Vladimir N Uversky

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. ncbi request reprint Conformational constraints for amyloid fibrillation: the importance of being unfolded
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Biochim Biophys Acta 1698:131-53. 2004
  2. ncbi request reprint Alpha-synuclein misfolding and neurodegenerative diseases
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Protein Pept Sci 9:507-40. 2008
  3. 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
  4. pmc Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses
    Eugenie Hebrard
    UMR 1097 Résistance des Plantes aux Bio agresseurs, IRD, CIRAD, Universite de Montpellier II, BP 64501, 34394 Montpellier Cedex 5, France
    Virol J 6:23. 2009
  5. pmc Protein disorder in the human diseasome: unfoldomics of human genetic diseases
    Uros Midic
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 10:S12. 2009
  6. pmc Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions
    Siyuan Ren
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 9:S26. 2008
  7. pmc Composition Profiler: a tool for discovery and visualization of amino acid composition differences
    Vladimir Vacic
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    BMC Bioinformatics 8:211. 2007
  8. 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
  9. pmc Mysterious oligomerization of the amyloidogenic proteins
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    FEBS J 277:2940-53. 2010
  10. pmc Nanotools for megaproblems: probing protein misfolding diseases using nanomedicine modus operandi
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Proteome Res 5:2505-22. 2006

Detail Information

Publications124 found, 100 shown here

  1. ncbi request reprint Conformational constraints for amyloid fibrillation: the importance of being unfolded
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Biochim Biophys Acta 1698:131-53. 2004
    ..The inherent flexibility of such an intermediate is essential in allowing the conformational rearrangements necessary to form the core cross-beta structure of the amyloid fibril...
  2. ncbi request reprint Alpha-synuclein misfolding and neurodegenerative diseases
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Protein Pept Sci 9:507-40. 2008
    ....
  3. 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...
  4. pmc Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses
    Eugenie Hebrard
    UMR 1097 Résistance des Plantes aux Bio agresseurs, IRD, CIRAD, Universite de Montpellier II, BP 64501, 34394 Montpellier Cedex 5, France
    Virol J 6:23. 2009
    ..To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins...
  5. pmc Protein disorder in the human diseasome: unfoldomics of human genetic diseases
    Uros Midic
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 10:S12. 2009
    ..2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases...
  6. pmc Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions
    Siyuan Ren
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 9:S26. 2008
    ..Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs)...
  7. pmc Composition Profiler: a tool for discovery and visualization of amino acid composition differences
    Vladimir Vacic
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    BMC Bioinformatics 8:211. 2007
    ..Composition Profiler is a web-based tool for semi-automatic discovery of enrichment or depletion of amino acids, either individually or grouped by their physico-chemical or structural properties...
  8. 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...
  9. pmc Mysterious oligomerization of the amyloidogenic proteins
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    FEBS J 277:2940-53. 2010
    ..This review provides an overview of some topics related to soluble oligomers and represents several illustrative examples of toxic, nontoxic, productive and off-pathway amyloid oligomers...
  10. pmc Nanotools for megaproblems: probing protein misfolding diseases using nanomedicine modus operandi
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Proteome Res 5:2505-22. 2006
    ....
  11. doi request reprint Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410W 10th Street, HS 5009, Indianapolis, IN, 46202, USA
    Protein J 28:305-25. 2009
    ..This review describes some of the most characteristic features of the IDP conformational behavior and the unique response of IDPs to changes in their environment...
  12. 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?..
  13. 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...
  14. 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...
  15. pmc Amyloidogenesis of natively unfolded proteins
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Alzheimer Res 5:260-87. 2008
    ..e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis...
  16. pmc Targeting intrinsically disordered proteins in neurodegenerative and protein dysfunction diseases: another illustration of the D(2) concept
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Expert Rev Proteomics 7:543-64. 2010
    ..Some of the aspects of IDPs, as well as their roles in neurodegeneration and protein dysfunction diseases, are discussed in this article, together with the peculiarities of IDPs as potential drug targets...
  17. 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...
  18. doi request reprint Systematic analysis of tropomodulin/tropomyosin interactions uncovers fine-tuned binding specificity of intrinsically disordered proteins
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Mol Recognit 24:647-55. 2011
    ..Knowing the residues responsible for isoform-specific affinity creates a tool suitable for studying the influence of Tmod/TM interactions on sarcomere assembly in muscle cells or actin dynamics in non-muscle cells...
  19. ncbi request reprint Neuropathology, biochemistry, and biophysics of alpha-synuclein aggregation
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
    J Neurochem 103:17-37. 2007
    ..This paper provides an overview of the biochemistry, biophysics, and neuropathology of alpha-synuclein aggregation...
  20. 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...
  21. ncbi request reprint Nanoimaging in protein-misfolding and -conformational diseases
    Vladimir N Uversky
    Indiana University School of Medicine, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, IN, USA
    Nanomedicine (Lond) 2:615-43. 2007
    ....
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  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. 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...
  30. 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...
  31. 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...
  32. ncbi request reprint Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli
    Irina Kataeva
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
    J Proteome Res 4:1942-51. 2005
    ..A suggestion has been made that the Wilkinson-Harrison model is not applicable to C. thermocellum proteins because it did not account for the peculiarities of protein sequences from thermophiles...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. pmc Protein disorder is positively correlated with gene expression in Escherichia coli
    Oleg Paliy
    Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio 45435, USA
    J Proteome Res 7:2234-45. 2008
    ..coli cultures and was not caused by a small subset of genes showing exceptionally high concordance in their disorder and expression levels. Global analysis was complemented by detailed consideration of several groups of proteins...
  38. 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
    ....
  39. 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)...
  40. 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...
  41. 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...
  42. pmc Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding
    Wei Lun Hsu
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
    Protein Sci 22:258-73. 2013
    ..The small number of residues involved in MoRFs and in their modifications by ASEs or PTMs may simplify the evolvability of signaling network diversity...
  43. 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
    ....
  44. 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...
  45. 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
    ....
  46. 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...
  47. pmc High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative
    Derrick E Johnson
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Struct Biol 180:201-15. 2012
    ..Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins...
  48. 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...
  49. 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
    ....
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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...
  57. 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
    ....
  58. 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...
  59. 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
    ....
  60. 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...
  61. 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
    ....
  62. 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...
  63. 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...
  64. ncbi 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...
  65. 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...
  66. ncbi request reprint Domain coupling in a multimodular cellobiohydrolase CbhA from Clostridium thermocellum
    Irina A Kataeva
    Department of Biochemistry and Molecular Biology, A216 Fred Davison Life Sciences Complex, University of Georgia, Athens, GA 30602, USA
    FEBS Lett 579:4367-73. 2005
    ..They denatured by mechanism simpler than expected from their modular architecture. The results indicate that domain coupling in thermophilic proteins constitutes a significant stabilizing factor...
  67. 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...
  68. 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...
  69. pmc Predictive Power Estimation Algorithm (PPEA)--a new algorithm to reduce overfitting for genomic biomarker discovery
    Jiangang Liu
    Translational Science, Lilly Research Laboratories, A Division of Eli Lilly and Co, Indianapolis, Indiana, United States of America
    PLoS ONE 6:e24233. 2011
    ..Thus, we believe that the PPEA model effectively addresses the over-fitting problem and can be used to facilitate genomic biomarker discovery for predictive toxicology and drug responses...
  70. 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...
  71. 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...
  72. ncbi request reprint Cryoenzymology: enzyme action in slow motion
    Ben M Dunn
    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
    Curr Protein Pept Sci 10:408-15. 2009
    ..This review describes the contribution of Prof. Anthony L. Fink to cryoenzymology and shows how his work shaped this exciting area...
  73. 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...
  74. 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...
  75. 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...
  76. ncbi request reprint Conformational behavior and aggregation of alpha-synuclein in organic solvents: modeling the effects of membranes
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 42:2720-30. 2003
    ..At least to some extent, these conformational effects mimic those observed in the presence of phospholipid vesicles, and can explain some of the observed effects of membranes on alpha-synuclein fibrillation...
  77. ncbi request reprint Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta- and gamma-synucleins
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 277:11970-8. 2002
    ..The lack of fibrils formed by beta-synuclein is most readily explained by the absence of a stretch of hydrophobic residues from the middle region of the protein. A model for the inhibition is proposed...
  78. ncbi request reprint Stimulation of insulin fibrillation by urea-induced intermediates
    Atta Ahmad
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 279:14999-5013. 2004
    ..The correlation between fibrillation and the partially unfolded monomer indicates that the latter is a critical amyloidogenic intermediate in insulin fibrillation...
  79. ncbi request reprint Conformational behavior of human alpha-synuclein is modulated by familial Parkinson's disease point mutations A30P and A53T
    Jie Li
    Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
    Neurotoxicology 23:553-67. 2002
    ....
  80. pmc Utilization of protein intrinsic disorder knowledge in structural proteomics
    Christopher J Oldfield
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Biochim Biophys Acta 1834:487-98. 2013
    ..Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed...
  81. 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)...
  82. 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
    ....
  83. 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...
  84. ncbi request reprint Biophysical constraints for protein structure prediction
    Olga Tcherkasskaya
    Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington DC, 20007, USA
    J Proteome Res 2:37-42. 2003
    ..In this regard, our analysis of 180 proteins in different conformational states allows prediction of the overall protein dimension based on the chain length, i.e., the protein molecular weight, with an accuracy of 10%...
  85. ncbi request reprint Structural transformations of oligomeric intermediates in the fibrillation of the immunoglobulin light chain LEN
    Pierre O Souillac
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 42:8094-104. 2003
    ....
  86. ncbi request reprint Characterization of the non-fibrillar α-synuclein oligomers
    Dong Pyo Hong
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Protein Pept Lett 18:230-40. 2011
    ..These findings suggest that these soluble oligomers are important players in the multi-pathway aggregation of α-synuclein and should be taken into account in studies on the molecular mechanisms of this protein fibrillation...
  87. 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...
  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. pmc A comparative analysis of viral matrix proteins using disorder predictors
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Virol J 5:126. 2008
    ..9 (Suppl. 2), S4) revealed that HIV matrix protein p17 possesses especially high levels of predicted intrinsic disorder (PID). In this study, we analyzed the PID patterns in matrix proteins of viruses related and unrelated to HIV-1...
  90. pmc Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Virol J 6:69. 2009
    ..The 1918 H1N1 virus was a highly virulent strain that killed 20-50 million people. The cause of its virulence remains poorly understood...
  91. ncbi request reprint Polymeric aspects of protein folding: a brief overview
    Olga Tcherkasskaya
    Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA
    Protein Pept Lett 10:239-45. 2003
    ..Several implications of these findings to protein folding are discussed...
  92. ncbi request reprint Partially folded intermediates in insulin fibrillation
    Atta Ahmad
    Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
    Biochemistry 42:11404-16. 2003
    ....
  93. ncbi request reprint Early events in the fibrillation of monomeric insulin
    Atta Ahmad
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 280:42669-75. 2005
    ..Both have significantly non-native conformations, and indicate that fibrillation occurs from a beta-rich structure significantly distinct from the native fold...
  94. pmc Guiding protein aggregation with macromolecular crowding
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Biochemistry 47:8993-9006. 2008
    ....
  95. ncbi request reprint Effect of association state and conformational stability on the kinetics of immunoglobulin light chain amyloid fibril formation at physiological pH
    Pierre O Souillac
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    J Biol Chem 277:12657-65. 2002
    ..Thus, increasing concentrations of urea, by triggering dissociation of dimeric LEN, lead to increased rates of fibrillation...
  96. ncbi request reprint Synergistic effects of pesticides and metals on the fibrillation of alpha-synuclein: implications for Parkinson's disease
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
    Neurotoxicology 23:527-36. 2002
    ..We propose a model in which environmentalfactors in conjunction with genetic susceptibility may form the underlying molecular basis for idiopathic PD...
  97. ncbi request reprint Methionine oxidation inhibits fibrillation of human alpha-synuclein in vitro
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    FEBS Lett 517:239-44. 2002
    ..This inhibitory effect was eliminated at low pH. The addition of oxidized alpha-synuclein to the unoxidized form led to a substantial inhibition of alpha-synuclein fibrillation...
  98. ncbi request reprint Role of protein-water interactions and electrostatics in alpha-synuclein fibril formation
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 43:3289-300. 2004
    ..Moderate concentrations of anions affected both the rates of nucleation and the elongation of alpha-synuclein fibrillation, primarily via their effect on the interaction of the protein with water...
  99. ncbi request reprint Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA
    Irina A Kataeva
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 7229, USA
    Protein Eng Des Sel 17:759-69. 2004
    ..The results indicate that inactivation of the GH9 module occurs as a result of multiple structural disturbances finally affecting the topology of the catalytic center...
  100. ncbi request reprint Certain metals trigger fibrillation of methionine-oxidized alpha-synuclein
    Ghiam Yamin
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 278:27630-5. 2003
    ..These findings indicate that a combination of oxidative stress and environmental metal pollution could play an important role in triggering the fibrillation of alpha-synuclein and thus possibly Parkinson's disease...
  101. ncbi request reprint Role of individual methionines in the fibrillation of methionine-oxidized alpha-synuclein
    Mark J Hokenson
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 43:4621-33. 2004
    ..The presence of zinc was shown to overcome the Met oxidation-induced inhibition. Interestingly, substitution of Met by Leu led to increased propensity for aggregation (soluble oligomers) but slower formation of fibrils...