proteins

Summary

Summary: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Top Publications

  1. Liu Q, Kwoh C, Li J. Binding affinity prediction for protein-ligand complexes based on ? contacts and B factor. J Chem Inf Model. 2013;53:3076-85 pubmed publisher
    ..atoms without covalent-bond oxygen/nitrogen, preferred contacts of metal ions, interfacial backbone atoms from proteins, or ? rings...
  2. Pavoni E, Vaccaro P, D Alessio V, De Santis R, Minenkova O. Simultaneous display of two large proteins on the head and tail of bacteriophage lambda. BMC Biotechnol. 2013;13:79 pubmed publisher
    ..copies of peptides or even large protein domains providing a powerful tool for screening libraries of peptides, proteins and cDNA...
  3. Schreyer A, Blundell T. CREDO: a structural interactomics database for drug discovery. Database (Oxford). 2013;2013:bat049 pubmed publisher
    ..The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo. ..
  4. Crowell A, Wall M, Doucette A. Maximizing recovery of water-soluble proteins through acetone precipitation. Anal Chim Acta. 2013;796:48-54 pubmed publisher
    ..increasing the ionic strength of the solution dramatically improves the precipitation efficiency of individual proteins, and proteome mixtures (ca. 80-100% yield)...
  5. van Blitterswijk M, DeJesus Hernandez M, Niemantsverdriet E, Murray M, Heckman M, Diehl N, et al. Association between repeat sizes and clinical and pathological characteristics in carriers of C9ORF72 repeat expansions (Xpansize-72): a cross-sectional cohort study. Lancet Neurol. 2013;12:978-88 pubmed publisher
  6. Wu Y, Chang G, Zhao Y, Zhang Y. Preparation of hollow nickel silicate nanospheres for separation of His-tagged proteins. Dalton Trans. 2014;43:779-83 pubmed publisher
    ..By taking advantage of the high affinity of Ni(2+) toward histidine-tagged (His-tagged) proteins, hollow NiSiO3 NSs can be used to enrich and separate His-tagged proteins directly from a mixture of lysed cells...
  7. Shi J, van Veelen P, Mahler M, Janssen G, Drijfhout J, Huizinga T, et al. Carbamylation and antibodies against carbamylated proteins in autoimmunity and other pathologies. Autoimmun Rev. 2014;13:225-30 pubmed publisher
    ..This review summarizes the current knowledge on carbamylation and the formation of anti-CarP antibodies and discusses their possibly important implications. ..
  8. Kishabongo A, Katchunga P, Van Aken E, Speeckaert M, Lagniau S, Husein D, et al. Glycated nail proteins: a new approach for detecting diabetes in developing countries. Trop Med Int Health. 2014;19:58-64 pubmed publisher
    To assess glycation of nail proteins as a tool in the diagnosis of diabetes...
  9. Dufrechou M, Vernhet A, Roblin P, Sauvage F, Poncet Legrand C. White wine proteins: how does the pH affect their conformation at room temperature?. Langmuir. 2013;29:10475-82 pubmed publisher
    Our studies focused on the determination of aggregation mechanisms of proteins occurring in wine at room temperature. Even if the wine pH range is narrow (2.8 to 3.7), some proteins are affected by this parameter...
  10. Xiang Z, Ren H, Hu Y, Coin I, Wei J, Cang H, et al. Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. Nat Methods. 2013;10:885-8 pubmed publisher
    Natural proteins often rely on the disulfide bond to covalently link side chains. Here we genetically introduce a new type of covalent bond into proteins by enabling an unnatural amino acid to react with a proximal cysteine...

Detail Information

Publications84

  1. Liu Q, Kwoh C, Li J. Binding affinity prediction for protein-ligand complexes based on ? contacts and B factor. J Chem Inf Model. 2013;53:3076-85 pubmed publisher
    ..atoms without covalent-bond oxygen/nitrogen, preferred contacts of metal ions, interfacial backbone atoms from proteins, or ? rings...
  2. Pavoni E, Vaccaro P, D Alessio V, De Santis R, Minenkova O. Simultaneous display of two large proteins on the head and tail of bacteriophage lambda. BMC Biotechnol. 2013;13:79 pubmed publisher
    ..copies of peptides or even large protein domains providing a powerful tool for screening libraries of peptides, proteins and cDNA...
  3. Schreyer A, Blundell T. CREDO: a structural interactomics database for drug discovery. Database (Oxford). 2013;2013:bat049 pubmed publisher
    ..The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo. ..
  4. Crowell A, Wall M, Doucette A. Maximizing recovery of water-soluble proteins through acetone precipitation. Anal Chim Acta. 2013;796:48-54 pubmed publisher
    ..increasing the ionic strength of the solution dramatically improves the precipitation efficiency of individual proteins, and proteome mixtures (ca. 80-100% yield)...
  5. van Blitterswijk M, DeJesus Hernandez M, Niemantsverdriet E, Murray M, Heckman M, Diehl N, et al. Association between repeat sizes and clinical and pathological characteristics in carriers of C9ORF72 repeat expansions (Xpansize-72): a cross-sectional cohort study. Lancet Neurol. 2013;12:978-88 pubmed publisher
  6. Wu Y, Chang G, Zhao Y, Zhang Y. Preparation of hollow nickel silicate nanospheres for separation of His-tagged proteins. Dalton Trans. 2014;43:779-83 pubmed publisher
    ..By taking advantage of the high affinity of Ni(2+) toward histidine-tagged (His-tagged) proteins, hollow NiSiO3 NSs can be used to enrich and separate His-tagged proteins directly from a mixture of lysed cells...
  7. Shi J, van Veelen P, Mahler M, Janssen G, Drijfhout J, Huizinga T, et al. Carbamylation and antibodies against carbamylated proteins in autoimmunity and other pathologies. Autoimmun Rev. 2014;13:225-30 pubmed publisher
    ..This review summarizes the current knowledge on carbamylation and the formation of anti-CarP antibodies and discusses their possibly important implications. ..
  8. Kishabongo A, Katchunga P, Van Aken E, Speeckaert M, Lagniau S, Husein D, et al. Glycated nail proteins: a new approach for detecting diabetes in developing countries. Trop Med Int Health. 2014;19:58-64 pubmed publisher
    To assess glycation of nail proteins as a tool in the diagnosis of diabetes...
  9. Dufrechou M, Vernhet A, Roblin P, Sauvage F, Poncet Legrand C. White wine proteins: how does the pH affect their conformation at room temperature?. Langmuir. 2013;29:10475-82 pubmed publisher
    Our studies focused on the determination of aggregation mechanisms of proteins occurring in wine at room temperature. Even if the wine pH range is narrow (2.8 to 3.7), some proteins are affected by this parameter...
  10. Xiang Z, Ren H, Hu Y, Coin I, Wei J, Cang H, et al. Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. Nat Methods. 2013;10:885-8 pubmed publisher
    Natural proteins often rely on the disulfide bond to covalently link side chains. Here we genetically introduce a new type of covalent bond into proteins by enabling an unnatural amino acid to react with a proximal cysteine...
  11. Gendron T, Bieniek K, Zhang Y, Jansen West K, Ash P, Caulfield T, et al. Antisense transcripts of the expanded C9ORF72 hexanucleotide repeat form nuclear RNA foci and undergo repeat-associated non-ATG translation in c9FTD/ALS. Acta Neuropathol. 2013;126:829-44 pubmed publisher
    ..also undergo repeat-associated non-ATG (RAN) translation resulting in the production of three aggregation-prone proteins. The goal of this study was to examine whether antisense transcripts resulting from bidirectional transcription ..
  12. Cocco S, Monasson R, Weigt M. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol. 2013;9:e1003176 pubmed publisher
    Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information...
  13. Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A. 2013;110:15674-9 pubmed publisher
    ..These conditions are currently met by 422 of the protein families collected in the Pfam database. ..
  14. Vahidi S, Stocks B, Konermann L. Partially disordered proteins studied by ion mobility-mass spectrometry: implications for the preservation of solution phase structure in the gas phase. Anal Chem. 2013;85:10471-8 pubmed publisher
    ..Collision cross sections (CCSs) measured by IM-MS provide a measure of analyte size. For native proteins and their complexes, many structural features can be preserved in the gas phase, making IM-MS a powerful approach ..
  15. Breslow D, Koslover E, Seydel F, Spakowitz A, Nachury M. An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier. J Cell Biol. 2013;203:129-47 pubmed publisher
    Specific proteins are concentrated within primary cilia, whereas others remain excluded...
  16. Breker M, Schuldiner M. The emergence of proteome-wide technologies: systematic analysis of proteins comes of age. Nat Rev Mol Cell Biol. 2014;15:453-64 pubmed publisher
    During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone...
  17. Huerta Cepas J, Capella Gutierrez S, Pryszcz L, Marcet Houben M, Gabaldón T. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 2014;42:D897-902 pubmed publisher
    ..is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species...
  18. Goyder M, Rebeaud F, Pfeifer M, Kalman F. Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins. Expert Rev Proteomics. 2013;10:489-501 pubmed publisher
    ..By contrast, venom proteins, which are receiving increasing interest as potential therapeutics, are a challenge for MS-based disulfide ..
  19. Karra E, O Daly O, Choudhury A, Yousseif A, Millership S, Neary M, et al. A link between FTO, ghrelin, and impaired brain food-cue responsivity. J Clin Invest. 2013;123:3539-51 pubmed publisher
    ..Our findings show that FTO regulates ghrelin, a key mediator of ingestive behavior, and offer insight into how FTO obesity-risk alleles predispose to increased energy intake and obesity in humans. ..
  20. Zhang Z, Lange O. Replica exchange improves sampling in low-resolution docking stage of RosettaDock. PLoS ONE. 2013;8:e72096 pubmed publisher
    ..Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied. ..
  21. Liu C, Mou S, Cai Y. FTO gene variant and risk of overweight and obesity among children and adolescents: a systematic review and meta-analysis. PLoS ONE. 2013;8:e82133 pubmed publisher
    ..However, the results have been inconsistent. In this study, we performed a meta-analysis to clarify the association of FTO gene polymorphisms with overweight/obesity risk among children and adolescents...
  22. Yang J, Wheeler S, Velikoff M, Kleaveland K, Lafemina M, Frank J, et al. Activated alveolar epithelial cells initiate fibrosis through secretion of mesenchymal proteins. Am J Pathol. 2013;183:1559-1570 pubmed publisher
    ..Activated fibroblasts overexpress matrix proteins and release factors that promote further recruitment of activated fibroblasts, leading to progressive fibrosis...
  23. Fox N, Brenner S, Chandonia J. SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014;42:D304-9 pubmed publisher
    Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database...
  24. Májek P, Riedelová Reicheltová Z, Suttnar J, Dyr J. Staining of proteins for 2D SDS-PAGE using Coomassie Blue--speed versus sensitivity?. Electrophoresis. 2013;34:1972-5 pubmed
    Several new fast staining protocols for the visualization of proteins separated by SDS-PAGE utilizing Coomassie Blue staining (CBS) have been described in literature...
  25. Leung K, Abou El Hassan M, Bremner R. A rapid and efficient method to purify proteins at replication forks under native conditions. Biotechniques. 2013;55:204-6 pubmed publisher
    ..Isolation of protein on nascent DNA (iPOND) is an elegant method for purifying replication fork proteins. Here, we present accelerated native iPOND (aniPOND), a simplification of the iPOND procedure with improved ..
  26. Hleap J, Susko E, Blouin C. Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. BMC Struct Biol. 2013;13:20 pubmed publisher
    ..We also described the evolutionary sub-domain architecture of the ?-amylase catalytic domain, identifying the already reported minimum functional TIM barrel. ..
  27. Yi X, Kabanov A. Brain delivery of proteins via their fatty acid and block copolymer modifications. J Drug Target. 2013;21:940-55 pubmed publisher
    ..With this general idea we began modifying proteins (antibodies, enzymes, hormones, etc...
  28. Mukhopadhyay A, Ray S, Maulik U. Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach. BMC Bioinformatics. 2014;15:26 pubmed publisher
    Discovering novel interactions between HIV-1 and human proteins would greatly contribute to different areas of HIV research. Identification of such interactions leads to a greater insight into drug target prediction...
  29. Mellacheruvu D, Wright Z, Couzens A, Lambert J, St Denis N, Li T, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. 2013;10:730-6 pubmed publisher
    ..polypeptides represent bona fide interactors versus those that are background contaminants (for example, proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task...
  30. Pawson A, Sharman J, Benson H, Faccenda E, Alexander S, Buneman O, et al. The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Res. 2014;42:D1098-106 pubmed publisher
  31. Gao M, Skolnick J. A comprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol. 2013;9:e1003302 pubmed publisher
    ..we present a large-scale study on a non-redundant set of about 20,000 known ligand-binding sites, or pockets, of proteins. We find that the structural space of protein pockets is crowded, likely complete, and may be represented by ..
  32. Medraño Fernández I, Fagioli C, Mezghrani A, Otsu M, Sitia R. Different redox sensitivity of endoplasmic reticulum associated degradation clients suggests a novel role for disulphide bonds in secretory proteins. Biochem Cell Biol. 2014;92:113-8 pubmed publisher
    To maintain proteostasis in the endoplasmic reticulum (ER), terminally misfolded secretory proteins must be recognized, partially unfolded, and dislocated to the cytosol for proteasomal destruction, in a complex process called ER-..
  33. Pruitt K, Brown G, Hiatt S, Thibaud Nissen F, Astashyn A, Ermolaeva O, et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014;42:D756-63 pubmed publisher
    ..We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.
  34. Grammel M, Hang H. Chemical reporters for biological discovery. Nat Chem Biol. 2013;9:475-84 pubmed publisher
    ..reporters in conjunction with bioorthogonal labeling methods can be used to image and retrieve nucleic acids, proteins, glycans, lipids and other metabolites in vitro, in cells as well as in whole organisms...
  35. Saptarshi S, Duschl A, Lopata A. Interaction of nanoparticles with proteins: relation to bio-reactivity of the nanoparticle. J Nanobiotechnology. 2013;11:26 pubmed publisher
    Interaction of nanoparticles with proteins is the basis of nanoparticle bio-reactivity. This interaction gives rise to the formation of a dynamic nanoparticle-protein corona...
  36. Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41:e166 pubmed publisher
    ..CNCI software is available at http://www.bioinfo.org/software/cnci. ..
  37. Yang J, Roy A, Zhang Y. Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics. 2013;29:2588-95 pubmed publisher
    ..The methods are tested on a set of 500 non-redundant proteins harboring 814 natural, drug-like and metal ion molecules...
  38. Polyansky A, Hlevnjak M, Zagrovic B. Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code. RNA Biol. 2013;10:1248-54 pubmed publisher
    ..we have recently explored the connection between the physicochemical properties of mRNAs and their cognate proteins at the proteome level...
  39. Das R, Pappu R. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc Natl Acad Sci U S A. 2013;110:13392-7 pubmed publisher
    The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units...
  40. Hernandez S, Ferragut G, Amela I, Pérez Pons J, Piñol J, Mozo Villarías A, et al. MultitaskProtDB: a database of multitasking proteins. Nucleic Acids Res. 2014;42:D517-20 pubmed publisher
    ..uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored...
  41. Kim J, Sumranjit J, Kang H, Chung S. Discovery of coumarin derivatives as fluorescence acceptors for intrinsic fluorescence resonance energy transfer of proteins. Mol Biosyst. 2014;10:30-3 pubmed publisher
    ..as acceptors for the intrinsic fluorescence resonance energy transfer (iFRET) of tryptophan residues in target proteins. The fluorescence properties such as quantum yields, iFRET efficiencies, and Förster distances of the prepared ..
  42. Manhart M, Morozov A. Path-based approach to random walks on networks characterizes how proteins evolve new functions. Phys Rev Lett. 2013;111:088102 pubmed
    ..After demonstrating our approach on two reaction rate problems, we present a biophysical model that describes how proteins evolve new functions while maintaining thermodynamic stability...
  43. Harding M, Hsin K. Mespeus--a database of metal interactions with proteins. Methods Mol Biol. 2014;1091:333-42 pubmed publisher
    ..uk/MESPEUS_10/) lists metal protein interactions whose geometry has been experimentally determined and allows them to be visualized. This can contribute to the modeling process. The use of Mespeus is described with a series of examples. ..
  44. Hu J, Rho H, Newman R, Zhang J, Zhu H, Qian J. PhosphoNetworks: a database for human phosphorylation networks. Bioinformatics. 2014;30:141-2 pubmed publisher
    ..PhosphoNetworks is expected to play a prominent role in proteomics and phosphorylation-related disease research. http://www.phosphonetworks.org ..
  45. David C, Jacobs D. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol. 2014;1084:193-226 pubmed publisher
    It has become commonplace to employ principal component analysis to reveal the most important motions in proteins. This method is more commonly known by its acronym, PCA...
  46. Finn R, Bateman A, Clements J, Coggill P, Eberhardt R, Eddy S, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222-30 pubmed publisher
    ..Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. ..
  47. Truong H, Kim B, Schafer N, Wolynes P. Funneling and frustration in the energy landscapes of some designed and simplified proteins. J Chem Phys. 2013;139:121908 pubmed publisher
    We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans...
  48. Mosca R, Pons T, Ceol A, Valencia A, Aloy P. Towards a detailed atlas of protein-protein interactions. Curr Opin Struct Biol. 2013;23:929-40 pubmed publisher
    ..The net result will be the definition of a detailed atlas spanning the universe of protein interactions to guide the everyday work of the biologist. ..
  49. Mei S. Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. PLoS ONE. 2013;8:e79606 pubmed publisher
    ..As regards with negative data construction, experiments show that exclusiveness of subcellular co-localized proteins is unbiased and more reliable than random sampling...
  50. Waite A, Bäumer D, East S, Neal J, Morris H, Ansorge O, et al. Reduced C9orf72 protein levels in frontal cortex of amyotrophic lateral sclerosis and frontotemporal degeneration brain with the C9ORF72 hexanucleotide repeat expansion. Neurobiol Aging. 2014;35:1779.e5-1779.e13 pubmed publisher
    ..These data suggest that a reduction in C9orf72 protein may be a consequence of the disease. ..
  51. Hu J, Kehr B, Reinert K. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics. 2014;30:540-8 pubmed publisher
    ..The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology...
  52. Mizielinska S, Lashley T, Norona F, Clayton E, Ridler C, Fratta P, et al. C9orf72 frontotemporal lobar degeneration is characterised by frequent neuronal sense and antisense RNA foci. Acta Neuropathol. 2013;126:845-57 pubmed publisher
    ..of the gene they reside in, by producing toxic aggregates of repeat RNA termed RNA foci, or by producing toxic proteins generated by repeat-associated non-ATG translation...
  53. Bauer B, Shemesh T, Chen Y, Rapoport T. A "push and slide" mechanism allows sequence-insensitive translocation of secretory proteins by the SecA ATPase. Cell. 2014;157:1416-29 pubmed publisher
    In bacteria, most secretory proteins are translocated across the plasma membrane by the interplay of the SecA ATPase and the SecY channel. How SecA moves a broad range of polypeptide substrates is only poorly understood...
  54. Nelson D, Randle S, Laman H. Beyond ubiquitination: the atypical functions of Fbxo7 and other F-box proteins. Open Biol. 2013;3:130131 pubmed publisher
    F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases...
  55. Miyamoto H, Endo H, Hashimoto N, Limura K, Isowa Y, Kinoshita S, et al. The diversity of shell matrix proteins: genome-wide investigation of the pearl oyster, Pinctada fucata. Zoolog Sci. 2013;30:801-16 pubmed publisher
    In molluscs, shell matrix proteins are associated with biomineralization, a biologically controlled process that involves nucleation and growth of calcium carbonate crystals...
  56. Roume H, Heintz Buschart A, Muller E, Wilmes P. Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods Enzymol. 2013;531:219-36 pubmed publisher
    ..isolation of concomitant metabolites, RNA (optionally split into large and small RNA fractions), DNA, and proteins. Depending on the nature of the sample, the methodology comprises different (pre)processing and preservation ..
  57. Mori K, Arzberger T, Grässer F, Gijselinck I, May S, Rentzsch K, et al. Bidirectional transcripts of the expanded C9orf72 hexanucleotide repeat are translated into aggregating dipeptide repeat proteins. Acta Neuropathol. 2013;126:881-93 pubmed publisher
    ..start codon, the repeat region is translated in all three reading frames into aggregating dipeptide-repeat (DPR) proteins, poly-(Gly-Ala), poly-(Gly-Pro) and poly-(Gly-Arg)...
  58. Donnelly C, Zhang P, Pham J, Haeusler A, Heusler A, Mistry N, et al. RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron. 2013;80:415-28 pubmed publisher
    ..These data indicate a toxic RNA gain-of-function mechanism as a cause of C9ORF72 ALS and provide candidate antisense therapeutics and candidate human pharmacodynamic markers for therapy. ..
  59. Quax T, Wolf Y, Koehorst J, Wurtzel O, van der Oost R, Ran W, et al. Differential translation tunes uneven production of operon-encoded proteins. Cell Rep. 2013;4:938-44 pubmed publisher
    ..Thus, modulation of translation efficiency appears to be a universal mode of control in bacteria and archaea that allows for differential production of operon-encoded proteins.
  60. Lui S, Tiana G. The network of stabilizing contacts in proteins studied by coevolutionary data. J Chem Phys. 2013;139:155103 pubmed publisher
    The primary structure of proteins, that is their sequence, represents one of the most abundant sets of experimental data concerning biomolecules...
  61. Mannini L, Cucco F, Quarantotti V, Krantz I, Musio A. Mutation spectrum and genotype-phenotype correlation in Cornelia de Lange syndrome. Hum Mutat. 2013;34:1589-96 pubmed publisher
    ..Phenotypic variability is seen both intra- and intergenically. This article reviews the spectrum of CdLS mutations with a particular emphasis on their correlation to the clinical phenotype. ..
  62. Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. J Biomol NMR. 2013;57:155-66 pubmed publisher
    ..A discussion on resolution and sensitivity in sedimented solutes is framed in this context. ..
  63. Omasits U, Ahrens C, Müller S, Wollscheid B. Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 2014;30:884-6 pubmed publisher
    ..of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics. The Protter web application is available at http://wlab.ethz...
  64. Belzil V, Bauer P, Prudencio M, Gendron T, Stetler C, Yan I, et al. Reduced C9orf72 gene expression in c9FTD/ALS is caused by histone trimethylation, an epigenetic event detectable in blood. Acta Neuropathol. 2013;126:895-905 pubmed publisher
    ..Confirming these exciting results using blood from a larger cohort of patients may establish this novel epigenetic event as a biomarker for c9FTD/ALS. ..
  65. Lin Y, Boutureira O, Lercher L, Bhushan B, Paton R, Davis B. Rapid cross-metathesis for reversible protein modifications via chemical access to Se-allyl-selenocysteine in proteins. J Am Chem Soc. 2013;135:12156-9 pubmed publisher
    ..This use of Se-relayed Seac CM on proteins has now enabled reactions with substrates (allyl GlcNAc, N-allyl acetamide) that were previously not possible for ..
  66. Kuhn M, Szklarczyk D, Pletscher Frankild S, Blicher T, von Mering C, Jensen L, et al. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014;42:D401-7 pubmed publisher
    ..Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms...
  67. Wall S, Smith M, Ricart K, Zhou F, Vayalil P, Oh J, et al. Detection of electrophile-sensitive proteins. Biochim Biophys Acta. 2014;1840:913-22 pubmed publisher
    ..of signaling are reactive species which can mediate the post-translational modification of specific groups of proteins, thereby effecting functional changes in the modified proteins...
  68. Zu T, Liu Y, Bañez Coronel M, Reid T, Pletnikova O, Lewis J, et al. RAN proteins and RNA foci from antisense transcripts in C9ORF72 ALS and frontotemporal dementia. Proc Natl Acad Sci U S A. 2013;110:E4968-77 pubmed publisher
    ..microsatellite expansion mutations can be bidirectionally transcribed and that these mutations express unexpected proteins by a unique mechanism, repeat-associated non-ATG (RAN) translation...
  69. Janda J, Meier A, Merkl R. CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. Bioinformatics. 2013;29:3029-35 pubmed publisher
    ..In contrast, five additionally tested 3D features did not increase the classification performance achieved with evolutionary signals deduced from the multiple sequence alignment. ..
  70. Bonet J, Planas Iglesias J, Garcia Garcia J, Marín López M, Fernandez Fuentes N, Oliva B. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Res. 2014;42:D315-9 pubmed publisher
    ..The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses. ..
  71. Kaur A, Ackels T, Kuo T, Cichy A, Dey S, Hays C, et al. Murine pheromone proteins constitute a context-dependent combinatorial code governing multiple social behaviors. Cell. 2014;157:676-88 pubmed publisher
    ..We find major urinary proteins (MUPs) sufficient to elicit countermarking, and unlike other vomeronasal ligands that are detected by ..
  72. Kristjansdottir B, Levan K, Partheen K, Sundfeldt K. Diagnostic performance of the biomarkers HE4 and CA125 in type I and type II epithelial ovarian cancer. Gynecol Oncol. 2013;131:52-8 pubmed publisher
    ..We especially wanted to investigate the levels of HE4 and CA125 with regard to the gene and histology-unifying model of type I and type II epithelial ovarian cancer (EOC)...
  73. Kononova O, Jones L, Barsegov V. Order statistics inference for describing topological coupling and mechanical symmetry breaking in multidomain proteins. J Chem Phys. 2013;139:121913 pubmed publisher
    Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains...
  74. Tinberg C, Khare S, Dou J, Doyle L, Nelson J, Schena A, et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 2013;501:212-216 pubmed publisher
    The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition...
  75. Lin T, Wu J, Chang D. Combining phylogenetic profiling-based and machine learning-based techniques to predict functional related proteins. PLoS ONE. 2013;8:e75940 pubmed publisher
    Annotating protein functions and linking proteins with similar functions are important in systems biology. The rapid growth rate of newly sequenced genomes calls for the development of computational methods to help experimental techniques...
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