1932

Abstract

The title, “Look to the past, Look to the present, and Look to the future,” the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-042910-155334
2011-06-09
2024-04-29
Loading full text...

Full text loading...

/deliver/fulltext/biophys/40/1/annurev-biophys-042910-155334.html?itemId=/content/journals/10.1146/annurev-biophys-042910-155334&mimeType=html&fmt=ahah

Literature Cited

  1. Acharya KR, Stuart DI, Phillips DC, Scheraga HA. 1.  1990. A critical evaluation of the predicted and X-ray structures of α-lactalbumin. J. Protein Chem. 9:549–63 [Google Scholar]
  2. Altmann KH, Scheraga HA. 2.  1990. Local structure in ribonuclease A. Effect of amino acid substitutions on the preferential formation of the native disulfide loop in synthetic peptides corresponding to residues Cys58-Cys72 of bovine pancreatic ribonuclease A. J. Am. Chem. Soc. 112:4926–31 [Google Scholar]
  3. Arnautova YA, Jagielska A, Scheraga HA. 3.  2006. A new force field (ECEPP-05) for peptides, proteins and organic molecules. J. Phys. Chem. B 110:5025–44 [Google Scholar]
  4. Arnautova YA, Scheraga HA. 4.  2008. Use of decoys to optimize an all-atom force field including hydration. Biophys. J. 95:2434–49 [Google Scholar]
  5. Arnautova YA, Vila JA, Martin OA, Scheraga HA. 5.  2009. What can we learn by computing 13Cα chemical shifts for X-ray protein models?. Acta Crystallogr. D 65:697–703 [Google Scholar]
  6. Arnautova YA, Vorobjev YN, Vila JA, Scheraga HA. 6.  2009. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Proteins Struct. Funct. Bioinform. 77:38–51 [Google Scholar]
  7. Backus JK, Laskowski M Jr, Scheraga HA, Nims LF. 7.  1952. Distribution of intermediate polymers in the fibrinogen-fibrin conversion. Arch. Biochem. Biophys. 41:354–66 [Google Scholar]
  8. Bixon M, Scheraga HA, Lifson S. 8.  1963. Effect of hydrophobic bonding on the stability of poly-L-alanine helices in water. Biopolymers 1:419–29 [Google Scholar]
  9. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 9.  1983. CHARMM: a program for macromolecular energy minimization, and dynamics calculations. J. Comp. Chem. 4:187–217 [Google Scholar]
  10. Czaplewski C, Kalinowski S, Liwo A, Scheraga HA. 10.  2009. Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α + β proteins. J. Chem. Theory Comput. 5:627–40 [Google Scholar]
  11. Donnelly TH, Laskowski M Jr, Notley N, Scheraga HA. 11.  1955. Equilibria in the fibrinogen-fibrin conversion. II. Reversibility of the polymerization steps. Arch. Biochem. Biophys. 56:369–87 [Google Scholar]
  12. Dunitz D, Scheraga HA. 12.  2004. Exercises in prognostication: crystal structures and protein folding. Proc. Natl. Acad. Sci. USA 101:14309–11 [Google Scholar]
  13. Dygert M, N, Scheraga HA. 13.  1975. Use of a symmetry condition to compute the conformation of gramicidin S. Macromolecules 8:750–61 [Google Scholar]
  14. Dyson HJ, Wright PE, Scheraga HA. 14.  2006. The role of hydrophobic interactions in initiation and propagation of protein folding. Proc. Natl. Acad. Sci. USA 103:13057–61 [Google Scholar]
  15. Einert TR, Staple DB, Kreuzer H-J, Netz BR. 15.  2010. A three-state model with loop entropy for the overstretching transition of DNA. Biophys. J. 99:578–87 [Google Scholar]
  16. Epand RM, Scheraga HA. 16.  1967. Enthalpy of stacking in single-stranded polyriboadenylic acid. J. Am. Chem. Soc. 89:3888–92 [Google Scholar]
  17. Everaers R, Kumar S, Simm C. 17.  2007. Unified distribution of poly- and oligonucleotide DNA melting: nearest-neighbor, Poland-Scheraga, and lattice models. Phys. Rev. E 75:041918 [Google Scholar]
  18. Ferry JD, Morrison PR. 18.  1947. Preparation and properties of serum and plasma proteins. VIII. The conversion of human fibrinogen to fibrin under various conditions. J. Am. Chem. Soc. 69:388–400 [Google Scholar]
  19. Frank HS, Evans MJ. 19.  1945. Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures; partial molal entropy in dilute solutions; structure and thermodynamics in aqueous electrolytes. J. Chem. Phys. 13:507–32 [Google Scholar]
  20. Gahl RF, Scheraga HA. 20.  2009. Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues. Biochemistry 48:2740–51 [Google Scholar]
  21. Gay DM.21.  1983. Algorithm 611: subroutine for unconstrained minimization using a model/trust-region approach. ACM Trans. Math. Soft. 9:503–4 [Google Scholar]
  22. Gibson KD, Scheraga HA. 22.  1967. Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. Proc. Natl. Acad. Sci. USA 58:420–27 [Google Scholar]
  23. M, Hesselink FT, N, Scheraga HA. 23.  1974. Molecular theory of the helix-coil transition in poly(amino acids). IV. Evaluation and analysis of s for poly(L-valine) in the absence and presence of water. Macromolecules 7:459–67 [Google Scholar]
  24. N, Scheraga HA. 24.  1969. Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. Chem. Phys. 51:4751–67 [Google Scholar]
  25. N, Scheraga HA. 25.  1976. On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules 9:535–42 [Google Scholar]
  26. Hao M-H, Scheraga HA. 26.  1998. Theory of two-state cooperative folding of proteins. Acc. Chem. Res. 31:433–40 [Google Scholar]
  27. Houry WA, Scheraga HA. 27.  1996. The nature of the unfolded state of ribonuclease A: effect of cis-trans X-Pro peptide bond isomerization. Biochemistry 35:11719–33 [Google Scholar]
  28. Imoto T, Johnson LN, North ACT, Phillips DC, Rupley JA. 28.  1972. Vertebrate lysozymes. The Enzymes, Vol. 7 PD Boyer 21665–868 New York/London: Academic [Google Scholar]
  29. Ingwall RT, Scheraga HA, Lotan N, Berger A, Katchalski E. 29.  1968. Conformational studies of poly-L-alanine in water. Biopolymers 6:331–68 [Google Scholar]
  30. Iwaoka M, Juminaga D, Scheraga HA. 30.  1998. Regeneration of three-disulfide mutants of bovine pancreatic ribonuclease A missing the 65–72 disulfide bond: characterization of a minor folding pathway of ribonuclease A and kinetic roles of Cys65 and Cys72. Biochemistry 37:4490–501 [Google Scholar]
  31. Katz S, Gutfreund K, Shulman S, Ferry JD. 31.  1952. The conversion of fibrinogen to fibrin: X. Light scattering studies of bovine fibrinogen. J. Am. Chem. Soc. 74:5706–9 [Google Scholar]
  32. Kauzmann W.32.  1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1–63 [Google Scholar]
  33. Kazmierkiewicz R, Liwo A, Scheraga HA. 33.  2002. Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method. J. Comput. Chem. 23:715–23 [Google Scholar]
  34. Kazmierkiewicz R, Liwo A, Scheraga HA. 34.  2003. Addition of side chains to a known backbone with defined side-chain centroids. Biophys. Chem. 100:261–80 Erratum 2003. Biophys. Chem. 106:91 [Google Scholar]
  35. Khalili M, Liwo A, Jagielska A, Scheraga HA. 35.  2005. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. J. Phys. Chem. B 109:13798–810 [Google Scholar]
  36. Khalili M, Liwo A, Scheraga HA. 36.  2006. Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. J. Mol. Biol. 355:536–47 [Google Scholar]
  37. Konishi Y, Ooi T, Scheraga HA. 37.  1982. Regeneration of ribonuclease A from the reduced protein. Energetic analysis. Biochemistry 21:4741–48 [Google Scholar]
  38. Konishi Y, Ooi T, Scheraga HA. 38.  1982. Regeneration of RNase A from the reduced protein: models of regeneration pathways. Proc. Natl. Acad. Sci. USA 79:5734–38 [Google Scholar]
  39. Laity JH, Lester CC, Shimotakahara S, Zimmerman DE, Montelione GT, Scheraga HA. 39.  1997. Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A. Biochemistry 36:12683–99 [Google Scholar]
  40. Laskowski M Jr, Scheraga HA. 40.  1954. Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups. J. Am. Chem. Soc. 76:6305–19 [Google Scholar]
  41. Laskowski M Jr, Scheraga HA. 41.  1956. Thermodynamic considerations of protein reactions. II. Modified reactivity of primary valence bonds. J. Am. Chem. Soc. 78:5793–98 [Google Scholar]
  42. Laskowski M Jr, Scheraga HA. 42.  1961. Thermodynamic considerations of protein reactions. III. Kinetics of protein denaturation. J. Am. Chem. Soc. 83:266–74 [Google Scholar]
  43. Lee J, Scheraga HA, Rackovsky S. 43.  1997. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J. Comput. Chem. 18:1222–32 [Google Scholar]
  44. Lewandowska A, Ołdziej S, Liwo A, Scheraga HA. 44.  2010. β-hairpin-forming peptides; models of early stages of protein folding. Biophys. Chem. 151:1–9 [Google Scholar]
  45. Li L-K, Riehm JP, Scheraga HA. 45.  1966. Structural studies of ribonuclease. XXIII. Pairing of the tyrosyl and carboxyl groups. Biochemistry 5:2043–48 [Google Scholar]
  46. Li Z, Scheraga HA. 46.  1987. Monte Carlo–minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA 84:6611–15 [Google Scholar]
  47. Liwo A, Arlukowicz P, Czaplewski C, Ołdziej S, Pillardy P, Scheraga HA. 47.  2002. A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc. Natl. Acad. Sci. USA 99:1937–42 [Google Scholar]
  48. Liwo A, Czaplewski C, Ołdziej S, Rojas AV, Kazmierkiewicz R. 48.  et al. 2008. Simulation of protein structure and dynamics with the coarse-grained UNRES force field. Coarse-Graining of Condensed Phase and Biomolecular Systems GA Voth 107–22 Boca Raton, FL: CRC Press [Google Scholar]
  49. Liwo A, Czaplewski C, Pillardy J, Scheraga HA. 49.  2001. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J. Chem. Phys. 115:2323–47 [Google Scholar]
  50. Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S. 50.  et al. 1998. A united-residue force field for off-lattice protein-structure simulations. III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J. Comput. Chem. 19:259–76 [Google Scholar]
  51. Liwo A, Khalili M, Czaplewski C, Kalinowski S, Ołdziej S. 51.  et al. 2007. Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J. Phys. Chem. B 111:260–85 [Google Scholar]
  52. Liwo A, Khalili M, Scheraga HA. 52.  2005. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. USA 102:2362–67 [Google Scholar]
  53. Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA. 53.  1999. Protein structure prediction by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA 96:5482–85 [Google Scholar]
  54. Liwo A, Ołdziej S, Czaplewski C, Kleinerman DS, Blood P, Scheraga HA. 54.  2010. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. J. Chem. Theory Comput. 6:890–909 [Google Scholar]
  55. Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. 55.  1997. A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J. Comput. Chem. 18:849–73 [Google Scholar]
  56. Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA. 56.  1997. A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization. J. Comput. Chem. 18:874–87 [Google Scholar]
  57. Lorand L. 57.  1950. Fibrin clots. Nature 166:694–95 [Google Scholar]
  58. Maisuradze GG, Liwo A, Ołdziej S, Scheraga HA. 58.  2010. Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. J. Am. Chem. Soc. 132:9444–52 [Google Scholar]
  59. Maisuradze GG, Liwo A, Scheraga HA. 59.  2009. Principal component analysis for protein folding dynamics. J. Mol. Biol. 385:312–29 [Google Scholar]
  60. Maisuradze GG, Liwo A, Scheraga HA. 60.  2009. How adequate are one- and two-dimensional free-energy landscapes for protein-folding dynamics?. Phys. Rev. Lett. 102:238102–1-4 [Google Scholar]
  61. Maisuradze GG, Liwo A, Scheraga HA. 61.  2010. Relation between free energy landscapes of proteins and dynamics. J. Chem. Theory Comput. 6:583–95 [Google Scholar]
  62. Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA. 62.  2010. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J. Phys. Chem. A 114:4471–85 [Google Scholar]
  63. Mandelkern L, Krigbaum WR, Scheraga HA, Flory PJ. 63.  1952. Sedimentation behavior of flexible chain molecules: polyisobutylene. J. Chem. Phys. 20:1392–97 [Google Scholar]
  64. Mattice WL, Scheraga HA. 64.  1984. Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel β sheet. Biopolymers 23:1701–24 [Google Scholar]
  65. Miller MH, Scheraga HA. 65.  1976. Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. I. Poly(glycyl-prolyl-prolyl). J. Polymer Sci. Polymer Symp. 54:171–200 [Google Scholar]
  66. Mirau PA, Bovey FA. 66.  1990. 2D and 3D NMR studies of polypeptide structure and function. Polymer Preprints, Division of Polymer Chemistry, POLY58, 199th A.C.S. August Meeting, Boston, MA 31:206 [Google Scholar]
  67. Momany FA, McGuire RF, Burgess AW, Scheraga HA. 67.  1975. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:2361–81 [Google Scholar]
  68. Montelione GT, Wüthrich K, Burgess AW, Nice EC, Wagner G. 68.  et al. 1992. Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. Biochemistry 31:236–49 Erratum 1992. Biochemistry 31:10138 [Google Scholar]
  69. Monthus C, Garel T. 69.  2005. Distribution of pseudo-critical temperatures and lack of self-averaging in disordered Poland-Scheraga models with different loop exponents. Eur. Phys. J. B 48:393–403 [Google Scholar]
  70. Nanias M, Chinchio M, Ołdziej S, Czaplewski C, Scheraga HA. 70.  2005. Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; comparison with MCM, CSA and CFMC. J. Comput. Chem. 26:1472–86 [Google Scholar]
  71. Nanias M, Czaplewski C, Scheraga HA. 71.  2006. Replica exchange and multicanonical algorithms with the coarse-grained united-residue (UNRES) force field. J. Chem. Theor. Comput. 2:513–28 [Google Scholar]
  72. Navon A, Ittah V, Landsman P, Scheraga HA, Haas E. 72.  2001. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry 40:105–18 [Google Scholar]
  73. Némethy G, Scheraga HA. 73.  1962. The structure of water and hydrophobic bonding in proteins. I. A model for the thermodynamic properties of liquid water. J. Chem. Phys. 36:3382–400 [Google Scholar]
  74. Némethy G, Scheraga HA. 74.  1962. The structure of water and hydrophobic bonding in proteins. II. A model for the thermodynamic properties of aqueous solutions of hydrocarbons. J. Chem. Phys. 36:3401–17 [Google Scholar]
  75. Némethy G, Scheraga HA. 75.  1962. The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J. Phys. Chem. 66:1773–89 Erratum 1963. J. Phys. Chem. 67:2888 [Google Scholar]
  76. Némethy G, Scheraga HA. 76.  1964. Structure of water and hydrophobic bonding in proteins. IV. The thermodynamic properties of liquid deuterium oxide. J. Chem. Phys. 41:680–89 [Google Scholar]
  77. Némethy G, Scheraga HA. 77.  1965. Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers 3:155–84 [Google Scholar]
  78. Némethy G, Scheraga HA, Kauzmann W. 78.  1968. Comments on the communication “a criticism of the term ‘hydrophobic bond’” by Joel H. Hildebrand. J. Phys. Chem. 72:1842 [Google Scholar]
  79. Némethy G, Steinberg IZ, Scheraga HA. 79.  1963. The influence of water structure and of hydrophobic interactions on the strength of side-chain hydrogen bonds in proteins. Biopolymers 1:43–69 [Google Scholar]
  80. Ni F, Gibson KD, Scheraga HA. 80.  1992. Nuclear magnetic resonance studies of thrombin-fibrinopeptide and thrombin-hirudin complexes. Thrombin: Structure and Function LJ Berliner 63–85 New York: Plenum [Google Scholar]
  81. Ni F, Konishi Y, Bullock LD, Rivetna MN, Scheraga HA. 81.  1989. High-resolution NMR studies of fibrinogen-like peptides in solution: structural basis for the bleeding disorder caused by a single mutation of Gly(12) to Val(12) in the Aα chain of human fibrinogen Rouen. Biochemistry 28:3106–19 [Google Scholar]
  82. Ooi T, Scott RA, Vanderkooi G, Scheraga HA. 82.  1967. Conformational analysis of macromolecules. IV. Helical structures of poly-L-alanine, poly-L-valine, poly-β-methyl-L-aspartate, poly-γ-methyl-L-glutamate, and poly-L-tyrosine. J. Chem. Phys. 46:4410–26 [Google Scholar]
  83. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. 83.  1999. Analyses and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins Struct. Funct. Genet. 37:S3149–70 [Google Scholar]
  84. Owicki JC, Scheraga HA. 84.  1977. Monte Carlo calculations in the isothermal-isobaric ensemble. 2. Dilute aqueous solution of methane. J. Am. Chem. Soc. 99:7413–18 [Google Scholar]
  85. Piela L, Kostrowicki J, Scheraga HA. 85.  1989. The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method. J. Phys. Chem. 93:3339–46 [Google Scholar]
  86. Piela L, Scheraga HA. 86.  1987. On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α-helix. Biopolymers 26:S33–58 [Google Scholar]
  87. Pincus MR, Scheraga HA. 87.  1981. Theoretical calculations on enzyme-substrate complexes: the basis of molecular recognition and catalysis. Acc. Chem. Res. 14:299–306 [Google Scholar]
  88. Poland D, Scheraga HA. 88.  1965. Comparison of theories of the helix-coil transition in polypeptides. J. Chem. Phys. 43:2071–74 Erratum 1965. J. Chem. Phys. 43:3774 [Google Scholar]
  89. Poland D, Scheraga HA. 89.  1966. Kinetics of the helix-coil transition in polyamino acids. J. Chem. Phys. 45:2071–90 [Google Scholar]
  90. Poland D, Scheraga HA. 90.  1966. Phase transitions in one dimension, and the helix-coil transition in polyamino acids. J. Chem. Phys. 45:1456–63 [Google Scholar]
  91. Poland D, Scheraga HA. 91.  1966. Occurrence of a phase transition in nucleic acid models. J. Chem. Phys. 45:1464–69 [Google Scholar]
  92. Poland D, Scheraga HA. 92.  1969. The equilibrium unwinding in finite chains of DNA. Physiol. Chem. Phys. 1:389–446 [Google Scholar]
  93. Poland D, Scheraga HA. 93.  1969. The Lifson-Allegra theories of the helix-coil transition for random copolymers: comparison with exact results and extension. Biopolymers 7:887–908 [Google Scholar]
  94. Poland D, Scheraga HA. 94.  1970. Theory of Helix-Coil Transitions in Biopolymers New York: Academic
  95. Rackovsky S, Scheraga HA. 95.  1984. Differential geometry and protein folding. Acc. Chem. Res. 17:209–14 [Google Scholar]
  96. Ripoll DR, Scheraga HA. 96.  1988. On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine). Biopolymers 27:1283–303 [Google Scholar]
  97. Rojas A, Liwo A, Browne D, Scheraga HA. 96a.  2010. Mechanism of fiber assembly: treatment of Aβ-peptide aggregation with a coarse-grained united-residue force field. J. Mol. Biol. 404:537–52 [Google Scholar]
  98. Rojas A, Liwo A, Scheraga HA. 97.  2007. Molecular dynamics with the united-residue (UNRES) force field. Ab initio folding simulations of multi-chain proteins. J. Phys. Chem. B 111:293–309 [Google Scholar]
  99. Roterman IK, Lambert MH, Gibson KD, Scheraga HA. 98.  1989. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. ϕ-ψ maps for N-acetyl alanine N′-methyl amide: comparisons, contrasts and simple experimental tests. J. Biomol. Struct. Dyn. 7:421–53 [Google Scholar]
  100. Rothwarf DM, Li Y-J, Scheraga HA. 99.  1998. Regeneration of bovine pancreatic ribonuclease A. Identification of two nativelike three-disulfide intermediates involved in separate pathways. Biochemistry 37:3760–66 [Google Scholar]
  101. Rothwarf DM, Li Y-J, Scheraga HA. 100.  1998. Regeneration of bovine pancreatic ribonuclease A. Detailed kinetic analysis of two independent folding pathways. Biochemistry 37:3767–76 [Google Scholar]
  102. Scheraga HA. 101.  1955. Non-Newtonian viscosity of solutions of ellipsoidal particles. J. Chem. Phys. 23:1526–32 [Google Scholar]
  103. Scheraga HA. 102.  1957. Tyrosyl-carboxylate ion hydrogen bonding in ribonuclease. Biochim. Biophys. Acta 23:196–97 [Google Scholar]
  104. Scheraga HA. 103.  1967. Structural studies of pancreatic ribonuclease. Fed. Proc. 26:1380–87 [Google Scholar]
  105. Scheraga HA. 104.  1968. Calculations of conformations of polypeptides. Adv. Phys. Org. Chem. 6:103–84 [Google Scholar]
  106. Scheraga HA. 105.  1996. Recent developments in the theory of protein folding: searching for the global energy minimum. Biophys. Chem. 59:329–39 [Google Scholar]
  107. Scheraga HA. 106.  1998. Theory of hydrophobic interactions. J. Biomol. Struct. Dyn. 16:447–60 [Google Scholar]
  108. Scheraga HA. 107.  2004. The thrombin-fibrinogen interaction. Biophys. Chem. 112:117–30 [Google Scholar]
  109. Scheraga HA, Backus JK. 108.  1951. Flow birefringence in solutions of N-hexadecyltrimethylammonium bromide. J. Am. Chem. Soc. 73:5108–12 [Google Scholar]
  110. Scheraga HA, Chou KC, Némethy G. 109.  1983. Interactions between the fundamental structures of polypeptide chains. Conformation in Biology R Srinivasan, RH Sarma 1–10 Schenectady, NY: Adenine [Google Scholar]
  111. Scheraga HA, Edsall JT, Gadd JO Jr. 110.  1951. Double refraction of flow: numerical evaluation of extinction angle and birefringence as a function of velocity gradient. J. Chem. Phys. 19:1101–8 [Google Scholar]
  112. Scheraga HA, Katchalsky A, Alterman Z. 111.  1969. Electrochemical properties of permeable multichain polyamino acids. J. Am. Chem. Soc. 91:7242–49 [Google Scholar]
  113. Scheraga HA, Khalili M, Liwo A. 112.  2007. Protein folding dynamics: overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 58:57–83 [Google Scholar]
  114. Scheraga HA, Konishi Y, Ooi T. 113.  1984. Multiple pathways for regenerating ribonuclease A. Adv. Biophys. 18:21–41 [Google Scholar]
  115. Scheraga HA, Laskowski M Jr. 114.  1957. The fibrinogen-fibrin conversion. Adv. Protein Chem. 12:1–131 [Google Scholar]
  116. Scheraga HA, Mandelkern L. 115.  1953. Consideration of the hydrodynamic properties of proteins. J. Am. Chem. Soc. 75:179–84 [Google Scholar]
  117. Sendak RA, Rothwarf DM, Wedemeyer WJ, Houry WA, Scheraga HA. 116.  1996. Kinetic and thermodynamic studies of the folding/unfolding of a tryptophan-containing mutant of ribonuclease A. Biochemistry 35:12978–92 [Google Scholar]
  118. Senet P, Maisuradze GG, Foulie C, Delarue P, Scheraga HA. 117.  2008. How main-chains of proteins explore the free-energy landscape in native states. Proc. Natl. Acad. Sci. USA 105:19708–13 [Google Scholar]
  119. Shimotakahara S, Rios CB, Laity JH, Zimmerman DE, Scheraga HA, Montelione GT. 118.  1997. NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms. Biochemistry 36:6915–29 [Google Scholar]
  120. Simon I, Glasser L, Scheraga HA, Manley RSJ. 119.  1988. Structure of cellulose. 2. Low-energy crystalline arrangements. Macromolecules 21:990–98 [Google Scholar]
  121. Smith-Gill SJ, Rupley JA, Pincus MR, Carty RP, Scheraga HA. 120.  1984. Experimental identification of a theoretically predicted “left-sided” binding mode for (GlcNAc) in the active site of lysozyme. Biochemistry 23:993–97 [Google Scholar]
  122. Steinberg IZ, Scheraga HA. 121.  1963. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238:172–81 [Google Scholar]
  123. Sturtevant JM, Laskowski M Jr, Donnelly TH, Scheraga HA. 122.  1955. Equilibria in the fibrinogen-fibrin conversion. III. Heats of polymerization and clotting of fibrin monomer. J. Am. Chem. Soc. 77:6168–72 [Google Scholar]
  124. Tanaka S, Scheraga HA. 123.  1975. Theory of the cooperative transition between two ordered conformations of poly(L-proline). III. Molecular theory in the presence of solvent. Macromolecules 8:516–21 [Google Scholar]
  125. Vila JA, Aramini JM, Rossi P, Kuzin A, Su M. 124.  et al. 2008. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc. Natl. Acad. Sci. USA 105:14389–94 [Google Scholar]
  126. Vila JA, Arnautova YA, Martin OA, Scheraga HA. 125.  2009. Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation. Proc. Natl. Acad. Sci. USA 106:16972–77 [Google Scholar]
  127. Vila JA, Arnautova YA, Scheraga HA. 126.  2008. Use of 13Cα chemical shifts for accurate determination of β-sheet structures in solution. Proc. Natl. Acad. Sci. USA 105:1891–96 [Google Scholar]
  128. Vila JA, Baldoni HA, Scheraga HA. 127.  2009. Performance of density functional models to reproduce observed 13Cα chemical shifts of proteins in solution. J. Comput. Chem. 30:884–92 [Google Scholar]
  129. Vila JA, Ripoll DR, Scheraga HA. 128.  2003. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc. Natl. Acad. Sci. USA 100:14812–16 [Google Scholar]
  130. Vila JA, Ripoll DR, Scheraga HA. 129.  2007. Use of 13Cα chemical shifts in protein-structure determination. J. Phys. Chem. B 111:6577–85 [Google Scholar]
  131. Vila JA, Scheraga HA. 130.  2008. Factors affecting the use of 13Cα chemical shifts to determine, refine and validate protein structures. Proteins Struct. Funct. Bioinform. 71:641–54 [Google Scholar]
  132. Vila JA, Scheraga HA. 131.  2009. Assessing the accuracy of protein structures by quantum mechanical computations of 13Cα chemical shifts. Acc. Chem. Res. 42:1545–53 [Google Scholar]
  133. Vila JA, Serrano P, Wüthrich K, Scheraga HA. 132.  2010. Sequential nearest-neighbor effects on computed 13Cα chemical shifts. J. Biomol. NMR 48:23–30 [Google Scholar]
  134. Vila JA, Villegas ME, Baldoni HA, Scheraga HA. 133.  2007. Predicting 13Cα chemical shifts for validation of protein structures. J. Biomol. NMR 38:221–35 [Google Scholar]
  135. Vournakis JN, Poland D, Scheraga HA. 134.  1967. Anti-cooperative interactions in single-strand oligomers of deoxyriboadenylic acid. Biopolymers 5:403–22 [Google Scholar]
  136. Vournakis JN, Scheraga HA, Rushizky GW, Sober HA. 135.  1966. Sober-neighbor-neighbor interactions in single-strand polynucleotides; optical rotatory dispersion studies of the ribonucleotide ApApCp. Biopolymers 4:33–41 [Google Scholar]
  137. Warme PK, Momany FA, Rumball SV, Tuttle RW, Scheraga HA. 136.  1974. Computation of structures of homologous proteins; α-lactalbumin from lysozyme. Biochemistry 13:768–82 [Google Scholar]
  138. Weiner SI, Kollman PA, Case DA, Singh UC, Ghio C. 137.  et al. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765–84 [Google Scholar]
  139. Wlodawer A, Svensson LA, Sjölin L, Gilliland GL. 138.  1988. Structure of phosphate-free ribonuclease A refined at 1.26 Å. Biochemistry 27:2705–17 [Google Scholar]
  140. Wojcik J, Altmann KH, Scheraga HA. 139.  1990. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutylglutamine-co-S-methylthio-L-cysteine). Biopolymers 30:121–34 [Google Scholar]
  141. Xu X, Rothwarf DM, Scheraga HA. 140.  1996. Nonrandom distribution of the one-disulfide intermediates in the regeneration of ribonuclease A. Biochemistry 35:6406–17 [Google Scholar]
  142. Xu X, Scheraga HA. 141.  1998. Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40–95] disulfide bond. Biochemistry 37:7561–71 [Google Scholar]
  143. Ye Y-J, Ripoll DR, Scheraga HA. 142.  1999. Kinetics of cooperative protein folding involving two separate conformational families. Comput. Theor. Polym. Sci. 9:359–70 [Google Scholar]
  144. Cote P, Senet P, Delarue P, Maisuradze GG, Scheraga HA. 143.  2010. Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations. Proc. Natl. Acad. Sci. USA 107:19844–49 [Google Scholar]
  145. He Y, Liwo A, Weinstein H, Scheraga HA. 144.  2011. PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J. Mol. Biol. 405:298–314 [Google Scholar]
/content/journals/10.1146/annurev-biophys-042910-155334
Loading
/content/journals/10.1146/annurev-biophys-042910-155334
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error