ca2+ conditions. Here, we used optical tweezers to study the folding behavior of individual NCS-1 molecules in the presence of Mg2+ and in the absence of divalent ions. Under tension, the Mg2+-bound state of NCS-1 unfolds and refolds in a three-state process by populating one intermediate state consisting of a folded C-domain and an unfolded N-domain. The interconversion at equilibrium between the different molecular states populated by NCS-1 was monitored in real time through constant-force measurements and the energy landscapes underlying the observed transitions were reconstructed through hidden Markov model analysis. Unlike what has been observed with the Ca2+-bound state, the presence of Mg2+ allows both the N- and C-domain to fold through all-or-none transitions with similar refolding rates. In the absence of divalent ions, NCS-1 unfolds and refolds reversibly in a two-state reaction involving only the C-domain, whereas the N-domain has no detectable transitions. Overall, the results allowed us to trace the progression of NCS-1 folding along its energy landscapes and provided a solid platform for understanding the conformational dynamics of similar EF-hand proteins. PMID:26153708

  19. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  20. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  1. Rv0216, a Conserved Hypothetical Protein from Myocbacterium Tuberculosis that is Essential for Bacterial Survival During Infection, has a Double Hotdog Fold

    SciTech Connect

    Castell,A.; Johansson, P.; Unge, T.; Jones, T.; Backbro, K.

    2005-01-01

    The Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three-dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R-specific hydration of 2-enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl-CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.

  2. A Novel ‘Roll-and-Slide’ Mechanism of DNA Folding in Chromatin. Implications for Nucleosome Positioning

    PubMed Central

    Tolstorukov, Michael Y.; Colasanti, Andrew V.; McCandlish, David; Olson, Wilma K.; Zhurkin, Victor B.

    2007-01-01

    How eukaryotic genomes encode the folding of DNA into nucleosomes and how this intrinsic organization of chromatin guides biological function are questions of wide interest. The physical basis of nucleosome positioning lies in the sequence-dependent propensity of DNA to adopt the tightly bent configuration imposed by the binding of the histone proteins. Traditionally, only DNA bending and twisting deformations are considered, while the effects of the lateral displacements of adjacent base pairs are neglected. We demonstrate, however, that these displacements play a much more important structural role than ever imagined. Specifically, the lateral Slide deformations observed at sites of local anisotropic bending of DNA define its superhelical trajectory in chromatin. Furthermore, the computed cost of deforming DNA on the nucleosome is sequence specific: in optimally positioned sequences the most easily deformed base-pair steps (CA:TG and TA) occur at sites of large positive Slide and negative Roll (where the DNA bends into the minor groove). These conclusions rest upon a treatment of DNA that goes beyond the conventional ribbon model, incorporating all essential degrees of freedom of ‘real’ duplexes in the estimation of DNA deformation energies. Indeed, only after lateral Slide displacements are considered, are we able to account for the sequence-specific folding of DNA found in nucleosome structures. The close correspondence between the predicted and observed nucleosome locations demonstrates the potential advantage of our 'structural' approach in the computer mapping of nucleosome positioning. PMID:17585938

  3. Universally Conserved Relationships between Nuclear Shape and Cytoplasmic Mechanical Properties in Human Stem Cells

    NASA Astrophysics Data System (ADS)

    Lozoya, Oswaldo A.; Gilchrist, Christopher L.; Guilak, Farshid

    2016-03-01

    The ability of cells to proliferate, differentiate, transduce extracellular signals and assemble tissues involves structural connections between nucleus and cytoskeleton. Yet, how the mechanics of these connections vary inside stem cells is not fully understood. To address those questions, we combined two-dimensional particle-tracking microrheology and morphological measures using variable reduction techniques to measure whether cytoplasmic mechanics allow for discrimination between different human adherent stem cell types and across different culture conditions. Here we show that nuclear shape is a quantifiable discriminant of mechanical properties in the perinuclear cytoskeleton (pnCSK) of various stem cell types. Also, we find the pnCSK is a region with different mechanical properties than elsewhere in the cytoskeleton, with heterogeneously distributed locations exhibiting subdiffusive features, and which obeys physical relations conserved among various stem cell types. Finally, we offer a prospective basis to discriminate between stem cell types by coupling perinuclear mechanical properties to nuclear shape.

  4. Universally Conserved Relationships between Nuclear Shape and Cytoplasmic Mechanical Properties in Human Stem Cells

    PubMed Central

    Lozoya, Oswaldo A.; Gilchrist, Christopher L.; Guilak, Farshid

    2016-01-01

    The ability of cells to proliferate, differentiate, transduce extracellular signals and assemble tissues involves structural connections between nucleus and cytoskeleton. Yet, how the mechanics of these connections vary inside stem cells is not fully understood. To address those questions, we combined two-dimensional particle-tracking microrheology and morphological measures using variable reduction techniques to measure whether cytoplasmic mechanics allow for discrimination between different human adherent stem cell types and across different culture conditions. Here we show that nuclear shape is a quantifiable discriminant of mechanical properties in the perinuclear cytoskeleton (pnCSK) of various stem cell types. Also, we find the pnCSK is a region with different mechanical properties than elsewhere in the cytoskeleton, with heterogeneously distributed locations exhibiting subdiffusive features, and which obeys physical relations conserved among various stem cell types. Finally, we offer a prospective basis to discriminate between stem cell types by coupling perinuclear mechanical properties to nuclear shape. PMID:26976044

  5. The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family.

    PubMed

    Sgourakis, Nikolaos G; Natarajan, Kannan; Ying, Jinfa; Vogeli, Beat; Boyd, Lisa F; Margulies, David H; Bax, Ad

    2014-09-01

    Immunoevasins are key proteins used by viruses to subvert host immune responses. Determining their high-resolution structures is key to understanding virus-host interactions toward the design of vaccines and other antiviral therapies. Mouse cytomegalovirus encodes a unique set of immunoevasins, the m02-m06 family, that modulates major histocompatibility complex class I (MHC-I) antigen presentation to CD8+ T cells and natural killer cells. Notwithstanding the large number of genetic and functional studies, the structural biology of immunoevasins remains incompletely understood, largely because of crystallization bottlenecks. Here we implement a technology using sparse nuclear magnetic resonance data and integrative Rosetta modeling to determine the structure of the m04/gp34 immunoevasin extracellular domain. The structure reveals a β fold that is representative of the m02-m06 family of viral proteins, several of which are known to bind MHC-I molecules and interfere with antigen presentation, suggesting its role as a diversified immune regulation module.

  6. Vibrational dynamics of vocal folds using nonlinear normal modes.

    PubMed

    Pinheiro, Alan P; Kerschen, Gaëtan

    2013-08-01

    Many previous works involving physical models, excised and in vivo larynges have pointed out nonlinear vibration in vocal folds during voice production. Moreover, theoretical studies involving mechanical modeling of these folds have tried to gain a profound understanding of the observed nonlinear phenomena. In this context, the present work uses the nonlinear normal mode theory to investigate the nonlinear modal behavior of 16 subjects using a two-mass mechanical modeling of the vocal folds. The free response of the conservative system at different energy levels is considered to assess the impact of the structural nonlinearity of the vocal fold tissues. The results show very interesting and complex nonlinear phenomena including frequency-energy dependence, subharmonic regimes and, in some cases, modal interactions, entrainment and bifurcations. PMID:23218815

  7. Stress, deformation, conservation, and rheology: a survey of key concepts in continuum mechanics

    USGS Publications Warehouse

    Major, J.J.

    2013-01-01

    This chapter provides a brief survey of key concepts in continuum mechanics. It focuses on the fundamental physical concepts that underlie derivations of the mathematical formulations of stress, strain, hydraulic head, pore-fluid pressure, and conservation equations. It then shows how stresses are linked to strain and rates of distortion through some special cases of idealized material behaviors. The goal is to equip the reader with a physical understanding of key mathematical formulations that anchor continuum mechanics in order to better understand theoretical studies published in geomorphology.

  8. Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

    PubMed Central

    Stolfi, Alberto; Lowe, Elijah K; Racioppi, Claudia; Ristoratore, Filomena; Brown, C Titus; Swalla, Billie J; Christiaen, Lionel

    2014-01-01

    Ascidians present a striking dichotomy between conserved phenotypes and divergent genomes: embryonic cell lineages and gene expression patterns are conserved between distantly related species. Much research has focused on Ciona or Halocynthia spp. but development in other ascidians remains poorly characterized. In this study, we surveyed the multipotent myogenic B7.5 lineage in Molgula spp. Comparisons to the homologous lineage in Ciona revealed identical cell division and fate specification events that result in segregation of larval, cardiac, and pharyngeal muscle progenitors. Moreover, the expression patterns of key regulators are conserved, but cross-species transgenic assays uncovered incompatibility, or ‘unintelligibility’, of orthologous cis-regulatory sequences between Molgula and Ciona. These sequences drive identical expression patterns that are not recapitulated in cross-species assays. We show that this unintelligibility is likely due to changes in both cis- and trans-acting elements, hinting at widespread and frequent turnover of regulatory mechanisms underlying otherwise conserved aspects of ascidian embryogenesis. DOI: http://dx.doi.org/10.7554/eLife.03728.001 PMID:25209999

  9. A conserved mechanism for vertebrate mesoderm specification in urodele amphibians and mammals.

    PubMed

    Swiers, Gemma; Chen, Yi-Hsien; Johnson, Andrew D; Loose, Matthew

    2010-07-01

    Understanding how mesoderm is specified during development is a fundamental issue in biology, and it has been studied intensively in embryos from Xenopus. The gene regulatory network (GRN) for Xenopus is surprisingly complex and is not conserved in vertebrates, including mammals, which have single copies of the key genes Nodal and Mix. Why the Xenopus GRN should express multiple copies of Nodal and Mix genes is not known. To understand how these expanded gene families evolved, we investigated mesoderm specification in embryos from axolotls, representing urodele amphibians, since urodele embryology is basal to amphibians and was conserved during the evolution of amniotes, including mammals. We show that single copies of Nodal and Mix are required for mesoderm specification in axolotl embryos, suggesting the ancestral vertebrate state. Furthermore, we uncovered a novel genetic interaction in which Mix induces Brachyury expression, standing in contrast to the relationship of these molecules in Xenopus. However, we demonstrate that this functional relationship is conserved in mammals by showing that it is involved in the production of mesoderm from mouse embryonic stem cells. From our results, we produced an ancestral mesoderm (m)GRN, which we suggest is conserved in vertebrates. The results are discussed within the context of a theory in which the evolution of mechanisms governing early somatic development is constrained by the ancestral germ line-soma relationship, in which germ cells are produced by epigenesis.

  10. The Crystal Structure of Dehi Reveals a New A-Haloacid Dehalogenase Fold And Active Site Mechanism

    SciTech Connect

    Schmidberger, J.W.; Wilce, J.A.; Weightman, A.J.; Whisstock, J.C.; Wilce, M.C.J.

    2009-05-27

    Haloacid dehalogenases catalyse the removal of halides from organic haloacids and are of interest for bioremediation and for their potential use in the synthesis of industrial chemicals. We present the crystal structure of the homodimer DehI from Pseudomonas putida strain PP3, the first structure of a group I {alpha}-haloacid dehalogenase that can process both L- and D-substrates. The structure shows that the DehI monomer consists of two domains of {approx}130 amino acids that have {approx}16% sequence identity yet adopt virtually identical and unique folds that form a pseudo-dimer. Analysis of the active site reveals the likely binding mode of both L- and D-substrates with respect to key catalytic residues. Asp189 is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of configuration of either L- or D-substrates in contrast to D-only enzymes. These details will assist with future bioengineering of dehalogenases.

  11. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

    NASA Astrophysics Data System (ADS)

    Pucheta-Martinez, Encarna; D’Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L.; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

    2016-07-01

    WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.

  12. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

    PubMed Central

    Pucheta-Martinez, Encarna; D’Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L.; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

    2016-01-01

    WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function. PMID:27456546

  13. A mechanism for repression of class II gene transcription through specific binding of NC2 to TBP-promoter complexes via heterodimeric histone fold domains.

    PubMed Central

    Goppelt, A; Stelzer, G; Lottspeich, F; Meisterernst, M

    1996-01-01

    Negative co-factor 2 (NC2) regulates transcription of the class II genes through binding to TFIID and inhibition of pre-initiation complex formation. We have isolated and cloned NC2, and investigated the molecular mechanism underlying repression of transcription. NC2 consists of two subunits, termed NC2alpha and NC2beta, the latter of which is identical to Dr1. The NC2 subunits dimerize and bind to TATA binding protein (TBP)-promoter complexes via histone fold domains of the H2A-H2B type. Repression of basal transcription requires the histone fold and carboxy-terminal domains of the NC2 subunits. Several mechanisms probably contribute to transcriptional repression. Binding of NC2 inhibits association of TFIIB with TBP-promoter complexes. NC2 binds directly to DNA, and binding of NC2 to TBP-promoter complexes affects the conformation of DNA, which could be one cause for the inhibition of TFIIB. In addition, multimerization of repressor-TBP complexes on DNA might inhibit the assembly of the pre-initiation complex. We suggest that binding of the repressor to TRP-promoter complexes establishes a mechanism that controls the rate of transcription by RNA polymerase II. Images PMID:8670811

  14. Mechanical stability model of progradational carbonate platform margins under tectonic loads: Deformation of Cretaceous carbonate platforms in the Sierra Madre Oriental fold-thrust belt (east central Mexico)

    NASA Astrophysics Data System (ADS)

    Contreras, Juan; Suter, Max

    2015-02-01

    Shortening in the Sierra Madre Oriental fold-thrust belt (east central Mexico) is localized along the margins of Cretaceous carbonate platforms and controlled by mechanical stratigraphy. The platform margins are deformed by imbricate series of thrust ramps, whereas the coeval basins and platform interiors are deformed by map-scale detachment folds. Here we present a finite element model to evaluate the influence of the boundary geometry and boundary conditions on the style of deformation observed at these basinward progradational platform margins. We calculate the stress distribution in a linearly elastic platform-basin transition zone under the action of horizontal tectonic stress, taking into account changes of rock mechanical properties across the platform margin, as well as their dependence on direction, and infer the resulting fracture patterns based on the Mohr-Coulomb failure criterion. Stress concentrations are predicted at the contacts between the massive rocks of the platform margin and the well-layered rocks of both, the platform interior and the adjacent basin. Brittle failure of the platform border can be mostly attributed to three effects: mechanical coupling between the carbonate platform and a substratum of moderate to low viscosity, variations in layering and texture that governed the mechanical properties of the involved carbonates as well as their dependence on direction, and the development of sharp domain boundary corners associated with progradational facies changes. In contrast, the dip of the basement and a possible taper of the overlying Upper Cretaceous shale toward the basin appear to have little influence on the mechanical failure of the platform margin.

  15. NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain.

    PubMed Central

    Szyperski, T; Pellecchia, M; Wall, D; Georgopoulos, C; Wüthrich, K

    1994-01-01

    DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution. Images PMID:7972061

  16. A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation.

    PubMed

    Jesus, Catarina S H; Almeida, Zaida L; Vaz, Daniela C; Faria, Tiago Q; Brito, Rui M M

    2016-08-31

    Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer's and Parkinson's. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo.

  17. A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation.

    PubMed

    Jesus, Catarina S H; Almeida, Zaida L; Vaz, Daniela C; Faria, Tiago Q; Brito, Rui M M

    2016-01-01

    Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer's and Parkinson's. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. PMID:27589730

  18. A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation

    PubMed Central

    Jesus, Catarina S. H.; Almeida, Zaida L.; Vaz, Daniela C.; Faria, Tiago Q.; Brito, Rui M. M.

    2016-01-01

    Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer’s and Parkinson’s. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. PMID:27589730

  19. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  20. Graphene folding on flat substrates

    SciTech Connect

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong; Zhang, Liuyang; Wang, Xianqiao

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57 eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  1. Predictive Computational Modeling of Chromatin Folding

    NASA Astrophysics Data System (ADS)

    di Pierro, Miichele; Zhang, Bin; Wolynes, Peter J.; Onuchic, Jose N.

    In vivo, the human genome folds into well-determined and conserved three-dimensional structures. The mechanism driving the folding process remains unknown. We report a theoretical model (MiChroM) for chromatin derived by using the maximum entropy principle. The proposed model allows Molecular Dynamics simulations of the genome using as input the classification of loci into chromatin types and the presence of binding sites of loop forming protein CTCF. The model was trained to reproduce the Hi-C map of chromosome 10 of human lymphoblastoid cells. With no additional tuning the model was able to predict accurately the Hi-C maps of chromosomes 1-22 for the same cell line. Simulations show unknotted chromosomes, phase separation of chromatin types and a preference of chromatin of type A to sit at the periphery of the chromosomes.

  2. Anisotropy of Magnetic Susceptibility: a petrofrabric tool for understanding mechanisms of fold and thrust belt evolution. Application in Malargüe FTB, Argentina

    NASA Astrophysics Data System (ADS)

    Branellec, Matthieu; Callot, Jean Paul; Aubourg, Charles; Nivière, Bertrand; Ringenbach, Jean Claude

    2013-04-01

    In fold and thrust belts (FTB), sedimentary beds are folded and faulted but rocks do not always show evidence of strong internal deformation. Nevertheless, several studies have demonstrated that a weak internal deformation (layer parallel shortening) can be recorded at the matrix scale before any macroscopic deformation. The Anisotropy of Magnetic susceptibility (AMS) provides information about the preferred orientation of billions of magnetic minerals. It enables the definition of a magnetic fabric, which may be visualized as an ellipsoid with principal axes K1 ≥ K2 ≥ K3. Basic elements of a magnetic fabric are the magnetic foliation (K1-K2 plane) and the magnetic lineation (K1 axe), when they are statistically defined. Both are related to strain-controlled petrofrabric. The Neuquén Basin is a wide intracratonic sag basin with complex and polyphased/diachronic evolution. The Pacific subduction and south Atlantic opening were the mechanisms controlling the large scale geodynamic framework. By late Triassic times, continental scale extension initiated fault-related narrow rift depocenters which later evolved toward a sag basin from middle Jurassic to upper Cretaceous. At that time, the basin started to record the compressive stress regime from the Pacific subduction. Three pulses of compressive deformation (Cretaceous, Paleogene and Miocene) are recorded in this retro-arc foreland setting. Approximately 300 samples have been collected from 30 sites in terrigenous rocks located along three cross sections from foothills to uplifted foreland area in Malargüe FTB. We mainly sample Kimmeridgian red beds of the Tordillo formation, Tithonian shales from the Vaca Muerta Fm, and late cretaceous red beds of the Neuquén Group. AMS fabrics are used as a proxy to measure accumulated microscopic finite strain and compares it with mesoscale (fractures) and macroscale structures (faults, folds…). This multi-scaled approach helps in defining a kinematic scenario for Malarg

  3. Fry and Rf/ϕ strain methods constraints and fold transection mechanisms in the NW Iberian Variscides

    NASA Astrophysics Data System (ADS)

    Soares, A.; Dias, R.

    2015-10-01

    Apúlia is a small Portuguese sector in NW of Central-Iberian Zone, that have been deformed in a non-coaxial sinistral transpressive regime during the first and main Variscan tectonic event (D1). This deformation give rise to a major NW-SE anticline, where the S1 N-S cleavage transect the inverted short NE limb; two and three-dimensional strains analysis have been done in the low metamorphic grade Ordovician quartzites of this limb using Fry and Rf/ϕ methods. The data show that most deformation was due to intergranular deformation mechanisms. The intragranular deformation leading to the distortion of strain markers and to cleavage was very incipient and a latter event in the D1 phase. The apparent plane strain ellipsoids (if no volume change is assumed) related to the intragranular mechanisms contrast with the more prolate strain ellipsoids related to the bulk deformation of Apúlia Quartzites. This constrictional bulk strain fabrics are characteristic of the sinistral transpressive regimes dominant in the northern sectors of the Central-Iberian Zone.

  4. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation.

    PubMed

    Coleman, Brantley D; Marivin, Arthur; Parag-Sharma, Kshitij; DiGiacomo, Vincent; Kim, Seongseop; Pepper, Judy S; Casler, Jason; Nguyen, Lien T; Koelle, Michael R; Garcia-Marcos, Mikel

    2016-03-01

    Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA-G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

  5. Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation

    PubMed Central

    Coleman, Brantley D.; Marivin, Arthur; Parag-Sharma, Kshitij; DiGiacomo, Vincent; Kim, Seongseop; Pepper, Judy S.; Casler, Jason; Nguyen, Lien T.; Koelle, Michael R.; Garcia-Marcos, Mikel

    2016-01-01

    Trimeric G protein signaling is a fundamental mechanism of cellular communication in eukaryotes. The core of this mechanism consists of activation of G proteins by the guanine-nucleotide exchange factor (GEF) activity of G protein coupled receptors. However, the duration and amplitude of G protein-mediated signaling are controlled by a complex network of accessory proteins that appeared and diversified during evolution. Among them, nonreceptor proteins with GEF activity are the least characterized. We recently found that proteins of the ccdc88 family possess a Gα-binding and activating (GBA) motif that confers GEF activity and regulates mammalian cell behavior. A sequence similarity-based search revealed that ccdc88 genes are highly conserved across metazoa but the GBA motif is absent in most invertebrates. This prompted us to investigate whether the GBA motif is present in other nonreceptor proteins in invertebrates. An unbiased bioinformatics search in Caenorhabditis elegans identified GBAS-1 (GBA and SPK domain containing-1) as a GBA motif-containing protein with homologs only in closely related worm species. We demonstrate that GBAS-1 has GEF activity for the nematode G protein GOA-1 and that the two proteins are coexpressed in many cells of living worms. Furthermore, we show that GBAS-1 can activate mammalian Gα-subunits and provide structural insights into the evolutionarily conserved determinants of the GBA–G protein interface. These results demonstrate that the GBA motif is a functional GEF module conserved among highly divergent proteins across evolution, indicating that the GBA-Gα binding mode is strongly constrained under selective pressure to mediate receptor-independent G protein activation in metazoans. PMID:26659249

  6. Conservative management of uncomplicated mechanical neck pain in a military aviator

    PubMed Central

    Green, Bart N.; Dunn, Andrew S.; Pearce, Solomon M.; Johnson, Claire D.

    2010-01-01

    Non-radicular neck pain arising from local musculoskeletal structures, known as mechanical neck pain or somatic dysfunction, is highly prevalent in the fighter jet aviator population. The management of this problem includes both therapeutic and aeromedical decisions. In addition to non-steroidal anti-inflammatory medications, waiver guides recommend therapeutic exercise and manipulative therapy as treatments for somatic spine pain in aviators, and such treatments are employed in many military locations. However, there are currently no published studies that describe the use of manipulative therapy for fighter jet aviators. We report the case of an F/A-18 instructor pilot who experienced long-term relief of uncomplicated mechanical neck pain following interdisciplinary management that included manipulation and a home exercise program. Diagnostic considerations, conservative treatment options, and aeromedical concerns are discussed. PMID:20520753

  7. Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism.

    PubMed

    Vasudevan, Dileep; Fu, Aigen; Luan, Sheng; Swaminathan, Kunchithapadam

    2012-06-01

    Cyclophilin38 (CYP38) is one of the highly divergent cyclophilins from Arabidopsis thaliana. Here, we report the crystal structure of the At-CYP38 protein (residues 83 to 437 of 437 amino acids) at 2.39-Å resolution. The structure reveals two distinct domains: an N-terminal helical bundle and a C-terminal cyclophilin β-barrel, connected by an acidic loop. Two N-terminal β-strands become part of the C-terminal cyclophilin β-barrel, thereby making a previously undiscovered domain organization. This study shows that CYP38 does not possess peptidyl-prolyl cis/trans isomerase activity and identifies a possible interaction of CYP38 with the E-loop of chlorophyll protein47 (CP47), a component of photosystem II. The interaction of CYP38 with the E-loop of CP47 is mediated through its cyclophilin domain. The N-terminal helical domain is closely packed together with the putative C-terminal cyclophilin domain and establishes a strong intramolecular interaction, thereby preventing the access of the cyclophilin domain to other proteins. This was further verified by protein-protein interaction assays using the yeast two-hybrid system. Furthermore, the non-Leucine zipper N-terminal helical bundle contains several new elements for protein-protein interaction that may be of functional significance. Together, this study provides the structure of a plant cyclophilin and explains a possible mechanism for autoinhibition of its function through an intramolecular interaction.

  8. New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF

    SciTech Connect

    Bae, Brian; Cobb, Ryan E.; DeSieno, Matthew A.; Zhao, Huimin; Nair, Satish K.

    2015-10-15

    The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5'-monophosphate-3-aminopropylphosphonate and cytidine 5'-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 {angstrom} resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-function studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.

  9. Mechanical study of the Chartreuse Fold-and-Thrust Belt: relationships between fluids overpressure and decollement within the Toarcian source-rock

    NASA Astrophysics Data System (ADS)

    Berthelon, Josselin; Sassi, William; Burov, Evgueni

    2016-04-01

    Many source-rocks are shale and constitute potential detachment levels in Fold-and-Thrust Belts (FTB): the toarcian Schistes-Cartons in the French Chartreuse FTB for example. Their mechanical properties can change during their burial and thermal maturation, as for example when large amount of hydrocarbon fluids are generated. A structural reconstruction of the Chartreuse FTB geo-history places the Toarcian Formation as the major decollement horizon. In this work, a mechanical analysis integrating the fluids overpressuring development is proposed to discuss on the validity of the structural interpretation. At first, an analogue of the Chartreuse Toarcian Fm, the albanian Posidonia Schist, is documented as it can provide insights on its initial properties and composition of its kerogen content. Laboratory characterisation documents the vertical evolution of the mineralogical, geochemical and mechanical parameters of this potential decollement layer. These physical parameters (i.e. Total Organic Carbon (TOC), porosity/permeability relationship, friction coefficient) are used to address overpressure buildup in the frontal part of the Chartreuse FTB with TEMISFlow Arctem Basin modelling approach (Faille et al, 2014) and the structural emplacement of the Chartreuse thrust units using the FLAMAR thermo-mechanical model (Burov et al, 2014). The hydro-mechanical modeling results highlight the calendar, distribution and magnitude of the overpressure that developed within the source-rock in the footwall of a simple fault-bend fold structure localized in the frontal part of the Chartreuse FTB. Several key geological conditions are required to create an overpressure able to fracture the shale-rocks and induce a significant change in the rheological behaviour: high TOC, low permeability, favourable structural evolution. These models highlight the importance of modeling the impact of a diffuse natural hydraulic fracturing to explain fluids propagation toward the foreland within

  10. Conservation Laws for Coupled Hydro-mechanical Processes in Unsaturated Porous Media: Theory and Implementation

    SciTech Connect

    Borja, R I; White, J A

    2010-02-19

    We develop conservation laws for coupled hydro-mechanical processes in unsaturated porous media using three-phase continuum mixture theory. From the first law of thermodynamics, we identify energy-conjugate variables for constitutive modeling at macroscopic scale. Energy conjugate expressions identified relate a certain measure of effective stress to the deformation of the solid matrix, the degree of saturation to the matrix suction, the pressure in each constituent phase to the corresponding intrinsic volume change of this phase, and the seepage forces to the corresponding pressure gradients. We then develop strong and weak forms of boundary-value problems relevant for 3D finite element modeling of coupled hydro-mechanical processes in unsaturated porous media. The paper highlights a 3D numerical example illustrating the advances in the solution of large-scale coupled finite element systems, as well as the challenges in developing more predictive tools satisfying the basic conservation laws and the observed constitutive responses for unsaturated porous materials.

  11. Molecular dynamics studies of protein folding and aggregation

    NASA Astrophysics Data System (ADS)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  12. Sandbox modelling of sequential thrusting in a mechanically two-layered system and its implications in fold-and-thrust belts

    NASA Astrophysics Data System (ADS)

    Saha, Puspendu; Bose, Santanu; Mandal, Nibir

    2016-10-01

    Many fold-and-thrust belts display multi-storied thrust sequences, characterizing a composite architecture of the thrust wedges. Despite dramatic progress in sandbox modelling over the last three decades, our understanding of such composite thrust-wedge mechanics is limited and demands a re-visit to the problem of sequential thrusting in mechanically layered systems. This study offers a new approach to sandbox modelling, designed with a two-layered sandpack simulating a mechanically weak Coulomb layer, resting coherently upon a stronger Coulomb layer. Our experimental models reproduce strikingly similar styles of the multi-storied frontal thrust sequences observed in natural fold-and- thrust belts. The upper weak horizon undergoes sequential thrusting at a high spatial frequency, forming numerous, closely spaced frontal thrusts, whereas the lower strong horizon produces widely spaced thrusts with progressive horizontal shortening. This contrasting thrust progression behaviour gives rise to composite thrust architecture in the layered sandpack. We show the evolution of such composite thrust sequences as a function of frictional strength (μb) at the basal detachment and thickness ratio (Tr) between the weak and strong layers. For any given values of Tr and μb, the two thrust sequences progress at different rates; the closely-spaced, upper thrust sequence advances forelandward at a faster rate than the widely-spaced, lower thrust sequence. Basal friction (μb) has little effects on the vergence of thrusts in the upper weak layer; they verge always towards foreland, irrespective of Tr values. But, the lower strong layer develops back-vergent thrusts when μb is low (∼0.36). In our experiments, closely spaced thrusts in the upper sequence experience intense reactivation due to their interaction with widely spaced thrusts in the lower sequence. The interaction eventually affects the wedge topography, leading to two distinct parts: inner and outer wedges

  13. Early Events in RNA Folding

    NASA Astrophysics Data System (ADS)

    Thirumalai, D.; Lee, Namkyung; Woodson, Sarah A.; Klimov, Dk

    2001-10-01

    We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.

  14. Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins

    PubMed Central

    Atherton, Joseph; Farabella, Irene; Yu, I-Mei; Rosenfeld, Steven S; Houdusse, Anne; Topf, Maya; Moores, Carolyn A

    2014-01-01

    Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 and kinesin-3 motor domains at multiple steps in their ATPase cycles—including their nucleotide-free states—at ∼7 Å resolution using cryo-electron microscopy. In both motors, microtubule binding promotes ordered conformations of conserved loops that stimulate ADP release, enhance microtubule affinity and prime the catalytic site for ATP binding. ATP binding causes only small shifts of these nucleotide-coordinating loops but induces large conformational changes elsewhere that allow force generation and neck linker docking towards the microtubule plus end. Family-specific differences across the kinesin–microtubule interface account for the distinctive properties of each motor. Our data thus provide evidence for a conserved ATP-driven mechanism for kinesins and reveal the critical mechanistic contribution of the microtubule interface. DOI: http://dx.doi.org/10.7554/eLife.03680.001 PMID:25209998

  15. Conserved mechanisms of vocalization coding in mammalian and songbird auditory midbrain

    PubMed Central

    Portfors, Christine V.

    2013-01-01

    The ubiquity of social vocalization among animals provides the opportunity to identify conserved mechanisms of auditory processing that subserve vocal communication. Identifying auditory coding properties that are shared across vocal communicators will provide insight into how human auditory processing leads to speech perception. Here, we compare auditory response properties and neural coding of social vocalizations in auditory midbrain neurons of mammalian and avian vocal communicators. The auditory midbrain is a nexus of auditory processing because it receives and integrates information from multiple parallel pathways and provides the ascending auditory input to the thalamus. The auditory midbrain is also the first region in the ascending auditory system where neurons show complex tuning properties that are correlated with the acoustics of social vocalizations. Single unit studies in mice, bats and zebra finches reveal shared principles of auditory coding including tonotopy, excitatory and inhibitory interactions that shape responses to vocal signals, nonlinear response properties that are important for auditory coding of social vocalizations and modulation tuning. Additionally, single neuron responses in the mouse and songbird midbrain are reliable, selective for specific syllables, and rely on spike timing for neural discrimination of distinct vocalizations. We propose that future research on auditory coding of vocalizations in mouse and songbird midbrain neurons adopt similar experimental and analytical approaches so that conserved principles of vocalization coding may be distinguished from those that are specialized for each species. PMID:23726970

  16. Conserved mechanisms of vocalization coding in mammalian and songbird auditory midbrain.

    PubMed

    Woolley, Sarah M N; Portfors, Christine V

    2013-11-01

    The ubiquity of social vocalizations among animals provides the opportunity to identify conserved mechanisms of auditory processing that subserve communication. Identifying auditory coding properties that are shared across vocal communicators will provide insight into how human auditory processing leads to speech perception. Here, we compare auditory response properties and neural coding of social vocalizations in auditory midbrain neurons of mammalian and avian vocal communicators. The auditory midbrain is a nexus of auditory processing because it receives and integrates information from multiple parallel pathways and provides the ascending auditory input to the thalamus. The auditory midbrain is also the first region in the ascending auditory system where neurons show complex tuning properties that are correlated with the acoustics of social vocalizations. Single unit studies in mice, bats and zebra finches reveal shared principles of auditory coding including tonotopy, excitatory and inhibitory interactions that shape responses to vocal signals, nonlinear response properties that are important for auditory coding of social vocalizations and modulation tuning. Additionally, single neuron responses in the mouse and songbird midbrain are reliable, selective for specific syllables, and rely on spike timing for neural discrimination of distinct vocalizations. We propose that future research on auditory coding of vocalizations in mouse and songbird midbrain neurons adopt similar experimental and analytical approaches so that conserved principles of vocalization coding may be distinguished from those that are specialized for each species. This article is part of a Special Issue entitled "Communication Sounds and the Brain: New Directions and Perspectives".

  17. Oxidative folding: recent developments.

    PubMed

    Szarka, András; Bánhegyi, Gábor

    2011-10-01

    Disulfide bond formation in proteins is an effective tool of both structure stabilization and redox regulation. The prokaryotic periplasm and the endoplasmic reticulum of eukaryotes were long considered as the only compartments for enzyme mediated formation of stable disulfide bonds. Recently, the mitochondrial intermembrane space has emerged as the third protein-oxidizing compartment. The classic view on the mechanism of oxidative folding in the endoplasmic reticulum has also been reshaped by new observations. Moreover, besides the structure stabilizing function, reversible disulfide bridge formation in some proteins of the endoplasmic reticulum, seems to play a regulatory role. This review briefly summarizes the present knowledge of the redox systems supporting oxidative folding, emphasizing recent developments. PMID:25962043

  18. The prosegment catalyzes native folding of Plasmodium falciparum plasmepsin II.

    PubMed

    Jaafar, Ahmad Haniff; Xiao, Huogen; Dee, Derek R; Bryksa, Brian C; Bhaumik, Prasenjit; Yada, Rickey Y

    2016-10-01

    Plasmepsin II is a malarial pepsin-like aspartic protease produced as a zymogen containing an N-terminal prosegment domain that is removed during activation. Despite structural similarities between active plasmepsin II and pepsin, their prosegments adopt different conformations in the respective zymogens. In contrast to pepsinogen, the proplasmepsin II prosegment is 80 residues longer, contains a transmembrane region and is non-essential for recombinant expression in an active form, thus calling into question the prosegment's precise function. The present study examines the role of the prosegment in the folding mechanism of plasmepsin II. Both a shorter (residues 77-124) and a longer (residues 65-124) prosegment catalyze plasmepsin II folding at rates more than four orders of magnitude faster compared to folding without prosegment. Native plasmepsin II is kinetically trapped and requires the prosegment both to catalyze folding and to shift the folding equilibrium towards the native conformation. Thus, despite low sequence identity and distinct zymogen conformations, the folding landscapes of plasmepsin II and pepsin, both with and without prosegment, are qualitatively identical. These results imply a conserved and unusual feature of the pepsin-like protease topology that necessitates prosegment-assisted folding. PMID:27378574

  19. Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

    PubMed Central

    Afanasyeva, Arina; Hirtreiter, Angela; Schreiber, Anne; Grohmann, Dina; Pobegalov, Georgii; McKay, Adam R.; Tsaneva, Irina; Petukhov, Michael; Käs, Emmanuel; Grigoriev, Mikhail; Werner, Finn

    2014-01-01

    Summary Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. PMID:24613487

  20. Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity.

    PubMed

    Fiore, Vincenzo G; Dolan, Raymond J; Strausfeld, Nicholas J; Hirth, Frank

    2015-12-19

    Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. PMID:26554043

  1. Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity

    PubMed Central

    Fiore, Vincenzo G.; Dolan, Raymond J.; Strausfeld, Nicholas J.; Hirth, Frank

    2015-01-01

    Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. PMID:26554043

  2. The parallel universe of RNA folding.

    PubMed

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  3. The effect of foreland palaeo-uplift on deformation mechanism in the Wupoer fold-and-thrust belt, NE Pamir: Constraints from analogue modelling

    NASA Astrophysics Data System (ADS)

    Wang, Chunyang; Cheng, Xiaogan; Chen, Hanlin; Ding, Weiwei; Lin, Xiubin; Wu, Lei; Li, Kang; Shi, Jun; Li, Yong

    2016-10-01

    Palaeo-uplifts often exist in fold-and-thrust belts. However, their effects on the deformational process have not yet been well understood. To evaluate such effects, six analogue models were systematically run based on geological features of the Wupoer fold-and-thrust belt (FTB), NE Pamir, where the Wulagen palaeo-uplift with overlying gypsum bed has been clearly identified. Our analogue results demonstrated that the palaeo-uplift (its location and inhomogenous distribution), accompanied with overlying gypsum bed that serves as ductile décollement, plays a critical role in localizing the front thrust fault and shaping it into arc form. The results indicate that the front thrust fault slides along the ductile décollement (gypsum bed), and breaks through onto the surface at the region where the palaeo-uplift develops, forming a piggy-back basin in the hanging wall. It suggests that the palaeo-uplift with consequent topographic variation of the overlying ductile décollement localizes the breakthrough point of the front thrust fault. In addition, the results indicate that the front thrust fault (Pamir Front Thrust, PFT) initially broke through in the location where it develops the Wulagen palaeo-uplift and propagated aside. This resulted in the distance between the PFT and the basement-involved fault (Main Pamir Thrust, MPT) to decrease from the region with palaeo-uplift to the areas aside without palaeo-uplift, thereby forming the arc-shaped PFT in map view. The results of this study also provide a revised geological model, which emphasizes the effect of décollement layer on absorbing the slip along the PFT. Our results provide a new mechanical interpretation of the deformation of Wupoer FTB, NE Pamir.

  4. The protein folding network

    NASA Astrophysics Data System (ADS)

    Rao, Francesco; Caflisch, Amedeo

    2004-03-01

    Networks are everywhere. The conformation space of a 20-residue antiparallel beta-sheet peptide [1], sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. As previously found for the World-Wide Web as well as for social and biological networks , the conformation space contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the network shows a hierarchical modularity [2] which is consistent with the funnel mechanism of folding [3] and is not observed for a random heteropolymer lacking a native state. Here we show that the conformation space network describes the free energy landscape without requiring projections into arbitrarily chosen reaction coordinates. The network analysis provides a basis for understanding the heterogeneity of the folding transition state and the existence of multiple pathways. [1] P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel beta-sheet peptide, PNAS 97, 10780-10785 (2000). [2] Ravasz, E. and Barabási, A. L. Hierarchical organization in complex networks. Phys. Rev. E 67, 026112 (2003). [3] Dill, K. and Chan, H From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997)

  5. Periodic folding of viscous sheets

    NASA Astrophysics Data System (ADS)

    Ribe, Neil M.

    2003-09-01

    The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

  6. Folding of Pollen Grains

    NASA Astrophysics Data System (ADS)

    Katifori, Eleni; Alben, Silas; Cerda, Enrique; Nelson, David; Dumais, Jacques

    2008-03-01

    At dehiscence, which occurs when the anther reaches maturity and opens, pollen grains dehydrate and their volume is reduced. The pollen wall deforms to accommodate the volume loss, and the deformation pathway depends on the initial turgid pollen grain geometry and the mechanical properties of the pollen wall. We demonstrate, using both experimental and theoretical approaches, that the design of the apertures (areas on the pollen wall where the stretching and the bending modulus are reduced) is critical for controlling the folding pattern, and ensures the pollen grain viability. An excellent fit to the experiments is obtained using a discretized version of the theory of thin elastic shells.

  7. Enhancing conservation, ecosystem services, and local livelihoods through a wildlife premium mechanism.

    PubMed

    Dinerstein, Eric; Varma, Keshav; Wikramanayake, Eric; Powell, George; Lumpkin, Susan; Naidoo, Robin; Korchinsky, Mike; Del Valle, Christian; Lohani, Shubash; Seidensticker, John; Joldersma, Dirk; Lovejoy, Thomas; Kushlin, Andrey

    2013-02-01

    We propose the wildlife premium mechanism as an innovation to conserve endangered large vertebrates. The performance-based payment scheme would allow stakeholders in lower-income countries to generate revenue by recovering and maintaining threatened fauna that can also serve as umbrella species (i.e., species whose protection benefits other species with which they co-occur). There are 3 possible options for applying the premium: option 1, embed premiums in a carbon payment; option 2, link premiums to a related carbon payment, but as independent and legally separate transactions; option 3, link premiums to noncarbon payments for conserving ecosystem services (PES). Each option presents advantages, such as incentive payments to improve livelihoods of rural poor who reside in or near areas harboring umbrella species, and challenges, such as the establishment of a subnational carbon credit scheme. In Kenya, Peru, and Nepal pilot premium projects are now underway or being finalized that largely follow option 1. The Kasigau (Kenya) project is the first voluntary carbon credit project to win approval from the 2 leading groups sanctioning such protocols and has already sold carbon credits totaling over $1.2 million since June 2011. A portion of the earnings is divided among community landowners and projects that support community members and has added over 350 jobs to the local economy. All 3 projects involve extensive community management because they occur on lands where locals hold the title or have a long-term lease from the government. The monitoring, reporting, and verification required to make premium payments credible to investors include transparent methods for collecting data on key indices by trained community members and verification of their reporting by a biologist. A wildlife premium readiness fund would enable expansion of pilot programs needed to test options beyond those presented here. PMID:23181423

  8. Kinetics and Mechanism of Calcium Hydroxide Conversion into Calcium Alkoxides: Implications in Heritage Conservation Using Nanolimes.

    PubMed

    Rodriguez-Navarro, Carlos; Vettori, Irene; Ruiz-Agudo, Encarnacion

    2016-05-24

    Nanolimes are alcohol dispersions of Ca(OH)2 nanoparticles used in the conservation of cultural heritage. Although it was believed that Ca(OH)2 particles were inert when dispersed in short-chain alcohols, it has been recently shown that they can undergo transformation into calcium alkoxides. Little is known, however, about the mechanism and kinetics of such a phase transformation as well as its effect on the performance of nanolimes. Here we show that Ca(OH)2 particles formed after lime slaking react with ethanol and isopropanol and partially transform (fractional conversion, α up to 0.08) into calcium ethoxide and isopropoxide, respectively. The transformation shows Arrhenius behavior, with apparent activation energy Ea of 29 ± 4 and 37 ± 6 kJ mol(-1) for Ca-ethoxide and Ca-isopropoxide conversion, respectively. High resolution transmission electron microscopy analyses of reactant and product phases show that the alkoxides replace the crystalline structure of Ca(OH)2 along specific [hkl] directions, preserving the external hexagonal (platelike) morphology of the parent phase. Textural and kinetic results reveal that this pseudomorphic replacement involves a 3D diffusion-controlled deceleratory advancement of the reaction front. The results are consistent with an interface-coupled dissolution-precipitation replacement mechanism. Analysis of the carbonation of Ca(OH)2 particles with different degree of conversion into Ca-ethoxide (α up to 0.08) and Ca-isopropoxide (α up to 0.04) exposed to air (20 °C, 80% relative humidity) reveals that Ca-alkoxides significantly reduce the rate of transformation into cementing CaCO3 and induce the formation of metastable vaterite, as opposed to stable calcite which forms in untransformed Ca(OH)2 samples. Similar effects are obtained when a commercial nanolime partially transformed into Ca-ethoxide is subjected to carbonation. Such effects may hamper/delay the strengthening or consolidation effects of nanolimes, thus having

  9. Kinetics and Mechanism of Calcium Hydroxide Conversion into Calcium Alkoxides: Implications in Heritage Conservation Using Nanolimes.

    PubMed

    Rodriguez-Navarro, Carlos; Vettori, Irene; Ruiz-Agudo, Encarnacion

    2016-05-24

    Nanolimes are alcohol dispersions of Ca(OH)2 nanoparticles used in the conservation of cultural heritage. Although it was believed that Ca(OH)2 particles were inert when dispersed in short-chain alcohols, it has been recently shown that they can undergo transformation into calcium alkoxides. Little is known, however, about the mechanism and kinetics of such a phase transformation as well as its effect on the performance of nanolimes. Here we show that Ca(OH)2 particles formed after lime slaking react with ethanol and isopropanol and partially transform (fractional conversion, α up to 0.08) into calcium ethoxide and isopropoxide, respectively. The transformation shows Arrhenius behavior, with apparent activation energy Ea of 29 ± 4 and 37 ± 6 kJ mol(-1) for Ca-ethoxide and Ca-isopropoxide conversion, respectively. High resolution transmission electron microscopy analyses of reactant and product phases show that the alkoxides replace the crystalline structure of Ca(OH)2 along specific [hkl] directions, preserving the external hexagonal (platelike) morphology of the parent phase. Textural and kinetic results reveal that this pseudomorphic replacement involves a 3D diffusion-controlled deceleratory advancement of the reaction front. The results are consistent with an interface-coupled dissolution-precipitation replacement mechanism. Analysis of the carbonation of Ca(OH)2 particles with different degree of conversion into Ca-ethoxide (α up to 0.08) and Ca-isopropoxide (α up to 0.04) exposed to air (20 °C, 80% relative humidity) reveals that Ca-alkoxides significantly reduce the rate of transformation into cementing CaCO3 and induce the formation of metastable vaterite, as opposed to stable calcite which forms in untransformed Ca(OH)2 samples. Similar effects are obtained when a commercial nanolime partially transformed into Ca-ethoxide is subjected to carbonation. Such effects may hamper/delay the strengthening or consolidation effects of nanolimes, thus having

  10. Is topsoil water repellency a mechanism for improving water conservation in depth?

    NASA Astrophysics Data System (ADS)

    Lozano, Elena; Jiménez-Pinilla, Patricia; Mataix-Solera, Jorge; Arcenegui, Vicky; Mataix-Beneyto, Jorge

    2013-04-01

    Soil water repellency (WR) is widespread in forest soils under different climatic conditions, soil types and vegetation covers (Doerr et al., 2000). It is normally characterized by a high spatial variability in persistence, showing wettable and water repellent patches. This phenomenon has a special interest in semiarid areas, such as the Mediterranean ecosystems, where water resources are limited. For that reason, it is thought to be a possible mechanism for improving water conservation in soil profile, which would minimize evaporation losses from the soil surface (Doerr et al., 2000; Robinson et al. 2010). The ecological function of having a patchy hydrophobic surface might be the means of transporting water deeper into the soil profile and away from surface evaporation. In addition, it may also inhibit the growth of other vegetal species. This could increase the resistance of plants to drought by increasing water availability through reducing losses to surface evaporation or other plants. Our aim was to test the hypothesis that soil WR improves the water conservation within the soil. We have compared the temporal evolution of soil moisture between samples with repellent and wettable layers. Repellent and wettable soil samples were collected from an agricultural area in Biar (Alicante, Spain). Samples were put in 100ml plastic pots (n=30). Each one had two layers (WR and wettable or both wettable) with depth around 2.5cm for superficial and 3.5cm for deeper wettable horizon. We measured the evolution under different initial conditions of soil water content (around 20% and 9%) and soil superficial WR persistence (wettable, slight, strong and severe soil (n=5 per treatment)). Pots were kept under laboratory conditions (between 30-50% of relative air humidity and ? 20°C). Soil water content was controlled daily by weight measurement. Our results showed a clear significant difference in evaporation rates, which were higher in samples with a wettable superficial layer

  11. Evaluation of management techniques to conserve water in a mechanical head wash blood removal system.

    PubMed

    Galloway, H O; Deotte, R E; Lawrence, T E

    2013-11-01

    This research objectively evaluated methods to conserve water in a mechanical beef head wash system. Digital images of pre-wash and post-wash beef heads were analyzed to quantify the percentage change in red saturation of the image, which was used as an objective measure of cleanliness. Three types of nozzles (fan, three-hole, venturi) and three water pressures (344, 516, 689kPa) were evaluated in a two-way treatment structure. An interaction (P=0.07) was observed between water pressure and nozzle type; the change in red saturation increased as pressure decreased for fan and three-hole nozzles which contrasted with venturi nozzles. The fan nozzle×516kPa pressure treatment used 25L of water per head washed and was used to evaluate the effect of three water temperatures (15, 38, 57°C). Water temperature did not impact (P=0.21) change in red saturation. Reducing water wastage and minimizing the use of heated water could have positive economic benefits to the beef processor. PMID:23793094

  12. Mechanisms controlling Pax6 isoform expression in the retina have been conserved between teleosts and mammals.

    PubMed

    Lakowski, Jörn; Majumder, Anirban; Lauderdale, James D

    2007-07-15

    The Pax6 gene plays several roles in retinal development, including control of cell proliferation, maintenance of the retinogenic potential of progenitor cells, and cell fate specification. Emerging evidence suggests that these different aspects of Pax6 gene function are mediated by different isoforms of the Pax6 protein; however, relatively little is known about the spatiotemporal expression of Pax6 isoforms in the vertebrate retina. Using bacterial artificial chromosome (BAC) technology, we modified a zebrafish Pax6a BAC such that we could distinguish paired-containing Pax6a transcripts from paired-less Pax6a transcripts. In the zebrafish, the spatial and temporal onset of expression of these transcripts suggests that the paired-less isoform is involved in the cell fate decision leading to the generation of amacrine cells; however, because of limitations associated with transient transgenic analysis, it was not feasible to establish whether this promoter was active in all amacrine cells or in a specific population of amacrine cells. By making mice transgenic for the zebrafish Pax6a BAC reporter transgene, we were able to show that paired-containing and paired-less Pax6a transcripts were differentially expressed in amacrine subpopulations. Our study also directly demonstrates the functional conservation of the regulatory mechanisms governing Pax6 transcription in teleosts and mammals.

  13. Evaluation of management techniques to conserve water in a mechanical head wash blood removal system.

    PubMed

    Galloway, H O; Deotte, R E; Lawrence, T E

    2013-11-01

    This research objectively evaluated methods to conserve water in a mechanical beef head wash system. Digital images of pre-wash and post-wash beef heads were analyzed to quantify the percentage change in red saturation of the image, which was used as an objective measure of cleanliness. Three types of nozzles (fan, three-hole, venturi) and three water pressures (344, 516, 689kPa) were evaluated in a two-way treatment structure. An interaction (P=0.07) was observed between water pressure and nozzle type; the change in red saturation increased as pressure decreased for fan and three-hole nozzles which contrasted with venturi nozzles. The fan nozzle×516kPa pressure treatment used 25L of water per head washed and was used to evaluate the effect of three water temperatures (15, 38, 57°C). Water temperature did not impact (P=0.21) change in red saturation. Reducing water wastage and minimizing the use of heated water could have positive economic benefits to the beef processor.

  14. The antiapoptotic activity of insect IAPs requires activation by an evolutionarily conserved mechanism.

    PubMed

    Tenev, T; Ditzel, M; Zachariou, A; Meier, P

    2007-06-01

    Apoptosis represents a fundamental biological process that relies on the activation of caspases. Inhibitor of apoptosis (IAP) proteins represent a group of negative regulators of both caspases and cell death. The current model dictates that IAPs suppress apoptosis by blocking the catalytic pocket of effector caspases thereby preventing substrate entry. Here, we provide evolutionary evidence for the functional interplay between insect IAPs and the N-end rule-associated ubiquitylation machinery in neutralising effector caspases and cell death. We find that IAPs require 'priming' in order to function as antiapoptotic molecules. Consistently, we demonstrate that the antiapoptotic activity of diverse insect IAPs is activated by effector caspases, providing the cell with a sensitive strategy to monitor and neutralise active caspases. Almost 300 million years of evolutionary selection pressure has preserved a caspase cleavage site in insect IAPs that, following processing by a caspase, exposes a binding motif for the N-end-rule-associated degradation machinery. Recruitment of this ubiquitylation machinery into the 'cleaved-IAP:caspase' complex provides a mechanism to negatively regulate effector caspases and block apoptosis. Furthermore, comparisons between cellular and several viral IAPs suggest differences in their modes of action, as OpIAP3, CpGV-IAP3 and HcNPV-IAP3 fail to associate with several effector caspases. Evolutionary conservation of the N-end-rule degradation pathway in IAP-mediated regulation of apoptosis further corroborates the physiological relevance of this ubiquitylation-associated process.

  15. A Conserved Inhibitory Mechanism of a Lycorine Derivative against Enterovirus and Hepatitis C Virus

    PubMed Central

    Guo, Yu; Wang, Yaxin; Cao, Lin; Wang, Peng; Qing, Jie; Zheng, Qizhen; Shang, Luqing

    2015-01-01

    Enterovirus 71 (EV71) (Picornaviridae family) and hepatitis C virus (HCV) (Flaviviridae family) are the causative agents of human hand, foot, and mouth disease (HFMD) and hepatitis C, resulting in a severe pandemic involving millions of infections in the Asia-Pacific region and worldwide. The great impact of EV71 and HCV on public health highlights the need to further our understanding of the biology of these two viruses and develop effective therapeutic antivirals. Here, we evaluated a total of 32 lycorine derivatives and demonstrated that 1-acetyllycorine suppressed the proliferation of multiple strains of EV71 in various cells. The results of the drug resistance analysis revealed that 1-acetyllycorine targeted a phenylalanine (F76) in EV71 2A protease (2Apro) to stabilize the conformation of a unique zinc finger. Most interestingly, the zinc binding site in EV71 2Apro is the exclusive homolog of HCV NS3 among all viruses. Further analysis revealed that 1-acetyllycorine also inhibits HCV with high efficacy, and the mutation on R118 in HCV NS3, which corresponds to F76 in EV71 2Apro, confers the resistance of HCV to 1-acetyllycorine. These results revealed a conserved mechanism of 1-acetyllycorine against EV71 and HCV through targeting viral proteases. We also documented the significant synergistic anti-EV71 and anti-HCV effects of 1-acetyllycorine with reported inhibitors, supporting potential combination therapy for the treatment of EV71 and HCV infections. PMID:26596952

  16. From tetrapods to primates: conserved developmental mechanisms in diverging ecological adaptations.

    PubMed

    Aboitiz, Francisco; Montiel, Juan F

    2012-01-01

    Primates are endowed with a brain about twice the size that of a mammal with the same body size, and humans have the largest brain relative to body size of all animals. This increase in brain size may be related to the acquisition of higher cognitive skills that permitted more complex social interactions, the evolution of culture, and the eventual ability to manipulate the environment. Nevertheless, in its internal structure, the primate brain shares a very conserved design with other mammals, being covered by a six-layered neocortex that, although expands disproportionately to other brain components, it does so following relatively well-defined allometric trends. Thus, the most fundamental events generating the basic design of the primate and human brain took place before the appearance of the first primate-like animal. Presumably, the earliest mammals already displayed a brain morphology radically different from that of their ancestors and that of their sister group, the reptiles, being characterized by the presence of an incipient neocortex that underwent an explosive growth in subsequent mammal evolution. In this chapter, we propose an integrative hypothesis for the origin of the mammalian neocortex, by considering the developmental modifications, functional networks, and ecological adaptations involved in the generation of this structure during the cretaceous period. Subsequently, the expansion of the primate brain is proposed to have relied on the amplification of the same, or very similar, developmental mechanisms as those involved in its primary origins, even in different ecological settings. PMID:22230620

  17. A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids.

    PubMed

    Sharma, Prashant P; Tarazona, Oscar A; Lopez, Davys H; Schwager, Evelyn E; Cohn, Martin J; Wheeler, Ward C; Extavour, Cassandra G

    2015-06-01

    The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of this anterior-most, appendage-bearing segment. While this homology statement implies a putative common mechanism for differentiation of deutocerebral appendages across arthropods, experimental data for deutocerebral appendage fate specification are limited to winged insects. Mandibulates (hexapods, crustaceans and myriapods) bear a characteristic pair of antennae on the deutocerebral segment, whereas chelicerates (e.g. spiders, scorpions, harvestmen) bear the eponymous chelicerae. In such hexapods as the fruit fly, Drosophila melanogaster, and the cricket, Gryllus bimaculatus, cephalic appendages are differentiated from the thoracic appendages (legs) by the activity of the appendage patterning gene homothorax (hth). Here we show that embryonic RNA interference against hth in the harvestman Phalangium opilio results in homeonotic chelicera-to-leg transformations, and also in some cases pedipalp-to-leg transformations. In more strongly affected embryos, adjacent appendages undergo fusion and/or truncation, and legs display proximal defects, suggesting conservation of additional functions of hth in patterning the antero-posterior and proximo-distal appendage axes. Expression signal of anterior Hox genes labial, proboscipedia and Deformed is diminished, but not absent, in hth RNAi embryos, consistent with results previously obtained with the insect G. bimaculatus. Our results substantiate a deep homology across arthropods of the mechanism whereby cephalic appendages are differentiated from locomotory appendages. PMID:25948691

  18. A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids.

    PubMed

    Sharma, Prashant P; Tarazona, Oscar A; Lopez, Davys H; Schwager, Evelyn E; Cohn, Martin J; Wheeler, Ward C; Extavour, Cassandra G

    2015-06-01

    The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of this anterior-most, appendage-bearing segment. While this homology statement implies a putative common mechanism for differentiation of deutocerebral appendages across arthropods, experimental data for deutocerebral appendage fate specification are limited to winged insects. Mandibulates (hexapods, crustaceans and myriapods) bear a characteristic pair of antennae on the deutocerebral segment, whereas chelicerates (e.g. spiders, scorpions, harvestmen) bear the eponymous chelicerae. In such hexapods as the fruit fly, Drosophila melanogaster, and the cricket, Gryllus bimaculatus, cephalic appendages are differentiated from the thoracic appendages (legs) by the activity of the appendage patterning gene homothorax (hth). Here we show that embryonic RNA interference against hth in the harvestman Phalangium opilio results in homeonotic chelicera-to-leg transformations, and also in some cases pedipalp-to-leg transformations. In more strongly affected embryos, adjacent appendages undergo fusion and/or truncation, and legs display proximal defects, suggesting conservation of additional functions of hth in patterning the antero-posterior and proximo-distal appendage axes. Expression signal of anterior Hox genes labial, proboscipedia and Deformed is diminished, but not absent, in hth RNAi embryos, consistent with results previously obtained with the insect G. bimaculatus. Our results substantiate a deep homology across arthropods of the mechanism whereby cephalic appendages are differentiated from locomotory appendages.

  19. A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids

    PubMed Central

    Sharma, Prashant P.; Tarazona, Oscar A.; Lopez, Davys H.; Schwager, Evelyn E.; Cohn, Martin J.; Wheeler, Ward C.; Extavour, Cassandra G.

    2015-01-01

    The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of this anterior-most, appendage-bearing segment. While this homology statement implies a putative common mechanism for differentiation of deutocerebral appendages across arthropods, experimental data for deutocerebral appendage fate specification are limited to winged insects. Mandibulates (hexapods, crustaceans and myriapods) bear a characteristic pair of antennae on the deutocerebral segment, whereas chelicerates (e.g. spiders, scorpions, harvestmen) bear the eponymous chelicerae. In such hexapods as the fruit fly, Drosophila melanogaster, and the cricket, Gryllus bimaculatus, cephalic appendages are differentiated from the thoracic appendages (legs) by the activity of the appendage patterning gene homothorax (hth). Here we show that embryonic RNA interference against hth in the harvestman Phalangium opilio results in homeonotic chelicera-to-leg transformations, and also in some cases pedipalp-to-leg transformations. In more strongly affected embryos, adjacent appendages undergo fusion and/or truncation, and legs display proximal defects, suggesting conservation of additional functions of hth in patterning the antero-posterior and proximo-distal appendage axes. Expression signal of anterior Hox genes labial, proboscipedia and Deformed is diminished, but not absent, in hth RNAi embryos, consistent with results previously obtained with the insect G. bimaculatus. Our results substantiate a deep homology across arthropods of the mechanism whereby cephalic appendages are differentiated from locomotory appendages. PMID:25948691

  20. Extracting Information from Folds in Rocks.

    ERIC Educational Resources Information Center

    Hudleston, Peter John

    1986-01-01

    Describes the three processes of folding in rocks: buckling, bending, and passive folding. Discusses how geometrical properties and strain distributions help to identify which processes produce natural folds, and also provides information about the mechanical properties of rocks, and the sense of shear in shear zones. (TW)

  1. Atomic-level description of ubiquitin folding

    PubMed Central

    Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.

    2013-01-01

    Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins. PMID:23503848

  2. Protein folding at atomic resolution: analysis of autonomously folding supersecondary structure motifs by nuclear magnetic resonance.

    PubMed

    Sborgi, Lorenzo; Verma, Abhinav; Sadqi, Mourad; de Alba, Eva; Muñoz, Victor

    2013-01-01

    The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism. PMID:22987355

  3. Is there an en route folding intermediate for Cold shock proteins?

    PubMed

    Huang, Lei; Shakhnovich, Eugene I

    2012-05-01

    Cold shock proteins (Csps) play an important role in cold shock response of a diverse number of organisms ranging from bacteria to humans. Numerous studies of the Csp from various species showed that a two-state folding mechanism is conserved and the transition state (TS) appears to be very compact. However, the atomic details of the folding mechanism of Csp remain unclear. This study presents the folding mechanism of Csp in atomic detail using an all-atom Go model-based simulations. Our simulations predict that there may exist an en route intermediate, in which β strands 1-2-3 are well ordered and the contacts between β1 and β4 are almost developed. Such an intermediate might be too unstable to be detected in the previous fluorescence energy transfer experiments. The transition state ensemble has been determined from the P(fold) analysis and the TS appears even more compact than the intermediate state.

  4. A repeated-measures analysis of the effects of soft tissues on wrist range of motion in the extant phylogenetic bracket of dinosaurs: Implications for the functional origins of an automatic wrist folding mechanism in Crocodilia.

    PubMed

    Hutson, Joel David; Hutson, Kelda Nadine

    2014-07-01

    A recent study hypothesized that avian-like wrist folding in quadrupedal dinosaurs could have aided their distinctive style of locomotion with semi-pronated and therefore medially facing palms. However, soft tissues that automatically guide avian wrist folding rarely fossilize, and automatic wrist folding of unknown function in extant crocodilians has not been used to test this hypothesis. Therefore, an investigation of the relative contributions of soft tissues to wrist range of motion (ROM) in the extant phylogenetic bracket of dinosaurs, and the quadrupedal function of crocodilian wrist folding, could inform these questions. Here, we repeatedly measured wrist ROM in degrees through fully fleshed, skinned, minus muscles/tendons, minus ligaments, and skeletonized stages in the American alligator Alligator mississippiensis and the ostrich Struthio camelus. The effects of dissection treatment and observer were statistically significant for alligator wrist folding and ostrich wrist flexion, but not ostrich wrist folding. Final skeletonized wrist folding ROM was higher than (ostrich) or equivalent to (alligator) initial fully fleshed ROM, while final ROM was lower than initial ROM for ostrich wrist flexion. These findings suggest that, unlike the hinge/ball and socket-type elbow and shoulder joints in these archosaurs, ROM within gliding/planar diarthrotic joints is more restricted to the extent of articular surfaces. The alligator data indicate that the crocodilian wrist mechanism functions to automatically lock their semi-pronated palms into a rigid column, which supports the hypothesis that this palmar orientation necessitated soft tissue stiffening mechanisms in certain dinosaurs, although ROM-restricted articulations argue against the presence of an extensive automatic mechanism. Anat Rec, 297:1228-1249, 2014. © 2014 Wiley Periodicals, Inc.

  5. Fog spontaneously folds mosquito wings

    NASA Astrophysics Data System (ADS)

    Dickerson, Andrew K.; Liu, Xing; Zhu, Ting; Hu, David L.

    2015-02-01

    The flexibility of insect wings confers aerodynamic benefits, but can also present a hazard if exposed to fog or dew. Fog can cause water to accumulate on wings, bending them into tight taco shapes and rendering them useless for flight. In this combined experimental and theoretical study, we use high-speed video to film the spontaneous folding of isolated mosquito wings due to the evaporation of a water drop. We predict shapes of the deformed wing using two-dimensional elastica theory, considering both surface tension and Laplace pressure. We also recommend fold-resistant geometries for the wings of flapping micro-aerial vehicles. Our work reveals the mechanism of insect wing folding and provides a framework for further study of capillarity-driven folding in both natural and biomimetic systems at small scales.

  6. Thick-skinned tectonics and basement control on geometry, kinematics and mechanics of fold-and-thrust belts. Insights from some cenozoic belts worldwide

    NASA Astrophysics Data System (ADS)

    Lacombe, Olivier; Bellahsen, Nicolas

    2015-04-01

    Fold-and-thrust belts (FTBs) form either in lower and upper plates at the expense of proximal parts of former passive margins during collision or within the upper plate of subduction orogens. In contrast, inner parts of mountain belts are likely made of stacked units from the distal passive margin domains that have undergone continental subduction and HP-LT metamorphism. There are increasing lines of evidence that the basement is involved in shortening in many FTBs worldwide, either pervasively (across the entire belt; tectonic inversion may even occur more forelandward than the mountain front) or mainly in their innermore domains where this basement is commonly exhumed. For thick-skinned FTBs that developed from former passive margins, the occurrence of weak mechanical layers within the proximal margin lithosphere (the middle and most of the lower crust are expectedly ductile) may explain that contractional deformation be distributed within most of the crust giving rise to basement-involved tectonic style. In contrast, because these weak crustal levels are usually lacking in distal parts of the margins as a result of thinning, these stronger lithospheric domains are more prone to localized deformation/subduction. Less understandable this way is the occurrence of thick-skinned wide domains within cold and strong interiors of upper plates of subduction zones, such as the Paleocene Laramide orogenic belt or the active Sierras Pampeanas belt. Structural, geophysical and thermochronological investigations within Cenozoic thick-skinned (or basement-involved thin-skinned) FTBs provide evidence for how the pre-orogenic and syn-orogenic deformation of the basement may control the geometry, kinematics and mechanics of FTBs. In this contribution, we examine some examples of FTBs where the basement is known to be involved in shortening and we review some aspects of the control exerted by the basement on the deformation. This control is demonstrated (1) at the scale of the

  7. Hydroxynitrile lyases with α/β-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms.

    PubMed

    Andexer, Jennifer N; Staunig, Nicole; Eggert, Thorsten; Kratky, Christoph; Pohl, Martina; Gruber, Karl

    2012-09-01

    Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies. PMID:22851196

  8. Hydroxynitrile Lyases with α/β-Hydrolase Fold: Two Enzymes with Almost Identical 3D Structures but Opposite Enantioselectivities and Different Reaction Mechanisms

    PubMed Central

    Andexer, Jennifer N; Staunig, Nicole; Eggert, Thorsten; Kratky, Christoph; Pohl, Martina; Gruber, Karl

    2012-01-01

    Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies. PMID:22851196

  9. Hydroxynitrile lyases with α/β-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms.

    PubMed

    Andexer, Jennifer N; Staunig, Nicole; Eggert, Thorsten; Kratky, Christoph; Pohl, Martina; Gruber, Karl

    2012-09-01

    Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies.

  10. Conserved components, but distinct mechanisms for the placement and assembly of the cell division machinery in unicellular and filamentous ascomycetes.

    PubMed

    Seiler, Stephan; Justa-Schuch, Daniela

    2010-12-01

    Cytokinesis is essential for cell proliferation, yet its molecular description is challenging, because >100 conserved proteins must be spatially and temporally co-ordinated. Despite the high importance of a tight co-ordination of cytokinesis with chromosome and organelle segregation, the mechanism for determining the cell division plane is one of the least conserved aspects of cytokinesis in eukaryotic cells. Budding and fission yeast have developed fundamentally distinct mechanisms to ensure proper nuclear segregation. The extent to which these pathways are conserved in multicellular fungi remains unknown. Recent progress indicates common components, but different mechanisms that are required for proper selection of the septation site in the different groups of Ascomycota. Cortical cues are used in yeast- and filament-forming species of the Saccharomycotina clade that are established at the incipient bud site or the hyphal tip respectively. In contrast, septum formation in the filament-forming Pezizomycotina species Aspergillus nidulans and Neurospora crassa seems more closely related to the fission yeast programme in that they may combine mitotic signals with a cell end-based marker system and Rho GTPase signalling. Thus, significant differences in the use and connection of conserved signalling modules become apparent that reflect the phylogenetic relationship of the analysed models. PMID:21091496

  11. Progress in fold recognition.

    PubMed

    Flöckner, H; Braxenthaler, M; Lackner, P; Jaritz, M; Ortner, M; Sippl, M J

    1995-11-01

    The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition.

  12. Let Them Fold

    ERIC Educational Resources Information Center

    Grant, Nicholas; Tobin, Alexander

    1972-01-01

    Directions are given for seven activities involving the folding of paper strips to illustrate geometric concepts. Properties of pentagons, triangles, hexagons, and Mobius bands resulting from the various foldings are discussed. (DT)

  13. Folded pendulum tiltmeter

    NASA Astrophysics Data System (ADS)

    Wu, Shuchao; Fan, Shuhua; Luo, Jun; Hsu, Houtse

    2002-05-01

    The application of the folded pendulum (FP) as a tiltmeter is proposed and some features of it have been studied both theoretically and experimentally. First, FP could have a quite low resonance frequency due to its mechanical structure. The period of our prototype FP is 6.2 s and the amplification factor is about 100. Second, FP is not sensitive to the environmental temperature variation but seriously affected by the temperature gradient. The experiment with a temperature gradient modulation shows that the static equilibrium position of the FP will change by 2.5 μrad if the temperature difference between the horizontal platform and the base of the FP is 0.1 °C. With a prototype FP, we have observed obvious tilt tides, and the calibration result shows that the resolution of the FP is about 1.2 nrad.

  14. Understanding Conservation of Laws in Mechanics: Students' Conceptual Change in Learning about Collisions.

    ERIC Educational Resources Information Center

    Grimellini-Tomasini, N.; And Others

    1993-01-01

    Reviews research on student learning about collisions in physics instruction. Focus is placed on the main differences between the spontaneous perspective in describing/interpreting collisions and the disciplinary perspective based upon the energy and linear momentum conservation laws. (PR)

  15. A Note on the Conservation of Mechanical Energy and the Galilean Principle of Relativity

    ERIC Educational Resources Information Center

    Santos, F. C.; Soares, V.; Tort, A. C.

    2010-01-01

    A reexamination of simple examples that we usually teach to our students in introductory courses is the starting point for a discussion about the principle of conservation of energy and Galilean invariance. (Contains 5 figures.)

  16. SELECTING INDICATORS OF BIODIVERSITY FOR CONSERVATION PLANNING: IDENTIFYING THE MECHANISMS BEHIND INDICATOR GROUP PERFORMANCE

    EPA Science Inventory

    Most conservation planning is constrained by time and funding. In particular, the selection of areas to protect biodiversity must often be completed with limited data on species distributions. Consequently, different groups of species have been proposed as indicators or surroga...

  17. Prolonged fasting identifies heat shock protein 10 as a Sirtuin 3 substrate: elucidating a new mechanism linking mitochondrial protein acetylation to fatty acid oxidation enzyme folding and function.

    PubMed

    Lu, Zhongping; Chen, Yong; Aponte, Angel M; Battaglia, Valentina; Gucek, Marjan; Sack, Michael N

    2015-01-23

    Although Sirtuin 3 (SIRT3), a mitochondrially enriched deacetylase and activator of fat oxidation, is down-regulated in response to high fat feeding, the rate of fatty acid oxidation and mitochondrial protein acetylation are invariably enhanced in this dietary milieu. These paradoxical data implicate that additional acetylation modification-dependent levels of regulation may be operational under nutrient excess conditions. Because the heat shock protein (Hsp) Hsp10-Hsp60 chaperone complex mediates folding of the fatty acid oxidation enzyme medium-chain acyl-CoA dehydrogenase, we tested whether acetylation-dependent mitochondrial protein folding contributes to this regulatory discrepancy. We demonstrate that Hsp10 is a functional SIRT3 substrate and that, in response to prolonged fasting, SIRT3 levels modulate mitochondrial protein folding. Acetyl mutagenesis of Hsp10 lysine 56 alters Hsp10-Hsp60 binding, conformation, and protein folding. Consistent with Hsp10-Hsp60 regulation of fatty acid oxidation enzyme integrity, medium-chain acyl-CoA dehydrogenase activity and fat oxidation are elevated by Hsp10 acetylation. These data identify acetyl modification of Hsp10 as a nutrient-sensing regulatory node controlling mitochondrial protein folding and metabolic function. PMID:25505263

  18. Proteopedia: Rossmann Fold: A Beta-Alpha-Beta Fold at Dinucleotide Binding Sites

    ERIC Educational Resources Information Center

    Hanukoglu, Israel

    2015-01-01

    The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (ß) and alpha helical (a) segments wherein the ß-strands are hydrogen bonded forming a ß-sheet. The initial beta-alpha-beta (ßaß) fold is the most conserved segment of Rossmann folds. As this segment…

  19. Geometry of Miura-folded metamaterials

    PubMed Central

    Schenk, Mark; Guest, Simon D.

    2013-01-01

    This paper describes two folded metamaterials based on the Miura-ori fold pattern. The structural mechanics of these metamaterials are dominated by the kinematics of the folding, which only depends on the geometry and therefore is scale-independent. First, a folded shell structure is introduced, where the fold pattern provides a negative Poisson’s ratio for in-plane deformations and a positive Poisson’s ratio for out-of-plane bending. Second, a cellular metamaterial is described based on a stacking of individual folded layers, where the folding kinematics are compatible between layers. Additional freedom in the design of the metamaterial can be achieved by varying the fold pattern within each layer. PMID:23401549

  20. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.

    PubMed Central

    Tsai, C. J.; Maizel, J. V.; Nussinov, R.

    1999-01-01

    We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers

  1. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: Re-entrant-Groove-Assisted VLS Growth of Boron Carbide Five-Fold Twinned Nanowires

    NASA Astrophysics Data System (ADS)

    Fu, Xin; Jiang, Jun; Liu, Chao; Yu, Zhi-Yang; Steffan, Lea; Yuan, Jun

    2009-08-01

    We report a preferential growth of boron carbide nanowires with a five-fold twinned internal structure. The nanowires are found to grow catalytically via iron boron nanoparticles, but unusually the catalytic particle is in contact with the low-energy surfaces of boron carbide with V-shaped contact lines. We propose that this catalytical growth may be caused by preferential nucleation at the re-entrant grooves due to the twinning planes, followed by rapid spreading of atomic steps. This is consistent with the observed temperature dependence of the five-fold twinned nanowire growth.

  2. Studying citizen science through adaptive management and learning feedbacks as mechanisms for improving conservation.

    PubMed

    Jordan, Rebecca; Gray, Steven; Sorensen, Amanda; Newman, Greg; Mellor, David; Newman, Greg; Hmelo-Silver, Cindy; LaDeau, Shannon; Biehler, Dawn; Crall, Alycia

    2016-06-01

    Citizen science has generated a growing interest among scientists and community groups, and citizen science programs have been created specifically for conservation. We examined collaborative science, a highly interactive form of citizen science, which we developed within a theoretically informed framework. In this essay, we focused on 2 aspects of our framework: social learning and adaptive management. Social learning, in contrast to individual-based learning, stresses collaborative and generative insight making and is well-suited for adaptive management. Adaptive-management integrates feedback loops that are informed by what is learned and is guided by iterative decision making. Participants engaged in citizen science are able to add to what they are learning through primary data collection, which can result in the real-time information that is often necessary for conservation. Our work is particularly timely because research publications consistently report a lack of established frameworks and evaluation plans to address the extent of conservation outcomes in citizen science. To illustrate how our framework supports conservation through citizen science, we examined how 2 programs enacted our collaborative science framework. Further, we inspected preliminary conservation outcomes of our case-study programs. These programs, despite their recent implementation, are demonstrating promise with regard to positive conservation outcomes. To date, they are independently earning funds to support research, earning buy-in from local partners to engage in experimentation, and, in the absence of leading scientists, are collecting data to test ideas. We argue that this success is due to citizen scientists being organized around local issues and engaging in iterative, collaborative, and adaptive learning.

  3. Studying citizen science through adaptive management and learning feedbacks as mechanisms for improving conservation.

    PubMed

    Jordan, Rebecca; Gray, Steven; Sorensen, Amanda; Newman, Greg; Mellor, David; Newman, Greg; Hmelo-Silver, Cindy; LaDeau, Shannon; Biehler, Dawn; Crall, Alycia

    2016-06-01

    Citizen science has generated a growing interest among scientists and community groups, and citizen science programs have been created specifically for conservation. We examined collaborative science, a highly interactive form of citizen science, which we developed within a theoretically informed framework. In this essay, we focused on 2 aspects of our framework: social learning and adaptive management. Social learning, in contrast to individual-based learning, stresses collaborative and generative insight making and is well-suited for adaptive management. Adaptive-management integrates feedback loops that are informed by what is learned and is guided by iterative decision making. Participants engaged in citizen science are able to add to what they are learning through primary data collection, which can result in the real-time information that is often necessary for conservation. Our work is particularly timely because research publications consistently report a lack of established frameworks and evaluation plans to address the extent of conservation outcomes in citizen science. To illustrate how our framework supports conservation through citizen science, we examined how 2 programs enacted our collaborative science framework. Further, we inspected preliminary conservation outcomes of our case-study programs. These programs, despite their recent implementation, are demonstrating promise with regard to positive conservation outcomes. To date, they are independently earning funds to support research, earning buy-in from local partners to engage in experimentation, and, in the absence of leading scientists, are collecting data to test ideas. We argue that this success is due to citizen scientists being organized around local issues and engaging in iterative, collaborative, and adaptive learning. PMID:26585836

  4. Structural and Mechanistic Analysis of a Novel Class of Shikimate Dehydrogenases: Evidence for a Conserved Catalytic Mechanism in the Shikimate Dehydrogenase Family

    SciTech Connect

    Peek, James; Lee, John; Hu, Shi; Senisterra, Guillermo; Christendat, Dinesh

    2011-10-27

    Shikimate dehydrogenase (SDH) catalyzes the reversible NADPH-dependent reduction of 3-dehydroshikimate to shikimate. This reaction represents the fourth step of the shikimate pathway, the essential route for the biosynthesis of the aromatic amino acids in plants, fungi, bacteria, and apicomplexan parasites. The absence of this pathway in animals makes it an attractive target for herbicides and antimicrobials. At least four functionally distinct enzyme classes, AroE, YdiB, SDH-like (SdhL), and AroE-like1 (Ael1), utilize shikimate as a substrate in vitro and form the SDH family. Crystal structures have been determined for AroE, YdiB, and SdhL. In this study, we have determined the first representative crystal structure of an Ael1 enzyme. We demonstrate that Ael1 shares a similar overall structure with the other members of the SDH family. This high level of structural conservation extends to the active sites of the enzymes. In particular, an ionizable active site lysine and aspartate are present in all SDH homologues. Two distinct biochemical roles have been reported for this Lys-Asp pair: as binding residues in YdiB and as a catalytic dyad in AroE and SdhL. Here, we establish that the residues function as a catalytic dyad in Ael1 and, interestingly, in at least one YdiB homologue. The conservation of three-dimensional fold, active site architecture, and catalytic mechanism among members of the SDH family will facilitate the design of drugs targeting the shikimate pathway.

  5. A Survey on Energy Conserving Mechanisms for the Internet of Things: Wireless Networking Aspects.

    PubMed

    Abbas, Zeeshan; Yoon, Wonyong

    2015-09-25

    The Internet of Things (IoT) is an emerging key technology for future industries and everyday lives of people, where a myriad of battery operated sensors, actuators, and smart objects are connected to the Internet to provide services such as mobile healthcare, intelligent transport system, environmental monitoring, etc. Since energy efficiency is of utmost importance to these battery constrained IoT devices, IoT-related standards and research works have focused on the device energy conserving issues. This paper presents a comprehensive survey on energy conserving issues and solutions in using diverse wireless radio access technologies for IoT connectivity, e.g., the 3rd Generation Partnership Project (3GPP) machine type communications, IEEE 802.11ah, Bluetooth Low Energy (BLE), and Z-Wave. We look into the literature in broad areas of standardization, academic research, and industry development, and structurally summarize the energy conserving solutions based on several technical criteria. We also propose future research directions regarding energy conserving issues in wireless networking-based IoT.

  6. A Survey on Energy Conserving Mechanisms for the Internet of Things: Wireless Networking Aspects

    PubMed Central

    Abbas, Zeeshan; Yoon, Wonyong

    2015-01-01

    The Internet of Things (IoT) is an emerging key technology for future industries and everyday lives of people, where a myriad of battery operated sensors, actuators, and smart objects are connected to the Internet to provide services such as mobile healthcare, intelligent transport system, environmental monitoring, etc. Since energy efficiency is of utmost importance to these battery constrained IoT devices, IoT-related standards and research works have focused on the device energy conserving issues. This paper presents a comprehensive survey on energy conserving issues and solutions in using diverse wireless radio access technologies for IoT connectivity, e.g., the 3rd Generation Partnership Project (3GPP) machine type communications, IEEE 802.11ah, Bluetooth Low Energy (BLE), and Z-Wave. We look into the literature in broad areas of standardization, academic research, and industry development, and structurally summarize the energy conserving solutions based on several technical criteria. We also propose future research directions regarding energy conserving issues in wireless networking-based IoT. PMID:26404275

  7. A Survey on Energy Conserving Mechanisms for the Internet of Things: Wireless Networking Aspects.

    PubMed

    Abbas, Zeeshan; Yoon, Wonyong

    2015-01-01

    The Internet of Things (IoT) is an emerging key technology for future industries and everyday lives of people, where a myriad of battery operated sensors, actuators, and smart objects are connected to the Internet to provide services such as mobile healthcare, intelligent transport system, environmental monitoring, etc. Since energy efficiency is of utmost importance to these battery constrained IoT devices, IoT-related standards and research works have focused on the device energy conserving issues. This paper presents a comprehensive survey on energy conserving issues and solutions in using diverse wireless radio access technologies for IoT connectivity, e.g., the 3rd Generation Partnership Project (3GPP) machine type communications, IEEE 802.11ah, Bluetooth Low Energy (BLE), and Z-Wave. We look into the literature in broad areas of standardization, academic research, and industry development, and structurally summarize the energy conserving solutions based on several technical criteria. We also propose future research directions regarding energy conserving issues in wireless networking-based IoT. PMID:26404275

  8. Investigating the Conservation of Mechanical Energy Using Video Analysis: Four Cases

    ERIC Educational Resources Information Center

    Bryan, J. A.

    2010-01-01

    Inexpensive video analysis technology now enables students to make precise measurements of an object's position at incremental times during its motion. Such capability now allows users to "examine", rather than simply "assume", energy conservation in a variety of situations commonly discussed in introductory physics courses. This article describes…

  9. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 12778, as Cycle 19.

  10. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {11863} during Cycle 17.

  11. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {10035} during Cycle 12.

  12. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 13149, as Cycle 20.

  13. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2011-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis, Proposal 12416, as Cycle 18.

  14. A galaxy of folds.

    PubMed

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains. PMID:19937658

  15. The Alternative complex III: properties and possible mechanisms for electron transfer and energy conservation.

    PubMed

    Refojo, Patrícia N; Teixeira, Miguel; Pereira, Manuela M

    2012-10-01

    Alternative complexes III (ACIII) are recently identified membrane-bound enzymes that replace functionally the cytochrome bc(1/)b(6)f complexes. In general, ACIII are composed of four transmembrane proteins and three peripheral subunits that contain iron-sulfur centers and C-type hemes. ACIII are built by a combination of modules present in different enzyme families, namely the complex iron-sulfur molybdenum containing enzymes. In this article a historical perspective on the investigation of ACIII is presented, followed by an overview of the present knowledge on these enzymes. Electron transfer pathways within the protein are discussed taking into account possible different locations (cytoplasmatic or periplasmatic) of the iron-sulfur containing protein and their contribution to energy conservation. In this way several hypotheses for energy conservation modes are raised including linear and bifurcating electron transfer pathways. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).

  16. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

    PubMed Central

    Schosserer, Markus; Minois, Nadege; Angerer, Tina B.; Amring, Manuela; Dellago, Hanna; Harreither, Eva; Calle-Perez, Alfonso; Pircher, Andreas; Gerstl, Matthias Peter; Pfeifenberger, Sigrid; Brandl, Clemens; Sonntagbauer, Markus; Kriegner, Albert; Linder, Angela; Weinhäusel, Andreas; Mohr, Thomas; Steiger, Matthias; Mattanovich, Diethard; Rinnerthaler, Mark; Karl, Thomas; Sharma, Sunny; Entian, Karl-Dieter; Kos, Martin; Breitenbach, Michael; Wilson, Iain B.H.; Polacek, Norbert; Grillari-Voglauer, Regina; Breitenbach-Koller, Lore; Grillari, Johannes

    2015-01-01

    Several pathways modulating longevity and stress resistance converge on translation by targeting ribosomal proteins or initiation factors, but whether this involves modifications of ribosomal RNA is unclear. Here, we show that reduced levels of the conserved RNA methyltransferase NSUN5 increase the lifespan and stress resistance in yeast, worms and flies. Rcm1, the yeast homologue of NSUN5, methylates C2278 within a conserved region of 25S rRNA. Loss of Rcm1 alters the structural conformation of the ribosome in close proximity to C2278, as well as translational fidelity, and favours recruitment of a distinct subset of oxidative stress-responsive mRNAs into polysomes. Thus, rather than merely being a static molecular machine executing translation, the ribosome exhibits functional diversity by modification of just a single rRNA nucleotide, resulting in an alteration of organismal physiological behaviour, and linking rRNA-mediated translational regulation to modulation of lifespan, and differential stress response. PMID:25635753

  17. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan.

    PubMed

    Schosserer, Markus; Minois, Nadege; Angerer, Tina B; Amring, Manuela; Dellago, Hanna; Harreither, Eva; Calle-Perez, Alfonso; Pircher, Andreas; Gerstl, Matthias Peter; Pfeifenberger, Sigrid; Brandl, Clemens; Sonntagbauer, Markus; Kriegner, Albert; Linder, Angela; Weinhäusel, Andreas; Mohr, Thomas; Steiger, Matthias; Mattanovich, Diethard; Rinnerthaler, Mark; Karl, Thomas; Sharma, Sunny; Entian, Karl-Dieter; Kos, Martin; Breitenbach, Michael; Wilson, Iain B H; Polacek, Norbert; Grillari-Voglauer, Regina; Breitenbach-Koller, Lore; Grillari, Johannes

    2015-01-30

    Several pathways modulating longevity and stress resistance converge on translation by targeting ribosomal proteins or initiation factors, but whether this involves modifications of ribosomal RNA is unclear. Here, we show that reduced levels of the conserved RNA methyltransferase NSUN5 increase the lifespan and stress resistance in yeast, worms and flies. Rcm1, the yeast homologue of NSUN5, methylates C2278 within a conserved region of 25S rRNA. Loss of Rcm1 alters the structural conformation of the ribosome in close proximity to C2278, as well as translational fidelity, and favours recruitment of a distinct subset of oxidative stress-responsive mRNAs into polysomes. Thus, rather than merely being a static molecular machine executing translation, the ribosome exhibits functional diversity by modification of just a single rRNA nucleotide, resulting in an alteration of organismal physiological behaviour, and linking rRNA-mediated translational regulation to modulation of lifespan, and differential stress response.

  18. Conserved mechanisms of Mycobacterium marinum pathogenesis within the environmental amoeba Acanthamoeba castellanii.

    PubMed

    Kennedy, George M; Morisaki, J Hiroshi; Champion, Patricia A DiGiuseppe

    2012-03-01

    Mycobacterium marinum is a waterborne mycobacterial pathogen. Due to their common niche, protozoa likely represent natural hosts for M. marinum. We demonstrate that the ESX-1 secretion system is required for M. marinum pathogenesis and that M. marinum utilizes actin-based motility in amoebae. Therefore, at least two virulence pathways used by M. marinum in macrophages are conserved during M. marinum infection of amoebae.

  19. Mathematics Through Paper Folding.

    ERIC Educational Resources Information Center

    Olson, Alton T.

    This booklet is a revised edition of Donovan Johnson's "Paper Folding for the Mathematics Class" (ED 077 711). It begins with directions for folding basic constructions such as as a straight line, the line perpendicular to a given line passing through a given point, and the bisector of an angle. Subsequent chapters cover concepts related to…

  20. Reduced alphabet for protein folding prediction.

    PubMed

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-04-01

    What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28-letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28-letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design.

  1. Microscopic interpretation of folding ϕ-values using the transition path ensemble.

    PubMed

    Best, Robert B; Hummer, Gerhard

    2016-03-22

    All-atom molecular dynamics simulations now allow us to create movies of proteins folding and unfolding. However, it is difficult to assess the accuracy of the folding mechanisms observed because experiments cannot yet directly resolve events occurring along the transition paths between unfolded and folded states. Protein folding ϕ-values provide residue-resolved information about folding mechanisms by comparing the effects of mutations on folding rates and stability, but determining ϕ-values by separately simulating mutant proteins would be computationally demanding and prone to large statistical errors. Here we use transition path theory to develop a method for computing ϕ-values directly from the transition path ensemble, without the need for additional simulations. This path-based approach uses the full transition path information available from equilibrium folding and unfolding trajectories, or from transition path sampling, and does not require identification of folding transition states. Applying our approach to a set of simulations of 10 small proteins by Shaw and coworkers [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520; Piana S, Lindorff-Larsen K, Shaw DE (2011) Biophys J100(9):L47-L49; and Piana S, Lindorff-Larsen K, Shaw DE (2013) Proc Natl Acad Sci USA 110(15):5915-5920], we find good agreement with experiments in most cases where data are available. We can further resolve the contributions to fractional ϕ-values coming from partial contact formation versus transition path heterogeneity. Although in some cases, there is substantial heterogeneity of folding mechanism, in others, such as Ubiquitin, the mechanism is strongly conserved.

  2. Microscopic interpretation of folding ϕ-values using the transition path ensemble

    PubMed Central

    Best, Robert B.; Hummer, Gerhard

    2016-01-01

    All-atom molecular dynamics simulations now allow us to create movies of proteins folding and unfolding. However, it is difficult to assess the accuracy of the folding mechanisms observed because experiments cannot yet directly resolve events occurring along the transition paths between unfolded and folded states. Protein folding ϕ-values provide residue-resolved information about folding mechanisms by comparing the effects of mutations on folding rates and stability, but determining ϕ-values by separately simulating mutant proteins would be computationally demanding and prone to large statistical errors. Here we use transition path theory to develop a method for computing ϕ-values directly from the transition path ensemble, without the need for additional simulations. This path-based approach uses the full transition path information available from equilibrium folding and unfolding trajectories, or from transition path sampling, and does not require identification of folding transition states. Applying our approach to a set of simulations of 10 small proteins by Shaw and coworkers [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520; Piana S, Lindorff-Larsen K, Shaw DE (2011) Biophys J 100(9):L47–L49; and Piana S, Lindorff-Larsen K, Shaw DE (2013) Proc Natl Acad Sci USA 110(15):5915–5920], we find good agreement with experiments in most cases where data are available. We can further resolve the contributions to fractional ϕ-values coming from partial contact formation versus transition path heterogeneity. Although in some cases, there is substantial heterogeneity of folding mechanism, in others, such as Ubiquitin, the mechanism is strongly conserved. PMID:26957599

  3. Stress and strain evolution of folding rocks

    NASA Astrophysics Data System (ADS)

    Llorens, Maria-Gema; Griera, Albert; Bons, Paul; Gomez-Rivas, Enrique; Weikusat, Ilka

    2015-04-01

    One of the main objectives of structural geology is to unravel rock deformation histories. Fold shapes can be used to estimate the orientation and amount of strain associated with folding. However, much more information on rheology and kinematics can potentially be extracted from fold geometries (Llorens et al., 2013a). We can study the development of folds, quantify the relationships between the different parameters that determine their geometries and estimate their mechanical evolution. This approach allows us to better understand and predict not only rock but also ice deformation. One of the main parameters in fold development is the viscosity contrast between the folding layer and the matrix in which it is embedded (m), since it determines the initial fold wavelength and the amplification rate of the developing folds. Moreover, non-linear viscous rheology influences fold geometry too (Llorens et al., 2013b). We present a series of 2-dimensional simulations of folding of viscous single layers in pure and simple shear. We vary different parameters in order to compare and determine their influence on the resulting fold patterns and the associated mechanical response of the material. To perform these simulations we use the software platform ELLE (www.elle.ws) with the non-linear viscous finite element code BASIL. The results show that layers thicken at the beginning of deformation in all simulations, and visible folds start earlier or later depending on the viscosity contrast. When folds start to nucleate the layer maximum shear strain decreases, moving away from the theoretical trend for homogeneous strain (no folding). This allows the accurate determination of the onset of folding. Maximum deviatoric stresses are higher in power-law than in linear-viscosity materials, and it is initially double in pure shear than in simple shear conditions. Therefore, folding a competent layer requires less work in simple than in pure shear. The maximum deviatoric stress

  4. The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism

    PubMed Central

    2012-01-01

    Background Hepatitis B virus (HBV) encodes an oncogenic factor, HBx, which is a multifunctional protein that can induce dysfunctional regulation of signaling pathways, transcription, and cell cycle progression, among other processes, through interactions with target host factors. The subcellular localization of HBx is both cytoplasmic and nuclear. This dynamic distribution of HBx could be essential to the multiple roles of the protein at different stages during HBV infection. Transactivational functions of HBx may be exerted both in the nucleus, via interaction with host DNA-binding proteins, and in the cytoplasm, via signaling pathways. Although there have been many studies describing different pathways altered by HBx, and its innumerable binding partners, the molecular mechanism that regulates its different roles has been difficult to elucidate. Methods In the current study, we took a bioinformatics approach to investigate whether the viral protein HBx might be regulated via phosphorylation by an evolutionarily conserved mechanism. Results We found that the phylogenetically conserved residues Ser25 and Ser41 (both within the negative regulatory domain), and Thr81 (in the transactivation domain) are predicted to be phosphorylated. By molecular 3D modeling of HBx, we further show these residues are all predicted to be exposed on the surface of the protein, making them easily accesible to these types of modifications. Furthermore, we have also identified Yin Yang sites that might have the potential to be phosphorylated and O-β-GlcNAc interplay at the same residues. Conclusions Thus, we propose that the different roles of HBx displayed in different subcellular locations might be regulated by an evolutionarily conserved mechanism of posttranslational modification, via phosphorylation. PMID:23079056

  5. Conserved molecular mechanisms underlying the effects of small molecule xenobiotic chemotherapeutics on cells

    PubMed Central

    SARIN, HEMANT

    2016-01-01

    For proper determination of the apoptotic potential of chemoxenobiotics in synergism, it is important to understand the modes, levels and character of interactions of chemoxenobiotics with cells in the context of predicted conserved biophysical properties. Chemoxenobiotic structures are studied with respect to atom distribution over molecular space, the predicted overall octanol-to-water partition coefficient (Log OWPC; unitless) and molecular size viz a viz van der Waals diameter (vdWD). The Log OWPC-to-vdWD (nm−1) parameter is determined, and where applicable, hydrophilic interacting moiety/core-to-vdWD (nm−1) and lipophilic incorporating hydrophobic moiety/core-to-vdWD (nm−1) parameters of their part-structures are determined. The cellular and sub-cellular level interactions of the spectrum of xenobiotic chemotherapies have been characterized, for which a classification system has been developed based on predicted conserved biophysical properties with respect to the mode of chemotherapeutic effect. The findings of this study are applicable towards improving the effectiveness of existing combination chemotherapy regimens and the predictive accuracy of personalized cancer treatment algorithms as well as towards the selection of appropriate novel xenobiotics with the potential to be potent chemotherapeutics for dendrimer nanoparticle-based effective transvascular delivery. PMID:26998284

  6. NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS SMOV as proposal 13555 {visit 5}.

  7. Conglobation in the pill bug, Armadillidium vulgare, as a water conservation mechanism.

    PubMed

    Smigel, Jacob T; Gibbs, Allen G

    2008-01-01

    Water balance of the terrestrial isopod, Armadillidium vulgare, was investigated during conglobation (rolling-up behavior). Water loss and metabolic rates were measured at 18 +/- 1 degrees C in dry air using flow-through respirometry. Water-loss rates decreased 34.8% when specimens were in their conglobated form, while CO2 release decreased by 37.1%. Water loss was also measured gravimetrically at humidities ranging from 6 to 75 %RH. Conglobation was associated with a decrease in water-loss rates up to 53 %RH, but no significant differences were observed at higher humidities. Our findings suggest that conglobation behavior may help to conserve water, in addition to its demonstrated role in protection from predation. PMID:20233103

  8. Conglobation in the Pill Bug, Armadillidium vulgare, as a Water Conservation Mechanism

    PubMed Central

    Smigel, Jacob T.; Gibbs, Allen G.

    2008-01-01

    Water balance of the terrestrial isopod, Armadillidium vulgare, was investigated during conglobation (rolling-up behavior). Water loss and metabolic rates were measured at 18 ± 1°C in dry air using flow-through respirometry. Water-loss rates decreased 34.8% when specimens were in their conglobated form, while CO2 release decreased by 37.1%. Water loss was also measured gravimetrically at humidities ranging from 6 to 75 %RH. Conglobation was associated with a decrease in water-loss rates up to 53 %RH, but no significant differences were observed at higher humidities. Our findings suggest that conglobation behavior may help to conserve water, in addition to its demonstrated role in protection from predation. PMID:20233103

  9. Beyond transcriptional silencing: Is methylcytosine a widely conserved eukaryotic DNA elimination mechanism?

    PubMed Central

    Bracht, John R.

    2014-01-01

    Methylation of cytosine DNA residues is a well-studied epigenetic modification with important roles in formation of heterochromatic regions of the genome, and also in tissue-specific repression of transcription. However, we recently found that the ciliate Oxytricha uses methylcytosine in a novel DNA elimination pathway important for programmed genome restructuring. Remarkably, mounting evidence suggests that methylcytosine can play a dual role in ciliates, repressing gene expression during some life-stages and directing DNA elimination in others. In this essay, I describe these recent advances in the DNA methylation field and discuss whether this unexpected novel role for methylcytosine in DNA elimination might be more widely conserved in eukaryotic biology, particularly in apoptotic pathways. PMID:24519896

  10. Targeting of nucleotide-binding proteins by HAMLET--a conserved tumor cell death mechanism.

    PubMed

    Ho, J C S; Nadeem, A; Rydström, A; Puthia, M; Svanborg, C

    2016-02-18

    HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) kills tumor cells broadly suggesting that conserved survival pathways are perturbed. We now identify nucleotide-binding proteins as HAMLET binding partners, accounting for about 35% of all HAMLET targets in a protein microarray comprising 8000 human proteins. Target kinases were present in all branches of the Kinome tree, including 26 tyrosine kinases, 10 tyrosine kinase-like kinases, 13 homologs of yeast sterile kinases, 4 casein kinase 1 kinases, 15 containing PKA, PKG, PKC family kinases, 15 calcium/calmodulin-dependent protein kinase kinases and 13 kinases from CDK, MAPK, GSK3, CLK families. HAMLET acted as a broad kinase inhibitor in vitro, as defined in a screen of 347 wild-type, 93 mutant, 19 atypical and 17 lipid kinases. Inhibition of phosphorylation was also detected in extracts from HAMLET-treated lung carcinoma cells. In addition, HAMLET recognized 24 Ras family proteins and bound to Ras, RasL11B and Rap1B on the cytoplasmic face of the plasma membrane. Direct cellular interactions between HAMLET and activated Ras family members including Braf were confirmed by co-immunoprecipitation. As a consequence, oncogenic Ras and Braf activity was inhibited and HAMLET and Braf inhibitors synergistically increased tumor cell death in response to HAMLET. Unlike most small molecule kinase inhibitors, HAMLET showed selectivity for tumor cells in vitro and in vivo. The results identify nucleotide-binding proteins as HAMLET targets and suggest that dysregulation of the ATPase/kinase/GTPase machinery contributes to cell death, following the initial, selective recognition of HAMLET by tumor cells. The findings thus provide a molecular basis for the conserved tumoricidal effect of HAMLET, through dysregulation of kinases and oncogenic GTPases, to which tumor cells are addicted.

  11. Structures of Xenopus Embryonic Epidermal Lectin Reveal a Conserved Mechanism of Microbial Glycan Recognition.

    PubMed

    Wangkanont, Kittikhun; Wesener, Darryl A; Vidani, Jack A; Kiessling, Laura L; Forest, Katrina T

    2016-03-11

    Intelectins (X-type lectins), broadly distributed throughout chordates, have been implicated in innate immunity. Xenopus laevis embryonic epidermal lectin (XEEL), an intelectin secreted into environmental water by the X. laevis embryo, is postulated to function as a defense against microbes. XEEL is homologous (64% identical) to human intelectin-1 (hIntL-1), which is also implicated in innate immune defense. We showed previously that hIntL-1 binds microbial glycans bearing exocyclic vicinal diol groups. It is unknown whether XEEL has the same ligand specificity. Also unclear is whether XEEL and hIntL-1 have similar quaternary structures, as XEEL lacks the corresponding cysteine residues in hIntL-1 that stabilize the disulfide-linked trimer. These observations prompted us to further characterize XEEL. We found that hIntL-1 and XEEL have similar structural features. Even without the corresponding intermolecular disulfide bonds present in hIntL-1, the carbohydrate recognition domain of XEEL (XEELCRD) forms a stable trimer in solution. The structure of XEELCRD in complex with d-glycerol-1-phosphate, a residue present in microbe-specific glycans, indicated that the exocyclic vicinal diol coordinates to a protein-bound calcium ion. This ligand-binding mode is conserved between XEEL and hIntL-1. The domain architecture of full-length XEEL is reminiscent of a barbell, with two sets of three glycan-binding sites oriented in opposite directions. This orientation is consistent with our observation that XEEL can promote the agglutination of specific serotypes of Streptococcus pneumoniae. These data support a role for XEEL in innate immunity, and they highlight structural and functional conservation of X-type lectins among chordates.

  12. NoFold: RNA structure clustering without folding or alignment.

    PubMed

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  13. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect

    Zheng, Zhongzhou; Sosnick, Tobin R.

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  14. Protein vivisection reveals elusive intermediates in folding.

    PubMed

    Zheng, Zhongzhou; Sosnick, Tobin R

    2010-04-01

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu-->Glu(-)) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  15. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study.

  16. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study. PMID:8179251

  17. Crystal structure of PXY-TDIF complex reveals a conserved recognition mechanism among CLE peptide-receptor pairs

    PubMed Central

    Zhang, Heqiao; Lin, Xiaoya; Han, Zhifu; Qu, Li-Jia; Chai, Jijie

    2016-01-01

    Plants can achieve amazing lifespans because of their continuous and repetitive formation of new organs by stem cells present within meristems. The balance between proliferation and differentiation of meristem cells is largely regulated by the CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE) peptide hormones. One of the well-characterized CLE peptides, CLE41/TDIF (tracheary elements differentiation inhibitory factor), functions to suppress tracheary element differentiation and promote procambial cell proliferation, playing important roles in vascular development and wood formation. The recognition mechanisms of TDIF or other CLE peptides by their respective receptors, however, remain largely elusive. Here we report the crystal structure of TDIF in complex with its receptor PXY, a leucine-rich repeat receptor kinase (LRR-RK). Our structure reveals that TDIF mainly adopts an “Ω”-like conformation binding to the inner surface of the LRR domain of PXY. Interaction between TDIF and PXY is predominately mediated by the relatively conserved amino acids of TDIF. Structure-based sequence alignment showed that the TDIF-interacting motifs are also conserved among other known CLE receptors. Our data provide a structural template for understanding the recognition mechanism of CLE peptides by their receptors, offering an opportunity for the identification of receptors of other uncharacterized CLE peptides. PMID:27055373

  18. Conservative treatment preferences and the plausible mechanism of Neer's stage 1 of shoulder impingement in younger people.

    PubMed

    2015-05-01

    The interaction of various factors in the vicious cycle (VC) of subacromial impingement syndrome (SIS) is complex and there are conservative treatment preferences for speedy rehabilitation. The mechanism of SIS is not fully understood and the inappropriate treatment priorities cause delay in rehabilitation. SIS is related to the reduction in the subacromial space (SS). Posterior capsular tightness (PCT) and rotator cuff (RC) dysfunction are the two basic mechanisms in this regard. PCT may cause anterosuperior translation of humeral head (HH) and anterior acromion tipping through scapular dyskinesis, thereby reducing the subacromial space. Alteration in the force couple of muscle secondary to scapular dyskinesis eventually causes injury to subacromial structures. The rotator cuff is important in centring the humeral head in the glenoid cavity and superior translation of humeral head occurs if their function is compromised. Posterior capsular tightness may affect the function of rotator cuff action which leads to early fatigue, dysfunction of these muscles and eventually impingement. Adhesive changes take place in various structures around the shoulder secondary to impingement pain and relative immobility, which further aggravates the problem. To reverse the vicious cycle, conservative intervention should therefore be directed to loosen posterior capsular tightness, restore rotator cuff function through appropriate exercise in a pain-free range through appropriate exercise, mobilisation of adhesion through teraservers friction or pain-free mobilisation or grade I and grade II manipulation. Depending on the level of irritability, pain control intervention could be considered alongside. PMID:26028390

  19. Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis

    PubMed Central

    Wiech, Eliza M; Cheng, Hai-Ping; Singh, Shaneen M

    2015-01-01

    The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present a theoretical structural model of the active form of ExoR protein, ExoRm, generated using computational methods. Our model suggests that ExoR possesses a super-helical fold comprising 12 α-helices forming six Sel1-like repeats, including two that were unidentified in previous studies. This fold is highly conducive to mediating protein–protein interactions and this is corroborated by the identification of putative protein binding sites on the surface of the ExoRm protein. Our studies reveal two novel insights: (a) an extended conformation of the third Sel1-like repeat that might be important for ExoR regulatory function and (b) a buried proteolytic site that implies a unique proteolytic mechanism. This study provides new and interesting insights into the structure of S. meliloti ExoR, lays the groundwork for elaborating the molecular mechanism of ExoRm cleavage, ExoRm–ExoS interactions, and studies of ExoR homologs in other bacterial host interactions. PMID:25492513

  20. Folding without charges

    PubMed Central

    Kurnik, Martin; Hedberg, Linda; Danielsson, Jens; Oliveberg, Mikael

    2012-01-01

    Surface charges of proteins have in several cases been found to function as “structural gatekeepers,” which avoid unwanted interactions by negative design, for example, in the control of protein aggregation and binding. The question is then if side-chain charges, due to their desolvation penalties, play a corresponding role in protein folding by avoiding competing, misfolded traps? To find out, we removed all 32 side-chain charges from the 101-residue protein S6 from Thermus thermophilus. The results show that the charge-depleted S6 variant not only retains its native structure and cooperative folding transition, but folds also faster than the wild-type protein. In addition, charge removal unleashes pronounced aggregation on longer timescales. S6 provides thus an example where the bias toward native contacts of a naturally evolved protein sequence is independent of charges, and point at a fundamental difference in the codes for folding and intermolecular interaction: specificity in folding is governed primarily by hydrophobic packing and hydrogen bonding, whereas solubility and binding relies critically on the interplay of side-chain charges. PMID:22454493

  1. Conservation of multivariate female preference functions and preference mechanisms in three species of trilling field crickets.

    PubMed

    Blankers, T; Hennig, R M; Gray, D A

    2015-03-01

    Divergence in mate recognition systems among closely related species is an important contributor to assortative mating and reproductive isolation. Here, we examine divergence in male song traits and female preference functions in three cricket species with songs consisting of long trills. The shape of female preference functions appears to be mostly conserved across species and follows the predictions from a recent model for song recognition. Multivariate preference profiles, combining the pulse and trill parameters, demonstrate selectivity for conspecific pulse rates and high trill duty cycles. The rules for integration across pulse and trill timescales were identical for all three species. Generally, we find greater divergence in male song traits than in associated female preferences. For pulse rate, we find a strong match between divergent male traits and female peak preferences. Preference functions for trill parameters and carrier frequency are similar between species and show less congruence between signal and preference. Differences among traits in the degree of trait-preference (mis)match may reflect the strength of preferences and the potential for linkage disequilibrium, selective constraints and alternative selective pressures, but appear unrelated to selection for mate recognition per se. PMID:25661511

  2. Conservation of multivariate female preference functions and preference mechanisms in three species of trilling field crickets.

    PubMed

    Blankers, T; Hennig, R M; Gray, D A

    2015-03-01

    Divergence in mate recognition systems among closely related species is an important contributor to assortative mating and reproductive isolation. Here, we examine divergence in male song traits and female preference functions in three cricket species with songs consisting of long trills. The shape of female preference functions appears to be mostly conserved across species and follows the predictions from a recent model for song recognition. Multivariate preference profiles, combining the pulse and trill parameters, demonstrate selectivity for conspecific pulse rates and high trill duty cycles. The rules for integration across pulse and trill timescales were identical for all three species. Generally, we find greater divergence in male song traits than in associated female preferences. For pulse rate, we find a strong match between divergent male traits and female peak preferences. Preference functions for trill parameters and carrier frequency are similar between species and show less congruence between signal and preference. Differences among traits in the degree of trait-preference (mis)match may reflect the strength of preferences and the potential for linkage disequilibrium, selective constraints and alternative selective pressures, but appear unrelated to selection for mate recognition per se.

  3. The presence of disulfide bonds reveals an evolutionarily conserved mechanism involved in mitochondrial protein translocase assembly

    PubMed Central

    Wrobel, Lidia; Sokol, Anna M.; Chojnacka, Magdalena; Chacinska, Agnieszka

    2016-01-01

    Disulfide bond formation is crucial for the biogenesis and structure of many proteins that are localized in the intermembrane space of mitochondria. The importance of disulfide bond formation within mitochondrial proteins was extended beyond soluble intermembrane space proteins. Tim22, a membrane protein and core component of the mitochondrial translocase TIM22, forms an intramolecular disulfide bond in yeast. Tim22 belongs to the Tim17/Tim22/Tim23 family of protein translocases. Here, we present evidence of the high evolutionary conservation of disulfide bond formation in Tim17 and Tim22 among fungi and metazoa. Topological models are proposed that include the location of disulfide bonds relative to the predicted transmembrane regions. Yeast and human Tim22 variants that are not oxidized do not properly integrate into the membrane complex. Moreover, the lack of Tim17 oxidation disrupts the TIM23 translocase complex. This underlines the importance of disulfide bond formation for mature translocase assembly through membrane stabilization of weak transmembrane domains. PMID:27265872

  4. Transcript profiling reveals mechanisms for lipid conservation during diapause in the mosquito, Aedes albopictus

    PubMed Central

    Reynolds, Julie A.; Poelchau, Monica F.; Rahman, Zahra; Armbruster, Peter A.; Denlinger, David L.

    2012-01-01

    The Asian tiger mosquito, Aedes albopictus, is a medically important invasive species whose geographic distribution has expanded dramatically during the past 20 years, and one of the key elements of its success is its capacity to survive long distance transport as a diapausing pharate first instar larva, encased within the chorion of the egg. We report that pharate larvae entering diapause are larger and contain 30% more lipid than their nondiapausing counterparts. To improve our understanding of the molecular regulation of lipid metabolism during diapause, we assessed the relative mRNA abundance of 21 genes using qRT-PCR. Elevated expression of lipid storage droplet protein 2 during embryonic development likely contributes to the higher amounts of lipid we noted in diapausing individuals. The conservation of lipids during diapause is reflected in downregulation of genes involved in lipid catabolism, including lipase 2, lipase 3, lipase 4, acyl-CoA dehydrogenase 4, and isovaleryl-CoA dehydrogenase. Two genes involved in fatty acid synthesis and modification, Δ(9)-desaturase, and fatty acyl-CoA elongase, were both upregulated in diapausing pharate larvae, suggesting roles for their gene products in generating unsaturated fatty acids to enhance membrane fluidity at low temperatures and generating precursors to the surface hydrocarbons needed to resist desiccation, respectively. Together, the results point to substantial distinctions in lipid metabolism within the embryo as a consequence of the diapause program, and these differences occur both before the actual onset of diapause as well as during the diapause state. PMID:22579567

  5. Conservation of clay-bearing stones: Understanding the swelling and damage mechanisms

    NASA Astrophysics Data System (ADS)

    Wangler, Timothy

    Certain sandstones used in historic monuments and decorative building facades may contain clays that swell upon wetting, producing differential strains during wetting and drying cycles and leading to the development of stresses that are on the order of the strength of the stone. This leads to damage observed in the field as buckling and surface delamination, damage expected to occur during a wetting cycle as a thin wet layer of stone goes into compression relative to the bulk of the dry stone. Clays swell due to hydration of counterbalancing cations that exist between the negatively charged aluminosilicate layers that make up a clay particle. This swelling has been observed to occur over two distinct ranges: short-range, discrete intracrystalline swelling, and long-range, continuous, osmotic swelling. Additionally, it has been shown that swelling can be reduced, but not eliminated, by exchanging the counterbalancing cations in the interlayer with alpha,o diaminoalkanes. In order to mitigate damage due to swelling, it is important to understand the mechanism by which clays swell, the mechanism by which alpha,o diaminoalkanes inhibit swelling, and the mechanism by which damage occurs on a macroscopic level. In this work, it is shown that for the sandstones studied, clays swell almost entirely via intracrystalline swelling and that alpha,o diaminoalkanes inhibit swelling via ion exchange and subsequently reduced rehydration. A buckling damage mechanism is verified experimentally and a flaw propagation mechanism in which flaws can grow to a critical buckling size is explored. An understanding of the development of stresses during wetting is explored via a novel warping experiment and swelling pressure experiments.

  6. Folded supersymmetry with a twist

    DOE PAGES

    Cohen, Timothy; Craig, Nathaniel; Lou, Hou Keong; Pinner, David

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. Asmore » a result, these models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.« less

  7. The M1 family of vertebrate aminopeptidases: role of evolutionarily conserved tyrosines in the enzymatic mechanism of aminopeptidase B.

    PubMed

    Cadel, Sandrine; Darmon, Cécile; Pernier, Julien; Hervé, Guy; Foulon, Thierry

    2015-02-01

    Aminopeptidase B (Ap-B), a member of the M1 family of Zn(2+)-aminopeptidases, removes basic residues at the NH2-terminus of peptides and is involved in the in vivo proteolytic processing of miniglucagon and cholecystokinin-8. M1 enzymes hydrolyze numerous different peptides and are implicated in many physiological functions. As these enzymes have similar catalytic mechanisms, their respective substrate specificity and/or catalytic efficiency must be based on subtle structural differences at or near the catalytic site. This leads to the hypothesis that each primary structure contains a consensus structural template, strictly necessary for aminopeptidase activity, and a specific amino acid environment localized in or outside the catalytic pocket that finely tunes the substrate specificity and catalytic efficiency of each enzyme. A multiple sequence alignment of M1 peptidases from vertebrates allowed to identify conserved tyrosine amino acids, which are members of this catalytic backbone. In the present work, site-directed mutagenesis and 3D molecular modeling of Ap-B were used to specify the role of four fully (Y281, Y229, Y414, and Y441) and one partially (Y409) conserved residues. Tyrosine to phenylalanine mutations allowed confirming the influence of the hydroxyl groups on the enzyme activity. These groups are implicated in the reaction mechanism (Y414), in substrate specificity and/or catalytic efficiency (Y409), in stabilization of essential amino acids of the active site (Y229, Y409) and potentially in the maintenance of its structural integrity (Y281, Y441). The importance of hydrogen bonds is verified by the Y229H substitution, which preserves the enzyme activity. These data provide new insights into the catalytic mechanism of Ap-B in the M1 family of aminopeptidases.

  8. Extracellular matrix elasticity and topography: material-based cues that affect cell function via conserved mechanisms.

    PubMed

    Janson, Isaac A; Putnam, Andrew J

    2015-03-01

    Chemical, mechanical, and topographic extracellular matrix (ECM) cues have been extensively studied for their influence on cell behavior. These ECM cues alter cell adhesion, cell shape, and cell migration and activate signal transduction pathways to influence gene expression, proliferation, and differentiation. ECM elasticity and topography, in particular, have emerged as material properties of intense focus based on strong evidence these physical cues can partially dictate stem cell differentiation. Cells generate forces to pull on their adhesive contacts, and these tractional forces appear to be a common element of cells' responses to both elasticity and topography. This review focuses on recently published work that links ECM topography and mechanics and their influence on differentiation and other cell behaviors. We also highlight signaling pathways typically implicated in mechanotransduction that are (or may be) shared by cells subjected to topographic cues. Finally, we conclude with a brief discussion of the potential implications of these commonalities for cell based therapies and biomaterial design.

  9. Systemic Acquired Resistance in Moss: Further Evidence for Conserved Defense Mechanisms in Plants

    PubMed Central

    Winter, Peter S.; Bowman, Collin E.; Villani, Philip J.; Dolan, Thomas E.; Hauck, Nathanael R.

    2014-01-01

    Vascular plants possess multiple mechanisms for defending themselves against pathogens. One well-characterized defense mechanism is systemic acquired resistance (SAR). In SAR, a plant detects the presence of a pathogen and transmits a signal throughout the plant, inducing changes in the expression of various pathogenesis-related (PR) genes. Once SAR is established, the plant is capable of mounting rapid responses to subsequent pathogen attacks. SAR has been characterized in numerous angiosperm and gymnosperm species; however, despite several pieces of evidence suggesting SAR may also exist in non-vascular plants6–8, its presence in non-vascular plants has not been conclusively demonstrated, in part due to the lack of an appropriate culture system. Here, we describe and use a novel culture system to demonstrate that the moss species Amblystegium serpens does initiate a SAR-like reaction upon inoculation with Pythium irregulare, a common soil-borne oomycete. Infection of A. serpens gametophores by P. irregulare is characterized by localized cytoplasmic shrinkage within 34 h and chlorosis and necrosis within 7 d of inoculation. Within 24 h of a primary inoculation (induction), moss gametophores grown in culture became highly resistant to infection following subsequent inoculation (challenge) by the same pathogen. This increased resistance was a response to the pathogen itself and not to physical wounding. Treatment with β-1,3 glucan, a structural component of oomycete cell walls, was equally effective at triggering SAR. Our results demonstrate, for the first time, that this important defense mechanism exists in a non-vascular plant, and, together with previous studies, suggest that SAR arose prior to the divergence of vascular and non-vascular plants. In addition, this novel moss – pathogen culture system will be valuable for future characterization of the mechanism of SAR in moss, which is necessary for a better understanding of the evolutionary history of SAR

  10. Fermilab Central Computing Facility: Energy conservation report and mechanical systems design optimization and cost analysis study

    SciTech Connect

    Krstulovich, S.F.

    1986-11-12

    This report is developed as part of the Fermilab Central Computing Facility Project Title II Design Documentation Update under the provisions of DOE Document 6430.1, Chapter XIII-21, Section 14, paragraph a. As such, it concentrates primarily on HVAC mechanical systems design optimization and cost analysis and should be considered as a supplement to the Title I Design Report date March 1986 wherein energy related issues are discussed pertaining to building envelope and orientation as well as electrical systems design.

  11. Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1β (IL-1β)

    PubMed Central

    Capraro, Dominique T.; Lammert, Heiko; Heidary, David K.; Roy, Melinda; Gross, Larry A.; Onuchic, José N.; Jennings, Patricia A.

    2013-01-01

    Deletion of the β-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1β into antagonist activity. Conversely, circular permutations of IL-1β conserve the functional folding route as well as the agonist activity. These two extremes in the folding-functional interplay beg the question of whether mutations in IL-1β would result in changes in the populations of heterogeneous folding routes and the signaling activity. A series of topologically equivalent water-mediated β-strand bridging interactions within the pseudosymmetric β-trefoil fold of IL-1β highlight the backbone water interactions that stabilize the secondary and tertiary structure of the protein. Additionally, conserved aromatic residues lining the central cavity appear to be essential for both stability and folding. Here, we probe these protein backbone-water molecule and side chain-side chain interactions and the role they play in the folding mechanism of this geometrically stressed molecule. We used folding simulations with structure-based models, as well as a series of folding kinetic experiments to examine the effects of the F42W core mutation on the folding landscape of IL-1β. This mutation alters water-mediated backbone interactions essential for maintaining the trefoil fold. Our results clearly indicate that this perturbation in the primary structure alters a structural water interaction and consequently modulates the population of folding routes accessed during folding and signaling activity. PMID:23972849

  12. An evolutionarily conserved negative feedback mechanism in the Hippo pathway reflects functional difference between LATS1 and LATS2

    PubMed Central

    Park, Gun-Soo; Oh, Hyangyee; Kim, Minchul; Kim, Tackhoon; Johnson, Randy L.; Irvine, Kenneth D.; Lim, Dae-Sik

    2016-01-01

    The Hippo pathway represses YAP oncoprotein activity through phosphorylation by LATS kinases. Although variety of upstream components has been found to participate in the Hippo pathway, the existence and function of negative feedback has remained uncertain. We found that activated YAP, together with TEAD transcription factors, directly induces transcription of LATS2, but not LATS1, to form a negative feedback loop. We also observed increased mRNA levels of Hippo upstream components upon YAP activation. To reveal the physiological role of this negative feedback regulation, we deleted Lats2 or Lats1 in the liver-specific Sav1-knockout mouse model which develops a YAP-induced tumor. Additional deletion of Lats2 severely enhanced YAP-induced tumorigenic phenotypes in a liver specific Sav1 knock-out mouse model while additional deletion of Lats1 mildly affected the phenotype. Only Sav1 and Lats2 double knock-down cells formed larger colonies in soft agar assay, thereby recapitulating accelerated tumorigenesis seen in vivo. Importantly, this negative feedback is evolutionarily conserved, as Drosophila Yorkie (YAP ortholog) induces transcription of Warts (LATS2 ortholog) with Scalloped (TEAD ortholog). Collectively, we demonstrated the existence and function of an evolutionarily conserved negative feedback mechanism in the Hippo pathway, as well as the functional difference between LATS1 and LATS2 in regulation of YAP. PMID:27006470

  13. Inhibition of protein synthesis by TOR inactivation revealed a conserved regulatory mechanism of the BiP chaperone in Chlamydomonas.

    PubMed

    Díaz-Troya, Sandra; Pérez-Pérez, María Esther; Pérez-Martín, Marta; Moes, Suzette; Jeno, Paul; Florencio, Francisco J; Crespo, José L

    2011-10-01

    The target of rapamycin (TOR) kinase integrates nutritional and stress signals to coordinately control cell growth in all eukaryotes. TOR associates with highly conserved proteins to constitute two distinct signaling complexes termed TORC1 and TORC2. Inactivation of TORC1 by rapamycin negatively regulates protein synthesis in most eukaryotes. Here, we report that down-regulation of TOR signaling by rapamycin in the model green alga Chlamydomonas reinhardtii resulted in pronounced phosphorylation of the endoplasmic reticulum chaperone BiP. Our results indicated that Chlamydomonas TOR regulates BiP phosphorylation through the control of protein synthesis, since rapamycin and cycloheximide have similar effects on BiP modification and protein synthesis inhibition. Modification of BiP by phosphorylation was suppressed under conditions that require the chaperone activity of BiP, such as heat shock stress or tunicamycin treatment, which inhibits N-linked glycosylation of nascent proteins in the endoplasmic reticulum. A phosphopeptide localized in the substrate-binding domain of BiP was identified in Chlamydomonas cells treated with rapamycin. This peptide contains a highly conserved threonine residue that might regulate BiP function, as demonstrated by yeast functional assays. Thus, our study has revealed a regulatory mechanism of BiP in Chlamydomonas by phosphorylation/dephosphorylation events and assigns a role to the TOR pathway in the control of BiP modification.

  14. Folds and Etudes

    ERIC Educational Resources Information Center

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  15. Overland flow generation mechanisms affected by topsoil treatment: Application to soil conservation

    NASA Astrophysics Data System (ADS)

    Hueso-González, P.; Ruiz-Sinoga, J. D.; Martínez-Murillo, J. F.; Lavee, H.

    2015-01-01

    Hortonian overland-flow is responsible for significant amounts of soil loss in Mediterranean geomorphological systems. Restoring the native vegetation is the most effective way to control runoff and sediment yield. During the seeding and plant establishment, vegetation cover may be better sustained if soil is amended with an external source. Four amendments were applied in an experimental set of plots: straw mulching (SM); mulch with chipped branches of Aleppo Pine (Pinus halepensis L.) (PM); TerraCottem hydroabsorbent polymer (HP); and sewage sludge (RU). Plots were afforested following the same spatial pattern, and amendments were mixed with the soil at the rate 10 Mg ha- 1. This research demonstrates the role played by the treatments in overland flow generation mechanism. On one hand, the high macroporosity of SM and PM, together with the fact that soil moisture increased with depth, explains weak overland flow and thus low sediment yield due to saturation conditions. Therefore, regarding overland flow and sediment yield, RU behaves similarly to SM and PM. On the other hand, when HP was applied, overland flow developed quickly with relatively high amounts. This, together with the decrease downward in soil moisture along the soil profile, proved that mechanisms of overland flow are of the Hortonian type.

  16. Conservative Mechanisms of Extracellular Trap Formation by Annelida Eisenia andrei: Serine Protease Activity Requirement

    PubMed Central

    Ortmann, Weronika; Kolaczkowska, Elzbieta

    2016-01-01

    Formation of extracellular traps (ETs) capturing and immobilizing pathogens is now a well-established defense mechanism added to the repertoire of vertebrate phagocytes. These ETs are composed of extracellular DNA (extDNA), histones and antimicrobial proteins. Formation of mouse and human ETs depends on enzymes (i) facilitating decondensation of chromatin by citrullination of histones, and (ii) serine proteases degrading histones. In invertebrates, initial reports revealed existence of ETs composed of extDNA and histones, and here we document for the first time that also coelomocytes, immunocompetent cells of an earthworm Eisenia andrei, cast ETs which successfully trap bacteria in a reactive oxygen species (ROS)-dependent and -independent manner. Importantly, the formation of ETs was observed not only when coelomocytes were studied ex vivo, but also in vivo, directly in the earthworm coelom. These ETs were composed of extDNA, heat shock proteins (HSP27) and H3 histones. Furthermore, the formation of E. andrei ETs depended on activity of serine proteases, including elastase-like activity. Moreover, ETs interconnected and hold together aggregating coelomocytes, a processes proceeding encapsulation. In conclusion, the study confirms ET formation by earthworms, and unravels mechanisms leading to ET formation and encapsulation in invertebrates. PMID:27416067

  17. Empathy as a driver of prosocial behaviour: highly conserved neurobehavioural mechanisms across species.

    PubMed

    Decety, Jean; Bartal, Inbal Ben-Ami; Uzefovsky, Florina; Knafo-Noam, Ariel

    2016-01-19

    Empathy reflects the natural ability to perceive and be sensitive to the emotional states of others, coupled with a motivation to care for their well-being. It has evolved in the context of parental care for offspring, as well as within kinship bonds, to help facilitate group living. In this paper, we integrate the perspectives of evolution, animal behaviour, developmental psychology, and social and clinical neuroscience to elucidate our understanding of the proximate mechanisms underlying empathy. We focus, in particular, on processing of signals of distress and need, and their relation to prosocial behaviour. The ability to empathize, both in animals and humans, mediates prosocial behaviour when sensitivity to others' distress is paired with a drive towards their welfare. Disruption or atypical development of the neural circuits that process distress cues and integrate them with decision value leads to callous disregard for others, as is the case in psychopathy. The realization that basic forms of empathy exist in non-human animals is crucial for gaining new insights into the underlying neurobiological and genetic mechanisms of empathy, enabling translation towards therapeutic and pharmacological interventions.

  18. Conservative Mechanisms of Extracellular Trap Formation by Annelida Eisenia andrei: Serine Protease Activity Requirement.

    PubMed

    Homa, Joanna; Ortmann, Weronika; Kolaczkowska, Elzbieta

    2016-01-01

    Formation of extracellular traps (ETs) capturing and immobilizing pathogens is now a well-established defense mechanism added to the repertoire of vertebrate phagocytes. These ETs are composed of extracellular DNA (extDNA), histones and antimicrobial proteins. Formation of mouse and human ETs depends on enzymes (i) facilitating decondensation of chromatin by citrullination of histones, and (ii) serine proteases degrading histones. In invertebrates, initial reports revealed existence of ETs composed of extDNA and histones, and here we document for the first time that also coelomocytes, immunocompetent cells of an earthworm Eisenia andrei, cast ETs which successfully trap bacteria in a reactive oxygen species (ROS)-dependent and -independent manner. Importantly, the formation of ETs was observed not only when coelomocytes were studied ex vivo, but also in vivo, directly in the earthworm coelom. These ETs were composed of extDNA, heat shock proteins (HSP27) and H3 histones. Furthermore, the formation of E. andrei ETs depended on activity of serine proteases, including elastase-like activity. Moreover, ETs interconnected and hold together aggregating coelomocytes, a processes proceeding encapsulation. In conclusion, the study confirms ET formation by earthworms, and unravels mechanisms leading to ET formation and encapsulation in invertebrates. PMID:27416067

  19. Epoxycarotenoid-mediated synthesis of abscisic acid in Physcomitrella patens implicating conserved mechanisms for acclimation to hyperosmosis in embryophytes.

    PubMed

    Takezawa, Daisuke; Watanabe, Naoki; Ghosh, Totan Kumar; Saruhashi, Masashi; Suzuki, Atsushi; Ishiyama, Kanako; Somemiya, Shinnosuke; Kobayashi, Masatomo; Sakata, Yoichi

    2015-04-01

    Plants acclimate to environmental stress signals such as cold, drought and hypersalinity, and provoke internal protective mechanisms. Abscisic acid (ABA), a carotenoid-derived phytohormone, which increases in response to the stress signals above, has been suggested to play a key role in the acclimation process in angiosperms, but the role of ABA in basal land plants such as mosses, including its biosynthetic pathways, has not been clarified. Targeted gene disruption of PpABA1, encoding zeaxanthin epoxidase in the moss Physcomitrella patens was conducted to determine the role of endogenous ABA in acclimation processes in mosses. The generated ppaba1 plants were found to accumulate only a small amount of endogenous ABA. The ppaba1 plants showed reduced osmotic acclimation capacity in correlation with reduced dehydration tolerance and accumulation of late embryogenesis abundant proteins. By contrast, cold-induced freezing tolerance was less affected in ppaba1, indicating that endogenous ABA does not play a major role in the regulation of cold acclimation in the moss. Our results suggest that the mechanisms for osmotic acclimation mediated by carotenoid-derived synthesis of ABA are conserved in embryophytes and that acquisition of the mechanisms played a crucial role in terrestrial adaptation and colonization by land plant ancestors. PMID:25545104

  20. Epoxycarotenoid-mediated synthesis of abscisic acid in Physcomitrella patens implicating conserved mechanisms for acclimation to hyperosmosis in embryophytes.

    PubMed

    Takezawa, Daisuke; Watanabe, Naoki; Ghosh, Totan Kumar; Saruhashi, Masashi; Suzuki, Atsushi; Ishiyama, Kanako; Somemiya, Shinnosuke; Kobayashi, Masatomo; Sakata, Yoichi

    2015-04-01

    Plants acclimate to environmental stress signals such as cold, drought and hypersalinity, and provoke internal protective mechanisms. Abscisic acid (ABA), a carotenoid-derived phytohormone, which increases in response to the stress signals above, has been suggested to play a key role in the acclimation process in angiosperms, but the role of ABA in basal land plants such as mosses, including its biosynthetic pathways, has not been clarified. Targeted gene disruption of PpABA1, encoding zeaxanthin epoxidase in the moss Physcomitrella patens was conducted to determine the role of endogenous ABA in acclimation processes in mosses. The generated ppaba1 plants were found to accumulate only a small amount of endogenous ABA. The ppaba1 plants showed reduced osmotic acclimation capacity in correlation with reduced dehydration tolerance and accumulation of late embryogenesis abundant proteins. By contrast, cold-induced freezing tolerance was less affected in ppaba1, indicating that endogenous ABA does not play a major role in the regulation of cold acclimation in the moss. Our results suggest that the mechanisms for osmotic acclimation mediated by carotenoid-derived synthesis of ABA are conserved in embryophytes and that acquisition of the mechanisms played a crucial role in terrestrial adaptation and colonization by land plant ancestors.

  1. Development of the external genitalia: conserved and divergent mechanisms of appendage patterning

    PubMed Central

    Cohn, Martin J.

    2011-01-01

    Over the past decade, the genetics of external genital development has begun to be understood. Male and female external genitalia develop from the genital tubercle. The early tubercle has a superficial resemblance to the limb bud, but an important distinction is that the limb consists only of mesoderm and ectoderm, whereas the genital tubercle also has an endodermal component, the urethral epithelium. Urethral epithelium, which expresses Sonic hedgehog, acts as a signaling region that controls outgrowth and pattern formation, and ultimately differentiates into the urethral tube. While there are intriguing parallels between limb and genital development, recent studies have identified some key differences, including the role of Fgf signaling. Our understanding of the mechanisms of genital development still lags far behind the limb, and major questions remain to be answered, including the molecular nature of the signals that initiate genital budding, sustain outgrowth, induce tissue polarity and orchestrate urethral tubulogenesis. PMID:21465625

  2. Evolutionary conservation of mechanisms for neural regionalization, proliferation and interconnection in brain development

    PubMed Central

    Reichert, Heinrich

    2008-01-01

    Comparative studies of brain development in vertebrate and invertebrate model systems demonstrate remarkable similarities in expression and action of developmental control genes during embryonic patterning, neural proliferation and circuit formation in the brain. Thus, comparable sets of developmental control genes are involved in specifying the early brain primordium as well as in regionalized patterning along its anteroposterior and dorsoventral axes. Furthermore, similar cellular and molecular mechanisms underlie the formation and proliferation of neural stem cell-like progenitors that generate the neurons in the central nervous systems. Finally, neural identity and some complex circuit interconnections in specific brain domains appear to be comparable in vertebrates and invertebrates and may depend on similar developmental control genes. PMID:18755655

  3. Steric constraints as folding coadjuvant

    NASA Astrophysics Data System (ADS)

    Tarragó, M. E.; Rocha, Luiz F.; Dasilva, R. A.; Caliri, A.

    2003-03-01

    Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

  4. Chaperonin-mediated Protein Folding

    PubMed Central

    Horwich, Arthur L.

    2013-01-01

    We have been studying chaperonins these past twenty years through an initial discovery of an action in protein folding, analysis of structure, and elucidation of mechanism. Some of the highlights of these studies were presented recently upon sharing the honor of the 2013 Herbert Tabor Award with my early collaborator, Ulrich Hartl, at the annual meeting of the American Society for Biochemistry and Molecular Biology in Boston. Here, some of the major findings are recounted, particularly recognizing my collaborators, describing how I met them and how our great times together propelled our thinking and experiments. PMID:23803606

  5. Modelling of lateral fold growth and fold linkage: Applications to fold-and-thrust belt tectonics

    NASA Astrophysics Data System (ADS)

    Grasemann, Bernhard; Schmalholz, Stefan

    2013-04-01

    We use a finite element model to investigate the three-dimensional fold growth and interference of two initially isolated fold segments. The most critical parameter, which controls the fold linkage mode, is the phase difference between the laterally growing fold hinge lines: 1) "Linear-linkage" yields a sub-cylindrical fold with a saddle at the location where the two initial folds linked. 2) "Oblique-linkage" produces a curved fold resembling a Type II refold structure. 3) "Oblique-no-linkage" results in two curved folds with fold axes plunging in opposite directions. 4) "Linear-no-linkage" yields a fold train of two separate sub-cylindrical folds with fold axes plunging in opposite directions. The transition from linkage to no-linkage occurs when the fold separation between the initially isolated folds is slightly larger than one half of the low-amplitude fold wavelength. The model results compare well with previously published plasticine analogue models and can be directly applied to the investigation of fold growth history in fold-and-thust belts. An excellent natural example of lateral fold linkage is described from the Zagros fold-and-thrust belt in the Kurdistan Region of Iraq. The fold growth in this region is not controlled by major thrust faults but the shortening of the Paleozoic to Cenozoic passive margin sediments of the Arabian plate occurred mainly by detachment folding. The sub-cylindrical anticlines with hinge-parallel lengths of more than 50 km have not developed from single sub-cylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification and lateral fold growth. Linkage points are marked by geomorphological saddle points which are structurally the lowermost points of antiforms and points of principal curvatures with opposite sign. Linkage points can significantly influence the migration of mineral-rich fluids and hydrocarbons and are therefore of great economic importance.

  6. Huddling by rat pups: group behavioral mechanisms of temperature regulation and energy conservation.

    PubMed

    Alberts, J R

    1978-04-01

    Body heat loss was attenuated and oxygen consumption was reduced by huddling in litters of developing rats. Rat pups derive physiological benefits from huddling similar to those enjoyed by adult mammals; these findings contrast with previous characterization of the altricial rat as poikilothermic. Huddling insulates by lessening the explosed body surface area of the participants, thus retarding heat loss and enhancing the efficiency of thermogenesis. These physical mechanisms of the clump are actively regulated by the pups. A novel quantitative measure of huddle size revealed a form of group regulatory behavior in rat pups whereby the surface expanded and contracted with increases and decreases in ambient temperature. The individual basis of this group regulatory activity was investigated by marking individual pups and observing them in huddles by means of time-lapse videography. It was found that individual animals circulate throught the huddle, frequently exchanging locations in the group. By studying the huddle positions of an anesthetized pup and a marked control sibling, dynamics of the pup flow were clarified. Ordinarily, the direction of movement was actively downward, into the pile; immobile pups "floated" on the surface. When the nest temperature was raised to thermoneutral, the direction of pup flow reversed and an immobile animal sank to the depths of the huddle. Through individual competitive adjustments the huddle behaves as a self-regulating unit which provides warmth and insulation to all its active members. PMID:670452

  7. Huddling by rat pups: group behavioral mechanisms of temperature regulation and energy conservation.

    PubMed

    Alberts, J R

    1978-04-01

    Body heat loss was attenuated and oxygen consumption was reduced by huddling in litters of developing rats. Rat pups derive physiological benefits from huddling similar to those enjoyed by adult mammals; these findings contrast with previous characterization of the altricial rat as poikilothermic. Huddling insulates by lessening the explosed body surface area of the participants, thus retarding heat loss and enhancing the efficiency of thermogenesis. These physical mechanisms of the clump are actively regulated by the pups. A novel quantitative measure of huddle size revealed a form of group regulatory behavior in rat pups whereby the surface expanded and contracted with increases and decreases in ambient temperature. The individual basis of this group regulatory activity was investigated by marking individual pups and observing them in huddles by means of time-lapse videography. It was found that individual animals circulate throught the huddle, frequently exchanging locations in the group. By studying the huddle positions of an anesthetized pup and a marked control sibling, dynamics of the pup flow were clarified. Ordinarily, the direction of movement was actively downward, into the pile; immobile pups "floated" on the surface. When the nest temperature was raised to thermoneutral, the direction of pup flow reversed and an immobile animal sank to the depths of the huddle. Through individual competitive adjustments the huddle behaves as a self-regulating unit which provides warmth and insulation to all its active members.

  8. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers

    PubMed Central

    Kho, Alvin T.; Zhao, Qing; Cai, Zhaohui; Butte, Atul J.; Kim, John Y.H.; Pomeroy, Scott L.; Rowitch, David H.; Kohane, Isaac S.

    2004-01-01

    Identification of common mechanisms underlying organ development and primary tumor formation should yield new insights into tumor biology and facilitate the generation of relevant cancer models. We have developed a novel method to project the gene expression profiles of medulloblastomas (MBs)—human cerebellar tumors—onto a mouse cerebellar development sequence: postnatal days 1-60 (P1-P60). Genomically, human medulloblastomas were closest to mouse P1-P10 cerebella, and normal human cerebella were closest to mouse P30-P60 cerebella. Furthermore, metastatic MBs were highly associated with mouse P5 cerebella, suggesting that a clinically distinct subset of tumors is identifiable by molecular similarity to a precise developmental stage. Genewise, down- and up-regulated MB genes segregate to late and early stages of development, respectively. Comparable results for human lung cancer vis-a-vis the developing mouse lung suggest the generalizability of this multiscalar developmental perspective on tumor biology. Our findings indicate both a recapitulation of tissue-specific developmental programs in diverse solid tumors and the utility of tumor characterization on the developmental time axis for identifying novel aspects of clinical and biological behavior. PMID:15075291

  9. The 27 February 1997 Sibi double-earthquake (Mw 6.9, 6.7) in the Sulaiman range of Pakistan - implications for the tectonics of fold-and-thrust belts and for earthquake triggering mechanisms

    NASA Astrophysics Data System (ADS)

    Nissen, E.; Craig, T. J.; McMullan, K.; Parsons, B. E.; Rickerby, A.; Wright, T. J.

    2011-12-01

    The Sulaiman mountains form an arcuate fold-and-thrust belt which accommodates oblique shortening between the Indian and Eurasian plates in western Pakistan. Despite being an important component of the India-Eurasia collision zone, little is known about the active tectonics of the range. The Mw ~7 Sibi earthquake of 27 February 1997 was the largest event to strike the Sulaiman mountains in the past eighty years, and provides an excellent opportunity to investigate the regional style of deformation. A pair of radar interferograms constructed from descending-track ERS-2 data reveals two distinct areas containing coseismic surface displacements, spaced ~50 km apart. We model these displacements to yield source parameters for the two sub-events. The larger (Mw 6.9) north-western sub-event occurred on a buried, S-dipping reverse fault, with slip confined to depths of between ~10 km and ~20 km. The elongate pattern of surface deformation lies oblique to the trend of local surface anticlines, suggesting that the fault responsible for this sub-event is disconnected from surface folding, possibly by a weak decollement. The smaller (Mw 6.7) south-eastern sub-event also involved reverse slip on a buried, S-dipping fault, but slip here reached shallower depths of ~4 km. Here, coseismic uplift is concentrated along a prominent surface anticline, which we interpret as a fault-propagation fold whose growth is driven by slip on the underlying thrust. These results suggest that (1) detachment folding and forced folding both contribute towards shortening of the Sulaiman mountains, (2) the range contains active S-dipping reverse faults despite the overall southwards propagation of thrusting, and (3) earthquakes can be generated within the thick sedimentary cover and are not restricted to the underlying basement. Finally, we merge the spatial information provided by InSAR with temporal constraints from seismic body-waveform modelling to investigate possible mechanisms for the

  10. The TLQP-21 Peptide Activates the G-protein-coupled receptor C3aR1 via a Folding-upon-Binding Mechanism

    PubMed Central

    Severini, Cinzia; Gopinath, Tata; Braun, Patrick D.; Sassano, Maria F.; Gurney, Allison; Roth, Bryan L.; Vulchanova, Lucy; Possenti, Roberta; Veglia, Gianluigi; Bartolomucci, Alessandro

    2014-01-01

    SUMMARY TLQP-21, a VGF-encoded peptide is emerging as a novel target for obesity-associated disorders. TLQP-21 is found in the sympathetic nerve terminals in the adipose tissue and targets the G-protein-coupled-receptor (GPCR) Complement-3a-Receptor1 (C3aR1). So far, the mechanisms of TLQP-21-induced receptor activation remained unexplored. Here, we report that TLQP-21 is intrinsically disordered and undergoes a disorder-to-order transition, adopting an α-helical conformation, upon targeting cells expressing the C3aR1. We determined that the hot spots for TLQP-21 are located at the C-terminus, with mutations in the last four amino acids progressively reducing the bioactivity and, a single site mutation (R21A) or C-terminal amidation abolishing its function completely. Interestingly, the human TLQP-21 sequence carrying a S20A substitution activates the human C3aR1 receptor with lower potency compared to the rodent sequence. These studies reveal the mechanism of action of TLQP-21 and provide molecular templates for designing agonists and antagonists to modulate C3aR1 functions. PMID:25456411

  11. Folded waveguide coupler

    DOEpatents

    Owens, Thomas L.

    1988-03-01

    A resonant cavity waveguide coupler for ICRH of a magnetically confined plasma. The coupler consists of a series of inter-leaved metallic vanes disposed withn an enclosure analogous to a very wide, simple rectangular waveguide that has been "folded" several times. At the mouth of the coupler, a polarizing plate is provided which has coupling apertures aligned with selected folds of the waveguide through which rf waves are launched with magnetic fields of the waves aligned in parallel with the magnetic fields confining the plasma being heated to provide coupling to the fast magnetosonic wave within the plasma in the frequency usage of from about 50-200 mHz. A shorting plate terminates the back of the cavity at a distance approximately equal to one-half the guide wavelength from the mouth of the coupler to ensure that the electric field of the waves launched through the polarizing plate apertures are small while the magnetic field is near a maximum. Power is fed into the coupler folded cavity by means of an input coaxial line feed arrangement at a point which provides an impedance match between the cavity and the coaxial input line.

  12. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  13. Local vs global motions in protein folding

    PubMed Central

    Maisuradze, Gia G.; Liwo, Adam; Senet, Patrick; Scheraga, Harold A.

    2013-01-01

    It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respectively, were analyzed. The key residues involved in the folding of the FBP28 WW domain are elucidated by this analysis. The correlations between local and global motions are found. It is shown that most of the residues in the folding trajectories of the system studied here move in a concerted fashion, following the dynamics of the whole system. This demonstrates how the choice of a pathway has to involve concerted movements in order for this protein to fold. This finding also sheds light on the effectiveness of principal component analysis (PCA) for the description of the folding dynamics of the system studied. It is demonstrated that the FEL along the PCs, computed by considering only several critically-placed residues, can correctly describe the folding dynamics. PMID:23914144

  14. A New Use for a Familiar Fold: the X-Ray Crystal Structure of GTP-Bound GTP Cyclohydrolase III From Methanocaldococcus Jannaschii Reveals a Two Metal Ion Catalytic Mechanism

    SciTech Connect

    Morrison, S.D.; Roberts, S.A.; Zegeer, A.M.; Montfort, W.R.; Bandarian, V.

    2009-05-26

    GTP cyclohydrolase (GCH) III from Methanocaldococcus jannaschii, which catalyzes the conversion of GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy), has been shown to require Mg{sup 2+} for catalytic activity and is activated by monovalent cations such as K{sup +} and ammonium [Graham, D. E., Xu, H., and White, R. H. (2002) Biochemistry 41, 15074-15084]. The reaction is formally identical to that catalyzed by a GCH II ortholog (SCO 6655) from Streptomyces coelicolor; however, SCO 6655, like other GCH II proteins, is a zinc-containing protein. The structure of GCH III complexed with GTP solved at 2 {angstrom} resolution clearly shows that GCH III adopts a distinct fold that is closely related to the palm domains of phosphodiesterases, such as DNA polymerase I. GCH III is a tetramer of identical subunits; each monomer is composed of an N- and a C-terminal domain that adopt nearly superimposible structures, suggesting that the protein has arisen by gene duplication. Three metal ions were located in the active site, two of which occupy positions that are analogous to those occupied by divalent metal ions in the structures of a number of palm domain containing proteins, such as DNA polymerase I. Two conserved Asp residues that coordinate the metal ions, which are also found in palm domain containing proteins, are observed in GCH III. Site-directed variants (Asp{yields}Asn) of these residues in GCH III are less active than wild-type. The third metal ion, most likely a potassium ion, is involved in substrate recognition through coordination of O6 of GTP. The arrangement of the metal ions in the active site suggests that GCH III utilizes two metal ion catalysis. The structure of GCH III extends the repertoire of possible reactions with a palm fold to include cyclohydrolase chemistry.

  15. Quantification of a Helical Origami Fold

    NASA Astrophysics Data System (ADS)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  16. Overland flow generation mechanisms affected by topsoil treatment: Application to soil conservation

    NASA Astrophysics Data System (ADS)

    González Paloma, Hueso; Juan Francisco, Martinez-Murillo; Damian, Ruiz-Sinoga Jose; Hanoch, Lavee

    2015-04-01

    Hortonian overland-flow is responsible for significant amounts of soil loss in Mediterranean geomorphological systems. Restoring the native vegetation is the most effective way to control runoff and sediment yield. During the seeding and plant establishment, vegetation cover may be better sustained if soil is amended with an external source. Four amendments were applied in an experimental set of plots: straw mulching (SM); mulch with chipped branches of Aleppo Pine (Pinus halepensis L.) (PM); TerraCotten hydroabsobent polymers (HP); sewage sludge (RU); and control (C). Plots were afforested following the same spatial pattern, and amendments were mixed with the soil at the rate 10 Mg ha-1. This research demonstrates the role played by the treatments in overland flow generation mechanism (runoff, overland flow and soil moisture along the soil profile). The general overland flow characteristics showed that in the C plots the average overland flow was 8.0 ± 22.0 l per event, and the HP plots produced a similar mean value (8.1 ± 20.1 l). The average overland flow per event was significantly less for soil amended with SM, PM or RU (2.7 ± 8.3 l; 1.3 ± 3.5 l and 2.2 ± 5.9 l, respectively). There was a similar trend with respect to the maximum overland flow. The mean sediment yield per event was relatively high in the C and HP plots (8.6 ± 27.8 kg and 14.8 ± 43.4 kg, respectively), while significantly lower values were registered in the SM, PM and RU plots (0.4 ± 1.0 kg; 0.2 ± 0.3 kg and 0.2 ± 0.3 kg, respectively). Very similar trends were found for the maximum sediment yield. Regarding to the soil moisture values, there was a difference in the trends between the C and HP plots and the SM, PM and RU plots. In the C and HP plots the general trend was for a decrease in soil moisture downward through the soil profile, while in the SM, PM and RU plots the soil moisture remained relatively constant or increased, except for the RU treatment in which the soil moisture

  17. Network measures for protein folding state discrimination

    PubMed Central

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  18. Network measures for protein folding state discrimination.

    PubMed

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  19. Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms

    PubMed Central

    Hutchins, Elizabeth D.; Markov, Glenn J.; Eckalbar, Walter L.; George, Rajani M.; King, Jesse M.; Tokuyama, Minami A.; Geiger, Lauren A.; Emmert, Nataliya; Ammar, Michael J.; Allen, April N.; Siniard, Ashley L.; Corneveaux, Jason J.; Fisher, Rebecca E.; Wade, Juli; DeNardo, Dale F.; Rawls, J. Alan; Huentelman, Matthew J.; Wilson-Rawls, Jeanne; Kusumi, Kenro

    2014-01-01

    Lizards, which are amniote vertebrates like humans, are able to lose and regenerate a functional tail. Understanding the molecular basis of this process would advance regenerative approaches in amniotes, including humans. We have carried out the first transcriptomic analysis of tail regeneration in a lizard, the green anole Anolis carolinensis, which revealed 326 differentially expressed genes activating multiple developmental and repair mechanisms. Specifically, genes involved in wound response, hormonal regulation, musculoskeletal development, and the Wnt and MAPK/FGF pathways were differentially expressed along the regenerating tail axis. Furthermore, we identified 2 microRNA precursor families, 22 unclassified non-coding RNAs, and 3 novel protein-coding genes significantly enriched in the regenerating tail. However, high levels of progenitor/stem cell markers were not observed in any region of the regenerating tail. Furthermore, we observed multiple tissue-type specific clusters of proliferating cells along the regenerating tail, not localized to the tail tip. These findings predict a different mechanism of regeneration in the lizard than the blastema model described in the salamander and the zebrafish, which are anamniote vertebrates. Thus, lizard tail regrowth involves the activation of conserved developmental and wound response pathways, which are potential targets for regenerative medical therapies. PMID:25140675

  20. Disparate Regulatory Mechanisms Control Fat3 and P75NTR Protein Transport through a Conserved Kif5-Interaction Domain

    PubMed Central

    Birkness, Jacqueline E.; Trinidad, Jonathan C.

    2016-01-01

    Directed transport delivers proteins to specific cellular locations and is one mechanism by which cells establish and maintain polarized cellular architectures. The atypical cadherin Fat3 directs the polarized extension of dendrites in retinal amacrine cells by influencing the distribution of cytoskeletal regulators during retinal development, however the mechanisms regulating the distribution of Fat3 remain unclear. We report a novel Kinesin/Kif5 Interaction domain (Kif5-ID) in Fat3 that facilitates Kif5B binding, and determines the distribution of Fat3 cytosolic domain constructs in neurons and MDCK cells. The Kif5-ID sequence is conserved in the neurotrophin receptor P75NTR, which also binds Kif5B, and Kif5-ID mutations similarly result in P75NTR mislocalization. Despite these similarities, Kif5B-mediated protein transport is differentially regulated by these two cargos. For Fat3, the Kif5-ID is regulated by alternative splicing, and the timecourse of splicing suggests that the distribution of Fat3 may switch between early and later stages of retinal development. In contrast, P75NTR binding to Kif5B is enhanced by tyrosine phosphorylation and thus has the potential to be dynamically regulated on a more rapid time scale. PMID:27788242

  1. Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms.

    PubMed

    Hutchins, Elizabeth D; Markov, Glenn J; Eckalbar, Walter L; George, Rajani M; King, Jesse M; Tokuyama, Minami A; Geiger, Lauren A; Emmert, Nataliya; Ammar, Michael J; Allen, April N; Siniard, Ashley L; Corneveaux, Jason J; Fisher, Rebecca E; Wade, Juli; DeNardo, Dale F; Rawls, J Alan; Huentelman, Matthew J; Wilson-Rawls, Jeanne; Kusumi, Kenro

    2014-01-01

    Lizards, which are amniote vertebrates like humans, are able to lose and regenerate a functional tail. Understanding the molecular basis of this process would advance regenerative approaches in amniotes, including humans. We have carried out the first transcriptomic analysis of tail regeneration in a lizard, the green anole Anolis carolinensis, which revealed 326 differentially expressed genes activating multiple developmental and repair mechanisms. Specifically, genes involved in wound response, hormonal regulation, musculoskeletal development, and the Wnt and MAPK/FGF pathways were differentially expressed along the regenerating tail axis. Furthermore, we identified 2 microRNA precursor families, 22 unclassified non-coding RNAs, and 3 novel protein-coding genes significantly enriched in the regenerating tail. However, high levels of progenitor/stem cell markers were not observed in any region of the regenerating tail. Furthermore, we observed multiple tissue-type specific clusters of proliferating cells along the regenerating tail, not localized to the tail tip. These findings predict a different mechanism of regeneration in the lizard than the blastema model described in the salamander and the zebrafish, which are anamniote vertebrates. Thus, lizard tail regrowth involves the activation of conserved developmental and wound response pathways, which are potential targets for regenerative medical therapies.

  2. II. Capsular vaso-mimicry formed by transgenic mammary tumor spheroids implanted ectopically into mouse dorsal skin fold: implications for cellular mechanisms of metastasis

    PubMed Central

    Witkiewicz, Halina

    2013-01-01

    Most cancer patients die of metastatic disease, not primary tumors, while biological mechanisms leading to metastases remain unclear and effective therapies are missing. Using a mouse dorsal skin chamber model we had observed that tumor growth and vasculature formation could be influenced by the way in vitro cultured (avascular) spheroids of N202 breast tumor cells were implanted; co-implantation of lactating breast tissue created stimulating microenvironment, whereas the absence of the graft resulted in temporary tumor dormancy. This report addressed the issue of cellular mechanisms of the vasculogenic switch that ended the dormancy. In situ ultrastructural analysis revealed that the tumors survived in ectopic microenvironment until some of host and tumor stem cells evolved independently into cells initiating the vasculogenic switch. The tumor cells that survived and proliferated under hypoxic conditions for three weeks were supported by erythrogenic autophagy of others. However, the host microenvironment first responded as it would to non-immunogenic foreign bodies, i.e., by encapsulating the tumor spheroids with collagen-producing fibroblasts. That led to a form of vaso-mimicry consisting of tumor cells amid tumor-derived erythrosomes (synonym of erythrocytes), megakaryocytes and platelets, and encapsulating them all, the host fibroblasts. Such capsular vaso-mimicry could potentially facilitate metastasis by fusing with morphologically similar lymphatic vessels or veins. Once incorporated into the host circulatory system, tumor cells could be carried away passively by blood flow, regardless of their genetic heterogeneity. The fake vascular segment would have permeability properties different from genuine vascular endothelium. The capsular vaso-mimicry was different from vasculogenic mimicry earlier observed in metastases-associated malignant tumors where channels formed by tumor cells were said to contain circulating blood. Structures similar to the vasculogenic

  3. Conserved mechanisms for germ cell-specific localization of nanos3 transcripts in teleost species with aquaculture significance.

    PubMed

    Škugor, Adrijana; Slanchev, Krasimir; Torgersen, Jacob Seilø; Tveiten, Helge; Andersen, Øivind

    2014-06-01

    The importance of the aquaculture production is increasing with the declining global fish stocks, but early sexual maturation in several farmed species reduces muscle growth and quality, and escapees could have a negative impact on wild populations. A possible solution to these problems is the production of sterile fish by ablation of the embryonic primordial germ cells (PGCs), a technique developed in zebrafish. Cell-specific regulation of mRNA stability is crucial for proper specification of the germ cell lineage and commonly involves microRNA (miRNA)-mediated degradation of targeted mRNAs in somatic cells. This study reports on the functional roles of conserved motifs in the 3' untranslated region (UTR) of the miRNA target gene nanos3 identified in Atlantic cod, Atlantic salmon, and zebrafish. The 3'UTR of cod nanos3 was sufficient for targeting the expression of green fluorescent protein (GFP) to the presumptive PGCs in injected embryos of the three phylogenetically distant species. 3'UTR elements of importance for PGC-specific expression were further examined by fusing truncated 3'UTR variants of cod nanos3 to GFP followed by injections in zebrafish embryos. The expression patterns of the GFP constructs in PGCs and somatic cells suggested that the proximal U-rich region is responsible for the PGC-specific stabilization of the endogenous nanos3 mRNA. Morpholino-mediated downregulation of the RNA-binding protein Dead end (DnD), a PGC-specific inhibitor of miRNA action, abolished the fluorescence of the PGCs in cod and zebrafish embryos, suggesting a conserved DnD-dependent mechanism for germ cell survival and migration.

  4. Four residues of propeptide are essential for precursor folding of nattokinase.

    PubMed

    Jia, Yan; Cao, Xinhua; Deng, Yu; Bao, Wei; Tang, Changyan; Ding, Hanjing; Zheng, Zhongliang; Zou, Guolin

    2014-11-01

    Subtilisin propeptide functions as an intramolecular chaperone that guides precursor folding. Nattokinase, a member of subtilisin family, is synthesized as a precursor consisting of a signal peptide, a propeptide, and a subtilisin domain, and the mechanism of its folding remains to be understood. In this study, the essential residues of nattokinase propeptide which contribute to precursor folding were determined. Deletion analysis showed that the conserved regions in propeptide were important for precursor folding. Single-site and multi-site mutagenesis studies confirmed the role of Tyr10, Gly13, Gly34, and Gly35. During stage (i) and (ii) of precursor folding, Tyr10 and Gly13 would form the part of interface with subtilisin domain. While Gly34 and Gly35 connected with an α-helix that would stabilize the structure of propeptide. The quadruple Ala mutation, Y10A/G13A/G34A/G35A, resulted in a loss of the chaperone function for the propeptide. This work showed the essential residues of propeptide for precursor folding via secondary structure and kinetic parameter analyses.

  5. Investigation of the Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily Pseudomonas sp. strain CBS3 4-Hydroxybenzoyl-CoA Thioesterase+

    PubMed Central

    Zhuang, Zhihao; Latham, John; Song, Feng; Zhang, Wenhai; Trujillo, Michael; Dunaway-Mariano, Debra

    2012-01-01

    The 4-hydroxybenzoyl-CoA (4-HB-CoA)1 thioesterase from Pseudomonas sp strain CBS3 catalyzes the final step of the 4-chlorobenzoate degradation pathway, which is the hydrolysis of 4-hydroxybenzoyl-CoA (4-HB-CoA) to coenzyme A (CoA) and 4-hydroxybenzoate. In previous work, X-ray structural analysis of the substrate-bound thioesterase provided evidence for the role of an active site Asp17 in nucleophilic catalysis (Thoden, J. B., Holden, H. M., Zhuang, Z., Dunaway-Mariano, D. (2002) X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase. J. Biol. Chem. 277, 27468–27476.). In the present study, kinetic techniques were used to test the catalytic mechanism that was suggested by the X-ray structural data. The time course for the multiple-turnover reaction of 50 µM [14C]4-HB-CoA catalyzed by 10 µM thioesterase supported a two-step pathway in which the second step is rate-limiting. Steady-state product inhibition studies revealed that CoA (Kis = 250 ± 70 µM, Kii = 900 ± 300 µM) and 4-HB (Kis = 1.2 ± 0.2 mM) binding is weak, suggesting that product release is not rate-limiting. A substantial D2O solvent kinetic isotope effect (3.8) on the steady-state kcat value (18 s−1) provided evidence that a chemical step involving proton transfer is the rate-limiting step. Taken together, the kinetic results support a two-chemical pathway. The microscopic rate constants governing the formation and consumption of the putative aspartyl17-(4-hydroxybenzoyl)anhydride intermediate were determined by simulation-based fitting of a kinetic model to time courses for the substrate binding reaction (5.0 µM 4-HB-CoA and 0.54 µM thioesterase), single-turnover reaction (5 µM [14C]4-HB-CoA catalyzed by 50 µM thioesterase), steady-state reaction (5.2 µM 4-HB-CoA catalyzed by 0.003 µM thioesterase) and transient-state multiple-turnover reaction (50 µM [14C]4-HB-CoA catalyzed by 10 µM thioesterase). Together with

  6. Idiopathic ulcerative laryngitis causing midmembranous vocal fold granuloma.

    PubMed

    Sinclair, Catherine F; Sulica, Lucian

    2013-02-01

    Idiopathic ulcerative laryngitis (IUL) is characterized by bilateral midmembranous vocal fold ulceration, which follows upper respiratory infection with cough. In contrast, granuloma of the membranous vocal fold can occur rarely following microlaryngoscopy, presumably secondary to surgical violation of deep tissue planes. We report a novel case of noniatrogenic membranous vocal fold granulation developing in a patient with IUL. Although the presence of granulation implied injury to the entire microstructure of the vibratory portion of the vocal fold, the lesion resolved with conservative management without adverse sequelae.

  7. Hippocampal-dorsolateral prefrontal coupling as a species-conserved cognitive mechanism: a human translational imaging study.

    PubMed

    Bähner, Florian; Demanuele, Charmaine; Schweiger, Janina; Gerchen, Martin F; Zamoscik, Vera; Ueltzhöffer, Kai; Hahn, Tim; Meyer, Patric; Flor, Herta; Durstewitz, Daniel; Tost, Heike; Kirsch, Peter; Plichta, Michael M; Meyer-Lindenberg, Andreas

    2015-06-01

    Hippocampal-prefrontal cortex (HC-PFC) interactions are implicated in working memory (WM) and altered in psychiatric conditions with cognitive impairment such as schizophrenia. While coupling between both structures is crucial for WM performance in rodents, evidence from human studies is conflicting and translation of findings is complicated by the use of differing paradigms across species. We therefore used functional magnetic resonance imaging together with a spatial WM paradigm adapted from rodent research to examine HC-PFC coupling in humans. A PFC-parietal network was functionally connected to hippocampus (HC) during task stages requiring high levels of executive control but not during a matched control condition. The magnitude of coupling in a network comprising HC, bilateral dorsolateral PFC (DLPFC), and right supramarginal gyrus explained one-fourth of the variability in an independent spatial WM task but was unrelated to visual WM performance. HC-DLPFC coupling may thus represent a systems-level mechanism specific to spatial WM that is conserved across species, suggesting its utility for modeling cognitive dysfunction in translational neuroscience. PMID:25578799

  8. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome.

    PubMed

    Dykeman, Eric C; Stockley, Peter G; Twarock, Reidun

    2013-09-01

    The current paradigm for assembly of single-stranded RNA viruses is based on a mechanism involving non-sequence-specific packaging of genomic RNA driven by electrostatic interactions. Recent experiments, however, provide compelling evidence for sequence specificity in this process both in vitro and in vivo. The existence of multiple RNA packaging signals (PSs) within viral genomes has been proposed, which facilitates assembly by binding coat proteins in such a way that they promote the protein-protein contacts needed to build the capsid. The binding energy from these interactions enables the confinement or compaction of the genomic RNAs. Identifying the nature of such PSs is crucial for a full understanding of assembly, which is an as yet untapped potential drug target for this important class of pathogens. Here, for two related bacterial viruses, we determine the sequences and locations of their PSs using Hamiltonian paths, a concept from graph theory, in combination with bioinformatics and structural studies. Their PSs have a common secondary structure motif but distinct consensus sequences and positions within the respective genomes. Despite these differences, the distributions of PSs in both viruses imply defined conformations for the packaged RNA genomes in contact with the protein shell in the capsid, consistent with a recent asymmetric structure determination of the MS2 virion. The PS distributions identified moreover imply a preferred, evolutionarily conserved assembly pathway with respect to the RNA sequence with potentially profound implications for other single-stranded RNA viruses known to have RNA PSs, including many animal and human pathogens.

  9. Polymer films removed from solid surfaces by nanostructured fluids: microscopic mechanism and implications for the conservation of cultural heritage.

    PubMed

    Raudino, Martina; Selvolini, Giulia; Montis, Costanza; Baglioni, Michele; Bonini, Massimo; Berti, Debora; Baglioni, Piero

    2015-03-25

    Complex fluids based on amphiphilic formulations are emerging, particularly in the field of conservation of works of art, as effective and safe liquid media for the removal of hydrophobic polymeric coatings. The comprehension of the cleaning mechanism is key to designing tailored fluids for this purpose. However, the interaction between nanostructured fluids and hydrophobic polymer films is still poorly understood. In this study, we show how the combination of confocal laser scanning microscopy (CLSM) and atomic force microscopy (AFM) provides interesting and complementary insight into this process. We focused on the interaction between an ethyl methacrylate/methyl acrylate 70:30 copolymer film deposited onto a glass surface and a water/nonionic surfactant/2-butanone (MEK) ternary system, with MEK being a good solvent and water being a nonsolvent for the polymer. Our results indicate a synergy between the organic solvent and the surfactant assemblies: MEK rapidly swells the outer layers of the polymer film allowing for the subsequent diffusion of solvent molecules, while the amphiphile decreases the interfacial energy between the polymeric coating and the liquid phase, favoring dewetting and dispersion of swollen polymer droplets in the aqueous phase. The chemical nature of the surfactant and the microstructure of the assemblies determine both the kinetics and the overall efficiency of polymer removal, as assessed by comparing the behavior of similar formulations containing an anionic surfactant (sodium dodecyl sulfate, SDS).

  10. Folding of non-Euclidean curved shells

    NASA Astrophysics Data System (ADS)

    Bende, Nakul; Evans, Arthur; Innes-Gold, Sarah; Marin, Luis; Cohen, Itai; Santangelo, Christian; Hayward, Ryan

    2015-03-01

    Origami-based folding of 2D sheets has been of recent interest for a variety of applications ranging from deployable structures to self-folding robots. Though folding of planar sheets follows well-established principles, folding of curved shells involves an added level of complexity due to the inherent influence of curvature on mechanics. In this study, we use principles from differential geometry and thin shell mechanics to establish fundamental rules that govern folding of prototypical creased shells. In particular, we show how the normal curvature of a crease line controls whether the deformation is smooth or discontinuous, and investigate the influence of shell thickness and boundary conditions. We show that snap-folding of shells provides a route to rapid actuation on time-scales dictated by the speed of sound. The simple geometric design principles developed can be applied at any length-scale, offering potential for bio-inspired soft actuators for tunable optics, microfluidics, and robotics. This work was funded by the National Science Foundation through EFRI ODISSEI-1240441 with additional support to S.I.-G. through the UMass MRSEC DMR-0820506 REU program.

  11. Folding funnels, binding funnels, and protein function.

    PubMed Central

    Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R.

    1999-01-01

    Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly

  12. Self-folding miniature elastic electric devices

    NASA Astrophysics Data System (ADS)

    Miyashita, Shuhei; Meeker, Laura; Tolley, Michael T.; Wood, Robert J.; Rus, Daniela

    2014-09-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor.

  13. Statistical properties of a folded elastic rod

    NASA Astrophysics Data System (ADS)

    Bayart, Elsa; Deboeuf, Stéphanie; Boué, Laurent; Corson, Francis; Boudaoud, Arezki; Adda-Bedia, Mokhtar

    2010-03-01

    A large variety of elastic structures naturally seem to be confined into environments too small to accommodate them; the geometry of folded structures span a wide range of length-scales. The elastic properties of these confined systems are further constrained by self-avoidance as well as by the dimensionality of both structures and container. To mimic crumpled paper, we devised an experimental setup to study the packing of a dimensional elastic object in 2D geometries: an elastic rod is folded at the center of a circular Hele-Shaw cell by a centripetal force. The initial configuration of the rod and the acceleration of the rotating disk allow to span different final folded configurations while the final rotation speed controls the packing intensity. Using image analysis we measure geometrical and mechanical properties of the folded configurations, focusing on length, curvature and energy distributions.

  14. Protein photo-folding and quantum folding theory.

    PubMed

    Luo, Liaofu

    2012-06-01

    The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from quantum folding theory by use of a field-theoretical method. All protein photo-folding processes are compared with common protein folding without the interaction of photons (non-radiative folding). It is demonstrated that there exists a common factor (thermo-averaged overlap integral of the vibration wave function, TAOI) for protein folding and protein photo-folding. Based on this finding it is predicted that (i) the stimulated photo-folding rates and the photon-protein resonance Raman scattering sections show the same temperature dependence as protein folding; (ii) the spectral line of the electronic transition is broadened to a band that includes an abundant vibration spectrum without and with conformational transitions, and the width of each vibration spectral line is largely reduced. The particular form of the folding rate-temperature relation and the abundant spectral structure imply the existence of quantum tunneling between protein conformations in folding and photo-folding that demonstrates the quantum nature of the motion of the conformational-electronic system.

  15. Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome

    PubMed Central

    Elcock, Adrian H

    2006-01-01

    Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (CI2), barnase, and Semliki forest virus protein (SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of CI2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which CI2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these

  16. Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design.

    PubMed

    Narasumani, Mohanalakshmi; Harrison, Paul M

    2015-12-18

    Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that 'fold on binding' to another molecule. Here, we perform bioinformatical parsing of human 'folding-on-binding' (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions ('Disordered-around-FB'), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding.

  17. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    NASA Astrophysics Data System (ADS)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  18. How the genome folds

    NASA Astrophysics Data System (ADS)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  19. Protein folding in the ER.

    SciTech Connect

    Stevens, F. J.; Argon, Y.; Biosciences Division; Univ. of Chicago

    1999-10-01

    The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

  20. A sweet code for glycoprotein folding.

    PubMed

    Caramelo, Julio J; Parodi, Armando J

    2015-11-14

    Glycoprotein synthesis is initiated in the endoplasmic reticulum (ER) lumen upon transfer of a glycan (Glc3Man9GlcNAc2) from a lipid derivative to Asn residues (N-glycosylation). N-Glycan-dependent quality control of glycoprotein folding in the ER prevents exit to Golgi of folding intermediates, irreparably misfolded glycoproteins and incompletely assembled multimeric complexes. It also enhances folding efficiency by preventing aggregation and facilitating formation of proper disulfide bonds. The control mechanism essentially involves four components, resident lectin-chaperones (calnexin and calreticulin) that recognize monoglucosylated polymannose protein-linked glycans, lectin-associated oxidoreductase acting on monoglucosylated glycoproteins (ERp57), a glucosyltransferase that creates monoglucosylated epitopes in protein-linked glycans (UGGT) and a glucosidase (GII) that removes the glucose units added by UGGT. This last enzyme is the only mechanism component sensing glycoprotein conformations as it creates monoglucosylated glycans exclusively in not properly folded glycoproteins or in not completely assembled multimeric glycoprotein complexes. Glycoproteins that fail to properly fold are eventually driven to proteasomal degradation in the cytosol following the ER-associated degradation pathway, in which the extent of N-glycan demannosylation by ER mannosidases play a relevant role in the identification of irreparably misfolded glycoproteins.

  1. Distribution of protein folds in the three superkingdoms of life.

    PubMed

    Wolf, Y I; Brenner, S E; Bash, P A; Koonin, E V

    1999-01-01

    A sensitive protein-fold recognition procedure was developed on the basis of iterative database search using the PSI-BLAST program. A collection of 1193 position-dependent weight matrices that can be used as fold identifiers was produced. In the completely sequenced genomes, folds could be automatically identified for 20%-30% of the proteins, with 3%-6% more detectable by additional analysis of conserved motifs. The distribution of the most common folds is very similar in bacteria and archaea but distinct in eukaryotes. Within the bacteria, this distribution differs between parasitic and free-living species. In all analyzed genomes, the P-loop NTPases are the most abundant fold. In bacteria and archaea, the next most common folds are ferredoxin-like domains, TIM-barrels, and methyltransferases, whereas in eukaryotes, the second to fourth places belong to protein kinases, beta-propellers and TIM-barrels. The observed diversity of protein folds in different proteomes is approximately twice as high as it would be expected from a simple stochastic model describing a proteome as a finite sample from an infinite pool of proteins with an exponential distribution of the fold fractions. Distribution of the number of domains with different folds in one protein fits the geometric model, which is compatible with the evolution of multidomain proteins by random combination of domains. [Fold predictions for proteins from 14 proteomes are available on the World Wide Web at. The FIDs are available by anonymous ftp at the same location.

  2. Folding Truss Structure

    NASA Technical Reports Server (NTRS)

    Warren, Aubrey D.

    1988-01-01

    Concept for foldable and deployable truss offers advantages of strength, rigidity, and mechanical simplicity. Structure consists of series of boxlike bays with 9-ft sides. Each box has panels on top and bottom and two sides. Two remaining sides open. Panels hinged at connecting edges. Adapted to terrestrial transportable structures, scaffolds, cranes, and rows of cubicles.

  3. Evolutionary optimization of protein folding.

    PubMed

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  4. Folding and faulting of an elastic continuum

    PubMed Central

    Gourgiotis, Panos A.

    2016-01-01

    Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called ‘chevrons’) and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures. PMID:27118925

  5. Physical experiments of transpressional folding

    NASA Astrophysics Data System (ADS)

    Tikoff, Basil; Peterson, Karl

    1998-06-01

    In order to understand the process of folding in obliquely convergent settings, we formed folds within a shear box capable of creating homogeneous transpressional deformations. Folds were created in a single layer of stiff mixed plasticine and silicone that overlay a Newtonian silicone, for a variety of plate convergence angles. As small amplitude folds became visible, they were parallel to the long axis of the horizontal finite strain ellipse. With increasing deformation, the fold hinges rotated parallel with the long axis of the horizontal finite strain ellipse for all angles of convergence. This parallelism indicates that fold hinges, once formed, rotate with the horizontal strain ellipse rather than as material lines. The experiments highlight several interesting effects of transpression dynamics. The fold hinges initiate parallel to either ṡ1 or ṡ2 and are parallel to either S1 or S2 with increasing deformation. Neither infinitesimal strain (stress) nor finite strain is resolvable solely from fold geometry. Further, the net amount of contraction determined by folding across the zone was overestimated in all cases except pure contraction. This effect is obvious for the case of wrenching, where folding implies that the zone contracts if elongation parallel to the fold hinge is not considered. Therefore, attempts to balance cross-sections in transpressional zones will tend to overestimate contraction unless the wrench component of deformation is addressed. This result is validated by applying the modeling results in folding in central California adjacent to the San Andreas fault, where cross-section balancing indicates higher amounts of contraction than predicted by plate motion.

  6. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {11891} during Cycle 17.

  7. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {12723} during Cycle 19.

  8. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  9. Generation of buckle folds in Naga fold thrust belt, north-east India

    NASA Astrophysics Data System (ADS)

    Saha, B.; Dietl, C.

    2009-04-01

    Naga fold thrust belt (NFTB), India, formed as a result of northward migration of the Indian plate initiated in Eocene and its subsequent collision with the Burmese plate during Oligocene. The NW-SE oriented compression generated a spectrum of structures; among them, we intend to focus on the folds- varying from gentle to tight asymmetric in geometry. Large recumbent folds are often associated with thrusting. Buckle folds forming under shallow crustal conditions are frequently reported from NFTB. Buckle folding occurs mainly within sandstones with intercalated shale layers which are in the study area typical for the Barail, Surma and Tipam Groups. We have tried to explain the controlling factors behind the variation of the buckle fold shapes and their varying wavelengths throughout the fold thrust belt with the aid of analogue (sand box) modelling. It is undoubted that competence contrast along with the layer parallel compressive stress are the major influencing factors in generation of buckle folds. Schmalholz and Podladchikov (1999) and Jeng et al. (2002) have shown that when low strain rate and low temperature are applicable, not only the viscosity contrast, but also the elasticity contrast govern the geometry of the developing buckle folds. Rocks deforming under high temperature and high pressure deform in pure viscous manner, whereas, rocks undergoing less confining stress and less temperature, are subjected to pure elastic deformation. However, they are the end members, and most of the deformations are a combination of these two end members, i.e. of viscoelastic nature. Our models are made up of sieved sand (0.5 mm grain size) and mica layers (1-5 mm) This interlayering imparts a mechanical anisotropy in the model. Mica is not a pure viscous material, rather it displays more elastic behaviour. The mica layers in the model produce bedding parallel slip during shortening through internal reorganization of the individual mica crystals leading to the thickening

  10. Folding superfunnel to describe cooperative folding of interacting proteins.

    PubMed

    Smeller, László

    2016-07-01

    This paper proposes a generalization of the well-known folding funnel concept of proteins. In the funnel model the polypeptide chain is treated as an individual object not interacting with other proteins. Since biological systems are considerably crowded, protein-protein interaction is a fundamental feature during the life cycle of proteins. The folding superfunnel proposed here describes the folding process of interacting proteins in various situations. The first example discussed is the folding of the freshly synthesized protein with the aid of chaperones. Another important aspect of protein-protein interactions is the folding of the recently characterized intrinsically disordered proteins, where binding to target proteins plays a crucial role in the completion of the folding process. The third scenario where the folding superfunnel is used is the formation of aggregates from destabilized proteins, which is an important factor in case of several conformational diseases. The folding superfunnel constructed here with the minimal assumption about the interaction potential explains all three cases mentioned above. Proteins 2016; 84:1009-1016. © 2016 Wiley Periodicals, Inc.

  11. Kinetics of Peptide Folding in Lipid Membranes

    PubMed Central

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  12. Effects of Knots on Protein Folding Properties

    PubMed Central

    Soler, Miguel A.; Faísca, Patrícia F. N.

    2013-01-01

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation. PMID:24023962

  13. Experimental investigation of protein folding and misfolding.

    PubMed

    Dobson, Christopher M

    2004-09-01

    Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.

  14. Towards a systematic classification of protein folds

    NASA Astrophysics Data System (ADS)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-10-01

    A lattice model Hamiltonian is suggested for protein structures that can explain the division into structural fold classes during the folding process. Proteins are described by chains of secondary structure elements, with the hinges in between being the important degrees of freedom. The protein structures are given a unique name, which simultaneously represent a linear string of physical coupling constants describing hinge spin interactions. We have defined a metric and a precise distance measure between the fold classes. An automated procedure is constructed in which any protein structure in the usual protein data base coordinate format can be transformed into the proposed chain representation. Taking into account hydrophobic forces we have found a mechanism for the formation of domains with a unique fold containing predicted magic numbers \\{4,6,9,12,16,18,...\\} of secondary structures and multiples of these domains. It is shown that the same magic numbers are robust and occur as well for packing on other nonclosed packed lattices. We have performed a statistical analysis of available protein structures and found agreement with the predicted preferred abundances of proteins with a predicted magic number of secondary structures. Thermodynamic arguments for the increased abundance and a phase diagram for the folding scenario are given. This includes an intermediate high symmetry phase, the parent structures, between the molten globule and the native states. We have made an exhaustive enumeration of dense lattice animals on a cubic lattice for acceptance number Z=4 and Z=5 up to 36 vertices.

  15. Recoverable and Programmable Collapse from Folding Pressurized Origami Cellular Solids.

    PubMed

    Li, S; Fang, H; Wang, K W

    2016-09-01

    We report a unique collapse mechanism by exploiting the negative stiffness observed in the folding of an origami solid, which consists of pressurized cells made by stacking origami sheets. Such a collapse mechanism is recoverable, since it only involves rigid folding of the origami sheets and it is programmable by pressure control and the custom design of the crease pattern. The collapse mechanism features many attractive characteristics for applications such as energy absorption. The reported results also suggest a new branch of origami study focused on its nonlinear mechanics associated with folding. PMID:27661691

  16. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  17. Structural Bridges through Fold Space

    PubMed Central

    Edwards, Hannah; Deane, Charlotte M.

    2015-01-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes. PMID:26372166

  18. Structural Bridges through Fold Space.

    PubMed

    Edwards, Hannah; Deane, Charlotte M

    2015-09-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes.

  19. Folding of β-barrel membrane proteins in lipid bilayers - Unassisted and assisted folding and insertion.

    PubMed

    Kleinschmidt, Jörg H

    2015-09-01

    In cells, β-barrel membrane proteins are transported in unfolded form to an outer membrane into which they fold and insert. Model systems have been established to investigate the mechanisms of insertion and folding of these versatile proteins into detergent micelles, lipid bilayers and even synthetic amphipathic polymers. In these experiments, insertion into lipid membranes is initiated from unfolded forms that do not display residual β-sheet secondary structure. These studies therefore have allowed the investigation of membrane protein folding and insertion in great detail. Folding of β-barrel membrane proteins into lipid bilayers has been monitored from unfolded forms by dilution of chaotropic denaturants that keep the protein unfolded as well as from unfolded forms present in complexes with molecular chaperones from cells. This review is aimed to provide an overview of the principles and mechanisms observed for the folding of β-barrel transmembrane proteins into lipid bilayers, the importance of lipid-protein interactions and the function of molecular chaperones and folding assistants. This article is part of a Special Issue entitled: Lipid-protein interactions.

  20. Novel sequences propel familiar folds.

    PubMed

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  1. Problem Solving through Paper Folding

    ERIC Educational Resources Information Center

    Wares, Arsalan

    2014-01-01

    The purpose of this article is to describe a couple of challenging mathematical problems that involve paper folding. These problem-solving tasks can be used to foster geometric and algebraic thinking among students. The context of paper folding makes some of the abstract mathematical ideas involved relatively concrete. When implemented…

  2. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as Cycle 20 proposal 13128.

  3. Multidimensional theory of protein folding

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2009-04-01

    Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.

  4. 3D fold growth rates in transpressional tectonic settings

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  5. Diversified Structural Basis of a Conserved Molecular Mechanism for pH-Dependent Dimerization in Spider Silk N-Terminal Domains.

    PubMed

    Otikovs, Martins; Chen, Gefei; Nordling, Kerstin; Landreh, Michael; Meng, Qing; Jörnvall, Hans; Kronqvist, Nina; Rising, Anna; Johansson, Jan; Jaudzems, Kristaps

    2015-08-17

    Conversion of spider silk proteins from soluble dope to insoluble fibers involves pH-dependent dimerization of the N-terminal domain (NT). This conversion is tightly regulated to prevent premature precipitation and enable rapid silk formation at the end of the duct. Three glutamic acid residues that mediate this process in the NT from Euprosthenops australis major ampullate spidroin 1 are well conserved among spidroins. However, NTs of minor ampullate spidroins from several species, including Araneus ventricosus ((Av)MiSp NT), lack one of the glutamic acids. Here we investigate the pH-dependent structural changes of (Av)MiSp NT, revealing that it uses the same mechanism but involves a non-conserved glutamic acid residue instead. Homology modeling of the structures of other MiSp NTs suggests that these harbor different compensatory residues. This indicates that, despite sequence variations, the molecular mechanism underlying pH-dependent dimerization of NT is conserved among different silk types. PMID:26033527

  6. Diversified Structural Basis of a Conserved Molecular Mechanism for pH-Dependent Dimerization in Spider Silk N-Terminal Domains.

    PubMed

    Otikovs, Martins; Chen, Gefei; Nordling, Kerstin; Landreh, Michael; Meng, Qing; Jörnvall, Hans; Kronqvist, Nina; Rising, Anna; Johansson, Jan; Jaudzems, Kristaps

    2015-08-17

    Conversion of spider silk proteins from soluble dope to insoluble fibers involves pH-dependent dimerization of the N-terminal domain (NT). This conversion is tightly regulated to prevent premature precipitation and enable rapid silk formation at the end of the duct. Three glutamic acid residues that mediate this process in the NT from Euprosthenops australis major ampullate spidroin 1 are well conserved among spidroins. However, NTs of minor ampullate spidroins from several species, including Araneus ventricosus ((Av)MiSp NT), lack one of the glutamic acids. Here we investigate the pH-dependent structural changes of (Av)MiSp NT, revealing that it uses the same mechanism but involves a non-conserved glutamic acid residue instead. Homology modeling of the structures of other MiSp NTs suggests that these harbor different compensatory residues. This indicates that, despite sequence variations, the molecular mechanism underlying pH-dependent dimerization of NT is conserved among different silk types.

  7. The Conservation of Structure and Mechanism of Catalytic Action in a Family of Thiamin Pyrophosphate (TPP)-dependent Enzymes

    NASA Technical Reports Server (NTRS)

    Dominiak, P.; Ciszak, Ewa

    2004-01-01

    Thiamin pyrophosphate (TPP)-dependent enzymes are a divergent family of TPP and metal ion binding proteins that perform a wide range of functions with the common decarboxylation steps of a -(O=)C-C(OH)- fragment of alpha-ketoacids and alpha- hydroxyaldehydes. To determine how structure and catalytic action are conserved in the context of large sequence differences existing within this family of enzymes, we have carried out an analysis of TPP-dependent enzymes of known structures. The common structure of TPP-dependent enzymes is formed at the interface of four alpha/beta domains from at least two subunits, which provide for two metal and TPP-binding sites. Residues around these catalytic sites are conserved for functional purpose, while those further away from TPP are conserved for structural reasons. Together they provide a network of contacts required for flip-flop catalytic action within TPP-dependent enzymes. Thus our analysis defines a TPP-action motif that is proposed for annotating TPP-dependent enzymes for advancing functional proteomics.

  8. DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination

    PubMed Central

    Graeber, Kai; Linkies, Ada; Steinbrecher, Tina; Mummenhoff, Klaus; Tarkowská, Danuše; Turečková, Veronika; Ignatz, Michael; Sperber, Katja; Voegele, Antje; de Jong, Hans; Urbanová, Terezie; Strnad, Miroslav; Leubner-Metzger, Gerhard

    2014-01-01

    Seed germination is an important life-cycle transition because it determines subsequent plant survival and reproductive success. To detect optimal spatiotemporal conditions for germination, seeds act as sophisticated environmental sensors integrating information such as ambient temperature. Here we show that the DELAY OF GERMINATION 1 (DOG1) gene, known for providing dormancy adaptation to distinct environments, determines the optimal temperature for seed germination. By reciprocal gene-swapping experiments between Brassicaceae species we show that the DOG1-mediated dormancy mechanism is conserved. Biomechanical analyses show that this mechanism regulates the material properties of the endosperm, a seed tissue layer acting as germination barrier to control coat dormancy. We found that DOG1 inhibits the expression of gibberellin (GA)-regulated genes encoding cell-wall remodeling proteins in a temperature-dependent manner. Furthermore we demonstrate that DOG1 causes temperature-dependent alterations in the seed GA metabolism. These alterations in hormone metabolism are brought about by the temperature-dependent differential expression of genes encoding key enzymes of the GA biosynthetic pathway. These effects of DOG1 lead to a temperature-dependent control of endosperm weakening and determine the optimal temperature for germination. The conserved DOG1-mediated coat-dormancy mechanism provides a highly adaptable temperature-sensing mechanism to control the timing of germination. PMID:25114251

  9. Fast events in protein folding

    SciTech Connect

    Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R.; Williams, S.

    1996-04-01

    The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.

  10. A Computational Study of the Effect of False Vocal Folds on Glottal Flow and Vocal Fold Vibration During Phonation

    PubMed Central

    Zheng, Xudong; Bielamowicz, Steve; Luo, Haoxiang; Mittal, Rajat

    2010-01-01

    The false vocal folds are believed to be components of the acoustic filter that is responsible for shaping the voice. However, the effects of false vocal folds on the vocal fold vibration and the glottal aerodynamic during phonation remain unclear. This effect has implications for computational modeling of phonation as well as for understanding laryngeal pathologies such as glottal incompetence resulting from unilateral vocal fold paralysis. In this study, a high fidelity, two-dimensional computational model, which combines an immersed boundary method for the airflow and a continuum, finite-element method for the vocal folds, is used to examine the effect of the false vocal folds on flow-induced vibration (FIV) of the true vocal folds and the dynamics of the glottal jet. The model is notionally based on a laryngeal CT scan and employs realistic flow conditions and tissue properties. Results show that the false vocal folds potentially have a significant impact on phonation. The false vocal folds reduce the glottal flow impedance and increase the amplitude as well as the mean glottal jet velocity. The false vocal folds also enhance the intensity of the monopole acoustic sources in the glottis. A mechanism for reduction in flow impedance due to the false vocal folds is proposed. PMID:19142730

  11. THE DELICATE BALANCE BETWEEN SECRETED PROTEIN FOLDING AND ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION IN HUMAN PHYSIOLOGY

    PubMed Central

    Guerriero, Christopher J.; Brodsky, Jeffrey L.

    2014-01-01

    Protein folding is a complex, error-prone process that often results in an irreparable protein by-product. These by-products can be recognized by cellular quality control machineries and targeted for proteasome-dependent degradation. The folding of proteins in the secretory pathway adds another layer to the protein folding “problem,” as the endoplasmic reticulum maintains a unique chemical environment within the cell. In fact, a growing number of diseases are attributed to defects in secretory protein folding, and many of these by-products are targeted for a process known as endoplasmic reticulum-associated degradation (ERAD). Since its discovery, research on the mechanisms underlying the ERAD pathway has provided new insights into how ERAD contributes to human health during both normal and diseases states. Links between ERAD and disease are evidenced from the loss of protein function as a result of degradation, chronic cellular stress when ERAD fails to keep up with misfolded protein production, and the ability of some pathogens to coopt the ERAD pathway. The growing number of ERAD substrates has also illuminated the differences in the machineries used to recognize and degrade a vast array of potential clients for this pathway. Despite all that is known about ERAD, many questions remain, and new paradigms will likely emerge. Clearly, the key to successful disease treatment lies within defining the molecular details of the ERAD pathway and in understanding how this conserved pathway selects and degrades an innumerable cast of substrates. PMID:22535891

  12. Acceleration of protein folding by four orders of magnitude through a single amino acid substitution

    PubMed Central

    Roderer, Daniel J. A.; Schärer, Martin A.; Rubini, Marina; Glockshuber, Rudi

    2015-01-01

    Cis prolyl peptide bonds are conserved structural elements in numerous protein families, although their formation is energetically unfavorable, intrinsically slow and often rate-limiting for folding. Here we investigate the reasons underlying the conservation of the cis proline that is diagnostic for the fold of thioredoxin-like thiol-disulfide oxidoreductases. We show that replacement of the conserved cis proline in thioredoxin by alanine can accelerate spontaneous folding to the native, thermodynamically most stable state by more than four orders of magnitude. However, the resulting trans alanine bond leads to small structural rearrangements around the active site that impair the function of thioredoxin as catalyst of electron transfer reactions by more than 100-fold. Our data provide evidence for the absence of a strong evolutionary pressure to achieve intrinsically fast folding rates, which is most likely a consequence of proline isomerases and molecular chaperones that guarantee high in vivo folding rates and yields. PMID:26121966

  13. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    NASA Astrophysics Data System (ADS)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    multi-scale dynamical problem when one considers the synergies between protein expression, spontaneous folding, chaperonin-assisted folding, protein targeting, the kinetics of post-translational modifications, protein degradation, and of course the drive to avoid aggregation. Further, there is growing recognition that cells not only tolerate but select for proteins that are intrinsically disordered. These proteins are essential for many crucial activities, and yet their inability to fold in isolation makes them prone to proteolytic processing and aggregation. In the series of papers that make up this special focus on protein folding in physical biology, leading researchers provide insights into diverse cross-sections of problems in protein folding. Barrick provides a concise review of what we have learned from the study of two-state folders and draws attention to how several unanswered questions are being approached using studies on large repeat proteins. Dissecting the contribution of hydration-mediated interactions to driving forces for protein folding and assembly has been extremely challenging. There is renewed interest in using hydrostatic pressure as a tool to access folding intermediates and decipher the role of partially hydrated states in folding, misfolding, and aggregation. Silva and Foguel review many of the nuances that have been uncovered by perturbing hydrostatic pressure as a thermodynamic parameter. As noted above, protein folding in vivo is expected to be considerably more complex than the folding of two-state proteins in dilute solutions. Lucent et al review the state-of-the-art in the development of quantitative theories to explain chaperonin-assisted folding in vivo. Additionally, they highlight unanswered questions pertaining to the processing of unfolded/misfolded proteins by the chaperone machinery. Zhuang et al present results that focus on the effects of surface tethering on transition state ensembles and folding mechanisms of a model two

  14. Protein folding by motion planning

    NASA Astrophysics Data System (ADS)

    Thomas, Shawna; Song, Guang; Amato, Nancy M.

    2005-12-01

    We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L. This research was supported in part by NSF CAREER Award CCR-9624315, NSF Grants ACI-9872126, EIA-9975018, EIA-0103742, EIA-9805823, ACR-0113971, CCR-0113974, EIA-9810937, EIA-0079874 and the Texas Higher Education Coordinating Board grant ATP-000512-0261-2001. ST was supported in part by an NSF Graduate Research Fellowship. GS was supported in part by an IBM PhD Fellowship.

  15. Electrochemistry of folded graphene edges.

    PubMed

    Ambrosi, Adriano; Bonanni, Alessandra; Pumera, Martin

    2011-05-01

    There is enormous interest in the investigation of electron transfer rates at the edges of graphene due to possible energy storage and sensing applications. While electrochemistry at the edges and the basal plane of graphene has been studied in the past, the new frontier is the electrochemistry of folded graphene edges. Here we describe the electrochemistry of folded graphene edges and compare it to that of open graphene edges. The materials were characterized in detail by high-resolution transmission electron microscopy, Raman spectroscopy, high-resolution X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy and cyclic voltammetry. We found that the heterogeneous electron transfer rate is significantly lower on folded graphene edges compared to open edge sites for ferro/ferricyanide, and that electrochemical properties of open edges offer lower potential detection of biomarkers than the folded ones. It is apparent, therefore, that for sensing and biosensing applications the folded edges are less active than open edges, which should then be preferred for such applications. As folded edges are the product of thermal treatment of multilayer graphene, such thermal procedures should be avoided when fabricating graphene for electrochemical applications.

  16. Self-folding graphene-polymer bilayers

    NASA Astrophysics Data System (ADS)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-01

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  17. Self-folding graphene-polymer bilayers

    SciTech Connect

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  18. Structure-Based Prediction of Protein-Folding Transition Paths.

    PubMed

    Jacobs, William M; Shakhnovich, Eugene I

    2016-09-01

    We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each transient state corresponds to the assembly of one or more discrete, cooperative units, which are determined directly from the native structure. We show that the transition state on a folding pathway is reached when a small number of critical contacts are formed between a specific set of substructures, after which folding proceeds downhill in free energy. This approach suggests a natural resolution for distinguishing parallel folding pathways and provides a simple means to predict the rate-limiting step in a folding reaction. Our theory identifies a common folding mechanism for proteins with diverse native structures and establishes general principles for the self-assembly of polymers with specific interactions. PMID:27602721

  19. Structure-Based Prediction of Protein-Folding Transition Paths

    NASA Astrophysics Data System (ADS)

    Jacobs, William M.; Shakhnovich, Eugene I.

    2016-09-01

    We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each transient state corresponds to the assembly of one or more discrete, cooperative units, which are determined directly from the native structure. We show that the transition state on a folding pathway is reached when a small number of critical contacts are formed between a specific set of substructures, after which folding proceeds downhill in free energy. This approach suggests a natural resolution for distinguishing parallel folding pathways and provides a simple means to predict the rate-limiting step in a folding reaction. Our theory identifies a common folding mechanism for proteins with diverse native structures and establishes general principles for the self-assembly of polymers with specific interactions.

  20. Examination of postmortem retinal folds: A non-invasive study.

    PubMed

    Oshima, Toru; Yoshikawa, Hiroshi; Ohtani, Maki; Mimasaka, Sohtaro

    2015-02-01

    The postmortem retinal fold has been previously documented, but its mechanism of formation is not known. All previous studies of the fold involved invasive techniques and the postmortem ocular fundus has yet to be non-invasively examined. Our study used the non-invasive techniques of monocular indirect ophthalmoscopy and ocular echography to examine 79 postmortem eyes of 42 bodies. We examined whether the postmortem retinal fold was associated with postmortem time, position, and/or age. Age was significantly associated with postmortem retinal fold formation (Mann-Whitney U test, P = 0.013), which led us to examine the effect of posterior vitreous detachment (PVD) on retinal folds. The absence of a PVD was statistically associated with the presence of a retinal fold (Fisher's exact test, P < 0.0001). Interestingly, the presence of a PVD was also significantly correlated with retinal fold height (Mann-Whitney U test, P < 0.0001). Therefore, we hypothesized that retinal folds result from postmortem vitreoretinal traction caused by eyeball flaccidity. We also believe that the loss of retinochoroidal hydrostatic pressure plays a role. It is important that forensic pathologists not confuse a postmortem retinal fold with traumatic retinal detachment or perimacular retinal folds caused by child abuse. When child abuse is suspected, forensic pathologists should perform enucleation and a subsequent histological examination for confirmation. PMID:25623189

  1. Influence of vein fabric on strain distribution and fold kinematics

    NASA Astrophysics Data System (ADS)

    Torremans, Koen; Muchez, Philippe; Sintubin, Manuel

    2014-05-01

    Abundant pre-folding, bedding-parallel fibrous dolomite veins in shale are found associated with the Nkana-Mindola stratiform Cu-Co deposit in the Central African Copperbelt, Zambia. These monomineralic veins extend for several meters along strike, with a fibrous infill orthogonal to low-tortuosity vein walls. Growth morphologies vary from antitaxial with a pronounced median surface to asymmetric syntaxial, always with small but quantifiable growth competition. Subsequently, these veins were folded. In this study, we aim to constrain the kinematic fold mechanism by which strain is accommodated in these veins, estimate paleorheology at time of deformation and investigate the influence of vein fabric on deformation during folding. Finally, the influence of the deformation on known metallogenetic stages is assessed. Various deformation styles are observed, ultimately related to vein attitude across tight to close lower-order, hectometre-scale folds. In fold hinges, at low to average dips, veins are (poly-)harmonically to disharmonically folded as parasitic folds in single or multilayer systems. With increasing distance from the fold hinge, parasitic fold amplitude decreases and asymmetry increases. At high dips in the limbs, low-displacement duplication thrusts of veins at low angles to bedding are abundant. Slickenfibres and slickenlines are sub-perpendicular to fold hinges and shallow-dipping slickenfibre-step lineations are parallel to local fold hinge lines. A dip isogon analysis of reconstructed fold geometries prior to homogeneous shortening reveals type 1B parallel folds for the veins and type 1C for the matrix. Two main deformation mechanisms are identified in folded veins. Firstly, undulatory extinction, subgrains and fluid inclusions planes parallel the fibre long axis, with deformation intensity increasing away from the fold hinges, indicate intracrystalline strain accumulation. Secondly, intergranular deformation through bookshelf rotation of fibres, via

  2. Double universality of a quantum phase transition in spinor condensates: modification of the Kibble-Żurek mechanism by a conservation law.

    PubMed

    Świsłocki, Tomasz; Witkowska, Emilia; Dziarmaga, Jacek; Matuszewski, Michał

    2013-01-25

    We consider a phase transition from an antiferromagnetic to a phase separated ground state in a spin-1 Bose-Einstein condensate of ultracold atoms. We demonstrate the occurrence of two scaling laws, for the number of spin domain seeds just after the phase transition, and for the number of spin domains in the final, stable configuration. Only the first scaling can be explained by the standard Kibble-Żurek mechanism. We explain the occurrence of two scaling laws by a model including postselection of spin domains due to the conservation of condensate magnetization.

  3. Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction

    PubMed Central

    Crowe, Brandon L.; Larue, Ross C.; Yuan, Chunhua; Hess, Sonja; Kvaratskhelia, Mamuka; Foster, Mark P.

    2016-01-01

    The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein–protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide comprising the ET binding motif (EBM) of MLV IN can disrupt the cognate interaction of Brd4 with NSD3, and that substitutions of Brd4 ET residues essential for binding MLV IN also impair interaction of Brd4 with a number of cellular partners involved in transcriptional regulation and chromatin remodeling. This suggests that γ-retroviruses have evolved the EBM to mimic a cognate interaction motif to achieve effective integration in host chromatin. Collectively, our findings identify key structural features of the ET domain of Brd4 that allow for interactions with both cellular and viral proteins. PMID:26858406

  4. Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction.

    PubMed

    Crowe, Brandon L; Larue, Ross C; Yuan, Chunhua; Hess, Sonja; Kvaratskhelia, Mamuka; Foster, Mark P

    2016-02-23

    The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein-protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide comprising the ET binding motif (EBM) of MLV IN can disrupt the cognate interaction of Brd4 with NSD3, and that substitutions of Brd4 ET residues essential for binding MLV IN also impair interaction of Brd4 with a number of cellular partners involved in transcriptional regulation and chromatin remodeling. This suggests that γ-retroviruses have evolved the EBM to mimic a cognate interaction motif to achieve effective integration in host chromatin. Collectively, our findings identify key structural features of the ET domain of Brd4 that allow for interactions with both cellular and viral proteins.

  5. Current Understanding and Future Directions for Vocal Fold Mechanobiology

    PubMed Central

    Li, Nicole Y.K.; Heris, Hossein K.; Mongeau, Luc

    2013-01-01

    The vocal folds, which are located in the larynx, are the main organ of voice production for human communication. The vocal folds are under continuous biomechanical stress similar to other mechanically active organs, such as the heart, lungs, tendons and muscles. During speech and singing, the vocal folds oscillate at frequencies ranging from 20 Hz to 3 kHz with amplitudes of a few millimeters. The biomechanical stress associated with accumulated phonation is believed to alter vocal fold cell activity and tissue structure in many ways. Excessive phonatory stress can damage tissue structure and induce a cell-mediated inflammatory response, resulting in a pathological vocal fold lesion. On the other hand, phonatory stress is one major factor in the maturation of the vocal folds into a specialized tri-layer structure. One specific form of vocal fold oscillation, which involves low impact and large amplitude excursion, is prescribed therapeutically for patients with mild vocal fold injuries. Although biomechanical forces affect vocal fold physiology and pathology, there is little understanding of how mechanical forces regulate these processes at the cellular and molecular level. Research into vocal fold mechanobiology has burgeoned over the past several years. Vocal fold bioreactors are being developed in several laboratories to provide a biomimic environment that allows the systematic manipulation of physical and biological factors on the cells of interest in vitro. Computer models have been used to simulate the integrated response of cells and proteins as a function of phonation stress. The purpose of this paper is to review current research on the mechanobiology of the vocal folds as it relates to growth, pathogenesis and treatment as well as to propose specific research directions that will advance our understanding of this subject. PMID:24812638

  6. Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase.

    PubMed

    Harris, T K; Wu, G; Massiah, M A; Mildvan, A S

    2000-02-22

    The MutT enzyme catalyzes the hydrolysis of nucleoside triphosphates (NTP) to NMP and PP(i) by nucleophilic substitution at the rarely attacked beta-phosphorus. The solution structure of the quaternary E-M(2+)-AMPCPP-M(2+) complex indicated that conserved residues Glu-53, -56, -57, and -98 are at the active site near the bound divalent cation possibly serving as metal ligands, Lys-39 is positioned to promote departure of the NMP leaving group, and Glu-44 precedes helix I (residues 47-59) possibly stabilizing this helix which contributes four catalytic residues to the active site [Lin, J. , Abeygunawardana, C., Frick, D. N., Bessman, M. J., and Mildvan, A. S. (1997) Biochemistry 36, 1199-1211]. To test these proposed roles, the effects of mutations of each of these residues on the kinetic parameters and on the Mn(2+), Mg(2+), and substrate binding properties were examined. The largest decreases in k(cat) for the Mg(2+)-activated enzyme of 10(4.7)- and 10(2.6)-fold were observed for the E53Q and E53D mutants, respectively, while 97-, 48-, 25-, and 14-fold decreases were observed for the E44D, E56D, E56Q, and E44Q mutations, respectively. Smaller effects on k(cat) were observed for mutations of Glu-98 and Lys-39. For wild type MutT and its E53D and E44D mutants, plots of log(k(cat)) versus pH exhibited a limiting slope of 1 on the ascending limb and then a hump, i.e., a sharply defined maximum near pH 8 followed by a plateau, yielding apparent pK(a) values of 7.6 +/- 0.3 and 8.4 +/- 0.4 for an essential base and a nonessential acid catalyst, respectively, in the active quaternary MutT-Mg(2+)-dGTP-Mg(2+) complex. The pK(a) of 7.6 is assigned to Glu-53, functioning as a base catalyst in the active quaternary complex, on the basis of the disappearance of the ascending limb of the pH-rate profile of the E53Q mutant, and its restoration in the E53D mutant with a 10(1.9)-fold increase in (k(cat))(max). The pK(a) of 8.4 is assigned to Lys-39 on the basis of the disappearance

  7. Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase.

    PubMed

    Harris, T K; Wu, G; Massiah, M A; Mildvan, A S

    2000-02-22

    The MutT enzyme catalyzes the hydrolysis of nucleoside triphosphates (NTP) to NMP and PP(i) by nucleophilic substitution at the rarely attacked beta-phosphorus. The solution structure of the quaternary E-M(2+)-AMPCPP-M(2+) complex indicated that conserved residues Glu-53, -56, -57, and -98 are at the active site near the bound divalent cation possibly serving as metal ligands, Lys-39 is positioned to promote departure of the NMP leaving group, and Glu-44 precedes helix I (residues 47-59) possibly stabilizing this helix which contributes four catalytic residues to the active site [Lin, J. , Abeygunawardana, C., Frick, D. N., Bessman, M. J., and Mildvan, A. S. (1997) Biochemistry 36, 1199-1211]. To test these proposed roles, the effects of mutations of each of these residues on the kinetic parameters and on the Mn(2+), Mg(2+), and substrate binding properties were examined. The largest decreases in k(cat) for the Mg(2+)-activated enzyme of 10(4.7)- and 10(2.6)-fold were observed for the E53Q and E53D mutants, respectively, while 97-, 48-, 25-, and 14-fold decreases were observed for the E44D, E56D, E56Q, and E44Q mutations, respectively. Smaller effects on k(cat) were observed for mutations of Glu-98 and Lys-39. For wild type MutT and its E53D and E44D mutants, plots of log(k(cat)) versus pH exhibited a limiting slope of 1 on the ascending limb and then a hump, i.e., a sharply defined maximum near pH 8 followed by a plateau, yielding apparent pK(a) values of 7.6 +/- 0.3 and 8.4 +/- 0.4 for an essential base and a nonessential acid catalyst, respectively, in the active quaternary MutT-Mg(2+)-dGTP-Mg(2+) complex. The pK(a) of 7.6 is assigned to Glu-53, functioning as a base catalyst in the active quaternary complex, on the basis of the disappearance of the ascending limb of the pH-rate profile of the E53Q mutant, and its restoration in the E53D mutant with a 10(1.9)-fold increase in (k(cat))(max). The pK(a) of 8.4 is assigned to Lys-39 on the basis of the disappearance

  8. Disassembly of yeast 80S ribosomes into subunits is a concerted action of ribosome-assisted folding of denatured protein.

    PubMed

    Chakraborty, Biprashekhar; Bhakta, Sayan; Sengupta, Jayati

    2016-01-22

    It has been shown by several groups that ribosome can assist folding of denatured protein in vitro and the process is conserved across the species. Domain V of large ribosomal rRNA which occupies the intersubunit side of the large subunit was identified as the key player responsible for chaperoning the folding process. Thus, it is conceivable that denatured protein needs to access the intersubunit space of the ribosome in order to get folded. In this study, we have investigated the mechanism of release of the protein from the eukaryotic ribosome following reactivation. We have observed significant splitting of yeast 80S ribosome when incubated with the denatured BCAII protein. Energy-free disassembly mechanism functions in low Mg(+2) ion concentration for prokaryotic ribosomes. Eukaryotic ribosomes do not show significant splitting even at low Mg(+2) ion concentration. In this respect, denatured protein-induced disassembly of eukaryotic ribosome without the involvement of any external energy source is intriguing. For prokaryotic ribosomes, it was reported that the denatured protein induces ribosome splitting into subunits in order to access domain V-rRNA. In contrast, our results suggest an alternative mechanism for eukaryotic ribosomal rRNA-mediated protein folding and subsequent separation of the subunits by which release of the activated-protein occurs.

  9. Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

    PubMed Central

    Chen, Chun-I; Keusch, Jeremy J; Klein, Dominique; Hess, Daniel; Hofsteenge, Jan; Gut, Heinz

    2012-01-01

    Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function. PMID:22588082

  10. Molecular and biochemical analysis of rainbow trout LCK suggests a conserved mechanism for T-cell signaling in gnathostomes

    USGS Publications Warehouse

    Laing, K.J.; Dutton, S.; Hansen, J.D.

    2007-01-01

    Two genes were identified in rainbow trout that display high sequence identity to vertebrate Lck. Both of the trout Lck transcripts are associated with lymphoid tissues and were found to be highly expressed in IgM-negative lymphocytes. In vitro analysis of trout lymphocytes indicates that trout Lck mRNA is up-regulated by T-cell mitogens, supporting an evolutionarily conserved function for Lck in the signaling pathways of T-lymphocytes. Here, we describe the generation and characterization of a specific monoclonal antibody raised against the N-terminal domains of recombinant trout Lck that can recognize Lck protein(s) from trout thymocyte lysates that are similar in size (???57 kDa) to mammalian Lck. This antibody also reacted with permeabilized lymphocytes during FACS analysis, indicating its potential usage for cellular analyses of trout lymphocytes, thus representing an important tool for investigations of salmonid T-cell function.

  11. Fermilab D-0 Experimental Facility: Energy conservation report and mechanical systems design optimization and cost analysis study

    SciTech Connect

    Krstulovich, S.F.

    1987-10-31

    This report is developed as part of the Fermilab D-0 Experimental Facility Project Title II Design Documentation Update. As such, it concentrates primarily on HVAC mechanical systems design optimization and cost analysis.

  12. Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi.

    PubMed

    Kwon, Min Jin; Arentshorst, Mark; Fiedler, Markus; de Groen, Florence L M; Punt, Peter J; Meyer, Vera; Ram, Arthur F J

    2014-02-01

    The filamentous fungus Aspergillus niger is an industrially exploited protein expression platform, well known for its capacity to secrete high levels of proteins. To study the process of protein secretion in A. niger, we established a GFP-v-SNARE reporter strain in which the trafficking and dynamics of secretory vesicles can be followed in vivo. The biological role of putative A. niger orthologues of seven secretion-specific genes, known to function in key aspects of the protein secretion machinery in Saccharomyces cerevisiae, was analysed by constructing respective gene deletion mutants in the GFP-v-SNARE reporter strain. Comparison of the deletion phenotype of conserved proteins functioning in the secretory pathway revealed common features but also interesting differences between S. cerevisiae and A. niger. Deletion of the S. cerevisiae Sec2p orthologue in A. niger (SecB), encoding a guanine exchange factor for the GTPase Sec4p (SrgA in A. niger), did not have an obvious phenotype, while SEC2 deletion in S. cerevisiae is lethal. Similarly, deletion of the A. niger orthologue of the S. cerevisiae exocyst subunit Sec3p (SecC) did not result in a lethal phenotype as in S. cerevisiae, although severe growth reduction of A. niger was observed. Deletion of secA, secH and ssoA (encoding SecA, SecH and SsoA the A. niger orthologues of S. cerevisiae Sec1p, Sec8p and Sso1/2p, respectively) showed that these genes are essential for A. niger, similar to the situation in S. cerevisiae. These data demonstrate that the orchestration of exocyst-mediated vesicle transport is only partially conserved in S. cerevisiae and A. niger. PMID:24295824

  13. Foreland basins and fold belts

    SciTech Connect

    Macqueen, R.W.; Leckie, D.A. )

    1992-01-01

    The papers in this book describe six foreland basins and fold belts in terms of their regional setting, stratigraphy, tectonics, and structure, and their oil and gas systems. All of the basins show general similarities, but each differs significantly in detail from the others, posing something of a problem in terms of arriving at a 'typical' foreland basin and fold belt. Some are major hydrocarbon producers; others are not. The major characteristics of the six foreland basins and fold belts are summarized in Tables 1 through 5, which provide a convenient means of comparing and contrasting these basins and their hydrocarbon resources. The Western Canada foreland basin and fold belt serves as the type example for several reasons. These include: its setting and clear relationship to a major orogene of Mesozoic-Cenozoic age; the fact that it is uncomplicated by later overprinting, segmentation, or cover rocks unlike the Ouachita, Eastern Venezuela, and U.S. Rocky Mountain foreland basins and fold belts); the fact that there is a large volume of publicly available data on the basin and an active exploration and research community; and the fact that it has reasonable oil and gas reserves in a well-defined stratigraphic framework.

  14. Domains in folding of model proteins.

    PubMed Central

    Abkevich, V. I.; Gutin, A. M.; Shakhnovich, E. I.

    1995-01-01

    By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were designed to have pronounced energy minimum target conformations of different length and shape. For short fully compact (36-mer) proteins, the all-or-none transition from the unfolded state to the native state was observed. This was not always the case for longer proteins. Among 12 designed sequences with the native structure of a fully compact 48-mer, a simple all-or-none transition was observed in only three cases. For the other nine sequences, three states of behavior-the native, denatured, and intermediate states-were found. The contiguous part of the native structure (domain) was conserved in the intermediate state, whereas the remaining part was completely unfolded and structureless. These parts melted separately from each other. PMID:7549881

  15. Rapid compaction during RNA folding

    NASA Astrophysics Data System (ADS)

    Russell, Rick; Millett, Ian S.; Tate, Mark W.; Kwok, Lisa W.; Nakatani, Bradley; Gruner, Sol M.; Mochrie, Simon G. J.; Pande, Vijay; Doniach, Sebastian; Herschlag, Daniel; Pollack, Lois

    2002-04-01

    We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

  16. Improved Method of Design for Folding Inflatable Shells

    NASA Technical Reports Server (NTRS)

    Johnson, Christopher J.

    2009-01-01

    An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One particularly difficult problem is that of mathematically defining fold lines on a gore pattern in a double- curvature region. Moreover, because the fold lines in a double-curvature region tend to be curved, there is a practical problem of how to implement the folds. Another problem is that of modifying the basic gore shapes and sizes for the various layers so that when they are folded as part of the integral structure, they do not mechanically interfere with each other at the fold lines. Heretofore, it has been a common practice to design an inflatable shell to be assembled in the deployed configuration, without regard for the need to fold it into compact form. Typically, the result has been that folding has been a difficult, time-consuming process resulting in a An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One

  17. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    PubMed Central

    Mohazab, Ali R.; Plotkin, Steven S.

    2013-01-01

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold , , , and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation “alignment”. The consensus minimal pathway is constructed and shown schematically for representative cases of an , , and knotted protein. An overlap parameter is defined between pathways; we find that proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding. PMID:23365638

  18. The dominant folding route minimizes backbone distortion in SH3.

    PubMed

    Lammert, Heiko; Noel, Jeffrey K; Onuchic, José N

    2012-01-01

    Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding.

  19. Autophagy, a Conserved Mechanism for Protein Degradation, Responds to Heat, and Other Abiotic Stresses in Capsicum annuum L.

    PubMed Central

    Zhai, Yufei; Guo, Meng; Wang, Hu; Lu, Jinping; Liu, Jinhong; Zhang, Chong; Gong, Zhenhui; Lu, Minghui

    2016-01-01

    Abiotic stresses negatively affect plants growth and development by inducing protein denaturation, and autophagy degrades the damaged proteins to alleviate their toxicity, however, little is known about the involvement of autophagy in pepper (Capsicum annuum L.) tolerances to abiotic stresses. In this study, we identified autophagy-related gene (ATG) members in the whole genome of pepper by HMM method and analyzed their expression profiles in response to heat and other abiotic stresses by quantitative real-time PCR. The results showed that the CaATG contained 15 core ATG members including 29 ATG proteins with their respective conserved functional domains, involving the whole process of autophagy. Under normal environmental condition, the expression of CaATG genes showed tissue- and developmental stage-specific patterns, while under abiotic stresses of salt, drought, heat, cold and carbohydrate starvation, the accumulation of autophagosome punctate increased and the expression level of CaATG genes changed with stress type-dependent pattern, which indicates the linkage of autophagy in pepper response to abiotic stresses. After treated with heat stress, both the number of up-regulated CaATG genes and the increment of autophagosome punctate were higher in pepper thermotolerant line R9 than those in thermosensitive line B6, implying an association of autophagy with heat tolerance. In addition, CaATG6 was predicted to interact with CaHSP90 family members. Our study suggests that autophagy is connected to pepper tolerances to heat and other abiotic stresses. PMID:26904087

  20. Autophagy, a Conserved Mechanism for Protein Degradation, Responds to Heat, and Other Abiotic Stresses in Capsicum annuum L.

    PubMed

    Zhai, Yufei; Guo, Meng; Wang, Hu; Lu, Jinping; Liu, Jinhong; Zhang, Chong; Gong, Zhenhui; Lu, Minghui

    2016-01-01

    Abiotic stresses negatively affect plants growth and development by inducing protein denaturation, and autophagy degrades the damaged proteins to alleviate their toxicity, however, little is known about the involvement of autophagy in pepper (Capsicum annuum L.) tolerances to abiotic stresses. In this study, we identified autophagy-related gene (ATG) members in the whole genome of pepper by HMM method and analyzed their expression profiles in response to heat and other abiotic stresses by quantitative real-time PCR. The results showed that the CaATG contained 15 core ATG members including 29 ATG proteins with their respective conserved functional domains, involving the whole process of autophagy. Under normal environmental condition, the expression of CaATG genes showed tissue- and developmental stage-specific patterns, while under abiotic stresses of salt, drought, heat, cold and carbohydrate starvation, the accumulation of autophagosome punctate increased and the expression level of CaATG genes changed with stress type-dependent pattern, which indicates the linkage of autophagy in pepper response to abiotic stresses. After treated with heat stress, both the number of up-regulated CaATG genes and the increment of autophagosome punctate were higher in pepper thermotolerant line R9 than those in thermosensitive line B6, implying an association of autophagy with heat tolerance. In addition, CaATG6 was predicted to interact with CaHSP90 family members. Our study suggests that autophagy is connected to pepper tolerances to heat and other abiotic stresses.

  1. Quantum theory on protein folding

    NASA Astrophysics Data System (ADS)

    Luo, LiaoFu

    2014-03-01

    The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds and stretching-bending vibrations the molecular torsion has the lowest energy and can be looked as the slow variable of the system. Simultaneously, from the multi-minima property of torsion potential the local conformational states are well defined. Following the idea that the slow variables slave the fast ones and using the nonadiabaticity operator method we deduce the Hamiltonian describing conformational change. It is shown that the influence of fast variables on the macromolecule can fully be taken into account through a phase transformation of slow variable wave function. Starting from the conformation-transition Hamiltonian the nonradiative matrix element was calculated and a general formulas for protein folding rate was deduced. The analytical form of the formula was utilized to study the temperature dependence of protein folding rate and the curious non-Arrhenius temperature relation was interpreted. By using temperature dependence data the multi-torsion correlation was studied. The decoherence time of quantum torsion state is estimated. The proposed folding rate formula gives a unifying approach for the study of a large class problems of biological conformational change.

  2. Semiempirical prediction of protein folds

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

    2001-08-01

    We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

  3. Unraveling metamaterial properties in zigzag-base folded sheets

    PubMed Central

    Eidini, Maryam; Paulino, Glaucio H.

    2015-01-01

    Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one–degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson’s ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson’s ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials. PMID:26601253

  4. Chaperones rescue luciferase folding by separating its domains.

    PubMed

    Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

    2014-10-10

    Over the last 50 years, significant progress has been made toward understanding how small single-domain proteins fold. However, very little is known about folding mechanisms of medium and large multidomain proteins that predominate the proteomes of all forms of life. Large proteins frequently fold cotranslationally and/or require chaperones. Firefly (Photinus pyralis) luciferase (Luciferase, 550 residues) has been a model of a cotranslationally folding protein whose extremely slow refolding (approximately days) is catalyzed by chaperones. However, the mechanism by which Luciferase misfolds and how chaperones assist Luciferase refolding remains unknown. Here we combine single-molecule force spectroscopy (atomic force microscopy (AFM)/single-molecule force spectroscopy) with steered molecular dynamic computer simulations to unravel the mechanism of chaperone-assisted Luciferase refolding. Our AFM and steered molecular dynamic results show that partially unfolded Luciferase, with the N-terminal domain remaining folded, can refold robustly without chaperones. Complete unfolding causes Luciferase to get trapped in very stable non-native configurations involving interactions between N- and C-terminal residues. However, chaperones allow the completely unfolded Luciferase to refold quickly in AFM experiments, strongly suggesting that chaperones are able to sequester non-natively contacting residues. More generally, we suggest that many chaperones, rather than actively promoting the folding, mimic the ribosomal exit tunnel and physically separate protein domains, allowing them to fold in a cotranslational-like sequential process.

  5. Root proliferation in decaying roots and old root channels: A nutrient conservation mechanism in oligotrophic mangrove forests?

    USGS Publications Warehouse

    McKee, K.L.

    2001-01-01

    1. In oligotrophic habitats, proliferation of roots in nutrient-rich microsites may contribute to overall nutrient conservation by plants. Peat-based soils on mangrove islands in Belize are characterized by the presence of decaying roots and numerous old root channels (0.1-3.5 cm diameter) that become filled with living and highly branched roots of Rhizophora mangle and Avicennia germinans. The objectives of this study were to quantify the proliferation of roots in these microsites and to determine what causes this response. 2. Channels formed by the refractory remains of mangrove roots accounted for only 1-2% of total soil volume, but the proportion of roots found within channels varied from 9 to 24% of total live mass. Successive generations of roots growing inside increasingly smaller root channels were also found. 3. When artificial channels constructed of PVC pipe were buried in the peat for 2 years, those filled with nutrient-rich organic matter had six times more roots than empty or sand-filled channels, indicating a response to greater nutrient availability rather than to greater space or less impedance to root growth. 4. Root proliferation inside decaying roots may improve recovery of nutrients released from decomposing tissues before they can be leached or immobilized in this intertidal environment. Greatest root proliferation in channels occurred in interior forest zones characterized by greater soil waterlogging, which suggests that this may be a strategy for nutrient capture that minimizes oxygen losses from the whole root system. 5. Improved efficiency of nutrient acquisition at the individual plant level has implications for nutrient economy at the ecosystem level and may explain, in part, how mangroves persist and grow in nutrient-poor environments.

  6. Origin of the vertebrate body plan via mechanically biased conservation of regular geometrical patterns in the structure of the blastula.

    PubMed

    Edelman, David B; McMenamin, Mark; Sheesley, Peter; Pivar, Stuart

    2016-09-01

    We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology-though all but neglected in previous accounts of both development and macroevolution-is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis-currently an elusive goal-will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences. PMID:27392530

  7. RNA folding pathways in stop motion.

    PubMed

    Bottaro, Sandro; Gil-Ley, Alejandro; Bussi, Giovanni

    2016-07-01

    We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions. PMID:27091499

  8. RNA folding pathways in stop motion

    PubMed Central

    Bottaro, Sandro; Gil-Ley, Alejandro; Bussi, Giovanni

    2016-01-01

    We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions. PMID:27091499

  9. A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity

    PubMed Central

    2016-01-01

    The balance between protein folding and misfolding is a crucial determinant of amyloid assembly. Transient intermediates that are sparsely populated during protein folding have been identified as key players in amyloid aggregation. However, due to their ephemeral nature, structural characterization of these species remains challenging. Here, using the power of nonuniformly sampled NMR methods we investigate the folding pathway of amyloidogenic and nonamyloidogenic variants of β2-microglobulin (β2m) in atomic detail. Despite folding via common intermediate states, we show that the decreased population of the aggregation-prone ITrans state and population of a less stable, more dynamic species ablate amyloid formation by increasing the energy barrier for amyloid assembly. The results show that subtle changes in conformational dynamics can have a dramatic effect in determining whether a protein is amyloidogenic, without perturbation of the mechanism of protein folding. PMID:27117876

  10. Structural origin of slow diffusion in protein folding.

    PubMed

    Chung, Hoi Sung; Piana-Agostinetti, Stefano; Shaw, David E; Eaton, William A

    2015-09-25

    Experimental, theoretical, and computational studies of small proteins suggest that interresidue contacts not present in the folded structure play little or no role in the self-assembly mechanism. Non-native contacts can, however, influence folding kinetics by introducing additional local minima that slow diffusion over the global free-energy barrier between folded and unfolded states. Here, we combine single-molecule fluorescence with all-atom molecular dynamics simulations to discover the structural origin for the slow diffusion that markedly decreases the folding rate for a designed α-helical protein. Our experimental determination of transition path times and our analysis of the simulations point to non-native salt bridges between helices as the source, which provides a quantitative glimpse of how specific intramolecular interactions influence protein folding rates by altering dynamics and not activation free energies.

  11. Exploring one-state downhill protein folding in single molecules

    PubMed Central

    Liu, Jianwei; Campos, Luis A.; Cerminara, Michele; Wang, Xiang; Ramanathan, Ravishankar; English, Douglas S.; Muñoz, Victor

    2012-01-01

    A one-state downhill protein folding process is barrierless at all conditions, resulting in gradual melting of native structure that permits resolving folding mechanisms step-by-step at atomic resolution. Experimental studies of one-state downhill folding have typically focused on the thermal denaturation of proteins that fold near the speed limit (ca. 106 s-1) at their unfolding temperature, thus being several orders of magnitude too fast for current single-molecule methods, such as single-molecule FRET. An important open question is whether one-state downhill folding kinetics can be slowed down to make them accessible to single-molecule approaches without turning the protein into a conventional activated folder. Here we address this question on the small helical protein BBL, a paradigm of one-state downhill thermal (un)folding. We decreased 200-fold the BBL folding-unfolding rate by combining chemical denaturation and low temperature, and carried out free-diffusion single-molecule FRET experiments with 50-μs resolution and maximal photoprotection using a recently developed Trolox-cysteamine cocktail. These experiments revealed a single conformational ensemble at all denaturing conditions. The chemical unfolding of BBL was then manifested by the gradual change of this unique ensemble, which shifts from high to low FRET efficiency and becomes broader at increasing denaturant. Furthermore, using detailed quantitative analysis, we could rule out the possibility that the BBL single-molecule data are produced by partly overlapping folded and unfolded peaks. Thus, our results demonstrate the one-state downhill folding regime at the single-molecule level and highlight that this folding scenario is not necessarily associated with ultrafast kinetics. PMID:22184219

  12. An iterative Riemann solver for systems of hyperbolic conservation law s, with application to hyperelastic solid mechanics

    SciTech Connect

    Miller, Gregory H.

    2003-08-06

    In this paper we present a general iterative method for the solution of the Riemann problem for hyperbolic systems of PDEs. The method is based on the multiple shooting method for free boundary value problems. We demonstrate the method by solving one-dimensional Riemann problems for hyperelastic solid mechanics. Even for conditions representative of routine laboratory conditions and military ballistics, dramatic differences are seen between the exact and approximate Riemann solution. The greatest discrepancy arises from misallocation of energy between compressional and thermal modes by the approximate solver, resulting in nonphysical entropy and temperature estimates. Several pathological conditions arise in common practice, and modifications to the method to handle these are discussed. These include points where genuine nonlinearity is lost, degeneracies, and eigenvector deficiencies that occur upon melting.

  13. Avibactam and Class C β-Lactamases: Mechanism of Inhibition, Conservation of the Binding Pocket, and Implications for Resistance

    PubMed Central

    Johnstone, M. R.; Ross, P. L.; McLaughlin, R. E.; Olivier, N. B.

    2014-01-01

    Avibactam is a novel non-β-lactam β-lactamase inhibitor that inhibits a wide range of β-lactamases. These include class A, class C, and some class D enzymes, which erode the activity of β-lactam drugs in multidrug-resistant pathogens like Pseudomonas aeruginosa and Enterobacteriaceae spp. Avibactam is currently in clinical development in combination with the β-lactam antibiotics ceftazidime, ceftaroline fosamil, and aztreonam. Avibactam has the potential to be the first β-lactamase inhibitor that might provide activity against class C-mediated resistance, which represents a growing concern in both hospital- and community-acquired infections. Avibactam has an unusual mechanism of action: it is a covalent inhibitor that acts via ring opening, but in contrast to other currently used β-lactamase inhibitors, this reaction is reversible. Here, we present a high-resolution structure of avibactam bound to a class C β-lactamase, AmpC, from P. aeruginosa that provided insight into the mechanism of both acylation and recyclization in this enzyme class and highlighted the differences observed between class A and class C inhibition. Furthermore, variants resistant to avibactam that identified the residues important for inhibition were isolated. Finally, the structural information was used to predict effective inhibition by sequence analysis and functional studies of class C β-lactamases from a large and diverse set of contemporary clinical isolates (P. aeruginosa and several Enterobacteriaceae spp.) obtained from recent infections to understand any preexisting variability in the binding pocket that might affect inhibition by avibactam. PMID:25022578

  14. Observation of Two Families of Folding Pathways of BBL

    PubMed Central

    Fan, Jue; Duan, Mojie; Li, Da-Wei; Wu, Hao; Yang, Haijun; Han, Li; Huo, Shuanghong

    2011-01-01

    BBL is an independent folding domain of a large multienzyme complex, 2-oxoglutarate dehydrogenase. The folding mechanism of BBL is under debate between the views of noncooperative downhill-type and classical two-state. Extensive replica exchange molecular dynamics simulations of BBL in explicit solvent have shown some non-two-state behaviors despite no definitive evidence of downhill folding. In this work, we postprocess the replica exchange data using our roadmap-based MaxFlux reaction path algorithm to reveal atomically detailed folding pathways. A connected graph is used to organize and visualize the folding pathways initiated from random coils. High structural and transition heterogeneity is seen in the early stage of folding. Two main parallel folding pathways emerge in the later stage; one path shows that tertiary contact and helix formation develop at different stages of folding, whereas the other path exhibits concurrence of secondary and tertiary structure formation to some extent. Because the native state of BBL is sensitive to experimental conditions, we speculate that the relative predominance of the two pathways may vary with the protein construct and solvent conditions, possibly leading to the seeming discrepancy of experimental results. Our roadmap-based reaction path algorithm is a general tool to extract path information from replica exchange. PMID:21575580

  15. When Do Semi-crystalline Polymer Fold during Crystallization?

    NASA Astrophysics Data System (ADS)

    Miyoshi, Toshikazu; Hong, You-Lee

    2014-03-01

    Semi-crystalline polymers are crystallized as folded chains in thin lamellae of ca. 5-20 nm from random coils in the melt and solution states. Lauritzen-Hoffman theory implied the crystallization process is dominated by sequential stem deposition on the growth front. Conversely, Allegra proposed a bundle model in which aggregates of 10-20 stems are produced by folding in the pre-stage of crystallization. The pre-folded chains are kinetically deposited on the growth front and thus determine the morphology at different crystallization temperatures. The folded chains preserve their own chain-folding directions, numbers, and fractions as a function of concentrations and supercooling, which would provide detailed chain-folding mechanism. We recently developed a new strategy using 13C-13C double-quantum NMR to investigate chain-trajectory of 13C selectively labeled polymer in bulk crystals. Here, we report how re-entrance sites, fraction, and number of folded chains of isotactic poly(1-butene) in form III single crystals depends on supercooling conditions and solvent effects. On the basis of molecular level structures, we will discuss about chain-folding process of iPB1 in dilute solutions. DMR-1105829.

  16. Detergent-assisted oxidative folding of delta-conotoxins.

    PubMed

    DeLa Cruz, R; Whitby, F G; Buczek, O; Bulaj, G

    2003-04-01

    Conotoxins comprise a diverse group of disulfide-rich peptides found in venoms of predatory Conus species. The native conformation of these peptides is marginally stable in comparison with alternative conformations, often resulting in low folding yields. The oxidative folding of hydrophobic delta-conotoxins was found to produce less than 1% of the native peptide [Bulaj, G. et al. (2001) Biochemistry 40, 13201]. In order to identify factors that might improve folding yields, we screened a number of additives including water-soluble polymers, detergents and osmolytes for their ability to increase steady-state accumulation of the native delta-conotoxin PVIA. The presence of a non-ionic detergent Tween and low temperature appeared to be the most effective factors in improving the oxidative folding. The detergent was also effective in promoting folding of other hydrophobic delta-conotoxins. Based on our findings, we discuss a possible mechanism for detergent-assisted folding and the general applicability of this mechanism to facilitating the proper folding of hydrophobic, cysteine-rich peptides.

  17. The West Nile virus assembly process evades the conserved antiviral mechanism of the interferon-induced MxA protein.

    PubMed

    Hoenen, Antje; Gillespie, Leah; Morgan, Garry; van der Heide, Peter; Khromykh, Alexander; Mackenzie, Jason

    2014-01-01

    Flaviviruses have evolved means to evade host innate immune responses. Recent evidence suggests this is due to prevention of interferon production and signaling in flavivirus-infected cells. Here we show that the interferon-induced MxA protein can sequester the West Nile virus strain Kunjin virus (WNVKUN) capsid protein in cytoplasmic tubular structures in an expression-replication system. This sequestering resulted in reduced titers of secreted WNVKUN particles. We show by electron microscopy, tomography and 3D modeling that these cytoplasmic tubular structures form organized bundles. Additionally we show that recombinant ER-targeted MxA can restrict production of infectious WNVKUN under conditions of virus infection. Our results indicate a co-ordinated and compartmentalized WNVKUN assembly process may prevent recognition of viral components by MxA, particularly the capsid protein. This recognition can be exploited if MxA is targeted to intracellular sites of WNVKUN assembly. This results in further understanding of the mechanisms of flavivirus evasion from the immune system.

  18. The West Nile virus assembly process evades the conserved antiviral mechanism of the interferon-induced MxA protein

    SciTech Connect

    Hoenen, Antje; Gillespie, Leah; Morgan, Garry; Heide, Peter van der; Khromykh, Alexander; Mackenzie, Jason

    2014-01-05

    Flaviviruses have evolved means to evade host innate immune responses. Recent evidence suggests this is due to prevention of interferon production and signaling in flavivirus-infected cells. Here we show that the interferon-induced MxA protein can sequester the West Nile virus strain Kunjin virus (WNV{sub KUN}) capsid protein in cytoplasmic tubular structures in an expression-replication system. This sequestering resulted in reduced titers of secreted WNV{sub KUN} particles. We show by electron microscopy, tomography and 3D modeling that these cytoplasmic tubular structures form organized bundles. Additionally we show that recombinant ER-targeted MxA can restrict production of infectious WNV{sub KUN} under conditions of virus infection. Our results indicate a co-ordinated and compartmentalized WNV{sub KUN} assembly process may prevent recognition of viral components by MxA, particularly the capsid protein. This recognition can be exploited if MxA is targeted to intracellular sites of WNV{sub KUN} assembly. This results in further understanding of the mechanisms of flavivirus evasion from the immune system. - Highlights: • We show that the ISG MxA can recognize the West Nile virus capsid protein. • Interaction between WNV C protein and MxA induces cytoplasmic fibrils. • MxA can be retargeted to the ER to restrict WNV particle release. • WNV assembly process is a strategy to avoid MxA recognition.

  19. Direct molecular dynamics observation of protein folding transition state ensemble.

    PubMed Central

    Ding, Feng; Dokholyan, Nikolay V; Buldyrev, Sergey V; Stanley, H Eugene; Shakhnovich, Eugene I

    2002-01-01

    The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50% probability to convert rapidly to the folded state and 50% chance to rapidly unfold, constitutes the basis of the modern interpretation of protein engineering experiments. It has been conjectured that conformations constituting the TSE in many proteins are the expanded and distorted forms of the native state built around a specific folding nucleus. This view has been supported by a number of on-lattice and off-lattice simulations. Here we report a direct observation and characterization of the TSE by molecular dynamic folding simulations of the C-Src SH3 domain, a small protein that has been extensively studied experimentally. Our analysis reveals a set of key interactions between residues, conserved by evolution, that must be formed to enter the kinetic basin of attraction of the native state. PMID:12496119

  20. The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

    SciTech Connect

    Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel; Korolev, Sergey

    2010-07-20

    Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragment adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.

  1. Ventricular-Fold Dynamics in Human Phonation

    ERIC Educational Resources Information Center

    Bailly, Lucie; Bernardoni, Nathalie Henrich; Müller, Frank; Rohlfs, Anna-Katharina; Hess, Markus

    2014-01-01

    Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricular-fold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample…

  2. Conformation and sequence evidence for two-fold symmetry in left-handed beta-helix fold.

    PubMed

    Shen, Xiaojuan

    2011-09-21

    The left-handed beta-helix (LβH) has received interest recently as it folds as a possible solution for the structure of misfolded proteins associated with prion and Huntington's diseases. Through a combination of sequence and structure analysis, we uncover a novel feature that is common to this unique fold: a two-fold symmetry in both sequence and structure, and this feature always coupled with extended loops in the middle of the helix. Since the results reveal a two-fold symmetric pattern both in the sequence and structure, it may indicate that the symmetry in tertiary structure is coded by the symmetry in primary sequence, which agrees with Anfisen's proposal that a protein's amino-acid sequence specify its three-dimensional structure. It may also indicate that LβH adopts a two-fold repeat pattern during the evolution process and symmetry helps maintaining the stability of the helix structure. The two-fold symmetric pattern and extended loops might be important in maintaining stability of helix proteins. This discovery can be useful in understanding the folding mechanisms of this protein fold and provide insights in the relation between sequences and structures.

  3. Conservative management.

    PubMed

    Kruis, W; Leifeld, L; Pfützer, R

    2012-01-01

    Treatment of diverticulitis comprises at least two options: conservative or surgical management. There is a recent trend to limit surgical treatment of acute diverticulitis and to favor conservative management. This review addresses general aspects of conservative patient care with special focus on the treatment of patients with a first attack of diverticulitis. The presentation does not include a discussion of specific drugs which is given in other sections of this issue.

  4. A Conserved Role for the NAM/miR164 Developmental Module Reveals a Common Mechanism Underlying Carpel Margin Fusion in Monocarpous and Syncarpous Eurosids

    PubMed Central

    Vialette-Guiraud, Aurélie C. M.; Chauvet, Aurélie; Gutierrez-Mazariegos, Juliana; Eschstruth, Alexis; Ratet, Pascal; Scutt, Charles P.

    2016-01-01

    The majority of angiosperms are syncarpous- their gynoecium is composed of two or more fused carpels. In Arabidopsis thaliana, this fusion is regulated through the balance of expression between CUP SHAPED COTYLEDON (CUC) genes, which are orthologs of the Petunia hybrida transcription factor NO APICAL MERISTEM (NAM), and their post-transcriptional regulator miR164. Accordingly, the expression of a miR164-insensitive form of A. thaliana CUC2 causes a radical breakdown of carpel fusion. Here, we investigate the role of the NAM/miR164 genetic module in carpel closure in monocarpous plants. We show that the disruption of this module in monocarpous flowers of A. thaliana aux1-22 mutants causes a failure of carpel closure, similar to the failure of carpel fusion observed in the wild-type genetic background. This observation suggested that closely related mechanisms may bring about carpel closure and carpel fusion, at least in A. thaliana. We therefore tested whether these mechanisms were conserved in a eurosid species that is monocarpous in its wild-type form. We observed that expression of MtNAM, the NAM ortholog in the monocarpous eurosid Medicago truncatula, decreases during carpel margin fusion, suggesting a role for the NAM/miR164 module in this process. We transformed M. truncatula with a miR164-resistant form of MtNAM and observed, among other phenotypes, incomplete carpel closure in the resulting transformants. These data confirm the underlying mechanistic similarity between carpel closure and carpel fusion which we observed in A. thaliana. Our observations suggest that the role of the NAM/miR164 module in the fusion of carpel margins has been conserved at least since the most recent common ancestor of the eurosid clade, and open the possibility that a similar mechanism may have been responsible for carpel closure at much earlier stages of angiosperm evolution. We combine our results with studies of early diverging angiosperms to speculate on the role of the NAM

  5. Two-ligand priming mechanism for potentiated phosphoinositide synthesis is an evolutionarily conserved feature of Sec14-like phosphatidylinositol and phosphatidylcholine exchange proteins

    PubMed Central

    Huang, Jin; Ghosh, Ratna; Tripathi, Ashutosh; Lönnfors, Max; Somerharju, Pentti; Bankaitis, Vytas A.

    2016-01-01

    Lipid signaling, particularly phosphoinositide signaling, plays a key role in regulating the extreme polarized membrane growth that drives root hair development in plants. The Arabidopsis AtSFH1 gene encodes a two-domain protein with an amino-terminal Sec14-like phosphatidylinositol transfer protein (PITP) domain linked to a carboxy-terminal nodulin domain. AtSfh1 is critical for promoting the spatially highly organized phosphatidylinositol-4,5-bisphosphate signaling program required for establishment and maintenance of polarized root hair growth. Here we demonstrate that, like the yeast Sec14, the AtSfh1 PITP domain requires both its phosphatidylinositol (PtdIns)- and phosphatidylcholine (PtdCho)-binding properties to stimulate PtdIns-4-phosphate [PtdIns(4)P] synthesis. Moreover, we show that both phospholipid-binding activities are essential for AtSfh1 activity in supporting polarized root hair growth. Finally, we report genetic and biochemical evidence that the two-ligand mechanism for potentiation of PtdIns 4-OH kinase activity is a broadly conserved feature of plant Sec14-nodulin proteins, and that this strategy appeared only late in plant evolution. Taken together, the data indicate that the PtdIns/PtdCho-exchange mechanism for stimulated PtdIns(4)P synthesis either arose independently during evolution in yeast and in higher plants, or a suitable genetic module was introduced to higher plants from a fungal source and subsequently exploited by them. PMID:27193303

  6. Antifungal mechanisms of a plant defensin MtDef4 are not conserved between the ascomycete fungi Neurospora crassa and Fusarium graminearum.

    PubMed

    El-Mounadi, Kaoutar; Islam, Kazi T; Hernández-Ortiz, Patricia; Read, Nick D; Shah, Dilip M

    2016-05-01

    Defensins play an important role in plant defense against fungal pathogens. The plant defensin, MtDef4, inhibits growth of the ascomycete fungi, Neurospora crassa and Fusarium graminearum, at micromolar concentrations. We have reported that MtDef4 is transported into the cytoplasm of these fungi and exerts its antifungal activity on intracellular targets. Here, we have investigated whether the antifungal mechanisms of MtDef4 are conserved in these fungi. We show that N. crassa and F. graminearum respond differently to MtDef4 challenge. Membrane permeabilization is required for the antifungal activity of MtDef4 against F. graminearum but not against N. crassa. We find that MtDef4 is targeted to different subcellular compartments in each fungus. Internalization of MtDef4 in N. crassa is energy-dependent and involves endocytosis. By contrast, MtDef4 appears to translocate into F. graminearum autonomously using a partially energy-dependent pathway. MtDef4 has been shown to bind to the phospholipid phosphatidic acid (PA). We provide evidence that the plasma membrane localized phospholipase D, involved in the biosynthesis of PA, is needed for entry of this defensin in N. crassa, but not in F. graminearum. To our knowledge, this is the first example of a defensin which inhibits the growth of two ascomycete fungi via different mechanisms. PMID:26801962

  7. Effects of positively charged redox molecules on disulfide-coupled protein folding.

    PubMed

    Okumura, Masaki; Shimamoto, Shigeru; Nakanishi, Takeyoshi; Yoshida, Yu-ichiro; Konogami, Tadafumi; Maeda, Shogo; Hidaka, Yuji

    2012-11-01

    In vitro folding of disulfide-containing proteins is generally regulated by redox molecules, such as glutathione. However, the role of the cross-disulfide-linked species formed between the redox molecule and the protein as a folding intermediate in the folding mechanism is poorly understood. In the present study, we investigated the effect of the charge on a redox molecule on disulfide-coupled protein folding. Several types of aliphatic thiol compounds including glutathione were examined for the folding of disulfide-containing-proteins, such as lysozyme and prouroguanylin. The results indicate that the positive charge and its dispersion play a critical role in accelerating disulfide-coupled protein folding.

  8. Analysis of tomato plasma membrane H(+)-ATPase gene family suggests a mycorrhiza-mediated regulatory mechanism conserved in diverse plant species.

    PubMed

    Liu, Junli; Liu, Jianjian; Chen, Aiqun; Ji, Minjie; Chen, Jiadong; Yang, Xiaofeng; Gu, Mian; Qu, Hongye; Xu, Guohua

    2016-10-01

    In plants, the plasma membrane H(+)-ATPase (HA) is considered to play a crucial role in regulating plant growth and respoding to environment stresses. Multiple paralogous genes encoding different isozymes of HA have been identified and characterized in several model plants, while limited information of the HA gene family is available to date for tomato. Here, we describe the molecular and expression features of eight HA-encoding genes (SlHA1-8) from tomato. All these genes are interrupted by multiple introns with conserved positions. SlHA1, 2, and 4 were widely expressed in all tissues, while SlHA5, 6, and 7 were almost only expressed in flowers. SlHA8, the transcripts of which were barely detectable under normal or nutrient-/salt-stress growth conditions, was strongly activated in arbuscular mycorrhizal (AM) fungal-colonized roots. Extreme lack of SlHA8 expression in M161, a mutant defective to AM fungal colonization, provided genetic evidence towards the dependence of its expression on AM symbiosis. A 1521-bp SlHA8 promoter could direct the GUS reporter expression specifically in colonized cells of transgenic tobacco, soybean, and rice mycorrhizal roots. Promoter deletion assay revealed a 223-bp promoter fragment of SlHA8 containing a variant of AM-specific cis-element MYCS (vMYCS) sufficient to confer the AM-induced activity. Targeted deletion of this motif in the corresponding promoter region causes complete abolishment of GUS staining in mycorrhizal roots. Together, these results lend cogent evidence towards the evolutionary conservation of a potential regulatory mechanism mediating the activation of AM-responsive HA genes in diverse mycorrhizal plant species.

  9. Improving protein fold recognition by random forest

    PubMed Central

    2014-01-01

    Background Recognizing the correct structural fold among known template protein structures for a target protein (i.e. fold recognition) is essential for template-based protein structure modeling. Since the fold recognition problem can be defined as a binary classification problem of predicting whether or not the unknown fold of a target protein is similar to an already known template protein structure in a library, machine learning methods have been effectively applied to tackle this problem. In our work, we developed RF-Fold that uses random forest - one of the most powerful and scalable machine learning classification methods - to recognize protein folds. Results RF-Fold consists of hundreds of decision trees that can be trained efficiently on very large datasets to make accurate predictions on a highly imbalanced dataset. We evaluated RF-Fold on the standard Lindahl's benchmark dataset comprised of 976 × 975 target-template protein pairs through cross-validation. Compared with 17 different fold recognition methods, the performance of RF-Fold is generally comparable to the best performance in fold recognition of different difficulty ranging from the easiest family level, the medium-hard superfamily level, and to the hardest fold level. Based on the top-one template protein ranked by RF-Fold, the correct recognition rate is 84.5%, 63.4%, and 40.8% at family, superfamily, and fold levels, respectively. Based on the top-five template protein folds ranked by RF-Fold, the correct recognition rate increases to 91.5%, 79.3% and 58.3% at family, superfamily, and fold levels. Conclusions The good performance achieved by the RF-Fold demonstrates the random forest's effectiveness for protein fold recognition. PMID:25350499

  10. Learning Protein Folding Energy Functions

    PubMed Central

    Guan, Wei; Ozakin, Arkadas; Gray, Alexander; Borreguero, Jose; Pandit, Shashi; Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey

    2014-01-01

    A critical open problem in ab initio protein folding is protein energy function design, which pertains to defining the energy of protein conformations in a way that makes folding most efficient and reliable. In this paper, we address this issue as a weight optimization problem and utilize a machine learning approach, learning-to-rank, to solve this problem. We investigate the ranking-via-classification approach, especially the RankingSVM method and compare it with the state-of-the-art approach to the problem using the MINUIT optimization package. To maintain the physicality of the results, we impose non-negativity constraints on the weights. For this we develop two efficient non-negative support vector machine (NNSVM) methods, derived from L2-norm SVM and L1-norm SVMs, respectively. We demonstrate an energy function which maintains the correct ordering with respect to structure dissimilarity to the native state more often, is more efficient and reliable for learning on large protein sets, and is qualitatively superior to the current state-of-the-art energy function. PMID:25311546

  11. Distinct folding pathways of two homologous disulfide proteins: bovine pancreatic trypsin inhibitor and tick anticoagulant peptide.

    PubMed

    Chang, Jui-Yoa

    2011-01-01

    The folding pathways of disulfide proteins vary substantially (Arolas et al., Trends Biochem Sci 31: 292-301, 2006). The diversity is mainly manifested by (a) the extent of heterogeneity of folding intermediates, (b) the extent of presence of native-like intermediates, and (c) the variation of folding kinetics. Even among structurally similar proteins, the difference can be enormous. This is demonstrated in this concise review with two structurally homologous kunitz-type protease inhibitors, bovine pancreatic trypsin inhibitor and tick anticoagulant peptide, as well as a group of cystine knot proteins. The diversity of their folding mechanisms is illustrated with two different folding techniques: (a) the conventional method of disulfide oxidation (oxidative folding), and (b) the novel method of disulfide scrambling (Chang, J Biol Chem 277: 120-126, 2002). This review also highlights the convergence of folding models concluded form the conventional conformational folding and those obtained by oxidative folding.

  12. A Hooke׳s law-based approach to protein folding rate.

    PubMed

    Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Prieto, Pablo J; Salgado, Jesús; García, Yamila; Sotomayor-Torres, Clivia M

    2015-01-01

    Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke׳s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics. PMID:25245368

  13. How the folding rates of two- and multistate proteins depend on the amino acid properties.

    PubMed

    Huang, Jitao T; Huang, Wei; Huang, Shanran R; Li, Xin

    2014-10-01

    Proteins fold by either two-state or multistate kinetic mechanism. We observe that amino acids play different roles in different mechanism. Many residues that are easy to form regular secondary structures (α helices, β sheets and turns) can promote the two-state folding reactions of small proteins. Most of hydrophilic residues can speed up the multistate folding reactions of large proteins. Folding rates of large proteins are equally responsive to the flexibility of partial amino acids. Other properties of amino acids (including volume, polarity, accessible surface, exposure degree, isoelectric point, and phase transfer energy) have contributed little to folding kinetics of the proteins. Cysteine is a special residue, it triggers two-state folding reaction and but inhibits multistate folding reaction. These findings not only provide a new insight into protein structure prediction, but also could be used to direct the point mutations that can change folding rate.

  14. Functional analysis of propeptide as an intramolecular chaperone for in vivo folding of subtilisin nattokinase.

    PubMed

    Jia, Yan; Liu, Hui; Bao, Wei; Weng, Meizhi; Chen, Wei; Cai, Yongjun; Zheng, Zhongliang; Zou, Guolin

    2010-12-01

    Here, we show that during in vivo folding of the precursor, the propeptide of subtilisin nattokinase functions as an intramolecular chaperone (IMC) that organises the in vivo folding of the subtilisin domain. Two residues belonging to β-strands formed by conserved regions of the IMC are crucial for the folding of the subtilisin domain through direct interactions. An identical protease can fold into different conformations in vivo due to the action of a mutated IMC, resulting in different kinetic parameters. Some interfacial changes involving conserved regions, even those induced by the subtilisin domain, blocked subtilisin folding and altered its conformation. Insight into the interaction between the subtilisin and IMC domains is provided by a three-dimensional structural model.

  15. Open Fissure Folds record coseismic loading and postseismic stress relaxation

    NASA Astrophysics Data System (ADS)

    Nüchter, Jens-Alexander

    2015-03-01

    Open Fissure Folds hosted by high pressure/low temperature metamorphic rocks of south Evia (Greece) are introduced, their structural and microstructural record is analysed, and a mechanical model is proposed. Open Fissure Folds are preserved as at least two parallel folded quartz-feldspar veins separated by narrow buckled rock columns. The veins originated as tensile cracks that propagated in the middle crust driven by high differential stress. Features diagnostic for Open Fissure Folds indicate that the rock columns represented the layers of high viscosity, and not the veins as consistently reported in many previous studies on folded veins. This record is taken to indicate that buckling of the rock columns initiated after arrest of the fractures and terminated prior to complete vein sealing. Accordingly, mechanical decoupling by open fissures allowed for buckling of the rock columns in response to episodic creep of the host rocks according to stress relaxation, as expected for postseismic deformation in the earthquake cycle. I propose that the parental fractures propagated in response to quasi-instantaneous coseismic loading of the middle crust. Buckling was attributed to transient postseismic creep and stress relaxation. Complete sealing of the veins occurred when stresses were largely relaxed. Each Open Fissure Fold records the stress and strain history of a single earthquake.

  16. Metal ion coupled protein folding and allosteric motions

    NASA Astrophysics Data System (ADS)

    Wang, Wei

    2014-03-01

    Many proteins need the help of cofactors for their successful folding and functioning. Metal ions, i.e., Zn2+, Ca2+, and Mg2+ etc., are typical biological cofactors. Binding of metal ions can reshape the energy landscapes of proteins, thereby modifying the folding and allosteric motions. For example, such binding may make the intrinsically disordered proteins have funneled energy landscapes, consequently, ensures their spontaneous folding. In addition, the binding may activate certain biological processes by inducing related conformational changes of regulation proteins. However, how the local interactions involving the metal ion binding can induce the global conformational motions of proteins remains elusive. Investigating such question requires multiple models with different details, including quantum mechanics, atomistic models, and coarse grained models. In our recent work, we have been developing such multiscale methods which can reasonably model the metal ion binding induced charge transfer, protonation/deprotonation, and large conformational motions of proteins. With such multiscale model, we elucidated the zinc-binding induced folding mechanism of classical zinc finger and the calcium-binding induced dynamic symmetry breaking in the allosteric motions of calmodulin. In addition, we studied the coupling of folding, calcium binding and allosteric motions of calmodulin domains. In this talk, I will introduce the above progresses on the metal ion coupled protein folding and allosteric motions. We thank the finacial support from NSFC and the 973 project.

  17. Vocal fold ion transport and mucin expression following acrolein exposure.

    PubMed

    Levendoski, Elizabeth Erickson; Sivasankar, M Preeti

    2014-05-01

    The vocal fold epithelium is exposed to inhaled particulates including pollutants during breathing in everyday environments. Yet, our understanding of the effects of pollutants on vocal fold epithelial function is extremely limited. The objective of this study was to investigate the effect of the pollutant acrolein on two vocal fold epithelial mechanisms: ion transport and mucin (MUC) synthesis. These mechanisms were chosen as each plays a critical role in vocal defense and in maintaining surface hydration which is necessary for optimal voice production. Healthy, native porcine vocal folds (N = 85) were excised and exposed to an acrolein or sham challenge. A 60-min acrolein, but not sham challenge significantly reduced ion transport and inhibited cyclic adenosine monophosphate-dependent, increases in ion transport. Decreases in ion transport were associated with reduced sodium absorption. Within the same timeline, no significant acrolein-induced changes in MUC gene or protein expression were observed. These results improve our understanding of the effects of acrolein on key vocal fold epithelial functions and inform the development of future investigations that seek to elucidate the impact of a wide range of pollutant exposures on vocal fold health.

  18. Folding and self-assembly of a small protein complex

    PubMed Central

    Sieradzan, Adam K.; Liwo, Adam; Hansmann, Ulrich H.E.

    2012-01-01

    The synthetic homotetrameric ββα (BBAT1) protein possesses a stable quaternary structure with a ββα fold. Because of its small size (a total of 84 residues), the homotetramer is an excellent model system with which to study the self-assembly and protein-protein interactions. We find from replica exchange molecular dynamics simulations with the coarse-grain UNRES force field that the folding and association pathway consists of three well-separated steps, where that association to a tetramer precedes and facilitates folding of the four chains. At room temperature the tetramer exists in an ensemble of diverse structures. The crystal structure becomes energetically favored only when the molecule is put in a dense and crystal-like environment. The observed picture of folding promoted by association may mirror the mechanism according to which intrinsically unfolded proteins assume their functional structure. PMID:24039552

  19. Five-fold twin formation during annealing of nanocrystalline Cu

    SciTech Connect

    Bringa, E M; Farkas, D; Caro, A; Wang, Y M; McNaney, J; Smith, R

    2009-05-20

    Contrary to the common belief that many-fold twins, or star twins, in nanophase materials are due to the action of significant external stresses, we report molecular dynamics simulations of annealing in 5 nm grain size samples annealed at 800 K for nearly 0.5 nsec at 0 external pressure showing the formation of five-fold star twins during annealing under the action of the large internal stresses responsible for grain growth and microstructural evolution. The structure of the many-fold twins is remarkably similar to those we have found to occur under uniaxial shock loading, of samples of nanocrystalline NiW with a grain size of {approx}5-30 nm. The mechanism of formation of the many-fold twins is discussed in the light of the simulations and experiments.

  20. Modern Analysis of Protein Folding by Differential Scanning Calorimetry.

    PubMed

    Ibarra-Molero, Beatriz; Naganathan, Athi N; Sanchez-Ruiz, Jose M; Muñoz, Victor

    2016-01-01

    Differential scanning calorimetry (DSC) is a very powerful tool for investigating protein folding and stability because its experimental output reflects the energetics of all conformations that become minimally populated during thermal unfolding. Accordingly, analysis of DSC experiments with simple thermodynamic models has been key for developing our understanding of protein stability during the past five decades. The discovery of ultrafast folding proteins, which have naturally broad conformational ensembles and minimally cooperative unfolding, opens the possibility of probing the complete folding free energy landscape, including those conformations at the top of the barrier to folding, via DSC. Exploiting this opportunity requires high-quality experiments and the implementation of novel analytical methods based on statistical mechanics. Here, we cover the recent exciting developments in this front, describing the new analytical procedures in detail as well as providing experimental guidelines for performing such analysis.

  1. Fungal infections of the folds (intertriginous areas).

    PubMed

    Metin, Ahmet; Dilek, Nursel; Demirseven, Duriye Deniz

    2015-01-01

    Superficial fungal infections are widespread, regardless of age and gender, in populations all around the world and may affect the skin and skin appendages. Although there are thousands of fungal infections from various genera and families in nature, those that are pathogenic for humans and nesting in skin folds are limited in number. The prevalence and distribution of these fungi vary according to the patients and certain environmental factors. Because the areas including the lids, external auditory canal, behind the ears, navel, inguinal region, and axillae, also called flexures, are underventilated and moist areas exposed to friction, they are especially sensitive to fungal infections. Fungi can both directly invade the skin, leading to infections, and indirectly stimulate immune mechanisms due to tissue interaction and their antigenic character and contribute to the development or exacerbation of secondary bacterial infections, seborrheic dermatitis, atopic dermatitis, and psoriasis. Superficial fungal infections can be classified and studied as dermatophyte infections, candidal infections, Malassezia infections, and other superficial infections independently from the involved skin fold areas. PMID:26051058

  2. Single-molecule spectroscopy of protein folding in a chaperonin cage

    PubMed Central

    Hofmann, Hagen; Hillger, Frank; Pfeil, Shawn H.; Hoffmann, Armin; Streich, Daniel; Haenni, Dominik; Nettels, Daniel; Lipman, Everett A.; Schuler, Benjamin

    2010-01-01

    Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage. PMID:20547872

  3. SbnG, a citrate synthase in Staphylococcus aureus: a new fold on an old enzyme.

    PubMed

    Kobylarz, Marek J; Grigg, Jason C; Sheldon, Jessica R; Heinrichs, David E; Murphy, Michael E P

    2014-12-01

    In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. We present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic gene clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. A structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production.

  4. Paper Folding for the Mathematics Class.

    ERIC Educational Resources Information Center

    Johnson, Donovan A.

    Directions are given for folding paper to show geometric figures and relationships. Topics covered are folding the basic constructions, geometric concepts concerning triangles and quadrilaterals, circle relationships, products and factors, polygon constructions, symmetry, conic sections, and recreations. (DT)

  5. Iodothyronine deiodinase gene analysis of the Pacific oyster Crassostrea gigas reveals possible conservation of thyroid hormone feedback regulation mechanism in mollusks

    NASA Astrophysics Data System (ADS)

    Huang, Wen; Xu, Fei; Qu, Tao; Li, Li; Que, Huayong; Zhang, Guofan

    2015-07-01

    Iodothyronine deiodinase catalyzes the initiation and termination of thyroid hormones (THs) effects, and plays a central role in the regulation of thyroid hormone level in vertebrates. In non-chordate invertebrates, only one deiodinase has been identified in the scallop Chlamys farreri. Here, two deiodinases were cloned in the Pacific oyster Crassostrea gigas ( CgDx and CgDy). The characteristic in-frame TGA codons and selenocysteine insertion sequence elements in the oyster deiodinase cDNAs supported the activity of them. Furthermore, seven orthologs of deiodinases were found by a tblastn search in the mollusk Lottia gigantea and the annelid Capitella teleta. A phylogenetic analysis revealed that the deiodinase gene originated from an common ancestor and a clade-specific gene duplication occurred independently during the differentiation of the mollusk, annelid, and vertebrate lineages. The distinct spatiotemporal expression patterns implied functional divergence of the two deiodinases. The expression of CgDx and CgDy was influenced by L-thyroxine T4, and putative thyroid hormone responsive elements were found in their promoters, which suggested that the oyster deiodinases were feedback regulated by TH. Epinephrine stimulated the expression level of CgDx and CgDy, suggesting an interaction effect between different hormones. This study provides the first evidence for the existence of a conserved TH feedback regulation mechanism in mollusks, providing insights into TH evolution.

  6. Drosophila Homologues of Adenomatous Polyposis Coli (APC) and the Formin Diaphanous Collaborate by a Conserved Mechanism to Stimulate Actin Filament Assembly*

    PubMed Central

    Jaiswal, Richa; Stepanik, Vince; Rankova, Aneliya; Molinar, Olivia; Goode, Bruce L.; McCartney, Brooke M.

    2013-01-01

    Adenomatous polyposis coli (APC) is a large multidomain protein that regulates the cytoskeleton. Recently, it was shown that vertebrate APC through its Basic domain directly collaborates with the formin mDia1 to stimulate actin filament assembly in the presence of nucleation barriers. However, it has been unclear whether these activities extend to homologues of APC and Dia in other organisms. Drosophila APC and Dia are each required to promote actin furrow formation in the syncytial embryo, suggesting a potential collaboration in actin assembly, but low sequence homology between the Basic domains of Drosophila and vertebrate APC has left their functional and mechanistic parallels uncertain. To address this question, we purified Drosophila APC1 and Dia and determined their individual and combined effects on actin assembly using both bulk fluorescence assays and total internal reflection fluorescence microscopy. Our data show that APC1, similar to its vertebrate homologue, bound to actin monomers and nucleated and bundled filaments. Further, Drosophila Dia nucleated actin assembly and protected growing filament barbed ends from capping protein. Drosophila APC1 and Dia directly interacted and collaborated to promote actin assembly in the combined presence of profilin and capping protein. Thus, despite limited sequence homology, Drosophila and vertebrate APCs exhibit highly related activities and mechanisms and directly collaborate with formins. These results suggest that APC-Dia interactions in actin assembly are conserved and may underlie important in vivo functions in a broad range of animal phyla. PMID:23558679

  7. Activation Barrier-Limited Folding and Conformational Sampling of a Dynamic Protein Domain.

    PubMed

    Dogan, Jakob; Toto, Angelo; Andersson, Eva; Gianni, Stefano; Jemth, Per

    2016-09-20

    Folding reaction mechanisms of globular protein domains have been extensively studied by both experiment and simulation and found to be highly concerted chemical reactions in which numerous noncovalent bonds form in an apparent two-state fashion. However, less is known regarding intrinsically disordered proteins because their folding can usually be studied only in conjunction with binding to a ligand. We have investigated by kinetics the folding mechanism of such a disordered protein domain, the nuclear coactivator-binding domain (NCBD) from CREB-binding protein. While a previous computational study suggested that NCBD folds without an activation free energy barrier, our experimental data demonstrate that NCBD, despite its highly dynamic structure, displays relatively slow folding (∼10 ms at 277 K) consistent with a barrier-limited process. Furthermore, the folding kinetics corroborate previous nuclear magnetic resonance data showing that NCBD exists in two folded conformations and one more denatured conformation at equilibrium and, thus, that the folding mechanism is a three-state mechanism. The refolding kinetics is limited by unfolding of the less populated folded conformation, suggesting that the major route for interconversion between the two folded states is via the denatured state. Because the two folded conformations have been suggested to bind distinct ligands, our results have mechanistic implications for conformational sampling in protein-protein interactions. PMID:27542287

  8. Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata

    PubMed Central

    Meijón, Mónica; Escandón, Mónica; Cañal, María Jesús

    2015-01-01

    Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species. PMID:25965766

  9. Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata.

    PubMed

    Valledor, Luis; Pascual, Jesús; Meijón, Mónica; Escandón, Mónica; Cañal, María Jesús

    2015-01-01

    Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species.

  10. Conservation Presentation.

    ERIC Educational Resources Information Center

    Friday, Gerald

    2001-01-01

    Introduces a project in which students teach about the importance of recycling and conservation by presenting demonstrations. Includes demonstrations on water, plastic, and other recycling products such as steel. (YDS)

  11. Dynamics of Folds in the Plane

    ERIC Educational Resources Information Center

    Krylov, Nikolai A.; Rogers, Edwin L.

    2011-01-01

    Take a strip of paper and fold a crease intersecting the long edges, creating two angles. Choose one edge and consider the angle with the crease. Fold the opposite edge along the crease, creating a new crease that bisects the angle. Fold again, this time using the newly created crease and the initial edge, creating a new angle along the chosen…

  12. Surgical revision of the upper eyelid fold.

    PubMed

    Cies, W A; Baylis, H I

    1975-12-01

    We performed surgery on 107 patients primarily with blepharoptosis and eyelid fold abnormalities, between 1973 and 1974. Production of an eyelid fold at the time of an initial blepharoptosis procedure should be a primary goal. Lack of a distinct symmetrical upper eyelid fold constituted a cosmetic blemish and necessitated revision.

  13. Towards a geomechanics classification of folded layered rock masses

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Zanchi, Andrea; Bianchi, Federico; Crosta, Giovanni B.

    2016-04-01

    Several schemes have been proposed in the last decades to account for the effects of structure and alteration of rock masses on their geo-mechanical properties. Among these, the Geological Strength Index (GSI) turned out as the most effective to account for complex geological conditions, including heavily fractured, heterogeneous (e.g. flysch-like) or tectonically disturbed rock masses. It is well known that folding has a direct impact on the type and degree of fracturing. Nevertheless, no classification scheme has been developed to introduce explicitly the effects of folding and associated fracturing on rock mass strength and deformability. In this perspective, we carried out an exploratory study aimed at establishing relationships between outcrop-scale folding and GSI in layered carbonate rock masses, exceptionally well exposed in a quarry near Bergamo (Lombardia, Southern Alps). A N-S trending, 350m long and 115m high benched rock face exposes a complete cross section of a sub-horizontal inclined fold involving Lower Jurassic cherty mudstones (Moltrasio Lms.) and marly limestones successions (Domaro Lms.). The main fold has an axial surface moderately dipping to the north and is characterised by polyharmonic folds at scales of metres to tens of metres. The site was documented by producing a digital outcrop through a high-resolution terrestrial photogrammetric survey from distances ranging from 70 to 130 m (18 camera stations, 395 pictures), using RTK GNSS measurements for camera station geo-referencing. Data processing by Structure-from-Motion (SfM) techniques resulted in detailed point clouds covering the entire slope with a cm-scale accuracy. In order to establish relationships between lithology, folding styles, and geomechanical properties of folded rock masses we performed a detailed structural analysis at 25 survey stations spread over all the different fold sectors. These surveys include: lithology, bedding attitude and thickness, brittle structures (e

  14. Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

    PubMed Central

    2015-01-01

    Background It is known that mRNA folding can affect and regulate various gene expression steps both in living organisms and in viruses. Previous studies have recognized functional RNA structures in the genome of the Dengue virus. However, these studies usually focused either on the viral untranslated regions or on very specific and limited regions at the beginning of the coding sequences, in a limited number of strains, and without considering evolutionary selection. Results Here we performed the first large scale comprehensive genomics analysis of selection for local mRNA folding strength in the Dengue virus coding sequences, based on a total of 1,670 genomes and 4 serotypes. Our analysis identified clusters of positions along the coding regions that may undergo a conserved evolutionary selection for strong or weak local folding maintained across different viral variants. Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized. In addition, up to 7% of these positions were found to be conserved in more than 90% of the viral genomes. Although some of the identified positions undergo frequent synonymous / non-synonymous substitutions, the selection for folding strength therein is preserved, and thus cannot be trivially explained based on sequence conservation alone. Conclusions The fact that many of the positions with significant folding related signals are conserved among different Dengue variants suggests that a better understanding of the mRNA structures in the corresponding regions may promote the development of prospective anti- Dengue vaccination strategies. The comparative genomics approach described here can be employed in the future for detecting functional regions in other pathogens with very high mutations rates. PMID:26449467

  15. Work done by titin protein folding assists muscle contraction

    PubMed Central

    Popa, Ionel; Kosuri, Pallav; Linke, Wolfgang A.; Fernández, Julio M.

    2016-01-01

    Current theories of muscle contraction propose that the power stroke of a myosin motor is the sole source of mechanical energy driving the sliding filaments of a contracting muscle. These models exclude titin, the largest protein in the human body, which determines the passive elasticity of muscles. Here, we show that stepwise unfolding/folding of titin Ig domains occurs in the elastic I band region of intact myofibrils at physiological sarcomere lengths and forces of 6-8 pN. We use single molecule techniques to demonstrate that unfolded titin Ig domains undergo a spontaneous stepwise folding contraction at forces below 10 pN, delivering up to 105 zJ of additional contractile energy, which is larger than the mechanical energy delivered by the power stroke of a myosin motor. Thus, it appears inescapable that folding of titin Ig domains is an important, but so far unrecognized contributor to the force generated by a contracting muscle. PMID:26854230

  16. Understanding Protein Non-Folding

    PubMed Central

    Uversky, Vladimir N.; Dunker, A. Keith

    2010-01-01

    This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: How were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? PMID:20117254

  17. Structural and Molecular Basis for the Novel Catalytic Mechanism and Evolution of DddP, an Abundant Peptidase-Like Bacterial Dimethylsulfoniopropionate Lyase: A New Enzyme from an Old Fold

    NASA Astrophysics Data System (ADS)

    Zhang, Y. Z.; Wang, P.; Chen, X. L.; Li, C. Y.; Gao, X.; Zhu, D.; Xie, B. B.; Qin, Q. L.; Zhang, X. Y.; Su, H. N.; Zhou, B. C.; Xun, L.

    2015-12-01

    The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO43- and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Further, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.

  18. Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.

    PubMed

    Wang, Peng; Chen, Xiu-Lan; Li, Chun-Yang; Gao, Xiang; Zhu, De-yu; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Su, Hai-Nan; Zhou, Bai-Cheng; Xun, Lu-ying; Zhang, Yu-Zhong

    2015-10-01

    The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria, and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds, but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO4 (3-) and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Furthermore, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production. PMID:26154071

  19. Folding of viscous sheets and filaments

    NASA Astrophysics Data System (ADS)

    Skorobogatiy, M.; Mahadevan, L.

    2000-12-01

    We consider the nonlinear folding behavior of a viscous filament or a sheet under the influence of an external force such as gravity. Everyday examples of this phenomenon are provided by the periodic folding of a sheet of honey as it impinges on toast, or the folding of a stream of shampoo as it falls on one's hand. To understand the evolution of a fold, we formulate and solve a free-boundary problem for the phenomenon, give scaling laws for the size of the folds and the frequency with which they are laid out, and verify these experimentally.

  20. Folding analysis of the most complex Stevedore's protein knot.

    PubMed

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  1. Material parameter computation for multi-layered vocal fold models.

    PubMed

    Schmidt, Bastian; Stingl, Michael; Leugering, Günter; Berry, David A; Döllinger, Michael

    2011-04-01

    Today, the prevention and treatment of voice disorders is an ever-increasing health concern. Since many occupations rely on verbal communication, vocal health is necessary just to maintain one's livelihood. Commonly applied models to study vocal fold vibrations and air flow distributions are self sustained physical models of the larynx composed of artificial silicone vocal folds. Choosing appropriate mechanical parameters for these vocal fold models while considering simplifications due to manufacturing restrictions is difficult but crucial for achieving realistic behavior. In the present work, a combination of experimental and numerical approaches to compute material parameters for synthetic vocal fold models is presented. The material parameters are derived from deformation behaviors of excised human larynges. The resulting deformations are used as reference displacements for a tracking functional to be optimized. Material optimization was applied to three-dimensional vocal fold models based on isotropic and transverse-isotropic material laws, considering both a layered model with homogeneous material properties on each layer and an inhomogeneous model. The best results exhibited a transversal-isotropic inhomogeneous (i.e., not producible) model. For the homogeneous model (three layers), the transversal-isotropic material parameters were also computed for each layer yielding deformations similar to the measured human vocal fold deformations.

  2. Anatomy and Histology of an Epicanthal Fold.

    PubMed

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  3. Geomorphology and fold growth, southern Tunisia.

    NASA Astrophysics Data System (ADS)

    Ahamadi, R.; Mercier, E.; Ouali, J.; van Vliet-Lanoë, B.; Mansy, J. L.; Launeau, P.; Rekis, F.

    2003-04-01

    At the northern edge of the Gafsa basin, a fold belt, the Metlaoui chain mostly rised from the Upper Miocene till today [1]. This region, endoreic since the Oligocene, is for lithologic and climate reasons a good laboratory to test various theories concerning fold growth. The origin of the fold belt is link to a main detachment level at the base of the Jurassic series (seismic profiles). The folding is facilitate with few strong calcareous beds by the dominance of soft lithologic series. This enhances the sliding along secondary detachment levels. Geomorphological, hydrological and chronological arguments prove that the folds mostly deformed as a "fault propagation fold" [2]. Furthermore, detailed field observations validate several features first observed by modelling of "fault propagation fold": 1) the stability of the roof of the fold, 2) the propagation of a knock-fold in front of the fold, disturbing the shape of pediments [3] and 3) the backward migration and extent of the backslope of the fold, in association with a backward migration of the depot centre of the syntectonic sedimentation. [1] Outtani, F., B. Addoum, E. Mercier, D. Frizon de Lamotte, J. Andrieux, Tectonophysics, 249, 233-248, 1995. [2] Suppe, J., and D.A. Medwedeff, , Eclogae geol. Helv., 83(3), 409-454, 1990. [3] Rafini S. and E. Mercier (2002). Sedimentary Geology, 146, 75-89

  4. STN1 OB Fold Mutation Alters DNA Binding and Affects Selective Aspects of CST Function

    PubMed Central

    Bhattacharjee, Anukana; Stewart, Jason; Chaiken, Mary; Price, Carolyn M.

    2016-01-01

    Mammalian CST (CTC1-STN1-TEN1) participates in multiple aspects of telomere replication and genome-wide recovery from replication stress. CST resembles Replication Protein A (RPA) in that it binds ssDNA and STN1 and TEN1 are structurally similar to RPA2 and RPA3. Conservation between CTC1 and RPA1 is less apparent. Currently the mechanism underlying CST action is largely unknown. Here we address CST mechanism by using a DNA-binding mutant, (STN1 OB-fold mutant, STN1-OBM) to examine the relationship between DNA binding and CST function. In vivo, STN1-OBM affects resolution of endogenous replication stress and telomere duplex replication but telomeric C-strand fill-in and new origin firing after exogenous replication stress are unaffected. These selective effects indicate mechanistic differences in CST action during resolution of different replication problems. In vitro binding studies show that STN1 directly engages both short and long ssDNA oligonucleotides, however STN1-OBM preferentially destabilizes binding to short substrates. The finding that STN1-OBM affects binding to only certain substrates starts to explain the in vivo separation of function observed in STN1-OBM expressing cells. CST is expected to engage DNA substrates of varied length and structure as it acts to resolve different replication problems. Since STN1-OBM will alter CST binding to only some of these substrates, the mutant should affect resolution of only a subset of replication problems, as was observed in the STN1-OBM cells. The in vitro studies also provide insight into CST binding mechanism. Like RPA, CST likely contacts DNA via multiple OB folds. However, the importance of STN1 for binding short substrates indicates differences in the architecture of CST and RPA DNA-protein complexes. Based on our results, we propose a dynamic DNA binding model that provides a general mechanism for CST action at diverse forms of replication stress. PMID:27690379

  5. Intermediates and the folding of proteins L and G

    SciTech Connect

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  6. Human variation in short regions predisposed to deep evolutionary conservation.

    PubMed

    Loots, Gabriela G; Ovcharenko, Ivan

    2010-06-01

    The landscape of the human genome consists of millions of short islands of conservation that are 100% conserved across multiple vertebrate genomes (termed "bricks"), the majority of which are located in noncoding regions. Several hundred thousand bricks are deeply conserved reaching the genomes of amphibians and fish. Deep phylogenetic conservation of noncoding DNA has been reported to be strongly associated with the presence of gene regulatory elements, introducing bricks as a proxy to the functional noncoding landscape of the human genome. Here, we report a significant overrepresentation of bricks in the promoters of transcription factors and developmental genes, where the high level of phylogenetic conservation correlates with an increase in brick overrepresentation. We also found that the presence of a brick dictates a predisposition to evolutionary constraint, with only 0.7% of the amniota brick central nucleotides being diverged within the primate lineage--an 11-fold reduction in the divergence rate compared with random expectation. Human single-nucleotide polymorphism (SNP) data explains only 3% of primate-specific variation in amniota bricks, thus arguing for a widespread fixation of brick mutations within the primate lineage and prior to human radiation. This variation, in turn, might have been utilized as a driving force for primate- and hominoid-specific adaptation. We also discovered a pronounced deviation from the evolutionary predisposition in the human lineage, with over 20-fold increase in the substitution rate at brick SNP sites over expected values. In addition, contrary to typical brick mutations, brick variation commonly encountered in the human population displays limited, if any, signatures of negative selection as measured by the minor allele frequency and population differentiation (F-statistical measure) measures. These observations argue for the plasticity of gene regulatory mechanisms in vertebrates--with evidence of strong purifying

  7. Pharyngeal wall fold influences on the collapsibility of the pharynx.

    PubMed

    Kairaitis, Kristina

    2012-09-01

    Obstructive sleep apnoea (OSA) is a disease that is characterised by recurrent pharyngeal obstruction during sleep. The pharynx is a hollow muscular tube lined with epithelium that performs the competing functions of breathing, where it is required to be open and swallowing where it is required to close. The mechanical process by which these large changes in luminal dimensions occur have not been considered, however in other biological tubes such as the oesophagus and the bronchial airways narrowing and closure occurs via folding of the mucosal surface. The transmural pressure (P) required to collapse a tube is related to the number of folds (n) formed during collapse by the equation P=n(2)-1, so that the more folds formed during narrowing and closure, the greater the transmural pressure required to collapse the tube. In biomechanical models, the bronchial airway is modelled as a 2-layer tube with an inner epithelial lining and an outer layer of muscle. These models predict that fold numbers will be reduced with thickening and stiffening of the outer layer, accompanied by an increase in collapsibility. We hypothesise that, similar to other biological tubes the pharynx narrows and closes via folding of the surface of the tube, and that the pharynx can also be modelled as a 2-layer tube. We further hypothesise that when compared to healthy subjects, subjects with OSA will have less pharyngeal wall folds during narrowing and closure, and that this reduction in fold numbers will contribute to an increase in pharyngeal collapsibility. In the absence of muscle activity, subjects with OSA have increased pharyngeal collapsibility when compared with healthy subjects, supporting an anatomical contribution to pharyngeal collapse. Histopathological studies of the pharyngeal epithelium in subjects with OSA demonstrate that, compared with age matched subjects, there is thickening of the epithelial surface with oedema of the submucosal layer, with a loss of tethering of the

  8. Conserved mechanism of PLAG1 activation in salivary gland tumors with and without chromosome 8q12 abnormalities: identification of SII as a new fusion partner gene.

    PubMed

    Aström, A K; Voz, M L; Kas, K; Röijer, E; Wedell, B; Mandahl, N; Van de Ven, W; Mark, J; Stenman, G

    1999-02-15

    chromosomal translocations and cryptic rearrangements, PLAG1 may also be activated by mutations or indirect mechanisms. Our findings establish a conserved mechanism of PLAG1 activation in salivary gland tumors with and without 8q12 aberrations, which indicates that such activation is a frequent event in these tumors.

  9. Folding of synthetic homogeneous glycoproteins in the presence of a glycoprotein folding sensor enzyme.

    PubMed

    Dedola, Simone; Izumi, Masayuki; Makimura, Yutaka; Seko, Akira; Kanamori, Akiko; Sakono, Masafumi; Ito, Yukishige; Kajihara, Yasuhiro

    2014-03-10

    UDP-glucose:glycoprotein glucosyltransferase (UGGT) plays a key role in recognizing folded and misfolded glycoproteins in the glycoprotein quality control system of the endoplasmic reticulum. UGGT detects misfolded glycoproteins and re-glucosylates them as a tag for misfolded glycoproteins. A flexible model to reproduce in vitro folding of a glycoprotein in the presence of UGGT in a mixture containing correctly folded, folding intermediates, and misfolded glycoproteins is described. The data demonstrates that UGGT can re-glucosylate all intermediates in the in vitro folding experiments, thus indicating that UGGT inspects not only final folded products, but also the glycoprotein folding intermediates.

  10. Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania).

    PubMed

    Mikó, István; Copeland, Robert S; Balhoff, James P; Yoder, Matthew J; Deans, Andrew R

    2014-01-01

    We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea). It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves.

  11. Folding Wings like a Cockroach: A Review of Transverse Wing Folding Ensign Wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania)

    PubMed Central

    Mikó, István; Copeland, Robert S.; Balhoff, James P.; Yoder, Matthew J.; Deans, Andrew R.

    2014-01-01

    We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea). It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves. PMID:24787704

  12. Conserved methionines in chloroplasts.

    PubMed

    Sundby, Cecilia; Härndahl, Ulrika; Gustavsson, Niklas; Ahrman, Emma; Murphy, Denis J

    2005-01-17

    Heat shock proteins counteract heat and oxidative stress. In chloroplasts, a small heat shock protein (Hsp21) contains a set of conserved methionines, which date back to early in the emergence of terrestrial plants. Methionines M49, M52, M55, M59, M62, M67 are located on one side of an amphipathic helix, which may fold back over two other conserved methionines (M97 and M101), to form a binding groove lined with methionines, for sequence-independent recognition of peptides with an overall hydrophobic character. The sHsps protect other proteins from aggregation by binding to their hydrophobic surfaces, which become exposed under stress. Data are presented showing that keeping the conserved methionines in Hsp21 in a reduced form is a prerequisite to maintain such binding. The chloroplast generates reactive oxygen species under both stress and unstressed conditions, but this organelle is also a highly reducing cellular compartment. Chloroplasts contain a specialized isoform of the enzyme, peptide methionine sulfoxide reductase, the expression of which is light-induced. Recombinant proteins were used to measure that this reductase can restore Hsp21 methionines after sulfoxidation. This paper also describes how methionine sulfoxidation-reduction can be directly assessed by mass spectrometry, how methionine-to-leucine substitution affects Hsp21, and discusses the possible role for an Hsp21 methionine sulfoxidation-reduction cycle in quenching reactive oxygen species. PMID:15680227

  13. Folds with vergence opposite to the sense of shear

    NASA Astrophysics Data System (ADS)

    Krabbendam, M.; Leslie, A. G.

    1996-06-01

    Near-similar folds with persistent NW-vergence occur in the southeast Highlands of Scotland and are interpreted to have formed in a regime of SE-directed non-coaxial shear. The sense of shear is corroborated by independent kinematic indicators. The folds are formed by a mechanism in which strongly partitioned shear produced an alternation of high strain zones, forming long limbs, and low strain zones, forming short limbs. Progressive strain results in the rotation and attenuation of strain markers in the long limbs and in the consumption of low strain zones. High strain may ultimately lead to the disappearance of the short limbs.

  14. Influence of glycosaminoglycan identity on vocal fold fibroblast behavior.

    PubMed

    Jimenez-Vergara, Andrea Carolina; Munoz-Pinto, Dany J; Becerra-Bayona, Silvia; Wang, Bo; Iacob, Alexandra; Hahn, Mariah S

    2011-11-01

    Poly(ethylene glycol) (PEG) hydrogels have recently begun to be studied for the treatment of scarred vocal fold lamina propria due, in part, to their tunable mechanical properties, resistance to fibroblast-mediated contraction, and ability to be polymerized in situ. However, pure PEG gels lack intrinsic biochemical signals to guide cell behavior and generally fail to mimic the frequency-dependent viscoelastic response critical to normal superficial lamina propria function. Recent results suggest that incorporation of viscoelastic bioactive substances, such as glycosaminoglycans (GAGs), into PEG networks may allow these gels to more closely approach the mechanical responses of normal vocal fold lamina propria while also stimulating desired vocal fold fibroblast behaviors. Although a number of vocal fold studies have examined the influence of hyaluronan (HA) on implant mechanics and vocal fold fibroblast responses, the effects of other GAG types have been relatively unexplored. This is significant, since recent studies have suggested that chondroitin sulfate C (CSC) and heparan sulfate (HS) are substantially altered in scarred lamina propria. The present study was therefore designed to evaluate the effects of CSC and HS incorporation on the mechanical response of PEG gels and vocal fold fibroblast behavior relative to HA. As with PEG-HA, the viscoelasticity of PEG-CSC and PEG-HS gels more closely approached that of the normal vocal fold lamina propria than pure PEG hydrogels. In addition, collagen I deposition and fibronectin production were significantly higher in CSC than in HA gels, and levels of the myofibroblast marker smooth muscle α-actin (SM α-actin) were greater in CSC and HS gels than in HA gels. Since collagen I, fibronectin, and SM α-actin are generally elevated in scarred lamina propria these results suggest that CSC and HS may be undesirable for vocal fold implants relative to HA. Investigation of various signaling intermediates indicated that

  15. Observation of Pollution Plume Capping by a Tropopause Fold

    NASA Technical Reports Server (NTRS)

    Cho, John Y. N.; Newell, Reginald E.; Browell, Edward V.; Grant, William B.; Butler, Carolyn F.; Fenn, Marta A.

    2001-01-01

    Airborne lidar measurements reveal a case in which a layer of high-ozone air extruding from a tropopause fold appears to cap a pollution plume and force it to spread out in the lower troposphere. The morphology of the high-ozone layer resembles a three-dimensional model of tropopause fold evolution that produces a low-altitude potential vorticity tube. This is a mechanism that can complete the irreversible transfer of air from the stratosphere, and can also affect pollution levels at the surface if the capping layer reaches the top of the boundary layer.

  16. Influence of glycosaminoglycan identity on vocal fold fibroblast behavior

    PubMed Central

    Jimenez-Vergara, Andrea Carolina; Munoz-Pinto, Dany J.; Becerra-Bayona, Silvia; Wang, Bo; Iacob, Alexandra; Hahn, Mariah S.

    2011-01-01

    Poly(ethylene glycol) (PEG) hydrogels have recently begun to be explored for the treatment of scarred vocal fold lamina propria due, in part, to their tunable mechanical properties, resistance to fibroblast-mediated contraction, and ability to be polymerized in situ. However, pure PEG gels lack intrinsic biochemical signals to guide cell behavior and generally fail to mimic the frequency-dependent viscoelastic response critical to normal superficial lamina propria function. Recent results suggest that incorporation of viscoelastic, bioactive substances, such as glycosaminoglycans (GAGs), into PEG networks may allow these gels to more closely approach the mechanical responses of normal vocal fold lamina propria while also stimulating desired vocal fold fibroblast behaviors. Although a number of vocal fold studies have examined the influence of hyaluronan (HA) on implant mechanics and vocal fold fibroblast responses, the effects of remaining GAG types have been relatively unexplored. This is significant since recent studies suggest that chondroitin sulfate C (CSC) and heparan sulfate (HS) are substantially altered in lamina propria scar. The present study was therefore designed to evaluate the effects of CSC and HS incorporation on PEG gel mechanical response and vocal fold fibroblast behavior relative to HA. As with PEG-HA, the viscoelasticity of PEG-CSC and PEG-HS gels more closely approached that of the normal vocal fold lamina propria than pure PEG hydrogels. In addition, collagen I deposition and fibronectin production were significantly higher in CSC than in HA gels, and levels myofibroblast marker SM-α-actin were greater in CSC and HS gels than in HA gels. Since collagen I, fibronectin, and SM-α-actin are generally elevated in lamina propria scar, these results suggest that CSC and HS may be undesirable for vocal fold implants relative to HA. Investigation of various signaling intermediates indicated that alterations in NFκB-p50, NFκB-p65, or pERK1

  17. Energy Conservation.

    ERIC Educational Resources Information Center

    Land, Amy A.

    This selection of class activities involves a sequence of 10 class sessions. The goal of the collection is to aid students in learning the concepts of energy conservation and to put this knowledge into practice. Attention is also given to the development of alternate energy sources. Each lesson includes an activity title, motivational hints,…

  18. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Instructional units deal with each aspect of conservation: forests, wildlife, rangelands, water, minerals, and soil. The area of the secondary school curriculum with which each is correlated is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the topic, questions to…

  19. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  20. Colorful Conservation

    ERIC Educational Resources Information Center

    Skophammer, Karen

    2011-01-01

    Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

  1. On the universe of protein folds.

    PubMed

    Kolodny, Rachel; Pereyaslavets, Leonid; Samson, Abraham O; Levitt, Michael

    2013-01-01

    In the fifty years since the first atomic structure of a protein was revealed, tens of thousands of additional structures have been solved. Like all objects in biology, proteins structures show common patterns that seem to define family relationships. Classification of proteins structures, which started in the 1970s with about a dozen structures, has continued with increasing enthusiasm, leading to two main fold classifications, SCOP and CATH, as well as many additional databases. Classification is complicated by deciding what constitutes a domain, the fundamental unit of structure. Also difficult is deciding when two given structures are similar. Like all of biology, fold classification is beset by exceptions to all rules. Thus, the perspectives of protein fold space that the fold classifications offer differ from each other. In spite of these ambiguities, fold classifications are useful for prediction of structure and function. Studying the characteristics of fold space can shed light on protein evolution and the physical laws that govern protein behavior.

  2. Dimerization of doublesex is mediated by a cryptic ubiquitin-associated domain fold: implications for sex-specific gene regulation.

    PubMed

    Bayrer, James R; Zhang, Wei; Weiss, Michael A

    2005-09-23

    Male- and female-specific isoforms of the Doublesex (DSX) transcription factor regulate somatic sexual differentiation in Drosophila. The isoforms (DSX(M) and DSX(F)) share an N-terminal DNA binding domain (the DM motif), broadly conserved among metazoan sex-determining pathways. DM-DNA recognition is enhanced by a C-terminal dimerization domain. The crystal structure of this domain, determined at a resolution of 1.6 A, reveals a novel dimeric arrangement of ubiquitin-associated (UBA) folds. Although this alpha-helical motif is well characterized in pathways of DNA repair and subcellular trafficking, to our knowledge this is its first report in a transcription factor. Dimerization is mediated by a non-canonical hydrophobic interface extrinsic to the putative ubiquitin binding surface. Key side chains at this interface, identified by alanine scanning mutagenesis, are conserved among DSX homologs. The mechanism of dimerization is thus unrelated to the low affinity domain swapping observed among ubiquitin-associated CUE domains. The unexpected observation of a ubiquitin-associated fold in DSX extends the repertoire of alpha-helical dimerization elements in transcription factors. The possibility that the ubiquitination machinery participates in the regulation of sexual dimorphism is discussed. PMID:16049008

  3. Acquired retinal folds in the cat.

    PubMed

    MacMillan, A D

    1976-06-01

    Retinal folds were found in 5 cats. The apparent cause of the folding was varied: in 1 cat the folds appeared after a localized retinal detachment; in 2 cats the condition accompanied other intraocular abnormalities associated with feline infectious peritonitis; 1 cat had active keratitis, and the retinal changes were thought to have been injury related; and 1 cat, bilaterally affected, had chronic glomerulonephritis. PMID:945253

  4. Differential conformational modulations of MreB folding upon interactions with GroEL/ES and TRiC chaperonin components

    PubMed Central

    Moparthi, Satish Babu; Carlsson, Uno; Vincentelli, Renaud; Jonsson, Bengt-Harald; Hammarström, Per; Wenger, Jérôme

    2016-01-01

    Here, we study and compare the mechanisms of action of the GroEL/GroES and the TRiC chaperonin systems on MreB client protein variants extracted from E. coli. MreB is a homologue to actin in prokaryotes. Single-molecule fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence polarization anisotropy report the binding interaction of folding MreB with GroEL, GroES and TRiC. Fluorescence resonance energy transfer (FRET) measurements on MreB variants quantified molecular distance changes occurring during conformational rearrangements within folding MreB bound to chaperonins. We observed that the MreB structure is rearranged by a binding-induced expansion mechanism in TRiC, GroEL and GroES. These results are quantitatively comparable to the structural rearrangements found during the interaction of β-actin with GroEL and TRiC, indicating that the mechanism of chaperonins is conserved during evolution. The chaperonin-bound MreB is also significantly compacted after addition of AMP-PNP for both the GroEL/ES and TRiC systems. Most importantly, our results showed that GroES may act as an unfoldase by inducing a dramatic initial expansion of MreB (even more than for GroEL) implicating a role for MreB folding, allowing us to suggest a delivery mechanism for GroES to GroEL in prokaryotes. PMID:27328749

  5. COS Side 2 NUV MAMA Fold Test

    NASA Astrophysics Data System (ADS)

    Bacinski, John

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {13128} during Cycle 20.This proposal is an exact duplication of nominal COS MAMA Fold Analysis {proposal 13128, Cycle 20}. Any changes 13128 or subsequent cycle submissions should be reflected in this proposal and vice versa.

  6. Functional stimuli responsive hydrogel devices by self-folding

    NASA Astrophysics Data System (ADS)

    Yoon, ChangKyu; Xiao, Rui; Park, JaeHyun; Cha, Jaepyeong; Nguyen, Thao D.; Gracias, David H.

    2014-09-01

    We describe a photolithographic approach to create functional stimuli responsive, self-folding, microscale hydrogel devices using thin, gradient cross-linked hinges and thick, fully cross-linked panels. The hydrogels are composed of poly (N-isopropylacrylamide-co-acrylic acid) (pNIPAM-AAc) with reversible stimuli responsive properties just below physiological temperatures. We show that a variety of three-dimensional structures can be formed and reversibly actuated by temperature or pH. We experimentally characterized the swelling and mechanical properties of pNIPAM-AAc and developed a finite element model to rationalize self-folding and its variation with hinge thickness and swelling ratio. Finally, we highlight applications of this approach in the creation of functional devices such as self-folding polymeric micro-capsules, untethered micro-grippers and thermally steered micro-mirror systems.

  7. Energy landscape exploration of the folding processes of biological molecules

    NASA Astrophysics Data System (ADS)

    Engel, Megan Clare

    For decades, scientists from every discipline have struggled to understand the mechanism of biological self-assembly, which allows proteins and nucleic acids to fold reliably into functional three-dimensional structures. Such an understanding may hold the key to eliminating diseases such as Alzheimer's and Parkinson's and to effective protein engineering. The current best framework for describing biological folding processes is that of statistical mechanical energy landscape theory, and one of the most promising experimental techniques for exploring molecular energy landscapes is single molecule force spectroscopy (SMFS), in which molecules are mechanically denatured. Theoretical advances have enabled the extraction of complete energy landscape profiles from SMFS data. Here, SMFS experiments performed using laser optical tweezers are analyzed to yield the first ever full landscape profile for an RNA pseudoknot. Further, a promising novel landscape reconstruction technique is validated for the first time using experimental data from a DNA hairpin.

  8. An overview of protein-folding techniques: issues and perspectives.

    PubMed

    Sikder, Abdur Rahman; Zomaya, Albert Y

    2005-01-01

    The importance of protein folding has been recognised for many years. Almost a half century ago, Linus Pauling discovered two quite simple, regular arrangements of amino acids--the alpha-helix and the beta-sheet that are found in almost every protein. In the early 1960s, Christian Anfinsen showed that the proteins actually "tie" themselves: If proteins become unfolded, they fold back into proper shape of their own accord; no shaper or folder is needed. The nature of the unfolded state plays a great role in understanding proteins. Alzheimer's disease, cystic fibrosis, mad cow disease, and many cancers are inherited emphysema. Recent discoveries show that all these apparently unrelated diseases result from protein folding gone wrong. Theoretical and computational studies have recently achieved noticeable success in reproducing various features of the folding mechanism of several small to medium-sized fast-folding proteins. This survey presents the state-of-the-art in protein structure prediction methods from a computer scientist perspective. PMID:18048125

  9. Adhesion and friction control localized folding in supported graphene

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Arroyo, M.

    2013-05-01

    Graphene deposited on planar surfaces often exhibits sharp and localized folds delimiting seemingly planar regions, as a result of compressive stresses transmitted by the substrate. Such folds alter the electronic and chemical properties of graphene, and therefore, it is important to understand their emergence, to either suppress them or control their morphology. Here, we study the emergence of out-of-plane deformations in supported and laterally strained graphene with high-fidelity simulations and a simpler theoretical model. We characterize the onset of buckling and the nonlinear behavior after the instability in terms of the adhesion and frictional material parameters of the graphene-substrate interface. We find that localized folds evolve from a distributed wrinkling linear instability due to the nonlinearity in the van der Waals graphene-substrate interactions. We identify friction as a selection mechanism for the separation between folds, as the formation of far apart folds is penalized by the work of friction. Our systematic analysis is a first step towards strain engineering of supported graphene, and is applicable to other compressed thin elastic films weakly coupled to a substrate.

  10. Molecular Dynamics of Peptide Folding at Aqueous Interfaces

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Chipot, Christophe; Chang, Sherwood (Technical Monitor)

    1997-01-01

    Even though most monomeric peptides are disordered in water they can adopt sequence-dependent, ordered structures, such as a-helices, at aqueous interfaces. This property is relevant to cellular signaling, membrane fusion, and the action of toxins and antibiotics. The mechanism of folding nonpolar peptides at the water-hexane interface was studied in the example of an 11-mer, of poly-L-leucine. Initially placed as a random coil on the water side of the interface, the peptide folded into an a-helix in 36 ns. Simultaneously, the peptide translocated into the hexane side of the interface. Folding was not sequential and involved a 3/10-helix as an intermediate. The folded peptide was either parallel to the interface or had its C-terminus exposed to water. An 11-mer, LQQLLQQLLQL, composed of leucine (L) and glutamine (G), was taken as a model amphiphilic peptide. It rapidly adopted an amphiphilic, disordered structure at the interface. Further folding proceeded through a series of amphiphilic intermediates.

  11. Guiding the folding pathway of DNA origami

    NASA Astrophysics Data System (ADS)

    Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.; Kwiatkowska, Marta; Turberfield, Andrew J.; Bath, Jonathan

    2015-09-01

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short `staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  12. Retinal and Choroidal Folds in Papilledema

    PubMed Central

    Sibony, Patrick A.; Kupersmith, Mark J.; Feldon, Steven E.; Wang, Jui-Kai; Garvin, Mona

    2015-01-01

    Purpose To determine the frequency, patterns, associations, and biomechanical implications of retinal and choroidal folds in papilledema due to idiopathic intracranial hypertension (IIH). Methods Retinal and choroidal folds were studied in patients enrolled in the IIH Treatment Trial using fundus photography (n = 165 study eyes) and spectral-domain optical coherence tomography (SD-OCT; n = 125). We examined the association between folds and peripapillary shape, retinal nerve fiber layer (RNFL) thickness, disc volume, Frisén grade, acuity, perimetric mean deviation, intraocular pressure, intracranial pressure, and refractive error. Results We identified three types of folds in IIH patients with papilledema: peripapillary wrinkles (PPW), retinal folds (RF), and choroidal folds (CF). Frequency, with photos, was 26%, 19%, and 1%, respectively; SD-OCT frequency was 46%, 47%, and 10%. At least one type of fold was present in 41% of patients with photos and 73% with SD-OCT. Spectral-domain OCT was more sensitive. Structural parameters related to the severity of papilledema were associated with PPW and RF, whereas anterior deformation of the peripapillary RPE/basement membrane layer was associated with CF and RF. Folds were not associated with vision loss at baseline. Conclusions Folds in papilledema are biomechanical signs of stress/strain on the optic nerve head and load-bearing structures induced by intracranial hypertension. Folds are best imaged with SD-OCT. The patterns of retinal and choroidal folds are the products of a complex interplay between the degree of papilledema and anterior deformation of the load-bearing structures (sclera and possibly the lamina cribrosa), both modulated by structural geometry and material properties of the optic nerve head. (ClinicalTrials.gov number, NCT01003639.) PMID:26335066

  13. What protein folding teaches us about biological function and molecular machines.

    PubMed

    Whitford, Paul C; Onuchic, José N

    2015-02-01

    Protein folding was the first area of molecular biology for which a systematic statistical-mechanical analysis of dynamics was developed. As a result, folding is described as a process by which a disordered protein chain diffuses across a high-dimensional energy landscape and finally reaches the folded ensemble. Folding studies have produced countless theoretical concepts that are generalizable to other biomolecular processes, such as the functional dynamics of molecular assemblies. Common themes in folding and function include the dominant role of excluded volume, that a balance between energetic roughness and geometrical effects guides dynamics, and that folding/functional landscapes are relatively smooth. Here, we discuss how insights into protein folding have been applied to investigate the functional dynamics of biomolecular assemblies.

  14. Heron conservation

    USGS Publications Warehouse

    Kushlan, J.A.; Hafner, H.

    2000-01-01

    Herons are large, popular and, in many cases, spectacular birds found in wetlands world-wide, both tropical and temperate, natural and man-made. Some populations are very small and localized, some have decreased, some have expanded their ranges, and a few are pests of human activities. In the fifteen years since the publication of the latest monographic treatment of the family, The Herons Handbook, there has been a tremendous increase in our knowledge of heron status and conservation requirements, set against a backdrop of increasing concern about the future of the world?s wetland habitats. This book provides a comprehensive update following two distinct threads. The status and conservation needs of herons are first presented on a regional basis, in a series of chapters set at a continental or subcontinental scale. Over 200 biologists and heron conservationists have contributed to the data summarized here, and the very latest census and survey results provide the most up-to-date and detailed picture of heron populations currently available. Chapters discussing several critical issues in heron conservation follow, tending to focus on the international nature of the problems.

  15. CFTR Folding Consortium: Methods Available for Studies of CFTR Folding and Correction

    PubMed Central

    Peters, Kathryn W.; Okiyoneda, Tsukasa; Balch, William E.; Braakman, Ineke; Brodsky, Jeffrey L.; Guggino, William B.; Penland, Christopher M.; Pollard, Harvey B.; Sorscher, Eric J.; Skach, William R.; Thomas, Philip J.; Lukacs, Gergely L.; Frizzell, Raymond A.

    2012-01-01

    The CFTR Folding Consortium (CFC) was formed in 2004 under the auspices of the Cystic Fibrosis Foundation and its drug discovery and development affiliate, CFF Therapeutics. A primary goal of the CFC is the development and distribution of reagents and assay methods designed to better understand the mechanistic basis of mutant CFTR misfolding and to identify targets whose manipulation may correct CFTR folding defects. As such, reagents available from the CFC primarily target wild-type CFTR NBD1 and its common variant, F508del, and they include antibodies, cell lines, constructs, and proteins. These reagents are summarized here, and two protocols are described for the detection of cell surface CFTR: (a) an assay of the density of expressed HA-tagged CFTR by ELISA and (b) the generation and use of an antibody to CFTR’s first extracellular loop for the detection of endogenous CFTR. Finally, we highlight a systematic collection of assays, the CFC Roadmap, which is being used to assess the cellular locus and mechanism of mutant CFTR correction. The Roadmap queries CFTR structure–function relations at levels ranging from purified protein to well-differentiated human airway primary cultures. PMID:21547742

  16. Simultaneous Alignment and Folding of Protein Sequences

    PubMed Central

    Waldispühl, Jérôme; O'Donnell, Charles W.; Will, Sebastian; Devadas, Srinivas; Backofen, Rolf

    2014-01-01

    Abstract Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/). PMID:24766258

  17. Protein folding: When ribosomes pick the structure

    NASA Astrophysics Data System (ADS)

    Sivertsson, Elin M.; Itzhaki, Laura S.

    2014-05-01

    Anfinsen's principle tells us that the folded structure of a protein is determined solely by its sequence. Now, it has been shown that the rate at which a polypeptide chain is synthesized in the cell can affect which of two alternative folded structures it adopts.

  18. Folding Polyominoes from One Level to Two

    ERIC Educational Resources Information Center

    Frederickson, Greg N.

    2011-01-01

    For any given polyomino, is it possible to cut it into pieces and then hinge the pieces, so that the polyomino folds up into a similar version of itself but two levels thick? While we don't know how to do this for every polyomino, the article does show how to cut, hinge, and fold polyominoes from several infinite classes, providing an…

  19. Substrate protein folds while it is bound to the ATP-independent chaperone Spy.

    PubMed

    Stull, Frederick; Koldewey, Philipp; Humes, Julia R; Radford, Sheena E; Bardwell, James C A

    2016-01-01

    Chaperones assist in the folding of many proteins in the cell. Although the most well-studied chaperones use cycles of ATP binding and hydrolysis to assist in protein folding, a number of chaperones have been identified that promote folding in the absence of high-energy cofactors. Precisely how ATP-independent chaperones accomplish this feat is unclear. Here we characterized the kinetic mechanism of substrate folding by the small ATP-independent chaperone Spy from Escherichia coli. Spy rapidly associates with its substrate, immunity protein 7 (Im7), thereby eliminating Im7's potential for aggregation. Remarkably, Spy then allows Im7 to fully fold into its native state while it remains bound to the surface of the chaperone. These results establish a potentially widespread mechanism whereby ATP-independent chaperones assist in protein refolding. They also provide compelling evidence that substrate proteins can fold while being continuously bound to a chaperone. PMID:26619265

  20. Substrate protein folds while it is bound to the ATP-independent chaperone Spy.

    PubMed

    Stull, Frederick; Koldewey, Philipp; Humes, Julia R; Radford, Sheena E; Bardwell, James C A

    2016-01-01

    Chaperones assist in the folding of many proteins in the cell. Although the most well-studied chaperones use cycles of ATP binding and hydrolysis to assist in protein folding, a number of chaperones have been identified that promote folding in the absence of high-energy cofactors. Precisely how ATP-independent chaperones accomplish this feat is unclear. Here we characterized the kinetic mechanism of substrate folding by the small ATP-independent chaperone Spy from Escherichia coli. Spy rapidly associates with its substrate, immunity protein 7 (Im7), thereby eliminating Im7's potential for aggregation. Remarkably, Spy then allows Im7 to fully fold into its native state while it remains bound to the surface of the chaperone. These results establish a potentially widespread mechanism whereby ATP-independent chaperones assist in protein refolding. They also provide compelling evidence that substrate proteins can fold while being continuously bound to a chaperone.

  1. Folded Supersymmetry and the LDP Paradox

    SciTech Connect

    Burdman, Gustavo; Chacko, Z.; Goh, Hock-Seng; Harnik, Roni

    2006-09-21

    We present a new class of models that stabilize the weak scale against radiative corrections up to scales of order 5 TeV without large corrections to precision electroweak observables. In these ''folded supersymmetric'' theories the one loop quadratic divergences of the Standard Model Higgs field are canceled by opposite spin partners, but the gauge quantum numbers of these new particles are in general different from those of the conventional superpartners. This class of models is built around the correspondence that exists in the large N limit between the correlation functions of supersymmetric theories and those of their non-supersymmetric orbifold daughters. By identifying the mechanism which underlies the cancellation of one loop quadratic divergences in these theories, we are able to construct simple extensions of the Standard Model which are radiatively stable at one loop. Ultraviolet completions of these theories can be obtained by imposing suitable boundary conditions on an appropriate supersymmetric higher dimensional theory compactified down to four dimensions. We construct a specific model based on these ideas which stabilizes the weak scale up to about 20 TeV and where the states which cancel the top loop are scalars not charged under Standard Model color. Its collider signatures are distinct from conventional supersymmetric theories and include characteristic events with hard leptons and missing energy.

  2. Similarities between protein folding and granular jamming

    PubMed Central

    Jose, Prasanth P; Andricioaei, Ioan

    2012-01-01

    Grains and glasses, widely different materials, arrest their motions upon decreasing temperature and external load, respectively, in common ways, leading to a universal jamming phase diagram conjecture. However, unified theories are lacking, mainly because of the disparate nature of the particle interactions. Here we demonstrate that folded proteins exhibit signatures common to both glassiness and jamming by using temperature- and force-unfolding molecular dynamics simulations. Upon folding, proteins develop a peak in the interatomic force distributions that falls on a universal curve with experimentally measured forces on jammed grains and droplets. Dynamical signatures are found as a dramatic slowdown of stress relaxation upon folding. Together with granular similarities, folding is tied not just to the jamming transition, but a more nuanced picture of anisotropy, preparation protocol and internal interactions emerges. Results have implications for designing stable polymers and can open avenues to link protein folding to jamming theory. PMID:23093180

  3. Geometry and wetting of capillary folding.

    PubMed

    Péraud, Jean-Philippe; Lauga, Eric

    2014-04-01

    Capillary forces are involved in a variety of natural phenomena, ranging from droplet breakup to the physics of clouds. The forces from surface tension can also be exploited in industrial applications provided the length scales involved are small enough. Recent experimental investigations showed how to take advantage of capillarity to fold planar structures into three-dimensional configurations by selectively melting polymeric hinges joining otherwise rigid shapes. In this paper we use theoretical calculations to quantify the role of geometry and fluid wetting on the final folded state. Considering folding in two and three dimensions, studying both hydrophilic and hydrophobic situations with possible contact-angle hysteresis, and addressing the shapes to be folded to be successively infinite, finite, curved, kinked, and elastic, we are able to derive an overview of the geometrical parameter space available for capillary folding.

  4. Prediction of sound from human vocal folds

    NASA Astrophysics Data System (ADS)

    Bodony, Daniel; Luo, Haoxiang; Mittal, Rajat

    2007-11-01

    The creation of voiced sounds in humans depends on the flow-induced vibration of the vocal folds within the larynx. The vocal folds, which are a complex structural system of cartilage and tissue, create an oscillatory ``glottal jet'' whose harmonic content partially determines the tone of the speech. In this work we will discuss the process of sound generation in the laynx by combining a fully coupled two-dimensional fluid-structure simulation of the incompressible flow field in the vicinity of the vocal folds to an acoustic analogy description of the sound field. The structural dynamics of the vocal folds are based on physically realistic properties and are coupled to the motion of the fluid via an immersed boundary method. Relationships between the sound produced and the vocal fold dynamics will be discussed.

  5. Visualizing chaperone-assisted protein folding.

    PubMed

    Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S; Martin, Raoul; Quan, Shu; Afonine, Pavel V; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C; Brooks, Charles L; Bardwell, James C A

    2016-07-01

    Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone. PMID:27239796

  6. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  7. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, R.R.; Cowan, T.E.

    1996-06-11

    Disclosed are fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figs.

  8. Folding and Finding RNA Secondary Structure

    PubMed Central

    Mathews, David H.; Moss, Walter N.; Turner, Douglas H.

    2010-01-01

    SUMMARY Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed. PMID:20685845

  9. The robustness and innovability of protein folds.

    PubMed

    Tóth-Petróczy, Agnes; Tawfik, Dan S

    2014-06-01

    Assignment of protein folds to functions indicates that >60% of folds carry out one or two enzymatic functions, while few folds, for example, the TIM-barrel and Rossmann folds, exhibit hundreds. Are there structural features that make a fold amenable to functional innovation (innovability)? Do these features relate to robustness--the ability to readily accumulate sequence changes? We discuss several hypotheses regarding the relationship between the architecture of a protein and its evolutionary potential. We describe how, in a seemingly paradoxical manner, opposite properties, such as high stability and rigidity versus conformational plasticity and structural order versus disorder, promote robustness and/or innovability. We hypothesize that polarity--differentiation and low connectivity between a protein's scaffold and its active-site--is a key prerequisite for innovability.

  10. Cortical Folding Pattern and its Consistency Induced by Biological Growth

    NASA Astrophysics Data System (ADS)

    Jalil Razavi, Mir; Zhang, Tuo; Liu, Tianming; Wang, Xianqiao

    2015-09-01

    Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s convoluted patterns can provide useful clues into normal and pathological brain function. In this paper, the cortical folding phenomenon is interpreted both analytically and computationally, and, in some cases, the findings are validated with experimental observations. The living human brain is modeled as a soft structure with a growing outer cortex and inner core to investigate its developmental mechanism. Analytical interpretations of differential growth of the brain model provide preliminary insight into critical growth ratios for instability and crease formation of the developing brain. Since the analytical approach cannot predict the evolution of cortical complex convolution after instability, non-linear finite element models are employed to study the crease formation and secondary morphological folds of the developing brain. Results demonstrate that the growth ratio of the cortex to core of the brain, the initial thickness, and material properties of both cortex and core have great impacts on the morphological patterns of the developing brain. Lastly, we discuss why cortical folding is highly correlated and consistent by presenting an intriguing gyri-sulci formation comparison.

  11. A study of Barstar folding events using boundary value simulations

    NASA Astrophysics Data System (ADS)

    Yunger, Jacob

    2007-12-01

    From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar-a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL-stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.

  12. [Protein structure: Folding and prions].

    PubMed

    Rey-Gayo, Antonio; Calbo Torrecilla, Francisco

    2002-04-01

    Transmissible spongiform encephalopathies have become a subject of prime social concern in recent years because of its relation to "mad cow disease" and their potential for transmission to humans. Among the most important scientific aspects of these diseases are the peculiar characteristics of the agent involved in their transmission. In this article we briefly describe the outstanding features of prions, the most widely accepted hypothesis for these diseases. We focus on the molecular characteristics of this protein, coded in the genome of the affected host, and describe the conformational alterations in the protein's tertiary structure that have been blamed for its pathologic activity. Our aim is to summarize the state-of-the-art knowledge on prions, the hypotheses proposed to explain mechanisms of disease transmission without agents containing genetic material, and some specific peculiarities of this new infectious agent. The links between this knowledge and possible therapeutic strategies to overcome the disease justify, once again, close interaction among chemistry, molecular biology, and medicine. PMID:11996702

  13. Construction and characterization of a novel vocal fold bioreactor.

    PubMed

    Zerdoum, Aidan B; Tong, Zhixiang; Bachman, Brendan; Jia, Xinqiao

    2014-01-01

    In vitro engineering of mechanically active tissues requires the presentation of physiologically relevant mechanical conditions to cultured cells. To emulate the dynamic environment of vocal folds, a novel vocal fold bioreactor capable of producing vibratory stimulations at fundamental phonation frequencies is constructed and characterized. The device is composed of a function generator, a power amplifier, a speaker selector and parallel vibration chambers. Individual vibration chambers are created by sandwiching a custom-made silicone membrane between a pair of acrylic blocks. The silicone membrane not only serves as the bottom of the chamber but also provides a mechanism for securing the cell-laden scaffold. Vibration signals, generated by a speaker mounted underneath the bottom acrylic block, are transmitted to the membrane aerodynamically by the oscillating air. Eight identical vibration modules, fixed on two stationary metal bars, are housed in an anti-humidity chamber for long-term operation in a cell culture incubator. The vibration characteristics of the vocal fold bioreactor are analyzed non-destructively using a Laser Doppler Vibrometer (LDV). The utility of the dynamic culture device is demonstrated by culturing cellular constructs in the presence of 200-Hz sinusoidal vibrations with a mid-membrane displacement of 40 µm. Mesenchymal stem cells cultured in the bioreactor respond to the vibratory signals by altering the synthesis and degradation of vocal fold-relevant, extracellular matrix components. The novel bioreactor system presented herein offers an excellent in vitro platform for studying vibration-induced mechanotransduction and for the engineering of functional vocal fold tissues. PMID:25145349

  14. Construction and Characterization of a Novel Vocal Fold Bioreactor

    PubMed Central

    Zerdoum, Aidan B.; Tong, Zhixiang; Bachman, Brendan; Jia, Xinqiao

    2014-01-01

    In vitro engineering of mechanically active tissues requires the presentation of physiologically relevant mechanical conditions to cultured cells. To emulate the dynamic environment of vocal folds, a novel vocal fold bioreactor capable of producing vibratory stimulations at fundamental phonation frequencies is constructed and characterized. The device is composed of a function generator, a power amplifier, a speaker selector and parallel vibration chambers. Individual vibration chambers are created by sandwiching a custom-made silicone membrane between a pair of acrylic blocks. The silicone membrane not only serves as the bottom of the chamber but also provides a mechanism for securing the cell-laden scaffold. Vibration signals, generated by a speaker mounted underneath the bottom acrylic block, are transmitted to the membrane aerodynamically by the oscillating air. Eight identical vibration modules, fixed on two stationary metal bars, are housed in an anti-humidity chamber for long-term operation in a cell culture incubator. The vibration characteristics of the vocal fold bioreactor are analyzed non-destructively using a Laser Doppler Vibrometer (LDV). The utility of the dynamic culture device is demonstrated by culturing cellular constructs in the presence of 200-Hz sinusoidal vibrations with a mid-membrane displacement of 40 µm. Mesenchymal stem cells cultured in the bioreactor respond to the vibratory signals by altering the synthesis and degradation of vocal fold-relevant, extracellular matrix components. The novel bioreactor system presented herein offers an excellent in vitro platform for studying vibration-induced mechanotransduction and for the engineering of functional vocal fold tissues. PMID:25145349

  15. Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

    PubMed Central

    Vijayabaskar, M. S.; Vishveshwara, Saraswathi

    2012-01-01

    There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or “sequence conservation” as the basis for their understanding. Recently “interaction energy” based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the “interaction conservation” viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design. PMID:22615547

  16. Direct osmolyte-macromolecule interactions confer entropic stability to folded states.

    PubMed

    Rodríguez-Ropero, Francisco; van der Vegt, Nico F A

    2014-07-01

    Protective osmolytes are chemical compounds that shift the protein folding/unfolding equilibrium toward the folded state under osmotic stresses. The most widely considered protection mechanism assumes that osmolytes are depleted from the protein's first solvation shell, leading to entropic stabilization of the folded state. However, recent theoretical and experimental studies suggest that protective osmolytes may directly interact with the macromolecule. As an exemplary and experimentally well-characterized system, we herein discuss poly(N-isopropylacrylamide) (PNiPAM) in water whose folding/unfolding equilibrium shifts toward the folded state in the presence of urea. On the basis of molecular dynamics simulations of this specific system, we propose a new microscopic mechanism that explains how direct osmolyte-macromolecule interactions confer stability to folded states. We show that urea molecules preferentially accumulate in the first solvation shell of PNiPAM driven by attractive van der Waals dispersion forces with the hydrophobic isopropyl groups, leading to the formation of low entropy urea clouds. These clouds provide an entropic driving force for folding, resulting in preferential urea binding to the folded state and a decrease of the lower folding temperature in agreement with experiment. The simulations further indicate that thermodynamic nonideality of the bulk solvent opposes this driving force and may lead to denaturation, as illustrated by simulations of PNiPAM in aqueous solutions with dimethylurea. The