Vladimir N Uversky

Summary

Affiliation: University of South Florida
Country: USA

Publications

  1. doi request reprint Intrinsically disordered proteins may escape unwanted interactions via functional misfolding
    Vladimir N Uversky
    Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
    Biochim Biophys Acta 1814:693-712. 2011
  2. pmc Analyzing thioflavin T binding to amyloid fibrils by an equilibrium microdialysis-based technique
    Irina M Kuznetsova
    Laboratory of Structural Dynamics, Stability and Folding of Proteins, The Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
    PLoS ONE 7:e30724. 2012
  3. pmc Ordered disorder of the astrocytic dystrophin-associated protein complex in the norm and pathology
    Insung Na
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
    PLoS ONE 8:e73476. 2013
  4. ncbi request reprint Disordered interactome of human papillomavirus
    Bin Xue
    Department of Molecular Medicine, University of South Florida, 12901 Bruce B Downs Blvd MDC07, Tampa, Florida 33612, USA
    Curr Pharm Des 20:1274-92. 2014
  5. doi request reprint Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612 Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
    Biopolymers 99:870-87. 2013
  6. doi request reprint A putative role of the Sup35p C-terminal domain in the cytoskeleton organization during yeast mitosis
    Insung Na
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
    Mol Biosyst 10:925-40. 2014
  7. doi request reprint Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems
    Leonid Breydo
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Mol Biosyst 9:3068-79. 2013
  8. pmc Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
    Maria de Lourdes Coelho Ribeiro
    Cancer Imaging Metabolism, H Lee Moffitt Cancer Center and Research Institute, United States Department of Molecular Medicine, University of South Florida, Tampa, Florida, United States
    Peerj 1:e2. 2013
  9. pmc Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing
    Poornima Bhat-Nakshatri
    Department of Surgery, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN 46202, USA
    BMC Med Genomics 6:21. 2013
  10. pmc A decade and a half of protein intrinsic disorder: biology still waits for physics
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
    Protein Sci 22:693-724. 2013

Collaborators

Detail Information

Publications122 found, 100 shown here

  1. doi request reprint Intrinsically disordered proteins may escape unwanted interactions via functional misfolding
    Vladimir N Uversky
    Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
    Biochim Biophys Acta 1814:693-712. 2011
    ....
  2. pmc Analyzing thioflavin T binding to amyloid fibrils by an equilibrium microdialysis-based technique
    Irina M Kuznetsova
    Laboratory of Structural Dynamics, Stability and Folding of Proteins, The Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
    PLoS ONE 7:e30724. 2012
    ..This approach is universal and can be used for determining the binding parameters of any dye interaction with a receptor, such as ANS binding to proteins in the molten globule state or to protein amorphous aggregates...
  3. pmc Ordered disorder of the astrocytic dystrophin-associated protein complex in the norm and pathology
    Insung Na
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
    PLoS ONE 8:e73476. 2013
    ..Curiously, the disorder-based binding regions are rarely affected by SNPs suggesting that these regions are crucial for the biological functions of their corresponding proteins. ..
  4. ncbi request reprint Disordered interactome of human papillomavirus
    Bin Xue
    Department of Molecular Medicine, University of South Florida, 12901 Bruce B Downs Blvd MDC07, Tampa, Florida 33612, USA
    Curr Pharm Des 20:1274-92. 2014
    ..This review analyzes the plentitude and demeanor of intrinsic disorder in proteins from HPVs and their cellular targets...
  5. doi request reprint Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612 Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
    Biopolymers 99:870-87. 2013
    ..2013 Wiley Periodicals, Inc. Biopolymers 99: 870-887, 2013. ..
  6. doi request reprint A putative role of the Sup35p C-terminal domain in the cytoskeleton organization during yeast mitosis
    Insung Na
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
    Mol Biosyst 10:925-40. 2014
    ..Based on the analysis of known and modeled structures of some effectors and partners we found possible protein-protein interactions. Based on our study, we propose that Sup35pC may serve as actin modulator during mitosis. ..
  7. doi request reprint Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems
    Leonid Breydo
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Mol Biosyst 9:3068-79. 2013
    ....
  8. pmc Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
    Maria de Lourdes Coelho Ribeiro
    Cancer Imaging Metabolism, H Lee Moffitt Cancer Center and Research Institute, United States Department of Molecular Medicine, University of South Florida, Tampa, Florida, United States
    Peerj 1:e2. 2013
    ..Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder...
  9. pmc Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing
    Poornima Bhat-Nakshatri
    Department of Surgery, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN 46202, USA
    BMC Med Genomics 6:21. 2013
    ..The endogenous targets of ERα:estradiol (E2)-mediated alternative splicing and the influence of extracellular kinases that phosphorylate ERα on E2-induced splicing are unknown...
  10. pmc A decade and a half of protein intrinsic disorder: biology still waits for physics
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
    Protein Sci 22:693-724. 2013
    ..This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs...
  11. doi request reprint The most important thing is the tail: multitudinous functionalities of intrinsically disordered protein termini
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
    FEBS Lett 587:1891-901. 2013
    ..This review covers some of the key functions of disordered protein termini and emphasizes that these tails are not simple flexible protrusions but are evolved to serve...
  12. ncbi request reprint Intrinsic disorder-based protein interactions and their modulators
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Curr Pharm Des 19:4191-213. 2013
    ..Some of the aspects of the intrinsic disorder-based protein interactions and modes of their regulation are considered in this review...
  13. doi request reprint Unusual biophysics of intrinsically disordered proteins
    Vladimir N Uversky
    Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
    Biochim Biophys Acta 1834:932-51. 2013
    ..This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly...
  14. doi request reprint MultIDIMensionality of IDIMs: intrinsic disorder in autoinhibition
    Vladimir N Uversky
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Structure 21:315-6. 2013
    ..The activity of some proteins is autoinhibited by their inhibitory modules (IMs). In this issue of Structure, Trudeau and colleagues showed multifarious roles of ID in controlling agility of IMs...
  15. doi request reprint Size-exclusion chromatography in structural analysis of intrinsically disordered proteins
    Vladimir N Uversky
    Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, USA
    Methods Mol Biol 896:179-94. 2012
    ..It also can be used to physically separate IDP conformers based on their hydrodynamic dimensions, thus providing a unique possibility for the independent analysis of their physicochemical properties...
  16. doi request reprint Intrinsically disordered proteins and novel strategies for drug discovery
    Vladimir N Uversky
    University of South Florida, Byrd Alzheimer s Research Institute, College of Medicine, Department of Molecular Medicine, 12901 Bruce B Downs Blvd, MDC07, Tampa, FL 33612, USA
    Expert Opin Drug Discov 7:475-88. 2012
    ....
  17. doi request reprint Multiparametric analysis of intrinsically disordered proteins: looking at intrinsic disorder through compound eyes
    Vladimir N Uversky
    Department of Molecular Medicine, University of South Florida, College of Medicine, Tampa, Florida 33612, USA
    Anal Chem 84:2096-104. 2012
    ..Intrinsically disordered proteins are highly abundant in various proteomes. They are different from ordered proteins at many levels, and their structural and functional characterization requires special experimental and computational tools...
  18. ncbi request reprint Molecular profiling: an essential technology enabling personalized medicine in breast cancer
    Jiangang Liu
    Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
    Curr Drug Targets 13:541-54. 2012
    ..This review analyzes some recent achievements in the development of such tools...
  19. ncbi request reprint The roles of intrinsic disorder in orchestrating the Wnt-pathway
    Bin Xue
    Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
    J Biomol Struct Dyn 29:843-61. 2012
    ..Intrinsically disordered APC helps the collection of β-catenin from cytoplasm, facilitates the b-catenin delivery to the binding sites on Axin, and controls the final detachment of β-catenin from Axin...
  20. pmc In-silico prediction of disorder content using hybrid sequence representation
    Marcin J Mizianty
    Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
    BMC Bioinformatics 12:245. 2011
    ..We show that these predictions may over-or under-predict the overall amount of disorder, which motivates development of novel tools for direct and accurate sequence-based prediction of the disorder content...
  21. ncbi request reprint SS-Stabilizing Proteins Rationally: Intrinsic Disorder-Based Design of Stabilizing Disulphide Bridges in GFP
    B S Melnik
    Institute of Protein Research, RAS, 142290 Pushchino, Moscow Region, Russia
    J Biomol Struct Dyn 29:817-24. 2012
    ..Therefore, our study represents a novel approach for the rational design of stabilizing disulphide bridges in proteins...
  22. doi request reprint Intrinsically disordered proteins from A to Z
    Vladimir N Uversky
    Department of Molecular Medicine, University of South Florida, FL 33612, USA
    Int J Biochem Cell Biol 43:1090-103. 2011
    ..This review summarizes some of the major discoveries and breakthroughs in the field of intrinsic disorder by representing related concepts and definitions...
  23. ncbi request reprint Analysis of molecular recognition features (MoRFs)
    Amrita Mohan
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    J Mol Biol 362:1043-59. 2006
    ..The results of this study will advance the understanding of protein-protein interactions and help towards the future development of useful protein-protein binding site predictors...
  24. pmc The unfoldomics decade: an update on intrinsically disordered proteins
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
    BMC Genomics 9:S1. 2008
    ..The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins...
  25. pmc Understanding the role of Arg96 in structure and stability of green fluorescent protein
    Olesya V Stepanenko
    Institute of Cytology, Russian Academy of Sciences, St Petersburg 194064, Russia
    Proteins 73:539-51. 2008
    ..These data taken together suggest that besides established earlier crucial catalytic role, Arg96 is important for the overall folding and conformational stability of GFP...
  26. pmc Unfoldomics of human diseases: linking protein intrinsic disorder with diseases
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 10:S7. 2009
    ..This raises questions regarding the involvement of IDPs and IDRs in various diseases...
  27. pmc Intrinsic disorder and functional proteomics
    Predrag Radivojac
    School of Informatics, Indiana University, Bloomington, Indiana, USA
    Biophys J 92:1439-56. 2007
    ..The future of the prediction of protein disorder and the future uses of such predictions in functional proteomics comprise the last section of this article...
  28. pmc Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder
    Jessica Walton Chen
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:888-98. 2006
    ..Although many think of such conserved domains as being ordered, in fact a significant number of them contain regions of disorder that are likely to be crucial to their functions...
  29. ncbi request reprint Prediction of intrinsic disorder and its use in functional proteomics
    Vladimir N Uversky
    School of Medicine, Indiana University, Indianapolis, USA
    Methods Mol Biol 408:69-92. 2007
    ..A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes...
  30. ncbi request reprint Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, "dimer2", and DsRed1
    Olesia V Stepanenko
    Institute of Cytology, Russian Academy of Sciences, St Petersburg 194064, Russia
    Biochemistry 43:14913-23. 2004
    ..This means that the quaternary structure, being an important stabilizing factor, does not represent the only circumstance dictating the dramatic variations between fluorescent proteins in their conformational stabilities...
  31. ncbi request reprint Coupled folding and binding with alpha-helix-forming molecular recognition elements
    Christopher J Oldfield
    Molecular Kinetics Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
    Biochemistry 44:12454-70. 2005
    ..Application of this algorithm to databases of genomics and functionally annotated proteins indicates that alpha-MoREs are likely to play important roles protein-protein interactions involved in signaling events...
  32. pmc TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder
    Andrew Campen
    Department of Computer and Information Science, Indiana University Purdue University Indianapolis, IN 46202, USA
    Protein Pept Lett 15:956-63. 2008
    ..A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/disindex.php)...
  33. pmc Characterization of molecular recognition features, MoRFs, and their binding partners
    Vladimir Vacic
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Proteome Res 6:2351-66. 2007
    ..Implications of these findings for the development of MoRF-partner interaction predictors are discussed. In addition, structural changes upon MoRF-to-partner complex formation were examined for several illustrative examples...
  34. ncbi request reprint Intrinsic disorder in the Protein Data Bank
    Tanguy Le Gall
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Biomol Struct Dyn 24:325-42. 2007
    ....
  35. ncbi request reprint Abundance of intrinsic disorder in protein associated with cardiovascular disease
    Yugong Cheng
    Molecular Kinetics, Inc, Indianapolis, Indiana 46268, USA
    Biochemistry 45:10448-60. 2006
    ..Thus, our data suggest that intrinsically disordered proteins might play key roles in cardiovascular disease...
  36. ncbi request reprint Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
    Proteins 53:855-62. 2003
    ..4 +/- 0.2 microM) leads only to a very moderate folding of this protein and CaD136 remains substantially unfolded within its tight complex with calmodulin. The biological significance of these observations is discussed...
  37. doi request reprint A new trend in the experimental methodology for the analysis of the thioflavin T binding to amyloid fibrils
    Irina M Kuznetsova
    Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Sciences, Tikhoretsky av 4, St Petersburg, 194064, Russia
    Mol Neurobiol 45:488-98. 2012
    ..Therefore, the proposed approach represents an important addition to the existing arsenal of means for the diagnostics and therapy of the neurodegenerative diseases...
  38. doi request reprint Molecular mechanisms of the anomalous thermal aggregation of green fluorescent protein
    Bogan S Melnik
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1814:1930-9. 2011
    ..As a result, at high temperatures, the GFP structure does not unfold but rather breaks, consequently leading to enhanced protein aggregation. This is very different from typical BCA-II behavior...
  39. pmc Intrinsic disorder in scaffold proteins: getting more from less
    Marc S Cortese
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Prog Biophys Mol Biol 98:85-106. 2008
    ..In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure...
  40. pmc Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms
    Pedro R Romero
    School of Informatics, Indiana University Purdue University Indianapolis, 535 West Michigan Street, IT475, Indianapolis, IN 46202, USA
    Proc Natl Acad Sci U S A 103:8390-5. 2006
    ..Associating alternative splicing with protein disorder enables the time- and tissue-specific modulation of protein function needed for cell differentiation and the evolution of multicellular organisms...
  41. pmc Analysis of structured and intrinsically disordered regions of transmembrane proteins
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Mol Biosyst 5:1688-1702. 2009
    ....
  42. ncbi request reprint Function and structure of inherently disordered proteins
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
    Curr Opin Struct Biol 18:756-64. 2008
    ....
  43. pmc Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    Yugong Cheng
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Biochemistry 46:13468-77. 2007
    ..87 +/- 0.10, 0.87 +/- 0.11, and 0.87 +/- 0.08 over 10 cross validations, respectively. We present the results of these analyses and validation examples to discuss the potential improvement of the alpha-MoRF-PredII prediction accuracy...
  44. ncbi request reprint Flexible nets. The roles of intrinsic disorder in protein interaction networks
    A Keith Dunker
    Department of Biochemistry and Molecular Biology, and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    FEBS J 272:5129-48. 2005
    ..An important research direction will be to determine what fraction of protein-protein interaction in regulatory networks relies on intrinsic disorder...
  45. ncbi request reprint Rational drug design via intrinsically disordered protein
    Yugong Cheng
    Molecular Kinetics Inc, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
    Trends Biotechnol 24:435-42. 2006
    ..This novel strategy, based on intrinsically disordered protein, has the potential to increase significantly the discovery rate for new molecule entities...
  46. pmc Intrinsic disorder in PTEN and its interactome confers structural plasticity and functional versatility
    Prerna Malaney
    Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, USA
    Sci Rep 3:2035. 2013
    ..Together, PTEN higher order functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR. Targeting PTEN IDR and its interaction hubs emerges as a new paradigm for treatment of PTEN related pathologies...
  47. pmc Fluorescence quantum yield of thioflavin T in rigid isotropic solution and incorporated into the amyloid fibrils
    Anna I Sulatskaya
    Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
    PLoS ONE 5:e15385. 2010
    ..43. Consequently, the ThT fluorescence quantum yield could be used to characterize the peculiarities of the fibrillar structure, which opens some new possibilities in the ThT use for structural characterization of the amyloid fibrils...
  48. doi request reprint Binding stoichiometry and affinity of fluorescent dyes to proteins in different structural states
    Anna I Sulatskaya
    Laboratory of Structural Dynamics, Stability and Folding of Proteins of the Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
    Methods Mol Biol 895:441-60. 2012
    ..All procedures are illustrated by interaction of 8-anilino-1-naphthalenesulfonate (ANS) with bovine serum albumin...
  49. ncbi request reprint Viral disorder or disordered viruses: do viral proteins possess unique features?
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Protein Pept Lett 17:932-51. 2010
    ..In this review, we focus on structural peculiarities of viral proteins and on the role of intrinsic disorder in their functions...
  50. pmc Archaic chaos: intrinsically disordered proteins in Archaea
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Syst Biol 4:S1. 2010
    ....
  51. pmc Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions
    Jessica Walton Chen
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:879-87. 2006
    ..Most regions of conserved predicted disorder detected were short, with less than 10% of those found exceeding 30 residues in length...
  52. doi request reprint Protein intrinsic disorder and induced pluripotent stem cells
    Bin Xue
    Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612, USA
    Mol Biosyst 8:134-50. 2012
    ....
  53. doi request reprint Role of metal ions in aggregation of intrinsically disordered proteins in neurodegenerative diseases
    Leonid Breydo
    Department of Molecular Medicine, College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, MDC07, Tampa, Florida 33612, USA
    Metallomics 3:1163-80. 2011
    ..This review examines the effects of metal ion binding on the aggregation pathways of IDPs found in neurodegenerative diseases...
  54. ncbi request reprint Structural and functional properties of IL-4delta2, an alternative splice variant of human IL-4
    Anatoly M Vasiliev
    Institute of Immunological Engineering, 142380 Lyubuchany, Moscow Region, Russia
    J Proteome Res 2:273-81. 2003
    ..IL-4delta2 interacts specifically with the alpha chain of IL-4R and competes effectively with IL-4 for the common binding sites. Thus, IL-4delta2 may act as a regulator of the cytokine net, being the natural antagonist of IL-4...
  55. ncbi request reprint Unraveling multistate unfolding of rabbit muscle creatine kinase
    Irina M Kuznetsova
    Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
    Biochim Biophys Acta 1596:138-55. 2002
    ..A model of CK unfolding, which takes into account both structural perturbations and association of partially folded intermediates has been elaborated...
  56. ncbi request reprint Intrinsic disorder in proteins associated with neurodegenerative diseases
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Front Biosci (Landmark Ed) 14:5188-238. 2009
    ..The major goals of this review are to show the interconnections between intrinsic disorder and human neurodegenerative diseases and to overview a recent progress in development of novel nanoimaging tools to follow protein aggregation...
  57. pmc SPA: Short peptide analyzer of intrinsic disorder status of short peptides
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Genes Cells 15:635-46. 2010
    ..As evident from the data analysis, this method provides more reliable prediction of the intrinsic disorder status of short peptides...
  58. doi request reprint Drugs for 'protein clouds': targeting intrinsically disordered transcription factors
    A Keith Dunker
    Institute for Intrinsically Disordered Protein Research, The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Opin Pharmacol 10:782-8. 2010
    ..However, challenges remain in the field of drug development for 'protein clouds'; such development is still in its earliest stage...
  59. pmc DisProt: the Database of Disordered Proteins
    Megan Sickmeier
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 35:D786-93. 2007
    ..In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at http://www.disprot.org...
  60. pmc PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Biochim Biophys Acta 1804:996-1010. 2010
    ..Increased understanding of the underlying mechanism by which such meta-predictors give improved predictions will likely promote the further development of protein disorder predictors. Access to PONDR-FIT is available at www.disprot.org...
  61. ncbi request reprint Intrinsically disordered proteins in human diseases: introducing the D2 concept
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Annu Rev Biophys 37:215-46. 2008
    ..From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept...
  62. ncbi request reprint A computational investigation of allostery in the catabolite activator protein
    Liwei Li
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Am Chem Soc 129:15668-76. 2007
    ..This finding prompted us to propose a new mechanism by which CAP triggers the transcription activation that is based on an order to disorder transition mediated by cAMP binding as well as DNA...
  63. ncbi request reprint Cracking the folding code. Why do some proteins adopt partially folded conformations, whereas other don't?
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
    FEBS Lett 514:181-3. 2002
    ..Thus, the competence of a protein to form equilibrium intermediate(s) may be determined by the bulk content of hydrophobic and charged amino acid residues rather than by the positioning of amino acids within the sequence...
  64. doi request reprint The crowd you're in with: effects of different types of crowding agents on protein aggregation
    Leonid Breydo
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA Electronic address
    Biochim Biophys Acta 1844:346-57. 2014
    ....
  65. ncbi request reprint Use of the phase diagram method to analyze the protein unfolding-refolding reactions: fishing out the "invisible" intermediates
    Irina M Kuznetsova
    Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
    J Proteome Res 3:485-94. 2004
    ..Advantages and disadvantages of the technique suggested are also discussed...
  66. ncbi request reprint The PTEN Long N-tail is intrinsically disordered: increased viability for PTEN therapy
    Prerna Malaney
    Morsani College of Medicine, MDC 64, Department of Pathology and Cell Biology, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL 33612, USA
    Mol Biosyst 9:2877-88. 2013
    ..An extensive analysis of this region is warranted to better exploit its structural and biophysical peculiarities to drug discovery and drug delivery applications. ..
  67. pmc The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation
    Konstantin K Turoverov
    Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology RAS, Tikhoretsky Ave 4, St Petersburg 194064, Russia
    Prog Biophys Mol Biol 102:73-84. 2010
    ....
  68. doi request reprint Dynamics of oligomer formation by denatured carbonic anhydrase II
    Dmitry A Prokhorov
    Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1784:834-42. 2008
    ..This work also demonstrates some novel NMR-based methodological approaches that provide useful information on protein self-association...
  69. ncbi request reprint Prediction of the association state of insulin using spectral parameters
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
    J Pharm Sci 92:847-58. 2003
    ..The results show that the spectral properties of the insulins reflect their state of association, and can be used to predict their oligomeric state...
  70. ncbi request reprint Structural and functional properties of Yersinia pestis Caf1 capsular antigen and their possible role in fulminant development of primary pneumonic plague
    Vyacheslav M Abramov
    Institute of Immunological Engineering, 142380 Lyubuchany, Moscow Region, Russia
    J Proteome Res 1:307-15. 2002
    ..The specificity of such interaction is confirmed by the inhibition of IL-1alpha binding by Caf1. The Caf1 role in pneumonic plague pathogenesis is discussed...
  71. pmc Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes
    Olesya V Stepanenko
    Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
    Curr Protein Pept Sci 9:338-69. 2008
    ....
  72. ncbi request reprint Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Russia
    J Proteome Res 1:149-59. 2002
    ..Zinc-loaded protein remains effectively unfolded. Possible implications of these findings to the functioning of PDEgamma are discussed...
  73. doi request reprint Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life
    Bin Xue
    aDepartment of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA
    J Biomol Struct Dyn 30:137-49. 2012
    ..This suggests that the increased disorder content in eukaryotic proteomes might be used by nature to deal with the increased cell complexity due to the appearance of the various cellular compartments...
  74. ncbi request reprint Abundance and functional roles of intrinsic disorder in allergenic proteins and allergen representative peptides
    Bin Xue
    Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, USA
    Proteins 79:2595-606. 2011
    ..These results suggest that intrinsic disorder and MoRFs may play functional roles in IgE-mediated allergy...
  75. ncbi request reprint Solution structure and dynamics of the chimeric SH3 domains, SHH- and SHA-"Bergeracs"
    Victor P Kutyshenko
    Institute of Theoretical and Experimental Biophysics of Russian Academy of Science, 142290 Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1794:1813-22. 2009
    ..In agreement with the experimental data, the predisposition for the increased intramolecular mobility was noticeably higher in SHA...
  76. pmc Intrinsic disorder in transcription factors
    Jiangang Liu
    School of Informatics, Indiana University Purdue University Indianapolis, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
    Biochemistry 45:6873-88. 2006
    ..Overall, our data reflected the fact that eukaryotes with well-developed gene transcription machinery require transcription factor flexibility to be more efficient...
  77. ncbi request reprint Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:1829-42. 2006
    ..The results of this analysis are consistent with the conclusion that high-risk HPVs are characterized by the increased amount of intrinsic disorder in transforming proteins E6 and E7...
  78. ncbi request reprint Acid denaturation and anion-induced folding of globular proteins: multitude of equilibium partially folded intermediates
    Vladimir N Uversky
    Institite for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Protein Pept Sci 10:447-55. 2009
    ..His papers are highly cited, clearly showing that the work of Tony Fink on anion-induced folding of globular proteins made a great impact to the protein folding field...
  79. pmc Protein intrinsic disorder toolbox for comparative analysis of viral proteins
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S4. 2008
    ..This exercise provides an example showing how the combined use of intrinsic disorder predictions and relational databases provides an improved understanding of the functional and structural behaviour of viral proteins...
  80. ncbi request reprint Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasome
    Uros Midic
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, USA
    Protein Pept Lett 16:1533-47. 2009
    ..Based on these observations the human-genetic-disease-associated unfoldome was created. This minireview describes several illustrative examples of ordered and intrinsically disordered members of the human diseasome...
  81. pmc Biophysics of Parkinson's disease: structure and aggregation of alpha-synuclein
    Vladimir N Uversky
    Institite for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Protein Pept Sci 10:483-99. 2009
    ..This review focuses on the contributions of Prof. Anthony L. Fink to the field and presents some recent developments in this exciting area...
  82. pmc CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions
    Bin Xue
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W 10th Street, HS 5009, Indianapolis, IN 46202, USA
    FEBS Lett 583:1469-74. 2009
    ..A consensus binary predictor, based on the artificial neural networks, NN-CDF, was developed by using output of the individual CDFs. The consensus method outperforms the individual predictors by 4-5% in the averaged accuracy...
  83. doi request reprint Sequential melting of two hydrophobic clusters within the green fluorescent protein GFP-cycle3
    Tatiana N Melnik
    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
    Biochemistry 50:7735-44. 2011
    ....
  84. ncbi request reprint The chicken-egg scenario of protein folding revisited
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292, Moscow Region, Pushchino, Russia
    FEBS Lett 515:79-83. 2002
    ..This correlation provides experimental support for the hypothesis that hydrophobic collapse occurs simultaneously with formation of secondary structure in the early stages of the protein folding...
  85. doi request reprint Stochastic machines as a colocalization mechanism for scaffold protein function
    Bin Xue
    Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
    FEBS Lett 587:1587-91. 2013
    ..This non-covalent, modular assembly process allows the various molecular machine components to be used in multiple processes...
  86. ncbi request reprint Local flexibility facilitates oxidization of buried methionine residues
    Kuiran Xu
    Department of Molecular Medicine, University of South Florida, 12901 Bruce B Downs Blvd, MDC7, Tampa Florida 33612 4799, USA
    Protein Pept Lett 19:688-97. 2012
    ..Our data are consistent with the hypothesis that protein structural flexibility represents another important factor favoring the oxidation process...
  87. ncbi request reprint HSF transcription factor family, heat shock response, and protein intrinsic disorder
    Sandy D Westerheide
    Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Curr Protein Pept Sci 13:86-103. 2012
    ..This review analyzes the abundance and functional roles of intrinsic disorder in various heat shock transcription factors and clearly shows that the heat shock response requires HSF flexibility to be more efficient...
  88. pmc MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
    Fatemeh Miri Disfani
    Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada
    Bioinformatics 28:i75-83. 2012
    ..However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains...
  89. ncbi request reprint The disordered amino-terminus of SIMPL interacts with members of the 70-kDa heat-shock protein family
    Erin Haag Breese
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University Cancer Center, Indianapolis, Indiana 46220, USA
    DNA Cell Biol 25:704-14. 2006
    ..Understanding the regulation of SIMPL through its interaction with Hsp70/Hsc70 may serve as a novel means of modulating tumor necrosis factor alpha signaling...
  90. pmc Understanding protein non-folding
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Biochim Biophys Acta 1804:1231-64. 2010
    ..about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases?..
  91. pmc The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, The Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Biomed Biotechnol 2010:568068. 2010
    ..Some of the computational and experimental tools for the unfoldome discovery are discussed in this review...
  92. ncbi request reprint Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling
    Vladimir N Uversky
    Molecular Kinetics, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
    J Mol Recognit 18:343-84. 2005
    ....
  93. pmc Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
    Christopher J Oldfield
    Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W, 10th Street, Indianapolis, IN 46202, USA
    BMC Genomics 9:S1. 2008
    ..febs j 2005, 272:5129-5148)...
  94. ncbi request reprint Comparing and combining predictors of mostly disordered proteins
    Christopher J Oldfield
    Molecular Kinetics, Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
    Biochemistry 44:1989-2000. 2005
    ....
  95. ncbi request reprint Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatment
    Marc S Cortese
    Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Proteome Res 4:1610-8. 2005
    ..In this way, large numbers of totally unstructured proteins could be identified with minimal effort...
  96. doi request reprint Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes
    Amrita Mohan
    School of Informatics, Indiana University, Bloomington, IN 47401, USA
    Mol Biosyst 4:328-40. 2008
    ..It also provides new insights into the evolution of intrinsic disorder in the context of adapting to a parasitic lifestyle and lays the foundation for further work on the subject...
  97. ncbi request reprint Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition
    Predrag Radivojac
    School of Informatics, Indiana University, Bloomington, Indiana, USA
    Proteins 63:398-410. 2006
    ..These findings add to the growing list of examples in which intrinsically disordered protein regions are indicated to provide the basis for cell signaling and regulation...
  98. ncbi request reprint How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin
    Serge E Permyakov
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    Protein Eng Des Sel 18:425-33. 2005
    ....
  99. pmc Protein intrinsic disorder in the acetylome of intracellular and extracellular Toxoplasma gondii
    Bin Xue
    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
    Mol Biosyst 9:645-57. 2013
    ....
  100. doi request reprint Sequence microheterogeneity of parvalbumin, the major fish allergen
    Yulia S Lapteva
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1834:1607-14. 2013
    ..Overall, sequence microheterogeneity is shown to be inherent to many of PAs and likely contributes to PA allergenicity. ..