V N Uversky

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. pmc The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, University of South Florida Tampa, FL 33612, USA Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
    F1000 Biol Rep 5:1. 2013
  5. ncbi request reprint Attachment of LcrV from Yersinia pestis at dual binding sites to human TLR-2 and human IFN-gamma receptor
    Vyacheslav M Abramov
    Institute of Immunological Engineering, 142380 Lyubuchany, Russia
    J Proteome Res 6:2222-31. 2007
  6. doi request reprint Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'
    Victor P Kutyshenko
    a Institute of Theoretical and Experimental Biophysics of Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
    J Biomol Struct Dyn 32:257-72. 2014
  7. 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
  8. ncbi request reprint Why are "natively unfolded" proteins unstructured under physiologic conditions?
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Proteins 41:415-27. 2000
  9. 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
  10. ncbi request reprint What does it mean to be natively unfolded?
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow, Russia
    Eur J Biochem 269:2-12. 2002

Detail Information

Publications116 found, 100 shown here

  1. 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
    ....
  2. 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...
  3. 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)...
  4. pmc The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, University of South Florida Tampa, FL 33612, USA Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
    F1000 Biol Rep 5:1. 2013
    ..Finally, we discuss whether 'intrinsically disordered protein' (IDP) represents a useful new concept...
  5. ncbi request reprint Attachment of LcrV from Yersinia pestis at dual binding sites to human TLR-2 and human IFN-gamma receptor
    Vyacheslav M Abramov
    Institute of Immunological Engineering, 142380 Lyubuchany, Russia
    J Proteome Res 6:2222-31. 2007
    ..The ability of LcrV to utilize human IFN-gamma (a major inflammatory effector of innate immunity) to minimize inflammation is insidious and may account in part for the severe symptoms of plague in man...
  6. doi request reprint Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'
    Victor P Kutyshenko
    a Institute of Theoretical and Experimental Biophysics of Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
    J Biomol Struct Dyn 32:257-72. 2014
    ....
  7. 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. ..
  8. ncbi request reprint Why are "natively unfolded" proteins unstructured under physiologic conditions?
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Proteins 41:415-27. 2000
    ....
  9. 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...
  10. ncbi request reprint What does it mean to be natively unfolded?
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow, Russia
    Eur J Biochem 269:2-12. 2002
    ..Finally, in comparison with the globular proteins, natively unfolded polypeptides possess 'turn out' responses to changes in the environment, as their structural complexities increase at high temperature or at extreme pH...
  11. ncbi request reprint A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences Pushchino, Moscow Region, Russia
    J Biomol Struct Dyn 21:211-34. 2003
    ..The peculiarities of this astonishing conformational behavior are analyzed to shed light on structural plasticity of this protein-chameleon...
  12. ncbi request reprint Amino acid determinants of alpha-synuclein aggregation: putting together pieces of the puzzle
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
    FEBS Lett 522:9-13. 2002
    ....
  13. 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...
  14. 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...
  15. ncbi request reprint Zn(2+)-mediated structure formation and compaction of the "natively unfolded" human prothymosin alpha
    V N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, 142292, Russia
    Biochem Biophys Res Commun 267:663-8. 2000
    ..It is possible that these structural changes may be important for the function of this protein...
  16. ncbi request reprint Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH
    V N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
    Biochemistry 38:15009-16. 1999
    ..It is possible that such conformational changes may be associated with the protein function...
  17. ncbi request reprint Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go?
    V N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
    Cell Mol Life Sci 60:1852-71. 2003
    ..This choice is dictated by the peculiarities of amino acid sequence and/or by the pressure of environmental factors. The aim of the present review is to outline some interesting features of these three routes...
  18. 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...
  19. pmc Natively unfolded proteins: a point where biology waits for physics
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
    Protein Sci 11:739-56. 2002
    ..In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed...
  20. 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...
  21. 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...
  22. ncbi request reprint Neurotoxicant-induced animal models of Parkinson's disease: understanding the role of rotenone, maneb and paraquat in neurodegeneration
    Vladimir N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
    Cell Tissue Res 318:225-41. 2004
    ..Suggested neurotoxicity mechanisms of these chemicals are considered, and the major lessons learned from the analysis of pesticide-induced PD models are discussed...
  23. ncbi request reprint Accelerated alpha-synuclein fibrillation in crowded milieu
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
    FEBS Lett 515:99-103. 2002
    ..Our results suggest that the major factor responsible for the accelerated fibrillation under crowded conditions is the excluded volume...
  24. ncbi request reprint Trimethylamine-N-oxide-induced folding of alpha-synuclein
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    FEBS Lett 509:31-5. 2001
    ..The latter conformation was significantly helical and probably represents the physiologically folded form of the protein...
  25. ncbi request reprint Effect of environmental factors on the kinetics of insulin fibril formation: elucidation of the molecular mechanism
    L Nielsen
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 40:6036-46. 2001
    ..A kinetic model, involving the association of monomeric partially folded intermediates, whose concentration is stimulated by the air-water interface, leading to formation of the critical nucleus and thence fibrils, is proposed...
  26. ncbi request reprint Pesticides directly accelerate the rate of alpha-synuclein fibril formation: a possible factor in Parkinson's disease
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    FEBS Lett 500:105-8. 2001
    ..These observations suggest one possible underlying molecular basis for Parkinson's disease...
  27. 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
    ....
  28. ncbi request reprint Structural and functional similarity between Yersinia pestis capsular protein Caf1 and human interleukin-1 beta
    V M Abramov
    Institute of Immunological Engineering, 142380 Lyubuchany, Moscow Region, Russia
    Biochemistry 40:6076-84. 2001
    ..pestis Yop virulon. Thus, these results help to explain the importance of Caf1 in the interaction of Y. pestis with the host immune system...
  29. ncbi request reprint Effect of familial Parkinson's disease point mutations A30P and A53T on the structural properties, aggregation, and fibrillation of human alpha-synuclein
    J Li
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 40:11604-13. 2001
    ..This increased propensity of these mutants to aggregate, relative to wild-type alpha-synuclein, would account for the correlation of these mutations with Parkinson's disease...
  30. ncbi request reprint Can grafting of an octapeptide improve the structure of a de novo protein?
    I Y Aphasizheva
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
    FEBS Lett 425:101-4. 1998
    ..This means that the structure of the artificial protein albebetin can be improved by a simple procedure of octapeptide grafting to its N-terminus...
  31. ncbi request reprint Metal-triggered structural transformations, aggregation, and fibrillation of human alpha-synuclein. A possible molecular NK between Parkinson's disease and heavy metal exposure
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 276:44284-96. 2001
    ..The results indicate that low concentrations of some metals can directly induce alpha-synuclein fibril formation...
  32. ncbi request reprint Accelerated fibrillation of alpha-synuclein induced by the combined action of macromolecular crowding and factors inducing partial folding
    L A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Curr Alzheimer Res 6:252-60. 2009
    ....
  33. 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...
  34. ncbi request reprint Stabilization of partially folded conformation during alpha-synuclein oligomerization in both purified and cytosolic preparations
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 276:43495-8. 2001
    ..These data suggest that partially folded alpha-synuclein, which is unstable in the monomeric form, is stabilized by self-assembly and that these oligomers may evolve into the fibril nucleus...
  35. ncbi request reprint Probing the mechanism of insulin fibril formation with insulin mutants
    L Nielsen
    University of California-Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA 95064, USA
    Biochemistry 40:8397-409. 2001
    ..A model for insulin fibril formation is proposed in which the formation of a partially folded intermediate is the precursor for associated species on the pathway to fibril formation...
  36. 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...
  37. 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...
  38. pmc Circularly permuted dihydrofolate reductase possesses all the properties of the molten globule state, but can resume functional tertiary structure by interaction with its ligands
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russia
    Protein Sci 5:1844-51. 1996
    ..Interaction of permuted protein with ligands leads to the structural adjustment and formation of active protein molecules...
  39. ncbi request reprint Rigidity of human alpha-fetoprotein tertiary structure is under ligand control
    V N Uversky
    Institutes of Protein Research, Russian Academy of Sciences, Moscow Region
    Biochemistry 36:13638-45. 1997
    ..In contrast, processes of HSA denaturation and unfolding are completely reversible. Release of ligands from HSA results only in a small decrease in stability but not transformation into the molten globule state...
  40. 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...
  41. 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...
  42. 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...
  43. ncbi request reprint Heparin and other glycosaminoglycans stimulate the formation of amyloid fibrils from alpha-synuclein in vitro
    Jeffrey A Cohlberg
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 41:1502-11. 2002
    ..Since there is some evidence that Lewy bodies may contain GAGs, these observations may be very relevant in the context of the etiology of Parkinson's disease...
  44. ncbi request reprint Effect of salts on the stability and folding of staphylococcal nuclease
    C Nishimura
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 40:2113-28. 2001
    ..The results suggest that, in general, marginally stable globular proteins will be significantly stabilized by salts under conditions where they have a substantial net charge...
  45. ncbi request reprint Protein engineering of de novo protein with predesigned structure and activity
    D A Dolgikh
    Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
    Appl Biochem Biotechnol 61:85-96. 1996
    ..It activates the blast transformation reaction of thymocyte cells even more efficiently than human interferon at low concentrations...
  46. ncbi request reprint Is Congo red an amyloid-specific dye?
    R Khurana
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    J Biol Chem 276:22715-21. 2001
    ..The fact that Congo red binds to native, partially folded conformations and amyloid fibrils of several proteins shows that it must be used with caution as a diagnostic test for the presence of amyloid fibrils in vitro...
  47. ncbi request reprint Conformational prerequisites for alpha-lactalbumin fibrillation
    John Goers
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 41:12546-51. 2002
    ....
  48. ncbi request reprint Recoverin is a zinc-binding protein
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    J Proteome Res 2:51-7. 2003
    ..Possible implications of these findings to the functioning of recoverin are discussed...
  49. ncbi request reprint Conformational prerequisites for formation of amyloid fibrils from histones
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    J Mol Biol 342:1305-24. 2004
    ..HCl increased the rate of fibrillation, although much less than NaCl. Different ions also differentially affected the rate of nucleation and the rate of fibril elongation...
  50. ncbi request reprint Forcing nonamyloidogenic beta-synuclein to fibrillate
    Ghiam Yamin
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 44:9096-107. 2005
    ..These new findings demonstrate the potential effect of environmental pollutants in generating an amyloidogenic, and potentially neurotoxic, conformation, in an otherwise benign protein...
  51. ncbi request reprint Nuclear localization of alpha-synuclein and its interaction with histones
    John Goers
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 42:8465-71. 2003
    ..e., injections of the herbicide paraquat). These observations indicate that translocation into the nucleus and binding with histones represent potential mechanisms underlying alpha-synuclein pathophysiology...
  52. ncbi request reprint Ligand-free form of human alpha-fetoprotein: evidence for the molten globule state
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
    FEBS Lett 410:280-4. 1997
    ..e., native protein molecule cannot be reconstituted from the ligand-free form of AFP by adding back ligands. A possible functional role of such a structural transformation is discussed...
  53. ncbi request reprint Structural properties of staphylococcal nuclease in oligomeric A-forms
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142292 Russia
    Biochemistry (Mosc) 63:463-9. 1998
    ..This suggests that association of a protein molecule in partially folded conformations can be an additional structure forming factor...
  54. pmc Association-induced folding of globular proteins
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 95:5480-3. 1998
    ..In addition, more globularity, as determined from Kratky plots of small-angle x-ray scattering data, was also noted in the associated states...
  55. ncbi request reprint Partially folded conformations in the folding pathway of bovine carbonic anhydrase II: a fluorescence spectroscopic analysis
    N A Bushmarina
    Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia
    Chembiochem 2:813-21. 2001
    ....
  56. ncbi request reprint Role of conformational changes in the heme-dependent regulation of human soluble guanylate cyclase
    D N Kosarikov
    Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132-4163, USA
    J Inorg Biochem 87:267-76. 2001
    ..This change is absent upon binding of NO, YC-1 or ODQ alone. Using this and previous data, we propose a working model for the mechanism of activation of sGC by NO and YC-1 and inhibition by ODQ...
  57. pmc Metal-controlled interdomain cooperativity in parvalbumins
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow, Russia
    Cell Calcium 46:163-75. 2009
    ....
  58. 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...
  59. 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...
  60. 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...
  61. pmc Structural characteristics of alpha-synuclein oligomers stabilized by the flavonoid baicalein
    Dong Pyo Hong
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    J Mol Biol 383:214-23. 2008
    ..This effect was rather similar to that of the monomeric protein, suggesting that targeted stabilization of certain alpha-synuclein oligomers might offer a potential strategy for the development of novel Parkinson's disease therapies...
  62. ncbi request reprint The effect of macromolecular crowding on protein aggregation and amyloid fibril formation
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    J Mol Recognit 17:456-64. 2004
    ..Pesticides and metals, which are linked to increased risk of Parkinson's disease by epidemiological studies, are shown to accelerate alpha-synuclein fibrillation under conditions of molecular crowding...
  63. ncbi request reprint Elucidation of the molecular mechanism during the early events in immunoglobulin light chain amyloid fibrillation. Evidence for an off-pathway oligomer at acidic pH
    Pierre O Souillac
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    J Biol Chem 277:12666-79. 2002
    ....
  64. 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...
  65. 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
    ....
  66. 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
    ....
  67. ncbi request reprint Evidence for a partially folded intermediate in alpha-synuclein fibril formation
    V N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 276:10737-44. 2001
    ..We propose a model for the fibrillation of alpha-synuclein in which the first step is the conformational transformation of the natively unfolded protein into the aggregation-competent partially folded intermediate...
  68. ncbi request reprint Mutating aspartate in the calcium-binding site of alpha-lactalbumin: effects on the protein stability and cation binding
    S E Permyakov
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    Protein Eng 14:785-9. 2001
    ..These results reaffirm that alanine substitution in site specific mutagenesis is not always a prudent choice. Substitutions must be conservative with only minimal changes in functional groups and side-chain volume...
  69. ncbi request reprint Structural effect of association on protein molecules in partially folded intermediates
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142292 Russia
    Biochemistry (Mosc) 63:456-62. 1998
    ..It is shown that association of non-native conformations of the protein molecule can be an additional structuring factor. The corresponding folding schemes and phase diagrams are suggested...
  70. ncbi request reprint Hyperphosphorylation induces structural modification of tau-protein
    V N Uversky
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region
    FEBS Lett 439:21-5. 1998
    ....
  71. pmc The effect of membranes on the in vitro fibrillation of an amyloidogenic light-chain variable-domain SMA
    Xiaoyun Meng
    Department of Chemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    J Mol Biol 381:989-99. 2008
    ..Thus, membranes may have significant effects on light-chain fibrillation and may contribute to the site selectivity observed in AL amyloidosis...
  72. 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...
  73. ncbi request reprint Human soluble guanylate cyclase: functional expression, purification and structural characterization
    D N Kosarikov
    Department of Chemistry and Biochemistry, San Francisco State University, California, USA
    Arch Biochem Biophys 388:185-97. 2001
    ..We used two hierarchical neural network methods to predict the secondary structure of sGC and found it to be consistent with the observed CD spectrum of sGC...
  74. pmc Methionine oxidation stabilizes non-toxic oligomers of alpha-synuclein through strengthening the auto-inhibitory intra-molecular long-range interactions
    Wenbo Zhou
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Biochim Biophys Acta 1802:322-30. 2010
    ..Finally, oxidation of methionines by H2O2 greatly inhibited alpha-Syn fibrillation in vitro, leading to the formation of relatively stable oligomers, which are not toxic to dopaminergic and GABAergic neurons...
  75. doi request reprint Apo-parvalbumin as an intrinsically disordered protein
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    Proteins 72:822-36. 2008
    ..The native rigid tertiary structure of PA is attained upon association of one (alpha-PA) or two (beta-PA) calcium ions per protein molecule, as follows from calorimetric and calcium titration data...
  76. 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...
  77. doi request reprint Molecular mechanisms underlying the flavonoid-induced inhibition of alpha-synuclein fibrillation
    Xiaoyun Meng
    Department of Chemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Biochemistry 48:8206-24. 2009
    ..The flavonoids inhibiting alpha-synuclein fibrillation and stabilizing the protein monomeric conformation can serve as a model for the development of therapeutic drugs in combating Parkinson's disease...
  78. ncbi request reprint Human alpha-fetoprotein as a Zn(2+)-binding protein. Tight cation binding is not accompanied by global changes in protein structure and stability
    Serge E Permyakov
    Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1586:1-10. 2002
    ..Such strong interactions without major structural consequences are highly unusual, and AFP may therefore be the first characterized representative of a new class of ligand-binding proteins...
  79. ncbi request reprint Ultraviolet illumination-induced reduction of alpha-lactalbumin disulfide bridges
    Eugene A Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    Proteins 51:498-503. 2003
    ..The effect observed has to be taken into account in any UV-region spectral studies of alpha-lactalbumin...
  80. ncbi request reprint Nitration inhibits fibrillation of human alpha-synuclein in vitro by formation of soluble oligomers
    Ghiam Yamin
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    FEBS Lett 542:147-52. 2003
    ..These observations suggest that nitration of soluble alpha-synuclein may be a protective factor in PD, rather than a causative one...
  81. ncbi request reprint Effects of nitration on the structure and aggregation of alpha-synuclein
    Vladimir N Uversky
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Brain Res Mol Brain Res 134:84-102. 2005
    ..The addition of nitrated alpha-synuclein inhibited fibrillation of non-modified alpha-synuclein at neutral pH. Potential implications of these findings to the etiology of Parkinson's disease are discussed...
  82. pmc At low concentrations, 3,4-dihydroxyphenylacetic acid (DOPAC) binds non-covalently to alpha-synuclein and prevents its fibrillation
    Wenbo Zhou
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    J Mol Biol 388:597-610. 2009
    ....
  83. 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...
  84. ncbi request reprint No need to be HAMLET or BAMLET to interact with histones: binding of monomeric alpha-lactalbumin to histones and basic poly-amino acids
    Serge E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
    Biochemistry 43:5575-82. 2004
    ..The data indicate that alpha-lactalbumin can be used as a basis for the design of antitumor agents, acting through disorganization of chromatin structure due to interaction between alpha-LA and histone proteins...
  85. doi request reprint Analysis of Ca2+/Mg2+ selectivity in alpha-lactalbumin and Ca(2+)-binding lysozyme reveals a distinct Mg(2+)-specific site in lysozyme
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    Proteins 78:2609-24. 2010
    ..The Ca(2+)/Mg(2+) selectivity of Mg(2+)-site of EQL is below an order of magnitude. EQL exhibits a distinct Mg(2+)-specific site, probably arising as an adaptation to the extracellular environment...
  86. pmc Polycation-induced oligomerization and accelerated fibrillation of human alpha-synuclein in vitro
    John Goers
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Protein Sci 12:702-7. 2003
    ..The results illustrate the potential critical role of electrostatic interactions in protein aggregation, and the potential role of naturally occurring polycations in modulating alpha-synuclein aggregation...
  87. 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...
  88. pmc Smoking and Parkinson's disease: does nicotine affect alpha-synuclein fibrillation?
    Dong Pyo Hong
    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Biochim Biophys Acta 1794:282-90. 2009
    ..This information can be used to understand the molecular mechanism of the nicotine and hydroquinone action to develop therapeutic solutions for PD...
  89. ncbi request reprint Effect of natural ligands on the structural properties and conformational stability of proteins
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142292 Russia
    Biochemistry (Mosc) 63:420-33. 1998
    ..Ligand-free forms of protein are classified from the viewpoint of structural property changes of a protein molecule...
  90. ncbi request reprint Equilibrium unfolding of partially folded staphylococcal nuclease A2- and A3-forms is accompanied by the formation of an intermediate state
    V N Uversky
    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142292 Russia
    Biochemistry (Mosc) 63:470-5. 1998
    ..A close structural similarity (including tendency for association) is shown between this intermediate and the least ordered A1-form, induced in the acid-unfolded nuclease by moderate sulfate or chloride concentrations...
  91. ncbi request reprint Recoverin as a redox-sensitive protein
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
    J Proteome Res 6:1855-63. 2007
    ..The Ca2+ modulated susceptibility of the recoverin thiol to reversible oxidation may be of potential importance for functioning of recoverin in photoreceptor cells...
  92. ncbi request reprint Conversion of human alpha-lactalbumin to an apo-like state in the complexes with basic poly-amino acids: toward understanding of the molecular mechanism of antitumor action of HAMLET
    Serge E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
    J Proteome Res 4:564-9. 2005
    ..The requirement for efficient conversion of alpha-lactalbumin to the LAMPA state is a poly-Lys(Arg) chain consisting of several tens of amino acid residues...
  93. 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...
  94. pmc Effect of methionine oxidation on the structural properties, conformational stability, and aggregation of immunoglobulin light chain LEN
    Dongmei Hu
    Department of Chemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 47:8665-77. 2008
    ..The methionine-oxidized LEN preferred to form amorphous aggregates instead of fibrils. The results indicated that the LEN oxidation may play an important role in amorphous deposition of the protein, but not in its fibrillation...
  95. 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...
  96. ncbi request reprint Native-like secondary structure of molten globules
    Konstantin S Vassilenko
    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
    Biochim Biophys Acta 1594:168-77. 2002
    ..9 for both the alpha-helix and the beta-structure. Thus, the secondary structure of proteins in the molten globule state is close to that in the native state...
  97. ncbi request reprint Peculiarities of copper binding to alpha-synuclein
    Atta Ahmad
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA
    J Biomol Struct Dyn 29:825-42. 2012
    ..Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding...
  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 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...
  100. ncbi request reprint Local flexibility in molecular function paradigm
    Jag Bhalla
    Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, Washington, DC 20007, USA
    Mol Cell Proteomics 5:1212-23. 2006
    ..Furthermore the local flexibility in protein molecules appears to be dependent on the molecular confinement and is essentially larger in extracellular proteins...
  101. 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...