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GFP Tagging of Sieve Element Occlusion (SEO) Proteins Results in Green Fluorescent Forisomes  

PubMed Central

Forisomes are Ca2+-driven, ATP-independent contractile protein bodies that reversibly occlude sieve elements in faboid legumes. They apparently consist of at least three proteins; potential candidates have been described previously as ‘FOR’ proteins. We isolated three genes from Medicago truncatula that correspond to the putative forisome proteins and expressed their green fluorescent protein (GFP) fusion products in Vicia faba and Glycine max using the composite plant methodology. In both species, expression of any of the constructs resulted in homogenously fluorescent forisomes that formed sieve tube plugs upon stimulation; no GFP fluorescence occurred elsewhere. Isolated fluorescent forisomes reacted to Ca2+ and chelators by contraction and expansion, respectively, and did not lose fluorescence in the process. Wild-type forisomes showed no affinity for free GFP in vitro. The three proteins shared numerous conserved motifs between themselves and with hypothetical proteins derived from the genomes of M. truncatula, Vitis vinifera and Arabidopsis thaliana. However, they showed neither significant similarities to proteins of known function nor canonical metal-binding motifs. We conclude that ‘FOR’-like proteins are components of forisomes that are encoded by a well-defined gene family with relatives in taxa that lack forisomes. Since the mnemonic FOR is already registered and in use for unrelated genes, we suggest the acronym SEO (sieve element occlusion) for this family. The absence of binding sites for divalent cations suggests that the Ca2+ binding responsible for forisome contraction is achieved either by as yet unidentified additional proteins, or by SEO proteins through a novel, uncharacterized mechanism. PMID:18784195

Pélissier, Hélène C.; Peters, Winfried S.; Collier, Ray; van Bel, Aart J. E.; Knoblauch, Michael



Calcium powered phloem protein of SEO gene family "Forisome" functions in wound sealing and act as biomimetic smart materials.  


Forisomes protein belongs to SEO gene family and is unique to Fabaceae family. These proteins are located in sieve tubes of phloem and function to prevent loss of nutrient-rich photoassimilates, upon mechanical injury/wounding. Forisome protein is also known as ATP independent, mechanically active proteins. Despite the wealth of information role of forisome in plants are not yet fully understood. Recent reports suggest that forisomes protein can act as ideal model to study self assembly mechanism for development of nanotechnological devices like microfluidic system application in space exploration mission. Improvement in micro instrument is highly demanding and has been a key technology by NASA in future space exploration missions. Based on its physical parameters, forisome are found to be ideal biomimetic materials for micro fluidic system because the conformational shifts can be replicated in vitro and are fully reversible over large number of cycles. By the use of protein engineering forisome recombinant protein can be tailored. Due to its unique ability to convert chemical energy into mechanical energy forisome has received much attention. For nanotechnological application and handling biomolecules such as DNA, RNA, protein and cell as a whole microfluidic system will be the most powerful technology. The discovery of new biomimetic smart materials has been a key factor in development of space science and its requirements in such a challenging environment. The field of microfludic, particularly in terms of development of its components along with identification of new biomimetic smart materials, deserves more attention. More biophysical investigation is required to characterize it to make it more suitable under parameters of performance. PMID:25763691

Srivastava, Vineet Kumar; Tuteja, Narendra



Calcium powered phloem protein of SEO gene family "Forisome" functions in wound sealing and act as biomimetic smart materials.  


Forisomes protein belongs to SEO gene family and is unique to Fabaceae family. These proteins are located in sieve tubes of phloem and function to prevent loss of nutrient-rich photoassimilates, upon mechanical injury/wounding. Forisome protein is also known as ATP independent, mechanically active proteins. Despite the wealth of information role of forisome in plants are not yet fully understood. Recent reports suggest that forisomes protein can act as ideal model to study self assembly mechanism for development of nanotechnological devices like microfluidic system application in space exploration mission. Improvement in micro instrument is highly demanding and has been a key technology by NASA in future space exploration missions. Based on its physical parameters, forisome are found to be ideal biomimetic materials for micro fluidic system because the conformational shifts can be replicated in vitro and are fully reversible over large number of cycles. By the use of protein engineering forisome recombinant protein can be tailored. Due to its unique ability to convert chemical energy into mechanical energy forisome has received much attention. For nanotechnological application and handling biomolecules such as DNA, RNA, protein and cell as a whole microfluidic system will be the most powerful technology. The discovery of new biomimetic smart materials has been a key factor in development of space science and its requirements in such a challenging environment. The field of microfludic, particularly in terms of development of its components along with identification of new biomimetic smart materials, deserves more attention. More biophysical investigation is required to characterize it to make it more suitable under parameters of performance. PMID:24905822

Srivastava, Vineet Kumar; Tuteja, Narendra



SEOS frame camera applications study  

NASA Technical Reports Server (NTRS)

A research and development satellite is discussed which will provide opportunities for observation of transient phenomena that fall within the fixed viewing circle of the spacecraft. The evaluation of possible applications for frame cameras, for SEOS, are studied. The computed lens characteristics for each camera are listed.



CEOS SEO and GISS Meeting  

NASA Technical Reports Server (NTRS)

The Committee on Earth Observation Satellites (CEOS) provides a brief to the Goddard Institute for Space Studies (GISS) regarding the CEOS Systems Engineering Office (SEO) and current work on climate requirements and analysis. A "system framework" is provided for the Global Earth Observation System of Systems (GEOSS). SEO climate-related tasks are outlined including the assessment of essential climate variable (ECV) parameters, use of the "systems framework" to determine relevant informational products and science models and the performance of assessments and gap analyses of measurements and missions for each ECV. Climate requirements, including instruments and missions, measurements, knowledge and models, and decision makers, are also outlined. These requirements would establish traceability from instruments to products and services allowing for benefit evaluation of instruments and measurements. Additionally, traceable climate requirements would provide a better understanding of global climate models.

Killough, Brian; Stover, Shelley



Earth resources applications of the Synchronous Earth Observatory Satellite (SEOS)  

NASA Technical Reports Server (NTRS)

The results are presented of a four month study to define earth resource applications which are uniquely suited to data collection by a geosynchronous satellite. While such a satellite could also perform many of the functions of ERTS, or its low orbiting successors, those applications were considered in those situations where requirements for timely observation limit the capability of ERTS or EOS. Thus, the application presented could be used to justify a SEOS.

Lowe, D. S.; Cook, J. J.



Flickr SEO Tip Sheet Feinberg Office of Communications  

E-print Network

Flickr SEO Tip Sheet Feinberg Office of Communications You've just edited all your photos at Feinberg School of Medicine, Chicago." Long image titles are OK. 4. Write a keyword rich description for each photo, and link back to the Feinberg site. Following your image description, insert something like

Engman, David M.


Yoonjung Seo Phone: +1(347)287-7022  

E-print Network

Yoonjung Seo Phone: +1(347)287-7022 Email: EDUCATION Columbia University, Fu to management · Actively involved in problem solving, investigating any test failure and revising SOPs (Standard-effectiveness of heart disease prevention and control, and tobacco policy · Analyzed data collected and generated


Raman spectra of haloselenate(IV) ions—the SeO 2Br - anion  

NASA Astrophysics Data System (ADS)

Compounds of the bromoselenite ion, MSeO 2Br(M + = ? 4Sb +, n-Bu 4N +) have been prepared and their Raman spectra studied. The spectra are consistent with C s symmetry. A normal coordinate analysis of the spectra of SeO 2F -, SeO 2Cl - and SeO 2Br - has been done and force constants determined. The SeX bonds are shown to be remarkably weak.

Milne, John; Lahaie, Pierre


Rich structural chemistry in scandium selenium/tellurium oxides: mixed-valent selenite-selenates, Sc2(SeO3)2(SeO4) and Sc2(TeO3)(SeO3)(SeO4), and ternary tellurite, Sc2(TeO3)3.  


Both single crystals and pure bulk phases of three new scandium selenium/tellurium oxides, Sc2(SeO3)2(SeO4), Sc2(TeO3)(SeO3)(SeO4), and Sc2(TeO3)3, have been synthesized through hydrothermal and solid-state reactions. X-ray diffractions were used to determine the structures and confirm the phase purities of the reported materials. Isostructural Sc2(SeO3)2(SeO4) and Sc2(TeO3)(SeO3)(SeO4) reveal three-dimensional frameworks with ScO7 pentagonal bipyramids, SeO3 (and TeO3) trigonal pyramids, and SeO4 tetrahedra. A novel ternary scandium tellurite, Sc2(TeO3)3, also shows a three-dimensional framework that is composed of ScO6 octahedra, ScO7-capped octahedra, and TeO3 trigonal pyramids. All three materials accommodate local asymmetric coordination moieties owing to the lone pairs on Se(4+) and Te(4+) cations. The effect of coordination environments of constituent cations on the frameworks, dimensionalities, and centricities of products is discussed. Thorough characterizations including elemental analyses, infrared and UV-vis diffuse reflectance spectroscopies, thermal analyses, and dipole moment calculations for the reported materials are reported. Crystal data: Sc2(SeO3)2(SeO4), monoclinic, space group P21/c (No. 14), a = 6.5294(2) Å, b = 10.8557(4) Å, c = 12.6281(6) Å, ? = 103.543(3)°, V = 870.21(6) Å(3), and Z = 4; Sc2(TeO3)(SeO3)(SeO4), monoclinic, space group P21/c (No. 14), a = 6.5345(12) Å, b = 10.970(2) Å, c = 12.559(2) Å, ? = 102.699(10)°, V = 878.3(6) Å(3), and Z = 4; Sc2(TeO3)3, monoclinic, space group P21/n (No. 14), a = 5.2345(3) Å, b = 24.3958(15) Å, c = 6.8636(4) Å, ? = 106.948(2)°, V = 838.42(9) Å(3), and Z = 4. PMID:24918773

Song, Seung Yoon; Lee, Dong Woo; Ok, Kang Min



Detection of calcium by a confocal laser scanning microscope in Na2SeO3-treated SW480 human colonic carcinoma cells  

NASA Astrophysics Data System (ADS)

A number of studies have demonstrated that perturbed cellular calcium homeostasis has been implicated in apoptosis. Some studies showed that selenium compounds were able to induce cell apoptosis. The main objective of this study is to evaluate effect of Na2SeO3 on intracellular Ca2+ levels in SW480 human colonic carcinoma cells. When SW480 cells were exposed to 25 to 100 micrometers ol/L Na2SeO3, we also found that Na2SeO3 was able to induce [Ca2+]i, disruption of mitochondrial membrane potential ((Delta) (psi) m) in SW480 cells by using a confocal laser scanning microscope. Ca2+ channel inhibitor CoCl2 and an intracellular Ca2+ chelator BAPTA completely inhibited [Ca2+]i increase. CoCl2, BAPTA and ruthenium red also inhibited disruption of (Delta) (psi) m. The results suggest that Na2SeO3 is able to increase [Ca2+]i mitochondria permeability transition and Ca2+ is from extracellular Ca2+.

Wang, Haitao; Liu, Yafeng; Zhang, Zhihong; Yang, Xiangliang; Xu, Hui-Bie F.



Fecal Calprotectin is an Accurate Tool and Correlated to Seo Index in Prediction of Relapse in Iranian Patients With Ulcerative Colitis  

PubMed Central

Background: The natural clinical course of Ulcerative Colitis (UC) is characterized by episodes of relapse and remission. Fecal Calprotectin (FC) is a relatively new marker of intestinal inflammation and is an available, non-expensive tool for predicting relapse of quiescent UC. The Seo colitis activity index is a clinical index for assessment of the severity of UC. Objectives: The present study aimed to evaluate the accuracy of FC and the Seo colitis activity index and their correlation in prediction of UC exacerbation. Patients and Methods: In this prospective cohort study, 157 patients with clinical and endoscopic diagnosis of UC selected randomly from 1273 registered patients in Fars province’s IBD registry center in Shiraz, Iran, were followed from October 2012 to October 2013 for 12 months or shorter, if they had a relapse. Two patients left the study before completion and one patient had relapse because of discontinuation of drugs. The participants' clinical and serum factors were evaluated every three months. Furthermore, stool samples were collected at the beginning of study and every three months and FC concentration (commercially available enzyme linked immunoassay) and the Seo Index were assessed. Then univariate analysis, multiple variable logistic regression, Receiver Operating Characteristics (ROC) curve analysis, and Pearson’s correlation test (r) were used for statistical analysis of data. Results: According to the results, 74 patients (48.1%) relapsed during the follow-up (33 men and 41 women). Mean ± SD of FC was 862.82 ± 655.97 ?g/g and 163.19 ± 215.85 ?g/g in relapsing and non-relapsing patients, respectively (P < 0.001). Multiple logistic regression analysis revealed that age, number of previous relapses, FC and the Seo index were significant predictors of relapse. ROC curve analysis of FC level and Seo activity index for prediction of relapse demonstrated area under the curve of 0.882 (P < 0.001) and 0.92 1(P < 0.001), respectively. Besides, FC level of 341 ?g/g was identified as the cut-off point with 11.2% and 79.7% relapse rate below and above this point, respectively. Additionally, Pearson correlation coefficient (r) between FC and the Seo index was significant in prediction of relapse (r = 0.63, P < 0.001). Conclusions: As a simple and noninvasive marker, FC is highly accurate and significantly correlated to the Seo activity index in prediction of relapse in the course of quiescent UC in Iranian patients.

Hosseini, Seyed Vahid; Jafari, Peyman; Taghavi, Seyed Alireza; Safarpour, Ali Reza; Rezaianzadeh, Abbas; Moini, Maryam; Mehrabi, Manoosh



An empirical analysis of health care IPOs and SEOs.  


This article reviews the extant literature regarding the three new issues phenomena: hot issue markets, first-day underpricing, and poor long-run performance as they apply to the heath care industry. Given the "creeping corporatization" of the heath care industry and the unique influence of nonmarket forces on it, we examine whether the three IPO phenomena exist within the industry. We find that hot issue markets, initial underpricing, and negative long-run abnormal returns and sales growth occur among both heath care IPOs and SEOs. Of particular interest, we find that firms are able to issue during times of excess heath care spending and subsequently underperform the market, apparently exploiting windows of opportunity. PMID:20515009

Brau, James C; Holloway, Jonathan M



Crystal structures of Na2SeO4·1.5H2O and Na2SeO4·10H2O.  


The crystal structures of Na2SeO4·1.5H2O (sodium selenate sesquihydrate) and Na2SeO4·10H2O (sodium selenate deca-hydrate) are isotypic with those of Na2CrO4·1.5H2O and Na2 XSeO4·10H2O (X = S, Cr), respectively. The asymmetric unit of the sesquihydrate contains two Na(+) cations, one SeO4 tetra-hedron and one and a half water mol-ecules, the other half being generated by twofold rotation symmetry. The coordination polyhedra of the cations are a distorted monocapped octa-hedron and a square pyramid; these [NaO x ] polyhedra are linked through common edges and corners into a three-dimensional framework structure, the voids of which are filled with the Se atoms of the SeO4 tetra-hedra. The structure is consolidated by O-H?O hydrogen bonds between coordinating water mol-ecules and framework O atoms. The asymmetric unit of the deca-hydrate consists of two Na(+) cations, one SeO4 tetra-hedron and ten water mol-ecules. Both Na(+) cations are octa-hedrally surrounded by water mol-ecules and by edge-sharing condensed into zigzag chains extending parallel to [001]. The SeO4 tetra-hedra and two uncoordinating water mol-ecules are situated between the chains and are connected to the chains through an intricate network of medium-strength O-H?O hydrogen bonds. PMID:25249853

Weil, Matthias; Bonneau, Barbara



Effects of sodium and potassium ions on a novel SeO2-B2O3-SiO2-P2O5-CaO bioactive system  

NASA Astrophysics Data System (ADS)

The study is focused on Na2O and/or K2O influence on a new sol-gel derived SeO2-B2O3-SiO2-P2O5-CaO bioactive system. The structural changes induced by Na2O and/or K2O addition were correlated with the samples behavior in simulated biological media. X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy were used to characterize the structure and the type of the chemical bonds. The morphology of the samples was characterized through scanning electron microscopy (SEM). XRD results pointed out a prevalent vitreous structure with an incipient hydroxyapatite (HA) crystalline phase. FTIR results revealed a complex network consisting of silicate, phosphate and borate units, as well as the development of both A- and B-type of carbonate-substituted HA. The bioactivity of the samples was tested in vitro following the evolution of the apatite layers self-assembled on the samples surface in simulated body fluid. Their biocompatibility was investigated after samples surface functionalization with protein. The results indicate that sodium and potassium addition improves the biocompatibility by enhancement of protein adherence on samples surface and without to prevent the samples bioactivity.

Trandafir, D. L.; Ponta, O.; Ciceo-Lucacel, R.; Simon, V.



Characterization of five subgroups of the sieve element occlusion gene family in Glycine max reveals genes encoding non-forisome P-proteins, forisomes and forisome tails.  


P-proteins are structural phloem proteins discussed to be involved in the rapid sealing of injured sieve elements. P-proteins are found in all dicotyledonous and some monocotyledonous plants, but additional crystalloid P-proteins, known as forisomes, have evolved solely in the Fabaceae. Both types are encoded by members of the sieve element occlusion (SEO) gene family, which comprises seven phylogenetic subgroups. The Fabaceae-specific subgroup 1 contains genes encoding forisome subunits in e.g. Medicago truncatula, Vicia faba, Dipteryx panamensis and Canavalia gladiata whereas basal subgroup 5 encodes P-proteins in Nicotiana tabacum (tobacco) and Arabidopsis thaliana. The function of remaining subgroups is still unknown. We chose Glycine max (soybean) as a model to investigate SEO proteins representing different subgroups in one species. We isolated native P-proteins to determine the SEO protein composition and analyzed the expression pattern, localization and structure of the G. max SEO proteins representing five of the subgroups. We found that subgroup 1 GmSEO genes encode forisome subunits, a member of subgroup 5 encodes a non-forisome P-protein and subgroup 2 GmSEO genes encode the components of forisome tails, which are present in a restricted selection of Fabaceaen species. We therefore present the first molecular characterization of a Fabaceae non-forisome P-protein and the first evidence that forisome tails are encoded by a phylogenetically-distinct branch of the SEO gene family. PMID:24928491

Zielonka, Sascia; Ernst, Antonia M; Hawat, Susan; Twyman, Richard M; Prüfer, Dirk; Noll, Gundula A



Japan, France Vying for Korea's Nuclear Project By Cho Jin-seo  

E-print Network

Japan, France Vying for Korea's Nuclear Project By Cho Jin-seo Staff Reporter France and Japan recently have sent high-ranking officials to South Korea, since it will play the key role in the selection in a meeting late this month and Korea is expected to be the key player in the vote. French Minister


Automatic Modeling of Virtual Humans and Body Clothing Nadia Magnenat-Thalmann, Hyewon Seo, Frederic Cordier  

E-print Network

Automatic Modeling of Virtual Humans and Body Clothing Nadia Magnenat-Thalmann, Hyewon Seo, parameterization techniques for modeling static shape (the variety of human body shapes) and dynamic shape (how the body shape changes as it moves) of virtual humans are classified, summarized and compared. Finally

Cordier, Frederic


Sodium selenite penta­hydrate, Na2SeO3·5H2O  

PubMed Central

In the crystal structure of Na2SeO3·5H2O [disodium selen­ate(IV) penta­hydrate], two Se, two selenite O atoms and one water O atom are located on a mirror plane, and one water O atom is located on a twofold rotation axis. The coordination of one Na+ cation is distorted trigonal bipyramidal, formed by three equatorial H2O ligands and two axial selenite O atoms. The other Na+ cation has an octa­hedral coordination by six water mol­ecules. The two independent SeO3 groups form almost undistorted trigonal pyramids, with Se—O bond lengths in the range 1.6856?(7)–1.7202?(10)?Å and O—Se—O angles in the range 101.98?(3)–103.11?(5)°, and both are ?2-O:O-bonded to a pair of Na+ cations. Hydrogen bonds involving all water molecules and selenite O atoms consolidate the crystal packing. Although anhydrous Na2SeO3 and Na2TeO3 are isotypic, the title compound is surprisingly not isotypic with Na2TeO3·5H2O. In the tellurite hydrate, all Na+ cations have an octa­hedral coordination and the TeO3 groups are bonded to Na+ only via one of their three O atoms. PMID:24454013

Mereiter, Kurt



A Rhizobium selenitireducens protein showing selenite reductase activity.  


Biobarriers remove, via precipitation, the metalloid selenite (SeO??²) from groundwater; a process that involves the biological reduction of soluble SeO??² to insoluble elemental red selenium (Se?). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitireducens at least two enzymes are potentially involved; one, a nitrite reductase reduces SeO??² to Se? but another protein may also be involved which is investigated in this study. Proteins from R. selenitireducens cells were precipitated with ammonium sulfate and run on native electrophoresis gels. When these gels were incubated with NADH and SeO??² a band of precipitated Se? developed signifying the presence of a SeO??² reducing protein. Bands were cut from the gel and analyzed for peptides via LCMSMS. The amino acid sequences associated with the bands indicated the presence of an NADH:flavin oxidoreductase that resembles YP_001326930 from Sinorhizobium medicae. The protein is part of a protein family termed old-yellow-enzymes (OYE) that contain a flavin binding domain. OYE enzymes are often involved in protecting cells from oxidative stress and, due in part to an active site that has a highly accessible binding pocket, are generally active on a wide range of substrates. This report is the first of an OYE enzyme being involved in SeO??² reduction. PMID:24474405

Hunter, W J



Emulating exhalative chemistry: synthesis and structural characterization of ilinskite, Na[Cu5O2](SeO3)2Cl3, and its K-analogue  

NASA Astrophysics Data System (ADS)

The K- and Na-synthetic analogues of the fumarolic mineral ilinskite have been synthesized by the chemical vapor transport (CVT) reactions method. The A[Cu5O2](SeO3)2Cl3 (A + = K+, Na+) compounds crystallize in the orthorhombic space group Pnma: a = 18.1691(6) Å, b = 6.4483(2) Å, c = 10.5684(4) Å, V = 1238.19(7) Å3, R 1 = 0.018 for 1957 unique reflections with F > 4? F for K[Cu5O2](SeO3)2Cl3 (KI), and a = 17.7489(18) Å, b = 6.4412(6) Å, c = 10.4880(12) Å, V = 1199.0(2) Å3, R 1 = 0.049 for 1300 unique reflections with F > 4? F for Na[Cu5O2](SeO3)2Cl3 (NaI). The crystal structures of KI and NaI are based upon the [O2Cu5]6+ sheets consisting of corner-sharing (OCu4)6+ tetrahedra. The Na-for-K substitution results in the significant expansion of the interlayer space and changes in local coordination of some of the Cu2+ cations. The A + cation coordination changes from fivefold (for Na+) to ninefold (for K+). The CVT reactions method provides a unique opportunity to model physicochemical conditions existing in fumarolic environments and may be used not only to model exhalative processes, but also to predict possible mineral phases that may form in fumaroles. In particular, the K analogue of ilinskite is not known in nature, whereas it may well form from volcanic gases in a K-rich local geochemical environment.

Kovrugin, Vadim M.; Siidra, Oleg I.; Colmont, Marie; Mentré, Olivier; Krivovichev, Sergey V.



Hydroxocobalamin association during cell culture results in pink therapeutic proteins  

PubMed Central

Process control of protein therapeutic manufacturing is central to ensuring the product is both safe and efficacious for patients. In this work, we investigate the cause of pink color variability in development lots of monoclonal antibody (mAb) and Fc-fusion proteins. Results show pink-colored product generated during manufacturing is due to association of hydroxocobalamin (OH-Cbl), a form of vitamin B12. OH-Cbl is not part of the product manufacturing process; however we found cyanocobalamin (CN-Cbl) in cell culture media converts to OH-Cbl in the presence of light. OH-Cbl can be released from mAb and Fc-fusion proteins by conversion with potassium cyanide to CN-Cbl, which does not bind. By exploiting the differential binding of CN-Cbl and OH-Cbl, we developed a rapid and specific assay to accurately measure B12 levels in purified protein. Analysis of multiple products and lots using this technique gives insight into color variability during manufacturing. PMID:23924851

Prentice, Kenneth M; Gillespie, Ronald; Lewis, Nathan; Fujimori, Kiyoshi; McCoy, Rebecca; Bach, Julia; Connell-Crowley, Lisa; Eakin, Catherine M



Cs(TaO2)3(SeO3)2 and Cs(TiOF)3(SeO3)2: Structural and Second Harmonic Generation Changes Induced by the Different d(0)-TM Coordination Octahedra.  


Two new cesium selenites containing TaO6 or TiO4F2 octahedra, namely, Cs(TaO2)3(SeO3)2 (1) and Cs(TiOF)3(SeO3)2 (2), have been prepared using standard high temperature solid-state method and hydrothermal reaction, respectively. Compound 1 crystallizes in P3?m1 and features an unusual [(TaO2)3(SeO3)2](-) sandwich-like double layer in which two [Ta(1)O3(SeO3)](3-) layers are bridged by central Ta(2)O6 octahedra via corner-sharing, whereas Cs(TiOF)3(SeO3)2 with a polar space group P63mc features an interesting hexagonal tungsten oxide (HTO) layered topology and presents a strong second harmonic generation (SHG) of about 5 × KDP (KH2PO4), which is much larger than those of A(VO2)3(QO3)2 (A = K, Tl, Rb, Cs, or NH4; Q = Se, Te) with a similar HTO layered structure. Cs(TiOF)3(SeO3)2 is also type-I phase matching. The SHG of above-mentioned HTO materials can be enhanced greatly with the replacement of VO6 octahedra by TiO4F2 octahedra. Furthermore, thermal stabilities, UV-vis diffuse reflectance spectra, infrared spectra, relationship between crystal structure and SHG, and theoretical calculations were also reported. PMID:25835387

Cao, Xue-Li; Hu, Chun-Li; Kong, Fang; Mao, Jiang-Gao



Insertion of Mutant Proteolipid Protein Results in Missorting of Myelin Proteins  

PubMed Central

Two brothers with a leukodystrophy, progressive spastic diplegia, and peripheral neuropathy were found to have proteinaceous aggregates in the peripheral nerve myelin sheath. The patients’ mother had only subclinical peripheral neuropathy, but the maternal grandmother had adult-onset leukodystrophy. Sequencing of the proteolipid protein (PLP) gene showed a point mutation IVS4 + 1 G?A within the donor splice site of intron 4. We identified one transcript with a deletion of exon 4 (?ex4, 169bp) encoding for PLP and DM20 proteins and lacking two transmembrane domains, and a second transcript with exon 4 + 10bp encoding three transmembrane domains. Immunohistochemistry showed abnormal aggregation in the myelin sheath of MBP and P0. Myelin-associated glycoprotein was present in the Schmidt–Lanterman clefts but significantly reduced in the periaxonal region. Using immunogold electron microscopy, we demonstrated the presence of mutated PLP/DM20 and the absence of the intact protein in the patient peripheral myelin sheath. We conclude that insertion of mutant PLP/DM20 with resulting aberrant distribution of other myelin proteins in peripheral nerve may constitute an important mechanism of dysmyelination in disorders associated with PLP mutations. PMID:14681886

Vaurs-Barriere, Catherine; Wong, Kondi; Weibel, Thais D.; Abu-Asab, Mones; Weiss, Michael D.; Kaneski, Christine R.; Mixon, Tong-Hui; Bonavita, Simona; Creveaux, Isabelle; Heiss, John D.; Tsokos, Maria; Goldin, Ehud; Quarles, Richard H.; Boespflug-Tanguy, Odile; Schiffmann, Raphael



Direct Synthesis of Gallium Nitride Nanowires Coated with Boron Carbonitride Layers Hee Won Seo, Seung Yong Bae, and Jeunghee Park*  

E-print Network

Direct Synthesis of Gallium Nitride Nanowires Coated with Boron Carbonitride Layers Hee Won Seo-crystalline wurtzite-structured gallium nitride nanowires. The graphitic outerlayers are composed of boron, carbonN nanorods.19 They also synthesized GaN nanorods coated with boron nitride (BN) layers.20 The mixture of Ga

Kim, Bongsoo


Protein Threading by Linear Programming: Theoretical Analysis and Computational Results  

Microsoft Academic Search

In a previous paper (Xu, Li, Kim, and Xu, Journal of Bioinformatics and Computational Biology, vol. 1, no. 1, pp. 95–117, 2003), we have used an integer programming approach to implement a protein threading program RAPTOR for protein 3D structure prediction, based on the threading model treating pairwise contacts rigorously and allowing variable gaps. We have solved the integer program

Jinbo Xu; Ming Li; Ying Xu



Magnetic properties of the superconducting state of iron-based superconductors Kangjun Seo,1 Chen Fang,1 B. Andrei Bernevig,2 and Jiangping Hu1  

E-print Network

Magnetic properties of the superconducting state of iron-based superconductors Kangjun Seo,1 Chen Fang,1 B. Andrei Bernevig,2 and Jiangping Hu1 1Department of Physics, Purdue University, West Lafayette

Hu, Jiangping


Cs7Nd11(SeO3)12Cl16: first noncentrosymmetric structure among alkaline-metal lanthanide selenite halides.  


Cs7Nd11(SeO3)12Cl16, the complex selenite chloride of cesium and neodymium, was synthesized in the NdOCl-SeO2-CsCl system. The compound has been characterized using single-crystal X-ray diffraction, electron diffraction, transmission electron microscopy, luminescence spectroscopy, and second-harmonic-generation techniques. Cs7Nd11(SeO3)12Cl16 crystallizes in an orthorhombic unit cell with a = 15.911(1) Å, b = 15.951(1) Å, and c = 25.860(1) Å and a noncentrosymmetric space group Pna2(1) (No. 33). The crystal structure of Cs7Nd11(SeO3)12Cl16 can be represented as a stacking of Nd11(SeO3)12 lamellas and CsCl-like layers. Because of the layered nature of the Cs7Nd11(SeO3)12Cl16 structure, it features numerous planar defects originating from occasionally missing the CsCl-like layer and violating the perfect stacking of the Nd11(SeO3)12 lamellas. Cs7Nd11(SeO3)12Cl16 represents the first example of a noncentrosymmetric structure among alkaline-metal lanthanide selenite halides. Cs7Nd11(SeO3)12Cl16 demonstrates luminescence emission in the near-IR region with reduced efficiency due to a high concentration of Nd(3+) ions causing nonradiative cross-relaxation. PMID:23477524

Berdonosov, Peter S; Akselrud, Lev; Prots, Yurii; Abakumov, Artem M; Smet, Philippe F; Poelman, Dirk; Van Tendeloo, Gustaaf; Dolgikh, Valery A



Synthesis, characterization, and structure-property relationships in two new polar oxides: Zn2(MoO4)(SeO3) and Zn2(MoO4)(TeO3).  


Two new noncentrosymmetric (NCS) polar oxide materials, Zn(2)(MoO(4))(AO(3)) (A = Se(4+) or Te(4+)), have been synthesized by hydrothermal and solid-state techniques. Their crystal structures have been determined, and characterization of their functional properties (second-harmonic generation, piezoelectricity, and polarization) has been performed. The isostructural materials exhibit a three-dimensional network consisting of ZnO(4), ZnO(6), MoO(4), and AO(3) polyhedra that share edges and corners. Powder second-harmonic generation (SHG) measurements using 1064 nm radiation indicate the materials exhibit moderate SHG efficiencies of 100 × and 80 × ?-SiO(2) for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively. Particle size vs SHG efficiency measurements indicate the materials are type 1 non-phase-matchable. Converse piezoelectric measurements resulted in d(33) values of ?14 and ?30 pm/V for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively, whereas pyroelectric measurements revealed coefficients of -0.31 and -0.64 ?C/m(2) K at 55 °C for Zn(2)(MoO(4))(SeO(3)) and Zn(2)(MoO(4))(TeO(3)), respectively. Frequency-dependent polarization measurements confirmed that all of the materials are nonferroelectric; that is, the macroscopic polarization is not reversible, or "switchable". Infrared, UV-vis, thermogravimetric, and differential thermal analysis measurements were also performed. First-principles density functional theory (DFT) electronic structure calculations were also done. Crystal data: Zn(2)(MoO(4))(SeO(3)), monoclinic, space group P2(1) (No. 4), a = 5.1809(4) Å, b = 8.3238(7) Å, c = 7.1541(6) Å, ? = 99.413(1)°, V = 305.2(1) Å(3), Z = 2; Zn(2)(MoO(4))(TeO(3)), monoclinic, space group P2(1) (No. 4), a = 5.178(4) Å, b = 8.409(6) Å, c = 7.241(5) Å, ? = 99.351(8)°, V = 311.1(4) Å(3), Z = 2. PMID:21557565

Nguyen, Sau Doan; Kim, Sang-Hwan; Halasyamani, P Shiv



The synthesis and crystal structures of the first rare-earth alkaline-earth selenite chlorides MNd 10(SeO 3) 12Cl 8 ( M=Ca and Sr)  

NASA Astrophysics Data System (ADS)

Two new alkaline-earth Nd selenite chlorides MNd 10(SeO 3) 12Cl 8 ( M=Ca, Sr) were obtained using crystal growth from alkaline-earth chloride melts in quartz tubes. These new compounds crystallize in the orthorhombic system in space group C cca (#68). The compounds were studied by energy dispersive X-ray spectroscopy (EDX) and X-ray diffraction. It was shown that both compounds adopt the same structure type, constructed by complex [M 11(SeO 3) 12] 8+ slabs separated by chloride anion layers perpendicular to the longest cell parameter. The SeO 3 groups show a pyramidal shape and may be described as SeO 3E tetrahedra. Such SeO 3 groups decorate the Nd-O skeletons forming the [M 11(SeO 3) 12] 8+ slabs.

Berdonosov, P. S.; Olenev, A. V.; Dolgikh, V. A.; Lightfoot, P.



Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results  

E-print Network

Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm

Istrail, Sorin


Protein crystal growth results from shuttle flight 51-F  

NASA Technical Reports Server (NTRS)

The protein crystal growth (PCG) experiments run on 51-F were analyzed. It was found that: (1) sample stability is increased over that observed during the experiments on flight 51-D; (2) the dialysis experiments produced lysozyme crystals that were significantly larger than those obtained in our identical ground-based studies; (3) temperature fluctuations apparently caused problems during the crystallization experiments on 51-F; (4) it is indicated that teflon tape stabilizes droplets on the syringe tips; (5) samples survived during the reentry and landing in glass tips that were not stoppered with plungers; (6) from the ground-based studies, it was expected that equilibration should be complete within 2 to 4 days for all of these vapor-diffusion experiments, thus it appears that the vapor diffusion rates are somewhat slower under microgravity conditions; (7) drop tethering was highly successful, all four of the tethered drops were stable, even though they contained MPD solutions; (8) the PCG experiments on 51-F were done to assess the hardware and experimental procedures that are developed for future flights, when temperature control will be available. Lysozyme crystals obtained by microdialysis are considerably larger than those obtained on the ground, using the identical apparatus and procedures.

Bugg, C. E.



RESEARCH ARTICLE Proteolipid Protein Cannot Replace P0  

E-print Network

of Peripheral Nervous System Myelin Xinghua Yin,1 Sumiko Kiryu-Seo,1 Grahame J. Kidd,1 M. Laura Feltri,2 Lawrence Wrabetz,2 and Bruce D. Trapp1 The central nervous system (CNS) of terrestrial vertebrates abundant protein of CNS myelin. However, PLP did not replace P0 in peripheral nervous system (PNS) myelin


Evolutionary Rate Covariation in Meiotic Proteins Results from Fluctuating Evolutionary Pressure in Yeasts and Mammals  

PubMed Central

Evolutionary rates of functionally related proteins tend to change in parallel over evolutionary time. Such evolutionary rate covariation (ERC) is a sequence-based signature of coevolution and a potentially useful signature to infer functional relationships between proteins. One major hypothesis to explain ERC is that fluctuations in evolutionary pressure acting on entire pathways cause parallel rate changes for functionally related proteins. To explore this hypothesis we analyzed ERC within DNA mismatch repair (MMR) and meiosis proteins over phylogenies of 18 yeast species and 22 mammalian species. We identified a strong signature of ERC between eight yeast proteins involved in meiotic crossing over, which seems to have resulted from relaxation of constraint specifically in Candida glabrata. These and other meiotic proteins in C. glabrata showed marked rate acceleration, likely due to its apparently clonal reproductive strategy and the resulting infrequent use of meiotic proteins. This correlation between change of reproductive mode and change in constraint supports an evolutionary pressure origin for ERC. Moreover, we present evidence for similar relaxations of constraint in additional pathogenic yeast species. Mammalian MMR and meiosis proteins also showed statistically significant ERC; however, there was not strong ERC between crossover proteins, as observed in yeasts. Rather, mammals exhibited ERC in different pathways, such as piRNA-mediated defense against transposable elements. Overall, if fluctuation in evolutionary pressure is responsible for ERC, it could reveal functional relationships within entire protein pathways, regardless of whether they physically interact or not, so long as there was variation in constraint on that pathway. PMID:23183665

Clark, Nathan L.; Alani, Eric; Aquadro, Charles F.




NSDL National Science Digital Library

Laboratory manual and supplemental resources that were developed for a college laboratory course in protein purification. The enzyme, Beta-galactosidase, is purified in two steps, with analysis and verification of results. Course materials are divided into four units: Why Proteins, Assays, The Purification Process, and Analysis and Verification. Powerpoint lectures and study guides are provided.

Mowery, Jeanette


Recent results and new hardware developments for protein crystal growth in microactivity  

NASA Technical Reports Server (NTRS)

Protein crystal growth experiments have been performed on 16 space shuttle missions since April, 1985. The initial experiments utilized vapor diffusion crystallization techniques similar to those used in laboratories for earth-based experiments. More recent experiments have utilized temperature induced crystallization as an alternative method for growing high quality protein crystals in microgravity. Results from both vapor diffusion and temperature induced crystallization experiments indicate that proteins grown in microgravity may be larger, display more uniform morphologies, and yield diffraction data to significantly higher resolutions than the best crystals of these proteins grown on earth.

Delucas, L. J.; Long, M. M.; Moore, K. M.; Smith, C.; Carson, M.; Narayana, S. V. L.; Carter, D.; Clark, A. D., Jr.; Nanni, R. G.; Ding, J.



Thallium selenate (Tl2SeO4) in a paraelastic phase by X-ray powder diffraction.  


The structure of thallium selenate, Tl2SeO4, in a paraelastic phase (above 661 K) has been analysed by Rietveld analysis of the X-ray powder diffraction pattern. Atomic parameters based on the isomorphic K2SO4 crystal in the paraelastic phase were used as the starting model. The structure was determined in the hexagonal space group P6(3)/mmc, with a = 6.2916 (2) A and c = 8.1964 (2) A. From the Rietveld refinement it was found that two orientations are possible for the SeO4 tetrahedra, in which one of their apices points randomly up and down with respect to [001]. One Tl atom lies at the origin with 3m symmetry, the other Tl and one of the O atoms occupy sites with 3m symmetry, the Se atom is at a site with 6m2 symmetry and the remaining O atom is at a site with m symmetry. Furthermore, it was also found that the Tl atoms display anomalously large positional disorder along [001] in the paraelastic phase. PMID:15805607

Matsuo, Yasumitsu; Tokoyoda, Yoshihide; Hatori, Junko; Komukae, Masaru; Ikehata, Seiichiro



The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone.  


Although protein folding is often described by motion on a funnel-shaped overall topology of the energy landscape, the many local interactions that can occur result in considerable landscape roughness which slows folding by increasing internal friction. Recent experimental results have brought to light that this roughness also causes unusual diffusional behaviour of the backbone of an unfolded protein, i.e. the relative motion of protein sections cannot be described by the normal diffusion equation, but shows strongly subdiffusional behaviour with a nonlinear time dependence of the mean square displacement, ?r(2)(t)??t(?) (?? 1). This results in significantly slower configurational equilibration than had been assumed hitherto. Analysis of the results also allows quantification of the energy landscape roughness, i.e. the root-mean-squared depth of local minima, yielding a value of 4-5kBT for a typical small protein. PMID:25412176

Volk, Martin; Milanesi, Lilia; Waltho, Jonathan P; Hunter, Christopher A; Beddard, Godfrey S



Modeling how reproductive ecology can drive protein diversification and result in linkage disequilibrium between sperm and egg proteins.  


Gamete-recognition proteins determine whether sperm and eggs are compatible at fertilization, and they often evolve rapidly. The source of selection driving the evolution of these proteins is still debated. It has been suggested that sexual conflict can result in proliferation of genetic variation and possibly linkage disequilibrium between sperm and egg proteins. Empirical evidence suggests that both male and female reproductive success can be predicted by their sperm ligand genotype, but why female success can be predicted by a protein expressed only in males is unknown. Here we use mathematical modeling to investigate the interaction between reproductive behavior and sperm availability on the evolution of sperm ligands and egg receptors. We consider haploid and diploid expression in gametes in two possible ecological scenarios, monogamous spawning and competitive spawning. Reproductive behavior plays an important role in determining possible outcomes resulting from sexual conflict. Sperm limitation selects for common genotypes regardless of mating behavior. Under conditions of sperm abundance, competitive spawning provides conditions for the persistence of allelic variation and gametic disequilibrium. With monogamous spawning, such conditions are more restrictive. PMID:20455709

Tomaiuolo, Maurizio; Levitan, Don R



Use of Composite Protein Database including Search Result Sequences for Mass Spectrometric Analysis of Cell Secretome  

PubMed Central

Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use. PMID:25822838

Shin, Jihye; Kim, Gamin; Kabir, Mohammad Humayun; Park, Seong Jun; Lee, Seoung Taek; Lee, Cheolju



Rational modification of protein stability by targeting surface sites leads to complicated results  

PubMed Central

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions. PMID:23798426

Xiao, Shifeng; Patsalo, Vadim; Shan, Bing; Bi, Yuan; Green, David F.; Raleigh, Daniel P.



A Low-power, Multi-channel Sensing System for Monitoring Patients M. Sheth, H. Cao, S. K. Thakar, Y-S. Seo, and J-C. Chiao  

E-print Network

complication to measurement accuracy. To overcome these issues, WISE (wireless intelligent sensor), Bluetooth-S. Seo, and J-C. Chiao Continuous collection and processing data from sensors attached on patients could provide accurate diagnosis and better care. A wireless communication system for sensors permitting

Chiao, Jung-Chih


Sr3Bi2(SeO3)6·H2O: A novel anionic layer consisting of second-order Jahn-Teller (SOJT) distortive cations  

NASA Astrophysics Data System (ADS)

A new layered bismuth selenite hydrate material, Sr3Bi2(SeO3)6·H2O has been synthesized through a hydrothermal reaction using SrCO3, Bi2O3, SeO2, and water as reagents. The crystal structure of the reported material has been determined by single crystal X-ray diffraction analysis. The anionic layered framework of Sr3Bi2(SeO3)6·H2O consists of polyhedra of second-order Jahn-Teller (SOJT) distortive cations, Bi3+ and Se4+. Attributable to the variable and asymmetric coordination geometry of the constituent cations, a rich structural chemistry including uni-dimensional bands and linkers is observed in the layer. The material is thermally stable up to about 390 °C and starts decomposing due to the sublimation of SeO2 above the temperature. The UV-vis diffuse reflectance spectrum suggests a band gap of 3.3 eV. Elemental analysis, infrared spectrum, local dipole moment calculations, and electronic structure calculations are also reported.

Ahn, Hyun Sun; Lee, Eun Pyo; Chang, Hong-Young; Lee, Dong Woo; Ok, Kang Min



Preparation and characterization of SeO2/TiO2 composite photocatalyst with excellent performance for sunset yellow azo dye degradation under natural sunlight illumination.  


To improve the solar light induced photocatalytic application performances of TiO2, in this study, the SeO2 modified TiO2 composite photocatalysts with various ratios of SeO2 to TiO2 were prepared by sol-gel method. The catalyst was characterized by X-ray diffraction (XRD), high resolution scanning electron microscope (HR-SEM), energy dispersive spectra (EDS), diffuse reflectance spectra (DRS), photoluminescence spectra (PL), X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) surface area measurement methods. The photocatalytic activity of SeO2/TiO2 was investigated for the degradation of sunset yellow (SY) in aqueous solution using solar light. The SeO2/TiO2 is found to be more efficient than prepared TiO2 and TiO2-P25 at pH 7 for the mineralization of SY. The effects of operational parameters such as the amount of photocatalyst, dye concentration and initial pH on photo mineralization of SY have been analyzed. The degradation was strongly enhanced in the presence of electron acceptors such as oxone, KIO4 and KBrO3. The kinetics of SY photodegradation was found to follow the pseudo-first order rate law and could be described in terms of Langmuir-Hinshelwood model. The mineralization of SY has been confirmed by COD measurements. The catalyst is found to be reusable. PMID:25528508

Rajamanickam, D; Dhatshanamurthi, P; Shanthi, M



Enhanced sensitivity to conformation in various proteins. Vibrational circular dichroism results  

SciTech Connect

Vibrational circular dichroism (VCD) spectra of several globular proteins dissolved in D2O are presented and compared to conventional UV-CD results. It can be seen that, for the alpha, beta, and alpha + beta categories of Levitt and Chothia, VCD evidences much larger band shape variations, including sign alteration, than does UV-CD. A direct parallel is seen between the VCD of the alpha-helix found in model polypeptides and the amide I' VCD of myoglobin. Since all structural aspects of the protein contribute to the VCD on a roughly equal footing, a similar correlation of the chymotrypsin amide I' VCD with that of beta-sheet models is not as clear. In addition, the VCD of random-coil-type proteins is found to be clearly related to VCD results from random-coil polypeptides. Finally, simulations are presented to postulate the expected VCD for protein structures having conformations that lie between the limiting cases discussed here.

Pancoska, P.; Yasui, S.C.; Keiderling, T.A. (Univ. of Illinois, Chicago (USA))



Overexpression of a Gluten Protein in Transgenic Wheat Results in Greatly Increased Dough Strength  

Microsoft Academic Search

The transgenic wheat line B73-6-1 contains additional genes encoding a gluten protein called HMW subunit 1Dx5, resulting in a four-fold increase in the proportion of this component in the seed proteins and corresponding increases in the proportions of total HMW subunits and total glutenins. This is associated with a dramatic increase in dough strength, as measured using a small scale

L Rooke; F Békés; R Fido; F Barro; P Gras; A. S Tatham; P Barcelo; P Lazzeri; P. R Shewry



Human 14-3-3 gamma protein results in abnormal cell proliferation in the developing eye of Drosophila melanogaster  

Microsoft Academic Search

BACKGROUND: 14-3-3 proteins are a family of adaptor proteins that participate in a wide variety of cellular processes. Recent evidence indicates that the expression levels of these proteins are elevated in some human tumors providing circumstantial evidence for their involvement in human cancers. However, the mechanism through which these proteins act in tumorigenesis is uncertain. RESULTS: To determine whether elevated

Sophia W Hong; Wenqing Qi; Marc Brabant; Giovanni Bosco; Jesse D Martinez



First results from the PROTEIN experiment on board the International Space Station  

NASA Astrophysics Data System (ADS)

On March 15 2009 Space Shuttle Discovery was launched, carrying the Process Unit of the Protein Crystallization Diagnostics Facility (PCDF) to the International Space Station. It contained the PROTEIN experiment, aiming at the in-situ observation of nucleation and crystal growth behaviour of proteins. After installation in the European Drawer Rack (EDR) and connection to the PCDF Electronics Unit, experiment runs were performed continuously for 4 months. It was the first time that protein crystallization experiments could be modified on-orbit in near real-time, based on data received on ground. The data included pseudo-dark field microscope images, interferograms, and Dynamic Light Scattering data. The Process Unit with space grown crystals was returned to ground on July 31 2009. Results for the model protein glucose isomerase (Glucy) from Streptomyces rubiginosus crystallized with ammonium sulfate will be reported concerning nucleation and the growth from Protein and Impurities Depletion Zones (PDZs). In addition, results of x-ray analyses for space-grown crystals will be given.

Decanniere, Klaas; Potthast, Lothar; Pletser, Vladimir; Maes, Dominique; Otalora, Fermin; Gavira, Jose A.; Pati, Luis David; Lautenschlager, Peter; Bosch, Robert


Protein Radical Formation Resulting from Eosinophil Peroxidase-catalyzed Oxidation of Sulfite*  

PubMed Central

Eosinophil peroxidase (EPO) is an abundant heme protein in eosinophils that catalyzes the formation of cytotoxic oxidants implicated in asthma, allergic inflammatory disorders, and cancer. It is known that some proteins with peroxidase activity (horseradish peroxidase and prostaglandin hydroperoxidase) can catalyze oxidation of bisulfite (hydrated sulfur dioxide), leading to the formation of sulfur trioxide anion radical (·SO3?). This free radical further reacts with oxygen to form peroxymonosulfate anion radical (?O3SOO·) and the very reactive sulfate anion radical (SO4??), which is nearly as strong an oxidant as the hydroxyl radical. However, the ability of EPO to generate reactive sulfur radicals has not yet been reported. Here we demonstrate that eosinophil peroxidase/H2O2 is able to oxidize bisulfite, ultimately forming the sulfate anion radical (SO4??), and that these reactive intermediates can oxidize target proteins to protein radicals, thereby initiating protein oxidation. We used immuno-spin trapping and confocal microscopy to study protein oxidation by EPO/H2O2 in the presence of bisulfite in a pure enzymatic system and in human promyelocytic leukemia HL-60 clone 15 cells, maturated to eosinophils. Polyclonal antiserum raised against the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) detected the presence of DMPO covalently attached to the proteins resulting from the DMPO trapping of protein free radicals. We found that sulfite oxidation mediated by EPO/H2O2 induced the formation of radical-derived DMPO spin-trapped human serum albumin and, to a lesser extent, of DMPO-EPO. These studies suggest that EPO-dependent oxidative damage may play a role in tissue injury in bisulfite-exacerbated eosinophilic inflammatory disorders. PMID:20501663

Ranguelova, Kalina; Chatterjee, Saurabh; Ehrenshaft, Marilyn; Ramirez, Dario C.; Summers, Fiona A.; Kadiiska, Maria B.; Mason, Ronald P.



Small structural differences of targeted anti-tumor toxins result in strong variation of protein expression.  


Targeted anti-tumor toxins consist of a toxic functional moiety that is chemically linked or recombinantly fused to a cell-directing ligand. Ribosome-inactivating proteins (RIPs), especially type I RIPs such as saporin or dianthin, are commonly used as toxin components. Although expression of type I RIP-based fusion proteins is well reported, the achievement of higher protein yields in heterologous expression systems through innovative strategies is of major interest. In the present study, the targeted toxins (his)saporin-EGF (SE) and (his)dianthin-EGF (DE) were expressed as fusion proteins under identical expression conditions. However, the total amount of DE was nearly two-times higher than SE. The identity of the heterologously expressed targeted toxins was confirmed by mass spectrometric studies. Their biological specific activity, monitored in real time, was almost equal. Sequence alignment shows 84% identity and a structural comparison revealed five major differences, two of which affect the secondary structure resulting in a loop (SE) to ?-strand (DE) conversion and one introduces a gap in SE (after position 57). In conclusion, these structural variations resulted in different protein expression levels while codon usage and toxicity to bacteria were excluded as a cause. Minor structural differences identified in this study may be considered responsible for the protection of DE from bacterial proteases and therefore may serve as a lead to modify certain domains in type I RIP-based targeted toxins. PMID:23867360

Gilabert-Oriol, Roger; Thakur, Mayank; Weise, Christoph; Dernedde, Jens; von Mallinckrodt, Benedicta; Fuchs, Hendrik; Weng, Alexander



Ingestion of Casein and Whey Proteins Result in Muscle Anabolism after Resistance Exercise  

Microsoft Academic Search

TIPTON, K. D., T. A. ELLIOTT, M. G. CREE, S. E. WOLF, A. P. SANFORD, and R. R. WOLFE. Ingestion of Casein and Whey Proteins Result in Muscle Anabolism after Resistance Exercise. Med. Sci. Sports Exerc., Vol. 36, No. 12, pp. 2073-2081, 2004. Purpose: Determination of the anabolic response to exercise and nutrition is important for individuals who may benefit




Arenavirus budding resulting from viral-protein-associated cell membrane curvature  

PubMed Central

Viral replication occurs within cells, with release (and onward infection) primarily achieved through two alternative mechanisms: lysis, in which virions emerge as the infected cell dies and bursts open; or budding, in which virions emerge gradually from a still living cell by appropriating a small part of the cell membrane. Virus budding is a poorly understood process that challenges current models of vesicle formation. Here, a plausible mechanism for arenavirus budding is presented, building on recent evidence that viral proteins embed in the inner lipid layer of the cell membrane. Experimental results confirm that viral protein is associated with increased membrane curvature, whereas a mathematical model is used to show that localized increases in curvature alone are sufficient to generate viral buds. The magnitude of the protein-induced curvature is calculated from the size of the amphipathic region hypothetically removed from the inner membrane as a result of translation, with a change in membrane stiffness estimated from observed differences in virion deformation as a result of protein depletion. Numerical results are based on experimental data and estimates for three arenaviruses, but the mechanisms described are more broadly applicable. The hypothesized mechanism is shown to be sufficient to generate spontaneous budding that matches well both qualitatively and quantitatively with experimental observations. PMID:23864502

Schley, David; Whittaker, Robert J.; Neuman, Benjamin W.



Loss of Photoreceptors Results in Upregulation of Synaptic Proteins in Bipolar Cells and Amacrine Cells  

PubMed Central

Deafferentation is known to cause significant changes in the postsynaptic neurons in the central nervous system. Loss of photoreceptors, for instance, results in remarkable morphological and physiological changes in bipolar cells and horizontal cells. Retinal ganglion cells (RGCs), which send visual information to the brain, are relatively preserved, but show aberrant firing patterns, including spontaneous bursts of spikes in the absence of photoreceptors. To understand how loss of photoreceptors affects the circuitry presynaptic to the ganglion cells, we measured specific synaptic proteins in two mouse models of retinal degeneration. We found that despite the nearly total loss of photoreceptors, the synaptophysin protein and mRNA levels in retina were largely unaltered. Interestingly, the levels of synaptophysin in the inner plexiform layer (IPL) were higher, implying that photoreceptor loss results in increased synaptophysin in bipolar and/or amacrine cells. The levels of SV2B, a synaptic protein expressed by photoreceptors and bipolar cells, were reduced in whole retina, but increased in the IPL of rd1 mouse. Similarly, the levels of syntaxin-I and synapsin-I, synaptic proteins expressed selectively by amacrine cells, were higher after loss of photoreceptors. The upregulation of syntaxin-I was evident as early as one day after the onset of photoreceptor loss, suggesting that it did not require any massive or structural remodeling, and therefore is possibly reversible. Together, these data show that loss of photoreceptors results in increased synaptic protein levels in bipolar and amacrine cells. Combined with previous reports of increased excitatory and inhibitory synaptic currents in RGCs, these results provide clues to understand the mechanism underlying the aberrant spiking in RGCs. PMID:24595229

Dagar, Sushma; Nagar, Saumya; Goel, Manvi; Cherukuri, Pitchaiah; Dhingra, Narender K.



Transiting Exoplanet Survey Satellite (TESS) Community Observer Program including the Science Enhancement Option Box (SEO Box) - 12 TB On-board Flash Memory for Serendipitous Science  

NASA Astrophysics Data System (ADS)

The Transiting Exoplanet Survey Satellite (TESS) will perform an all-sky survey in a low-inclination, low-Earth orbit. TESS's 144 GB of raw data collected each orbit will be stacked, cleaned, cut, compressed and downloaded. The Community Observer Program is a Science Enhancement Option (SEO) that takes advantage of the low-radiation environment, technology advances in flash memory, and the vast amount of astronomical data collected by TESS. The Community Observer Program requires the addition of a 12 TB "SEO Box” inside the TESS Bus. The hardware can be built using low-cost Commercial Off-The-Shelf (COTS) components and fits within TESS's margins while accommodating GSFC gold rules. The SEO Box collects and stores a duplicate of the TESS camera data at a "raw” stage ( 4.3 GB/orbit, after stacking and cleaning) and makes them available for on-board processing. The sheer amount of onboard storage provided by the SEO Box allows the stacking and storing of several months of data, allowing the investigator to probe deeper in time prior to a given event. Additionally, with computation power and data in standard formats, investigators can utilize data-mining techniques to investigate serendipitous phenomenon, including pulsating stars, eclipsing binaries, supernovae or other transient phenomena. The Community Observer Program enables ad-hoc teams of citizen scientists to propose, test, refine and rank algorithms for on-board analysis to support serendipitous science. Combining "best practices” of online collaboration, with careful moderation and community management, enables this `crowd sourced’ participatory exploration with a minimal risk and impact on the core TESS Team. This system provides a powerful and independent tool opening a wide range of opportunity for science enhancement and secondary science. Support for this work has been provided by NASA, the Kavli Foundation, Google, and the Smithsonian Institution.

Schingler, Robert; Villasenor, J. N.; Ricker, G. R.; Latham, D. W.; Vanderspek, R. K.; Ennico, K. A.; Lewis, B. S.; Bakos, G.; Brown, T. M.; Burgasser, A. J.; Charbonneau, D.; Clampin, M.; Deming, L. D.; Doty, J. P.; Dunham, E. W.; Elliot, J. L.; Holman, M. J.; Ida, S.; Jenkins, J. M.; Jernigan, J. G.; Kawai, N.; Laughlin, G. P.; Lissauer, J. J.; Martel, F.; Sasselov, D. D.; Seager, S.; Torres, G.; Udry, S.; Winn, J. N.; Worden, S. P.




NSDL National Science Digital Library

Protein structure: Primary protein structure is a sequence of amino acids. Secondary protein structure occurs when the amino acids in the sequence are linked by hydrogen bonds. Tertiary protein structure occurs when certain attractions are present between alpha helices and pleated sheets. Quaternary protein structure is a protein consisting of more than one amino acid chain.

Darryl Leja (National Human Genome Research Institute REV)



Synthesis, Crystal Structure and Thermal Decomposition of the New Cadmium Selenite Chloride, Cd4(SeO3)2OCl2  

PubMed Central

A synthetic study in the Cd-Se-O-Cl system led to formation of the new oxochloride compound Cd4(SeO3)2OCl2 via solid state reactions. The compound crystallizes in the orthorhombic space group Fmmm with cell parameters a?=?7.3610(3) Å, b?=?15.4936(2) Å, c?=?17.5603(3) Å, Z?=?8, S?=?0.969, F(000)?=?2800, R?=?0.0185, Rw?=?0.0384. Single crystal X-ray data were collected at 293 K. The crystal structure can be considered as layered and the building units are distorted [Cd(1)O6] octahedra, distorted [Cd(2)O8] cubes, irregular [Cd(3)O4Cl2] polyhedra and SeO3E trigonal pyramids. There are two crystallographically unique Cl atoms that both are half occupied. Thermogravimetric studies show that the compound starts to decompose at 500°C. The crystal structure of the new compound is closely related to the previously described compound Cd4(SeO3)2Cl4(H2O). PMID:24844633

Rabbani, Faiz; Ajaz, Humayun; Zimmermann, Iwan; Johnsson, Mats



SAP deficiency results in a striking alteration of the protein profile in activated CD4 T cells.  


Deficiency in a protein called signaling lymphocytic activation molecule-associated protein (SAP) causes X-linked lymphoproliferative disease (XLP) and helper T cell-dependent antibody defects. To identify proteins regulated by SAP, we performed proteomic analyses of SAP deficient vs wild type T cells. Our results reveal protein species whose abundances are profoundly altered by SAP. Our work therefore identifies candidate cellular mediators of SAP-dependent T cell help. PMID:16823987

Kamperschroer, Cris; Swain, Susan L; Grussenmeyer, Thomas; Lefkovits, Ivan



Enhanced sensitivity to conformation in various proteins. Vibrational circular dichroism results  

Microsoft Academic Search

Vibrational circular dichroism (VCD) spectra of several globular proteins dissolved in D2O are presented and compared to conventional UV-CD results. It can be seen that, for the alpha, beta, and alpha + beta categories of Levitt and Chothia, VCD evidences much larger band shape variations, including sign alteration, than does UV-CD. A direct parallel is seen between the VCD of

Petr Pancoska; Sritana C. Yasui; Timothy A. Keiderling



Aging results in an unusual expression of Drosophila heat shock proteins  

SciTech Connect

The authors used high-resolution two-dimensional polyacrylamide gel electrophoresis to evaluate the effect of aging on the heat shock response in Drosophila melanogaster. Although the aging process is not well understood at the molecular level, recent observations suggest that quantitative changes in gene expression occur as these fruit flies approach senescence. Such genetic alterations are in accord with our present data, which clearly show marked differences in the synthesis of heat shock proteins between young and old fruit flies. In 10-day-old flies, a heat shock of 20 min results in the expression of 14 new proteins as detectable by two-dimensional electrophoresis of ({sup 35}S)methionine-labeled polypeptides, whereas identical treatment of 45-day-old flies leads to the expression of at least 50 new or highly up-regulated proteins. In addition, there is also a concomitant increase in the rate of synthesis of a number of the normal proteins in the older animals. Microdensitometric determinations of the low molecular weight heat shock polypeptides on autoradiographs of five age groups revealed that their maximum expression occurs at 47 days for a population of flies with a mean life span of 33.7 days. Moreover, a heat shock effect similar to that observed in senescent flies occurs in young flies fed canavanine, an arginine analogue, before heat shock.

Fleming, J.E.; Walton, J.K.; Dubitsky, R.; Bensch, K.G. (Linus Pauling Institute of Science and Medicine, Palo Alto, CA (USA))



Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142  

SciTech Connect

Cyanothece sp. ATCC 51142 is a diazotrophic cyanobacterium notable for its ability to perform oxygenic photosynthesis and dinitrogen fixation in the same single cell. Previous transcriptional analysis revealed that the existence of these incompatible cellular processes largely depends on tightly synchronized expression programs involving ,30% of genes in the genome. To expand upon current knowledge, we have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for,5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark conditions exhibited periodic oscillations in their abundances. Our results suggest that altered enzyme activities at different phases during the diurnal cycle can be attributed to changes in the abundance of related proteins and key compounds. The integration of global proteomics and transcriptomic data further revealed that post-transcriptional events are important for temporal regulation of processes such as photosynthesis in Cyanothece 51142. This analysis is the first comprehensive report on global quantitative proteomics in a unicellular diazotrophic cyanobacterium and uncovers novel findings about diurnal rhythms.

Stockel, Jana; Jacobs, Jon M.; Elvitigala, Thanura R.; Liberton, Michelle L.; Welsh, Eric A.; Polpitiya, Ashoka D.; Gritsenko, Marina A.; Nicora, Carrie D.; Koppenaal, David W.; Smith, Richard D.; Pakrasi, Himadri B.



The Results of Mancini's test depend on the presence bound metal cations in the test protein.  


Samples of human serum gamma-globulin with specifically bound copper or zinc cations were studied in Mancini's radial immunodiffusion test with human antibodies to IgG (H+L). The intensity of antibody binding to zinc-modified protein was 10-20% higher in comparison with the reference sample, while detection of gamma-globulin with bound copper by antibodies was 20-30% lower than in the corresponding reference sample. Comparison with the results of native gamma-globulin testing indicates limitations of Mancini's method as the quantitative assay for practical diagnosis, because under certain clinical conditions the traditional method can give over- and underestimated results. PMID:19110593

Cheknyov, S B; Denisova, E A; Mongush, E M; Shukhovtseva, Yu V



Protein crystal growth results from the United States Microgravity Laboratory-1 mission  

NASA Technical Reports Server (NTRS)

Protein crystal growth experiments have been performed by this laboratory on 18 Space Shuttle missions since April, 1985. In addition, a number of microgravity experiments also have been performed and reported by other investigators. These Space Shuttle missions have been used to grow crystals of a variety of proteins using vapor diffusion, liquid diffusion, and temperature-induced crystallization techniques. The United States Microgravity Laboratory - 1 mission (USML-1, June 25 - July 9, 1992) was a Spacelab mission dedicated to experiments involved in materials processing. New protein crystal growth hardware was developed to allow in orbit examination of initial crystal growth results, the knowledge from which was used on subsequent days to prepare new crystal growth experiments. In addition, new seeding hardware and techniques were tested as well as techniques that would prepare crystals for analysis by x-ray diffraction, a capability projected for the planned Space Station. Hardware that was specifically developed for the USML-1 mission will be discussed along with the experimental results from this mission.

Delucas, Lawrence J.; Moore, K. M.; Vanderwoerd, M.; Bray, T. L.; Smith, C.; Carson, M.; Narayana, S. V. L.; Rosenblum, W. M.; Carter, D.; Clark, A. D, Jr.



The sieve element occlusion gene family in dicotyledonous plants  

PubMed Central

Sieve element occlusion (SEO) genes encoding forisome subunits have been identified in Medicago truncatula and other legumes. Forisomes are structural phloem proteins uniquely found in Fabaceae sieve elements. They undergo a reversible conformational change after wounding, from a condensed to a dispersed state, thereby blocking sieve tube translocation and preventing the loss of photoassimilates. Recently, we identified SEO genes in several non-Fabaceae plants (lacking forisomes) and concluded that they most probably encode conventional non-forisome P-proteins. Molecular and phylogenetic analysis of the SEO gene family has identified domains that are characteristic for SEO proteins. Here, we extended our phylogenetic analysis by including additional SEO genes from several diverse species based on recently published genomic data. Our results strengthen the original assumption that SEO genes seem to be widespread in dicotyledonous angiosperms, and further underline the divergent evolution of SEO genes within the Fabaceae. PMID:21422825

Jekat, Stephan B; Nordzieke, Steffen; Reineke, Anna R; Müller, Boje; Bornberg-Bauer, Erich; Noll, Gundula A





... sources, such as fruits, vegetables, grains, nuts and seeds, lack one or more essential amino acids. Vegetarians ... protein came from animal sources. Diabetes Again, protein quality matters more than protein quantity when it comes ...


Divergent Evolution of CHD3 Proteins Resulted in MOM1 Refining Epigenetic Control in Vascular Plants  

PubMed Central

Arabidopsis MOM1 is required for the heritable maintenance of transcriptional gene silencing (TGS). Unlike many other silencing factors, depletion of MOM1 evokes transcription at selected loci without major changes in DNA methylation or histone modification. These loci retain unusual, bivalent chromatin properties, intermediate to both euchromatin and heterochromatin. The structure of MOM1 previously suggested an integral nuclear membrane protein with chromatin-remodeling and actin-binding activities. Unexpected results presented here challenge these presumed MOM1 activities and demonstrate that less than 13% of MOM1 sequence is necessary and sufficient for TGS maintenance. This active sequence encompasses a novel Conserved MOM1 Motif 2 (CMM2). The high conservation suggests that CMM2 has been the subject of strong evolutionary pressure. The replacement of Arabidopsis CMM2 by a poplar motif reveals its functional conservation. Interspecies comparison suggests that MOM1 proteins emerged at the origin of vascular plants through neo-functionalization of the ubiquitous eukaryotic CHD3 chromatin remodeling factors. Interestingly, despite the divergent evolution of CHD3 and MOM1, we observed functional cooperation in epigenetic control involving unrelated protein motifs and thus probably diverse mechanisms. PMID:18725928

?aikovski, Marian; Yokthongwattana, Chotika; Habu, Yoshiki; Nishimura, Taisuke; Mathieu, Olivier; Paszkowski, Jerzy



The antibody against a nuclear autoantigenic sperm protein can result in reproductive failure  

Microsoft Academic Search

To study whether the antibody against the testis form of the nuclear autoantigenic sperm protein (tNASP) could result in reproductive failure, we successfully cloned and expressed a 339-bp cDNA fragment of mouse tNASP (mtNASP). Using mouse as a model, recombinant mtNASP (rmtNASP) and a synthetic peptide, human tNASP393-408 (htNASP393–408), were investigated for their antifertility effect. Active immunization with rmtNASP or

Min Wang; Jian-Li Shi; Guo-Yan Cheng; Yan-Qing Hu; Chen Xu



Correlating labeling chemistry and in-vitro test results with the biological behavior of radiolabeled proteins  

SciTech Connect

Monoclonal antibodies possess enormous potential for delivery of therapeutic amounts of radionuclides to target antigens in vivo, in particular for tumor imaging and therapy. Translation of this concept into practice has encountered numerous problems. Specifically whereas general protein radiolabeling methods are applicable to antibodies, immunological properties of the antibodies are often compromised resulting in reduced in-vivo specificity for the target antigens. The bifunctional chelating agent approach shows the most promise, however, development of other agents will be necessary for widespread usefulness of this technique. The effects of labeling chemistry on the in-vivo behavior of several monoclonal antibodies are described. 30 refs., 4 figs., 10 tabs.

Srivastava, S.C.; Meinken, G.E.



Sulfoxidation with hydrogen peroxide catalyzed by [SeO(4){WO(O(2))(2)}(2)](2-).  


The selenium-containing dinuclear peroxotungstate, [(n-C(4)H(9))(4)N](2)[SeO(4){WO(O(2))(2)}(2)] (I), acts as a homogeneous catalyst for the selective oxidation of various kinds of cyclic mono- and disulfides with 30% aqueous H(2)O(2). The cyclic disulfides were selectively oxidized to the corresponding monosulfoxides with one equivalent of H(2)O(2) with respect to the sulfides. In the presence of two equivalents of H(2)O(2), the oxidation of dibenzothiophene gave the corresponding sulfone in 98% yield under the mild conditions. The negative Hammett rho value (-0.62) for the competitive oxidation of p-substituted thioanisoles and the low X(SO) (X(SO) = (nucleophilic oxidation)/(total oxidation)) value of 0.14 for the I-catalyzed oxidation of thianthrene 5-oxide (SSO) revealed that I is a strong electrophilic oxidant. The reactivities of the di- and tetranuclear peroxotungstates with XO(4)(n-) ligands (X = Se(vi), As(v), P(v), S(vi), and Si(iv)) were strongly dependent on the kinds of hetero atoms. The reaction rates for the sulfoxidation decreased with an increase in the X(SO) values and a peroxotungstate with a stronger electrophilicity was more active for the sulfoxidation. The kinetic and mechanistic investigations showed that the electrophilic attack of the peroxo oxygen at the sulfur atom is a key step in the sulfoxidation. The computational investigation supported the high chemoselectivitiy for the sulfoxidation of diallyl sulfide. PMID:20454716

Kamata, Keigo; Hirano, Tomohisa; Ishimoto, Ryo; Mizuno, Noritaka



Mutations in Flavobacterium johnsoniae sprE result in defects in gliding motility and protein secretion.  


Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Transposon mutagenesis was used to identify sprE, which is involved in gliding. Mutations in sprE resulted in the formation of nonspreading colonies on agar. sprE mutant cells in wet mounts were almost completely deficient in attachment to and movement on glass, but a small percentage of cells exhibited slight movements, indicating that the motility machinery was not completely disrupted. SprE is a predicted lipoprotein with a tetratricopeptide repeat domain. SprE is similar in sequence to Porphyromonas gingivalis PorW, which is required for secretion of gingipain protease virulence factors. Disruption of F. johnsoniae sprE resulted in decreased extracellular chitinase activity and decreased secretion of the cell surface motility protein SprB. Reduced secretion of cell surface components of the gliding machinery, such as SprB, may account for the defects in gliding. Orthologs of sprE are found in many gliding and nongliding members of the phylum Bacteroidetes, suggesting that similar protein secretion systems are common among members of this large and diverse group of bacteria. PMID:21784937

Rhodes, Ryan G; Samarasam, Mudiarasan Napoleon; Van Groll, Eric J; McBride, Mark J



Mutations in Flavobacterium johnsoniae sprE Result in Defects in Gliding Motility and Protein Secretion?†  

PubMed Central

Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Transposon mutagenesis was used to identify sprE, which is involved in gliding. Mutations in sprE resulted in the formation of nonspreading colonies on agar. sprE mutant cells in wet mounts were almost completely deficient in attachment to and movement on glass, but a small percentage of cells exhibited slight movements, indicating that the motility machinery was not completely disrupted. SprE is a predicted lipoprotein with a tetratricopeptide repeat domain. SprE is similar in sequence to Porphyromonas gingivalis PorW, which is required for secretion of gingipain protease virulence factors. Disruption of F. johnsoniae sprE resulted in decreased extracellular chitinase activity and decreased secretion of the cell surface motility protein SprB. Reduced secretion of cell surface components of the gliding machinery, such as SprB, may account for the defects in gliding. Orthologs of sprE are found in many gliding and nongliding members of the phylum Bacteroidetes, suggesting that similar protein secretion systems are common among members of this large and diverse group of bacteria. PMID:21784937

Rhodes, Ryan G.; Samarasam, Mudiarasan Napoleon; Van Groll, Eric J.; McBride, Mark J.



TGF-?1 conjugated to gold nanoparticles results in protein conformational changes and attenuates the biological function.  


Gold nanoparticles (AuNPs) are widely used as carriers or therapeutic agents due to their great biocompatibility and unique physical properties. Transforming growth factor-beta 1 (TGF-?1), a member of the cysteine-knot structural superfamily, plays a pivotal role in many diseases and is known as an immunosuppressive agent that attenuates immune response resulting in tumor growth. The results reported herein reflect strong interactions between TGF-?1 and the surface of AuNPs when incubated with serum-containing medium, and demonstrate a time- and dose-dependent pattern. Compared with other serum proteins that can also bind to the AuNP surface, AuNP-TGF?1 conjugate is a thermodynamically favored compound. Epithelial cells undergo epithelial-mesenchymal transition (EMT) upon treatment with TGF-?1; however, treatment with AuNPs reverses this effect, as detected by cell morphology and expression levels of EMT markers. TGF-?1 is found to bind to AuNPs through S-Au bonds by X-ray photoelectron spectroscopy. Fourier transform infrared spectroscopy is employed to analyze the conformational changes of TGF-?1 on the surface of AuNPs. The results indicate that TGF-?1 undergoes significant conformational changes at both secondary and tertiary structural levels after conjugation to the AuNP surface, which results in the deactivation of TGF-?1 protein. An in vivo experiment also shows that addition of AuNPs attenuates the growth of TGF-?1-secreting murine bladder tumor 2 cells in syngeneic C3H/HeN mice, but not in immunocompromised NOD-SCID mice, and this is associated with an increase in the number of tumor-infiltrating CD4? and CD8? T lymphocytes and a decrease in the number of intrasplenic Foxp3(+) lymphocytes. The findings demonstrate that AuNPs may be a promising agent for modulating tumor immunity through inhibiting immunosuppressive TGF-?1 signaling. PMID:23335450

Tsai, Yuh-Shyan; Chen, Yu-Hung; Cheng, Pai-Chiao; Tsai, Hsin-Tzu; Shiau, Ai-Li; Tzai, Tzong-Shin; Wu, Chao-Liang



Disrupted Proteolipid Protein Trafficking Results in Oligodendrocyte Apoptosis in an Animal Model of Pelizaeus-Merzbacher Disease  

Microsoft Academic Search

Pelizaeus-Merzbacher disease (PMD) is a dysmyelinating disease resulting from mutations, dele- tions, or duplications of the proteolipid protein ( PLP ) gene. Distinguishing features of PMD include pleio- tropy and a range of disease severities among patients. Previously, we demonstrated that, when expressed in transfected fibroblasts, many naturally occurring mu- tant PLP alleles encode proteins that accumulate in the endoplasmic

Alexander Gow; Cherie M. Southwood; Robert A. Lazzarini





... meet their protein needs. With some planning, a vegetarian diet can easily meet the recommended protein needs of ... the American Dietetic Association and Dietitians of Canada: Vegetarian diets. JADA , 2003; 103(6) 748 – 765. 2 Source ...


Mutual Fund Trading Pressure: Firm-Level Stock Price Impact and Timing of SEOs  

E-print Network

We use price pressure resulting from purchases by mutual funds with large capital inflows to identify overvalued equity. This is a relatively exogenous overvaluation indicator as it is associated with who is buying—buyers ...

Khan, Mozaffar Nayim


Compromised Mitochondrial Fatty Acid Synthesis in Transgenic Mice Results in Defective Protein Lipoylation and Energy Disequilibrium  

PubMed Central

A mouse model with compromised mitochondrial fatty acid synthesis has been engineered in order to assess the role of this pathway in mitochondrial function and overall health. Reduction in the expression of mitochondrial malonyl CoA-acyl carrier protein transacylase, a key enzyme in the pathway encoded by the nuclear Mcat gene, was achieved to varying extents in all examined tissues employing tamoxifen-inducible Cre-lox technology. Although affected mice consumed more food than control animals, they failed to gain weight, were less physically active, suffered from loss of white adipose tissue, reduced muscle strength, kyphosis, alopecia, hypothermia and shortened lifespan. The Mcat-deficient phenotype is attributed primarily to reduced synthesis, in several tissues, of the octanoyl precursors required for the posttranslational lipoylation of pyruvate and ?-ketoglutarate dehydrogenase complexes, resulting in diminished capacity of the citric acid cycle and disruption of energy metabolism. The presence of an alternative lipoylation pathway that utilizes exogenous free lipoate appears restricted to liver and alone is insufficient for preservation of normal energy metabolism. Thus, de novo synthesis of precursors for the protein lipoylation pathway plays a vital role in maintenance of mitochondrial function and overall vigor. PMID:23077570

Smith, Stuart; Witkowski, Andrzej; Moghul, Ayesha; Yoshinaga, Yuko; Nefedov, Michael; de Jong, Pieter; Feng, Dejiang; Fong, Loren; Tu, Yiping; Hu, Yan; Young, Stephen G.; Pham, Thomas; Cheung, Carling; Katzman, Shana M.; Brand, Martin D.; Quinlan, Casey L.; Fens, Marcel; Kuypers, Frans; Misquitta, Stephanie; Griffey, Stephen M.; Tran, Son; Gharib, Afshin; Knudsen, Jens; Hannibal-Bach, Hans Kristian; Wang, Grace; Larkin, Sandra; Thweatt, Jennifer; Pasta, Saloni



Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber  

PubMed Central

Protein deficiency is the most crucial factor that affects physical growth and development and that increases morbidity and mortality especially in developing countries. Efforts have been made to improve protein quality and quantity in crop plants but with limited success. Here, we report the development of transgenic potatoes with enhanced nutritive value by tuber-specific expression of a seed protein, AmA1 (Amaranth Albumin 1), in seven genotypic backgrounds suitable for cultivation in different agro-climatic regions. Analyses of the transgenic tubers revealed up to 60% increase in total protein content. In addition, the concentrations of several essential amino acids were increased significantly in transgenic tubers, which are otherwise limited in potato. Moreover, the transgenics also exhibited enhanced photosynthetic activity with a concomitant increase in total biomass. These results are striking because this genetic manipulation also resulted in a moderate increase in tuber yield. The comparative protein profiling suggests that the proteome rebalancing might cause increased protein content in transgenic tubers. Furthermore, the data on field performance and safety evaluation indicate that the transgenic potatoes are suitable for commercial cultivation. In vitro and in vivo studies on experimental animals demonstrate that the transgenic tubers are also safe for human consumption. Altogether, these results emphasize that the expression of AmA1 is a potential strategy for the nutritional improvement of food crops. PMID:20855595

Chakraborty, Subhra; Chakraborty, Niranjan; Agrawal, Lalit; Ghosh, Sudip; Narula, Kanika; Shekhar, Shubhendu; Naik, Prakash S.; Pande, P. C.; Chakrborti, Swarup Kumar; Datta, Asis



DMBC: SEO (Search Engine Optimization) search engines in a natural, non-promoted or advertised way.  

E-print Network

A holistic approach to the development of a website. Design & content, social media, and beyond are all priority in search results ontrol: Low e you linking to? Embrace relevant and meaningful social media and purposes. Link Building ­ All social media should point back to your homepage · inks: Add additional

Stowell, Michael


Altered protein prenylation in Sertoli cells is associated with adult infertility resulting from childhood mumps infection  

PubMed Central

Mumps commonly affects children 5–9 yr of age, and can lead to permanent adult sterility in certain cases. However, the etiology of this long-term effect remains unclear. Mumps infection results in progressive degeneration of the seminiferous epithelium and, occasionally, Sertoli cell–only syndrome. Thus, the remaining Sertoli cells may be critical to spermatogenesis recovery after orchitis healing. Here, we report that the protein farnesylation/geranylgeranylation balance is critical for patients’ fertility. The expression of geranylgeranyl diphosphate synthase 1 (GGPPS) was decreased due to elevated promoter methylation in the testes of infertile patients with mumps infection history. When we deleted GGPPS in mouse Sertoli cells, these cells remained intact, whereas the adjacent spermatogonia significantly decreased after the fifth postnatal day. The proinflammatory MAPK and NF-?B signaling pathways were constitutively activated in GGPPS?/? Sertoli cells due to the enhanced farnesylation of H-Ras. GGPPS?/? Sertoli cells secreted an array of cytokines to stimulate spermatogonia apoptosis, and chemokines to induce macrophage invasion into the seminiferous tubules. Invaded macrophages further blocked spermatogonia development, resulting in a long-term effect through to adulthood. Notably, this defect could be rescued by GGPP administration in EMCV-challenged mice. Our results suggest a novel mechanism by which mumps infection during childhood results in adult sterility. PMID:23825187

Wang, Xiu-Xing; Ying, Pu; Diao, Fan; Wang, Qiang; Ye, Dan; Jiang, Chen; Shen, Ning; Xu, Na; Chen, Wei-Bo; Lai, Shan-Shan; Jiang, Shan; Miao, Xiao-Li; Feng, Jin; Tao, Wei-Wei; Zhao, Ning-Wei; Yao, Bing; Xu, Zhi-Peng; Sun, Hai-Xiang; Sha, Jia-Hao; Huang, Xing-Xu; Shi, Qing-Hua; Tang, Hong



SANS study of interaction of silica nanoparticles with BSA protein and their resultant structure  

NASA Astrophysics Data System (ADS)

Small angle neutron scattering (SANS) has been carried out to study the interaction of anionic silica nanoparticles (88 Å) with globular protein Bovine Serum Albumin (BSA) (M.W. 66.4 kD) in aqueous solution. The measurements have been carried out on fixed concentration (1 wt %) of Ludox silica nanoparticles with varying concentration of BSA (0-5 wt %) at pH7. Results show that silica nanoparticles and BSA coexist as individual entities at low concentration of BSA where electrostatic repulsive interactions between them prevent their aggregation. However, as the concentration of BSA increases (? 0.5 wt %), it induces the attractive depletion interaction among nanoparticles leading to finally their aggregation at higher BSA concentration (2 wt %). The aggregates are found to be governed by the diffusion limited aggregation (DLA) morphology of fractal nature having fractal dimension about 2.4.

Yadav, Indresh; Aswal, V. K.; Kohlbrecher, J.



Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders  

PubMed Central

Background Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery, suffer from the disadvantages of being random, time-consuming and expensive. To accelerate the process, traditional structure- or ligand-based VLS approaches are combined with experimental high-throughput screening, HTS. Often a single protein or, at most, a protein family is considered. Large scale VLS benchmarking across diverse protein families is rarely done, and the reported success rate is very low. Here, we demonstrate the experimental HTS validation of a novel VLS approach, FINDSITEcomb, across a diverse set of medically-relevant proteins. Results For eight different proteins belonging to different fold-classes and from diverse organisms, the top 1% of FINDSITEcomb’s VLS predictions were tested, and depending on the protein target, 4%-47% of the predicted ligands were shown to bind with ?M or better affinities. In total, 47 small molecule binders were identified. Low nanomolar (nM) binders for dihydrofolate reductase and protein tyrosine phosphatases (PTPs) and micromolar binders for the other proteins were identified. Six novel molecules had cytotoxic activity (<10 ?g/ml) against the HCT-116 colon carcinoma cell line and one novel molecule had potent antibacterial activity. Conclusions We show that FINDSITEcomb is a promising new VLS approach that can assist drug discovery. PMID:24936211



Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles.  

PubMed Central

We previously applied the Poisson-Boltzmann equation to atomic models of phospholipid bilayers and basic peptides to calculate their electrostatic interactions from first principles (Ben-Tal, N., B. Honig, R. M. Peitzsch, G. Denisov, and S. McLaughlan. 1996. Binding of small basic peptides to membranes containing acidic lipids. Theoretical models and experimental results. Biophys. J. 71:561-575). Specifically, we calculated the molar partition coefficient, K (the reciprocal of the lipid concentration at which 1/2 the peptide is bound), of simple basic peptides (e.g., pentalysine) with phospholipid vesicles. The theoretical predictions agreed well with experimental measurements of the binding, but the agreement could have been fortuitous because the structure(s) of these flexible peptides is not known. Here we use the same theoretical approach to calculate the membrane binding of two small proteins of known structure: charybdotoxin (CTx) and iberiotoxin (IbTx); we also measure the binding of these proteins to phospholipid vesicles. The theoretical model describes accurately the dependence of K on the ionic strength and mol % acidic lipid in the membrane for both CTx (net charge +4) and IbTx (net charge +2). For example, the theory correctly predicts that the value of K for the binding of CTx to a membrane containing 33% acidic lipid should decrease by a factor of 10(5) when the salt concentration increases from 10 to 200 mM. We discuss the limitations of the theoretical approach and also consider a simple extension of the theory that incorporates nonpolar interactions. Images FIGURE 1 FIGURE 4 PMID:9336168

Ben-Tal, N; Honig, B; Miller, C; McLaughlin, S



Dysfunction of nitric oxide induces protein kinase C activation resulting in vasospasm after subarachnoid hemorrhage.  


We hypothesize that the interaction between protein kinase C (PKC) and nitric oxide (NO) plays a role in the modulation of cerebral vascular tone, and the disturbance of this interaction following subarachnoid hemorrhage (SAH) results in vasospasm. To prove this hypothesis with direct evidence, PKC activities of smooth muscle cells of canine basilar arteries in the control and in the SAH groups were measured by an enzyme immunoassay method. N omega-nitro-L arginine (L-NA), an inhibitor of NO production, enhanced PKC activity. This enhancement was inhibited neither by 8-bromo-guanosine 3',5'-cyclic monophosphate (8-bromo-cGMP) nor SIN-1, a NO releasing agent. PKC activity in the SAH was significantly higher than in the control; however, no further enhancement was produced with L-NA. In the SAH, PKC activity was not inhibited either by 8-bromo-cGMP or SIN-1. We conclude that NO maintains an appropriate vascular tone through inactivation of PKC, and that this effect is disturbed following SAH, resulting in PKC-dependent vascular contraction, such as vasospasm. On the other hand, once PKC has been activated, NO precursors do not inhibit PKC. These facts indicate NO inactivates PKC through the inhibition of phosphatidylinositol breakdown. PMID:9329037

Nishizawa, S; Yamamoto, S; Yokoyama, T; Uemura, K




NSDL National Science Digital Library

Paul Anderson explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide.

Paul Anderson




ERIC Educational Resources Information Center

Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

Doolittle, Russell F.



Transcriptional activation by TAL1 and FUS-CHOP proteins expressed in acute malignancies as a result of chromosomal abnormalities.  

PubMed Central

Proteins that appear to participate in transcriptional control of gene expression are increasingly implicated in leukemias and malignant solid tumors. We report here that the N-terminal domains of the proteins TAL1 (ectopically activated in T-cell acute leukemias after chromosomal abnormalities caused by V-D-J recombinase error) (V, variable; D, diversity; J, joining) and FUS-CHOP (a liposarcoma tumor-specific fusion protein that is produced as a result of a chromosomal translocation) can function as transcription activators of specific responsive reporter genes. The result with TAL1 provides evidence that transcriptional activation can be mediated by a gene activated by translocation in T-cell acute leukemias. In the case of the liposarcoma, transactivation by the FUS-CHOP protein occurs because the FUS transcriptional activation domain is added to the DNA-binding CHOP protein normally lacking such activity. Therefore, the association of transcriptional activation and DNA-binding elements is a common consequence in proteins activated or newly created as fusion proteins after chromosomal translocations in acute leukemias and in malignant solid tumors. Images PMID:8058726

Sánchez-García, I; Rabbitts, T H



Heterologous Activation of Protein Kinase C Stimulates Phosphorylation of -Opioid Receptor at Serine 344, Resulting  

E-print Network

Heterologous Activation of Protein Kinase C Stimulates Phosphorylation of -Opioid Receptor of the current study is to investigate the effect of opioid-independent, heterologous activation of protein kinase C (PKC) on the responsiveness of opioid receptor and the underlying molecular mechanisms. Our

Tian, Weidong


Loss of Clcc1 Results in ER Stress, Misfolded Protein Accumulation, and Neurodegeneration.  


Folding of transmembrane and secretory proteins occurs in the lumen of the endoplasmic reticulum (ER) before transportation to the cell surface and is monitored by the unfolded protein response (UPR) signaling pathway. The accumulation of unfolded proteins in the ER activates the UPR that restores ER homeostasis by regulating gene expression that leads to an increase in the protein-folding capacity of the ER and a decrease in the ER protein-folding load. However, prolonged UPR activity has been associated with cell death in multiple pathological conditions, including neurodegeneration. Here, we report a spontaneous recessive mouse mutation that causes progressive cerebellar granule cell death and peripheral motor axon degeneration. By positional cloning, we identify the mutation in this strain as a retrotransposon insertion in the Clcc1 gene, which encodes a putative chloride channel localized to the ER. Furthermore, we demonstrate that the C3H/HeSnJ inbred strain has late onset cerebellar degeneration due to this mutation. Interestingly, acute knockdown of Clcc1 expression in cultured cells increases sensitivity to ER stress. In agreement, GRP78, the major HSP70 family chaperone in the ER, is upregulated in Clcc1-deficient granule cells in vivo, and ubiquitinated proteins accumulate in these neurons before their degeneration. These data suggest that disruption of chloride homeostasis in the ER disrupts the protein-folding capacity of the ER, leading to eventual neuron death. PMID:25698737

Jia, Yichang; Jucius, Thomas J; Cook, Susan A; Ackerman, Susan L



Moderate energy restriction with high protein diet results in healthier outcome in women  

PubMed Central

Background The present study compares two different weight reduction regimens both with a moderately high protein intake on body composition, serum hormone concentration and strength performance in non-competitive female athletes. Methods Fifteen normal weighted women involved in recreational resistance training and aerobic training were recruited for the study (age 28.5 ± 6.3 yr, height 167.0 ± 7.0 cm, body mass 66.3 ± 4.2 kg, body mass index 23.8 ± 1.8, mean ± SD). They were randomized into two groups. The 1 KG group (n = 8; energy deficit 1100 kcal/day) was supervised to reduce body weight by 1 kg per week and the 0.5 KG group (n = 7; energy deficit 550 kcal/day) by 0.5 kg per week, respectively. In both groups protein intake was kept at least 1.4 g/kg body weight/day and the weight reduction lasted four weeks. At the beginning of the study the energy need was calculated using food and training diaries. The same measurements were done before and after the 4-week weight reduction period including total body composition (DXA), serum hormone concentrations, jumping ability and strength measurements Results During the 4-week weight reduction period there were no changes in lean body mass and bone mass, but total body mass, fat mass and fat percentage decreased significantly in both groups. The changes were greater in the 1 KG group than in the 0.5 KG group in total body mass (p < 0.001), fat mass (p < 0.001) and fat percentage (p < 0.01). Serum testosterone concentration decreased significantly from 1.8 ± 1.0 to 1.4 ± 0.9 nmol/l (p < 0.01) in 1 KG and the change was greater in 1 KG (30%, p < 0.001) than in 0.5 KG (3%). On the other hand, SHBG increased significantly in 1 KG from 63.4 ± 17.7 to 82.4 ± 33.0 nmol/l (p < 0.05) during the weight reducing regimen. After the 4-week period there were no changes in strength performance in 0.5 KG group, however in 1 KG maximal strength in bench press decreased (p < 0.05) while endurance strength in squat and counter movement jump improved (p < 0.05) Conclusion It is concluded that a weight reduction by 0.5 kg per week with ~1.4 g protein/kg body weight/day can be recommended to normal weighted, physically active women instead of a larger (e.g. 1 kg per week) weight reduction because the latter may lead to a catabolic state. Vertical jumping performance is improved when fat mass and body weight decrease. Thus a moderate weight reduction prior to a major event could be considered beneficial for normal built athletes in jumping events. PMID:20205751



Targeted disruption of a G protein a subunit gene results in reduced pathogenicity in Fusarium oxysporum  

Microsoft Academic Search

The cloning of fga1, the gene encoding a G protein ! subunit, was performed by standard PCR techniques and by screening a Fusarium oxysporum genomic library, using the PCR product as a probe. The full-length open reading frame spanned 1,059 nucleotides and the deduced primary structure of the protein (353 amino acid residues) showed high identity to those of G

Sona Jain; Kouichi Akiyama; Kenjiro Mae; Tomizo Ohguchi; Renkichi Takata



Heme binding to albuminoid proteins is the result of recent evolution.  


We hypothesize that the structure of the heme binding site of paralogous albuminoids alpha-fetoprotein and serum albumin has evolved from the ancestor vitamin D binding protein through the 'phylogenetic intermediate' afamin, the most recently discovered albuminoid. Heme binding to plasma proteins should serve not only as a buffer for heme homeostasis, avoiding heme binding to lipoproteins with the consequent oxidative stress, but also for heme transfer to the liver, complementing the function of hemopexin. PMID:17654119

Fasano, Mauro; Fanali, Gabriella; Leboffe, Loris; Ascenzi, Paolo



Loss of C. elegans BBS-7 and BBS-8 protein function results in cilia defects and compromised intraflagellar transport  

PubMed Central

Bardet-Biedl syndrome (BBS) is a genetically heterogeneous developmental disorder whose molecular basis is largely unknown. Here, we show that mutations in the Caenorhabditis elegans bbs-7 and bbs-8 genes cause structural and functional defects in cilia. C. elegans BBS proteins localize predominantly at the base of cilia, and like proteins involved in intraflagellar transport (IFT), a process necessary for cilia biogenesis and maintenance, move bidirectionally along the ciliary axoneme. Importantly, we demonstrate that BBS-7 and BBS-8 are required for the normal localization/motility of the IFT proteins OSM-5/Polaris and CHE-11, and to a notably lesser extent, CHE-2. We propose that BBS proteins play important, selective roles in the assembly and/or function of IFT particle components. Our findings also suggest that some of the cardinal and secondary symptoms of BBS, such as obesity, diabetes, cardiomyopathy, and learning defects may result from cilia dysfunction. PMID:15231740

Blacque, Oliver E.; Reardon, Michael J.; Li, Chunmei; McCarthy, Jonathan; Mahjoub, Moe R.; Ansley, Stephen J.; Badano, Jose L.; Mah, Allan K.; Beales, Philip L.; Davidson, William S.; Johnsen, Robert C.; Audeh, Mark; Plasterk, Ronald H.A.; Baillie, David L.; Katsanis, Nicholas; Quarmby, Lynne M.; Wicks, Stephen R.; Leroux, Michel R.



Effect of a High-Protein Diet on Kidney Function in Healthy Adults: Results From the OmniHeart Trial  

PubMed Central

Background Consumption of a diet high in protein can cause glomerular hyperfiltration, a potentially maladaptive response, which may accelerate the progression of kidney disease. Study Design An ancillary study of the OmniHeart trial, a randomized 3-period crossover feeding trial testing the effects of partial replacement of carbohydrate with protein on kidney function. Setting & Participants Healthy adults (N=164) with prehypertension or stage 1 hypertension at a community-based research clinic with a metabolic kitchen. Intervention Participants were fed each of 3 diets for 6 weeks. Feeding periods were separated by a 2- to 4-week washout period. Weight was held constant on each diet. The 3 diets emphasized carbohydrate, protein, or unsaturated fat; dietary protein was either 15% (carbohydrate and unsaturated fat diets) or 25% (protein diet) of energy intake. Outcomes Fasting serum creatinine, cystatin C, and ?2-microglobulin levels, estimated glomerular filtration rate (eGFR). Measurements Serum creatinine, cystatin C, and ?2-microglobulin collected at the end of each feeding period. Results Baseline cystatin C-based eGFR was 92.0±16.3 (SD) mL/min/1.73 m2. Compared with the carbohydrate and unsaturated fat diets, the protein diet increased cystatin C-based eGFR by ~4 mL/min/1.73 m2 (P < 0.001). The effects of the protein diet on kidney function were independent of changes in blood pressure. There was no significant difference between the carbohydrate and unsaturated fat diets. Limitations Participants did not have kidney disease at baseline. Conclusions A healthy diet rich in protein increased eGFR. Whether long-term consumption of a high-protein diet leads to kidney disease is uncertain. PMID:23219108

Juraschek, Stephen P.; Appel, Lawrence J.; Anderson, Cheryl A.M.; Miller, Edgar R.



Abstract--Most high-throughput experimental results of protein-protein interactions (PPIs) are seemingly inconsistent  

E-print Network

, this concordance also held true for more general inter-platform and intra-species comparisons (Pearson correlation have low concordance with each other. Recently, tandem affinity purification followed by mass (association scores), and the resulting DDI profiles of association scores allowed us to evaluate the inherent


Total Protein Concentration and Diagnostic Test Results for Gray Wolf (Canis lupus) Serum using Nobuto Filter Paper Strips.  


Nobuto filter paper strips are widely used for storing blood-serum samples, but the recovery of proteins from these strips following rehydration is unknown. Poor recovery of proteins could reduce the concentration of antibodies and antigens and reduce the sensitivity of diagnostic assays. We compared the protein concentration, and its association with test sensitivity, of eluted Nobuto strip samples with paired sera. We collected and froze serum from five gray wolves (Canis lupus) for 8 mo. When thawed, we used a spectrophotometer (absorbance 280 nm) to determine the serum protein concentration for paired sera and Nobuto eluates for each animal in 2-fold serial dilutions. Total protein concentration was similar for both sample storage methods (Nobuto eluates and control sera), except for the undiluted samples in which Nobuto eluates had higher total protein concentrations. Both sample storage methods appear to produce similar results using the SNAP® 4Dx® Test to detect antibodies against pathogens causing Lyme disease, anaplasmosis, and ehrlichiosis as well as antigen for canine heartworm disease. PMID:25574804

Jara, Rocío F; Sepúlveda, Carolina; Ip, Hon S; Samuel, Michael D



Results of a screening programme to identify plants or plant extracts that inhibit ruminal protein degradation.  


One aim of the EC Framework V project, 'Rumen-up' (QLK5-CT-2001-00 992), was to find plants or plant extracts that would inhibit the nutritionally wasteful degradation of protein in the rumen. A total of 500 samples were screened in vitro using 14C-labelled casein in a 30-min incubation with ruminal digesta. Eight were selected for further investigation using a batch fermentation system and soya protein and bovine serum albumin as proteolysis substrates; proteolysis was monitored over 12 h by the disappearance of soluble protein and the production of branched SCFA and NH3. Freeze-dried, ground foliage of Peltiphyllum peltatum, Helianthemum canum, Arbutus unedo, Arctostaphylos uva-ursi and Knautia arvensis inhibited proteolysis (P < 0.05), while Daucus carota, Clematis vitalba and Erica arborea had little effect. Inhibition by the first four samples appeared to be caused by the formation of insoluble tannin-protein complexes. The samples were rich in phenolics and inhibition was reversed by polyethyleneglycol. In contrast, K. arvensis contained low concentrations of phenolics and no tannins, had no effect in the 30-min assay, yet inhibited the degradation rate of soluble protein (by 14 %, P < 0.0001) and the production of branched SCFA (by 17 %, P < 0.05) without precipitating protein in the 12-h batch fermentation. The effects showed some resemblance to those obtained in parallel incubations containing 3 mum-monensin, suggesting that K. arvensis may be a plant-derived feed additive that can suppress growth and activity of key proteolytic ruminal micro-organisms in a manner similar to that already well known for monensin. PMID:17445338

Selje, N; Hoffmann, E M; Muetzel, S; Ningrat, R; Wallace, R J; Becker, K



Accumulation of mutant huntingtin fragments in aggresome-like inclusion bodies as a result of insufficient protein degradation.  


The huntingtin exon 1 proteins with a polyglutamine repeat in the pathological range (51 or 83 glutamines), but not with a polyglutamine tract in the normal range (20 glutamines), form aggresome-like perinuclear inclusions in human 293 Tet-Off cells. These structures contain aggregated, ubiquitinated huntingtin exon 1 protein with a characteristic fibrillar morphology. Inclusion bodies with truncated huntingtin protein are formed at centrosomes and are surrounded by vimentin filaments. Inhibition of proteasome activity resulted in a twofold increase in the amount of ubiquitinated, SDS-resistant aggregates, indicating that inclusion bodies accumulate when the capacity of the ubiquitin-proteasome system to degrade aggregation-prone huntingtin protein is exhausted. Immunofluorescence and electron microscopy with immunogold labeling revealed that the 20S, 19S, and 11S subunits of the 26S proteasome, the molecular chaperones BiP/GRP78, Hsp70, and Hsp40, as well as the RNA-binding protein TIA-1, the potential chaperone 14-3-3, and alpha-synuclein colocalize with the perinuclear inclusions. In 293 Tet-Off cells, inclusion body formation also resulted in cell toxicity and dramatic ultrastructural changes such as indentations and disruption of the nuclear envelope. Concentration of mitochondria around the inclusions and cytoplasmic vacuolation were also observed. Together these findings support the hypothesis that the ATP-dependent ubiquitin-proteasome system is a potential target for therapeutic interventions in glutamine repeat disorders. PMID:11359930

Waelter, S; Boeddrich, A; Lurz, R; Scherzinger, E; Lueder, G; Lehrach, H; Wanker, E E



Recombinant PNPLA3 protein shows triglyceride hydrolase activity and its I148M mutation results in loss of function.  


The patatin-like phospholipase domain containing 3 (PNPLA3, also called adiponutrin, ADPN) is a membrane-bound protein highly expressed in the liver. The genetic variant I148M (rs738409) was found to be associated with progression of chronic liver disease. We aimed to establish a protein purification protocol in a yeast system (Pichia pastoris) and to examine the human PNPLA3 enzymatic activity, substrate specificity and the I148M mutation effect. hPNPLA3 148I wild type and 148M mutant cDNA were cloned into P. pastoris expression vectors. Yeast cells were grown in 3L fermentors. PNPLA3 protein was purified from membrane fractions by Ni-affinity chromatography. Enzymatic activity was assessed using radiolabeled substrates. Both 148I wild type and 148M mutant proteins are localized to the membrane. The wild type protein shows a predominant lipase activity with mild lysophosphatidic acid acyl transferase activity (LPAAT) and the I148M mutation results in a loss of function of both these activities. Our data show that PNPLA3 has a predominant lipase activity and I148M mutation results in a loss of function. PMID:24369119

Pingitore, Piero; Pirazzi, Carlo; Mancina, Rosellina M; Motta, Benedetta M; Indiveri, Cesare; Pujia, Arturo; Montalcini, Tiziana; Hedfalk, Kristina; Romeo, Stefano



Millions of years of life's struggle for survival in different environments have resulted in proteins providing  

E-print Network

energy from the environment to repairing and replicating their own code. Good solu- tions to biological problems can also be good solutions to human problems -- proteins are widely used in the food, chemicals the details. Evolution, however, had no difficulty generating these impressive molecules. Despite

Arnold, Frances H.


TATA Binding Protein Discriminates between Different Lesions on DNA, Resulting in a Transcription Decrease  

Microsoft Academic Search

DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription- competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic




Diminished Self-Chaperoning Activity of the DF508 Mutant of CFTR Results in Protein Misfolding  

E-print Network

design strategies of cystic fibrosis treatment. Here we show that the deletion of Phe508 alters Chapel Hill, Chapel Hill, North Carolina, United States of America, 3 Cystic Fibrosis Research Center The absence of a functional ATP Binding Cassette (ABC) protein called the Cystic Fibrosis Transmembrane

Dokholyan, Nikolay V.


Analysis of proteins in bronchoalveolar lavage fluids during pulmonary edema resulting from nitrogen dioxide and cadmium exposure  

SciTech Connect

We have developed a new HPLC method by which quantitative measurements can be made on the biochemical constituents of the extracellular fluid lining of the lung as sampled by bronchoalveolar lavage. Nine of the fractions are proteins, two are phospholipids, and two fractions remained unidentified. Rats were subjected to the intrapulmonary deposition of cadmium, a treatment model known to induce pulmonary edema and cause a translocation of blood compartment proteins into the lung's alveolar space compartment. Resulting pulmonary edema was hallmarked by /approximately/25-fold increases in three major blood compartment-derived HPLC protein fractions, two of which have been identified as albumin and immunoglobulin(s). Analysis of lavage fluid from rats exposed to 100 ppM NO/sub 2/ for 15 min, an exposure regimen which also produces pulmonary edema, indicated that the three blood compartment proteins in the lavage fluids were elevated 35- to 72-fold over controls 24 h after exposure. These results demonstrate that HPLC can be used to provide a highly sensitive method for detection and quantitation of pulmonary edema that can occur in acute lung injuries resulting from environmental insults.

Gurley, L.R.; London, J.E.; Dethloff, L.A.; Lehnert, B.E.



Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans  

PubMed Central

Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section. PMID:18842128

Sela, Noa; Stern, Adi; Makalowski, Wojciech; Pupko, Tal; Ast, Gil



Protein High-Force Pulling Simulations Yield Low-Force Results  

PubMed Central

All-atom explicit-solvent molecular dynamics simulations are used to pull with extremely large constant force (750–3000 pN) on three small proteins. The introduction of a nondimensional timescale permits direct comparison of unfolding across all forces. A crossover force of approximately 1100 pN divides unfolding dynamics into two regimes. At higher forces, residues sequentially unfold from the pulling end while maintaining the remainder of the protein force-free. Measurements of hydrodynamic viscous stresses are made easy by the high speeds of unfolding. Using an exact low-Reynolds-number scaling, these measurements can be extrapolated to provide, for the first time, an estimate of the hydrodynamic force on low-force unfolding. Below 1100 pN, but surprisingly still at extremely large applied force, intermediate states and cooperative unfoldings as seen at much lower forces are observed. The force-insensitive persistence of these structures indicates that decomposition into unfolded fragments requires a large fluctuation. This finding suggests how proteins are constructed to resist transient high force. The progression of helix and sheet unfolding is also found to be insensitive to force. The force-insensitivity of key aspects of unfolding opens the possibility that numerical simulations can be accelerated by high applied force while still maintaining critical features of unfolding. PMID:22529933

Lichter, Seth; Rafferty, Benjamin; Flohr, Zachary; Martini, Ashlie



Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences.  


Repetitive nucleotide or amino acid sequences are often engineered into probes and biosensors to achieve functional readouts and robust signal amplification. However, these repeated sequences are notoriously prone to aberrant deletion and degradation, impacting the ability to correctly detect and interpret biological functions. Here, we introduce a facile and generalizable approach to solve this often unappreciated problem by modifying the nucleotide sequences of the target mRNA to make them nonrepetitive but still functional ("synonymous"). We first demonstrated the procedure by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and showed a dramatic improvement in signal and reproducibility in single-RNA detection in live cells. The same approach was extended to enhancing the stability of engineered fluorescent biosensors containing a fluorescent resonance energy transfer (FRET) pair of fluorescent proteins on which a great majority of systems thus far in the field are based. Using the synonymous modification to FRET biosensors, we achieved correct expression of full-length sensors, eliminating the aberrant truncation products that often were assumed to be due to nonspecific proteolytic cleavages. Importantly, the biological interpretations of the sensor are significantly different when a correct, full-length biosensor is expressed. Thus, we show here a useful and generally applicable method to maintain the integrity of expressed genes, critical for the correct interpretation of probe readouts. PMID:25877922

Wu, Bin; Miskolci, Veronika; Sato, Hanae; Tutucci, Evelina; Kenworthy, Charles A; Donnelly, Sara K; Yoon, Young J; Cox, Dianne; Singer, Robert H; Hodgson, Louis



A comprehensive platform to investigate protein-metal ion interactions by affinity capillary electrophoresis.  


In this work, the behavior of several metal ions with different globular proteins was investigated by affinity capillary electrophoresis. Screening was conducted by applying a proper rinsing protocol developed by our group. The use of 0.1M EDTA in the rinsing solution successfully desorbs metal ions from the capillary wall. The mobility ratio was used to evaluate the precision of the method. Excellent precision for repeated runs was achieved for different protein metal ion interactions (RSD% of 0.05-1.0%). Run times were less than 6min for all of the investigated interactions. The method has been successfully applied for the interaction study of Li(+), Na(+), Mg(2+), Ca(2+), Ba(2+), Al(3+), Ga(3+), La(3+), Pd(2+), Ir(3+), Ru(3+), Rh(3+), Pt(2+), Pt(4+), Os(3+), Au(3+), Au(+), Ag(+), Cu(1+), Cu(2+), Fe(2+), Fe(3+), Co(2+), Ni(2+), Cr(3+), V(3+), MoO4(2-) and SeO3(2-) with bovine serum albumin, ovalbumin, ?-lactoglobulin and myoglobin. Different interaction values were obtained for most of the tested metal ions even for that in the same metal group. Results were discussed and compared in view of metal and semimetal group's interaction behavior with the tested proteins. The calculated normalized difference of mobility ratios for each protein-metal ion interaction and its sign (positive and negative) has been successfully used to detect the interaction and estimate further coordination of the bound metal ion, respectively. The comprehensive platform summarizes all the obtained interaction results, and is valuable for any future protein-metal ion investigation. PMID:25638307

Alhazmi, Hassan A; Nachbar, Markus; Albishri, Hassan M; El-Hady, Deia Abd; Redweik, Sabine; El Deeb, Sami; Wätzig, Hermann



Th(VO3)2(SeO3) and Ln(VO3)2(IO3) (Ln = Ce, Pr, Nd, Sm, and Eu): unusual cases of aliovalent substitution.  


Th(VO3)2(SeO3) and Ln(VO3)2(IO3) (Ln = Ce, Pr, Nd, Sm, and Eu) have been prepared and characterized. Surprisingly, these compounds are isotypic and rather extreme examples of aliovalent substitution (Th(IV)vs. Ln(III); Se(IV)O3(2-)vs. I(V)O3(-)) are possible in this structure type. PMID:24590373

Eaton, Teresa; Lin, Jian; Cross, Justin N; Stritzinger, Jared T; Albrecht-Schmitt, Thomas E



Chemical and Structural Evolution in the Th-SeO3(2-)/SeO4(2-) System: from Simple Selenites to Cluster-Based Selenate Compounds.  


While extensive success has been gained in the structural chemistry of the U-Se system, the synthesis and characterization of Th-based Se structures are widely unexplored. Here, four new Th-Se compounds, ?-Th(SeO3)2, ?-Th(SeO3)2, Th(Se2O5)2, and Th3O2(OH)2(SeO4)3, have been obtained from mild hydrothermal or low-temperature (180-220 °C) flux conditions and were subsequently structurally and spectroscopically characterized. The crystal structures of ?-Th(SeO3)2 and ?-Th(SeO3)2 are based on ThO8 and SeO3 polyhedra, respectively, featuring a three-dimensional (3D) network with selenite anions filling in the Th channels along the a axis. Th(Se2O5)2 is a 3D framework composed of isolated ThO8 polyhedra interconnected by [Se2O5](2-) dimers. Th3O2(OH)2(SeO4)3 is also a 3D framework constructed by octahedral hexathorium clusters [Th6(?3-O)4(?3-OH)4](12+), which are interlinked by selenate groups SeO4(2-). The positions of the vibrational modes associated with both Se(IV)O3(2-) and Se(VI)O4(2-) units, respectively, were determined for four compounds, and the Raman spectra of ?- and ?-Th(SeO3)2 are compared and discussed in detail. PMID:25719971

Xiao, Bin; Langer, Eike; Dellen, Jakob; Schlenz, Hartmut; Bosbach, Dirk; Suleimanov, Evgeny V; Alekseev, Evgeny V



Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes.  


We analyze how artificial targeting of Suppressor of Under-Replication (SUUR) and HP1 proteins affects DNA replication in the "open," euchromatic regions. Normally these regions replicate early in the S phase and display no binding of either SUUR or HP1. These proteins were expressed as fusions with DNA-binding domain of GAL4 and recruited to multimerized UAS integrated in three euchromatic sites of the polytene X chromosome: 3B, 8D, and 18B. Using PCNA staining as a marker of ongoing replication, we showed that targeting of SUUR(GAL4DBD) and HP1(GAL4DBD) results in delayed replication of appropriate euchromatic regions. Specifically, replication at these regions starts early, much like in the absence of the fusion proteins; however, replication completion is significantly delayed. Notably, delayed replication was insufficient to induce underreplication. Recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on expression of a mini-white reporter, found near UAS. Whereas SUUR(GAL4DBD) had no measurable influence on mini-white expression, HP1(GAL4DBD) targeting silenced mini-white, even in the absence of functional SU(VAR)3-9. Furthermore, recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on the protein composition of target regions. HP1(GAL4DBD) but not SUUR(GAL4DBD) could displace an open chromatin marker, CHRIZ, from the tethering sites. PMID:25398563

Pokholkova, Galina V; Koryakov, Dmitry E; Pindyurin, Alexey V; Kozhevnikova, Elena N; Belyakin, Stepan N; Andreyenkov, Oleg V; Belyaeva, Elena S; Zhimulev, Igor F



High-pressure protein crystallography (HPPX): instrumentation, methodology and results on lysozyme crystals.  


A new set-up and associated methodology for the collection of angle-dispersive diffraction data from protein crystals submitted to high hydrostastic pressure have been developed on beamline ID30 at the ESRF. The instrument makes use of intense X-rays of ultra-short wavelength emitted by two collinear undulators, and combines a membrane-driven diamond-anvil cell mounted on a two-axis goniometer and an imaging-plate scanner. Sharp and clean diffraction pictures from tetragonal crystals of hen egg-white lysozyme (tHEWL) and orthorhombic crystals of bovine erythrocyte Cu, Zn superoxide dismutase (SOD) were recorded at room temperature and pressures up to 0.915 and 1.00 GPa, respectively. The compressibility of tHEWL was determined from unit-cell parameters determined at 24 different pressures up to 0.915 GPa. High-pressure diffraction data sets from several crystals of tHEWL were collected and analyzed. Merging of data recorded on different crystals at 0.30 and 0.58 GPa produced two sets of structure amplitudes with good resolution, completeness, redundancy and R(sym) values. A third set at 0.69 GPa was of a similar quality except a lower completeness. The three structures have been refined. The pressure-induced loss of crystalline order in a tHEWL crystal beyond 0.82 GPa was captured through a series of diffraction pictures. PMID:11524565

Fourme, R; Kahn, R; Mezouar, M; Girard, E; Hoerentrup, C; Prangé, T; Ascone, I



Phosphorylation of serine-46 in HPr, a key regulatory protein in bacteria, results in stabilization of its solution structure.  

PubMed Central

The serine-phosphorylated form of histidine-containing protein (HPr), a component of the phosphoenolpyruvate:sugar phosphotransferase system from Bacillus subtilis, has been characterized by NMR spectroscopy and solvent denaturation studies. The results indicate that phosphorylation of Ser 46, the N-cap of alpha-helix-B, does not cause a conformational change but rather stabilizes the helix. Amide proton exchange rates in helix-B are decreased and phosphorylation stabilizes the protein to solvent and thermal denaturation, with a delta delta G of 0.7-0.8 kcal mol-1. A mutant in which Ser 46 is replaced by aspartic acid shows a similar stabilization, indicating that an electrostatic interaction between the negatively charged groups and the helix macrodipole contributes significantly to the stabilization. PMID:8580838

Pullen, K.; Rajagopal, P.; Branchini, B. R.; Huffine, M. E.; Reizer, J.; Saier, M. H.; Scholtz, J. M.; Klevit, R. E.



Do endocrine disrupting chemicals threaten Mediterranean swordfish? Preliminary results of vitellogenin and Zona radiata proteins in Xiphias gladius.  


Endocrine Disrupting Chemicals (EDCs) have the potential to alter hormone pathways that regulate reproductive processes in wildlife and fishes. In this research the hypothesis that Mediterranean top predator species (such as large pelagic fish) are potentially at risk due to EDCs is investigated. These marine organisms tend to accumulate high concentrations of EDCs such as polyhalogenated aromatic hydrocarbons (PHAHs). The potential effects of EDCs on a fish species of commercial interest, the top predator Xiphias gladius (swordfish), were investigated using vitellogenin (Vtg) and Zona radiata proteins (Zrp) as diagnostic and prognostic biomarkers. Dramatic induction of typically female proteins (Vtg and Zrp) was detected by ELISA and Western Blot in adult males of the species. These results are the first warning of the potential risk for reproductive function of Mediterranean top predators, and suggest the need for continuous monitoring of this fragile marine environment. PMID:11763150

Fossi, M C; Casini, S; Ancora, S; Moscatelli, A; Ausili, A; Notarbartolo-di-Sciara, G




Technology Transfer Automated Retrieval System (TEKTRAN)

Transgenic Arabidopsis thaliana plants which express genes encoding insect, Dendroides canadensis, antifreeze proteins (AFP) were produced by Agrobacterium-mediated transformation. The antifreeze protein genes, both with and without the signal peptide sequence (for protein secretion), were expresse...


Frustration and Dzyaloshinsky-Moriya anisotropy in the kagome francisites Cu3Bi (SeO3)2 O2X (X = Br , Cl )  

NASA Astrophysics Data System (ADS)

We investigate the antiferromagnetic canting instability of the spin-1/2 kagome ferromagnet, as realized in the layered cuprates Cu3Bi (SeO3)2 O2X (X = Br , Cl ). While the local canting can be explained in terms of competing exchange interactions, the direction of the ferrimagnetic order parameter fluctuates strongly even at short distances on account of frustration which gives rise to an infinite ground state degeneracy at the classical level. In analogy with the kagome antiferromagnet, the accidental degeneracy is fully lifted only by nonlinear 1 /S corrections, rendering the selected uniform canted phase very fragile even for spins-1/2, as shown explicitly by coupled-cluster calculations. To account for the observed ordering, we show that the minimal description of these systems must include the microscopic Dzyaloshinsky-Moriya interactions, which we obtain from density-functional band-structure calculations. The model explains all qualitative properties of the kagome francisites, including the detailed nature of the ground state and the anisotropic response under a magnetic field. The predicted magnon excitation spectrum and quantitative features of the magnetization process call for further experimental investigations of these compounds.

Rousochatzakis, Ioannis; Richter, Johannes; Zinke, Ronald; Tsirlin, Alexander A.



Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.  


Methods developed originally to analyze domain motions from simulation [Proteins 27:425-437, 1997] are adapted and extended for the analysis of X-ray conformers and for proteins with more than two domains. The method can be applied as an automatic procedure to any case where more than one conformation is available. The basis of the methodology is that domains can be recognized from the difference in the parameters governing their quasi-rigid body motion, and in particular their rotation vectors. A clustering algorithm is used to determine clusters of rotation vectors corresponding to main-chain segments that form possible dynamic domains. Domains are accepted for further analysis on the basis of a ratio of interdomain to intradomain fluctuation, and Chasles' theorem is used to determine interdomain screw axes. Finally residues involved in the interdomain motion are identified. The methodology is tested on citrate synthase and the M6I mutant of T4 lysozyme. In both cases new aspects to their conformational change are revealed, as are individual residues intimately involved in their dynamics. For citrate synthase the beta sheet is identified to be part of the hinging mechanism. In the case of T4 lysozyme, one of the four transitions in the pathway from the closed to the open conformation, furnished four dynamic domains rather than the expected two. This result indicates that the number of dynamic domains a protein possesses may not be a constant of the motion. PMID:9489922

Hayward, S; Berendsen, H J



RNA editing in wheat mitochondria results in the conservation of protein sequences  

Microsoft Academic Search

RNA editing is a process that results in the production of a messenger RNA with nucleotide sequences that differ from those of the template DNA1, and provides another mechanism for modulating gene expression. The phenomenon was initially described in the mitochondria of protozoa2, 3. Here we report that RNA editing is also required for the correct expression of plant mitochondria!

José M. Gualberto; Lorenzo Lamattina; Géraldine Bonnard; Jacques-Henry Weil; Jean-Michel Grienenberger



Upregulation of elastase proteins results in aortic dilatation in mucopolysaccharidosis I mice  

E-print Network

-L-iduronidase (IDUA) deficiency. It results in fragmentation of elastin fibers in the aorta and heart valves via and dermatan sulfate. Elastin fragmentation causes aortic dilatation and valvular insufficiency, which can insufficiency due to reduced structural integrity of the valve. Dog [4,5] and mouse [3,6,7] models of MPS I also

Ponder, Katherine P.



ERIC Educational Resources Information Center

Describes the Collegiate Results Instrument (CRI), which measures a range of collegiate outcomes for alumni 6 years after graduation. The CRI was designed to target alumni from institutions across market segments and assess their values, abilities, work skills, occupations, and pursuit of lifelong learning. (EV)

Zemsky, Robert; Shaman, Susan; Shapiro, Daniel B.



Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring.  


Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3-13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease. PMID:25799107

de Pagter, Mirjam S; van Roosmalen, Markus J; Baas, Annette F; Renkens, Ivo; Duran, Karen J; van Binsbergen, Ellen; Tavakoli-Yaraki, Masoumeh; Hochstenbach, Ron; van der Veken, Lars T; Cuppen, Edwin; Kloosterman, Wigard P



Disruption of the Basal Body Protein POC1B Results in Autosomal-Recessive Cone-Rod Dystrophy  

PubMed Central

Exome sequencing revealed a homozygous missense mutation (c.317C>G [p.Arg106Pro]) in POC1B, encoding POC1 centriolar protein B, in three siblings with autosomal-recessive cone dystrophy or cone-rod dystrophy and compound-heterozygous POC1B mutations (c.199_201del [p.Gln67del] and c.810+1G>T) in an unrelated person with cone-rod dystrophy. Upon overexpression of POC1B in human TERT-immortalized retinal pigment epithelium 1 cells, the encoded wild-type protein localized to the basal body of the primary cilium, whereas this localization was lost for p.Arg106Pro and p.Gln67del variant forms of POC1B. Morpholino-oligonucleotide-induced knockdown of poc1b translation in zebrafish resulted in a dose-dependent small-eye phenotype, impaired optokinetic responses, and decreased length of photoreceptor outer segments. These ocular phenotypes could partially be rescued by wild-type human POC1B mRNA, but not by c.199_201del and c.317C>G mutant human POC1B mRNAs. Yeast two-hybrid screening of a human retinal cDNA library revealed FAM161A as a binary interaction partner of POC1B. This was confirmed in coimmunoprecipitation and colocalization assays, which both showed loss of FAM161A interaction with p.Arg106Pro and p.Gln67del variant forms of POC1B. FAM161A was previously implicated in autosomal-recessive retinitis pigmentosa and shown to be located at the base of the photoreceptor connecting cilium, where it interacts with several other ciliopathy-associated proteins. Altogether, this study demonstrates that POC1B mutations result in a defect of the photoreceptor sensory cilium and thus affect cone and rod photoreceptors. PMID:25018096

Roosing, Susanne; Lamers, Ideke J.C.; de Vrieze, Erik; van den Born, L. Ingeborgh; Lambertus, Stanley; Arts, Heleen H.; Boldt, Karsten; de Baere, Elfride; Klaver, Caroline C.W.; Coppieters, Frauke; Koolen, David A.; Lugtenberg, Dorien; Neveling, Kornelia; van Reeuwijk, Jeroen; Ueffing, Marius; van Beersum, Sylvia E.C.; Zonneveld-Vrieling, Marijke N.; Peters, Theo A.; Hoyng, Carel B.; Kremer, Hannie; Hetterschijt, Lisette; Letteboer, Stef J.F.; van Wijk, Erwin; Roepman, Ronald; den Hollander, Anneke I.; Cremers, Frans P.M.



GAS41 amplification results in overexpression of a new spindle pole protein.  


Amplification is a hallmark of many human tumors but the role of most amplified genes in human tumor development is not yet understood. Previously, we identified a frequently amplified gene in glioma termed glioma-amplified sequence 41 (GAS41). Using the TCGA data portal and performing experiments on HeLa and TX3868, we analyzed the role of GAS41 amplification on GAS41 overexpression and the effect on the cell cycle. Here we show that GAS41 amplification is associated with overexpression in the majority of cases. Both induced and endogenous overexpression of GAS41 leads to an increase in multipolar spindles. We showed that GAS41 is specifically associated with pericentrosome material. As result of an increased GAS41 expression we found bipolar spindles with misaligned chromosomes. This number was even increased by a combined overexpression of GAS41 and a reduced expression of NuMA. We propose that GAS41 amplification may have an effect on the highly altered karyotype of glioblastoma via its role during spindle pole formation. PMID:22619067

Schmitt, Jana; Fischer, Ulrike; Heisel, Sabrina; Strickfaden, Hilmar; Backes, Christina; Ruggieri, Alessia; Keller, Andreas; Chang, Paul; Meese, Eckart



Deletion of an ATP-binding cassette protein subfamily C transporter in Leishmania donovani results in increased virulence.  


Genome comparison of Leishmania species sequenced to date has identified several hundred differentially distributed genes which are present as functional genes in some species but as pseudogenes or absent in others. It is not clear whether these differentially distributed genes are important for disease, redundant or even harmful for a particular Leishmania species though a few of these genes have been implicated in Leishmania infection tissue tropism. The L. infantum LinJ.24.1510 gene is an ATP-binding cassette transporter protein subfamily C member which is present in L. donovani complex species and L. mexicana but absent in L. major and L. braziliensis and its substrate is unknown. Experimental deletion of this gene from L. donovani has resulted in an increase in growth as axenic amastigotes and increased virulence in infecting mice. To our knowledge, this is the first gene identified in Leishmania where its deletion results in hypervirulence. PMID:22841683

Zhang, Wen-Wei; Matlashewski, Greg



Directed evolution of the suicide protein O?-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability.  


Here we present a biophysical, structural, and computational analysis of the directed evolution of the human DNA repair protein O(6)-alkylguanine-DNA alkyltransferase (hAGT) into SNAP-tag, a self-labeling protein tag. Evolution of hAGT led not only to increased protein activity but also to higher stability, especially of the alkylated protein, suggesting that the reactivity of the suicide enzyme can be influenced by stabilizing the product of the irreversible reaction. Whereas wild-type hAGT is rapidly degraded in cells after alkyl transfer, the high stability of benzylated SNAP-tag prevents proteolytic degradation. Our data indicate that the intrinstic stability of a key ? helix is an important factor in triggering the unfolding and degradation of wild-type hAGT upon alkyl transfer, providing new insights into the structure-function relationship of the DNA repair protein. PMID:22280500

Mollwitz, Birgit; Brunk, Elizabeth; Schmitt, Simone; Pojer, Florence; Bannwarth, Michael; Schiltz, Marc; Rothlisberger, Ursula; Johnsson, Kai



Tamm-Horsfall protein in patients with kidney dama...[Urol Res. 2004] -PubMed Result Urol Res. 2004 May;32(2):79-83. Links  

E-print Network

Tamm-Horsfall protein in patients with kidney dama...[Urol Res. 2004] - PubMed Result Urol Res. 2004 May;32(2):79-83. Links Tamm-Horsfall protein in patients with kidney damage and diabetes in diabetic and control kidney tissue specimens with or without kidney damage. Immunogold labeling

Abraham, Nader G.


Loss of glial fibrillary acidic protein results in decreased glutamate transport and inhibition of PKA-induced EAAT2 cell surface trafficking  

Microsoft Academic Search

Loss of the astrocyte-specific intermediate filament protein, glial fibrillary acidic protein (GFAP) results in an increased susceptibility to ischemic insult, enhanced hippocampal LTP, and decreased cerebellar long-term depression (LTD). Because glutamate receptor activation plays a key role in cell death and cellular plasticity responses, we wanted to determine if alterations in glial glutamate transport could contribute to the GFAP null

Ethan G Hughes; Jamie L Maguire; Melanie T McMinn; Rachael E Scholz; Margaret L Sutherland



Promoter Hypomethylation Results in Increased Expression of Protein Phosphatase 2A in T Cells from Patients with Systemic Lupus Erythematosus  

PubMed Central

The catalytic subunit ? isoform of protein phosphatase 2A (PP2Ac?) activity, protein, and mRNA have been found increased in systemic lupus erythematosus (SLE) T cells and to contribute to decreased IL-2 production. The PP2Ac? promoter activity is controlled epigenetically through the methylation of a CpG within a cAMP response element (CRE) motif defined by its promoter. We considered that hypomethylation may account for the increased expression of PP2Ac? in patients with SLE. Using bisulfite sequencing, we found that SLE T cells displayed decreased DNA methylation in the promoter region compared with normal T cells. More importantly, we found that the CRE-defined CpG, which binds p-CREB, is significantly less methylated in SLE compared with normal T cells, and the levels of methylation correlated with decreased amounts of DNA methyltransferase 1 transcripts. Methylation intensity correlated inversely with levels of PP2Ac? mRNA and SLE disease activity. Chromatin immunoprecipitation assays revealed more binding of p-CREB to the CRE site in SLE T cells, resulting in increased expression of PP2Ac?. We propose that PP2Ac? represents a new methylation-sensitive gene that, like the previously reported CD70 and CD11a, contributes to the pathogenesis of SLE. PMID:21346232

Sunahori, Katsue; Juang, Yuang-Taung; Kyttaris, Vasileios C.; Tsokos, George C.



Disruption of srtA gene in Streptococcus suis results in decreased interactions with endothelial cells and extracellular matrix proteins.  


Streptococcus suis, a major pathogen of swine, is an emerging zoonotic agent which causes meningitis and septic shock. In this study, we investigated the ability of S. suis mutant strain (SRTDeltaA) lacking the sortase A gene (srtA) to interact with host cells and extracellular matrix (ECM) proteins, as well as its virulence in a mouse infection model. We demonstrated that mutant SRTDeltaA had reduced capacity to adhere to and invade porcine brain microvascular endothelial cells compared to the wild-type strain. In addition, mutant SRTDeltaA also showed significantly less adherence to plasma fibronectin, cellular fibronectin and collagen type I. However, disruption of srtA had little effect on the virulence of S. suis in a mouse intraperitoneal model of infection. These results indicate that surface proteins anchored by sortase A are required for a normal level of bacterial binding. However, other factors may also be important for S. suis virulence and interaction with host tissues. PMID:17954016

Vanier, G; Sekizaki, T; Domínguez-Punaro, M C; Esgleas, M; Osaki, M; Takamatsu, D; Segura, M; Gottschalk, M



Accumulation of a Brazil nut albumin in seeds of transgenic canola results in enhanced levels of seed protein methionine  

Microsoft Academic Search

We have increased the methionine content of the seed proteins of a commercial winter variety of canola by expressing a chimeric gene encoding a methionine-rich seed protein from Brazil nut in the seeds of transgenic plants. Transgenic canola seeds accumulate the heterologous methionine-rich protein at levels which range from 1.7% to 4.0% of the total seed protein and contain up

Susan B. Altenbach; Chiung-Chi Kuo; Lisa C. Staraci; Karen W. Pearson; Connie Wainwright; Anca Georgescu; Jeffrey Townsend



Two Novel Mutations in the C-Terminal Region of Centrosomal Protein 290 (CEP290) Result in Classic Joubert Syndrome.  


Joubert syndrome is a neurologic disorder with a pathognomonic "molar tooth sign" on brain imaging. The purpose of this study was to identify potential mutations in a Chinese patient with Joubert syndrome by targeted massively parallel sequencing. Taking advantage of high-throughput DNA sequencing technologies, 18 Joubert-causing genes of a Chinese patient with classic Joubert syndrome were sequenced at a time, and 2 novel variants in the CEP290 gene (c.7323_7327delAGAAG and c.6012-2A>G) were identified in this patient. Sanger validation showed that 2 variants were inherited from each parents, respectively. Both variants are located in the C-terminal region of the CEP290 protein and are predicted to be deleterious. The results support that the combination of targeted genes enrichment and next-generation sequencing is valuable molecular diagnostic tool and suitable for clinical application. PMID:24850569

Wang, Lixia; Yang, Yun; Song, Jieping; Mao, Liangwei; Wei, Xiaoming; Sun, Yan; Yang, Shuang; Mu, Feng; Wang, Hairong; Niu, Yanfeng



Nd 5O 4Cl[AsO 3] 2 and Gd 5O 4Br 3[SeO 3] 2: Two lanthanoid oxide halides with complex "lone-pair" oxoanions  

NASA Astrophysics Data System (ADS)

Both compounds, neodymium oxide chloride oxoarsenate(III) Nd 5O 4Cl[AsO 3] 2 and gadolinium oxide bromide oxoselenate(IV) Gd 5O 4Br 3[SeO 3] 2, were prepared by solid-state reactions from mixtures of the corresponding binary oxides and halides, and their crystal structures have been determined by X-ray diffraction of single crystals. They crystallize monoclinically ( a = 1241.62(9) pm, b = 565.78(4) pm, c = 902.03(7) pm, ? = 116.454(3)° for Nd 5O 4Cl[AsO 3] 2 and a = 1243.70(9) pm, b = 549.91(4) pm, c = 1005.28(8) pm, ? = 91.869(3)° for Gd 5O 4Br 3[SeO 3] 2) in space group C2/ m with two formula units per unit cell. The non-isotypic crystal structures contain three crystallographically different M 3+ cations (M = Nd and Gd). The coordination sphere of (M1) 3+ consists of eight oxygen atoms (CN = 8) exclusively, whereas (M2) 3+ carries six oxygen atoms and one X - anion (X = Cl and Br, CN = 7) in each case. For (M3) 3+, however, CN = 8 is realized by six oxygen atoms and two Cl - anions in Nd 5O 4Cl[AsO 3] 2, but five oxygen atoms and three Br - anions in Gd 5O 4Br 3[SeO 3] 2. The isolated pyramidal [AsO 3] 3-/[SeO 3] 2- anions ( d(As 3+-O 2-) = 175-179; d(Se 4+-O 2-) = 165-174 pm) originate from three oxygen atoms (O2 and two O3), which surround the As 3+/Se 4+ cations together with the stereochemically active non-bonding electron pair ( lone pair) ? 1-tetrahedrally (?(O-As-O) = 95-102; ?(O-Se-O) = 95-96°). Both crystal structures are built up of corrugated two-dimensional lanthanoid-oxygen layers {[}?2 consisting of edge- and corner-shared [OM 4] 10+ tetrahedra ( d(O 2--Nd 3+) = 228-242; d(O 2--Gd 3+) = 226-235 pm). The single Cl - anion in the neodymium and the two crystallographically independent Br - anions in the gadolinium compound reside in between these sheets, where the lone-pair electrons at the As 3+/Se 4+ cations point into the center of channels, which are formed by lanthanoid-oxygen layers and halide chains.

Kang, Dong-Hee; Wontcheu, Joseph; Schleid, Thomas



Perinatal Protein Malnutrition Affects Mitochondrial Function in Adult and Results in a Resistance to High Fat Diet-Induced Obesity  

PubMed Central

Epidemiological findings indicate that transient environmental influences during perinatal life, especially nutrition, may have deleterious heritable health effects lasting for the entire life. Indeed, the fetal organism develops specific adaptations that permanently change its physiology/metabolism and that persist even in the absence of the stimulus that initiated them. This process is termed “nutritional programming”. We previously demonstrated that mothers fed a Low-Protein-Diet (LPD) during gestation and lactation give birth to F1-LPD animals presenting metabolic consequences that are different from those observed when the nutritional stress is applied during gestation only. Compared to control mice, adult F1-LPD animals have a lower body weight and exhibit a higher food intake suggesting that maternal protein under-nutrition during gestation and lactation affects the energy metabolism of F1-LPD offspring. In this study, we investigated the origin of this apparent energy wasting process in F1-LPD and demonstrated that minimal energy expenditure is increased, due to both an increased mitochondrial function in skeletal muscle and an increased mitochondrial density in White Adipose Tissue. Importantly, F1-LPD mice are protected against high-fat-diet-induced obesity. Clearly, different paradigms of exposure to malnutrition may be associated with differences in energy expenditure, food intake, weight and different susceptibilities to various symptoms associated with metabolic syndrome. Taken together these results demonstrate that intra-uterine environment is a major contributor to the future of individuals and disturbance at a critical period of development may compromise their health. Consequently, understanding the molecular mechanisms may give access to useful knowledge regarding the onset of metabolic diseases. PMID:25118945

Jousse, Céline; Muranishi, Yuki; Parry, Laurent; Montaurier, Christophe; Even, Patrick; Launay, Jean-Marie; Carraro, Valérie; Maurin, Anne-Catherine; Averous, Julien; Chaveroux, Cédric; Bruhat, Alain; Mallet, Jacques; Morio, Béatrice; Fafournoux, Pierre



Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels  

PubMed Central

Background Plasmodium falciparum, the causative agent of severe human malaria, has evolved to become resistant to previously successful antimalarial chemotherapies, most notably chloroquine and the antifolates. The prevalence of resistant strains has necessitated the discovery and development of new chemical entities with novel modes-of-action. Although much effort has been invested in the creation of analogues based on existing drugs and the screening of chemical and natural compound libraries, a crucial shortcoming in current Plasmodial drug discovery efforts remains the lack of an extensive set of novel, validated drug targets. A requirement of these targets (or the pathways in which they function) is that they prove essential for parasite survival. The polyamine biosynthetic pathway, responsible for the metabolism of highly abundant amines crucial for parasite growth, proliferation and differentiation, is currently under investigation as an antimalarial target. Chemotherapeutic strategies targeting this pathway have been successfully utilized for the treatment of Trypanosomes causing West African sleeping sickness. In order to further evaluate polyamine depletion as possible antimalarial intervention, the consequences of inhibiting P. falciparum spermidine synthase (PfSpdSyn) were examined on a morphological, transcriptomic, proteomic and metabolic level. Results Morphological analysis of P. falciparum 3D7 following application of the PfSpdSyn inhibitor cyclohexylamine confirmed that parasite development was completely arrested at the early trophozoite stage. This is in contrast to untreated parasites which progressed to late trophozoites at comparable time points. Global gene expression analyses confirmed a transcriptional arrest in the parasite. Several of the differentially expressed genes mapped to the polyamine biosynthetic and associated metabolic pathways. Differential expression of corresponding parasite proteins involved in polyamine biosynthesis was also observed. Most notably, uridine phosphorylase, adenosine deaminase, lysine decarboxylase (LDC) and S-adenosylmethionine synthetase were differentially expressed at the transcript and/or protein level. Several genes in associated metabolic pathways (purine metabolism and various methyltransferases) were also affected. The specific nature of the perturbation was additionally reflected by changes in polyamine metabolite levels. Conclusions This study details the malaria parasite's response to PfSpdSyn inhibition on the transcriptomic, proteomic and metabolic levels. The results corroborate and significantly expand previous functional genomics studies relating to polyamine depletion in this parasite. Moreover, they confirm the role of transcriptional regulation in P. falciparum, particularly in this pathway. The findings promote this essential pathway as a target for antimalarial chemotherapeutic intervention strategies. PMID:20385001



Targeted disruption of a G protein ? subunit gene results in reduced growth and pathogenicity in Rhizoctonia solani  

Microsoft Academic Search

Cloning and disruption of Rga1, the gene encoding the G protein ? subunit in the rice sheath blight fungus Rhizoctonia solani, was investigated. The deduced primary structure of the Rga1-encoded protein showed high identity to those of G? subunits from other filamentous fungi. Disruption of Rga1 led to decreased vegetative growth and pathogenicity. The Rga1 disruptant showed altered colony morphology.

Kanlayani Charoensopharat; Nuntipa Aukkanit; Sudarat Thanonkeo; Weerasak Saksirirat; Pornthap Thanonkeo; Kouichi Akiyama




EPA Science Inventory

Measurements of neuron-specific (neurotypic) and glia-specific (fliotypic) proteins were used to characterize the toxic effects of TET on the developing CNS. Six proteins, each of which is associated with specific aspects of neuronal and glial development, were evaluated as follo...



Technology Transfer Automated Retrieval System (TEKTRAN)

A study was conducted to evaluate the effect of protein source and nutrient density on fish growth, feed efficiency, digestibility and plasma amino acid concentrations. A four by two factorial treatment arrangement with four protein sources (fishmeal/barley, plant concentrates, plant meals, animal ...


A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results.  


MS/MS and database searching has emerged as a valuable technology for rapidly analyzing protein expression, localization, and post-translational modifications. The probability-based search engine Mascot has found widespread use as a tool to correlate tandem mass spectra with peptides in a sequence database. Although the Mascot scoring algorithm provides a probability-based model for peptide identification, the independent peptide scores do not correlate with the significance of the proteins to which they match. Herein, we describe a heuristic method for organizing proteins identified at a specified false-discovery rate using Mascot-matched peptides. We call this method PROVALT, and it uses peptide matches from a random database to calculate false-discovery rates for protein identifications and reduces a complex list of peptide matches to a nonredundant list of homologous protein groups. This method was evaluated using Mascot-identified peptides from a Trypanosoma cruzi epimastigote whole-cell lysate, which was separated by multidimensional LC and analyzed by MS/MS. PROVALT was then compared with the two traditional methods of protein identification when using Mascot, the single peptide score and cumulative protein score methods, and was shown to be superior to both in regards to the number of proteins identified and the inclusion of lower scoring nonrandom peptide matches. PMID:15703444

Weatherly, D Brent; Atwood, James A; Minning, Todd A; Cavola, Cameron; Tarleton, Rick L; Orlando, Ron



Acylation-stimulating protein (ASP)/complement C3adesArg deficiency results in increased energy expenditure in mice.  


Acylation-stimulating protein (ASP) acts as a paracrine signal to increase triglyceride synthesis in adipocytes. In mice, C3 (the precursor to ASP) knock-out (KO) results in ASP deficiency and leads to reduced body fat and leptin levels yet they are hyperphagic. In the present study, we investigated the mechanism for this energy repartitioning. Compared with wild-type (WT) mice, male and female C3(-/-) ASP-deficient mice had elevated oxygen consumption (VO2) in both the active (dark) and resting (light) phases of the diurnal cycle: +8.9% males (p < 0.05) +9.4% females (p < 0.05). Increased physical activity (movement) was observed during the dark phase in female but not in male KO animals. Female WT mice moved 16.9 +/- 2.4 m whereas KO mice moved 30.1 +/- 5.4 m, over 12 h, +78.4%, p < 0.05). In contrast, there was no difference in physical activity in male mice, but a repartitioning of dietary fat following intragastric fat administration was noted. This was reflected by increased fatty acid oxidation in liver and muscle in KO mice, with increased UCP2 (inguinal fat) and UCP3 (muscle) mRNA expression (p = 0.005 and 0.036, respectively). Fatty acid uptake into brown adipose tissue (BAT) and white adipose tissue (WAT) was reduced as reflected by a decrease in the fatty acid incorporation into lipids (BAT -68%, WAT -29%. The decrease of FA incorporation was normalized by intraperitoneal administration of ASP at the time of oral fat administration. These results suggest that ASP deficiency results in energy repartitioning through different mechanisms in male and female mice. PMID:14615480

Xia, Zhunan; Stanhope, Kimber L; Digitale, Erin; Simion, Oana-Maria; Chen, Lanying; Havel, Peter; Cianflone, Katherine



Agricultural illustrations of 19th century Korea: 'Imwon gyeongjeji' (Treatises on Management of Forest and Garden) by Seo Yugu.  


The generative relationship between text and image has long been established. Its structure evolved historically as a result of varying understandings of the functions of art and technology. Agriculture illustration, which emerged in China during the Song dynasty, is a prime example of this creative dialogue in which aspects of both disciplines were combined. Political, technological, and aesthetic concerns informed the reformulations of this new genre. This paper will address agricultural illustrations on nineteenth-century Korea, when notable changes occurred in the visualization of agricultural texts. It will explore changes in the understanding of the roles of agriculture, technology, and labor through an analysis of shifts in modes of illustration and the texts selected. The relationship between technology and visual representations during late Joseon Korea will be contextualized through an exploration of the evolution of technical drawing in East Asia. This paper will suggest that the recognition of imagery's ability to convey textual and technical information provided an important alternative paradigm for the presentation and use of knowledge. PMID:22171414

Chung, Hyung-Min



A gene trap knockout of the Tiam-1 protein results in malformation of the early embryonic brain.  


Tiam-1 has been implicated in the development of the central nervous system. However, the in vivo function of Tiam-1 has not been fully determined in the developing mouse brain. In this study, we generated Tiam-1 knockout mice using a Tiam-1 gene-trapped embryonic stem cell line. Insertion of a gene trap vector into a genomic site downstream of exon 5 resulted in a mutant allele encoding a truncated protein fused with the ?-geo LacZ gene. Primary mouse embryonic fibroblasts lacking Tiam-1 revealed a significant decrease in Rac activity and cell proliferation. In addition, whole-mount embryonic LacZ expression analysis demonstrated that Tiam-1 is specifically expressed in regions of the developing brain, such as the caudal telencephalon and rostral diencephalon. More importantly, mouse embryos deficient in Tiam-1 gene expression displayed a severe defect in embryonic brain development, including neural tube closure defects or a dramatic decrease in brain size. These findings suggest that embryonic Tiam-1 expression plays a critical role during early brain development in mice. PMID:22661025

Yoo, Sooyeon; Kim, Yujin; Lee, Haeryung; Park, Sungjeong; Park, Soochul



Attenuation of bone morphogenetic protein signaling during amphibian limb development results in the generation of stage-specific defects.  


The vertebrate limb is one of the most intensively studied organs in the field of developmental biology. Limb development in tetrapod vertebrates is highly conserved and dependent on the interaction of several important molecular pathways. The bone morphogenetic protein (BMP) signaling cascade is one of these pathways and has been shown to be crucial for several aspects of limb development. Here, we have used a Xenopus laevis transgenic line, in which expression of the inhibitor Noggin is under the control of the heat-shock promoter hsp70 to examine the effects of attenuation of BMP signaling at different stages of limb development. Remarkably different phenotypes were produced at different stages, illustrating the varied roles of BMP in development of the limb. Very early limb buds appeared to be refractory to the effects of BMP attenuation, developing normally in most cases. Ectopic limbs were produced by overexpression of Noggin corresponding to a brief window of limb development at about stage 49/50, as recently described by Christen et al. (2012). Attenuation of BMP signaling in stage 51 or 52 tadpoles lead to a reduction in the number of digits formed, resulting in hypodactyly or ectrodactyly, as well as occasional defects in the more proximal tibia-fibula. Finally, inhibition at stage 54 (paddle stage) led to the formation of dramatically shortened digits resulting from loss of distal phalanges. Transcriptome analysis has revealed the possibility that more Noggin-sensitive members of the BMP family could be involved in limb development than previously suspected. Our analysis demonstrates the usefulness of heat-shock-driven gene expression as an effective method for inhibiting a developmental pathway at different times during limb development. PMID:23981117

Jones, Tamsin E M; Day, Robert C; Beck, Caroline W



Crowding Induces Differences in the Diffusion of Thermophilic and Mesophilic Proteins: A New Look at Neutron Scattering Results  

PubMed Central

The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior. PMID:22261067

Marcos, Enrique; Mestres, Pau; Crehuet, Ramon



Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.  


The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior. PMID:22261067

Marcos, Enrique; Mestres, Pau; Crehuet, Ramon



Mechanisms of cross-talk between G-protein-coupled receptors resulting in enhanced release of intracellular Ca2+.  

PubMed Central

Alteration in [Ca(2+)](i) (the intracellular concentration of Ca(2+)) is a key regulator of many cellular processes. To allow precise regulation of [Ca(2+)](i) and a diversity of signalling by this ion, cells possess many mechanisms by which they are able to control [Ca(2+)](i) both globally and at the subcellular level. Among these are many members of the superfamily of GPCRs (G-protein-coupled receptors), which are characterized by the presence of seven transmembrane domains. Typically, those receptors able to activate PLC (phospholipase C) enzymes cause release of Ca(2+) from intracellular stores and influence Ca(2+) entry across the plasma membrane. It has been well documented that Ca(2+) signalling by one type of GPCR can be influenced by stimulation of a different type of GPCR. Indeed, many studies have demonstrated heterologous desensitization between two different PLC-coupled GPCRs. This is not surprising, given our current understanding of negative-feedback regulation and the likely shared components of the signalling pathway. However, there are also many documented examples of interactions between GPCRs, often coupling preferentially to different signalling pathways, which result in a potentiation of Ca(2+) signalling. Such interactions have important implications for both the control of cell function and the interpretation of in vitro cell-based assays. However, there is currently no single mechanism that adequately accounts for all examples of this type of cross-talk. Indeed, many studies either have not addressed this issue or have been unable to determine the mechanism(s) involved. This review seeks to explore a range of possible mechanisms to convey their potential diversity and to provide a basis for further experimental investigation. PMID:12790797

Werry, Tim D; Wilkinson, Graeme F; Willars, Gary B



Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres.  


Double-stranded regions of the telomeres are recognized by proteins containing Myb-like domains conferring specificity toward telomeric repeats. Although biochemical and structural studies revealed basic molecular principles involved in DNA binding, relatively little is known about evolutionary pathways leading to various types of Myb domain-containing proteins in divergent species of eukaryotes. Recently we identified a novel type of telomere-binding protein YlTay1p from the yeast Yarrowia lipolytica containing two Myb domains (Myb1, Myb2) very similar to the Myb domain of mammalian TRF1 and TRF2. In this study we prepared mutant versions of YlTay1p lacking Myb1, Myb2, or both Myb domains and found that YlTay1p carrying either Myb domain exhibits preferential affinity to both Y. lipolytica (GGGTTAGTCA)(n) and human (TTAGGG)(n) telomeric sequences. Quantitative measurements of the protein binding to telomeric DNA revealed that the presence of both Myb domains is required for a high affinity of YlTay1p to either telomeric repeat. Additionally, we performed detailed thermodynamic analysis of the YlTay1p interaction with its cognate telomeric DNA, which is to our knowledge the first energetic description of a full-length telomeric-protein binding to DNA. Interestingly, when compared with human TRF1 and TRF2 proteins, YlTay1p exhibited higher affinity not only for Y. lipolytica telomeres but also for human telomeric sequences. The duplication of the Myb domain region in YlTay1p thus produces a synergistic effect on its affinity toward the cognate telomeric sequence, alleviating the need for homodimerization observed in TRF-like proteins possessing a single Myb domain. PMID:22815473

Visacka, Katarina; Hofr, Ctirad; Willcox, Smaranda; Necasova, Ivona; Pavlouskova, Jana; Sepsiova, Regina; Wimmerova, Michaela; Simonicova, Lucia; Nosek, Jozef; Fajkus, Jiri; Griffith, Jack D; Tomaska, Lubomir



How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.  


A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. PMID:22933379

Mascarenhas, Nahren Manuel; Kästner, Johannes



Analysis of proteins in bronchoalveolar lavage fluids during pulmonary edema resulting from nitrogen dioxide and cadmium exposure  

Microsoft Academic Search

We have developed a new HPLC method by which quantitative measurements can be made on the biochemical constituents of the extracellular fluid lining of the lung as sampled by bronchoalveolar lavage. Nine of the fractions are proteins, two are phospholipids, and two fractions remained unidentified. Rats were subjected to the intrapulmonary deposition of cadmium, a treatment model known to induce

L. R. Gurley; J. E. London; L. A. Dethloff; B. E. Lehnert



Conformational changes of hapten-protein conjugates resulting in improved broad-specificity and sensitivity of an ELISA for organophosphorus pesticides  

Technology Transfer Automated Retrieval System (TEKTRAN)

The type of hapten linkage to the carrier protein can play an important role in determining the nature of the resulting antibody response. Generic haptens using three types of linkers were synthesized (a monocarboxylic acid, an unsaturated hydrocarbon, and a carboxamido spacer). These haptens were...


An HLA-A2-restricte d Tyrosinase Antigen on Melanoma Cells Results from Posttranslational Modification and Suggests a Novel Pathway for Processing of Membrane Proteins  

Microsoft Academic Search

Summary T lymphocytes recognize antigens consisting ofpeptides presented by class I and II major histo- compatibility complex (MHC) molecules. The peptides identified so far have been predictable from the amino acid sequences of proteins. We have identified the natural peptide target of a CTL clone that recognizes the tyrosinase gene product on melanoma cells. The peptide results from posttranslational conversion

Jonathan C. A. Skipper; Ronald C. Hendrickson; Jeffrey Shabanowitz; Thomas Wolfel; Craig L. Slingluff; Thierry Boon; Donald F. Hunt; H. Engelhard


Cationization of immunoglobulin G results in enhanced organ uptake of the protein after intravenous administration in rats and primate  

SciTech Connect

Cationization of proteins in general enhances the cellular uptake of these macromolecules, and cationized antibodies are known to retain antigen binding properties. Therefore, cationized antibodies may be therapeutic and allow for intracellular immunization. The present studies test the hypothesis that the tissue uptake of cationized immunoglobulin G (IgG) after intravenous administration may be greatly increased relative to the uptake of native proteins. The pharmacokinetics of cationized immunoglobulin G clearance from blood, and the volume of distribution of the cationized or native protein (albumin, IgG) for 10 organs was measured both in anesthetized rats and in an anesthetized adult Macaca irus cynomologous monkey. Initial studies on brain showed that serum factors inhibited uptake of 125I-cationized IgG, but not 3H-cationized IgG. The blood-brain barrier permeability surface area product for 3H-cationized IgG was 0.57 {plus minus} 0.04 microliters min-1 g-1. The ratio of the volume of distribution of the 3-H-cationized IgG compared to 3H-labeled native albumin ranged from 0.9 (testis) to 15.7 (spleen) in the rat at 3 hr after injection, and a similarly enhanced organ uptake was observed in the primate. In conclusion, these studies demonstrate that cationization of immunoglobulin greatly increases organ uptake of the plasma protein compared to native immunoglobulins, and suggest that cationization of monoclonal antibodies may represent a potential new strategy for enhancing the intracellular delivery of these proteins.

Triguero, D.; Buciak, J.L.; Pardridge, W.M. (Department of Medicine, University of California, Los Angeles School of Medicine (USA))



Loss of lysosomal membrane protein NCU-G1 in mice results in spontaneous liver fibrosis with accumulation of lipofuscin and iron in Kupffer cells.  


Human kidney predominant protein, NCU-G1, is a highly conserved protein with an unknown biological function. Initially described as a nuclear protein, it was later shown to be a bona fide lysosomal integral membrane protein. To gain insight into the physiological function of NCU-G1, mice with no detectable expression of this gene were created using a gene-trap strategy, and Ncu-g1(gt/gt) mice were successfully characterized. Lysosomal disorders are mainly caused by lack of or malfunctioning of proteins in the endosomal-lysosomal pathway. The clinical symptoms vary, but often include liver dysfunction. Persistent liver damage activates fibrogenesis and, if unremedied, eventually leads to liver fibrosis/cirrhosis and death. We demonstrate that the disruption of Ncu-g1 results in spontaneous liver fibrosis in mice as the predominant phenotype. Evidence for an increased rate of hepatic cell death, oxidative stress and active fibrogenesis were detected in Ncu-g1(gt/gt) liver. In addition to collagen deposition, microscopic examination of liver sections revealed accumulation of autofluorescent lipofuscin and iron in Ncu-g1(gt/gt) Kupffer cells. Because only a few transgenic mouse models have been identified with chronic liver injury and spontaneous liver fibrosis development, we propose that the Ncu-g1(gt/gt) mouse could be a valuable new tool in the development of novel treatments for the attenuation of fibrosis due to chronic liver damage. PMID:24487409

Kong, Xiang Y; Nesset, Cecilie Kasi; Damme, Markus; Løberg, Else-Marit; Lübke, Torben; Mæhlen, Jan; Andersson, Kristin B; Lorenzo, Petra I; Roos, Norbert; Thoresen, G Hege; Rustan, Arild C; Kase, Eili T; Eskild, Winnie



Life-long protein malnutrition in the rat (Rattus norvegicus) results in altered patterns of craniofacial growth and smaller individuals  

PubMed Central

Dietary protein is a limiting factor in mammalian growth, significantly affecting the non-linear trajectories of skeletal growth. Young females may be particularly vulnerable to protein malnutrition if the restriction is not lifted before they become reproductive. With such early malnutrition, limited amino acids would be partitioned between two physiological objectives, successful reproduction vs. continued growth. Thus, the consequences of protein malnutrition could affect more than one generation. However, few studies have quantified these cross-generational effects. Our objective was to test for differences in skeletal growth in a second generation of malnourished rats compared with rats malnourished only post-weaning, the first generation and with controls. In this longitudinal study we modelled the growth of 22 craniofacial measurements with the logistic Gompertz equation, and tested for differences in the equation's parameters among the diet groups. The female offspring of post-weaning malnourished dams did not catch up in size to the first generation or to controls, although certain aspects of their craniofacial skeleton were less affected than others. The second generation's growth trajectories resembled the longer and slower growth of the first malnourished generation. There was a complex interaction between developmental processes and early nutritional environment, which affected variation of adult size. PMID:16761979

Lobe, Shannon L; Bernstein, Marica C; German, Rebecca Z



Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly  

PubMed Central

Replication of plus-stranded RNA viruses is greatly affected by numerous host-encoded proteins that act as restriction factors. Cyclophilins, which are a large family of cellular prolyl isomerases, have been found to inhibit Tomato bushy stunt tombusvirus (TBSV) replication in a Saccharomyces cerevisiae model based on genome-wide screens and global proteomics approaches. In this report, we further characterize single-domain cyclophilins, including the mammalian cyclophilin A and plant Roc1 and Roc2, which are orthologs of the yeast Cpr1p cyclophilin, a known inhibitor of TBSV replication in yeast. We found that recombinant CypA, Roc1, and Roc2 strongly inhibited TBSV replication in a cell-free replication assay. Additional in vitro studies revealed that CypA, Roc1, and Roc2 cyclophilins bound to the viral replication proteins, and CypA and Roc1 also bound to the viral RNA. These interactions led to inhibition of viral RNA recruitment, the assembly of the viral replicase complex, and viral RNA synthesis. A catalytically inactive mutant of CypA was also able to inhibit TBSV replication in vitro due to binding to the replication proteins and the viral RNA. Overexpression of CypA and its mutant in yeast or plant leaves led to inhibition of tombusvirus replication, confirming that CypA is a restriction factor for TBSV. Overall, the current work has revealed a regulatory role for the cytosolic single-domain Cpr1-like cyclophilins in RNA virus replication. PMID:24089553

Kovalev, Nikolay



Cyclophilin A binds to the viral RNA and replication proteins, resulting in inhibition of tombusviral replicase assembly.  


Replication of plus-stranded RNA viruses is greatly affected by numerous host-encoded proteins that act as restriction factors. Cyclophilins, which are a large family of cellular prolyl isomerases, have been found to inhibit Tomato bushy stunt tombusvirus (TBSV) replication in a Saccharomyces cerevisiae model based on genome-wide screens and global proteomics approaches. In this report, we further characterize single-domain cyclophilins, including the mammalian cyclophilin A and plant Roc1 and Roc2, which are orthologs of the yeast Cpr1p cyclophilin, a known inhibitor of TBSV replication in yeast. We found that recombinant CypA, Roc1, and Roc2 strongly inhibited TBSV replication in a cell-free replication assay. Additional in vitro studies revealed that CypA, Roc1, and Roc2 cyclophilins bound to the viral replication proteins, and CypA and Roc1 also bound to the viral RNA. These interactions led to inhibition of viral RNA recruitment, the assembly of the viral replicase complex, and viral RNA synthesis. A catalytically inactive mutant of CypA was also able to inhibit TBSV replication in vitro due to binding to the replication proteins and the viral RNA. Overexpression of CypA and its mutant in yeast or plant leaves led to inhibition of tombusvirus replication, confirming that CypA is a restriction factor for TBSV. Overall, the current work has revealed a regulatory role for the cytosolic single-domain Cpr1-like cyclophilins in RNA virus replication. PMID:24089553

Kovalev, Nikolay; Nagy, Peter D



Exposure to vehicle emissions results in altered blood brain barrier permeability and expression of matrix metalloproteinases and tight junction proteins in mice  

PubMed Central

Background Traffic-generated air pollution-exposure is associated with adverse effects in the central nervous system (CNS) in both human exposures and animal models, including neuroinflammation and neurodegeneration. While alterations in the blood brain barrier (BBB) have been implicated as a potential mechanism of air pollution-induced CNS pathologies, pathways involved have not been elucidated. Objectives To determine whether inhalation exposure to mixed vehicle exhaust (MVE) mediates alterations in BBB permeability, activation of matrix metalloproteinases (MMP) -2 and ?9, and altered tight junction (TJ) protein expression. Methods Apolipoprotein (Apo) E?/? and C57Bl6 mice were exposed to either MVE (100 ?g/m3 PM) or filtered air (FA) for 6 hr/day for 30 days and resulting BBB permeability, expression of ROS, TJ proteins, markers of neuroinflammation, and MMP activity were assessed. Serum from study mice was applied to an in vitro BBB co-culture model and resulting alterations in transport and permeability were quantified. Results MVE-exposed Apo E?/? mice showed increased BBB permeability, elevated ROS and increased MMP-2 and ?9 activity, compared to FA controls. Additionally, cerebral vessels from MVE-exposed mice expressed decreased levels of TJ proteins, occludin and claudin-5, and increased levels of inducible nitric oxide synthase (iNOS) and interleukin (IL)-1? in the parenchyma. Serum from MVE-exposed animals also resulted in increased in vitro BBB permeability and altered P-glycoprotein transport activity. Conclusions These data indicate that inhalation exposure to traffic-generated air pollutants promotes increased MMP activity and degradation of TJ proteins in the cerebral vasculature, resulting in altered BBB permeability and expression of neuroinflammatory markers. PMID:24344990



Protein C Thr315Ala variant results in gain of function but manifests as type II deficiency in diagnostic assays.  


Protein C (PC) is a vitamin K-dependent plasma glycoprotein, which upon activation by thrombin in complex with thrombomodulin (TM), regulates the coagulation cascade through a feedback loop inhibition mechanism. PC deficiency is associated with an increased risk of venous thromboembolism (VTE). A recent cohort study aimed at establishing a normal PC range identified a healthy PC-deficient subject whose PC antigen level of 65% and activity levels of 50% (chromogenic assay) and 36% (clotting assay) were markedly low. The proband has a negative family history of VTE. Genetic analysis revealed the proband has a heterozygous missense mutation in which Thr-315 of the PC heavy chain has been substituted with Ala. We expressed this mutant in HEK-293 cells and purified it to homogeneity. A similar decrease in both anticoagulant and anti-inflammatory activities of the activated protein C mutant was observed in plasma- and cell-based assays. Interestingly, we discovered if functional assays were coupled to PC activation by the thrombin-TM complex, the variant exhibits improved activities in all assays. Sequence analysis revealed Thr-315 is a consensus N-linked glycosylation site for Asn-313 and that its elimination significantly (?four- to fivefold) improves the maximum velocity of PC activation by the thrombin-TM complex, explaining the basis for the proband's negative VTE pedigree. PMID:25651845

Ding, Qiulan; Yang, Likui; Dinarvand, Peyman; Wang, Xuefeng; Rezaie, Alireza R



Disruption of the A-Kinase Anchoring Domain in Flagellar Radial Spoke Protein 3 Results in Unregulated Axonemal cAMP-dependent Protein Kinase Activity and Abnormal Flagellar Motility  

PubMed Central

Biochemical studies of Chlamydomonas flagellar axonemes revealed that radial spoke protein (RSP) 3 is an A-kinase anchoring protein (AKAP). To determine the physiological role of PKA anchoring in the axoneme, an RSP3 mutant, pf14, was transformed with an RSP3 gene containing a mutation in the PKA-binding domain. Analysis of several independent transformants revealed that the transformed cells exhibit an unusual phenotype: a fraction of the cells swim normally; the remainder of the cells twitch feebly or are paralyzed. The abnormal/paralyzed motility is not due to an obvious deficiency of radial spoke assembly, and the phenotype cosegregates with the mutant RSP3. We postulated that paralysis was due to failure in targeting and regulation of axonemal cAMP-dependent protein kinase (PKA). To test this, reactivation experiments of demembranated cells were performed in the absence or presence of PKA inhibitors. Importantly, motility in reactivated cell models mimicked the live cell phenotype with nearly equal fractions of motile and paralyzed cells. PKA inhibitors resulted in a twofold increase in the number of motile cells, rescuing paralysis. These results confirm that flagellar RSP3 is an AKAP and reveal that a mutation in the PKA binding domain results in unregulated axonemal PKA activity and inhibition of normal motility. PMID:16571668

Gaillard, Anne R.; Fox, Laura A.; Rhea, Jeanne M.; Craige, Branch



Accumulation of radium in ferruginous protein bodies formed in lung tissue: association of resulting radiation hotspots with malignant mesothelioma and other malignancies  

PubMed Central

While exposure to fibers and particles has been proposed to be associated with several different lung malignancies including mesothelioma, the mechanism for the carcinogenesis is not fully understood. Along with mineralogical observation, we have analyzed forty-four major and trace elements in extracted asbestos bodies (fibers and proteins attached to them) with coexisting fiber-free ferruginous protein bodies from extirpative lungs of individuals with malignant mesothelioma. These observations together with patients’ characteristics suggest that inhaled iron-rich asbestos fibers and dust particles, and excess iron deposited by continuous cigarette smoking would induce ferruginous protein body formation resulting in ferritin aggregates in lung tissue. Chemical analysis of ferruginous protein bodies extracted from lung tissues reveals anomalously high concentrations of radioactive radium, reaching millions of times higher concentration than that of seawater. Continuous and prolonged internal exposure to hotspot ionizing radiation from radium and its daughter nuclides could cause strong and frequent DNA damage in lung tissue, initiate different types of tumour cells, including malignant mesothelioma cells, and may cause cancers. PMID:19644223

Nakamura, Eizo; Makishima, Akio; Hagino, Kyoko; Okabe, Kazunori



Accumulation of radium in ferruginous protein bodies formed in lung tissue: association of resulting radiation hotspots with malignant mesothelioma and other malignancies.  


While exposure to fibers and particles has been proposed to be associated with several different lung malignancies including mesothelioma, the mechanism for the carcinogenesis is not fully understood. Along with mineralogical observation, we have analyzed forty-four major and trace elements in extracted asbestos bodies (fibers and proteins attached to them) with coexisting fiber-free ferruginous protein bodies from extirpative lungs of individuals with malignant mesothelioma. These observations together with patients' characteristics suggest that inhaled iron-rich asbestos fibers and dust particles, and excess iron deposited by continuous cigarette smoking would induce ferruginous protein body formation resulting in ferritin aggregates in lung tissue. Chemical analysis of ferruginous protein bodies extracted from lung tissues reveals anomalously high concentrations of radioactive radium, reaching millions of times higher concentration than that of seawater. Continuous and prolonged internal exposure to hotspot ionizing radiation from radium and its daughter nuclides could cause strong and frequent DNA damage in lung tissue, initiate different types of tumour cells, including malignant mesothelioma cells, and may cause cancers. PMID:19644223

Nakamura, Eizo; Makishima, Akio; Hagino, Kyoko; Okabe, Kazunori



RNA interference-mediated depletion of N-ethylmaleimide sensitive fusion protein and synaptosomal associated protein of 25 kDa results in the inhibition of blood feeding of the Gulf Coast tick, Amblyomma maculatum.  


The signalling pathways in tick salivary glands that control 'sialo-secretome' secretion at the tick-host interface remain elusive; however, this complex process is essential for successful feeding and manipulation of the host haemostatic response. Exocytosis of the sialo-secretome in the salivary glands requires a core of soluble N-ethylmaleimide-sensitive fusion (NSF) attachment proteins (SNAPs) and receptor proteins (SNAREs). SNAREs have been identified as the key components in regulating the sialo-secretome in the salivary gland cells. In this study, we utilized RNA interference to investigate the functional role of two Amblyomma maculatum?SNARE complex proteins, AmNSF and AmSNAP-25, in the tick salivary glands during extended blood feeding on the vertebrate host. Knock-down of AmNSF and AmSNAP-25 resulted in death, impaired feeding on the host, lack of engorgement and inhibited oviposition in ticks. Depletion also led to important morphological changes in the collapse of the Golgi apparatus in the salivary gland cells. Our results imply a functional significance of AmNSF and AMSNAP-25 in prolonged tick feeding, and survival on the host. Further characterization of the factors that regulate exocytosis may lead to novel approaches to prevent tick-borne diseases. PMID:23437815

Browning, R; Karim, S



Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus  

PubMed Central

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites. PMID:19119418

Botosso, Viviane F.; de A. Zanotto, Paolo M.; Ueda, Mirthes; Arruda, Eurico; Gilio, Alfredo E.; Vieira, Sandra E.; Stewien, Klaus E.; Peret, Teresa C. T.; Jamal, Leda F.; Pardini, Maria I. de M. C.; Pinho, João R. R.; Massad, Eduardo; Sant'Anna, Osvaldo A.; Holmes, Eddie C.; Durigon, Edison L.



C-reactive protein as an adverse prognostic marker for men with castration-resistant prostate cancer (CRPC): confirmatory results  

PubMed Central

We previously reported that higher serum concentrations of C-reactive protein (CRP) are associated with shorter survival in men with castration-resistant prostate cancer (CRPC). To confirm this finding in an independent data set, we used 119 CRPC patients enrolled in 6 phase II clinical trials and examined the relationship of CRP, alkaline phosphatase, hemoglobin, age, ECOG PS, and prostate specific antigen (PSA) with survival. Median follow-up was 19.7 months (0.9–98.5 months) and 89% have died. After analyzing the form of the risk function using the generalized additive model method, univariate and multivariate Cox proportional hazard models were used to assess associations between baseline individual categorical and continuous variables. Quartiles of CRP were: 1: 0–1.0, 1.1–4.9, 5.0–17.0, and 17.1 to 311 mg/L. In a Cox multivariate model, log2(CRP) (HR 1.106 p=0.013) as well as hemoglobin and alkaline phosphatase were independently associated with survival, confirming that higher CRP is associated with shorter survival in CRPC. Since CRP is a marker of inflammation, this finding suggests that inflammation may play an important role in the natural history of advanced prostate cancer. CRP is a readily measurable biomarker that has the potential to improve prognostic models and should be validated in a prospective clinical trial. PMID:20207556

Prins, Renee C.; Rademacher, Brooks L.; Mongoue-Tchokote, Solange; Alumkal, Joshi J.; Graff, Julie N.; Eilers, Kristine M.; Beer, Tomasz M.



Depletion of the RNA-Binding Protein RBP33 Results in Increased Expression of Silenced RNA Polymerase II Transcripts in Trypanosoma brucei  

PubMed Central

We have characterized the RNA-binding protein RBP33 in Trypanosoma brucei, and found that it localizes to the nucleus and is essential for viability. The subset of RNAs bound to RBP33 was determined by immunoprecipitation of ribonucleoprotein complexes followed by deep sequencing. Most RBP33-bound transcripts are predicted to be non-coding. Among these, over one-third are located close to the end of transcriptional units (TUs) or have an antisense orientation within a TU. Depletion of RBP33 resulted in an increase in the level of RNAs derived from regions that are normally silenced, such as strand-switch regions, retroposon and repeat sequences. Our work provides the first example of an RNA-binding protein involved in the regulation of gene silencing in trypanosomes. PMID:25215501

Fernández-Moya, Sandra M.; Carrington, Mark; Estévez, Antonio M.



Genetic Divergence of Rotavirus Nonstructural Protein 4 Results in Distinct Serogroup-Specific Viroporin Activity and Intracellular Punctate Structure Morphologies  

PubMed Central

Nonstructural protein 4 (NSP4) viroporin activity is critical for the replication and assembly of serogroup A rotavirus (RVA); however, the dramatic primary sequence divergence of NSP4s across serogroups raises the possibility that viroporin activity is not a common feature among RVs. We tested for NSP4 viroporin activity from divergent strains, including RVA (EC and Ty-1), RVB (IDIR), and RVC (Cowden). Canonical viroporin motifs were identified in RVA, RVB, and RVC NSP4s, but the arrangement of basic residues and the amphipathic ?-helices was substantially different between serogroups. Using Escherichia coli and mammalian cell expression, we showed that each NSP4 tested had viroporin activity, but serogroup-specific viroporin phenotypes were identified. Only mammalian RVA and RVC NSP4s induced BL21-pLysS E. coli cell lysis, a classical viroporin activity assay. In contrast, RVA, RVB, and RVC NSP4 expression was universally cytotoxic to E. coli and disrupted reduction-oxidation activities, as measured by a new redox dye assay. In mammalian cells, RVB and RVC NSP4s were initially localized in the endoplasmic reticulum (ER) and trafficked into punctate structures that were mutually exclusive with RVA NSP4. The punctate structures partially localized to the ER-Golgi intermediate compartment (ERGIC) but primarily colocalized with punctate LC3, a marker for autophagosomes. Similar to RVA NSP4, expression of RVB and RVC NSP4s significantly elevated cytosolic calcium levels, demonstrating that despite strong primary sequence divergence, RV NSP4 has maintained viroporin activity across serogroups A to C. These data suggest that elevated cytosolic calcium is a common critical process for all rotavirus strains. PMID:22357281

Hyser, Joseph M.; Utama, Budi; Crawford, Sue E.



Anti-depressant medication use and C-reactive protein: Results from two population-based studies  

PubMed Central

The use of anti-depressant medication has been linked to cardiovascular disease (CVD). We examined the association between anti-depressant medication use and a marker of low grade systemic inflammation as a potential pathway linking anti-depressant use and CVD in two population based studies. Data were collected in a representative sample of 8,131 community dwelling adults (aged 47.4 ± 15.9 yrs, 46.7% male) from the Scottish Health Surveys (SHS). The use of anti-depressant medication was coded according to the British National Formulary and blood was drawn for the measurement of C-reactive protein (CRP). In a second study, we attempted to replicate our findings using longitudinal data from the Whitehall II study (n=4584, aged 55.5 ± 5.9 yrs, mean follow-up 5.5 years). Antidepressants were used in 5.6% of the SHS sample, with selective serotonin reuptake inhibitors (SSRIs) being the most common. There was a higher risk of elevated CRP (>3 mg/L) in users of tricyclic antidepressant (TCA) medication (multivariate adjusted odds ratio (OR) = 1.52, 95% CI, 1.07 – 2.15), but not in SSRI users (multivariate adjusted OR = 1.07, 95% CI, 0.81 – 1.42). A longitudinal association between any antidepressant use and subsequent CRP was confirmed in the Whitehall cohort. In summary, the use of anti-depressants was associated with elevated levels of systemic inflammation independently from the symptoms of mental illness and cardiovascular co-morbidity. This might be a potential mechanism through which antidepressant medication increases CVD risk. Further data are required to explore the effects of dosage and duration of antidepressant treatment. PMID:20863880

Hamer, Mark; Batty, G. David; Marmot, Michael G.; Singh-Manoux, Archana; Kivimäki, Mika



Unique thermodynamic relationships for ?fHo and ?fGo for crystalline inorganic salts. I. Predicting the possible existence and synthesis of Na2SO2 and Na2SeO2.  


The concept that equates oxidation and pressure has been successfully utilized in explaining the structural changes observed in the M(2)S subnets of M(2)SO(x) (x = 3, 4) compounds (M = Na, K) when compared with the structures (room- and high-pressure phases) of their parent M(2)S `alloy' [Martínez-Cruz et al. (1994), J. Solid State Chem. 110, 397-398; Vegas (2000), Crystallogr. Rev. 7, 189-286; Vegas et al. (2002), Solid State Sci. 4, 1077-1081]. These structural changes suggest that if M(2)SO(2) would exist, its cation array might well have an anti-CaF(2) structure. On the other hand, in an analysis of the existing thermodynamic data for M(2)S, M(2)SO(3) and M(2)SO(4) we have identified, and report, a series of unique linear relationships between the known ?(f)H(o) and ?(f)G(o) values of the alkali metal (M) sulfide (x = 0) and their oxyanion salts M(2)SO(x) (x = 3 and 4), and the similarly between M(2)S(2) disulfide (x = 0) and disulfur oxyanion salts M(2)S(2)O(x) (x = 3, 4, 5, 6 and 7) and the number of O atoms in their anions x. These linear relationships appear to be unique to sulfur compounds and their inherent simplicity permits us to interpolate thermochemical data (?(f)H(o)) for as yet unprepared compounds, M(2)SO (x = 1) and M(2)SO(2) (x = 2). The excellent linearity indicates the reliability of the interpolated data. Making use of the volume-based thermodynamics, VBT [Jenkins et al. (1999), Inorg. Chem. 38, 3609-3620], the values of the absolute entropies were estimated and from them, the standard ?(f)S(o) values, and then the ?(f)G(o) values of the salts. A tentative proposal is made for the synthesis of Na(2)SO(2) which involves bubbling SO(2) through a solution of sodium in liquid ammonia. For this attractive thermodynamic route, we estimate ?G(o) to be approximately -500 kJ mol(-1). However, examination of the stability of Na(2)SO(2) raises doubts and Na(2)SeO(2) emerges as a more attractive target material. Its synthesis is likely to be easier and it is stable to disproportionation into Na(2)S and Na(2)SeO(4). Like Na(2)SO(2), this compound is predicted to have an anti-CaF(2) Na(2)Se subnet. PMID:22992796

Vegas, Angel; Liebman, Joel F; Jenkins, H Donald Brooke



Nonablative skin rejuvenation devices and the role of heat shock protein 70: results of a human skin explant model  

NASA Astrophysics Data System (ADS)

Nonablative thermal laser therapy with a 1540-nm laser induces controlled, spatially determined thermal damage, allowing subsequent collagen remodeling while preserving the epidermis. A photorejuvenation effect using nonthermal nonablative stimulation of cells with low energy and narrow band light has been termed photomodulation. Light emitting diodes (LEDs) are narrow band emitters that lead to photomodulation via stimulation of mitochondrial cell organelles. In a previous study, we demonstrated in a human skin explant model that heat shock protein 70 (HSP70) plays a pivotal role in the initiation of skin remodeling after ablative fractional photothermolysis. To test its importance in nonablative laser therapy and photomodulation, the spatio-temporal expression of HSP70 is investigated in response to a 1540-nm laser treatment and six different LED therapies. An Er:glass laser is used with a 1-Hz repetition rate, 30-J/cm2 fluence, and a hand piece with a 2-mm spot size. Nonthermal nonablative treatment is performed using two LED (LEDA SCR red light: 635 nm, 40 to 120 W/cm2, 40 to 120 J/cm2 LEDA SCR yellow light: 585 nm, 16 to 35 W/cm2, 20 to 100 J/cm2 spot size 16×10 cm). Immediate responses as well as responses 1, 3, or 7 days postprocedure are studied; untreated skin explants serve as control. Immunohistochemical investigation (HSP70) is performed in all native, nontreated, and Er:glass laser- or LED-treated samples (n=175). Nonablative laser therapy leads to a clear time-dependent induction of epidermally expressed HSP70, peaking between one to three days post-treatment. In contrast, none of the various LED treatments up-regulated the HSP70 expression in our skin explant model. HSP70 is up-regulated by nonablative but thermal laser devices, but does not seem to play a significant role in the induction of skin remodeling induced by photomodulation. The maximum of HSP70 expression is reached later after Er:glass laser intervention compared to ablative fractional (AFP) treatment.

Helbig, Doris; Moebius, Anne; Simon, Jan C.; Paasch, Uwe



Differences in folate?protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate  

SciTech Connect

Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. In mammalian liver it reduces S-adenosylmethionine levels by using it to methylate glycine, producing N-methylglycine (sarcosine) and S-adenosylhomocysteine. GNMT is inhibited by binding two molecules of 5-methyltetrahydrofolate (mono- or polyglutamate forms) per tetramer of the active enzyme. Inhibition is sensitive to the status of the N-terminal valine of GNMT and to polyglutamation of the folate inhibitor. It is inhibited by pentaglutamate form more efficiently compared to monoglutamate form. The native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein expressed in E. coli where the N-terminus is not acetylated. In this work we used a protein crystallography approach to evaluate the structural basis for these differences. We show that in the folate-GNMT complexes with the native enzyme, two folate molecules establish three and four hydrogen bonds with the protein. In the folate-recombinant GNMT complex only one hydrogen bond is established. This difference results in more effective inhibition by folate of the native liver GNMT activity compared to the recombinant enzyme.

Luka, Zigmund; Pakhomova, Svetlana; Loukachevitch, Lioudmila V.; Newcomer, Marcia E.; Wagner, Conrad (Vanderbilt); (LSU)



First results on label-free detection of DNA and protein molecules using a novel integrated sensor technology based on gravimetric detection principles.  


A novel integrated bio-sensor technology based on thin-film bulk acoustic wave resonators on silicon is presented and the feasibility of detecting DNA and protein molecules proofed. The detection principle of these sensors is label-free and relies on a resonance frequency shift caused by mass loading of an acoustic resonator, a principle very well known from quartz crystal micro balances. Integrated ZnO bulk acoustic wave resonators with resonance frequencies around 2 GHz have been fabricated, employing an acoustic mirror for isolation from the silicon substrate. DNA oligos have been thiol-coupled to the gold electrode by on-wafer dispensing. In a further step, samples have either been hybridised or alternatively a protein has been coupled to the receptor. The measurement results show the new bio-sensor being capable of both, detecting proteins as well as the DNA hybridisation without using a label. Due to the substantially higher oscillation frequency, these sensors already show much higher sensitivity and resolution comparable to quartz crystal micro balances. The potential for these sensors and sensors arrays as well as technological challenges will be discussed in detail. PMID:14683645

Gabl, R; Feucht, H-D; Zeininger, H; Eckstein, G; Schreiter, M; Primig, R; Pitzer, D; Wersing, W



Immunization of Aotus monkeys with recombinant Plasmodium falciparum hybrid proteins does not reproducibly result in protection from malaria infection.  


Plasmodium falciparum antigens SERP, HRPII, MSAI, and 41-3 have shown promise as vaccine components. This study aimed at reproducing and extending previous results using three hybrid molecules. Antibody responses were reproduced in Aotus monkeys, but solid protection from a P. falciparum blood-stage challenge that showed an unintendedly enhanced pathogenicity was not observed. PMID:9423884

Kocken, C H; Hundt, E; Knapp, B; Brazel, D; Enders, B; Narum, D L; Wubben, J A; Thomas, A W



Overproduction of a single protein, Pc-Pex11p, results in 2-fold enhanced penicillin production by Penicillium chrysogenum  

Microsoft Academic Search

Current industrial production of ?-lactam antibiotics, using the filamentous fungus Penicillium chrysogenum, is the result of many years of strain improvement by classical mutagenesis. More efficient production strains showed significant increases in the number and volume fraction of microbodies in their cells, organelles that harbor key enzymes involved in the biosynthesis of ?-lactam antibiotics. We have isolated the P. chrysogenum

Jan A. K. W. Kiel; Ida J. van der Klei; Marco A. van den Berg; Roel A. L. Bovenberg; Marten Veenhuis



Feeding soy protein isolate prevents impairment of bone acquisition by western diets as a result of insulin signaling in bone  

Technology Transfer Automated Retrieval System (TEKTRAN)

Excessive consumption of high fat/high cholesterol “Western” diets during postnatal life results in increased energy intake, development of obesity and systemic insulin resistance. However, how this diet impairs bone development and remodeling is not well understood, and no effective dietary interve...


Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.  


There is a tendency in the literature to be critical of scoring functions when docking programs perform poorly. The assumption is that existing scoring functions need to be enhanced or new ones developed in order to improve the performance of docking programs for tasks such as pose prediction and virtual screening. However, failures can result from either sampling or scoring (or a combination of the two), although less emphasis tends to be given to the former. In this work, we use the programs GOLD and Glide on a high-quality data set to explore whether failures in pose prediction and binding affinity estimation can be attributable more to sampling or scoring. We show that identification of the correct pose (docking power) can be improved by incorporating ligand strain into the scoring function or rescoring an ensemble of diverse docking poses with MM-GBSA in a postprocessing step. We explore the use of nondefault docking settings and find that enhancing ligand sampling also improves docking power, again suggesting that sampling is more limiting than scoring for the docking programs investigated in this work. In cross-docking calculations (docking a ligand to a noncognate receptor structure) we observe a significant reduction in the accuracy of pose ranking, as expected and has been reported by others; however, we demonstrate that these alternate poses may in fact be more complementary between the ligand and the rigid receptor conformation, emphasizing that treating the receptor rigidly is an artificial constraint on the docking problem. We simulate protein flexibility by the use of multiple crystallographic conformations of a protein and demonstrate that docking results can be improved with this level of protein sampling. This work indicates the need for better sampling in docking programs, especially for the receptor. This study also highlights the variable descriptive value of RMSD as the sole arbiter of pose replication quality. It is shown that ligand poses within 2 Å of the crystallographic one can show dramatic differences in calculated relative protein-ligand energies. MM-GBSA rescoring of distinct poses overcomes some of the sensitivities of pose ranking experienced by the docking scoring functions due to protein preparation and binding site definition. PMID:25266271

Greenidge, P A; Kramer, C; Mozziconacci, J-C; Sherman, W



Structure of L-arabinose-binding protein from Escherichia coli at 5 A resolution and preliminary results at 3.5 A.  

PubMed Central

The three-dimensional crystal structure of the L-arabinose-binding protein from E. coli, an essential component in the active transport of L-arabinose, has been solved at 5 A resolution using the method of multiple isomorphous replacement. Five heavy atom derivatives were used. A preliminary 3.5 A electron density map has also been calculated. The results indicate that the molecule is ellipsoidal with approximate dimensions 68 A X 38 A X 30 A. Two similar domains within the molecule (which is a single polypeptide chain) are related by an approximate noncrystallographic rotation-translation axis. This relationship involves approximately 20% of the structure. Images PMID:781669

Phillips, G N; Mahajan, V K; Siu, A K; Quiocho, F A



Interactive intoxicating and ameliorating effects of tannic acid, aluminum (Al3+), copper (Cu2+), and selenate (SeO42-) in wheat roots. A descriptive and mathematical assessment  

Technology Transfer Automated Retrieval System (TEKTRAN)

Tannic acids and tannins are polyphenolic compounds produced by plants and are important components of soil and water organic matter. Tannic acids and tannins form complexes with proteins, metals, and soil particulate matter and perform several physiological and ecological functions. The tannic ac...


Direct Interaction between Protein Kinase Cu(PKCu) and 14-3-3tin T Cells: 14-3-3 Overexpression Results in Inhibition of PKCuTranslocation and Function  

Microsoft Academic Search

Recent studies have documented direct interactions between 14-3-3 proteins and several oncogene and proto-oncogene products involved in signal transduction pathways. Studies on the effects of 14-3-3 proteins on protein kinase C (PKC) activity in vitro have reported conflicting results, and previous attempts to demon- strate a direct association between PKC and 14-3-3 were unsuccessful. Here, we examined potential physical and




The G protein-coupled estrogen receptor-1, GPER-1, promotes fibrillogenesis via a Shc-dependent pathway resulting in anchorage-independent growth.  


The G protein-coupled estrogen receptor-1, GPER-1, coordinates fibronectin (FN) matrix assembly and release of heparan-bound epidermal growth factor (HB-EGF). This mechanism of action results in the recruitment of FN-engaged integrin ?5?1 to fibrillar adhesions and the formation of integrin ?5?1-Shc adaptor protein complexes. Here, we show that GPER-1 stimulation of murine 4 T1 or human SKBR3 breast cancer cells with 17?-estradiol (E2?) promotes the formation of focal adhesions and actin stress fibers and results in increased cellular adhesion and haptotaxis on FN, but not collagen. These actions are also induced by the xenoestrogen, bisphenol A, and the estrogen receptor (ER) antagonist, ICI 182, 780, but not the inactive stereoisomer, 17?-estradiol (E2?). In addition, we show that GPER-1 stimulation of breast cancer cells allows for FN-dependent, anchorage-independent growth and FN fibril formation in "hanging drop" assays, indicating that these GPER-1-mediated actions occur independently of adhesion to solid substrata. Stable expression of Shc mutant Y317F lacking its primary tyrosyl phosphorylation site disrupts E2?-induced focal adhesion and actin stress fiber formation and abolishes E2?-enhanced haptotaxis on FN and anchorage-dependent growth. Collectively, these data demonstrate that E2? action via GPER-1 enhances cellular adhesivity and FN matrix assembly and allows for anchorage-independent growth, cellular events that may allow for cellular survival, and tumor progression. PMID:25096985

Magruder, Hilary T; Quinn, Jeffrey A; Schwartzbauer, Jean E; Reichner, Jonathan; Huang, Allan; Filardo, Edward J



Acute leukemias of different lineages have similar MLL gene fusions encoding related chimeric proteins resulting from chromosomal translocation  

SciTech Connect

The MLL gene, on human chromosome 11q23, undergoes chromosomal translocation in acute leukemias, resulting in gene fusion with AF4 (chromosome 4) and ENL (chromosome 19). The authors report here translocation of MLL with nine different chromosomes and two paracentric chromosome 11 deletions in early B cell, B- or T-cell lineage, or nonlymphocytic acute leukemias. The mRNA translocation junction from 22t(4;11) patients, including six adult leukemias, and nine t(11;19) tumors reveals a remarkable conservation of breakpoints within MLL, AF4, or ENL genes, irrespective of tumor phenotype. Typically, the breakpoints are upstream of the zinc-finger region of MLL, and deletion of this region can accompany translocation, supporting the der(11) chromosome as the important component in leukemogenesis. Partial sequence of a fusion between MLL and the AFX1 gene from chromosome X shows the latter to be rich in Ser/Pro codons, like the ENL mRNA. These data suggest that the heterogeneous 11q23 abnormalities might cause attachment of Ser/Pro-rich segments to the NH[sub 2] terminus of MLL, lacking the zinc-finger region, and that translocation occurs in early hematopoietic cells, before commitment to distinct lineages. 36 refs., 2 figs.

Corral, J.; Forster, A.; Thompson, S.; Rabbitts, T.H. (Medical Research Council Laboratory of Molecular Biology, Cambridge (United Kingdom)); Lampert, F. (Kinderklinik-Universitaet Giessen (Germany)); Kaneko, Y. (Saitama Cancer Centre, Saitama (Japan)); Slater, R.; Kroes, W.G. (Univ. of Amsterdam (Netherlands)); Van Der Schoot, C.E. (Central Laboratory of the Netherlands Red Cross, Amsterdam (Netherlands)); Ludwig, W.D. (Institut fur Humangenetik und Antrhopologie, Heidelberg (Germany)); Karpas, A. (Univ. of Cambridge (United Kingdom)); Pocock, C.; Cotter, F. (Institute of Child Health, London (United Kingdom))



Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  

SciTech Connect

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.; Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.



Sugared water consumption by adult offspring of mothers fed a protein-restricted diet during pregnancy results in increased offspring adiposity: the second hit effect.  


Poor maternal nutrition predisposes offspring to metabolic disease. This predisposition is modified by various postnatal factors. We hypothesised that coupled to the initial effects of developmental programming due to a maternal low-protein diet, a second hit resulting from increased offspring postnatal sugar consumption would lead to additional changes in metabolism and adipose tissue function. The objective of the present study was to determine the effects of sugared water consumption (5% sucrose in the drinking-water) on adult offspring adiposity as a 'second hit' following exposure to maternal protein restriction during pregnancy. We studied four offspring groups: (1) offspring of mothers fed the control diet (C); (2) offspring of mothers fed the restricted protein diet (R); (3) offspring of control mothers that drank sugared water (C-S); (4) offspring of restricted mothers that drank sugared water (R-S). Maternal diet in pregnancy was considered the first factor and sugared water consumption as the second factor - the second hit. Body weight and total energy consumption, before and after sugared water consumption, were similar in all the groups. Sugared water consumption increased TAG, insulin and cholesterol concentrations in both the sexes of the C-S and R-S offspring. Sugared water consumption increased leptin concentrations in the R-S females and males but not in the R offspring. There was also an interaction between sugared water and maternal diet in males. Sugared water consumption increased adipocyte size and adiposity index in both females and males, but the interaction with maternal diet was observed only in females. Adiposity index and plasma leptin concentrations were positively correlated in both the sexes. The present study shows that a second hit during adulthood can amplify the effects of higher adiposity arising due to poor maternal pregnancy diet in an offspring sex dependent fashion. PMID:24124655

Cervantes-Rodríguez, M; Martínez-Gómez, M; Cuevas, E; Nicolás, L; Castelán, F; Nathanielsz, P W; Zambrano, E; Rodríguez-Antolín, J



Rapamycin and Chloroquine: The In Vitro and In Vivo Effects of Autophagy-Modifying Drugs Show Promising Results in Valosin Containing Protein Multisystem Proteinopathy  

PubMed Central

Mutations in the valosin containing protein (VCP) gene cause hereditary Inclusion body myopathy (hIBM) associated with Paget disease of bone (PDB), frontotemporal dementia (FTD), more recently termed multisystem proteinopathy (MSP). Affected individuals exhibit scapular winging and die from progressive muscle weakness, and cardiac and respiratory failure, typically in their 40s to 50s. Histologically, patients show the presence of rimmed vacuoles and TAR DNA-binding protein 43 (TDP-43)-positive large ubiquitinated inclusion bodies in the muscles. We have generated a VCPR155H/+ mouse model which recapitulates the disease phenotype and impaired autophagy typically observed in patients with VCP disease. Autophagy-modifying agents, such as rapamycin and chloroquine, at pharmacological doses have previously shown to alter the autophagic flux. Herein, we report results of administration of rapamycin, a specific inhibitor of the mechanistic target of rapamycin (mTOR) signaling pathway, and chloroquine, a lysosomal inhibitor which reverses autophagy by accumulating in lysosomes, responsible for blocking autophagy in 20-month old VCPR155H/+ mice. Rapamycin-treated mice demonstrated significant improvement in muscle performance, quadriceps histological analysis, and rescue of ubiquitin, and TDP-43 pathology and defective autophagy as indicated by decreased protein expression levels of LC3-I/II, p62/SQSTM1, optineurin and inhibiting the mTORC1 substrates. Conversely, chloroquine-treated VCPR155H/+ mice revealed progressive muscle weakness, cytoplasmic accumulation of TDP-43, ubiquitin-positive inclusion bodies and increased LC3-I/II, p62/SQSTM1, and optineurin expression levels. Our in vitro patient myoblasts studies treated with rapamycin demonstrated an overall improvement in the autophagy markers. Targeting the mTOR pathway ameliorates an increasing list of disorders, and these findings suggest that VCP disease and related neurodegenerative multisystem proteinopathies can now be included as disorders that can potentially be ameliorated by rapalogs. PMID:25884947

Nalbandian, Angèle; Llewellyn, Katrina J.; Nguyen, Christopher; Yazdi, Puya G.; Kimonis, Virginia E.



A Spontaneous Deletion within the Desmoglein 3 Extracellular Domain of Mice Results in Hypomorphic Protein Expression, Immunodeficiency, and a Wasting Disease Phenotype.  


Desmoglein 3 is a transmembrane component of desmosome complexes that mediate epidermal cell-to-cell adhesion and tissue integrity. Antibody blockade of desmoglein 3 function in pemphigus vulgaris patients leads to skin blistering (acantholysis) and oral mucosa lesions. Desmoglein 3 deficiency in mice leads to a phenotype characterized by cyclic alopecia in addition to the dramatic skin and mucocutaneous acantholysis observed in pemphigus patients. In this study, mice that developed an overt squeaky (sqk) phenotype were identified with obstructed airways, cyclic hair loss, and severe immunodeficiency subsequent to the development of oral lesions and malnutrition. Single-nucleotide polymorphism-based quantitative trait loci mapping revealed a genetic deletion that resulted in expression of a hypomorphic desmoglein 3 protein with a truncation of an extracellular cadherin domain. Because hypomorphic expression of a truncated desmoglein 3 protein led to a spectrum of severe pathology not observed in mice deficient in desmoglein 3, similar human genetic alterations may also disrupt desmosome function and induce a disease course distinct from pathogenesis of pemphigus vulgaris. PMID:25542773

Kountikov, Evgueni I; Poe, Jonathan C; Maclver, Nancie J; Rathmell, Jeffrey C; Tedder, Thomas F



Mutations in the TIR1 auxin receptor that increase affinity for auxin/indole-3-acetic acid proteins result in auxin hypersensitivity.  


The phytohormone auxin regulates virtually every aspect of plant development. The hormone directly mediates the interaction between the two members of the auxin coreceptor complex, a TRANSPORT INHIBITOR RESPONSE (TIR1)/AUXIN SIGNALING F-BOX protein and an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor. To learn more about the interaction between these proteins, a mutant screen was performed using the yeast (Saccharomyces cerevisiae) two-hybrid system in Arabidopsis (Arabidopsis thaliana). Two tir1 mutations were identified that increased interaction with Aux/IAAs. The D170E and M473L mutations increase affinity between TIR1 and the degron motif of Aux/IAAs and enhance the activity of the SCF(TIR1) complex. This resulted in faster degradation of Aux/IAAs and increased transcription of auxin-responsive genes in the plant. Plants carrying the pTIR1:tir1 D170E/M473L-Myc transgene exhibit diverse developmental defects during plant growth and display an auxin-hypersensitive phenotype. This work demonstrates that changes in the leucine-rich repeat domain of the TIR1 auxin coreceptor can alter the properties of SCF(TIR1). PMID:23539280

Yu, Hong; Moss, Britney L; Jang, Seunghee S; Prigge, Michael; Klavins, Eric; Nemhauser, Jennifer L; Estelle, Mark



Isoflurane anesthesia results in reversible ultrastructure and occludin tight junction protein expression changes in hippocampal blood-brain barrier in aged rats.  


The underlying mechanism of isoflurane-induced cognitive dysfunction in older individuals is unknown. In this study, the effects of isoflurane exposure on the hippocampal blood-brain barrier (BBB) in aged rats were investigated because it was previously shown that BBB disruption involves in cognitive dysfunction. Twenty-month-old rats randomly received 1.5% isoflurane or vehicle gas as control. Hippocampal BBB ultrastructure was analyzed by transmission electron microscopy and expression of tight junction proteins was measured by western blot analysis. BBB permeability was detected with sodium fluorescein extravasation and further confirmed by immunoglobulin G immunohistochemistry. Spatial learning and memory were assessed by the Morris water maze test. Isoflurane anesthesia resulted in reversible time-dependent BBB ultrastructure morphological damage and significant decreases in expression of the tight junction proteins occludin, which contributed to sodium fluorescein and IgG leakage. Rats with isoflurane exposure also showed significant cognitive deficits in the Morris water maze test. This in vivo data indicate that occludin down-regulation may be one of the mediators of isoflurane-induced hippocampus BBB disruption, and may contribute to hippocampus-dependent cognitive impairment after isoflurane exposure in aged rats. PMID:25524410

Cao, Yiyun; Ni, Cheng; Li, Zhengqian; Li, Lunxu; Liu, Yajie; Wang, Chunyi; Zhong, Yanfeng; Cui, Dehua; Guo, Xiangyang



Misfolding of collagen X chains harboring Schmid metaphyseal chondrodysplasia mutations results in aberrant disulfide bond formation, intracellular retention, and activation of the unfolded protein response.  


Collagen X is a short chain collagen expressed specifically by the hypertrophic chondrocytes of the cartilage growth plate during endochondral bone formation. Accordingly, COL10A1 mutations disrupt growth plate function and cause Schmid metaphyseal chondrodysplasia (SMCD). SMCD mutations are almost exclusively located in the NC1 domain, which is crucial for both trimer formation and extracellular assembly. Several mutations are expected to reduce the level of functional collagen X due to NC1 domain misfolding or exclusion from stable trimer formation. However, other mutations may be tolerated within the structure of the assembled NC1 trimer, allowing mutant chains to exert a dominant-negative impact within the extracellular matrix. To address this, we engineered SMCD mutations that are predicted either to prohibit subunit folding and assembly (NC1del10 and Y598D, respectively) or to allow trimerization (N617K and G618V) and transfected these constructs into 293-EBNA and SaOS-2 cells. Although expected to form stable trimers, G618V and N617K chains (like Y598D and NC1del10 chains) were secreted very poorly compared with wild-type collagen X. Interestingly, all mutations resulted in formation of an unusual SDS-stable dimer, which dissociated upon reduction. As the NC1 domain sulfhydryl group is not solvent-exposed in the correctly folded NC1 monomer, disulfide bond formation would result only from a dramatic conformational change. In cells expressing mutant collagen X, we detected significantly increased amounts of the spliced form of X-box DNA-binding protein mRNA and up-regulation of BiP, two key markers for the unfolded protein response. Our data provide the first clear evidence for misfolding of SMCD collagen X mutants, and we propose that solvent exposure of the NC1 thiol may trigger the recognition and degradation of mutant collagen X chains. PMID:15695517

Wilson, Richard; Freddi, Susanna; Chan, Danny; Cheah, Kathryn S E; Bateman, John F



Homozygosity for a partial deletion of apoprotein A-V signal peptide results in intracellular missorting of the protein and chylomicronemia in a breast-fed infant.  


Deficiency of apoprotein A-V (apoA-V) can cause hypertriglyceridemia. In an 11 months old boy presenting with a severe hypertriglyceridemia, a formerly unknown 24 nucleotide deletion in exon 2 of the APOA5 gene was detected. The homozygous mutation results in an eight amino acid loss in the signal peptide sequence (c.16_39del; p.Ala6_Ala13del). Screening of control persons proved that this deletion is a rare mutation. Hypertriglyceridemia in the patient was only found at the time when he was breast fed, while after weaning, triglyceride levels were close to normal. Under both dietary conditions, apoA-V protein was undetectable in plasma while post-heparin plasma lipoprotein lipase activity was normal. Expression analysis of normal and mutated protein by Western blot and immunofluorescence in apoA-V deficient primary hepatocytes revealed that, due to changes in the signal peptide, mutated apoA-V was intracellularly missorted to lipid droplets and not secreted. Wild type apoA-V, instead, was not targeted to lipid droplets but transported via endosomal compartments to the plasma membrane for secretion. It is concluded that the c.16_39del mutation in the APOA5 gene leads to hepatic missorting and impaired secretion, which consequently results in undetectable apoA-V plasma levels. The absence of apoA-V in plasma leads under conditions of fat-rich diets to severe chylomicronemia, suggestive for a modulatory role of apoA-V for lipoprotein lipase mediated intravascular triglyceride lipolysis. PMID:24529129

Albers, Kirstin; Schlein, Christian; Wenner, Kirsten; Lohse, Peter; Bartelt, Alexander; Heeren, Joerg; Santer, René; Merkel, Martin



ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.  


Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. PMID:25392418

Sehnal, David; Svobodová Va?eková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Ko?a, Jaroslav



ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank  

PubMed Central

Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. PMID:25392418

Sehnal, David; Svobodová Va?eková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Ko?a, Jaroslav



Disruption of Fyn SH3 Domain Interaction with a Proline-Rich Motif in Liver Kinase B1 Results in Activation of AMP-Activated Protein Kinase  

PubMed Central

Fyn-deficient mice display increased AMP-activated Protein Kinase (AMPK) activity as a result of Fyn-dependent regulation of Liver Kinase B1 (LKB1) in skeletal muscle. Mutation of Fyn-specific tyrosine sites in LKB1 results in LKB1 export into the cytoplasm and increased AMPK activation site phosphorylation. This study characterizes the structural elements responsible for the physical interaction between Fyn and LKB1. Effects of point mutations in the Fyn SH2/SH3 domains and in the LKB1 proline-rich motif on 1) Fyn and LKB1 binding, 2) LKB1 subcellular localization and 3) AMPK phosphorylation were investigated in C2C12 muscle cells. Additionally, novel LKB1 proline-rich motif mimicking cell permeable peptides were generated to disrupt Fyn/LKB1 binding and investigate the consequences on AMPK activity in both C2C12 cells and mouse skeletal muscle. Mutation of either Fyn SH3 domain or the proline-rich motif of LKB1 resulted in the disruption of Fyn/LKB1 binding, re-localization of 70% of LKB1 signal in the cytoplasm and a 2-fold increase in AMPK phosphorylation. In vivo disruption of the Fyn/LKB1 interaction using LKB1 proline-rich motif mimicking cell permeable peptides recapitulated Fyn pharmacological inhibition. We have pinpointed the structural elements within Fyn and LKB1 that are responsible for their binding, demonstrating the functionality of this interaction in regulating AMPK activity. PMID:24586906

Yamada, Eijiro; Bastie, Claire C.



Thermodynamic model for the solubility of BaSeO4(cr) in the aqueous Ba2+-SeO42--Na+-H+-OH--H2O system: Extending to high selenate concentrations  

SciTech Connect

The solubility of Ba(SeO4, SO4) precipitates was determined as a function of the BaSeO4 mole fractions, ranging from 0.0015 to 0.3830, and time with an equilibration period extending to as long as 302 days. Equilibrium/steady state conditions in this system are reached in ? 65 days. Pitzer’s ion interaction model was used to calculate solid and aqueous phase activity coefficients. Thermodynamic analyses showed that the data do not satisfy Gibbs-Duhem equation, thereby demonstrating that a single-solid solution phase does not control both the selenate and sulfate concentrations. Our extensive data with log10 [Ba]) ranging from -3.6 to -5.9, log10 [SeO4]) ranging from -3.6 to -5.2, and log10 [SO4] ranging from -4.0 to -5.3 can be explained with the formation of an ideal BaSeO4 solid solution phase that controls the selenium concentrations and a slightly disordered/less-crystalline BaSO4(s) (log10 K0sp = -9.5 instead of -10.05 for barite) that controls the sulfate concentrations. In these experiments the BaSO4 component of the solid solution phase never reaches thermodynamic equilibrium with the aqueous phase. Thermodynamic interpretations of the data show that both the ideal BaSeO4 solid solution phase and less-crystalline BaSO4(s) phase are in equilibrium with each other in the entire range of BaSeO4 mole fractions investigated in this study.

Rai, Dhanpat; Felmy, Andrew R.; Moore, Dean A.; Kitamura, Akira; Yoshikawa, Hideki; Doi, Reisuke; Yoshida, Yasushi



Downregulation of Cellular c-Jun N-Terminal Protein Kinase and NF-?B Activation by Berberine May Result in Inhibition of Herpes Simplex Virus Replication  

PubMed Central

Berberine is a quaternary ammonium salt from the protoberberine group of isoquinoline alkaloids. Some reports show that berberine exhibits anti-inflammatory, antitumor, and antiviral properties by modulating multiple cellular signaling pathways, including p53, nuclear factor ?B (NF-?B), and mitogen-activated protein kinase. In the present study, we investigated the antiviral effect of berberine against herpes simplex virus (HSV) infection. Current antiherpes medicines such as acyclovir can lessen the recurring activation when used early at infection but are unable to prevent or cure infections where treatment has selected for resistant mutants. In searching for new antiviral agents against herpesvirus infection, we found that berberine reduced viral RNA transcription, protein synthesis, and virus titers in a dose-dependent manner. To elucidate the mechanism of its antiviral activity, the effect of berberine on the individual steps of viral replication cycle of HSV was investigated via time-of-drug addition assay. We found that berberine acted at the early stage of HSV replication cycle, between viral attachment/entry and genomic DNA replication, probably at the immediate-early gene expression stage. We further demonstrated that berberine significantly reduced HSV-induced NF-?B activation, as well as I?B-? degradation and p65 nuclear translocation. Moreover, we found that berberine also depressed HSV-induced c-Jun N-terminal kinase (JNK) phosphorylation but had little effect on p38 phosphorylation. Our results suggest that the berberine inhibition of HSV infection may be mediated through modulating cellular JNK and NF-?B pathways. PMID:24913175

Song, Siwei; Qiu, Min; Chu, Ying; Chen, Deyan; Wang, Xiaohui; Su, Airong



High temperature redox reactions with uranium: Synthesis and characterization of Cs(UO2)Cl(SeO3), Rb2(UO2)3O2(SeO3)2, and RbNa5U2(SO4)7  

NASA Astrophysics Data System (ADS)

Cs(UO2)Cl(SeO3) (1), Rb2(UO2)3O2(SeO3)3 (2), and RbNa5U2(SO4)7 (3) single crystals were synthesized using CsCl, RbCl, and a CuCl/NaCl eutectic mixture as fluxes, respectively. Their lattice parameters and space groups are as follows: P21/n (a=6.548(1) Å, b=11.052(2) Å, c=10.666(2) Å and ?=93.897(3)°), P1bar (a=7.051(2) Å, b=7.198(2) Å, c=8.314(2) Å, ?=107.897(3)°, ?=102.687(3)° and ?=100.564(3)°) and C2/c (a=17.862(4) Å, b=6.931(1) Å, c=20.133(4) Å and ?=109.737(6)°. The small anionic building units found in these compounds are SeO32- and SO42- tetrahedra, oxide, and chloride. The crystal structure of the first compound is composed of [(UO2)2Cl2(SeO3)2]2- chains separated by Cs+ cations. The structure of (2) is constructed from [(UO2)3O11]16- chains further connected through selenite units into layers stacked perpendicularly to the [0 1 0] direction, with Rb+ cations intercalating between them. The structure of compound (3) is made of uranyl sulfate layers formed by edge and vertex connections between dimeric [U2O16] and [SO4] polyhedra. These layers contain unusual sulfate-metal connectivity as well as large voids.

Babo, Jean-Marie; Albrecht-Schmitt, Thomas E.



Activation of extracellular signal-regulated protein kinase1,2 results in down-regulation of decorin expression in fibroblasts.  

PubMed Central

Decorin is a small leucine-rich extracellular matrix proteoglycan, the expression of which is down-regulated in proliferating and malignantly transformed cells. In the present study we show that the expression of decorin in fibroblasts is suppressed by epidermal growth factor (EGF) and PMA, and that the effect of both is potently inhibited by blocking the extracellular signal-regulated protein kinase (ERK)1,2 signalling pathway (Raf/MEK1,2/ERK1,2) with the specific MAPK/ERK kinase (MEK)1,2 inhibitor, PD98059. In addition, specific activation of ERK1,2 by adenovirus-mediated expression of constitutively active MEK1 in dermal fibroblasts results in marked reduction in decorin mRNA abundance and production. Co-transfection of NIH-3T3 fibroblasts with human decorin promoter/chloramphenicol acetyltransferase (CAT) construct (pDEC--879/CAT) in combination with the expression vectors for constitutively active Raf-1 and MEK1 markedly suppressed decorin promoter activity. Co-transfections of human decorin promoter 5'-deletion constructs with constitutively active MEK1 expression vector identified the region -278 to -188 as essential for ERK1,2 mediated down-regulation of decorin promoter activity. These results show that activation of the ERK1,2 signalling pathway by a mitogenic growth factor, a tumour promoter or transformation suppresses decorin gene expression in fibroblasts, which in turn may promote proliferation and migration of normal and malignant cells. PMID:10861206

Laine, P; Reunanen, N; Ravanti, L; Foschi, M; Santra, M; Iozzo, R V; Kähäri, V M



Inhibition of calcium/calmodulin-dependent protein kinase type IV results in suppression of autoimmunity and organ pathology in lupus-prone mice  

PubMed Central

Objective Systemic lupus erythematousus (SLE) is a chronic inflammatory disease associated with aberrant immune cell function. Treatment involves the use of indiscriminate immunosuppression with significant side effects. SLE T cells express high levels of calcium/calmodulin-dependent protein kinase type IV (CaMKIV) which translocates to the nucleus upon engagement of the T cell receptor (TCR)/CD3 and accounts for abnormal T cell function. We hypothesized that inhibition of CaMKIV should improve disease pathology. Methods We treated MRL/lpr mice with KN-93, a CaMKIV inhibitor, starting either at week 8 or week 12 of age through week 16 and evaluated skin lesions, proteinuria, kidney histopathology, pro-inflammatory cytokine production and co-stimulatory molecule expression. We also determined the effect of silencing of CaMKIV on IFN-? expression by human SLE T cells. Results We report that CaMKIV inhibition in MRL/lpr mice results in significant suppression of nephritis, skin disease, decreased expression of the co-stimulatory molecules CD86 and CD80 on B cells and suppression of IFN-? and TNF-? production. In human SLE T cells, silencing of CaMKIV resulted in suppression of IFN-? production. Conclusion We conclude that suppression of CaMKIV mitigates disease development in lupus-prone mice by suppressing cytokine production and co-stimulatory molecule expression. Specific silencing of CaMKIV in human T cells results in similar suppression of IFN-? production. Our data justify the development of small molecule CaMKIV inhibitors for the treatment of patients with SLE. PMID:20954187

Ichinose, Kunihiro; Juang, Yuang-Taung; Crispín, José C.; Kis-Toth, Katalin; Tsokos, George C.



Rats fed soy protein isolate (SPI) have impaired hepatic CYP1A1 induction by polycyclic aromatic hydrocarbons as a result of interference with aryl hydrocarbon receptor signaling  

Technology Transfer Automated Retrieval System (TEKTRAN)

Consumption of soy diet has been found to reduce cancer incidence in animals and is associated with reduced cancer risk in humans. Previously, we have demonstrated that female Sprague-Dawley rats fed purified AIN-93G diets with soy protein isolate (SPI) as the sole protein source had reduced CYP1A1 ...


Effect of laser wavelength and protein solder concentration on acute tissue repair using laser welding: initial results in a canine ureter model.  


Successful tissue approximation can be performed using low power laser energy combined with human albumin solder. In vitro studies were undertaken to investigate the acute repair strengths achieved using different laser wavelengths. Furthermore, we evaluated the change in repair strength with that resulted from changes in protein solder concentration. Intraluminal bursting pressure following ureterotomy repair was measured for the following laser wavelengths: 532, 808, 1,320, 2,100, and 10,600 nm. The tissue absorption characteristics of the 808-nm diode and the KTP-532-nm lasers required the addition of the exogenous chromophores indocyanine green and fluorescein, respectively. A 40% human albumin solder was incorporated in the repair of a 1.0-cm longitudinal defect in the canine ureter. Following determination of an optimal welding wavelength, human albumin solder of varying concentrations (25%, 38%, 45%, and 50%) were prepared and tested. The 1,320-nm YAG laser achieved the highest acute bursting pressure and was the most effective in this model. Of the concentrations of albumin tested, 50% human albumin yielded the greatest bursting pressures. We conclude that of the laser wavelengths evaluated, the 1,320-nm YAG achieves the strongest tissue weld in the acute ex vivo dog ureter model. In addition, when this laser system is used, the acute strength of a photothermal weld appears to be directly proportional to the concentration of human albumin solder in the range of 25 to 50%. PMID:9422452

Wright, E J; Poppas, D P



Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein  

PubMed Central

A battery of thermodynamic, kinetic, and structural approaches has indicated that the small ?-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ?7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ?15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any given condition because the native structure is less stable for the protonated form. PMID:24205082

Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Muñoz, Victor



Homozygosity for a Missense Mutation in SERPINH1, which Encodes the Collagen Chaperone Protein HSP47, Results in Severe Recessive Osteogenesis Imperfecta  

PubMed Central

Osteogenesis imperfecta (OI) is characterized by bone fragility and fractures that may be accompanied by bone deformity, dentinogenesis imperfecta, short stature, and shortened life span. About 90% of individuals with OI have dominant mutations in the type I collagen genes COL1A1 and COL1A2. Recessive forms of OI resulting from mutations in collagen-modifying enzymes and chaperones CRTAP, LEPRE1, PPIB, and FKBP10 have recently been identified. We have identified an autosomal-recessive missense mutation (c.233T>C, p.Leu78Pro) in SERPINH1, which encodes the collagen chaperone-like protein HSP47, that leads to a severe OI phenotype. The mutation results in degradation of the endoplasmic reticulum resident HSP47 via the proteasome. Type I procollagen accumulates in the Golgi of fibroblasts from the affected individual and a population of the secreted type I procollagen is protease sensitive. These findings suggest that HSP47 monitors the integrity of the triple helix of type I procollagen at the ER/cis-Golgi boundary and, when absent, the rate of transit from the ER to the Golgi is increased and helical structure is compromised. The normal 3-hydroxylation of the prolyl residue at position 986 of the triple helical domain of pro?1(I) chains places the role of HSP47 downstream from the CRTAP/P3H1/CyPB complex that is involved in prolyl 3-hydroxylation. Identification of this mutation in SERPINH1 gives further insight into critical steps of the collagen biosynthetic pathway and the molecular pathogenesis of OI. PMID:20188343

Christiansen, Helena E.; Schwarze, Ulrike; Pyott, Shawna M.; AlSwaid, Abdulrahman; Al Balwi, Mohammed; Alrasheed, Shatha; Pepin, Melanie G.; Weis, Mary Ann; Eyre, David R.; Byers, Peter H.



Cytochrome b Mutation Y268S Conferring Atovaquone Resistance Phenotype in Malaria Parasite Results in Reduced Parasite bc1 Catalytic Turnover and Protein Expression*  

PubMed Central

Atovaquone is an anti-malarial drug used in combination with proguanil (e.g. MalaroneTM) for the curative and prophylactic treatment of malaria. Atovaquone, a 2-hydroxynaphthoquinone, is a competitive inhibitor of the quinol oxidation (Qo) site of the mitochondrial cytochrome bc1 complex. Inhibition of this enzyme results in the collapse of the mitochondrial membrane potential, disruption of pyrimidine biosynthesis, and subsequent parasite death. Resistance to atovaquone in the field is associated with point mutations in the Qo pocket of cytochrome b, most notably near the conserved Pro260-Glu261-Trp262-Tyr263 (PEWY) region in the ef loop). The effect of this mutation has been extensively studied in model organisms but hitherto not in the parasite itself. Here, we have performed a molecular and biochemical characterization of an atovaquone-resistant field isolate, TM902CB. Molecular analysis of this strain reveals the presence of the Y268S mutation in cytochrome b. The Y268S mutation is shown to confer a 270-fold shift of the inhibitory constant (Ki) for atovaquone with a concomitant reduction in the Vmax of the bc1 complex of ?40% and a 3-fold increase in the observed Km for decylubiquinol. Western blotting analyses reveal a reduced iron-sulfur protein content in Y268S bc1 suggestive of a weakened interaction between this subunit and cytochrome b. Gene expression analysis of the TM902CB strain reveals higher levels of expression, compared with the 3D7 (atovaquone-sensitive) control strain in bc1 and cytochrome c oxidase genes. It is hypothesized that the observed differential expression of these and other key genes offsets the fitness cost resulting from reduced bc1 activity. PMID:22282497

Fisher, Nicholas; Abd Majid, Roslaini; Antoine, Thomas; Al-Helal, Mohammed; Warman, Ashley J.; Johnson, David J.; Lawrenson, Alexandre S.; Ranson, Hilary; O'Neill, Paul M.; Ward, Stephen A.; Biagini, Giancarlo A.



Subversion of Protein Kinase CA Signaling in Hematopoietic Progenitor Cells Results in the Generation of a B-Cell Chronic Lymphocytic Leukemia-Like Population In vivo  

Microsoft Academic Search

B-cell chronic lymphocytic leukemia (B-CLL) is characterized by the accumulation of long-lived mature B cells with the distinctive phenotype CD19hi CD5+ CD23+ IgMlo, which are refractory to apoptosis. An increased level of apoptosis has been observed on treatment of human B-CLL cells with protein kinase C (PKC) inhibitors, suggesting that this family of protein kinases mediate survival signals within B-CLL

Rinako Nakagawa; Jae Won Soh; Alison M. Michie


Technical decision making with higher order structure data: utilization of differential scanning calorimetry to elucidate critical protein structural changes resulting from oxidation.  


Differential scanning calorimetry (DSC) is a useful tool for monitoring thermal stability of the molecular conformation of proteins. Here, we present an example of the sensitivity of DSC to changes in stability arising from a common chemical degradation pathway, oxidation. This Note is part of a series of industry case studies demonstrating the application of higher order structure data for technical decision making. For this study, six protein products from three structural classes were evaluated at multiple levels of oxidation. For each protein, the melting temperature (Tm ) decreased linearly as a function of oxidation; however, differences in the rate of change in Tm , as well as differences in domain Tm stability were observed across and within structural classes. For one protein, analysis of the impact of oxidation on protein function was also performed. For this protein, DSC was shown to be a leading indicator of decreased antigen binding suggesting a subtle conformation change may be underway that can be detected using DSC prior to any observable impact on product potency. Detectable changes in oxidized methionine by mass spectrometry (MS) occurred at oxidation levels below those with a detectable conformational or functional impact. Therefore, by using MS, DSC, and relative potency methods in concert, the intricate relationship between a primary structural modification, changes in conformational stability, and functional impact can be elucidated. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:1548-1554, 2015. PMID:25561411

Arthur, Kelly K; Dinh, Nikita; Gabrielson, John P



Rhizobium selenitireducens proteins involved in the reduction of selenite to elemental selenium  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microbial based bioremediation barriers can remove the metalloid selenite (SeO3–2) from flowing groundwater. The organisms associated with the process include microorganisms from within the bacterial and archaeal domains that can reduce soluble SeO3–2 to the insoluble and reddish-colored elemental ...


BBS7 is required for BBSome formation and its absence in mice results in Bardet-Biedl syndrome phenotypes and selective abnormalities in membrane protein trafficking  

PubMed Central

Summary Bardet-Biedl Syndrome (BBS) is a pleiotropic and genetically heterozygous disorder caused independently by numerous genes (BBS1–BBS17). Seven highly conserved BBS proteins (BBS1, 2, 4, 5, 7, 8 and 9) form a complex known as the BBSome, which functions in ciliary membrane biogenesis. BBS7 is both a unique subunit of the BBSome and displays direct physical interaction with a second BBS complex, the BBS chaperonin complex. To examine the in vivo function of BBS7, we generated Bbs7 knockout mice. Bbs7?/? mice show similar phenotypes to other BBS gene mutant mice including retinal degeneration, obesity, ventriculomegaly and male infertility characterized by abnormal spermatozoa flagellar axonemes. Using tissues from Bbs7?/? mice, we show that BBS7 is required for BBSome formation, and that BBS7 and BBS2 depend on each other for protein stability. Although the BBSome serves as a coat complex for ciliary membrane proteins, BBS7 is not required for the localization of ciliary membrane proteins polycystin-1, polycystin-2, or bitter taste receptors, but absence of BBS7 leads to abnormal accumulation of the dopamine D1 receptor to the ciliary membrane, indicating that BBS7 is involved in specific membrane protein localization to cilia. PMID:23572516

Zhang, Qihong; Nishimura, Darryl; Vogel, Tim; Shao, Jianqiang; Swiderski, Ruth; Yin, Terry; Searby, Charles; Carter, Calvin S.; Kim, GunHee; Bugge, Kevin; Stone, Edwin M.; Sheffield, Val C.



BBS7 is required for BBSome formation and its absence in mice results in Bardet-Biedl syndrome phenotypes and selective abnormalities in membrane protein trafficking.  


Bardet-Biedl Syndrome (BBS) is a pleiotropic and genetically heterozygous disorder caused independently by numerous genes (BBS1-BBS17). Seven highly conserved BBS proteins (BBS1, 2, 4, 5, 7, 8 and 9) form a complex known as the BBSome, which functions in ciliary membrane biogenesis. BBS7 is both a unique subunit of the BBSome and displays direct physical interaction with a second BBS complex, the BBS chaperonin complex. To examine the in vivo function of BBS7, we generated Bbs7 knockout mice. Bbs7(-/-) mice show similar phenotypes to other BBS gene mutant mice including retinal degeneration, obesity, ventriculomegaly and male infertility characterized by abnormal spermatozoa flagellar axonemes. Using tissues from Bbs7(-/-) mice, we show that BBS7 is required for BBSome formation, and that BBS7 and BBS2 depend on each other for protein stability. Although the BBSome serves as a coat complex for ciliary membrane proteins, BBS7 is not required for the localization of ciliary membrane proteins polycystin-1, polycystin-2, or bitter taste receptors, but absence of BBS7 leads to abnormal accumulation of the dopamine D1 receptor to the ciliary membrane, indicating that BBS7 is involved in specific membrane protein localization to cilia. PMID:23572516

Zhang, Qihong; Nishimura, Darryl; Vogel, Tim; Shao, Jianqiang; Swiderski, Ruth; Yin, Terry; Searby, Charles; Carter, Calvin S; Kim, Gunhee; Bugge, Kevin; Stone, Edwin M; Sheffield, Val C



F box protein FBXL2 exerts human lung tumor suppressor-like activity by ubiquitin-mediated degradation of cyclin D3 resulting in cell cycle arrest  

PubMed Central

Dyregulated behavior of cell cycle proteins and their control by ubiquitin E3 ligases is an emerging theme in human lung cancer. Here we identified and characterized the activity of a novel F box protein, termed FBXL2, belonging to the SCF (Skip-Cullin1-F-box protein) E3 ligase family. Ectopically expressed FBXL2 triggered G2/M phase arrest, induced chromosomal anomalies, and increased apoptosis of transformed lung epithelia by mediating polyubiquitination and degradation of the mitotic regulator, cyclin D3. Unlike other F box proteins that target phosphodegrons within substrates, FBXL2 uniquely recognizes a canonical calmodulin-binding motif within cyclin D3 to facilitate its polyubiquitination. Calmodulin bound and protected cyclin D3 from FBXL2 by direct intermolecular competition with the F box protein for access within this motif. The chemotherapeutic agent vinorelbine increased apoptosis of human lung carcinoma cells by inducing FBXL2 expression and cyclin D3 degradation, an effect accentuated by calmodulin knockdown. Depletion of endogenous FBXL2 stabilized cyclin D3 levels, accellerated cancer cell growth, and increased cell viability after vinorelbine treatment. Last, ectopic expression of FBXL2 significantly inhibited the growth and migration of tumorogenic cells and tumor formation in athymic nude mice. These observations implicate SCFFBXL2 as an indispensible regulator of mitosis that serves as a tumor suppressor. PMID:22020328

Chen, Bill B.; Glasser, Jennifer R.; Coon, Tiffany A.; Mallampalli, Rama K.



Protein Foods  


... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...


Binding of selenium-75 to blood and liver cytosolic proteins in the preruminant calf  

SciTech Connect

Labeled selenite (75Se) administered to calves in milk replacer, containing .2 or 5 ppm Se, was rapidly absorbed with peak blood 75Se at 6 h. Gel filtration and dialysis treatment of plasma and erythrocyte hemolysates showed that initially 75Se was transported in blood as 75SeO3= or loosely bound to plasma and erythrocyte proteins. At high Se intake, albumin became a transport protein for some of the plasma 75Se, and proportionately more blood radioactivity was carried in the erythrocytes. At 72 h after dosing, most plasma 75Se was tightly bound to protein in glutathione peroxidase fraction with low peroxidase activity, possibly Se transport protein. At 72 h, distribution of 75Se in erythrocyte was 35 to 40% in glutathione peroxidase, 50% in hemoglobin, and 5% in a selenite plus selenopolypeptide fraction. Erythrocyte peroxidase activity was mostly in the glutathione peroxidase fraction (57%) and hemoglobin (38%). Molecular weight estimate for erythrocyte glutathione peroxidase was 84,200 daltons; about 90% of blood peroxidase activity was in erythrocytes. High Se intake had no marked effect on distribution of 75Se among liver cytosolic proteins. About 35% of 75Se was in glutathione peroxidase fraction, having most of the peroxidase activity, 25% in void volume, 11 to 18% in a selenite plus selenopolypeptide fraction, and small amounts in selenoproteins of about 12,000 and 50,000 daltons.

Jenkins, K.J.; Hidiroglou, M.



Bacteriophage Protein–Protein Interactions  

PubMed Central

Bacteriophages T7, ?, P22, and P2/P4 (from Escherichia coli), as well as ?29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage–host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages ? and T7. For example, the ?55 proteins encoded by the T7 genome are connected by ?43 interactions with another ?15 between the phage and its host. The chapter compiles published interactions for the well-studied phages ? (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ?29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage ? and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology. PMID:22748812

Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggård-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian



Muscle Uncoupling Protein 3 Expression Is Unchanged by Chronic Ephedrine/Caffeine Treatment: Results of a Double Blind, Randomised Clinical Trial in Morbidly Obese Females  

PubMed Central

Ephedrine/caffeine combination (EC) has been shown to induce a small-to-moderate weight loss in obese patients. Several mechanisms have been proposed, among which an increased thermogenic capacity of skeletal muscle consequent to the EC-induced up-regulation of uncoupling protein 3 (UCP3) gene expression. We did a parallel group double-blind, placebo-controlled, 4-week trial to investigate this hypothesis. Thirteen morbidly obese women (25–52 years of age, body-mass index 48.0±4.0 kg/m2, range 41.1–57.6) were randomly assigned to EC (200/20 mg, n?=?6) or to placebo (n?=?7) administered three times a day orally, before undergoing bariatric surgery. All individuals had an energy-deficit diet equal to about 70% of resting metabolic rate (RMR) diet (mean 5769±1105 kJ/day). The RMR analysed by intention to treat and the UCP3 (long and short isoform) mRNA levels in rectus abdominis were the primary outcomes. Body weight, plasma levels of adrenaline, noradrenaline, triglycerides, free fatty acids, glycerol, TSH, fT4, and fT3 were assessed, as well as fasting glucose, insulin and HOMA index, at baseline and at the end of treatments. Body weight loss was evident in both groups when compared to baseline values (overall ?5.2±3.2%, p<0.0001) without significant differences between the treated groups. EC treatment increased the RMR (+9.2±6.8%, p?=?0.020), differently from placebo which was linked to a reduction of RMR (?7.6±6.5%, p?=?0.029). No significant differences were seen in other metabolic parameters. Notably, no changes of either UCP3 short or UCP3 long isoform mRNA levels were evident between EC and placebo group. Our study provides evidence that 4-week EC administration resulted in a pronounced thermogenic effect not related to muscle UCP3 gene expression and weight loss in morbidly obese females under controlled conditions. Trial Registration NCT02048215 PMID:24905629

Bracale, Renata; Petroni, Maria Letizia; Davinelli, Sergio; Bracale, Umberto; Scapagnini, Giovanni; Carruba, Michele O.; Nisoli, Enzo



MART-1 peptide vaccination plus IMP321 (LAG-3Ig fusion protein) in patients receiving autologous PBMCs after lymphodepletion: results of a Phase I trial  

PubMed Central

Background Immunotherapy offers a promising novel approach for the treatment of cancer and both adoptive T-cell transfer and immune modulation lead to regression of advanced melanoma. However, the potential synergy between these two strategies remains unclear. Methods We investigated in 12 patients with advanced stage IV melanoma the effect of multiple MART-1 analog peptide vaccinations with (n?=?6) or without (n?=?6) IMP321 (LAG-3Ig fusion protein) as an adjuvant in combination with lymphodepleting chemotherapy and adoptive transfer of autologous PBMCs at day (D) 0 (Trial registration No: NCT00324623). All patients were selected on the basis of ex vivo detectable MART-1-specific CD8 T-cell responses and immunized at D0, 8, 15, 22, 28, 52, and 74 post-reinfusion. Results After immunization, a significant expansion of MART-1-specific CD8 T cells was measured in 83% (n?=?5/6) and 17% (n?=?1/6) of patients from the IMP321 and control groups, respectively (P?2-, >4- and >6-fold higher at D15, D30 and D60 (P?



A single amino acid substitution in the hemagglutinin-neuraminidase protein of Newcastle disease virus results in increased fusion and decreased neuraminidase activities without changes in virus pathotype  

Technology Transfer Automated Retrieval System (TEKTRAN)

Newcastle disease virus (NDV) attachment to the host cell is mediated by the hemagglutinin-neuraminidase (HN), a multifunctional protein that has receptor recognition, neuraminidase and fusion promotion activities. The process that correlates receptor binding and fusion triggering is poorly understo...


A serine-to-threonine substitution in the triazine herbicide-binding protein in potato cells results in atrazine resistance without impairing productivity.  

PubMed Central

A mutation of the psbA gene was identified in photoautotrophic potato (Solanum tuberosum L. cv Superior x U.S. Department of Agriculture line 66-142) cells selected for resistance to 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine (atrazine). Photoaffinity labeling with 6-azido-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine detected a thylakoid membrane protein with a M(r) of 32,000 in susceptible, but not in resistant, cells. This protein was identified as the secondary quinone acceptor of photosystem II (QB) protein. Atrazine resistance in selected cells was attributable to a mutation from AGT (serine) to ACT (threonine) in codon 264 of the psbA gene that encodes the QB protein. Although the mutant cells exhibited extreme levels of resistance to atrazine, no concomitant reductions in photosynthetic electron transport or cell growth rates compared to the unselected cells were detected. This is in contrast with the losses in productivity observed in atrazine-resistant mutants that contain a glycine-264 alteration. PMID:8022941

Smeda, R J; Hasegawa, P M; Goldsbrough, P B; Singh, N K; Weller, S C



Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics.  


Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed. The Gateway system is a versatile framework to construct a variety of expression clones for various experiments. We have constructed 33 275 human Gateway entry clones from full-length cDNAs, representing to our knowledge the largest collection in the world. Utilizing these clones with a highly efficient cell-free protein synthesis system based on wheat germ extract, we have systematically and comprehensively produced and analyzed human proteins in vitro. Sequence information for both amino acids and nucleotides of open reading frames of cDNAs cloned into Gateway entry clones and in vitro expression data using those clones can be retrieved from the Human Gene and Protein Database (HGPD, HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones. PMID:19073703

Maruyama, Yukio; Wakamatsu, Ai; Kawamura, Yoshifumi; Kimura, Kouichi; Yamamoto, Jun-ichi; Nishikawa, Tetsuo; Kisu, Yasutomo; Sugano, Sumio; Goshima, Naoki; Isogai, Takao; Nomura, Nobuo



Clinical implications of p53 tumor suppressor gene mutation and protein expression in esophageal adenocarcinomas: Results of a ten-year prospective study  

Microsoft Academic Search

Objective: This study was undertaken to characterize the spectrum of p53 alterations (mutations and protein expression) in surgically resected esophageal adenocarcinomas, and to correlate molecular alterations with clinicopathologic findings and outcome. Methods: Between 1991 and 2001, 91 consecutive patients with esophageal adenocarcinomas underwent subtotal esophagectomy. No patient received induction therapy. Strict clinicopathologic criteria were used to define primary esophageal adenocarcinomas.

Alan G. Casson; Susan C. Evans; Amy Gillis; Geoffrey A. Porter; Paul Veugelers; S. Jane Darnton; Duane L. Guernsey; Pierre Hainaut



Effects of proteins on protein diffusion  

PubMed Central

Despite increased attention, little is known about how the crowded intracellular environment affects basic phenomena like protein diffusion. Here, we use NMR to quantify the rotational and translational diffusion of a 7.4-kDa test protein, chymotrypsin inhibitor 2 (CI2), in solutions of glycerol, synthetic polymers, proteins, and cell lysates. As expected, translational diffusion and rotational diffusion decrease with increasing viscosity. In glycerol, for example, the decrease follows the Stokes-Einstein and Stokes-Einstein-Debye laws. Synthetic polymers cause negative deviation from the Stokes Laws and affect translation more than rotation. Surprisingly, however, protein crowders have the opposite effect, causing positive deviation and reducing rotational diffusion more than translational diffusion. Indeed, bulk proteins severely attenuate the rotational diffusion of CI2 in crowded protein solutions. Similarly, CI2 diffusion in cell lysates is comparable to its diffusion in crowded protein solutions, supporting the biological relevance of the results. The rotational attenuation is independent of the size and total charge of the crowding protein, suggesting that the effect is general. The difference between the behavior of synthetic polymers and protein crowders suggests that synthetic polymers may not be suitable mimics of the intracellular environment. NMR relaxation data reveal that the source of the difference between synthetic polymers and proteins is the presence of weak interactions between the proteins and CI2. In summary, weak but non-specific, non-covalent chemical interactions between proteins appear to fundamentally impact protein diffusion in cells. PMID:20560582

Wang, Yaqiang; Li, Conggang; Pielak, Gary J.



Mutation of the elongin C binding domain of human respiratory syncytial virus non-structural protein 1 (NS1) results in degradation of NS1 and attenuation of the virus  

PubMed Central

Background Human respiratory syncytial virus (RSV) is an important cause of lower respiratory tract disease in the paediatic population, immunocompromised individuals and the elderly worldwide. However, despite global efforts over the past several decades there are no commercially available vaccines. RSV encodes 2 non-structural proteins, NS1 and NS2, that are type I interferon antagonists. RSV restricts type I interferon signaling and the expression of antiviral genes by degrading STAT2. It has been proposed that NS1 binds to elongin C to form a ubiquitin ligase (E3) complex that targets STAT2 for ubiquitination and proteosomal degradation. Results Here, we have engineered a live recombinant RSV in which the 3 consensus amino acids of the NS1 elongin C binding domain have been replaced with alanine (NS1F-ELCmut). Mutation of this region of NS1 resulted in attenuation of RSV replication in A549 cells to levels similar to that observed when the NS1 gene is completely deleted (?NS1). This mutation also resulted in moderate attenuation in Vero cells. Attenuation was correlated to intracellular degradation of the mutated NS1 protein. Time course analysis showed that mutant NS1 protein accumulated in cytoplasmic bodies that contained the lysosomal marker LAMP1. However lack of cleavage of LC3 suggested that autophagy was not involved. Induction of IFN-? mRNA expression also was observed in association with the degradation of NS1 protein and attenuation of viral growth. Conclusions These results indicate that the elongin C binding region of NS1 is crucial for survival of the protein and that disruption of this region results in the degradation of NS1 and restriction of RSV replication. PMID:21600055



Overexpression of the Gene Encoding the Multidrug Resistance-Associated Protein Results in Increased ATP-Dependent Glutathione S-Conjugate Transport  

Microsoft Academic Search

The multidrug resistance-associated protein (MRP) is a 180- to 195-kDa glycoprotein associated with multidrug resistance of human tumor cells. MRP is mainly located in the plasma membrane and it confers resistance by exporting natural product drugs out of the cell. Here we demonstrate that overexpression of the MRP gene in human cancer cells increases the ATP-dependent glutathione S-conjugate carrier activity

Michael Muller; Coby Meijer; Guido J. R. Zaman; Piet Borst; Rik J. Scheper; Nanno H. Mulder; Elisabeth G. E. de Vries; Peter L. M. Jansen



Deficiency of Protein Kinase CA in Mice Results in Impairment of Epidermal Hyperplasia and Enhancement of Tumor Formation in Two-Stage Skin Carcinogenesis  

Microsoft Academic Search

We generated a mouse strain lacking protein kinase CA (PKCA) and evaluated the significance of the enzyme in epithelial hyperplasia and tumor formation. PKCA-deficient mice exhibited increased susceptibility to tumor formation in two-stage skin carcinogenesis by single application of 7,12- dimethylbenz(a)anthracene (DMBA) for tumor initiation and repeated applications of 12-O-tetradecanoylphorbol-13- acetate (TPA) for tumor promotion. Tumor formation was not enhanced

Takeshi Hara; Yuriko Saito; Takaaki Hirai; Kenji Nakamura; Kazuki Nakao; Motoya Katsuki; Kazuhiro Chida



Encephalitogenic potential of the myelin basic protein peptide (amino acids 83–99) in multiple sclerosis: Results of a phase II clinical trial with an altered peptide ligand  

Microsoft Academic Search

Myelin-specific T lymphocytes are considered essential in the pathogenesis of multiple sclerosis. The myelin basic protein peptide (a.a. 83–99) represents one candidate antigen; therefore, it was chosen to design an altered peptide ligand, CGP77116, for specific immunotherapy of multiple sclerosis. A magnetic resonance imaging-controlled phase II clinical trial with this altered peptide ligand documented that it was poorly tolerated at

Bibiana Bielekova; Bonnie Goodwin; Nancy Richert; Irene Cortese; Takayuki Kondo; Ghazaleh Afshar; Bruno Gran; Joan Eaton; Jack Antel; Joseph A. Frank; Henry F. McFarland; Roland Martin



Escherichia coli cold shock protein CsdA effects an increase in septation and the resultant formation of coccobacilli at low temperature  

Microsoft Academic Search

Bacterial shape is controlled by peptidoglycan assembly along the lateral wall and at the septum site. In contrast to rods\\u000a at 37°C, the wild-type strain formed coccobacilli at 12°C, indicating a prevailing shift toward septal peptidoglycan synthesis\\u000a at low temperature. Escherichia coli cold shock protein CsdA is a DEAD-box RNA helicase with an extended variable region at the carboxyl terminus.

Ashley Pierce; Devyn Gillette; Pamela G. Jones



Predicting Protein Phenotypes Based on Protein-Protein Interaction Network  

PubMed Central

Background Identifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins. Methodology/Principal Findings Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only the most likely phenotype, a series of possible phenotypes for the query protein were generated and ranked acording to the tethering potential score. As a result, the first order prediction accuracy of our method achieved 65.4% evaluated by Jackknife test of 1,267 proteins in budding yeast, much higher than the success rate (15.4%) of a random guess. And the likelihood of the first 3 predicted phenotypes including all the real phenotypes of the proteins was 70.6%. Conclusions/Significance The candidate phenotypes predicted by our method provided useful clues for the further validation. In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms. PMID:21423698

Liu, Xiao-Jun; Cai, Yu-Dong



A single amino acid change resulting in loss of fluorescence of eGFP in a viral fusion protein confers fitness and growth advantage to the recombinant vesicular stomatitis virus  

SciTech Connect

Using a recombinant vesicular stomatitis virus encoding eGFP fused in-frame with an essential viral replication protein, the phosphoprotein P, we show that during passage in culture, the virus mutates the nucleotide C289 within eGFP of the fusion protein PeGFP to A or T, resulting in R97S/C amino acid substitution and loss of fluorescence. The resultant non-fluorescent virus exhibits increased fitness and growth advantage over its fluorescent counterpart. The growth advantage of the non-fluorescent virus appears to be due to increased transcription and replication activities of the PeGFP protein carrying the R97S/C substitution. Further, our results show that the R97S/C mutation occurs prior to accumulation of mutations that can result in loss of expression of the gene inserted at the G-L gene junction. These results suggest that fitness gain is more important for the recombinant virus than elimination of expression of the heterologous gene.

Dinh, Phat X.; Panda, Debasis; Das, Phani B.; Das, Subash C.; Das, Anshuman [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States) [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); The Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); Pattnaik, Asit K., E-mail: [School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States); The Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0900 (United States)



Protein Analysis  

NSDL National Science Digital Library

This workbook allows the analysis of sample or imported protein sequences. The model can analyze protein sequences up to 500 amino acids long. The program analyzes five aspects of the protein sequence: the highest potential charge along the protein sequence, the amino acid composition of the protein sequence, the isoelectric point of the protein sequence at varying pHs, the hydrophobicity to predict surface and membrane spanning regions of the protein sequence and the protein structure using the Chau and Fassman algorithm.

John Jungck (Beloit College; Biology)



The common missense mutation D489N in TRIM32 causing limb girdle muscular dystrophy 2H leads to loss of the mutated protein in knock-in mice resulting in a Trim32-null phenotype.  


Mutations in tripartite motif protein 32 (TRIM32) are responsible for several hereditary disorders that include limb girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathy (STM) and Bardet Biedl syndrome. Most LGMD2H mutations in TRIM32 are clustered in the NHL ?-propeller domain at the C-terminus and are predicted to interfere with homodimerization. To get insight into TRIM32's role in the pathogenesis of LGMD2H and to create an accurate model of disease, we have generated a knock-in mouse (T32KI) carrying the c.1465G > A (p.D489N) mutation in murine Trim32 corresponding to the human LGMD2H/STM pathogenic mutation c.1459G > A (p.D487N). Our data indicate that T32KI mice have both a myopathic and a neurogenic phenotype, very similar to the one described in the Trim32-null mice that we created previously. Analysis of Trim32 gene expression in T32KI mice revealed normal mRNA levels, but a severe reduction in mutant TRIM32 (D489N) at the protein level. Our results suggest that the D489N pathogenic mutation destabilizes the protein, leading to its degradation, and results in the same mild myopathic and neurogenic phenotype as that found in Trim32-null mice. Thus, one potential mechanism of LGMD2H might be destabilization of mutated TRIM32 protein leading to a null phenotype. PMID:21775502

Kudryashova, Elena; Struyk, Arie; Mokhonova, Ekaterina; Cannon, Stephen C; Spencer, Melissa J



Single Point Mutations Result in the Miss-Sorting of Glut4 to a Novel Membrane Compartment Associated with Stress Granule Proteins  

PubMed Central

Insulin increases cellular glucose uptake and metabolism in the postprandial state by acutely stimulating the translocation of the Glut4 glucose transporter from intracellular membrane compartments to the cell surface in muscle and fat cells. The intracellular targeting of Glut4 is dictated by specific structural motifs within cytoplasmic domains of the transporter. We demonstrate that two leucine residues at the extreme C-terminus of Glut4 are critical components of a motif (IRM, insulin responsive motif) involved in the sorting of the transporter to insulin responsive vesicles in 3T3L1 adipocytes. Light microscopy, immunogold electron microscopy, subcellular fractionation, and sedimentation analysis indicate that mutations in the IRM cause the aberrant targeting of Glut4 to large dispersed membrane vesicles that are not insulin responsive. Proteomic characterization of rapidly and slowly sedimenting membrane vesicles (RSVs and SSVs) that were highly enriched by immunoadsorption for either wild-type Glut4 or an IRM mutant revealed that the major vesicle fraction containing the mutant transporter (IRM-RSVs) possessed a relatively small and highly distinct protein population that was enriched for proteins associated with stress granules. We suggest that the IRM is critical for an early step in the sorting of Glut4 to insulin-responsive subcellular membrane compartments and that IRM mutants are miss-targeted to relatively large, amorphous membrane vesicles that may be involved in a degradation pathway for miss-targeted or miss-folded proteins or represent a transitional membrane compartment that Glut4 traverses en route to insulin responsive storage compartments. PMID:23874650

Song, XiaoMei; Lichti, Cheryl F.; Townsend, R. Reid; Mueckler, Mike



Rats fed soy protein isolate (SPI) have impaired hepatic CYP1A1 induction by polycyclic aromatic hydrocarbons as a result of interference with aryl hydrocarbon receptor signaling  

SciTech Connect

Consumption of soy diets has been found to reduce cancer incidence in animals and is associated with reduced cancer risk in humans. Previously, we have demonstrated that female Sprague-Dawley rats fed purified AIN-93G diets with soy protein isolate (SPI) as the sole protein source had reduced CYP1A1 induction and basal aryl hydrocarbon receptor (AhR) levels relative to those fed the same diet containing casein (CAS). In the present study, the molecular mechanisms underlying reduced AhR expression have been studied. The SPI-effect on AhR was not observed after feeding diets containing the purified soy isoflavones genistein or daidzein. Rat hepatoma FGC-4 cells were treated with the serum obtained from rats fed CAS- or SPI-containing diets. Reduced AhR levels (P < 0.05) were observed after 24 h exposure to SPI-serum without any changes in the overall expression of chaperone proteins-HSP90 and XAP2. SPI-serum-stimulated AhR degradation was inhibited by treating the cells with the proteasome inhibitor, MG132, and was observed to be preceded by ubiquitination of the receptor. A reduced association of XAP2 with the immunoprecipitated AhR complex was observed. SPI-serum-mediated AhR degradation was preceded by nuclear translocation of the receptor. However, the translocated receptor was found to be unable to heterodimerize with ARNT or to bind to XRE elements on the CYP1A1 enhancer. These data suggest that feeding SPI-containing diets antagonizes AhR signaling by a novel mechanism which differs from those established for known AhR antagonists.

Singhal, Rohit [Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Badger, Thomas M. [Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Children's Nutrition Center, Little Rock, AR 72202 (United States); Ronis, Martin J. [Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Children's Nutrition Center, Little Rock, AR 72202 (United States)], E-mail:



Protein Crystallization  

NASA Technical Reports Server (NTRS)

Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

Chernov, Alexander A.



Vaccination with a Fusion Protein That Introduces HIV-1 Gag Antigen into a Multitrimer CD40L Construct Results in Enhanced CD8+ T Cell Responses and Protection from Viral Challenge by Vaccinia-Gag  

PubMed Central

CD40 ligand (CD40L, CD154) is a membrane protein that is important for the activation of dendritic cells (DCs) and DC-induced CD8+ T cell responses. To be active, CD40L must cluster CD40 receptors on responding cells. To produce a soluble form of CD40L that clusters CD40 receptors necessitates the use of a multitrimer construct. With this in mind, a tripartite fusion protein was made from surfactant protein D (SPD), HIV-1 Gag as a test antigen, and CD40L, where SPD serves as a scaffold for the multitrimer protein complex. This SPD-Gag-CD40L protein activated CD40-bearing cells and bone marrow-derived DCs in vitro. Compared to a plasmid for Gag antigen alone (pGag), DNA vaccination of mice with pSPD-Gag-CD40L induced an increased number of Gag-specific CD8+ T cells with increased avidity for major histocompatibility complex class I-restricted Gag peptide and improved vaccine-induced protection from challenge by vaccinia-Gag virus. The importance of the multitrimeric nature of the complex was shown using a plasmid lacking the N terminus of SPD that produced a single trimer fusion protein. This plasmid, pTrimer-Gag-CD40L, was only weakly active on CD40-bearing cells and did not elicit strong CD8+ T cell responses or improve protection from vaccinia-Gag challenge. An adenovirus 5 (Ad5) vaccine incorporating SPD-Gag-CD40L was much stronger than Ad5 expressing Gag alone (Ad5-Gag) and induced complete protection (i.e., sterilizing immunity) from vaccinia-Gag challenge. Overall, these results show the potential of a new vaccine design in which antigen is introduced into a construct that expresses a multitrimer soluble form of CD40L, leading to strongly protective CD8+ T cell responses. PMID:24227853

Gupta, Sachin; Termini, James M.; Raffa, Francesca N.; Williams, Cindi-Ann; Kornbluth, Richard S.



Selection for low or high primary dormancy in Lolium rigidum Gaud seeds results in constitutive differences in stress protein expression and peroxidase activity  

PubMed Central

Seed dormancy in wild Lolium rigidum Gaud (annual ryegrass) populations is highly variable and not well characterized at the biochemical level. To identify some of the determinants of dormancy level in these seeds, the proteomes of subpopulations selected for low and high levels of primary dormancy were compared by two-dimensional polyacrylamide gel electrophoresis of extracts from mature, dry seeds. High-dormancy seeds showed higher expression of small heat shock proteins, enolase, and glyoxalase I than the low-dormancy seeds. The functional relevance of these differences in protein expression was confirmed by the fact that high-dormancy seeds were more tolerant to high temperatures imposed at imbibition and had consistently higher glyoxalase I activity over 0–42?d dark stratification. Higher expression of a putative glutathione peroxidase in low-dormancy seeds was not accompanied by higher activity, but these seeds had a slightly more oxidized glutathione pool and higher total peroxidase activity. Overall, these biochemical and physiological differences suggest that L. rigidum seeds selected for low dormancy are more prepared for rapid germination via peroxidase-mediated cell wall weakening, whilst seeds selected for high dormancy are constitutively prepared to survive environmental stresses, even in the absence of stress during seed development. PMID:20974739

Goggin, Danica E.; Powles, Stephen B.; Steadman, Kathryn J.



Enterovirus 71 VP1 Activates Calmodulin-Dependent Protein Kinase II and Results in the Rearrangement of Vimentin in Human Astrocyte Cells  

PubMed Central

Enterovirus 71 (EV71) is one of the main causative agents of foot, hand and mouth disease. Its infection usually causes severe central nervous system diseases and complications in infected infants and young children. In the present study, we demonstrated that EV71 infection caused the rearrangement of vimentin in human astrocytoma cells. The rearranged vimentin, together with various EV71 components, formed aggresomes-like structures in the perinuclear region. Electron microscopy and viral RNA labeling indicated that the aggresomes were virus replication sites since most of the EV71 particles and the newly synthesized viral RNA were concentrated here. Further analysis revealed that the vimentin in the virus factories was serine-82 phosphorylated. More importantly, EV71 VP1 protein is responsible for the activation of calmodulin-dependent protein kinase II (CaMK-II) which phosphorylated the N-terminal domain of vimentin on serine 82. Phosphorylation of vimentin and the formation of aggresomes were required for the replication of EV71 since the latter was decreased markedly after phosphorylation was blocked by KN93, a CaMK-II inhibitor. Thus, as one of the consequences of CaMK-II activation, vimentin phosphorylation and rearrangement may support virus replication by playing a structural role for the formation of the replication factories. Collectively, this study identified the replication centers of EV71 in human astrocyte cells. This may help us understand the replication mechanism and pathogenesis of EV71 in human. PMID:24073199

Haolong, Cong; Du, Ning; Hongchao, Tian; Yang, Yang; Wei, Zhang; Hua, Zhang; Wenliang, Zhang; Lei, Song; Po, Tien



ProteinProtein Interactions  

E-print Network

to nitrocellulose or PVDF membrane, and then incubating with a probe of interest. The probe is typically a protein, samples are run on SDS-PAGE gels, transferred to nitrocellulose or PVDF, and then overlaid with a soluble

Hall, Randy A


Night-time consumption of protein or carbohydrate results in increased morning resting energy expenditure in active college-aged men.  


The purpose of the present study was to investigate whether whey protein (WP), casein protein (CP), carbohydrate (CHO) or a non-energy-containing placebo (PLA) consumed before sleep alters morning appetite and resting energy expenditure (REE) in active men. A total of eleven men (age: 23·6 (sem 1·0) years; body fat: 16·3 (sem 2·5) %) participated in this randomised, double-blind, cross-over study. A single dose of WP (30 g), CP (30 g), CHO (33 g) or PLA was consumed 30 min before sleep, and each trial was separated by 48-72 h. The next morning (05.00-08.00 hours), measurements of satiety, hunger and desire to eat and REE were taken. After a 30 min equilibration period, REE in the supine position was measured for 60 min. An analysis of 10 min mean intervals over the final 50 min of the measurement period was conducted. Statistical analyses were conducted using repeated-measures ANOVA for metabolic variables, and a one-way ANOVA was used for measuring changes in appetite markers. Group differences were examined by Tukey's post hoc analysis. There were no significant differences in appetite measures among the groups. There was a main group effect for REE. The predicted REE was significantly greater after consumption of the WP (8151 (sem 67) kJ/d), CP (8126 (sem 67) kJ/d) and CHO (7988 (sem 67) kJ/d) than after that of the PLA (7716 (sem 67) kJ/d, P <0·0001). There were no significant differences between the WP and CP groups in any metabolic measurements. Night-time consumption of WP, CP or CHO, in the hours close to sleep, elicits favourable effects on the next-morning metabolism when compared with that of a PLA in active young men. PMID:23768612

Madzima, Takudzwa A; Panton, Lynn B; Fretti, Sarah K; Kinsey, Amber W; Ormsbee, Michael J



Oligomeric protein structure networks: insights into protein-protein interactions  

PubMed Central

Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues) with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb). A few predictions of interface hot spots have also been made based on the results obtained from this analysis, which await experimental verification. Conclusion The construction and analysis of oligomeric protein structure networks and their comparison with monomeric protein structure networks provide insights into protein association. Further, the interface hubs identified using the present method can be effective targets for interface de-stabilizing mutations. We believe this analysis will significantly enhance our knowledge of the principles behind protein association and also aid in protein design. PMID:16336694

Brinda, KV; Vishveshwara, Saraswathi



Stochastic interpolation of rainfall data from rain gages and radar using Cokriging: 2. Results  

NASA Astrophysics Data System (ADS)

Various estimation procedures using ordinary, universal, and disjunctive cokriging are evaluated in merging rain gage measurements and radar rainfall data. The estimation procedures and the simulation experiments were described in part 1 (Seo et al., this issue) of this two-part work. In this part, the experiments are described in detail. An objective comparison scheme, devised to compare a large number of estimators, is also described. The results are presented focusing upon (1) the potential of radar-gage estimation using cokriging over radar-only estimation and gage-only estimation under widely varying conditions of gage network density and the error characteristics of radar rainfall, (2) the potential for using universal or disjunctive cokriging over ordinary cokriging, (3) how the uncertain second-order statistics affect the estimators, due to lack of rain gage measurements, and (4) how the statistical characteristics of ground truth rainfall affect the estimators.

Seo, Dong-Jun; Krajewski, Witold F.; Azimi-Zonooz, Ali; Bowles, David S.



Protein Condensation  

NASA Astrophysics Data System (ADS)

Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.



Protein Condensation  

NASA Astrophysics Data System (ADS)

Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.



Research Results  

NASA Astrophysics Data System (ADS)

Research on Global Carbon Emission and Sequestration NSFC Funded Project Made Significant Progress in Quantum Dynamics Functional Human Blood Protein Obtained from Rice How Giant Pandas Thrive on a Bamboo Diet New Evidence of Interpersonal Violence from 129,000 Years Ago Found in China Aptamer-Mediated Efficient Capture and Release of T Lymphocytes on Nanostructured Surfaces BGI Study Results on Resequencing 50 Accessions of Rice Cast New Light on Molecular Breeding BGI Reports Study Results on Frequent Mutation of Genes Encoding UMPP Components in Kidney Cancer Research on Habitat Shift Promoting Species Diversification



[The results of application of the rapid quantitative assay for fatty acid-binding protein at the onset of acute coronary syndrome].  


Fatty acid-binding protein (FABP) appearing in blood within a few hours of acute coronary syndrome (ACS) is a marker of myocardial necrosis. We estimated the diagnostic value of rapid immunochromatographic test for FABP in patients with ACS and compared it with other cardiomarkers: troponin 1 (Tn1), myoglobin and creatin phosphokinase-MB (CPK-MB). The study included 100 patients aged 61.3 +/- 12.9 yr hospitalized with ACS within 2 hr after beginning of anginous pain. FABP was detected by CardioFABP test, Tn1, myoglobin and CPK-MB by quantitative assays. Blood samples were taken 2, 6, and 24 hr after the onset of anginous pain. Acute myocardial infarction was diagnosed in 79 patients, unstable angina in 9, FC 3-4 angina of effort in 4, vasospastic angina in 1, non-coronary pathology in 7. Sensitivity of FABP, Tn1, myoglobin and CPK-MB 2 hr after onset of pain was 84.8; 34.2, 65.8; 22.8% respectively: it was 98.7: 92.4; 96.2; 82.3% in 6 hr and 56; 100; n/d; 86.7% in 24 hr. Specificity of FABP was 100% in all time intervals. It is concluded that FABP level determined by rapid qualitative assay within 2-6 hr after onset of ACS is a more sensitive cardiomarker than Tn1, myoglobin and CPK-MB for diagnostics of ACS. PMID:23659068

Kalinchenko, R M; Kopylov, F Iu; Syrkin, A L; Gitel', E P; Novikova, O V



DOCKGROUND resource for studying protein-protein interfaces  

Microsoft Academic Search

Motivation: Public resources for studying protein interfaces are necessary for better understanding of molecular recognition and developing intermolecular potentials, search procedures, and scor- ing functions for the prediction of protein complexes. Results: The first release of the DOCKGROUND resource implements a comprehensive database of co-crystallized (bound-bound) protein- protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated)

Dominique Douguet; Huei-chi Chen; Andrey Tovchigrechko; Ilya A. Vakser



Protein C  


Protein C is a normal substance in the body that prevents blood clotting. A blood test can be done ... forming (anticoagulants), such as warfarin (Coumadin), decrease protein C and protein S levels. Your doctor may ask you ...


Total protein  


The total protein test measures the total amount of two classes of proteins found in the fluid portion of your blood. These are albumin and globulin. Proteins are important parts of all cells and tissues. ...


Dietary Proteins  


Protein is in every living cell in the body. Our bodies need protein from the foods we eat to build and maintain bones, muscles and skin. We get proteins in our diet from meat, dairy products, nuts ...


Influence of insulin-like growth factor binding protein (IGFBP)-1 and IGFBP-3 on bone health: results from the European Male Ageing Study.  


The aim of this study was to determine the influence of insulin-like growth factor binding protein (IGFBP)-1, IGFBP-3, and IGF-I on calcaneal ultrasound parameters in middle-aged and elderly European men. Men aged 40-79 years were recruited from population registers for participation in the European Male Ageing Study (EMAS). Subjects were invited by letter to complete a postal questionnaire and to attend for an interviewer-assisted questionnaire, quantitative ultrasound (QUS) of the calcaneus, and a fasting blood sample from which serum levels of IGFBP-1, IGFBP-3, IGF-I, estradiol (E(2)), and SHBG were assayed. The questionnaires included the Physical Activity Scale for the Elderly (PASE) and questions about smoking and alcohol consumption. Estimated bone mineral density (eBMD) was derived as a function of the QUS parameters speed of sound and broadband ultrasound attenuation. Height and weight were measured in all subjects. 3057 men, mean age 59.7 years (standard deviation 11.0) were included in the analysis. After adjusting for age, center, and BMI, higher levels of IGFBP-1 were associated with lower eBMD. Higher levels of both IGFBP-3 and IGF-I were associated with higher eBMD. After further adjustment for PASE score, current smoking, alcohol consumption, free E(2), and SHBG, IGFBP-3 and IGF-I, though not IGFBP-1, remained significantly associated with eBMD. IGFBP-1 was associated with bone health, though the effect could be explained by other factors. IGFBP-3 and IGF-I were independent determinants of bone health in middle-aged and elderly European men. PMID:21503646

Pye, Stephen R; Almusalam, Bader; Boonen, Steven; Vanderschueren, Dirk; Borghs, Herman; Gielen, Evelien; Adams, Judith E; Ward, Kate A; Bartfai, Gyorgy; Casanueva, Felipe F; Finn, Joseph D; Forti, Gianni; Giwercman, Aleksander; Han, Thang S; Huhtaniemi, Ilpo T; Kula, Krzysztof; Labrie, Fernand; Lean, Michael E J; Pendleton, Neil; Punab, Margus; Silman, Alan J; Wu, Frederick C W; O'Neill, Terence W



Corresponding author: TaeWon Seo E-mail:  

E-print Network

adhesive pads[8,9] . Although these robots can climb sloped walls, they cannot climb various shaped walls environments or in climbing a verti- cal wall, since their center of mass is close to the loco- motor surface for parameter design, dynamic analysis, and optimization in biomimetic robot research. The proposed kinematic

Kim, Jongwon


Photoswitchable cyan fluorescent protein for protein tracking.  


In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications. PMID:15502815

Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A



Protein solubility modeling.  


A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. PMID:10397850

Agena, S M; Pusey, M L; Bogle, I D



Protein solubility modeling  

NASA Technical Reports Server (NTRS)

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Agena, S. M.; Pusey, M. L.; Bogle, I. D.



Computational Prediction of Protein–Protein Interaction Networks: Algo-rithms and Resources  

PubMed Central

Protein interactions play an important role in the discovery of protein functions and pathways in biological processes. This is especially true in case of the diseases caused by the loss of specific protein-protein interactions in the organism. The accuracy of experimental results in finding protein-protein interactions, however, is rather dubious and high throughput experimental results have shown both high false positive beside false negative information for protein interaction. Computational methods have attracted tremendous attention among biologists because of the ability to predict protein-protein interactions and validate the obtained experimental results. In this study, we have reviewed several computational methods for protein-protein interaction prediction as well as describing major databases, which store both predicted and detected protein-protein interactions, and the tools used for analyzing protein interaction networks and improving protein-protein interaction reliability. PMID:24396273

Zahiri, Javad; Bozorgmehr, Joseph Hannon; Masoudi-Nejad, Ali



A missense mutation in the transmembrane domain of CESA4 affects protein abundance in the plasma membrane and results in abnormal cell wall biosynthesis in rice  

Microsoft Academic Search

Cellulose synthase (CESA) is a critical catalytic subunit of the cellulose synthase complex responsible for glucan chain elongation.\\u000a Our knowledge about how CESA functions is still very limited. Here, we report the functional characterization of a rice mutant,\\u000a brittle culm11, that shows growth retardation and dramatically reduced plant strength. Map-based cloning revealed that all the mutant phenotypes\\u000a result from a

Baocai Zhang; Lingwei Deng; Qian Qian; Guangyan Xiong; Dali Zeng; Rui Li; Longbiao Guo; Jiayang Li; Yihua Zhou



Transcriptional Regulation of the Protocadherin ? Cluster during Her-2 Protein-induced Mammary Tumorigenesis Results from Altered N-Glycan Branching*  

PubMed Central

Changes in the levels of N-acetylglucosaminyltransferase V (GnT-V) can alter the function of several types of cell surface receptors and adhesion molecules by causing altered N-linked glycan branching. Using a her-2 mammary tumor mouse model, her-2 receptor signaling was down-regulated by GnT-V knock-out, resulting in a significant delay in the onset of her-2-induced mammary tumors. To identify the genes that contributed to this GnT-V regulation of early events in tumorigenesis, microarray analysis was performed using her-2 induced mammary tumors from wild-type and GnT-V-null mice. We found that 142 genes were aberrantly expressed (>2.0-fold) with 64 genes up-regulated and 78 genes down-regulated after deletion of GnT-V. Among differentially expressed genes, the expression of a subgroup of the cadherin superfamily, the protocadherin ? (Pcdh?) cluster, was up-regulated in GnT-V-null tumors. Altered expression of the Pcdh? cluster in GnT-V-null tumors was not due to changes in promoter methylation; instead, impaired her-2-mediated signaling pathways were implicated at least in part resulting from reduced microRNA-21 expression. Overexpression of Pcdh? genes inhibited tumor cell growth, decreased the proportion of tumor-initiating cells, and decreased tumor formation in vivo, demonstrating that expression of the Pcdh? gene cluster can serve as an inhibitor of the transformed phenotype. Our results suggest the up-regulation of the Pcdh? gene cluster as a mechanism for reduced her-2-mediated tumorigenesis resulting from GnT-V deletion. PMID:22665489

Guo, Huabei; Nairn, Alison; dela Rosa, Mitche; Nagy, Tamas; Zhao, Shaying; Moremen, Kelley; Pierce, Michael



DNA immunization of HLA transgenic mice with a plasmid expressing mycobacterial heat shock protein 65 results in HLA class I- and II-restricted T cell responses that can be augmented by cytokines.  


Infection with Mycobacterium tuberculosis (MTB) remains a major cause of morbidity and mortality world-wide. An effective vaccination strategy is the immunization with plasmid DNA (pDNA), expressing an antigen (Ag) from a pathogen in vivo, which results in specific immune response against the encoded protein as well as the pathogen itself or cells infected with it. To test the ability to induce HLA-restricted T cell immune response against a mycobacterial antigen in humans by pDNA vaccination, we have used transgenic mice that express HLA class I (A*0201/Kb) or HLA class II (DRB1*0301) molecules. pDNA immunization with mycobacterial heat shock protein 65 (Mhsp65)-expressing plasmid (P3M.65) resulted in HLA-II-restricted, Ag-specific T cell-mediated immune responses characterized by proliferation and cytokine production. These T cell responses could be further augmented by the coinjection of P3M.65 and plasmid expressing murine GM-CSF. Furthermore, coimmunizing HLA-I transgenic mice with P3M.65 and a plasmid expressing murine IFN-gamma induced a specific cytotoxic T lymphocyte response restricted by HLA-A2. These results represent the first evidence of a concomitant in vivo induction of HLA class I- as well as class II-restricted T cell responses by pDNA immunization, which is induced or augmented by the codelivery of cytokine-expressing plasmids, supporting its potential use in clinical trials. PMID:11560772

Charo, J; Sundbäck, M; Geluk, A; Ottenhoff, T; Kiessling, R



Protein Analysis  

NASA Astrophysics Data System (ADS)

Proteins are an abundant component in all cells, and almost all except storage proteins are important for biological functions and cell structure. Food proteins are very complex. Many have been purified and characterized. Proteins vary in molecular mass, ranging from approximately 5000 to more than a million Daltons. They are composed of elements including hydrogen, carbon, nitrogen, oxygen, and sulfur. Twenty ?-amino acids are the building blocks of proteins; the amino acid residues in a protein are linked by peptide bonds. Nitrogen is the most distinguishing element present in proteins. However, nitrogen content in various food proteins ranges from 13.4 to 19.1% (1) due to the variation in the specific amino acid composition of proteins. Generally, proteins rich in basic amino acids contain more nitrogen.

Chang, Sam K. C.


Protein adsorption to hydrocephalus shunt catheters: CSF protein adsorption  

PubMed Central

OBJECTIVE—To assess the quantity and nature of the proteins that adsorb to hydrocephalus shunt catheters after implantation, and to determine whether sufficient could accumulate to obstruct the catheter.?DESIGN—Elution of proteins from 102 explanted shunt catheters, with protein assay and electrophoresis of the eluate, and scanning electron microscopy (SEM) of the catheters.?RESULTS—The amount of protein elutable was extremely low, and significant protein, apart from a thin film, was not found on SEM. Qualitative analysis disclosed that most of the adsorbed protein was albumin.?CONCLUSIONS—Protein deposition on hydrocephalus catheters does not occur in sufficient quantities to cause catheter obstruction.?? PMID:9598681

Brydon, H.; Keir, G.; Thompson, E.; Bayston, R.; Hayward, R.; Harkness, W.



Protein Complexes in Bacteria  

PubMed Central

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter



Constitutive or seed-specific overexpression of Arabidopsis G-protein ? subunit 3 (AGG3) results in increased seed and oil production and improved stress tolerance in Camelina sativa.  


Heterotrimeric G-proteins consisting of G?, G? and G? subunits play an integral role in mediating multiple signalling pathways in plants. A novel, recently identified plant-specific G? protein, AGG3, has been proposed to be an important regulator of organ size and mediator of stress responses in Arabidopsis, whereas its potential homologs in rice are major quantitative trait loci for seed size and panicle branching. To evaluate the role of AGG3 towards seed and oil yield improvement, the gene was overexpressed in Camelina sativa, an oilseed crop of the Brassicaceae family. Analysis of multiple homozygous T4 transgenic Camelina lines showed that constitutive overexpression of AGG3 resulted in faster vegetative as well as reproductive growth accompanied by an increase in photosynthetic efficiency. Moreover, when expressed constitutively or specifically in seed tissue, AGG3 was found to increase seed size, seed mass and seed number per plant by 15%-40%, effectively resulting in significantly higher oil yield per plant. AGG3 overexpressing Camelina plants also exhibited improved stress tolerance. These observations draw a strong link between the roles of AGG3 in regulating two critical yield parameters, seed traits and plant stress responses, and reveal an effective biotechnological tool to dramatically increase yield in agricultural crops. PMID:24102738

Roy Choudhury, Swarup; Riesselman, Adam J; Pandey, Sona



Protein- protein interaction detection system using fluorescent protein microdomains  


The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)



Physics of protein motility and motor proteins  

NASA Astrophysics Data System (ADS)

Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor Xianchao Meng, Min Yu and Yunxin Zhang Microtubule organization by kinesin motors and microtubule crosslinking protein MAP65 Joshua Pringle, Amutha Muthukumar, Amanda Tan, Laura Crankshaw, Leslie Conway and Jennifer L Ross Backtracking dynamics of RNA polymerase: pausing and error correction Mamata Sahoo and Stefan Klumpp First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor Ajeet K Sharma and Debashish Chowdhury

Kolomeisky, Anatoly B.



Protein function prediction via graph kernels  

Microsoft Academic Search

Motivation: Computational approaches to protein function prediction infer protein function by finding proteins with simi- lar sequence, structure, surface clefts, chemical properties, aminoacidmotifs, interactionpartnersorphylogeneticprofiles. Wepresentanewapproachthatcombinessequential, structu- ral and chemical information into one graph model of proteins. We predict functional class membership of enzymes and non- enzymes using graph kernels and Support Vector Machine classification on these protein graphs. Results: Our

Karsten M. Borgwardt; Cheng Soon Ong; Stefan Schönauer; S. V. N. Vishwanathan; Alexander J. Smola; Hans-peter Kriegel



Protein Bracelets  

NSDL National Science Digital Library

In this activity, learners use beads, which represent amino acids, to create protein bracelets. Learners examine the relationship between amino acids and proteins. Learners also discover that different arrangements of amino acids create different kinds of proteins.

Note: Have a bracelet already created so students can see what they are working to create.

Arizona Science Center



Protein Structure  

ERIC Educational Resources Information Center

Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

Asmus, Elaine Garbarino



Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association.  

PubMed Central

A hydrophobic folding unit cutting algorithm, originally developed for dissecting single-chain proteins, has been applied to a dataset of dissimilar two-chain protein-protein interfaces. Rather than consider each individual chain separately, the two-chain complex has been treated as a single chain. The two-chain parsing results presented in this work show hydrophobicity to be a critical attribute of two-state versus three-state protein-protein complexes. The hydrophobic folding units at the interfaces of two-state complexes suggest that the cooperative nature of the two-chain protein folding is the outcome of the hydrophobic effect, similar to its being the driving force in a single-chain folding. In analogy to the protein-folding process, the two-chain, two-state model complex may correspond to the formation of compact, hydrophobic nuclei. On the other hand, the three-state model complex involves binding of already folded monomers, similar to the association of the hydrophobic folding units within a single chain. The similarity between folding entities in protein cores and in two-state protein-protein interfaces, despite the absence of some chain connectivities in the latter, indicates that chain linkage does not necessarily affect the native conformation. This further substantiates the notion that tertiary, non-local interactions play a critical role in protein folding. These compact, hydrophobic, two-chain folding units, derived from structurally dissimilar protein-protein interfaces, provide a rich set of data useful in investigations of the role played by chain connectivity and by tertiary interactions in studies of binding and of folding. Since they are composed of non-contiguous pieces of protein backbones, they may also aid in defining folding nuclei. PMID:9232644

Tsai, C. J.; Nussinov, R.



Ultrafiltration of pegylated proteins  

NASA Astrophysics Data System (ADS)

There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine groups in the PEGylated proteins. Ultrafiltration experiments were performed using PEGylated alpha-lactalbumin, ovalbumin, and bovine serum albumin. In contrast to the size exclusion chromatography data, the sieving coefficient of the PEGylated proteins depended upon both the number and size of the attached PEG chains due to the elongation or deformation of the PEG associated with the filtrate flux. Sieving coefficients at low filtrate flux were in good agreement with predictions of available hydrodynamic models, with significant elongation occurring when the Deborah number for the PEG chain exceeded 0.001. The effects of electrostatic interactions on the ultrafiltration of PEGylated proteins were examined using electrically-charged membranes generated by covalent attachment of sulphonic acid groups to the base cellulosic membrane. Transmission of PEGylated proteins through charged membranes was dramatically reduced at low ionic strength due to strong electrostatic interactions, despite the presence of the neutral PEG. The experimental results were in good agreement with model calculations developed for the partitioning of charged spheres into charged cylindrical pores. The experimental and theoretical results provide the first quantitative analysis of the effects of PEGylation on transport through semipermeable ultrafiltration membranes. The results from small-scale ultrafiltration experiments were used to develop a two-stage diafiltration process to purify PEGylated alpha-lactalbumin. The first-stage used a neutral membrane to remove the unreacted protein by exploiting differences in size. The second stage used a negatively-charged membrane to remove hydrolyzed PEG, with the PEGylated product retained by strong electrostatic interactions. This process provided a purification factor greater than 1000 with respect to the unreacted protein and greater than 20-fold with respect to the PEG with an overall yield of PEGylated alpha-lactalbumin of 78%. These results provide the first demonstration of the potential of using ultrafiltration for the purificatio

Molek, Jessica R.


Protein Dynamics in an RNA Binding Protein  

NASA Astrophysics Data System (ADS)

Using ^15N NMR relaxation measurements, analyzed with the Lipari-Szabo formalism, we have found that the human U1A RNA binding protein has ps-ns motions in those loops that make contact with RNA. Specific mutations can alter the extent and pattern of motions, and those proteins inevitably lose RNA binding affinity. Proteins with enhanced mobility of loops and termini presumably lose affinity due to increased conformational sampling by those parts of the protein that interact directly with RNA. There is an entropic penalty associated with locking down those elements upon RNA binding, in addition to a loss of binding efficiency caused by the increased number of conformations adopted by the protein. However, in addition to local conformational heterogeneity, analysis of molecular dynamics trajectories by Reorientational Eigenmode Dynamics reveals that loops of the wild type protein undergo correlated motions that link distal sites across the binding surface. Mutations that disrupt correlated motions result in weaker RNA binding, implying that there is a network of interactions across the surface of the protein. (KBH was a Postdoctoral Fellow with Al Redfield from 1985-1990). This work was supported by the NIH (to KBH) and NSF (SAS).

Hall, Kathleen



Production of specific antibodies against protein A fusion proteins.  

PubMed Central

The gene for Staphylococcal protein A was fused to the coding sequence of bacterial beta-galactosidase, alkaline phosphatase and human insulin-like growth factor I (IGF-I). The fusion proteins, expressed in bacteria, were purified by affinity chromatography on IgG-Sepharose and antibodies were raised in rabbits. All three fusion proteins elicited specific antibodies against both the inserted protein sequences and the protein A moiety. In the case of IGF-I, the protein A moiety in the fusion protein may act as an adjuvant since native IGF-I alone is a poor immunogen. The results suggest that the protein A fusion system can be used for efficient antibody production against peptides or proteins expressed from cloned or synthetic genes. To facilitate such gene fusions a set of optimized vectors have been constructed. Images Fig. 2. Fig. 3. Fig. 4. Fig. 6. PMID:3096719

Löwenadler, B; Nilsson, B; Abrahmsén, L; Moks, T; Ljungqvist, L; Holmgren, E; Paleus, S; Josephson, S; Philipson, L; Uhlén, M



The Halophile Protein Database  

PubMed Central

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: PMID:25468930

Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj



Quantification of the Influence of Protein-Protein Interactions on Adsorbed Protein Structure and Bioactivity  

PubMed Central

While protein-surface interactions have been widely studied, relatively little is understood at this time regarding how protein-surface interaction effects are influenced by protein-protein interactions and how these effects combine with the internal stability of a protein to influence its adsorbed-state structure and bioactivity. The objectives of this study were to develop a method to study these combined effects under widely varying protein-protein interaction conditions using hen egg-white lysozyme (HEWL) adsorbed on silica glass, poly(methyl methacrylate), and polyethylene as our model systems. In order to vary protein-protein interaction effects over a wide range, HEWL was first adsorbed to each surface type under widely varying protein solution concentrations for 2 h to saturate the surface, followed by immersion in pure buffer solution for 15 h to equilibrate the adsorbed protein layers in the absence of additionally adsorbing protein. Periodic measurements were made at selected time points of the areal density of the adsorbed protein layer as an indicator of the level of protein-protein interaction effects within the layer, and these values were then correlated with measurements of the adsorbed protein’s secondary structure and bioactivity. The results from these studies indicate that protein-protein interaction effects help stabilize the structure of HEWL adsorbed on silica glass, have little influence on the structural behavior of HEWL on HDPE, and actually serve to destabilize HEWL’s structure on PMMA. The bioactivity of HEWL on silica glass and HDPE was found to decrease in direct proportion to the degree of adsorption-induce protein unfolding. A direct correlation between bioactivity and the conformational state of adsorbed HEWL was less apparent on PMMA, thus suggesting that other factors influenced HEWL’s bioactivity on this surface, such as the accessibility of HEWL’s bioactive site being blocked by neighboring proteins or the surface itself. The developed methods provide an effective means to characterize the influence of protein-protein interaction effects and provide new molecular-level insights into how protein-protein interaction effects combine with protein-surface interaction and internal protein stability effects to influence the structure and bioactivity of adsorbed protein. PMID:23751416

Wei, Yang; Thyparambil, Aby A.; Latour, Robert A.



Mdm20 protein functions with Nat3 protein to acetylate Tpm1 protein and regulate  

E-print Network

Mdm20 protein functions with Nat3 protein to acetylate Tpm1 protein and regulate tropomyosin-terminally acetylate Tpm1p, an abundant form of tropomyosin that binds and stabilizes actin filaments and cables. The F-actin-binding activity of unacety- lated Tpm1p is reduced severely relative to the acetylated form. These results

Shaw, Janet M.


A novel intronic splice site deletion of the IL-2 receptor common gamma chain results in expression of a dysfunctional protein and T-cell-positive X-linked Severe combined immunodeficiency.  


X-linked severe combined immunodeficiency is caused by mutations in the IL-2 receptor common gamma chain and classically presents in the first 6 months of life with predisposition to bacterial, viral and fungal infections. In most instances, affected individuals are lymphopenic with near complete absence of T cells and NK cells. We report a boy who presented at 12 months of age with Pneumocystis jiroveci pneumonia and a family history consistent with X-linked recessive inheritance. He had a normal lymphocyte count including the presence of T cells and a broad T-cell-receptor diversity, as well as normal surface expression of the common gamma chain (CD132) protein. He however had profound hypogammaglobulinaemia, and IL-2-induced STAT5 phosphorylation was absent. Sequencing of IL-2RG demonstrated a 12-base pair intronic deletion close to the canonical splice site of exon 5, which resulted in a variety of truncated IL2RG mRNA species. A review of the literature identified 4 other patients with T-cell-positive X-SCID, with the current patient being the first associated with an mRNA splicing defect. This case raises the question of how a dysfunctional protein incapable of mediating STAT5 phosphorylation might nonetheless support T-cell development. Possible explanations are that STAT5-mediated signal transduction may be less relevant to IL7-receptor-mediated T-cell development than are other IL7R-induced intracellular transduction pathways or that a low level of STAT5 phosphorylation, undetectable in the laboratory, may be sufficient to support some T-cell development. PMID:25443657

Gray, P E A; Logan, G J; Alexander, I E; Poulton, S; Roscioli, T; Ziegler, J



Dramatic Structural Changes Resulting from the Loss of a Crucial Hydrogen Bond in the Hinge Region Involved in C-Terminal Helix Swapping in SurE: A Survival Protein from Salmonella typhimurium  

PubMed Central

Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two ? strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 Å and 2.35 Å resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2– H234 NE2 hydrogen bond (2.89 Å in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE. PMID:23409101

Mathiharan, Yamuna Kalyani; Pappachan, Anju; Savithri, H. S.; Murthy, Mathur R. N.



RGS Proteins  

Microsoft Academic Search

For several years, the model for the transduction of G protein-mediated signals consisted of three components: a heptahelical\\u000a receptor, a heterotrimeric G protein, and an effector (1). The heptahelical receptor, which spans the membrane seven times, is coupled to a G protein complex consisting of an ?-subunit\\u000a in the guanosine-5?-diphosphate-bound form (?-GDP) and a ??-dimer. Upon agonist binding to the

Ryan W. Richman; María A. Diversé-Pierluissi


Transport Proteins  

NSDL National Science Digital Library

This Teaching Resource provides and describes two animated lessons that illustrate general properties of transport proteins. The lesson called “transport protein classes” depicts major classes and subclasses of transport proteins. The “transporters, mechanism of action” lesson explains how transporters and P class ATPase (adenosine triphosphatase) pumps function. These animations serve as valuable resources for any collegiate-level course that describes these important factors. Courses that might use them include introductory biology, biochemistry, cell biology, physiology, and biophysics.

Jack D. Thatcher (Lewisburg; West Virginia School of Osteopathic Medicine REV)



Physicochemical mechanisms of protein regulation by phosphorylation  

PubMed Central

Phosphorylation offers a dynamic way to regulate protein activity and subcellular localization, which is achieved through its reversibility and fast kinetics. Adding or removing a dianionic phosphate group somewhere on a protein often changes the protein’s structural properties, its stability and dynamics. Moreover, the majority of signaling pathways involve an extensive set of protein–protein interactions, and phosphorylation can be used to regulate and modulate protein–protein binding. Losses of phosphorylation sites, as a result of disease mutations, might disrupt protein binding and deregulate signal transduction. In this paper we focus on the effects of phosphorylation on protein stability, dynamics, and binding. We describe several physico-chemical mechanisms of protein regulation through phosphorylation and pay particular attention to phosphorylation in protein complexes and phosphorylation in the context of disorder–order and order–disorder transitions. Finally we assess the role of multiple phosphorylation sites in a protein molecule, their possible cooperativity and function. PMID:25147561

Nishi, Hafumi; Shaytan, Alexey; Panchenko, Anna R.



Proteolytic cleavage of the reovirus sigma 3 protein results in enhanced double-stranded RNA-binding activity: identification of a repeated basic amino acid motif within the C-terminal binding region.  

PubMed Central

The reovirus capsid protein sigma 3 was examined for double-stranded RNA (dsRNA)-binding activity by Northwestern (RNA-protein) blot analysis. Treatment of virion-derived sigma 3 protein with Staphylococcus aureus V8 protease led to an increase in the dsRNA-binding activity associated with the C-terminal fragment of the protein. Recombinant C-terminal fragments of the sigma 3 protein were expressed in Escherichia coli from the S4 cDNA of reovirus serotype 1. These truncated sigma 3 proteins displayed proteolytic processing and dsRNA-binding activity similar to those observed for native, virion-derived sigma 3 protein as measured by Northwestern blot analysis. Construction of a modified pET3c vector, pET3Exo, allowed the production of 3'-terminal deletions of the S4 cDNA by using exonuclease III and rapid screening of the induced truncated sigma 3 proteins. An 85-amino-acid domain within the C-terminal portion of the sigma 3 protein which was responsible for dsRNA-binding activity was identified. The 85-amino-acid domain possessed a repeated basic amino acid motif which was conserved in all three serotypes of reovirus. Deletion of one of the basic motifs, predicted to be an amphipathic alpha-helix, destroyed dsRNA-binding activity. Images PMID:1501278

Miller, J E; Samuel, C E



Envelope proteins in Neisseria.  


The proteins of the cell envelope of Neisseria sicca strain ATCC 9913 have been examined by SDS - polyacrylamide gel electrophoresis. Some 20 proteins were resolved from the total envelope fraction, and nearly all of these were found to be localized in the outer membrane. Preparations of the "free-endotoxin" fraction differ from the outer membrane only in lacking a few minor proteins. The behavior of several of the envelope proteins on electrophoresis can be modified by changing the temperature of sample solubilization, and also by alteration of the growth medium. Experiments with phosphate-limited cultures showed that certain periplasmic proteins are closely associated with free endotoxin. Mutations which result in altered outer membrane permeability to antibiotics were found to cause changes in cell envelope protein composition. A comparison of the envelope proteins of eight species of non-pathogenic Neisseria showed that each had a characteristic composition. A classification of the organisms based on the relatedness of the protein patterns seen on SDS-polyacrylamide gels was in close agreement with classifications based on more usual methods. PMID:1104115

Russell, R R; Johnson, K G; McDonald, I J



Small Molecule Inhibitors to Disrupt Protein-protein Interactions of Heat Shock Protein 90 Chaperone Machinery  

PubMed Central

Heat shock protein 90 (Hsp90) is an adenosine triphosphate dependent molecular chaperone in eukaryotic cells that regulates the activation and maintenance of numerous regulatory and signaling proteins including epidermal growth factor receptor, human epidermal growth factor receptor 2, mesenchymal-epithelial transition factor, cyclin-dependent kinase-4, protein kinase B, hypoxia-inducible factor 1?, and matrix metalloproteinase-2. Since many of Hsp90 clients are oncogenic proteins, Hsp90 has become an attractive therapeutic target for treatment of cancer. To discover small molecule inhibitors targeting Hsp90 chaperone machinery, several strategies have been employed, which results in three classes of inhibitors such as N-terminal inhibitors, C-terminal inhibitors, and inhibitors disrupting protein-protein interactions of Hsp90 chaperone machinery. Developing small molecule inhibitors that modulate protein-protein interactions of Hsp90 is a challenging task, although it offers many alternative opportunities for therapeutic intervention. The lack of well-defined binding pocket and starting points for drug design challenges medicinal chemists to discover small molecule inhibitors disrupting protein-protein interactions of Hsp90. The present review will focus on the current studies on small molecule inhibitors disrupting protein-protein interactions of Hsp90 chaperone machinery, provide biological background on the structure, function and mechanism of Hsp90’s protein-protein interactions, and discuss the challenges and promise of its small molecule modulations.

Seo, Young Ho



Protein-protein interaction databases: keeping up with growing interactomes.  


Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction data. Protein-protein interactions have been retrieved from six major databases, integrated and the results compared. The six databases (the Biological General Repository for Interaction Datasets [BioGRID], the Molecular INTeraction database [MINT], the Biomolecular Interaction Network Database [BIND], the Database of Interacting Proteins [DIP], the IntAct molecular interaction database [IntAct] and the Human Protein Reference Database [HPRD]) differ in scope and content; integration of all datasets is non-trivial owing to differences in data annotation. With respect to human protein-protein interaction data, HPRD seems to be the most comprehensive. To obtain a complete dataset, however, interactions from all six databases have to be combined. To overcome this limitation, meta-databases such as the Agile Protein Interaction Database (APID) offer access to integrated protein-protein interaction datasets, although these also currently have certain restrictions. PMID:19403463

Lehne, Benjamin; Schlitt, Thomas



Electronic transport via proteins.  


A central vision in molecular electronics is the creation of devices with functional molecular components that may provide unique properties. Proteins are attractive candidates for this purpose, as they have specific physical (optical, electrical) and chemical (selective binding, self-assembly) functions and offer a myriad of possibilities for (bio-)chemical modification. This Progress Report focuses on proteins as potential building components for future bioelectronic devices as they are quite efficient electronic conductors, compared with saturated organic molecules. The report addresses several questions: how general is this behavior; how does protein conduction compare with that of saturated and conjugated molecules; and what mechanisms enable efficient conduction across these large molecules? To answer these questions results of nanometer-scale and macroscopic electronic transport measurements across a range of organic molecules and proteins are compiled and analyzed, from single/few molecules to large molecular ensembles, and the influence of measurement methods on the results is considered. Generalizing, it is found that proteins conduct better than saturated molecules, and somewhat poorer than conjugated molecules. Significantly, the presence of cofactors (redox-active or conjugated) in the protein enhances their conduction, but without an obvious advantage for natural electron transfer proteins. Most likely, the conduction mechanisms are hopping (at higher temperatures) and tunneling (below ca. 150-200 K). PMID:25256438

Amdursky, Nadav; Marchak, Debora; Sepunaru, Lior; Pecht, Israel; Sheves, Mordechai; Cahen, David



Interfacial Protein-Protein Associations  

PubMed Central

While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface – with areas of high protein density (i.e. strongly-interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e. partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e. clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage. PMID:24274729

Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.



Protein based Block Copolymers  

PubMed Central

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251

Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.



Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study  

PubMed Central

Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting protein-protein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at:

Xue, Li C.; Jordan, Rafael A.; EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant



Predictions of Protein-Protein Interfaces within Membrane Protein Complexes  

PubMed Central

Background Prediction of interaction sites within the membrane protein complexes using the sequence data is of a great importance, because it would find applications in modification of molecules transport through membrane, signaling pathways and drug targets of many diseases. Nevertheless, it has gained little attention from the protein structural bioinformatics community. Methods In this study, a wide variety of prediction and classification tools were applied to distinguish the residues at the interfaces of membrane proteins from those not in the interfaces. Results The tuned SVM model achieved the high accuracy of 86.95% and the AUC of 0.812 which outperforms the results of the only previous similar study. Nevertheless, prediction performances obtained using most employed models cannot be used in applied fields and needs more effort to improve. Conclusion Considering the variety of the applied tools in this study, the present investigation could be a good starting point to develop more efficient tools to predict the membrane protein interaction site residues. PMID:23919118

Asadabadi, Ebrahim Barzegari; Abdolmaleki, Parviz



Co-immunization with an optimized plasmid-encoded immune stimulatory interleukin, high-mobility group box 1 protein, results in enhanced interferon-? secretion by antigen-specific CD8 T cells  

PubMed Central

DNA vaccination is a novel immunization strategy that has great potential for the development of vaccines and immune therapeutics. This strategy has been highly effective in mice, but is less immunogenic in non-human primates and in humans. Enhancing DNA vaccine potency remains a challenge. It is likely that antigen-presenting cells (APCs), and especially dendritic cells (DCs), play a significant role in the presentation of the vaccine antigen to the immune system. A new study reports the synergistic recruitment, expansion and activation of DCs in vivo by high-mobility group box 1 (HMGB1) protein. Such combinational strategies for delivering vaccine in a single, simple platform will hypothetically bolster the cellular immunity in vivo. Here, we combined plasmid encoding human immunodeficiency virus-1 (HIV-1) Gag and Env with an HMGB1 plasmid as a DNA adjuvant in BALB/c mice (by intramuscular immunization via electroporation), and humoral and cellular responses were measured. Co-administration of this potent immunostimulatory adjuvant strongly enhanced the cellular interferon-? (IFN-?) and humoral immune response compared with that obtained in mice immunized with vaccine only. Our results show that co-immunization with HMGB1 can have a strong adjuvant activity, driving strong cellular and humoral immunity that may be an effective immunological adjuvant in DNA vaccination against HIV-1. PMID:19740322

Muthumani, Gowtham; Laddy, Dominick J; Sundaram, Senthil G; Fagone, Paolo; Shedlock, Devon J; Kannan, Senthil; Wu, Ling; Chung, Christopher W; Lankaraman, Karthikbabu Mallil; Burns, John; Muthumani, Karuppiah; Weiner, David B



Silencing of ANGPTL 3 (angiopoietin-like protein 3) in human hepatocytes results in decreased expression of gluconeogenic genes and reduced triacylglycerol-rich VLDL secretion upon insulin stimulation  

PubMed Central

Homozygosity of loss-of-function mutations in ANGPTL3 (angiopoietin-like protein 3)-gene results in FHBL2 (familial combined hypolipidaemia, OMIM #605019) characterized by the reduction of all major plasma lipoprotein classes, which includes VLDL (very-low-density lipoprotein), LDL (low-density lipoprotein), HDL (high-density lipoprotein) and low circulating NEFAs (non-esterified fatty acids), glucose and insulin levels. Thus complete lack of ANGPTL3 in humans not only affects lipid metabolism, but also affects whole-body insulin and glucose balance. We used wild-type and ANGPTL3-silenced IHHs (human immortalized hepatocytes) to investigate the effect of ANGPTL3 silencing on hepatocyte-specific VLDL secretion and glucose uptake. We demonstrate that both insulin and PPAR? (peroxisome-proliferator-activated receptor ?) agonist rosiglitazone down-regulate the secretion of ANGPTL3 and TAG (triacylglycerol)-enriched VLDL1-type particles in a dose-dependent manner. Silencing of ANGPTL3 improved glucose uptake in hepatocytes by 20–50% and influenced down-regulation of gluconeogenic genes, suggesting that silencing of ANGPTL3 improves insulin sensitivity. We further show that ANGPTL3-silenced cells display a more pronounced shift from the secretion of TAG-enriched VLDL1-type particles to secretion of lipid poor VLDL2-type particles during insulin stimulation. These data suggest liver-specific mechanisms involved in the reported insulin-sensitive phenotype of ANGPTL3-deficient humans, featuring lower plasma insulin and glucose levels. PMID:25495645

Tikka, Anna; Soronen, Jarkko; Laurila, Pirkka-Pekka; Metso, Jari; Ehnholm, Christian; Jauhiainen, Matti



EDITORIAL: Precision proteins Precision proteins  

NASA Astrophysics Data System (ADS)

Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the large molecular weight, net negative charge and hydrophilicity of synthetic small interfering RNAs makes it hard for the molecules to cross the plasma membrane and enter the cell cytoplasm. Immune responses can also diminish the effectiveness of this approach. In this issue, Shiri Weinstein and Dan Peer from Tel Aviv University provide an overview of the challenges and recent progress in the use of nanocarriers for delivering RNAi effector molecules into target tissues and cells more effectively [5]. Also in this issue, researchers in Korea report new results that demonstrate the potential of nanostructures in neural network engineering [6]. Min Jee Jang et al report directional growth of neurites along linear carbon nanotube patterns, demonstrating great progress in neural engineering and the scope for using nanotechnology to treat neural diseases. Modern medicine cannot claim to have abolished the pain and suffering that accompany disease. But a comparison between the ghastly and often ineffective iron implements of early medicine and the smart gadgets and treatments used in hospitals today speaks volumes for the extraordinary progress that has been made, and the motivation behind this research. References [1] Wallis F 2000 Signs and senses: diagnosis and prognosis in early medieval pulse and urine texts Soc. Hist. Med. 13 265-78 [2] Arntz Y, Seelig J D, Lang H P, Zhang J, Hunziker P, Ramseyer J P, Meyer E, Hegner M and Gerber Ch 2003 Label-free protein assay based on a nanomechanical cantiliever array Nanotechnology 14 86-90 [3] Gowtham S, Scheicher R H, Pandey R, Karna S P and Ahuja R 2008 First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes Nanotechnology 19 125701 [4] Wang H-N and Vo-Dinh T 2009 Multiplex detection of breast cancer biomarkers using plasmonic molecular sentinel nanoprobes Nanotechnology 20 065101 [5] Weinstein S and Peer D 2010 RNAi nanomedicines: challenges and opportunities within the immune system Nanotechnology 21 232001 [6] Jang M J, Namgung S, Hong S, and Nam Y 2010 Directional neurite gro

Demming, Anna



Protein Phosphatases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein phosphatases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the importance of phosphatases in physiology, recognized by the award of a Nobel Prize in 1992, and then proceeds to describe the two types of protein phosphatases: serine/threonine and tyrosine phosphatases. The information covered includes the structure, regulation, and substrate specificity of protein phosphatases, with an emphasis on their importance in disease and clinical settings.

Stephen R. Salton (Mount Sinai School of Medicine; Department of Neuroscience REV)



Arsenite-induced apoptosis is prevented by selenite in A375 cell line.  


Arsenic trioxide induces apoptosis and clinical remission in patients diagnosed with acute promyelocytic leukemia. The human malignant melanoma A375 cells were treated with NaAsO2 (0.1–130 ?M) and also treated with combined 10 ?M NaAsO2 and 10 ?M Na2SeO3. NaAsO2 arrested cell growth in the G1 phase and induced apoptosis in a concentration- and time-dependent manner. In contrast, administration of Na2SeO3 antagonized the cell growth inhibition and apoptosis induced by NaAsO2. The NaAsO2 treatment resulted in a marked increase in p53 protein as early as 4 h and in Bcl-2 protein level by 12 h. In addition, p53 downregulation accompanied the combined treatment of NaAsO2 and Na2SeO3. Thus, our results indicate upregulation of p53 and Bcl-2 play acrucial role in the NaAsO2-induced G1 arrest and apoptosis of A375 cells and that downregulation p53 appears to contribute to the inhibition by Na2SeO3 of the effects induced by NaAsO2. PMID:20390378

Wang, Zhi-Fang; Guo, Xiong



Analytical Evaluation of the Diazyme Glycated Serum Protein Assay on the Siemens ADVIA 1800: Comparison of Results Against HbA1c for Diagnosis and Management of Diabetes.  


Hemoglobin A1c (HbA1c) is considered the gold standard for assessment of glycemic control in diabetic patients. HbA1c is inadequate in individuals homozygous or compound heterozygous for hemoglobin variants or in conditions with an altered red blood cell turnover. In these cases glycated albumin (GA) is proposed as an alternative assay. We aimed to evaluate the analytical performance of the Diazyme glycated serum protein (GSP) assay on an automated analyzer, to establish a reference interval (RI), and to compare from a clinical perspective, GSP/GA with glycated Hb (glyHb) results. Validation studies followed the CLSI guidelines and included precision, linearity, interferences, concordance of results with glyHb, and RI calculation. GSP was analyzed on representative samples with previously ordered HbA1c and albumin from the Dyna LIFE : DX laboratory. Samples from patients with bisalbuminemia, hemoglobinopathies, and multiple myeloma were also included. Within-run and total imprecision was <3.0% at both levels of control, analytical sensitivity was 5.31 ?mol/L, and linearity was verified from 10 to 1150 ?mol/L (total allowable error of 5%). Clinical concordance between %GA and glyHb was substantial (n = 175, R (2) = .91, kappa = .78, P = .167). GSP RI was 160 to 340 ?mol/L or if expressed as %GA 10.5 to 17.5%. Analytical performance of the Diazyme GSP assay on the Siemens ADVIA 1800 is acceptable for clinical use. The RI obtained was higher than that suggested by the manufacturer. PMID:25591854

Rodriguez-Capote, Karina; Tovell, Kayla; Holmes, Deborah; Dayton, Janice; Higgins, Trefor N



Proteins S100A8 and S100A9 are potential biomarkers for renal cell carcinoma in the early stages: Results from a proteomic study integrated with bioinformatics analysis.  


In order to investigate the two members of the EF?hand Ca2+ binding protein S100 family, S100A8 and S100A9, in renal cell carcinoma (RCC), serum samples were collected from patients with RCC, transitional cell carcinoma in the kidney, benign renal masses and normal controls. The samples were analyzed by isobaric tags for relative and absolute quantification technology to identify the differential expression of S100A8 and S100A9 in the respective groups. Hierarchical clustering analysis was then conducted for the samples and the relevant selected gene. The cross?platform analysis for the external validation was performed by means of The Cancer Genome Atlas database, containing the gene/microRNA expression pattern and clinical information of patients with RCC. Immunohistochemical staining was used to verify the expression of S100A8 and S100A9 in the four groups. As a result, serum and mRNA expression levels of S100A8 and S100A9 were found to be upregulated in patients with RCC compared with the other three groups, which was consistent with the result of the upregulated expression of mRNA levels in RCC tissue. The overexpression of S100A8 and S100A9 in cancer cells was also confirmed by immunohistochemistry. In addition, bioinformatics revealed that let?7, a microRNA formerly identified as an inhibiting factor of RCC was downregulated in RCC, which contrasted with S100A8. It was also complementary to the sequence at the 3' untranslated region terminal of S100A8. Therefore, indicating that S100A8 and S100A9 may serve as biomarkers for the detection of RCC. PMID:25673070

Zhang, Limin; Jiang, Haowen; Xu, Gang; Wen, Hui; Gu, Bin; Liu, Jun; Mao, Shanghua; Na, Rong; Jing, Yan; Ding, Qiang; Zhang, Yuanfang



Direct polymerization of proteins.  


We report the synthesis of active polymers of superfolder green fluorescent protein (sfGFP) in one step using Click chemistry. Up to six copies of the non-natural amino acids (nnAAs) p-azido-l-phenylalanine (pAzF) or p-propargyloxy-l-phenylalanine (pPaF) were site-specifically inserted into sfGFP by cell-free protein synthesis (CFPS). sfGFP containing two or three copies of these nnAAs were coupled by copper-catalyzed azide-alkyne cycloaddition to synthesize linear or branched protein polymers, respectively. The protein polymers retained ?63% of their specific activity (i.e., fluorescence) after coupling. Polymerization of a concentrated solution of triply substituted sfGFP resulted in fluorescent macromolecular particles. Our method can be generalized to synthesize polymers of a protein or copolymers of any two or more proteins, and the conjugation sites can be determined exactly by standard genetic manipulation. Polymers of proteins and small molecules can also be created with this technology to make a new class of scaffolds or biomaterials. PMID:24200191

Albayrak, Cem; Swartz, James R



Reclamation of Whey Protein with Carboxymethylcellulose1  

Microsoft Academic Search

Molecular complex formation between anionic hydrocolloids and proteins was used. to recover proteins from whey with carboxymethylcellulose. A predetermined amount of the hydrocolloid was mixed with acidified whey and the resulting complex removed by centrifugation. More than 90% of the protein was recovered in an acidic fraction (Fraction I) at pH 3.2. Following removal of this complex, addi- tional protein

P. M. T. Hansen; J. Hidalgo; I. A. Gould



REVIEW ARTICLE The Proteins of Morbilliviruses  

Microsoft Academic Search

viruses. By 1977 a small number of publications relating to the study of morbillivirus proteins, describing mainly virion proteins separated in tube-gel disc electrophoresis, had given rise to conflicting reports resulting from the difficulties in purifying the virus free from host proteins and from the inability of these viruses to shut off host protein synthesis. Since then, a reappraisal has




Structure-Immunogenicity Relationships of Therapeutic Proteins  

Microsoft Academic Search

As more recombinant human proteins become available on the market, the incidence of immunogenicity problems is rising. The antibodies formed against a therapeutic protein can result in serious clinical effects, such as loss of efficacy and neutralization of the endogenous protein with essential biological functions. Here we review the literature on the relations between the immunogenicity of the therapeutic proteins

Suzanne Hermeling; Daan J. A. Crommelin; Huub Schellekens; Wim Jiskoot



Protein Purification  

NSDL National Science Digital Library

This animation produced by WGBH and Digizyme, Inc. demonstrates how a protein of interest is isolated from other contents in a transformed bacterial cell—a process called purification—using a lab technique called hydrophobic interaction chromatography.



Evolution of Chloroplast J Proteins  

PubMed Central

Hsp70 chaperones are involved in multiple biological processes and are recruited to specific processes by designated J domain-containing cochaperones, or J proteins. To understand the evolution and functions of chloroplast Hsp70s and J proteins, we identified the Arabidopsis chloroplast J protein constituency using a combination of genomic and proteomic database searches and individual protein import assays. We show that Arabidopsis chloroplasts have at least 19 J proteins, the highest number of confirmed J proteins for any organelle. These 19 J proteins are classified into 11 clades, for which cyanobacteria and glaucophytes only have homologs for one clade, green algae have an additional three clades, and all the other 7 clades are specific to land plants. Each clade also possesses a clade-specific novel motif that is likely used to interact with different client proteins. Gene expression analyses indicate that most land plant-specific J proteins show highly variable expression in different tissues and are down regulated by low temperatures. These results show that duplication of chloroplast Hsp70 in land plants is accompanied by more than doubling of the number of its J protein cochaperones through adding new J proteins with novel motifs, not through duplications within existing families. These new J proteins likely recruit chloroplast Hsp70 to perform tissue specific functions related to biosynthesis rather than to stress resistance. PMID:23894646

Chiu, Chi-Chou; Chen, Lih-Jen; Su, Pai-Hsiang; Li, Hsou-min



Your Kidney Test Results  


... and can damage blood vessels in the kidneys. Serum Albumin Normal: 3.4 to 5.0* Your Result: Albumin is a protein that helps measure how well you are eating. Bicarbonate Normal: More than 22 Your Result: Bicarbonate measures the acid level in your blood. Blood Urea Nitrogen (BUN) Normal: ...


PROTEIN DESIGN: Proteins from Scratch  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. It is not easy to predict a protein's structure from its linear amino acid sequence, and the reverse problem--designing a protein that will assume a particular folded shape--is even harder. But on page 82 in this issue, Dahiyat and Mayo have succeeded in creating a zinc finger fold de novo, which forms the same shaped protein as the natural one but without the usual stabilizing zinc ion. In his Perspective, DeGrado explains why this problem has been so intractable and where we can go now that Dahiyat and Mayo have paved the way.

William F. DeGrado (University of Pennsylvania School of Medicine; Department of Biochemistry and Biophysics)



Protein crystal growth in microgravity  

NASA Technical Reports Server (NTRS)

Major advances have been made in several of the experimental aspects of protein crystallography, leaving protein crystallization as one of the few remaining bottlenecks. As a result, it has become important that the science of protein crystal growth is better understood and that improved methods for protein crystallization are developed. Preliminary experiments with both small molecules and proteins indicate that microgravity may beneficially affect crystal growth. For this reason, a series of protein crystal growth experiments using the Space Shuttle was initiated. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth. Various optical techniques are being utilized to monitor the crystal growth process from the incipient or nucleation stage and throughout the growth phase. The eventual goal of these studies is to develop a system which utilizes optical monitoring for dynamic control of the crystallization process.

Rosenblum, William M.; Delucas, Lawrence J.; Wilson, William W.



Protein structure modeling with MODELLER.  


Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In this chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences. PMID:24573470

Webb, Benjamin; Sali, Andrej



Retinal proteins as model systems for membrane protein folding.  


Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks. PMID:24333783

Tastan, Oznur; Dutta, Arpana; Booth, Paula; Klein-Seetharaman, Judith



Predicting Protein Interactions by Brownian Dynamics Simulations  

PubMed Central

We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions. PMID:22500075

Meng, Xuan-Yu; Xu, Yu; Zhang, Hong-Xing; Mezei, Mihaly; Cui, Meng



Prediction of thermodynamic instabilities of protein solutions from simple protein-protein interactions  

NASA Astrophysics Data System (ADS)

Statistical thermodynamics of protein solutions is often studied in terms of simple, microscopic models of particles interacting via pairwise potentials. Such modelling can reproduce the short range structure of protein solutions at equilibrium and predict thermodynamics instabilities of these systems. We introduce a square well model of effective protein-protein interaction that embeds the solvent’s action. We modify an existing model [45] by considering a well depth having an explicit dependence on temperature, i.e. an explicit free energy character, thus encompassing the statistically relevant configurations of solvent molecules around proteins. We choose protein solutions exhibiting demixing upon temperature decrease (lysozyme, enthalpy driven) and upon temperature increase (haemoglobin, entropy driven). We obtain satisfactory fits of spinodal curves for both the two proteins without adding any mean field term, thus extending the validity of the original model. Our results underline the solvent role in modulating or stretching the interaction potential.

D'Agostino, Tommaso; Solana, José Ramón; Emanuele, Antonio



Characterization of protein complexes and subcomplexes in protein-protein interaction databases.  


The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions. This paper provides a novel characterization of subcomplexes in protein interaction databases, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity, and gene ontology (GO) terms. The paper introduces the concept of "nested group" as a way to represent subcomplexes and estimates that around 15% of those nested group with the higher Jaccard index may be a result of data artifacts in protein interaction databases, while a number of them can be found in biologically important modular structures or dynamic structures. We also found that network centralities, enrichment in essential proteins, GO terms related to regulation, imperfect 5-clique motifs, and higher GO homogeneity can be used to identify proteins in nested complexes. PMID:25722891

Zaki, Nazar; Mohamed, Elfadil A; Mora, Antonio



Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases  

PubMed Central

The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions. This paper provides a novel characterization of subcomplexes in protein interaction databases, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity, and gene ontology (GO) terms. The paper introduces the concept of “nested group” as a way to represent subcomplexes and estimates that around 15% of those nested group with the higher Jaccard index may be a result of data artifacts in protein interaction databases, while a number of them can be found in biologically important modular structures or dynamic structures. We also found that network centralities, enrichment in essential proteins, GO terms related to regulation, imperfect 5-clique motifs, and higher GO homogeneity can be used to identify proteins in nested complexes. PMID:25722891

Zaki, Nazar; Mohamed, Elfadil A.; Mora, Antonio



A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies  

PubMed Central

Foreign viral proteins expressed by rabies virus (RV) have been shown to induce potent humoral and cellular immune responses in immunized animals. In addition, highly attenuated and, therefore, very safe RV-based vectors have been constructed. Here, an RV-based vaccine vehicle was utilized as a novel vaccine against severe acute respiratory syndrome coronavirus (SARS-CoV). For this approach, the SARS-CoV nucleocapsid protein (N) or envelope spike protein (S) genes were cloned between the RV glycoprotein G and polymerase L genes. Recombinant vectors expressing SARS-CoV N or S protein were recovered and their immunogenicity was studied in mice. A single inoculation with the RV-based vaccine expressing SARS-CoV S protein induced a strong SARS-CoV-neutralizing antibody response. The ability of the RV-SARS-CoV S vector to confer immunity after a single inoculation makes this live vaccine a promising candidate for eradication of SARS-CoV in animal reservoirs, thereby reducing the risk of transmitting the infection to humans. PMID:15831955

Faber, Milosz; Lamirande, Elaine W.; Roberts, Anjeanette; Rice, Amy B.; Koprowski, Hilary; Dietzschold, Bernhard; Schnell, Matthias J.



Cotton and Protein Interactions  

SciTech Connect

The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.



Recombinant protein production technology  

Technology Transfer Automated Retrieval System (TEKTRAN)

Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...


Impact of Protein Supplementation and Care and Support on Body Composition and CD4 Count among HIV-Infected Women Living in Rural India: Results from a Randomized Pilot Clinical Trial  

PubMed Central

Body composition in HIV-infected individuals is subject to many influences. We conducted a pilot six-month randomized trial of 68 WLA (women living with AIDS) from rural India. High protein intervention combined with education and supportive care delivered by HIV-trained village women (Asha [Activated Social Health Activist] Life [AL]) was compared to standard protein with usual care delivered by village community assistants (Usual Care [UC]). Measurements included CD4 counts, ART adherence, socio-demographics, disease characteristics (questionnaires); and anthropometry (bioimpedance analyzer). Repeated measures analysis of variance modeled associations. AL significantly gained in BMI, muscle mass, fat mass, ART adherence, and CD4 counts compared to UC, with higher weight and muscle mass gains among ART adherent (? 66%) participants who had healthier immunity (CD4 ? 450). BMI of WLA improved through high protein supplementation combined with education and supportive care. Future research is needed to determine which intervention aspect was most responsible. PMID:23370835

Nyamathi, Adeline; Sinha, Sanjeev; Ganguly, Kalyan K; Ramakrishna, Padma; Suresh, P.; Carpenter, Catherine L



Impact of protein supplementation and care and support on body composition and CD4 count among HIV-infected women living in rural India: results from a randomized pilot clinical trial.  


Body composition in HIV-infected individuals is subject to many influences. We conducted a pilot 6-month randomized trial of 68 women living with AIDS (WLA) from rural India. High protein intervention combined with education and supportive care delivered by HIV-trained village women (activated social health activist [Asha] life [AL]) was compared to standard protein with usual care delivered by village community assistants (usual care [UC]). Measurements included CD4 counts, ART adherence, socio-demographics, disease characteristics (questionnaires); and anthropometry (bioimpedance analyzer). Repeated measures analysis of variance modeled associations. AL significantly gained in BMI, muscle mass, fat mass, ART adherence, and CD4 counts compared to UC, with higher weight and muscle mass gains among ART adherent (?66%) participants who had healthier immunity (CD4 ?450). BMI of WLA improved through high protein supplementation combined with education and supportive care. Future research is needed to determine which intervention aspect was most responsible. PMID:23370835

Nyamathi, Adeline; Sinha, Sanjeev; Ganguly, Kalyan K; Ramakrishna, Padma; Suresh, P; Carpenter, Catherine L



Protein damage, repair and proteolysis.  


Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression. PMID:23107776

Chondrogianni, Niki; Petropoulos, Isabelle; Grimm, Stefanie; Georgila, Konstantina; Catalgol, Betul; Friguet, Bertrand; Grune, Tilman; Gonos, Efstathios S



Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study  

PubMed Central

Background Proteins that interact in vivo tend to reside within the same or "adjacent" subcellular compartments. This observation provides opportunities to reveal protein subcellular localization in the context of the protein-protein interaction (PPI) network. However, so far, only a few efforts based on heuristic rules have been made in this regard. Results We systematically and quantitatively validate the hypothesis that proteins physically interacting with each other probably share at least one common subcellular localization. With the result, for the first time, four graph-based semi-supervised learning algorithms, Majority, ?2-score, GenMultiCut and FunFlow originally proposed for protein function prediction, are introduced to assign "multiplex localization" to proteins. We analyze these approaches by performing a large-scale cross validation on a Saccharomyces cerevisiae proteome compiled from BioGRID and comparing their predictions for 22 protein subcellular localizations. Furthermore, we build an ensemble classifier to associate 529 unlabeled and 137 ambiguously-annotated proteins with subcellular localizations, most of which have been verified in the previous experimental studies. Conclusions Physical interaction of proteins has actually provided an essential clue for their co-localization. Compared to the local approaches, the global algorithms consistently achieve a superior performance. PMID:22759426



Integrating experimental and literature protein-protein interaction data for protein complex prediction  

PubMed Central

Background Accurate determination of protein complexes is crucial for understanding cellular organization and function. High-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data, allowing prediction of protein complexes from PPI networks. However, the high-throughput data often includes false positives and false negatives, making accurate prediction of protein complexes difficult. Method The biomedical literature contains large quantities of PPI data that, along with high-throughput experimental PPI data, are valuable for protein complex prediction. In this study, we employ a natural language processing technique to extract PPI data from the biomedical literature. This data is subsequently integrated with high-throughput PPI and gene ontology data by constructing attributed PPI networks, and a novel method for predicting protein complexes from the attributed PPI networks is proposed. This method allows calculation of the relative contribution of high-throughput and biomedical literature PPI data. Results Many well-characterized protein complexes are accurately predicted by this method when apply to two different yeast PPI datasets. The results show that (i) biomedical literature PPI data can effectively improve the performance of protein complex prediction; (ii) our method makes good use of high-throughput and biomedical literature PPI data along with gene ontology data to achieve state-of-the-art protein complex prediction capabilities. PMID:25708571



Inferring ProteinProtein Interactions from Multiple Protein Domain Combinations  

E-print Network

­protein interaction and domain data of Saccharomyces cerevisiae and Drosophila melanogaster we introduce a novel) and Saccharomyces cerevisiae (2­7). Most recently, attention focused on the first protein­protein interaction maps

Izaguirre, Jesús A.


Protein quality of chickpea ( Cicer arietinum L.) protein hydrolysates  

Microsoft Academic Search

Chickpea protein isolate (CPI) was used as the starting material in the production of chickpea protein hydrolysates (CPHs). To obtain a highly extensive hydrolysate with a degree of hydrolysis higher than 50%, a sequential utilisation of endoprotease (Alcalase) and exoprotease (Flavourzyme) was necessary. Molecular weight patterns of CPHs were determined by gel filtration chromatography. As a result of the enzymatic

Alfonso Clemente; Javier Vioque; Raúl Sánchez-Vioque; Justo Pedroche; Juan Bautista; Francisco Millán



Comparative analysis of five protein-protein interaction corpora  

Microsoft Academic Search

Background: Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate. Results: We present the first comparative evaluation of the diverse

Sampo Pyysalo; Antti Airola; Juho Heimonen; Jari Björne; Filip Ginter; Tapio Salakoski



Improving protein function prediction using domain and protein complexes in PPI networks  

PubMed Central

Background Characterization of unknown proteins through computational approaches is one of the most challenging problems in silico biology, which has attracted world-wide interests and great efforts. There have been some computational methods proposed to address this problem, which are either based on homology mapping or in the context of protein interaction networks. Results In this paper, two algorithms are proposed by integrating the protein-protein interaction (PPI) network, proteins’ domain information and protein complexes. The one is domain combination similarity (DCS), which combines the domain compositions of both proteins and their neighbors. The other is domain combination similarity in context of protein complexes (DSCP), which extends the protein functional similarity definition of DCS by combining the domain compositions of both proteins and the complexes including them. The new algorithms are tested on networks of the model species of Saccharomyces cerevisiae to predict functions of unknown proteins using cross validations. Comparing with other several existing algorithms, the results have demonstrated the effectiveness of our proposed methods in protein function prediction. Furthermore, the algorithm DSCP using experimental determined complex data is robust when a large percentage of the proteins in the network is unknown, and it outperforms DCS and other several existing algorithms. Conclusions The accuracy of predicting protein function can be improved by integrating the protein-protein interaction (PPI) network, proteins’ domain information and protein complexes. PMID:24655481



A new protein structure representation for efficient protein function prediction.  


One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average. PMID:25343279

Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F



Smoking interacts with HLA-DRB1 shared epitope in the development of anti-citrullinated protein antibody-positive rheumatoid arthritis: results from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA)  

PubMed Central

Introduction Rheumatoid arthritis (RA) is a multifactorial autoimmune disease in which genetic and environmental factors interact in the etiology. In this study, we investigated whether smoking and HLA-DRB1 shared-epitope (SE) alleles interact differently in the development of the two major subgroups of rheumatoid arthritis (RA), anti-citrullinated proteins antibody (ACPA)-positive and ACPA-negative disease, in a multiethnic population of Asian descent. Methods A case-control study comprising early diagnosed RA cases was carried out in Malaysia between 2005 and 2009. In total, 1,076 cases and 1,612 matched controls participated in the study. High-resolution HLA-DRB1 genotyping was performed for shared-epitope (SE) alleles. All participants answered a questionnaire on a broad range of issues, including smoking habits. The odds ratio (OR) of developing ACPA-positive and ACPA-negative disease was calculated for smoking and the presence of any SE alleles separately. Potential interaction between smoking history (defined as "ever" and "never" smoking) and HLA-DRB1 SE alleles also was calculated. Results In our multiethnic study, both the SE alleles and smoking were associated with an increased risk of developing ACPA-positive RA (OR SE alleles, 4.7; 95% confidence interval (CI), 3.6 to 6.2; OR smoking, 4.1; 95% CI, 1.9 to 9.2). SE-positive smokers had an odds ratio of ACPA-positive RA of 25.6 (95% CI, 10.4 to 63.4), compared with SE-negative never-smokers. The interaction between smoking and SE alleles was significant (attributable proportion due to interaction (AP) was 0.7 (95% CI, 0.5 to 1.0)). The HLA-DRB1*04:05 SE allele, which is common in Asian populations, but not among Caucasians, was associated with an increased risk of ACPA-positive RA, and this allele also showed signs of interaction with smoking (AP, 0.4; 95% CI, -0.1 to 0.9). Neither smoking nor SE alleles nor their combination was associated with an increased risk of ACPA-negative RA. Conclusions The risk of developing ACPA-positive RA is associated with a strong gene-environment interaction between smoking and HLA-DRB1 SE alleles in a Malaysian multiethnic population of Asian descent. This interaction seems to apply also between smoking and the specific HLA-DRB1*04:05 SE allele, which is common in Asian populations but not in Caucasians. PMID:22537824



Evolutionary Rate Heterogeneity of Core and Attachment Proteins in Yeast Protein Complexes  

PubMed Central

In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core protein subunits are the main functional elements, whereas attachment proteins act as modifiers or activators in protein complexes. In this article, using the current data set of yeast protein complexes, we found that core proteins are evolving at a faster rate than attachment proteins in spite of their functional importance. Interestingly, our investigation revealed that attachment proteins are present in a higher number of macromolecular complexes than core proteins. We also observed that the protein complex number (defined as the number of protein complexes in which a protein subunit belongs) has a stronger influence on gene/protein essentiality than multifunctionality. Finally, our results suggest that the observed differences in the rates of protein evolution between core and attachment proteins are due to differences in protein complex number and expression level. Moreover, we conclude that proteins which are present in higher numbers of macromolecular complexes enhance their overall expression level by increasing their transcription rate as well as translation rate, and thus the protein complex number imposes a strong selection pressure on the evolution of yeast proteome. PMID:23814130

Chakraborty, Sandip; Ghosh, Tapash Chandra



Protein-Protein Interaction Detection: Methods and Analysis  

PubMed Central

Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Thus, in silico methods which include sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, phylogenetic tree, phylogenetic profile, and gene expression-based approaches were developed. Elucidation of protein interaction networks also contributes greatly to the analysis of signal transduction pathways. Recent developments have also led to the construction of networks having all the protein-protein interactions using computational methods for signaling pathways and protein complex identification in specific diseases. PMID:24693427

Rao, V. Srinivasa; Srinivas, K.; Sujini, G. N.; Kumar, G. N. Sunand



Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET)  

Microsoft Academic Search

Bioluminescence resonance energy transfer (BRET) is a straightforward biophysical technique for studying protein-protein interactions. It requires: (1) that proteins of interest and suitable controls be labeled with either a donor or acceptor molecule, (2) placement of these labeled proteins in the desired environment for assessing their potential interaction, and (3) use of suitable detection instrumentation to monitor resultant energy transfer.

Karin A Eidne; Kevin D G Pfleger



Gradual Soil Water Depletion Results in Reversible Changes of Gene Expression, Protein Profiles, Ecophysiology, and Growth Performance in Populus euphratica, a Poplar Growing in Arid Regions1[W][OA  

PubMed Central

The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated. PMID:17158588

Bogeat-Triboulot, Marie-Béatrice; Brosché, Mikael; Renaut, Jenny; Jouve, Laurent; Le Thiec, Didier; Fayyaz, Payam; Vinocur, Basia; Witters, Erwin; Laukens, Kris; Teichmann, Thomas; Altman, Arie; Hausman, Jean-François; Polle, Andrea; Kangasjärvi, Jaakko; Dreyer, Erwin



Protein Adsorption in Three Dimensions  

PubMed Central

Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and initially-adsorbed protein. Interphase protein concentration CI increases as VI decreases, resulting in slow reduction in interfacial energetics. Steady-state is governed by a net partition coefficient P=(/CBCI). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This “adsorption-dehydration” step is the significant free-energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent-surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, protein adsorption monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle ? ? 65°. Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting ? < 65° . For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ?Gadso is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein adsorption to any surface by competing with

Vogler, Erwin A.



Protein adsorption in three dimensions.  


Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the "protein-adsorption problem" to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations C(B). This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume V(I) by expulsion of either-or-both interphase water and initially adsorbed protein. Interphase protein concentration C(I) increases as V(I) decreases, resulting in slow reduction in interfacial energetics. Steady state is governed by a net partition coefficient P=(C(I)/C(B)). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This "adsorption-dehydration" step is the significant free energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, adsorbent capacity monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle ??65(°). Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting ?<65(°). For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ?G(ads)(o) is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein adsorption to any surface by competing with adsorbing protein mol

Vogler, Erwin A



Isotope-coded protein label.  


A great variety of technologies using stable isotope labeling in combination with mass spectrometry have been described being tools to identify and relatively quantify proteins within complex mixtures. Here, we present a method, termed isotope-coded protein label (ICPL), which is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on tagging stable isotope derivatives at the free amino groups of intact proteins, the method is applicable to any protein sample, including extracts from tissues or body fluids. All separation methods currently employed in proteome studies can be used to reduce complexity on the protein level. After enzymatic cleavage of the protein fractions, the ratios of peptides from different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides representing different expression levels in the different proteomic states are further analyzed by tandem-mass spectrometry to identify respective proteins. For quantification of proteins from multiplexed ICPL experiments, ICPLQuant was developed, a software package especially designed to cover the whole ICPL workflow. The ICPL method results in accurate and reproducible quantification of proteins and high sequence coverage, indispensable for a comprehensive detection of posttranslational modifications and discrimination of protein isoforms. PMID:22665300

Kellermann, Josef; Lottspeich, Friedrich



DNA to Protein  

NSDL National Science Digital Library

Explore the relationship between the genetic code on the DNA strand and the resulting protein and rudimentary shape it forms. Through models of transcription and translation, you will discover this relationship and the resilience to mutations built into our genetic code. Start by exploring DNA?s double helix with an interactive 3D model. Highlight base pairs, look at one or both strands, and turn hydrogen bonds on or off. Next, watch an animation of transcription, which creates RNA from DNA, and translation, which ?reads? the RNA codons to create a protein.



Nucleation precursors in protein crystallization.  


Protein crystal nucleation is a central problem in biological crystallography and other areas of science, technology and medicine. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors. Here, methods of detection and characterization of the precursors are reviewed: dynamic light scattering, atomic force microscopy and Brownian microscopy. Data for several proteins provided by these methods have demonstrated that the nucleation precursors are clusters consisting of protein-dense liquid, which are metastable with respect to the host protein solution. The clusters are several hundred nanometres in size, the cluster population occupies from 10(-7) to 10(-3) of the solution volume, and their properties in solutions supersaturated with respect to crystals are similar to those in homogeneous, i.e. undersaturated, solutions. The clusters exist owing to the conformation flexibility of the protein molecules, leading to exposure of hydrophobic surfaces and enhanced intermolecular binding. These results indicate that protein conformational flexibility might be the mechanism behind the metastable mesoscopic clusters and crystal nucleation. Investigations of the cluster properties are still in their infancy. Results on direct imaging of cluster behaviors and characterization of cluster mechanisms with a variety of proteins will soon lead to major breakthroughs in protein biophysics. PMID:24598910

Vekilov, Peter G; Vorontsova, Maria A



Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding  

E-print Network

Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate, the results show that protein folding intermediates are ensembles of different structural forms direct experi- mental evidence in support of a basic tenet of energy landscape theory for protein folding


Regulation of Gluconeogenesis by a Novel Protein Phosphatase  

E-print Network

of FoxO proteins………………………………………………...7 FoxO proteins and Akt……………………………………………………...11 Protein phosphatase………………………………………………………...12 CHAPTER II IDENTIFICATION OF SMP5 AS A FOXO1/3A PHOSPHATASE......15 Introduction... ................................................................................................................15 Materials and methods ...............................................................................................16 Results and discussion...

Cao, Jin



Breakfast Proteins  

NSDL National Science Digital Library

In this activity, learners construct a cereal chain as a model of how proteins are made in the cell. Learners build their chain off of an initial template which represents a single copy of DNA and hand-written notes, replicating the process of transcription and translation. In this model, the letters of the chain correspond to the colors of the cereal (not the amino acids).

Julie Yu



Protein Factory  

NSDL National Science Digital Library

In this activity, learners take on the role of various parts of the cell in order to model the process of protein synthesis. Each learner receives a card describing, step by step, what s/he should be doing. Learners play the roles of either RNA codons, an RNA polymerase, messenger RNA, a ribosome, or transfer RNA. This activity is designed for a large group of 30 learners, but could be used with smaller groups of at least 10 learners.



Protein Kinases  

NSDL National Science Digital Library

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of protein kinases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the genomics and evolutionary relationships among kinases and then proceeds to describe the structure-function relationships of specific kinases, the molecular mechanisms underlying substrate specificity, and selected issues in regulation of kinase activity.

Avrom Caplan (Mount Sinai School of Medicine; Department of Pharmacology and Biological Chemistry REV)



The role of the unfolded protein response in the heart  

Microsoft Academic Search

The misfolding of nascent proteins, or the unfolding of proteins after synthesis is complete, can occur in response to numerous environmental stresses, or as a result of mutations that de-stabilize protein structure. Cells have developed elaborate protein quality control systems that recognize improperly folded proteins and either refold them or facilitate their degradation. One such quality control system is the

Christopher C. Glembotski



The ablation of glial fibrillary acidic protein-positive cells from the adult central nervous system results in the loss of forebrain neural stem cells but not retinal stem cells  

Microsoft Academic Search

The adult mammalian forebrain subependyma contains neural stem cells (NSCs) capable of self-renewal and multilineage differentia- tion. The in vivo identification of NSCs has not been definitively addressed using a loss of function approach. Using a transgenic mouse expressing herpes-simplex virus thymidine kinase from the glial fibrillary acidic protein (GFAP) promotor, we have selectively killed dividing GFAP-positive cells in the

Cindi M. Morshead; A. Denize Garcia; Michael V. Sofroniew; Derek van der Kooy



Naturally occurring R225W mutation of the gene encoding AMP-activated protein kinase (AMPK)? 3 results in increased oxidative capacity and glucose uptake in human primary myotubes  

Microsoft Academic Search

Aims\\/hypothesis  AMP-activated protein kinase (AMPK) has a broad role in the regulation of glucose and lipid metabolism making it a promising\\u000a target in the treatment of type 2 diabetes mellitus. We therefore sought to characterise for the first time the effects of\\u000a chronic AMPK activation on skeletal muscle carbohydrate metabolism in carriers of the rare gain-of-function mutation of the\\u000a gene encoding

S. A. Crawford; S. R. Costford; C. Aguer; S. C. Thomas; R. A. deKemp; J. N. DaSilva; D. Lafontaine; M. Kendall; R. Dent; R. S. B. Beanlands; R. McPherson; M.-E. Harper



Proteomic Analysis of Membrane Proteins of Vero Cells: Exploration of Potential Proteins Responsible for Virus Entry  

PubMed Central

Vero cells are highly susceptible to many viruses in humans and animals, and its membrane proteins (MPs) are responsible for virus entry. In our study, the MP proteome of the Vero cells was investigated using a shotgun LC-MS/MS approach. Six hundred twenty-seven proteins, including a total of 1839 peptides, were identified in MP samples of the Vero cells. In 627 proteins, 307 proteins (48.96%) were annotated in terms of biological process of gene ontology (GO) categories; 356 proteins (56.78%) were annotated in terms of molecular function of GO categories; 414 proteins (66.03%) were annotated in terms of cellular components of GO categories. Of 627 identified proteins, seventeen proteins had been revealed to be virus receptor proteins. The resulting protein lists and highlighted proteins may provide valuable information to increase understanding of virus infection of Vero cells. PMID:24286161

Guo, Donghua; Zhu, Qinghe; Zhang, Hong



C4BPAL1, a member of the human regulator of complement activation (RCA) gene cluster that resulted from the duplication of the gene coding for the [alpha]-chain of C4b-binding protein  

SciTech Connect

The regulator of complement activation (RCA) gene cluster evolved by multiple gene duplications to produce a family of genes coding for proteins that collectively control the activation of the complement system. The authors report here the characterization of C4BPAL1, a member of the human RCA gene cluster that arose from the duplication of the C4BPA gene after the separation of rodent and primate lineages. C4BPAL1 maps 20 kb downstream of the C4BPA gene and is in the same 5[prime] to 3[prime] orientation found for all RCA genes characterized thus far. It includes nine exon-like regions homologous to exons 2-8, 11, and 12 of the C4BPA gene. Analysis of the C4BPAL1 sequence suggests that it is currently a pseudogene in humans. However, comparisons between C4BPAL1 and the human and murine C4BPA genes show sequence conservation, which strongly suggests that, for a long period of time, C4BPAL1 has been a functional gene coding for a protein with structural requirements similar to those of the [alpha]-chain of C4b-binding protein. 50 refs., 5 figs., 1 tab.

Sanchez-Corral, P.; Pardo-Manuel de Villena, F.; Rey-Campos, J.; Rodriguez de Cordoba, S. (Unidad de Immunologia, Madrid (Spain))



Benchtop Detection of Proteins  

NASA Technical Reports Server (NTRS)

A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein complexes while allowing any remaining unbound dye/antibody pairs to flow away. The retained dye/antibody/protein complexes are transferred to a cuvette, wherein they are irradiated with light from a miniature near-infrared laser delivered via a fiber-optic cable. The resulting fluorescence from the dye(s) is measured by use of a miniature spectrometer, the output of which is digitized, then analyzed by laptop computer. The software running in the computer identifies the protein species by the wavelengths of their spectral peaks and determines the amounts of the proteins, and thus, one day, microbes of the various species from the intensities of the peaks. The abovementioned removal of the unbound dye/antibody pairs during centrifugation prevents false positive readings. The process proves successful in detecting proteins in solution and thus can now be employed for use in microbe detection.

Scardelletti, Maximilian C.; Varaljay, Vanessa



Water-protein interactions from high-resolution protein crystallography.  

PubMed Central

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level. PMID:15306376

Nakasako, Masayoshi



Twitter SEO Tip Sheet Feinberg Office of Communications  

E-print Network

relevant media. Images and videos are popular on Twitter (and other social media sites) and consistently. For assistance on assessing your need and developing your social media presence, contact Nicole Mladic at 312 a link shortener like bitly when uploading but these keywords will make the media more valuable. Video

Engman, David M.


Seo 104 CCS/DOCENTES Local : Sala do Conselho -CCS  

E-print Network


Floeter, Sergio Ricardo



E-print Network

social media for marketing and increased traffic Learn how to utilize search engine optimization and web optimization issues will be dis- cussed; e-mail marketing campaign, e-commerce strategy and social (949) 824-3413 Program Benefits Understand how search engines (Google, Yahoo, Bing, Bidu) rank websites

Rose, Michael R.


Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes.  

PubMed Central

The adsorption free energy of charged proteins on mixed membranes, containing varying amounts of (oppositely) charged lipids, is calculated based on a mean-field free energy expression that accounts explicitly for the ability of the lipids to demix locally, and for lateral interactions between the adsorbed proteins. Minimization of this free energy functional yields the familiar nonlinear Poisson-Boltzmann equation and the boundary condition at the membrane surface that allows for lipid charge rearrangement. These two self-consistent equations are solved simultaneously. The proteins are modeled as uniformly charged spheres and the (bare) membrane as an ideal two-dimensional binary mixture of charged and neutral lipids. Substantial variations in the lipid charge density profiles are found when highly charged proteins adsorb on weakly charged membranes; the lipids, at a certain demixing entropy penalty, adjust their concentration in the vicinity of the adsorbed protein to achieve optimal charge matching. Lateral repulsive interactions between the adsorbed proteins affect the lipid modulation profile and, at high densities, result in substantial lowering of the binding energy. Adsorption isotherms demonstrating the importance of lipid mobility and protein-protein interactions are calculated using an adsorption equation with a coverage-dependent binding constant. Typically, at bulk-surface equilibrium (i.e., when the membrane surface is "saturated" by adsorbed proteins), the membrane charges are "overcompensated" by the protein charges, because only about half of the protein charges (those on the hemispheres facing the membrane) are involved in charge neutralization. Finally, it is argued that the formation of lipid-protein domains may be enhanced by electrostatic adsorption of proteins, but its origin (e.g., elastic deformations associated with lipid demixing) is not purely electrostatic. PMID:11023883

May, S; Harries, D; Ben-Shaul, A



BIOCHEMISTRY: How Do Proteins Interact?  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. New results provide support for the hypothesis that interactions between proteins involve selection from an ensemble of different conformations.

David D. Boehr (The Scripps Research Institute; Department of Molecular Biology and Skaggs Institute for Chemical Biology)



Analysis of membrane binding equilibria of peripheral proteins: allowance for excluded area of bound protein.  


When peripheral proteins bind to phospholipid membranes lacking discrete binding sites, steric repulsion between bound protein molecules may result in a reduction of the surface area available to additional bound protein by an amount significantly greater than the actual area occupied by bound protein. An approximate treatment of this effect demonstrates that neglect of area exclusion by bound protein may lead to significant errors in the evaluation of equilibrium association constants and the fractional coverage of membrane surface area. PMID:19837044

Minton, Allen P



Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes  

SciTech Connect

Protein-protein and protein-salt interactions have been obtained for ovalbumin in solutions of ammonium sulfate and for lysozyme in solutions of ammonium sulfate, sodium chloride, potassium isothiocyanate, and potassium chloride. The two-body interactions between ovalbumin molecules in concentrated ammonium-sulfate solutions can be described by the DLVO potentials plus a potential that accounts for the decrease in free volume available to the protein due to the presence of the salt ions. The interaction between ovalbumin and ammonium sulfate is unfavorable, reflecting the kosmotropic nature of sulfate anions. Lysozyme-lysozyme interactions cannot be described by the above potentials because anion binding to lysozyme alters these interactions. Lysozyme-isothiocyanate complexes are strongly attractive due to electrostatic interactions resulting from bridging by the isothiocyanate ion. Lysozyme-lysozyme interactions in sulfate solutions are more repulsive than expected, possibly resulting from a larger excluded volume of a lysozyme-sulfate bound complex or perhaps, hydration forces between the lysozyme-sulfate complexes.

Curtis, R.A.; Blanch, H.W. [Univ. of California, Berkeley, CA (United States). Dept. of Chemical Engineering] [Univ. of California, Berkeley, CA (United States). Dept. of Chemical Engineering; Prausnitz, J.M. [Lawrence Berkeley Lab., CA (United States)] [Lawrence Berkeley Lab., CA (United States)



Mathematics of protein pathological misfolding.  


"Protein folding is defined as a process by which a polypeptide chain performs a search in conformational space with the objective of achieving the so-called native conformation to global free-energy minimum under a given set of physiochemical conditions of the medium." Misfolding then, is the process by which this objective is not achieved. Protein Folding Quality Assessment (PFQA), is characterized by a three-parameter distribution function Phi(T) referred to as the PFQA function. It uses results of protein folding processes to assess the output quality of protein folding. Protein misfolding is implicated in the initial cause of many conformational diseases. Folding of cytosolic protein can be regarded as the performance of the protein after it is produced or manufactured by the synthesis processes. Protein folding through different mechanisms and pathways has been extensively covered in [J.D. Bryngelson, P.G. Wolynes, Spin glass and statistical mechanics of protein folding, Proc. Natl. Acad. Sci. USA 84 (1987) 7524; J. Wang, Statistics, pathways and dynamics of single molecule folding, J. Chem. Phys. 118 (2) (2003) 953; N.D. Socci, J.N. Onuchic, P.G. Wolynes, Diffusive dynamics of the reaction coordinates for protein folding funnels, J. Chem. Phys. 104 (14) (1996); D. Thirumalai, From minimal models to real proteins, time scales for protein folding kinetics, J. Phys. I France 5 (1995) 1457]. The model is based on growth models of Ratkowsky, Richards, etc. [D.A. Ratkowski, T.J. Reeds, Choosing near-linear parameters logistic model for radio-ligand and related assays, Biometrics 42 (1986) 575] for a three-parameters model to handle the quality assessment of the folding process. Thus a complete distribution can be found, thanks to the scale, location and shape parameters. PMID:17157330

Armah, Ebenezer O



Identifying protein complexes based on density and modularity in protein-protein interaction network  

PubMed Central

Background Identifying protein complexes is crucial to understanding principles of cellular organization and functional mechanisms. As many evidences have indicated that the subgraphs with high density or with high modularity in PPI network usually correspond to protein complexes, protein complexes detection methods based on PPI network focused on subgraph's density or its modularity in PPI network. However, dense subgraphs may have low modularity and subgraph with high modularity may have low density, which results that protein complexes may be subgraphs with low modularity or with low density in the PPI network. As the density-based methods are difficult to mine protein complexes with low density, and the modularity-based methods are difficult to mine protein complexes with low modularity, both two methods have limitation for identifying protein complexes with various density and modularity. Results To identify protein complexes with various density and modularity, including those have low density but high modularity and those have low modularity but high density, we define a novel subgraph's fitness, f?, as f?= (density)?*(modularity)1-?, and propose a novel algorithm, named LF_PIN, to identify protein complexes by expanding seed edges to subgraphs with the local maximum fitness value. Experimental results of LF-PIN in S.cerevisiae show that compared with the results of fitness equal to density (? = 1) or equal to modularity (? = 0), the LF-PIN identifies known protein complexes more effectively when the fitness value is decided by both density and modularity (0results of seven competing protein complex detection methods (CMC, Core-Attachment, CPM, DPClus, HC-PIN, MCL, and NFC) in S.cerevisiae and E.coli, LF-PIN outperforms other seven methods in terms of matching with known complexes and functional enrichment. Moreover, LF-PIN has better performance in identifying protein complexes with low density or with low modularity. Conclusions By considering both the density and the modularity, LF-PIN outperforms other protein complexes detection methods that only consider density or modularity, especially in identifying known protein complexes with low density or low modularity. PMID:24565048



Health Benefits of Texturized Whey Proteins  

Technology Transfer Automated Retrieval System (TEKTRAN)

Whey proteins are an important class of food ingredients used in many functional foods to boost protein content. Using the extrusion texturization process to partially open the native globular structures of whey proteins changed their conformation to the molten globular state, resulting in a new cla...


A surprising simplicity to protein folding  

Microsoft Academic Search

The polypeptide chains that make up proteins have thousands of atoms and hence millions of possible inter-atomic interactions. It might be supposed that the resulting complexity would make prediction of protein structure and protein-folding mechanisms nearly impossible. But the fundamental physics underlying folding may be much simpler than this complexity would lead us to expect: folding rates and mechanisms appear

David Baker



Correlation of C-reactive protein haplotypes with serum C-reactive protein level and response to anti-tumor necrosis factor therapy in UK rheumatoid arthritis patients: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort  

PubMed Central

Introduction In many European countries, restrictions exist around the prescription of anti-tumor necrosis factor (anti-TNF) treatments for rheumatoid arthritis (RA). Eligibility and response to treatment is assessed by using the disease activity score 28 (DAS28) algorithm, which incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Although DAS28-CRP provides a more reliable measure of disease activity, functional variants exist within the CRP gene that affect basal CRP production. Therefore, we aimed to determine the relation between functional genetic variants at the CRP gene locus and levels of serum CRP in RA patients, and whether these variants, alone or in combination, are correlated with DAS28-CRP and change in DAS28-CRP after anti-TNF treatment. Methods DNA samples from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS) were genotyped for rs1205, rs1800947, and rs3091244 by using either TaqMan or the Sequenom MassARRAY iPLEX system. Estimated haplotypes were constructed for each sample by using the expectation maximization algorithm implemented in the haplo.stats package within the R statistical program. CRP values were log transformed, and the association between single nucleotide polymorphisms (SNPs), haplotypes of SNPs and baseline CRP, baseline DAS28-CRP, and change in DAS28-CRP were evaluated by using linear regression in STATA v.10. Results Baseline CRP measurements were available for 599 samples with 442 also having data 6 months after treatment with an anti-TNF. For these 442 samples, the study had > 80% power to detect a clinically meaningful difference of 0.6 DAS28 Units for an allele frequency of 5%. Estimated haplotype frequencies corresponded with previous frequencies reported in the literature. Overall, no significant association was observed between any of the markers investigated and baseline CRP levels. Further, CRP haplotypes did not correlate with baseline CRP (P = 0.593), baseline DAS28-CRP (P = 0.540), or change in DAS28-CRP after treatment with an anti-TNF over a 6-month period (P = 0.302). Conclusions Although CRP genotype may influence baseline CRP levels, in patients with very active disease, no such association was found. This suggests that genetic variation at the CRP locus does not influence DAS28-CRP, which may continue to be used in determining eligibility for and response to anti-TNF treatment, without adjusting for CRP genotype. PMID:23039402



Mining literature for protein-protein interactions  

Microsoft Academic Search

Motivation: A central problem in bioinformatics is how to capture information from the vast current scientific literature in a form suitable for analysis by computer. We address the special case of information on protein-protein interactions, and show that the frequencies of words in Medline abstracts can be used to determine whether or not a given paper discusses protein-protein interactions. For

Edward M. Marcotte; Ioannis Xenarios; David Eisenberg



The 3;21 translocation in myelodysplasia results in a fusion transcript between the AML1 gene and the gene for EAP, a highly conserved protein associated with the Epstein-Barr virus small RNA EBER 1.  

PubMed Central

In the 8;21 translocation, the AML1 gene, located at chromosome band 21q22, is translocated to chromosome 8 (q22), where it is fused to the ETO gene and transcribed as a chimeric gene. AML1 is the human homolog of the recently cloned mouse gene pebp2 alpha B, homologous to the DNA binding alpha subunit of the polyoma enhancer factor pebp2. AML1 is also involved in a translocation with chromosome 3 that is seen in patients with therapy-related acute myeloid leukemia and myelodysplastic syndrome and in chronic myelogenous leukemia in blast crisis. We have isolated a fusion cDNA clone from a t(3;21) library derived from a patient with therapy-related myelodysplastic syndrome; this clone contains sequences from AML1 and from EAP, which we have now localized to band 3q26. EAP has previously been characterized as a highly expressed small nuclear protein of 128 residues (EBER 1) associated with Epstein-Barr virus small RNA. The fusion clone contains the DNA binding 5' part of AML1 that is fused to ETO in the t(8;21) and, in addition, at least one other exon. The translocation replaces the last nine codons of AML1 with the last 96 codons of EAP. The fusion does not maintain the correct reading frame of EAP and may not lead to a functional chimeric protein. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 PMID:8395054

Nucifora, G; Begy, C R; Erickson, P; Drabkin, H A; Rowley, J D



Mutation of a Conserved Residue (D123) Required for Oligomerization of Human Immunodeficiency Virus Type 1 Nef Protein Abolishes Interaction with Human Thioesterase and Results in Impairment of Nef Biological Functions  

PubMed Central

Nef is a myristoylated protein of 27 to 35 kDa that is conserved in primate lentiviruses. In vivo, Nef is required for high viral load and full pathological effects. In vitro, Nef has at least four activities: induction of CD4 and major histocompatibility complex (MHC) class I downregulation, enhancement of viral infectivity, and alteration of T-cell activation pathways. We previously reported that the Nef protein from human immunodeficiency virus type 1 interacts with a novel human thioesterase (hTE). In the present study, by mutational analysis, we identified a region of the Nef core, extending from the residues D108 to W124, that is involved both in Nef-hTE interaction and in Nef-induced CD4 downregulation. This region of Nef is located on the oligomer interface and is in close proximity to the putative CD4 binding site. One of the mutants carrying a mutation in this region, targeted to the conserved residue D123, was also found to be defective in two other functions of Nef, MHC class I downmodulation and enhancement of viral infectivity. Furthermore, mutation of this residue affected the ability of Nef to form dimers, suggesting that the oligomerization of Nef may be critical for its multiple functions. PMID:10799608

Liu, Lang Xia; Heveker, Nikolaus; Fackler, Oliver T.; Arold, Stefan; Le Gall, Sylvie; Janvier, Katy; Peterlin, B. Matija; Dumas, Christian; Schwartz, Olivier; Benichou, Serge; Benarous, Richard



Hepatitis C Virus Core Protein Is a Dimeric Alpha-Helical Protein Exhibiting Membrane Protein Features  

PubMed Central

The building block of hepatitis C virus (HCV) nucleocapsid, the core protein, together with viral RNA, is composed of different domains involved in RNA binding and homo-oligomerization. The HCV core protein 1-169 (CHCV169) and its N-terminal region from positions 1 to 117 (CHCV117) were expressed in Escherichia coli and purified to homogeneity suitable for biochemical and biophysical characterizations. The overall conformation and the oligomeric properties of the resulting proteins CHCV169 and CHCV117 were investigated by using analytical centrifugation, circular dichroism, intrinsic fluorescence measurements, and limited proteolysis. Altogether, our results show that core protein (CHCV169) behaves as a membranous protein and forms heterogeneous soluble micelle-like aggregates of high molecular weight in the absence of detergent. In contrast, it behaves, in the presence of mild detergent, as a soluble, well-folded, noncovalent dimer. Similar to findings observed for core proteins of HCV-related flaviviruses, the HCV core protein is essentially composed of ?-helices (50%). In contrast, CHCV117 is soluble and monodispersed in the absence of detergent but is unfolded. It appears that the folding of the highly basic domain from positions 2 to 117 (2-117 domain) depends on the presence of the 117-169 hydrophobic domain, which contains the structural determinants ensuring the binding of core with cellular membranes. Finally, our findings provide valuable information for further investigations on isolated core protein, as well as for attempts to reconstitute nucleocapsid particles in vitro. PMID:16103187

Boulant, Steeve; Vanbelle, Christophe; Ebel, Christine; Penin, François; Lavergne, Jean-Pierre



Purification of Proteins Fused to Maltose-Binding Protein Mario Lebendiker and Tsafi Danieli  

E-print Network

on amylose­ agarose columns, resulting in a protein that is often 70­90% pure. In addition to protein, Amylose­ agarose, TEV protease MBP is one of the oldest and most popular fusion partners being used

Lebendiker, Mario


Measurements of Protein Crystal Face Growth Rates  

NASA Technical Reports Server (NTRS)

Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

Gorti, S.



Exogenous amyloidogenic proteins function as seeds in amyloid ?-protein aggregation.  


Amyloid ?-protein (A?) aggregation is considered to be a critical step in the neurodegeneration of Alzheimer's disease (AD). In addition to A?, many proteins aggregate into the amyloid state, in which they form elongated fibers with spines comprising stranded ?-sheets. However, the cross-seeding effects of other protein aggregates on A? aggregation pathways are not completely clear. To investigate the cross-seeding effects of exogenous and human non-CNS amyloidogenic proteins on A? aggregation pathways, we examined whether and how sonicated fibrils of casein, fibroin, sericin, actin, and islet amyloid polypeptide affected A?40 and A?42 aggregation pathways using the thioflavin T assay and electron microscopy. Interestingly, the fibrillar seeds of all amyloidogenic proteins functioned as seeds. The cross-seeding effect of actin was stronger but that of fibroin was weaker than that of other proteins. Furthermore, our nuclear magnetic resonance spectroscopic studies identified the binding sites of A? with the amyloidogenic proteins. Our results indicate that the amyloidogenic proteins, including those contained in foods and cosmetics, contribute to A? aggregation by binding to A?, suggesting their possible roles in the propagation of A? amyloidosis. PMID:24440525

Ono, Kenjiro; Takahashi, Ryoichi; Ikeda, Tokuhei; Mizuguchi, Mineyuki; Hamaguchi, Tsuyoshi; Yamada, Masahito



Green fluorescent protein as a reporter of prion protein folding  

PubMed Central

Background The amino terminal half of the cellular prion protein PrPc is implicated in both the binding of copper ions and the conformational changes that lead to disease but has no defined structure. However, as some structure is likely to exist we have investigated the use of an established protein refolding technology, fusion to green fluorescence protein (GFP), as a method to examine the refolding of the amino terminal domain of mouse prion protein. Results Fusion proteins of PrPc and GFP were expressed at high level in E.coli and could be purified to near homogeneity as insoluble inclusion bodies. Following denaturation, proteins were diluted into a refolding buffer whereupon GFP fluorescence recovered with time. Using several truncations of PrPc the rate of refolding was shown to depend on the prion sequence expressed. In a variation of the format, direct observation in E.coli, mutations introduced randomly in the PrPc protein sequence that affected folding could be selected directly by recovery of GFP fluorescence. Conclusion Use of GFP as a measure of refolding of PrPc fusion proteins in vitro and in vivo proved informative. Refolding in vitro suggested a local structure within the amino terminal domain while direct selection via fluorescence showed that as little as one amino acid change could significantly alter folding. These assay formats, not previously used to study PrP folding, may be generally useful for investigating PrPc structure and PrPc-ligand interaction. PMID:16939649

Vasiljevic, Snezana; Ren, Junyuan; Yao, YongXiu; Dalton, Kevin; Adamson, Catherine S; Jones, Ian M



Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system.  


In this study, the amount of protein synthesized using an in vitro protein synthesis system composed of only highly purified components (the PURE system) was optimized. By varying the concentrations of each system component, we determined the component concentrations that result in the synthesis of 0.38 mg/mL green fluorescent protein (GFP) in batch mode and 3.8 mg/mL GFP in dialysis mode. In dialysis mode, protein concentrations of 4.3 and 4.4 mg/mL were synthesized for dihydrofolate reductase and ?-galactosidase, respectively. Using the optimized system, the synthesized protein represented 30% (w/w) of the total protein, which is comparable to the level of overexpressed protein in Escherichia coli cells. This optimized reconstituted in vitro protein synthesis system may potentially be useful for various applications, including in vitro directed evolution of proteins, artificial cell assembly, and protein structural studies. PMID:24880499

Kazuta, Yasuaki; Matsuura, Tomoaki; Ichihashi, Norikazu; Yomo, Tetsuya



Scaffolding proteins in G-protein signaling  

Microsoft Academic Search

Heterotrimeric G proteins are ubiquitous signaling partners of seven transmembrane-domain G-protein-coupled receptors (GPCRs), the largest (and most important pharmacologically) receptor family in mammals. A number of scaffolding proteins have been identified that regulate various facets of GPCR signaling. In this review, we summarize current knowledge concerning those scaffolding proteins that are known to directly bind heterotrimeric G proteins, and discuss

Alexandra V Andreeva; Mikhail A Kutuzov; Tatyana A Voyno-Yasenetskaya



Length, protein protein interactions, and complexity  

NASA Astrophysics Data System (ADS)

The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large-scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein interactions has driven the selection of longer proteins, as they are more able to distinguish among a larger number of distinct interactions due to their greater average surface area. Annotated protein sequences available from the SWISS-PROT database were analyzed for 13 eukaryotes, eight bacteria, and two archaea species. The number of subcellular locations to which each protein is associated is used as a measure of the number of interactions to which a protein participates. Two databases of yeast protein-protein interactions were used as another measure of the number of interactions to which each S. cerevisiae protein participates. Protein length is shown to correlate with both number of subcellular locations to which a protein is associated and number of interactions as measured by yeast two-hybrid experiments. Protein length is also shown to correlate with the probability that the protein is encoded by an essential gene. Interestingly, average protein length and number of subcellular locations are not significantly different between all human proteins and protein targets of known, marketed drugs. Increased protein length appears to be a significant mechanism by which the increasing complexity of protein-protein interaction networks is accommodated within the natural evolution of species. Consideration of protein length may be a valuable tool in drug design, one that predicts different strategies for inhibiting interactions in aberrant and normal pathways.

Tan, Taison; Frenkel, Daan; Gupta, Vishal; Deem, Michael W.



Character and evolution of protein protein interfaces  

NASA Astrophysics Data System (ADS)

Protein-protein interactions create the macromolecular assemblies and sequential signaling pathways essential for cell function. Their number far exceeds the number of proteins themselves and their experimental characterization, while improving, remains relatively slow. For these reasons, novel computational methods have important roles to play in understanding the physical basis of protein interactions, and in constraining the molecular basis of their specificity. This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees.

Res, Ivica; Lichtarge, Olivier



Site-directed analysis on protein hydrophobicity.  


Hydrophobicity of a protein is considered to be one of the major intrinsic factors dictating the protein aggregation propensity. Understanding how protein hydrophobicity is determined is, therefore, of central importance in preventing protein aggregation diseases and in the biotechnological production of human therapeutics. Traditionally, protein hydrophobicity is estimated based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acid residues depends on the protein context. To this end, we analyze the hydration free energy-free energy change on hydration quantifying the hydrophobicity-of the wild-type and 21 mutants of amyloid-beta protein associated with Alzheimer's disease by performing molecular dynamics simulations and integral-equation calculations. From detailed analysis of mutation effects on the protein hydrophobicity, we elucidate how the protein global factor such as the total charge as well as underlying protein conformations influence the hydrophobicity of amino acid residues. Our results provide a unique insight into the protein hydrophobicity for rationalizing and predicting the protein aggregation propensity on mutation, and open a new avenue to design aggregation-resistant proteins as biotherapeutics. PMID:24817476

Chong, Song-Ho; Ham, Sihyun



Protein Quality Control in the Nucleus  

PubMed Central

In their natural environment, cells are regularly exposed to various stress conditions that may lead to protein misfolding, but also in the absence of stress, misfolded proteins occur as the result of mutations or failures during protein synthesis. Since such partially denatured proteins are prone to aggregate, cells have evolved several elaborate quality control systems to deal with these potentially toxic proteins. First, various molecular chaperones will seize the misfolded protein and either attempt to refold the protein or target it for degradation via the ubiquitin-proteasome system. The degradation of misfolded proteins is clearly compartmentalized, so unique degradation pathways exist for misfolded proteins depending on whether their subcellular localization is ER/secretory, mitochondrial, cytosolic or nuclear. Recent studies, mainly in yeast, have shown that the nucleus appears to be particularly active in protein quality control. Thus, specific ubiquitin-protein ligases located in the nucleus, target not only misfolded nuclear proteins, but also various misfolded cytosolic proteins which are transported to the nucleus prior to their degradation. In comparison, much less is known about these mechanisms in mammalian cells. Here we highlight recent advances in our understanding of nuclear protein quality control, in particular regarding substrate recognition and proteasomal degradation. PMID:25010148

Nielsen, Sofie V.; Poulsen, Esben G.; Rebula, Caio A.; Hartmann-Petersen, Rasmus



The Two-Hybrid System: A Method to Identify and Clone Genes for Proteins that Interact with a Protein of Interest  

Microsoft Academic Search

We describe a method that detects proteins capable of interacting with a known protein and that results in the immediate availability of the cloned genes for these interacting proteins. Plasmids are constructed to encode two hybrid proteins. One hybrid consists of the DNA-binding domain of the yeast transcriptional activator protein GAL4 fused to the known protein; the other hybrid consists

Cheng-Ting Chien; Paul L. Bartel; Rolf Sternglanz



Dynamics of protein conformations  

NASA Astrophysics Data System (ADS)

A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

Stepanova, Maria



Contribution of sarcoplasmic proteins to myofibrillar proteins gelation.  


Surimi, a refined protein extract, is produced by solubilizing myofibrillar proteins during the comminuting and salting stages of manufacturing. The resulting paste gels on heating to produce kamaboko or a range of analog shellfish such as crab claw, filament sticks, fish mushroom, and so on. The myosin molecule is the major myofibrillar protein in gelation. It is believed that washing steps during the traditional surimi process play an important role in enhancing the gel properties of the resultant kamaboko by removing water-soluble (sarcoplasmic, Sp-P) proteins. By contrast, some researchers claim that retaining Sp-P or adding it into the surimi gel network not only does not interfere with the action of myofibrillar proteins during the sol-gel transition step but also improves the gel characteristics of the resultant kamaboko. It seems that retention of Sp-P or their addition into raw surimi does enhance the textural properties of kamaboko gel perhaps by functioning as a proteinase inhibitor, particularly against trypsin and trypsin-like proteinases but this depends on the type of applied surimi process. Among different types of Sp-P, it has been claimed that some proteins such as endogenous transglutaminase (TGase) play a more important role than other Sp-P in bond formation, by catalyzing the cross-linking of myosin heavy chain (MHC) molecules during low-temperature setting of surimi, resulting a more elastic kamaboko gel. PMID:22224956

Jafarpour, Ali; Gorczyca, Elisabeth M



Quantitative study of protein-protein interactions by quartz nanopipettes.  


In this report, protein-modified quartz nanopipettes were used to quantitatively study protein-protein interactions in attoliter sensing volumes. As shown by numerical simulations, the ionic current through the conical-shaped nanopipette is very sensitive to the surface charge variation near the pore mouth. With the appropriate modification of negatively charged human neuroglobin (hNgb) onto the inner surface of a nanopipette, we were able to detect concentration-dependent current change when the hNgb-modified nanopipette tip was exposed to positively charged cytochrome c (Cyt c) with a series of concentrations in the bath solution. Such current change is due to the adsorption of Cyt c to the inner surface of the nanopipette through specific interactions with hNgb. In contrast, a smaller current change with weak concentration dependence was observed when Cyt c was replaced with lysozyme, which does not specifically bind to hNgb. The equilibrium dissociation constant (KD) for the Cyt c-hNgb complex formation was derived and the value matched very well with the result from surface plasmon resonance measurement. This is the first quantitative study of protein-protein interactions by a conical-shaped nanopore based on charge sensing. Our results demonstrate that nanopipettes can potentially be used as a label-free analytical tool to quantitatively characterize protein-protein interactions. PMID:25060094

Tiwari, Purushottam Babu; Astudillo, Luisana; Miksovska, Jaroslava; Wang, Xuewen; Li, Wenzhi; Darici, Yesim; He, Jin



Contact Density Affects Protein Evolutionary Rate from Bacteria to Animals  

Microsoft Academic Search

The density of contacts or the fraction of buried sites in a protein structure is thought to be related to a protein’s designability,\\u000a and genes encoding more designable proteins should evolve faster than other genes. Several recent studies have tested this\\u000a hypothesis but have found conflicting results. Here, we investigate how a gene’s evolutionary rate is affected by its protein’s

Tong Zhou; D. Allan Drummond; Claus O. Wilke



Dual targeting of peroxisomal proteins  

PubMed Central

Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed. PMID:24151469

Ast, Julia; Stiebler, Alina C.; Freitag, Johannes; Bölker, Michael



Water at interface with proteins  

E-print Network

Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of the hydration water and the dynamics of protein. These works have generated a large amount of data whose interpretation is debated. New experiments measure the dynamics of water at low temperature on the surface of proteins, finding a qualitative change (crossover) that might be related to the slowing down and stop of the protein's activity (protein glass transition), possibly relevant for the safe preservation of organic material at low temperature. To better understand the experimental data several scenarios have been discussed. Here, we review these experiments and discuss their interpretations in relation with the anomalous properties of water. We summarize the results for the thermodynamics and dynamics of supercooled water at an interface. We consider also the effect of water on protein stability, making a step in the direction of understanding, by means of Monte Carlo simulations and theoretical calculations, how the interplay of water cooperativity and hydrogen bonds interfacial strengthening affects the protein cold denaturation.

Giancarlo Franzese; Valentino Bianco; Svilen Iskrov



Effect of sepsis on calcium uptake and content in skeletal muscle and regulation in vitro by calcium of total and myofibrillar protein breakdown in control and septic muscle: Results from a preliminary study  

SciTech Connect

Because high calcium concentration in vitro stimulates muscle proteolysis, calcium has been implicated in the pathogenesis of increased muscle breakdown in different catabolic conditions. Protein breakdown in skeletal muscle is increased during sepsis, but the effect of sepsis on muscle calcium uptake and content is not known. In this study the influence of sepsis, induced in rats by cecal ligation and puncture, on muscle calcium uptake and content was studied. Sixteen hours after cecal ligation and puncture or sham operation, calcium content of the extensor digitorum longus (EDL) and soleus (SOL) muscles was determined with an atomic absorption spectrometer. Calcium uptake was measured in intact SOL muscles incubated in the presence of calcium 45 (45Ca) for between 1 and 120 minutes. Total and myofibrillar protein breakdown was determined in SOL muscles, incubated in the presence of different calcium concentrations (0; 2.5; 5.0 mmol/L), and measured as release into the incubation medium of tyrosine and 3-methylhistidine (3-MH), respectively. Calcium content was increased by 51% (p less than 0.001) during sepsis in SOL and by 10% (p less than 0.05) in EDL muscle. There was no difference in 45Ca uptake between control and septic muscles during the early phase (1 to 5 minutes) of incubation. During more extended incubation (30 to 120 minutes), muscles from septic rats took up significantly more 45Ca than control muscles (p less than 0.05). Tyrosine release by incubated SOL muscles from control and septic rats was increased when calcium was added to the incubation medium, and at a calcium concentration of 2.5 mmol/L, the increase in tyrosine release was greater in septic than in control muscle. Addition of calcium to the incubation medium did not affect 3-MH release in control or septic muscle.

Benson, D.W.; Hasselgren, P.O.; Hiyama, D.T.; James, J.H.; Li, S.; Rigel, D.F.; Fischer, J.E.



HMPAS: Human Membrane Protein Analysis System  

PubMed Central

Background Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources related with membrane proteins. However, most of these resources are built for specific well-known membrane protein groups, making it difficult to find common and specific features of various membrane protein groups. Methods We collected human membrane proteins from the dispersed resources and predicted novel membrane protein candidates by using ortholog information and our membrane protein classifiers. The membrane proteins were classified according to the type of interaction with the membrane, subcellular localization, and molecular function. We also made new feature dataset to characterize the membrane proteins in various aspects including membrane protein topology, domain, biological process, disease, and drug. Moreover, protein structure and ICD-10-CM based integrated disease and drug information was newly included. To analyze the comprehensive information of membrane proteins, we implemented analysis tools to identify novel sequence and functional features of the classified membrane protein groups and to extract features from protein sequences. Results We constructed HMPAS with 28,509 collected known membrane proteins and 8,076 newly predicted candidates. This system provides integrated information of human membrane proteins individually and in groups organized by 45 subcellular locations and 1,401 molecular functions. As a case study, we identified associations between the membrane proteins and diseases and present that membrane proteins are promising targets for diseases related with nervous system and circulatory system. A web-based interface of this system was constructed to facilitate researchers not only to retrieve organized information of individual proteins but also to use the tools to analyze the membrane proteins. Conclusions HMPAS provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups. In this system, user can acquire the information of individual proteins and specified groups focused on their conserved sequence features, involved cellular processes, and diseases. HMPAS may contribute as a valuable resource for the inference of novel cellular mechanisms and pharmaceutical targets associated with the human membrane proteins. HMPAS is freely available at PMID:24564858



Membrane bending by protein-protein crowding.  


Curved membranes are an essential feature of dynamic cellular structures, including endocytic pits, filopodia protrusions and most organelles. It has been proposed that specialized proteins induce curvature by binding to membranes through two primary mechanisms: membrane scaffolding by curved proteins or complexes; and insertion of wedge-like amphipathic helices into the membrane. Recent computational studies have raised questions about the efficiency of the helix-insertion mechanism, predicting that proteins must cover nearly 100% of the membrane surface to generate high curvature, an improbable physiological situation. Thus, at present, we lack a sufficient physical explanation of how protein attachment bends membranes efficiently. On the basis of studies of epsin1 and AP180, proteins involved in clathrin-mediated endocytosis, we propose a third general mechanism for bending fluid cellular membranes: protein-protein crowding. By correlating membrane tubulation with measurements of protein densities on membrane surfaces, we demonstrate that lateral pressure generated by collisions between bound proteins drives bending. Whether proteins attach by inserting a helix or by binding lipid heads with an engineered tag, protein coverage above ~20% is sufficient to bend membranes. Consistent with this crowding mechanism, we find that even proteins unrelated to membrane curvature, such as green fluorescent protein (GFP), can bend membranes when sufficiently concentrated. These findings demonstrate a highly efficient mechanism by which the crowded protein environment on the surface of cellular membranes can contribute to membrane shape change. PMID:22902598

Stachowiak, Jeanne C; Schmid, Eva M; Ryan, Christopher J; Ann, Hyoung Sook; Sasaki, Darryl Y; Sherman, Michael B; Geissler, Phillip L; Fletcher, Daniel A; Hayden, Carl C



Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties  

PubMed Central

Background With the huge amount of uncharacterized protein sequences generated in the post-genomic age, it is highly desirable to develop effective computational methods for quickly and accurately predicting their functions. The information thus obtained would be very useful for both basic research and drug development in a timely manner. Methodology/Principal Findings Although many efforts have been made in this regard, most of them were based on either sequence similarity or protein-protein interaction (PPI) information. However, the former often fails to work if a query protein has no or very little sequence similarity to any function-known proteins, while the latter had similar problem if the relevant PPI information is not available. In view of this, a new approach is proposed by hybridizing the PPI information and the biochemical/physicochemical features of protein sequences. The overall first-order success rates by the new predictor for the functions of mouse proteins on training set and test set were 69.1% and 70.2%, respectively, and the success rate covered by the results of the top-4 order from a total of 24 orders was 65.2%. Conclusions/Significance The results indicate that the new approach is quite promising that may open a new avenue or direction for addressing the difficult and complicated problem. PMID:21283518

Shi, Xiaohe; Lu, Wen-Cong; Cai, Yu-Dong; Chou, Kuo-Chen



Evolutionary optimization of protein folding.  


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

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



Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces  

PubMed Central

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei



Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins  

PubMed Central

HIV type 1 (HIV-1) is characterized by its rapid genetic evolution, leading to challenges in anti-HIV therapy. However, the sequence variations in HIV-1 proteins are not randomly distributed due to a combination of functional constraints and genetic drift. In this study, we examined patterns of sequence variability for evidence of linked sequence changes (termed as coevolution or covariation) in 15 HIV-1 proteins. It shows that the percentage of charged residues in the coevolving residues is significantly higher than that in all the HIV-1 proteins. Most of the coevolving residues are spatially proximal in the protein structures and tend to form relatively compact and independent units in the tertiary structures, termed as “protein sectors”. These protein sectors are closely associated with anti-HIV drug resistance, T cell epitopes, and antibody binding sites. Finally, we explored candidate peptide inhibitors based on the protein sectors. Our results can establish an association between the coevolving residues and molecular functions of HIV-1 proteins, and then provide us with valuable knowledge of pathology of HIV-1 and therapeutics development. PMID:25671429

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei



Integrated analysis of residue coevolution and protein structures capture key protein sectors in HIV-1 proteins.  


HIV type 1 (HIV-1) is characterized by its rapid genetic evolution, leading to challenges in anti-HIV therapy. However, the sequence variations in HIV-1 proteins are not randomly distributed due to a combination of functional constraints and genetic drift. In this study, we examined patterns of sequence variability for evidence of linked sequence changes (termed as coevolution or covariation) in 15 HIV-1 proteins. It shows that the percentage of charged residues in the coevolving residues is significantly higher than that in all the HIV-1 proteins. Most of the coevolving residues are spatially proximal in the protein structures and tend to form relatively compact and independent units in the tertiary structures, termed as "protein sectors". These protein sectors are closely associated with anti-HIV drug resistance, T cell epitopes, and antibody binding sites. Finally, we explored candidate peptide inhibitors based on the protein sectors. Our results can establish an association between the coevolving residues and molecular functions of HIV-1 proteins, and then provide us with valuable knowledge of pathology of HIV-1 and therapeutics development. PMID:25671429

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei



Protein imprinting in polyacrylamide-based gels  

PubMed Central

Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

Zayats, Maya; Brenner, Andrew J.; Searson, Peter C.



Protein Crystal Based Nanomaterials  

NASA Technical Reports Server (NTRS)

This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

Bell, Jeffrey A.; VanRoey, Patrick



Application Note for protein  

E-print Network

Application Note Dynabeads® for protein complex isolation Studying the way proteins function and interact is an exciting area of research. By looking at protein structures, researchers can identify how cofactors and other molecules influence enzymatic or protein activity. Isolating complete protein complexes

Lebendiker, Mario


Shotgun protein sequencing.  

SciTech Connect

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

Faulon, Jean-Loup Michel; Heffelfinger, Grant S.



Distinguishing Proteins From Arbitrary Amino Acid Sequences  

PubMed Central

What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy



Distinguishing proteins from arbitrary amino acid sequences.  


What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

Yau, Stephen S-T; Mao, Wei-Guang; Benson, Max; He, Rong Lucy



Human Glycolipid Transfer Protein  

PubMed Central

Glycolipid transfer protein (GLTP) is a soluble 24 kDa protein that selectively accelerates the intermembrane transfer of glycolipids in vitro. Little is known about the GLTP structure and dynamics. Here, we report the cloning of human GLTP and characterize the environment of the three tryptophans (Trps) of the protein using fluorescence spectroscopy. Excitation at 295 nm yielded an emission maximum (?max) near 347 nm, indicating a relatively polar average environment for emitting Trps. Quenching with acrylamide at physiological ionic strength or with potassium iodide resulted in linear Stern—Volmer plots, suggesting accessibility of emitting Trps to soluble quenchers. Insights into reversible conformational changes accompanying changes in GLTP activity were provided by addition and rapid dilution of urea while monitoring changes in Trp or 1-anilinonaphthalene-8-sulfonic acid fluorescence. Incubation of GLTP with glycolipid liposomes caused a blue shift in the Trp emission maximum but diminished the fluorescence intensity. The blue-shifted emission maximum, centered near 335 nm, persisted after separation of glycolipid liposomes from GLTP, consistent with formation of a GLTP—glycolipid complex at a glycolipid-liganding site containing Trp. The results provide the first insights into human GLTP structural dynamics by fluorescence spectroscopy, including global conformational changes that accompany GLTP folding into an active conformational state as well as more subtle conformational changes that play a role in GLTP-mediated transfer of glycolipids between membranes, and establish a foundation for future studies of membrane rafts using GLTP. PMID:15287756

Li, Xin-Min; Malakhova, Margarita L.; Lin, Xin; Pike, Helen M.; Chung, Taeowan; Molotkovsky, Julian G.; Brown, Rhoderick E.



A simple physical model for binding energy hot spots in protein–protein complexes  

PubMed Central

Protein–protein recognition plays a central role in most biological processes. Although the structures of many protein–protein complexes have been solved in molecular detail, general rules describing affinity and selectivity of protein–protein interactions do not accurately account for the extremely diverse nature of the interfaces. We investigate the extent to which a simple physical model can account for the wide range of experimentally measured free energy changes brought about by alanine mutation at protein–protein interfaces. The model successfully predicts the results of alanine scanning experiments on globular proteins (743 mutations) and 19 protein–protein interfaces (233 mutations) with average unsigned errors of 0.81 kcal/mol and 1.06 kcal/mol, respectively. The results test our understanding of the dominant contributions to the free energy of protein–protein interactions, can guide experiments aimed at the design of protein interaction inhibitors, and provide a stepping-stone to important applications such as interface redesign. PMID:12381794

Kortemme, Tanja; Baker, David



Conventional and novel G? protein families constitute the heterotrimeric G-protein signaling network in soybean.  


Heterotrimeric G-proteins comprised of G?, G? and G? proteins are important signal transducers in all eukaryotes. The G? protein of the G-protein heterotrimer is crucial for its proper targeting at the plasma membrane and correct functioning. G? proteins are significantly smaller and more diverse than the G? and G? proteins. In model plants Arabidopsis and rice that have a single G? and G? protein, the presence of two canonical G? proteins provide some diversity to the possible heterotrimeric combinations. Our recent analysis of the latest version of the soybean genome has identified ten G? proteins which belong to three distinct families based on their C-termini. We amplified the full length cDNAs, analyzed their detailed expression profile by quantitative PCR, assessed their localization and performed yeast-based interaction analysis to evaluate interaction specificity with different G? proteins. Our results show that ten G? genes are retained in the soybean genome and have interesting expression profiles across different developmental stages. Six of the newly identified proteins belong to two plant-specific G? protein families. Yeast-based interaction analyses predict some degree of interaction specificity between different G? and G? proteins. This research thus identifies a highly diverse G-protein network from a plant species. Homologs of these novel proteins have been previously identified as QTLs for grain size and yield in rice. PMID:21853116

Choudhury, Swarup Roy; Bisht, Naveen C; Thompson, Rheannon; Todorov, Oleg; Pandey, Sona



The Geobiochemistry of Methanogen Proteins  

NASA Astrophysics Data System (ADS)

A principle of geobiochemistry is that adaptation over evolutionary time includes a thermodynamic drive to minimize costs of making biomolecules like proteins and lipids. If so, then biomolecule abundances will reflect, at least in part, their relative stabilities at the conditions imposed by external environments. We tested this hypothesis by comparing relative stabilities of 138 orthologous proteins between a representative lake-sediment methanogen (Methanoculleus marisnigri) and a representative rumen methanogen (Methanospirillum hungatei) at the compositional constraints of their respective environments. Chemical affinities of the proteins were calculated based on pH, temperature, and concentrations of dissolved hydrogen, bicarbonate, ammonia, and hydrogen sulfide, together with standard Gibbs energies of formation of proteins from the elements predicted with a group additivity algorithm for unfolded proteins [1]. Methanogens were chosen as they are chemoautotrophs and their metabolism proceeds at relatively small affinities. Also, they are found in a variety of compositionally varying habitats like rumen, sediments, hydrothermal systems and sewage. The methanogens selected belong to the same order of taxonomy and are closely related. Preliminary results show that a majority of the proteins belonging to the rumen methanogen (66%) are more stable in the rumen environment, while a majority of the proteins belonging to the lake-sediment methanogen (58%) are more stable at sediment conditions. In a separate observation, it was noted that while the complete protein ';proteasome subunit alpha' of another rumen methanogen (Methanobrevibacter smithii) was less stable in its more reducing habitat as compared to a sewage methanogen (Methanothermobacter thermoautotophicus), its first 26 amino acid residues (N terminal) were in fact more stable in its own environment. These 26 residues are reported to be unique as compared to other proteasome proteins and are suggested to be performing a structural role [2]. These findings suggest that adaptation of microbes to their geochemical environment is accompanied by minimization of the energetic costs of protein biosynthesis, which can be tested further by including methanogens in other environments like hot springs, submarine hydrothermal vents and peatlands. Comparative analyses will reveal which proteins and protein regions follow this energy-minimization strategy and which are excluded. It will then be possible to characterize proteins in terms of the extent to which their sequences are influenced by external geochemical forces. 1. Dick, J. M. (2008). Calculation of the relative metastabilities of proteins using the CHNOSZ software package. Geochem. Trans, 9(10). DOI: 10.1186/1467-4866-9-10. 2. Zwickl P., Grziwa A., Puehler G., Dahlmann B., Lottspeich F. and Baumeister W. (1992) Primary structure of the Thermoplasma proteasome and its implications for the structure, function, and evolution of the multicatalytic proteinase. Biochemistry 31, 964-972. DOI: 10.1021/bi00119a004.

Prasad, A.; Shock, E.



Protein expression of sensory and motor nerves  

PubMed Central

The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

Ren, Zhiwu; Wang, Yu; Peng, Jiang; Zhang, Li; Xu, Wenjing; Liang, Xiangdang; Zhao, Qing; Lu, Shibi



Protein structure alignment beyond spatial proximity  

PubMed Central

Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures. PMID:23486213

Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo



Potential Survival Benefit of Anti-Apoptosis Protein: Survivin-Derived Peptide Vaccine with and without Interferon Alpha Therapy for Patients with Advanced or Recurrent Urothelial Cancer—Results from Phase I Clinical Trials  

PubMed Central

We previously identified a human leukocyte antigen (HLA)-A24-restricted antigenic peptide, survivin-2B80–88, a member of the inhibitor of apoptosis protein family, recognized by CD8+cytotoxic T lymphocytes (CTL). In a phase I clinical trial of survivin-2B80-88 vaccination for metastatic urothelial cancer (MUC), we achieved clinical and immunological responses with safety. Moreover, our previous study indicated that interferon alpha (IFN?) enhanced the effects of the vaccine for colorectal cancer. Therefore, we started a new phase I clinical trial of survivin-2B80–88 vaccination with IFN? for MUC patients. Twenty-one patients were enrolled and no severe adverse event was observed. HLA-A24/survivin-2B80–88 tetramer analysis and ELISPOT assay revealed a significant increase in the frequency of the peptide-specific CTLs after vaccination in nine patients. Six patients had stable disease. The effects of IFN? on the vaccination were unclear for MUC. Throughout two trials, 30 MUO patients received survivin-2B80–88 vaccination. Patients receiving the vaccination had significantly better overall survival than a comparable control group of MUO patients without vaccination (P = 0.0009). Survivin-2B80–88 vaccination may be a promising therapy for selected patients with MUC refractory to standard chemotherapy. This trial was registered with UMIN00005859. PMID:24363758

Kitamura, Hiroshi; Nishida, Sachiyo; Takahashi-Takaya, Akari; Kawami, Sachiyo; Torigoe, Toshihiko; Hirohashi, Yoshihiko; Tsukamoto, Taiji; Sato, Noriyuki; Masumori, Naoya



Implications of protein polymorphism on protein phase behaviour.  


The phase behaviour of small globular proteins is often modeled by approximating them as spherical particles with fixed internal structure. However, changes in the local environment of a protein can lead to changes in its conformation rendering this approximation invalid. We present a simple two-state model in which protein conformation is not conserved and where the high-energy, non-native state is stabilised by pair-wise attractive interactions. The resulting phase behaviour is remarkably complex, non-universal and exhibits re-entrance. The model calculations show a demarcation between a regime where conformational transitioning is largely enslaved by phase separation and one where this is not the case. In the latter regime, which is characterised by a large free energy difference between the native and the non-native state, we deduce that the kinetics of the phase transition strongly depend on the average conformation of the proteins prior to their condensation. For condensation to occur in this regime within a dispersion of native proteins, nucleation of a cluster of proteins in the non-native state is required. We argue that our theory supports the distinction between common phase separation and the nucleated assembly of non-native supramolecular aggregates in protein dispersions. PMID:25629931

Stegen, J; van der Schoot, P



Non-classical protein secretion in bacteria  

PubMed Central

Background We present an overview of bacterial non-classical secretion and a prediction method for identification of proteins following signal peptide independent secretion pathways. We have compiled a list of proteins found extracellularly despite the absence of a signal peptide. Some of these proteins also have known roles in the cytoplasm, which means they could be so-called "moon-lightning" proteins having more than one function. Results A thorough literature search was conducted to compile a list of currently known bacterial non-classically secreted proteins. Pattern finding methods were applied to the sequences in order to identify putative signal sequences or motifs responsible for their secretion. We have found no signal or motif characteristic to any majority of the proteins in the compiled list of non-classically secreted proteins, and conclude that these proteins, indeed, seem to be secreted in a novel fashion. However, we also show that the apparently non-classically secreted proteins are still distinguished from cellular proteins by properties such as amino acid composition, secondary structure and disordered regions. Specifically, prediction of disorder reveals that bacterial secretory proteins are more structurally disordered than their cytoplasmic counterparts. Finally, artificial neural networks were used to construct protein feature based methods for identification of non-classically secreted proteins in both Gram-positive and Gram-negative bacteria. Conclusion We present a publicly available prediction method capable of discriminating between this group of proteins and other proteins, thus allowing for the identification of novel non-classically secreted proteins. We suggest candidates for non-classically secreted proteins in Escherichia coli and Bacillus subtilis. The prediction method is available online. PMID:16212653

Bendtsen, Jannick D; Kiemer, Lars; Fausbøll, Anders; Brunak, Søren



Tic62: a protein family from metabolism to protein translocation  

PubMed Central

Background The function and structure of protein translocons at the outer and inner envelope membrane of chloroplasts (Toc and Tic complexes, respectively) are a subject of intensive research. One of the proteins that have been ascribed to the Tic complex is Tic62. This protein was proposed as a redox sensor protein and may possibly act as a regulator during the translocation process. Tic62 is a bimodular protein that comprises an N-terminal module, responsible for binding to pyridine nucleotides, and a C-terminal module which serves as a docking site for ferredoxin-NAD(P)-oxido-reductase (FNR). This work focuses on evolutionary analysis of the Tic62-NAD(P)-related protein family, derived from the comparison of all available sequences, and discusses the structure of Tic62. Results Whereas the N-terminal module of Tic62 is highly conserved among all oxyphototrophs, the C-terminal region (FNR-binding module) is only found in vascular plants. Phylogenetic analyses classify four Tic62-NAD(P)-related protein subfamilies in land plants, closely related to members from cyanobacteria and green sulphur bacteria. Although most of the Tic62-NAD(P)-related eukaryotic proteins are localized in the chloroplast, one subgroup consists of proteins without a predicted transit peptide. The N-terminal module of Tic62 contains the structurally conserved Rossman fold and probably belongs to the extended family of short-chain dehydrogenases-reductases. Key residues involved in NADP-binding and residues that may attach the protein to the inner envelope membrane of chloroplasts or to the Tic complex are proposed. Conclusion The Tic62-NAD(P)-related proteins are of ancient origin since they are not only found in cyanobacteria but also in green sulphur bacteria. The FNR-binding module at the C-terminal region of the Tic62 proteins is probably a recent acquisition in vascular plants, with no sequence similarity to any other known motifs. The presence of the FNR-binding domain in vascular plants might be essential for the function of the protein as a Tic component and/or for its regulation. PMID:17374152

Balsera, Mónica; Stengel, Anna; Soll, Jürgen; Bölter, Bettina



Protein Structure Prediction by Protein Threading  

Microsoft Academic Search

\\u000a The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on “the inverse protein folding problem” laid the foundation of protein structure prediction by protein threading. By using\\u000a simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility\\u000a and protein secondary structure, the authors derived a simple and yet

Ying Xu; Zhijie Liu; Liming Cai; Dong Xu



Protein in diet  


... basic structure of protein is a chain of amino acids. You need protein in your diet to help ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a number ...


Physicochemical properties of artificial proteins that accelerate nucleation of crystalline calcium phosphate  

NASA Astrophysics Data System (ADS)

We have created 18 artificial proteins by embedding two calcification motifs found in a protein involved in bone and dentin formation. The relationship between the physicochemical properties of the proteins and their in vitro mineralization activities was investigated. Two slightly acidic proteins nucleated octacalcium phosphate (OCP) at a low protein concentration from a solution where precipitation did not occur without the proteins. Among 16 basic proteins, only one protein nucleated OCP at the same protein concentration. At a higher protein concentration, four proteins self-assembled to become large aggregates, and these four proteins nucleated OCP. Among 14 proteins without the self-assembling property, only five proteins nucleated OCP. None of the proteins formed ?-helix or ß-sheet structures. These results suggest that the proteins that had the self-assembling property appeared to exhibit nucleation activity with high frequency and that the formation of the ordered backbone conformation was not required for proteins to promote nucleation.

Tsuji, Toru; Onuma, Kazuo; Yamamoto, Akira; Iijima, Mayumi; Shiba, Kiyotaka



S100 proteins modulate protein phosphatase 5 function: a link between CA2+ signal transduction and protein dephosphorylation.  


PP5 is a unique member of serine/threonine phosphatases comprising a regulatory tetratricopeptide repeat (TPR) domain and functions in signaling pathways that control many cellular responses. We reported previously that Ca(2+)/S100 proteins directly associate with several TPR-containing proteins and lead to dissociate the interactions of TPR proteins with their client proteins. Here, we identified protein phosphatase 5 (PP5) as a novel target of S100 proteins. In vitro binding studies demonstrated that S100A1, S100A2, S100A6, and S100B proteins specifically interact with PP5-TPR and inhibited the PP5-Hsp90 interaction. In addition, the S100 proteins activate PP5 by using a synthetic phosphopeptide and a physiological protein substrate, Tau. Overexpression of S100A1 in COS-7 cells induced dephosphorylation of Tau. However, S100A1 and permanently active S100P inhibited the apoptosis signal-regulating kinase 1 (ASK1) and PP5 interaction, resulting the inhibition of dephosphorylation of phospho-ASK1 by PP5. The association of the S100 proteins with PP5 provides a Ca(2+)-dependent regulatory mechanism for the phosphorylation status of intracellular proteins through the regulation of PP5 enzymatic activity or PP5-client protein interaction. PMID:22399290

Yamaguchi, Fuminori; Umeda, Yoshinori; Shimamoto, Seiko; Tsuchiya, Mitsumasa; Tokumitsu, Hiroshi; Tokuda, Masaaki; Kobayashi, Ryoji




Technology Transfer Automated Retrieval System (TEKTRAN)

Soybean seed yield and protein concentration often show a strong negative correlation. Initial results of our study indicate that development of soybean lines with high yield and high protein concentration is possible by selecting for protein concentration first. We evaluated the relationship of yie...


Protein–protein docking: is the glass half-full or half-empty?  

Microsoft Academic Search

Are current docking methods capable of building complexes from putative component protein structures? Results of recent computational studies, including those of the CAPRI (Critical Assessment of Protein Interactions) competition, were used to determine the key properties for successful docking and introduce a classification of protein complexes based on docking difficulty. Enzyme–inhibitor complexes could be determined with reasonable accuracy – possibly

Sandor Vajda; Carlos J. Camacho



Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis  

Microsoft Academic Search

BACKGROUND: Cancer serum protein profiling by mass spectrometry has uncovered mass profiles that are potentially diagnostic for several common types of cancer. However, direct mass spectrometric profiling has a limited dynamic range and difficulties in providing the identification of the distinctive proteins. We hypothesized that distinctive profiles may result from the differential expression of relatively abundant serum proteins associated with

Wei-Min Gao; Rork Kuick; Randal P Orchekowski; David E Misek; Ji Qiu; Alissa K Greenberg; William N Rom; Dean E Brenner; Gilbert S Omenn; Brian B Haab; Samir M Hanash