The Protein Physics Lab
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Selected publications of the
Theoretical and Experimental teams

  1. Galzitskaya OV, Ivankov DN, Finkelstein AV. Folding nuclei in proteins. FEBS Lett. 2001 Feb 2;489(2-3):113-8. Review. PMID: 11165233

  2. Reva BA, Finkelstein AV, Skolnick J. Derivation and testing residue-residue mean-force potentials for use in protein structure recognition. Methods Mol Biol. 2000;143:155-74. No abstract available. PMID: 11084906

  3. Mirny LA, Finkelstein AV, Shakhnovich EI. Statistical significance of protein structure prediction by threading. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9978-83. PMID: 10954732

  4. Galzitskaya OV, Skoogarev AV, Ivankov DN, Finkelstein AV. Folding nuclei in 3D protein structures. Pac Symp Biocomput. 2000;:131-42. PMID: 10902163

  5. Rykunov DS, Lobanov MY, Finkelstein AV. Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures. Proteins. 2000 Aug 15;40(3):494-501. PMID: 10861941

  6. Galzitskaya OV, Surin AK, Nakamura H. Optimal region of average side-chain entropy for fast protein folding. Protein Sci. 2000 Mar;9(3):580-6. PMID: 10752620

  7. Galzitskaya O, Caflisch A. Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations. J Mol Graph Model. 1999 Feb;17(1):19-27. PMID: 10660907

  8. Galzitskaya OV, Finkelstein AV. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11299-304. PMID: 10500171

  9. Reva BA, Skolnick J, Finkelstein AV. Averaging interaction energies over homologs improves protein fold recognition in gapless threading. Proteins. 1999 May 15;35(3):353-9. PMID: 10328270

  10. Reva BA, Rykunov DS, Finkelstein AV, Skolnick J. Optimization of protein structure on lattices using a self-consistent field approach. J Comput Biol. 1998 Fall;5(3):531-8. PMID: 9773348

  11. Badretdinov AYa, Finkelstein AV. How homologs can help to predict protein folds even though they cannot be predicted for individual sequences. J Comput Biol. 1998 Fall;5(3):369-76. PMID: 9773338

  12. Reva BA, Finkelstein AV, Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Fold Des. 1998;3(2):141-7. PMID: 9565758

  13. Galzitskaya O, Finkelstein AV. Folding rate dependence on the chain length of RNA-like heteropolymers. Fold Des. 1998;3(2):69-78. PMID: 9565751

  14. Reva BA, Finkelstein AV, Sanner M, Olson AJ, Skolnick J. Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein Eng. 1997 Oct;10(10):1123-30. PMID: 9488137

  15. Reva BA, Finkelstein AV, Sanner MF, Olson AJ. Residue-residue mean-force potentials for protein structure recognition. Protein Eng. 1997 Aug;10(8):865-76. PMID: 9415437

  16. Finkelstein AV. Can protein unfolding simulate protein folding? Protein Eng. 1997 Aug;10(8):843-5. No abstract available. PMID: 9415434

  17. Reva BA, Finkelstein AV, Sanner MF, Olson AJ. Accurate mean-force pairwise-residue potentials for discrimination of protein folds. Pac Symp Biocomput. 1997;:373-84. PMID: 9390307

  18. Abdullaev ZK, Latypov RF, Badretdinov AY, Dolgikh DA, Finkelstein AV, Uversky VN, Kirpichnikov MP. S6 permutein shows that the unusual target topology is not responsible for the absence of rigid tertiary structure in de novo protein albebetin. FEBS Lett. 1997 Sep 8;414(2):243-6. PMID: 9315694

  19. Finkelstein AV. Protein structure: what is it possible to predict now? Curr Opin Struct Biol. 1997 Feb;7(1):60-71. Review. PMID: 9032057

  20. Finkelstein AV, Badretdinov AYa. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. Fold Des. 1997;2(2):115-21. PMID: 9135984

  21. Reva BA, Finkelstein AV, Rykunov DS, Olson AJ. Building self-avoiding lattice models of proteins using a self-consistent field optimization. Proteins. 1996 Sep;26(1):1-8. PMID: 8880925

  22. Reva BA, Finkelstein AV, Sanner MF, Olson AJ. Adjusting potential energy functions for lattice models of chain molecules. Proteins. 1996 Jul;25(3):379-88. PMID: 8844872

  23. Reva BA, Finkelstein AV. Search for the most stable folds of protein chains: II. Computation of stable architectures of beta-proteins using a self-consistent molecular field theory. Protein Eng. 1996 May;9(5):399-411. PMID: 8795040

  24. Finkelstein AV, Reva BA. Search for the most stable folds of protein chains: I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction. Protein Eng. 1996 May;9(5):387-97. PMID: 8795039

  25. Finkelstein AV, Gutin AM, Badretdinov AY. Perfect temperature for protein structure prediction and folding. Proteins. 1995 Oct;23(2):151-62. PMID: 8592697

  26. Finkelstein AV, Badretdinov AYa, Gutin AM. Why do protein architectures have Boltzmann-like statistics? Proteins. 1995 Oct;23(2):142-50. PMID: 8592696

  27. Galzitskaya OV, Finkelstein AV. Folding of chains with random and edited sequences: similarities and differences. Protein Eng. 1995 Sep;8(9):883-92. PMID: 8746726

  28. Rykunov DS, Reva BA, Finkelstein AV. Accurate general method for lattice approximation of three-dimensional structure of a chain molecule. Proteins. 1995 Jun;22(2):100-9. PMID: 7567958

  29. Finkelstein AV. Predicted beta-structure stability parameters under experimental test. Protein Eng. 1995 Feb;8(2):207-9. PMID: 7630890

  30. Reva BA, Rykunov DS, Olson AJ, Finkelstein AV. Constructing lattice models of protein chains with side groups. J Comput Biol. 1995 Winter;2(4):527-35. PMID: 8634904

  31. Finkelstein AV, Gutin AM, Badretdinov AYa. Boltzmann-like statistics of protein architectures. Origins and consequences. Subcell Biochem. 1995;24:1-26. Review. No abstract available. PMID: 7900172

  32. Chemeris VV, Dolgikh DA, Fedorov AN, Finkelstein AV, Kirpichnikov MP, Uversky VN, Ptitsyn OB. A new approach to artificial and modified proteins: theory-based design, synthesis in a cell-free system and fast testing of structural properties by radiolabels. Protein Eng. 1994 Aug;7(8):1041-52. PMID: 7809031

  33. Kuwajima K, Semisotnov GV, Finkelstein AV, Sugai S, Ptitsyn OB. Secondary structure of globular proteins at the early and the final stages in protein folding. FEBS Lett. 1993 Nov 22;334(3):265-8. PMID: 8243629

  34. Finkelstein AV, Gutun AM, Badretdinov AYa. Why are the same protein folds used to perform different functions? FEBS Lett. 1993 Jun 28;325(1-2):23-8. Review. PMID: 8513888

  35. Finkelstein AV, Nakamura H. Weak points of antiparallel beta-sheets. How are they filled up in globular proteins? Protein Eng. 1993 Jun;6(4):367-72. PMID: 8332593

  36. Finkelstein AV, Roytberg MA. Computation of biopolymers: a general approach to different problems. Biosystems. 1993;30(1-3):1-19. PMID: 7690608

  37. Reva BA, Finkelstein AV. A new approach to the design of a sequence with the highest affinity for a molecular surface. Protein Eng. 1992 Oct;5(7):625-8. PMID: 1480616

  38. Finkelstein AV, Reva BA. Search for the stable state of a short chain in a molecular field. Protein Eng. 1992 Oct;5(7):617-24. PMID: 1282717

  39. Fedorov AN, Dolgikh DA, Chemeris VV, Chernov BK, Finkelstein AV, Schulga AA, Alakhov YuB, Kirpichnikov MP, Ptitsyn OB. De novo design, synthesis and study of albebetin, a polypeptide with a predetermined three-dimensional structure. Probing the structure at the nanogram level. J Mol Biol. 1992 Jun 20;225(4):927-31. PMID: 1613798

  40. Sander C, Vriend G, Bazan F, Horovitz A, Nakamura H, Ribas L, Finkelstein AV, Lockhart A, Merkl R, Perry LJ, et al. Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins. 1992 Feb;12(2):105-10. PMID: 1603799

  41. Finkelstein AV, Reva BA. A search for the most stable folds of protein chains. Nature. 1991 Jun 6;351(6326):497-9. PMID: 2046752

  42. Finkelstein AV. Rate of beta-structure formation in polypeptides. Proteins. 1991;9(1):23-7. PMID: 2017433

  43. Finkelstein AV, Badretdinov AY, Ptitsyn OB. Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins. 1991;10(4):287-99. PMID: 1946339

  44. Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem. 1990;59:1007-39. Review. No abstract available. PMID: 2197975

  45. Finkelstein AV, Janin J. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 1989 Oct;3(1):1-3. No abstract available. PMID: 2813338

  46. Finkelstein AV, Shakhnovich EI. Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution. Biopolymers. 1989 Oct;28(10):1681-94. PMID: 2597724

  47. Shakhnovich EI, Finkelstein AV. Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition. Biopolymers. 1989 Oct;28(10):1667-80. PMID: 2597723

  48. Ptitsyn OB, Finkelstein AV. Prediction of protein secondary structure based on physical theory. Histones. Protein Eng. 1989 Mar;2(6):443-7. PMID: 2710781

  49. Murzin AG, Finkelstein AV. General architecture of the alpha-helical globule. J Mol Biol. 1988 Dec 5;204(3):749-69. PMID: 3225849

  50. Mesyanzhinov VV, Peletskaya EN, Zhdanov VM, Efimov AV, Finkelstein AV, Ivanovsky DI. Prediction of secondary structure, spatial organization and distribution of antigenic determinants for hepatitis A virus proteins. J Biomol Struct Dyn. 1987 Oct;5(2):447-58. PMID: 2482756

  51. Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol. 1987;50(3):171-90. Review. No abstract available. PMID: 3332386

  52. Ptitsyn OB, Finkelstein AV, Murzin AG. Structural model for interferons. FEBS Lett. 1985 Jul 8;186(2):143-8. PMID: 3924661

  53. Finkelstein AV, Bendzko P, Rapoport TA. Recognition of signal sequences. FEBS Lett. 1983 Sep 19;161(2):176-9. PMID: 6617872

  54. Ptitsyn OB, Finkelstein AV. Theory of protein secondary structure and algorithm of its prediction. Biopolymers. 1983 Jan;22(1):15-25. No abstract available. PMID: 6673754

  55. Ptitsyn OB, Finkelstein AV, Kirpichnikov MP, Skryabin KG. cI and lexA repressors consist of three cro-like domains. FEBS Lett. 1982 Oct 4;147(1):11-5. No abstract available. PMID: 6216121

  56. Ptitsyn OB, Finkelstein AV. Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding? Q Rev Biophys. 1980 Aug;13(3):339-86. Review. No abstract available. PMID: 7012894

  57. Ptitsyn OB, Finkelstein AV, Falk P. Principal folding pathway and topology of all-beta proteins. FEBS Lett. 1979 May 1;101(1):1-5. No abstract available. PMID: 446719

  58. Finkelstein AV. Did the primitive ribosomal RNA code primitive ribosomal protein? FEBS Lett. 1977 Oct 15;82(2):169-71. No abstract available. PMID: 913584

  59. Finkelstein AV. Theory of protein molecule self-organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain. Biopolymers. 1977 Mar;16(3):525-9. No abstract available. PMID: 843600

  60. Finkelstein AV, Ptitsyn OB, Kozitsyn SA. Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments. Biopolymers. 1977 Mar;16(3):497-524. No abstract available. PMID: 843599

  61. Finkelstein AV, Ptitsyn OB. Theory of protein molecule self-organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain. Biopolymers. 1977 Mar;16(3):469-95. No abstract available. PMID: 843598

  62. Finkelstein AV, Ptitsyn OB. A theory of protein molecule self-organization. IV. Helical and irregular local structures of unfolded protein chains. J Mol Biol. 1976 May 5;103(1):15-24. No abstract available. PMID: 957423

  63. Finkelstein AV, Kozitsyn SA, Ptitsyn OB. Prediction of the three-dimensional structure for ribosomal protein L25. FEBS Lett. 1975 Dec 1;60(1):137-40. No abstract available. PMID: 1227950

  64. Schulz GE, Barry CD, Friedman J, Chou PY, Fasman GD, Finkelstein AV, Lim VI, Pititsyn OB, Kabat EA, Wu TT, Levitt M, Robson B, Nagano K. Comparison of predicted and experimentally determined secondary structure of adenyl kinase. Nature. 1974 Jul 12;250(462):140-2. No abstract available. PMID: 4367211

  65. Ptitsyn OB, Denesyuk AI, Finkelstein AV, Lim VI. Prediction of the secondary structure of the L7, L12 proteins of the E. coli ribosome. FEBS Lett. 1973 Aug 1;34(1):55-7. No abstract available. PMID: 4580998

  66. Finkelstein AV, Ptitsyn OB. Statistical analysis of the correlation among amino acid residues in helical, beta-structural and non-regular regions of globular proteins. J Mol Biol. 1971 Dec 28;62(3):613-24. No abstract available. PMID: 5167562

  67. Ptitsyn O.B., Finkelstein A.V. - Connection between primary and secondary structure of globular proteins. - Biofizika (USSR) 1970, 15: 757-767.

  1. Szilagyi AN, Kotova NV, Semisotnov GV, Vas M.
    Incomplete refolding of a fragment of the N-terminal domain of pig muscle 3-phosphoglycerate kinase that lacks a subdomain Comparison with refolding of the complementary C-terminal fragment. Eur J Biochem. 2001 Mar;268(6):1851-60. PMID: 11248706
  2. Timchenko AA, Melnik BS, Kihara H, Kimura K, Semisotnov GV.
    GroES co-chaperonin small-angle X-ray scattering study shows ring orifice increase in solution. FEBS Lett. 2000 Apr 14;471(2-3):211-4. PMID: 10767425
  3. Surin AK, Kotova NV, Marchenkova SI, Marchenkov VV, Semisotnov GV.
    [Monomeric form of the molecular chaperone GroEL: structure, stability, and oligomerization]. Bioorg Khim. 1999 May;25(5):358-64. Russian. PMID: 10495893
  4. Korotkov KV, Plotnikov AN, Motuz LP, Vasilenko KS, Semisotnov GV, Alakhov IB.
    [Characteristics of N-terminal 60-kDa fragment of elongation factor 2]. Bioorg Khim. 1998 Mar;24(3):171-4. Russian. PMID: 9612557
  5. Arai M, Ikura T, Semisotnov GV, Kihara H, Amemiya Y, Kuwajima K.
    Kinetic refolding of beta-lactoglobulin. Studies by synchrotron X-ray scattering, and circular dichroism, absorption and fluorescence spectroscopy. J Mol Biol. 1998 Jan 9;275(1):149-62. PMID: 9451446
  6. Veprintsev DB, Permyakov SE, Permyakov EA, Rogov VV, Cawthern KM, Berliner LJ.
    Cooperative thermal transitions of bovine and human apo-alpha-lactalbumins: evidence for a new intermediate state. FEBS Lett. 1997 Aug 4;412(3):625-8. PMID: 9276479
  7. Surin AK, Kotova NV, Marchenkova SI, Sokolovskii IV, Rodionova NA, Iaklichkin SI, Semisotnov GV.
    [Denatured transitions of the molecular chaperone GroEL from Escherichia coli]. Bioorg Khim. 1997 Apr;23(4):251-6. Russian. PMID: 9221726
  8. Surin AK, Kotova NV, Kashparov IA, Marchenkov VV, Marchenkova SYu, Semisotnov GV.
    Ligands regulate GroEL thermostability. FEBS Lett. 1997 Apr 1;405(3):260-2. PMID: 9108300
  9. Semisotnov GV, Kihara H, Kotova NV, Kimura K, Amemiya Y, Wakabayashi K, Serdyuk IN, Timchenko AA, Chiba K, Nikaido K, Ikura T, Kuwajima K.
    Protein globularization during folding. A study by synchrotron small-angle X-ray scattering. J Mol Biol. 1996 Oct 4;262(4):559-74. PMID: 8893863
  10. Plotnikov AN, Vasilenko KS, Kirkitadze MD, Kotova NV, Motuz LP, Korotkov KV, Semisotnov GV, Alakhov IB.
    [Biosynthesis and conformational state of 17-kDa and 27-kDa N-terminal fragments of elongation factor EF-2 in solution]. Bioorg Khim. 1996 Jul;22(7):489-502. Russian. PMID: 8992954
  11. Kuwajima K, Semisotnov GV, Finkelstein AV, Sugai S, Ptitsyn OB.
    Secondary structure of globular proteins at the early and the final stages in protein folding. FEBS Lett. 1993 Nov 22;334(3):265-8. PMID: 8243629
  12. Uverskii VN, Semisotnov GV, Ptitsyn OB.
    [Molten globule unfolding by strong denaturing agents occurs by the "all or nothing" principle]. Biofizika. 1993 Jan-Feb;38(1):37-46. Russian. PMID: 8471644
  13. Uversky VN, Semisotnov GV, Pain RH, Ptitsyn OB.
    'All-or-none' mechanism of the molten globule unfolding. FEBS Lett. 1992 Dec 7;314(1):89-92. PMID: 1451808
  14. Semisotnov GV, Vas M, Chemeris VV, Kashparova NJ, Kotova NV, Razgulyaev OI, Sinev MA.
    Refolding kinetics of pig muscle and yeast 3-phosphoglycerate kinases and of their proteolytic fragments. Eur J Biochem. 1991 Dec 18;202(3):1083-9. PMID: 1765069
  15. Semisotnov GV, Rodionova NA, Razgulyaev OI, Uversky VN, Gripas' AF, Gilmanshin RI.
    Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers. 1991 Jan;31(1):119-28. PMID: 2025683
  16. Cleland JL, Wang DI.
    Refolding and aggregation of bovine carbonic anhydrase B: quasi-elastic light scattering analysis. Biochemistry. 1990 Dec 18;29(50):11072-8. PMID: 2125502
  17. Semisotnov GV, Uversky VN, Sokolovsky IV, Gutin AM, Razgulyaev OI, Rodionova NA.
    Two slow stages in refolding of bovine carbonic anhydrase B are due to proline isomerization. J Mol Biol. 1990 Jun 5;213(3):561-8. PMID: 2112610
  18. Vas M, Sinev MA, Kotova NV, Semisotnov GV.
    Reactivation of 3-phosphoglycerate kinase from its unfolded proteolytic fragments. Eur J Biochem. 1990 May 20;189(3):575-9. PMID: 2351137
  19. Goldberg ME, Semisotnov GV, Friguet B, Kuwajima K, Ptitsyn OB, Sugai S.
    An early immunoreactive folding intermediate of the tryptophan synthease beta 2 subunit is a 'molten globule'. FEBS Lett. 1990 Apr 9;263(1):51-6. PMID: 1691989
  20. Ptitsyn OB, Pain RH, Semisotnov GV, Zerovnik E, Razgulyaev OI.
    Evidence for a molten globule state as a general intermediate in protein folding. FEBS Lett. 1990 Mar 12;262(1):20-4. PMID: 2318308
  21. Semisotnov GV, Kutyshenko VP, Ptitsyn OB.
    [Intramolecular mobility of a protein in a "molten globule" state. A study of carbonic anhydrase by 1H-NMR]. Mol Biol (Mosk). 1989 May-Jun;23(3):808-15. Russian. PMID: 2505063
  22. Rodionova NA, Semisotnov GV, Kutyshenko VP, Uverskii VN, Bolotina IA.
    [Staged equilibrium of carbonic anhydrase unfolding in strong denaturants]. Mol Biol (Mosk). 1989 May-Jun;23(3):683-92. Russian. PMID: 2505062
  23. Gil'manshin RI, Ptitsyn OB, Semisotnov GV.
    [Kinetics of the renaturation of bovine alpha-lactalbumin]. Biofizika. 1988 Mar-Apr;33(2):204-7. Russian. PMID: 3390469
  24. Semisotnov GV, Rodionova NA, Kutyshenko VP, Ebert B, Blanck J, Ptitsyn OB.
    Sequential mechanism of refolding of carbonic anhydrase B. FEBS Lett. 1987 Nov 16;224(1):9-13. PMID: 2824244
  25. Dolgikh DA, Abaturov LV, Bolotina IA, Brazhnikov EV, Bychkova VE, Gilmanshin RI, Lebedev YuO, Semisotnov GV, Tiktopulo EI, Ptitsyn OB, et al.
    Compact state of a protein molecule with pronounced small-scale mobility: bovine alpha-lactalbumin. Eur Biophys J. 1985;13(2):109-21. PMID: 3843533
  26. Dolgikh DA, Gilmanshin RI, Brazhnikov EV, Bychkova VE, Semisotnov GV, Venyaminov SYu, Ptitsyn OB.
    Alpha-Lactalbumin: compact state with fluctuating tertiary structure? FEBS Lett. 1981 Dec 28;136(2):311-5. No abstract available. PMID: 7327267
  27. Kashparov IA, Semisotnov GV, Alakhov YB.
    Interaction of the N-terminal and C-terminal domains of elongation factor G on formation of complexes with guanyl nucleotides. Eur J Biochem. 1981 Aug;118(2):417-21. PMID: 7285933
  28. Kashparov IA, Semisotnov GV, Alakhov IB.
    [Properties and role of tryptophan residues in the polypeptide chain of elongation factor G from E. coli]. Biokhimiia. 1981 Aug;46(8):1488-98. Russian. PMID: 7023551
  29. Bychkova VE, Semisotnov GV, Ptitsyn OB, Gudkova OV, Mitin IV.
    [Compact structure of random copolymers of hydrophobic and hydrophilic amino acid residues]. Mol Biol (Mosk). 1980 Mar-Apr;14(2):278-86. Russian. PMID: 7383026

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