Hostname: page-component-78c5997874-94fs2 Total loading time: 0 Render date: 2024-11-13T11:16:51.034Z Has data issue: false hasContentIssue false
  • English
  • Français

My 65 years in protein chemistry

Published online by Cambridge University Press:  08 April 2015

Harold A. Scheraga
Harold A. Scheraga*
Affiliation:
Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, USA
*
*Author for correspondence: Harold A. Scheraga, Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, USA Email: has5@cornell.edu
Get access Rights & Permissions [Opens in a new window]

Abstract

This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein–protein interactions and to nucleic acids and to protein–nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.

Keywords

Hydrogen bondshydrophobic interactionsstructurethermodynamicsfolding pathwaysexperimental and theoretical studies of protein foldingECEPPUNRES
Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 48 , Issue 2 , May 2015 , pp. 117 - 177
Copyright
Copyright © Cambridge University Press 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

27. References

Ananthanarayanan, V. S., Andreatta, R. H., Poland, D. & Scheraga, H. A. (1971). Helix-coil stability constants for the naturally occurring amino acids in water. III. Glycine parameters from random poly(hydroxybutylglutamine-co-glycine). Macromolecules 4, 417–424.CrossRefGoogle Scholar
Andreatta, R. H., Liem, R. K. H. & Scheraga, H. A. (1971). Mechanism of action of thrombin on fibrinogen. I. Synthesis of fibrinogen like peptides, and their proteolysis by thrombin and trypsin. Proceedings of the National Academy of Sciences of the United States of America 68, 253–256.CrossRefGoogle ScholarPubMed
Anfinsen, C. B. (1973). Principles that govern the folding of protein chains. Science 181, 223–230.CrossRefGoogle ScholarPubMed
Anfinsen, C. B. & Scheraga, H. A. (1975). Experimental and theoretical aspects of protein folding. Advances in Protein Chemistry 29, 205–300.CrossRefGoogle ScholarPubMed
Arnautova, Y. A., Jagielska, A. & Scheraga, H. A. (2006). A new force field (ECEPP-05) for peptides, proteins and organic molecules. Journal of Physical Chemistry B 110, 5025–5044.CrossRefGoogle ScholarPubMed
Arnautova, Y. A., Vila, J. A., Martin, O. A. & Scheraga, H. A. (2009). What can we learn by computing 13Cα chemical shifts for X-ray protein models? Acta Crystallographica, D65, 697–703.Google Scholar
Backus, J. K., Laskowski, M. JR, Scheraga, H. A. & Nims, L. F. (1952). Distribution of intermediate polymers in the fibrinogen-fibrin conversion. Archives of Biochemistry and Biophysics 41, 354–366.CrossRefGoogle ScholarPubMed
Bixon, M., Scheraga, H. A. & Lifson, S. (1963). Effect of hydrophobic bonding on the stability of poly–L–alanine helices in water. Biopolymers 1, 419–429.CrossRefGoogle Scholar
Bradbury, J. H. & Scheraga, H. A. (1966). Structural studies of ribonuclease. XXIV. The application of nuclear magnetic resonance spectroscopy to distinguish between the histidine residues of ribonuclease. Journal of the American Chemical Society 88, 4240–4246.CrossRefGoogle Scholar
Buchan, D. W. A., Minneci, F., Nugent, T. C. O., Bryson, K. & Jones, D. T. (2013). Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Research 41, W340–W348.CrossRefGoogle ScholarPubMed
Burgess, A. W. & Scheraga, H. A. (1975). A hypothesis for the pathway of the thermally-induced unfolding of bovine pancreatic ribonuclease. Journal of Theoretical Biology 53, 403–420.CrossRefGoogle ScholarPubMed
Cerf, R. & Scheraga, H. A. (1952). Flow birefringence in solutions of macromolecules. Chemical Reviews 51, 185–261.CrossRefGoogle Scholar
Chen, J., Brooks, C. L. III & Scheraga, H. A. (2008). Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. Journal of Physical Chemistry B 112, 242–249.CrossRefGoogle ScholarPubMed
Chou, K. C., Némethy, G. & Scheraga, H. A. (1990). Energetics of interactions of regular structural elements in proteins. Accounts of Chemical Research 23, 134–141.CrossRefGoogle Scholar
Cote, Y., Senet, P., Delarue, P., Maisuradze, G. G. & Scheraga, H. A. (2010). Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations. Proceedings of the National Academy of Sciences of the United States of America 107, 19844–19849.CrossRefGoogle ScholarPubMed
Cote, Y., Senet, P., Delarue, P., Maisuradze, G. G. & Scheraga, H. A. (2012). Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proceedings of the National Academy of Sciences of the United States of America 109, 10346–10351.CrossRefGoogle ScholarPubMed
Cuesta-López, S., Menoni, H., Angelov, D. and Peyrard, M. (2011). Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions. Nucleic Acids Research 39, 5276–5283.CrossRefGoogle ScholarPubMed
Czaplewski, C., Kalinowski, S., Liwo, A. & Scheraga, H. A. (2009). Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α + β proteins. Journal of Chemical Theory and Computation 5, 627–640.CrossRefGoogle Scholar
Das, S., Ghosh, S., Dasgupta, D., Sen, U. & Mukhopadhyay, D. (2012). Biophysical studies with AICD-47 reveal unique binding behavior characteristic of an unfolded domain. Biochemical and Biophysical Research Communications 425, 201–206.CrossRefGoogle ScholarPubMed
Davydov, A. S. (1973). The theory of contraction of proteins under their excitation. Journal of Theoretical Biology 38, 559–569.CrossRefGoogle ScholarPubMed
Debye, P. & Bueche, A. M. (1948). Intrinsic viscosity, diffusion, and sedimentation rate of polymers in solution. Journal of Chemical Physics 16, 573–579.CrossRefGoogle Scholar
Donnely, T. H., Laskowski, M. JR, Notley, N. & Scheraga, H. A. (1955). Equilibria in the fibrinogen-fibrin conversion. II. Reversibility of the polymerization steps. Archives of Biochemistry and Biophysics 56, 369–387.CrossRefGoogle Scholar
Dygert, M., Gō, N. & Scheraga, H. A. (1975). Use of a symmetry condition to compute the conformation of gramicidin S. Macromolecules 8, 750–761.CrossRefGoogle Scholar
Dyson, H. J., Wright, P. E. & Scheraga, H. A. (2006). The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences of the United States of America 103, 13057–13061.CrossRefGoogle ScholarPubMed
Edsall, J. T. (1949). The size and shape of protein molecules. Fortschritte der Chemischen Forschung, Bd. 1, S. 119–174.CrossRefGoogle Scholar
Edsall, J. T., Gilbert, G. A. & Scheraga, H. A. (1955). The Non–clotting component of the human plasma fraction I–1 (“Cold Insoluble Globulin”). Journal of the American Chemical Society 77, 157–161.CrossRefGoogle Scholar
Epand, R. M. & Scheraga, H. A. (1967). Enthalpy of stacking in single–stranded polyriboadenylic acid. Journal of the American Chemical Society 89, 3888–3892.CrossRefGoogle Scholar
Erenrich, E. H., Andreatta, R. H. & Scheraga, H. A. (1970). Experimental verification of predicted helix sense of two polyamino acids. Journal of the American Chemical Society 92, 1116–1119.CrossRefGoogle Scholar
Ferry, J. D. & Morrison, P. R. (1947). Preparation and properties of serum and plasma proteins. VIII. The conversion of human fibrinogen to fibrin under various conditions. Journal of the American Chemical Society 69, 388–400.CrossRefGoogle Scholar
Fisher, M. E. (1966). Effect of excluded volume of phase transitions in biopolymers. Journal of Chemical Physics 45, 1469–1473.CrossRefGoogle Scholar
Flory, P. J. & Fox, T. G. (1951). Treatment of intrinsic viscosities. Journal of the American Chemical Society 73, 1904–1908.CrossRefGoogle Scholar
Fossy, S. A., Némethy, G., Gibson, K. D. & Scheraga, H. A. (1991). Conformational energy studies of β-sheets of model silk fibroin peptides. I. Sheets of Poly(Ala–Gly) chains. Biopolymers 31, 1529–1541.CrossRefGoogle Scholar
Frank, H. S. (1958). Covalency in the hydrogen bond and the properties of water and ice. Proceedings of the Royal Society London A 247, 481–492.Google Scholar
Frank, H. S. & Wen, W. Y. (1957). Ion-solvent interaction. Structural aspect of ion-solvent interaction in aqueous solutions: a suggested picture of water structure. Discussions of the Faraday Society 24, 133–140.CrossRefGoogle Scholar
Gahl, R. F., & Scheraga, H. A. (2009). Oxidative folding pathway of onconase, a ribonuclease homologue: Insight into oxidative folding mechanisms from a study of two homologues. Biochemistry 48, 2740–2751.CrossRefGoogle ScholarPubMed
Gay, J. G. & Berne, B. J. (1981). Modification of the overlay potential to mimic a linear site-site potential. Journal of the American Chemical Society 74, 3316–3319.Google Scholar
Gō, M., Gō, N. & Scheraga, H. A. (1970). Molecular theory of the helix–coil transition in polyamino acids. II. Numerical evaluation of s and σ for polyglycine and poly-L-alanine in the absence (for s and σ) and presence (for σ) of solvent. Journal of Chemical Physics 52, 2060–2079.CrossRefGoogle Scholar
Gō, M., Gō, N. & Scheraga, H. A. (1971). Molecular theory of the helix–coil transition in polyamino acids. III. Evaluation and analysis of s and σ for polyglycine and poly-L- alanine in water. Journal of Chemical Physics 54, 4489–4503.CrossRefGoogle Scholar
Gō, M., Hesselink, F. T., Gō, N. & Scheraga, H. A. (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, 459–467.CrossRefGoogle Scholar
Gō, M. & Scheraga, H. A. (1984). Molecular theory of the helix–coil transition in polyamino acids. V. Explanation of the different conformational behavior of valine, isoleucine and leucine in aqueous solution. Biopolymers 23, 1961–1977.CrossRefGoogle ScholarPubMed
Gō, N., Gō, M. & Scheraga, H. A. (1968). Molecular theory of the helix-coil transition in polyamino acids. I Formulation. Proceedings of the National Academy of Sciences of the United States of America 59, 1030–1037.CrossRefGoogle ScholarPubMed
Gō, N., Lewis, P. N. & Scheraga, H. A. (1970). Calculation of the conformation of the pentapeptide cyclo(glycylglycylgly-cylprolylprolyl). II. Statistical weights. Macromolecules 3, 628–634.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1969). Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. Journal of Chemical Physics 51, 4751–4767.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1970a). Ring closure and local conformational deformations of chain molecules. Macromolecules 3, 178–187.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1970b). Calculation of the conformation of the pentapeptide cyclo-(Glycylglycylglycylprolyl-prolyl). I. A complete energy map. Macromolecules 3, 188–194.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1973a). Ring closure in chain molecules with Cn, I or S2n symmetry. Macromolecules 6, 273–281.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1973b). Calculation of the conformation of cyclo-hexaglycyl. Macromolecules 6, 525–535.CrossRefGoogle Scholar
Gō, N. & Scheraga, H. A. (1976). On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules 9, 535–542.CrossRefGoogle Scholar
Golas, E., Maisuradze, G. G., Senet, P., Oldziej, S., Czaplewski, C., Scheraga, H. A. & Liwo, A. (2012). Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. Journal of Chemical Theory and Computation 8, 1750–1764.CrossRefGoogle ScholarPubMed
Griffith, J. H. & Scheraga, H. A. (2004). Statistical thermodynamics of aqueous solutions. I. Water structure, solutions with non-polar solutes, and hydrophobic interactions. Journal of Molecular Structure: THEOCHEM 682, 97–113.CrossRefGoogle Scholar
Hall, C. E. (1956). Visualization of individual macromolecules with the electron microscope. Proceedings of the National Academy of Sciences of the United States of America 42, 801–806.CrossRefGoogle Scholar
Han, D. S. & Weinstein, H. (2008). Auto-inhibition in the multi-domain protein PICK 1 revealed by dynamic models of its quaternary structure. Biophysical Journal 94, 67–76.Google Scholar
Hansmann, U. H. E. (1997). Parallel tempering algorithm for conformational studies of biological molecules. Chemical Physics Letters 18, 849–873.Google Scholar
Hao, M. H. & Scheraga, H. A. (1998a). Molecular mechanisms for cooperative folding of proteins. Journal of Molecular Biology 277, 973–983.CrossRefGoogle ScholarPubMed
Hao, M. H. & Scheraga, H. A. (1998b). A Theory of two-state cooperative folding of proteins. Accounts of Chemical Research 31, 433–440.CrossRefGoogle Scholar
He, Y., Liwo, A., Weinstein, H. & Scheraga, H. A. (2011). PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. Journal of Molecular Biology 405, 298–314.CrossRefGoogle Scholar
He, Y., Maciejczyk, M., Oldziej, S., Scheraga, H. A. & Liwo, A. (2013a). Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix. Physical Review Letters 110, 098101.CrossRefGoogle ScholarPubMed
He, Y., Mozelewska, M. A., Krupa, P., Sieradzan, A. K., Wirecki, T. K., Liwo, A., Kachlishvili, K., Rackovsky, S., Jagiela, D., Slusarz, R., Czaplewski, C. R., Oldziej, S. & Scheraga, H. A. (2013b). Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proceedings of the National Academy of Sciences of the United States of America 110, 14936–14941.CrossRefGoogle Scholar
He, Y., Xiao, Y., Liwo, A. & Scheraga, H. A. (2009). Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. Journal of Computational Chemistry 30, 2127–2135.CrossRefGoogle ScholarPubMed
Hermans, J. JR & Scheraga, H. A. (1961a). Structural studies of ribonuclease. V. Reversible change of configuration. Journal of the American Chemical Society 83, 3283–3292.CrossRefGoogle Scholar
Hermans, J. JR & Scheraga, H. A. (1961b). Structural studies of ribonuclease. VI. Abnormal ionizable groups. Journal of the American Chemical Society 83, 3293–3300.CrossRefGoogle Scholar
Houry, W. A., Rothwarf, D. M. & Scheraga, H. A. (1994). A very fast phase in the refolding of disulfide-intact ribonuclease A: implications for the refolding and unfolding pathways. Biochemistry 33, 2516–2530.CrossRefGoogle ScholarPubMed
Hughesman, C. B., Turner, R. F. B. & Haynes, C. (2011a). Correcting for heat capacity and 5′-TA type terminal nearest neighbors improves prediction of DNA melting temperatures using nearest-neighbor thermodynamic models. Biochemistry 50, 2642–2649.CrossRefGoogle Scholar
Hughesman, C. B., Turner, R. F. B. & Haynes, C. (2011b). Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA. Biochemistry 50, 5354–5368.CrossRefGoogle ScholarPubMed
Hung, A. Y. & Sheng, M. (2002). PDZ domains: structural modules for protein complex assembly. Journal of Biology and Chemistry 277, 5699–5702.CrossRefGoogle ScholarPubMed
Imoto, T., Johnson, L. N., North, A. C. T., Phillips, D. C. & Rupley, J. A. (1972). Vertebrate lysozymes. In “The Enzymes”, 3rd edn, vol. 7 (ed. Boyer, P. D.), pp. 665–868. New York: Academic Press.Google Scholar
Ingwall, R. T., Scheraga, H. A., Lotan, N., Berger, A. & Katchalski, E. (1968). Conformational studies of poly–L–alanine in water. Biopolymers 6, 331–368.CrossRefGoogle ScholarPubMed
Isogai, Y., Némethy, G. & Scheraga, H. A. (1977). Enkephalin: conformational analysis by means of empirical energy calculations. Proceedings of the National Academy of Sciences of the United States of America 74, 414–418.CrossRefGoogle ScholarPubMed
Iwaoka, M., Juminaga, D. & Scheraga, H. A. (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, 4490–4501.CrossRefGoogle ScholarPubMed
Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195–202.CrossRefGoogle ScholarPubMed
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637.CrossRefGoogle ScholarPubMed
Kachlishvili, K., Maisuradze, G. G., Martin, O. A., Liwo, A., Vila, J. A. & Scheraga, H. A. (2014). Accounting for a mirror – image conformation as a subtle effect in protein folding. Proceedings of the National Academy of Sciences of the United States of America 111, 8458–8463.CrossRefGoogle ScholarPubMed
Kaźmierkiewicz, R., Liwo, A. & Scheraga, H. A. (2002). Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method. Journal of Computational Chemistry 23, 715–723.CrossRefGoogle ScholarPubMed
Kaźmierkiewicz, R., Liwo, A. & Scheraga, H. A. (2003). Addition of side chains to a known backbone with defined side-chain centroids. Biophysical Chemistry 100, 261–280. Erratum: Biophysical Chemistry 106, 91.CrossRefGoogle ScholarPubMed
Kevrekidis, P. G. (2009). The Discrete Nonlinear Schrödinger Equation: Mathematical Analysis, Numerical Computations and Physical Perspectives. Springer Verlag, Berlin.CrossRefGoogle Scholar
Khalili, M., Liwo, A., Rakowski, F., Grochowski, P. & Scheraga, H. A. (2005a). Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. Journal of Physical Chemistry B 109, 13785–13797.CrossRefGoogle ScholarPubMed
Khalili, M., Liwo, A., Jagielska, A., & Scheraga, H. A. (2005b). Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. Journal of Physical Chemistry, B 109, 13798–13810.CrossRefGoogle ScholarPubMed
Khalili, M., Liwo, A. & Scheraga, H. A. (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. Journal of Molecular Biology 355, 536–547.CrossRefGoogle Scholar
Kidera, A., Konishi, Y., Oka, M., Ooi, T. & Scheraga, H. A. (1985a). Statistical Analysis of the Physical Properties of the 20 Naturally Occurring Amino Acids. Journal of Protein Chemistry 4, 23–55.CrossRefGoogle Scholar
Kidera, A., Konishi, Y., Ooi, T. & Scheraga, H. A. (1985b). Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids. Journal of Protein Chemistry 4, 265–297.CrossRefGoogle Scholar
Kim, P. S., & Baldwin, R. L. (1982). Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annual Reviews of Biochemistry 51, 459–489.CrossRefGoogle ScholarPubMed
Kirkwood, J. G. & Riseman, J. (1948). The intrinsic viscosities and diffusion constants of flexible macromolecules in solution. Journal of Chemical Physics 16, 565–573.CrossRefGoogle Scholar
Kityk, R., Kopp, J., Sinning, I. & Mayer, M. P. (2013). Structure and dynamics of the ATP – bound open conformation of Hsp70 chaperones. Molecular Cell 48, 863–874.CrossRefGoogle Scholar
Kostrowicki, J., Piela, L., Cherayil, B. J. & Scheraga, H. A. (1991). Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms. Journal of Physical Chemistry 95, 4113–4119.CrossRefGoogle Scholar
Kostrowicki, J., & Scheraga, H. A. (1992). Application of the diffusion equation method for global optimization to oligopeptides. Journal of Physical Chemistry 96, 7442–7449.CrossRefGoogle Scholar
Kostrowicki, J. & Scheraga, H. A. (1996). Some approaches to the multiple-minima problem in protein folding, in “Global minimization of nonconvex energy functions: molecular conformation and protein folding”, (eds. P. M. Pardalos, D. Shalloway & G. Xue). DIMACS: Series in Discrete Mathematics and Theoretical Computer Science (American Mathematical Society) 23, 123–132.Google Scholar
Krakow, W., Endres, G. F., Siegel, B. M. & Scheraga, H. A. (1972). An electron microscopic investigation of the polymerization of bovine fibrin monomer. Journal of Molecular Biology 71, 95–103.CrossRefGoogle ScholarPubMed
Kresheck, G. C. & Scheraga, H. A. (1966). Structural studies of ribonuclease. XXV. Enthalpy changes accompanying acid denaturation. Journal of the American Chemical Society 88, 4588–4591.CrossRefGoogle ScholarPubMed
Kresheck, G. C., Hamori, E., Davenport, G. & Scheraga, H. A. (1966). Determination of the dissociation rate of dodecylpyridinium iodide micelles by a temperature- jump technique. Journal of the American Chemical Society 88, 246–253.CrossRefGoogle Scholar
Krokhotin, A., Liwo, A., Maisuradze, G. G., Niemi, A. J. & Scheraga, H. A. (2014). Kinks, loops and protein folding, with protein A as an example. Journal of Chemical Physics 140, 025101-1–025101-17.CrossRefGoogle ScholarPubMed
Krokhotin, A., Liwo, A., Niemi, A. J. & Scheraga, H. A. (2012). Coexistence of phases in a protein heterodimer. Journal of Chemical Physics 137, 035101-1–035101-13.CrossRefGoogle Scholar
Krokhotin, A., Niemi, A. & Peng, X. (2011). Soliton concept and protein structure. Physical Review E 85, 031906-1–0319068-8.Google Scholar
Krupa, P., Sieradzan, A. K., Rackovsky, S., Beranowski, M., Oldziej, S. M., Scheraga, H. A., Liwo, A. & Czaplewski, C. (2013). Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. Journal of Chemical Theory and Computation 9, 4620–4632.CrossRefGoogle ScholarPubMed
Kubo, R. (1962). Generalized cumulant expansion method. Journal of the Physical Society of Japan 17, 1100–1120.CrossRefGoogle Scholar
Lam, A. R., Rodriguez, J. J., Rojas, A., Scheraga, H. A. & Mukamel, S. (2013). Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy. Journal of Physical Chemistry A 117, 342–350.CrossRefGoogle ScholarPubMed
Laskowski, M. JR, Rakowitz, D. H. & Scheraga, H. A. (1952). Equilibria in the fibrinogen-fibrin conversion. Journal of the American Chemical Society 74, 280.CrossRefGoogle Scholar
Laskowski, M. JR & Scheraga, H. A. (1954). Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups. Journal of the American Chemical Society 76, 6305–6319.CrossRefGoogle Scholar
Laskowski, M. JR & Scheraga, H. A. (1956). Thermodynamic considerations of protein reactions. II. Modified reactivity of primary valence bonds. Journal of the American Chemical Society 78, 5793–5798.CrossRefGoogle Scholar
Laskowski, M. JR & Scheraga, H. A. (1961). Thermodynamic considerations of protein reactions. III. Kinetics of protein denaturation. Journal of the American Chemical Society 83, 266–274.CrossRefGoogle Scholar
Lee, J., Liwo, A., Ripoll, D. R., Pillardy, J., Saunders, J. A., Gibson, K. D. & Scheraga, H. A. (2000). Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets. International Journal of Quantum Chemistry 71, 90–117.3.0.CO;2-L>CrossRefGoogle Scholar
Lee, J. & Scheraga, H. A. (1999). Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin. International Journal of Quantum Chemistry 75, 255–265.3.0.CO;2-V>CrossRefGoogle Scholar
Lee, J., Scheraga, H. A. & Rackovsky, S. (1997). New optimization method for conformational energy calculations on polypeptides: conformational space annealing. Journal of Computational Chemistry 18, 1222–1232.3.0.CO;2-7>CrossRefGoogle Scholar
Lee, J., Scheraga, H. A. & Rackovsky, S. (1998). Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 46, 103–115.3.0.CO;2-Q>CrossRefGoogle ScholarPubMed
Lee, J., Liwo, A., Ripoll, D. R., Pillardy, J. & Scheraga, H. A. (1999a). Calculation of protein conformation by global optimization of a potential energy function. Proteins: Structure, Function and Genetics, Supplement 3, 204–208.3.0.CO;2-F>CrossRefGoogle Scholar
Lee, J., Liwo, A. & Scheraga, H. A. (1999b). Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10–55 fragment of staphylococcal protein A and to apo calbindin D9K. Proceedings of the National Academy of Sciences of the United States of America 96, 2025–2030.CrossRefGoogle Scholar
Levenberg, K. (1944). A method for the solution of certain non-linear problems in least squares. Quarterly of Applied Mathematics 2, 164–168.CrossRefGoogle Scholar
Lewis, P. N., Gō, N., Gō, M., Kotelchuck, D. & Scheraga, H. A. (1970). Helix probability profiles of denatured proteins and their correlation with native structures. Proceedings of the National Academy of Sciences of the United States of America 65, 810–815.CrossRefGoogle ScholarPubMed
Lewis, P. N. & Scheraga, H. A. (1971a). Predictions of structural homologies in cytochrome c proteins. Archives of Biochemistry and Biophysics 144, 576–583.CrossRefGoogle ScholarPubMed
Lewis, P. N. & Scheraga, H. A. (1971b). Prediction of structural homology between bovine α-lactalbumin and hen egg white lysozyme. Archives of Biochemistry and Biophysics 144, 584–588.CrossRefGoogle ScholarPubMed
Li, L. K., Riehm, J. P. & Scheraga, H. A. (1966). Structural studies of ribonuclease. XXIII. Pairing of the tyrosyl and carboxyl groups. Biochemistry 5, 2043–2048.CrossRefGoogle Scholar
Li, Z. & Scheraga, H. A. (1984). Real-space renormalization group treatment of the helix-coil transition in a homopolyamino acid chain. Journal of Physical Chemistry 88, 6580–6586.CrossRefGoogle Scholar
Li, Z. & Scheraga, H. A. (1987). Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proceedings of the National Academy of Sciences of the United States of America 84, 6611–6615.CrossRefGoogle Scholar
Li, Z. & Scheraga, H. A. (1988). Structure and free energy of complex thermodynamic systems. Journal of Molecular Structure: THEOCHEM 179, 333–352.CrossRefGoogle Scholar
Lifson, S. & Roig, A. (1961). On the theory of helix–coil transition in polypeptides. Journal of Chemical Physics 34, 1963–1974.CrossRefGoogle Scholar
Liwo, A., Arlukowicz, P., Czaplewski, C., Oldziej, S., Pillardy, J. & Scheraga, H. A. (2002). A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proceedings of the National Academy of Sciences of the United States of America 99, 1937–1942.CrossRefGoogle Scholar
Liwo, A., Arlukowicz, P., Oldziej, S., Czaplewski, C., Makowski, M. & Scheraga, H. A. (2004). Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 1. Tests of the approach using simple lattice protein models. Journal of Physical Chemistry B 108, 16918–16933.CrossRefGoogle Scholar
Liwo, A., Czaplewski, C., Oldziej, S., Rojas, A. V., Kaźmierkiewicz, R., Makowski, M., Murarka, R. K. & Scheraga, H. A. (2008). Simulation of protein structure and dynamics with the coarse-grained UNRES force field. In Coarse-Graining of Condensed Phase and Biomolecular Systems, (ed. Voth, G. A.), pp. 107–122. CRC Press.Google Scholar
Liwo, A., Czaplewski, C., Pillardy, J. & Scheraga, H. A. (2001). Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. Journal of Chemical Physics 115, 2323–2347.CrossRefGoogle Scholar
Liwo, A., Kaźmierkiewicz, R., Czaplewski, C., Groth, M., Oldziej, S., Wawak, R. J., Rackovsky, S., Pincus, M. R. & Scheraga, H. A. (1998). United-residue force field for off-lattice protein-structure simulations; III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. Journal of Computational Chemistry 19, 259–276.3.0.CO;2-S>CrossRefGoogle Scholar
Liwo, A., Khalili, M., Czaplewski, C., Kalinowski, S., Oldziej, S., Wachucik, K. & Scheraga, H. A. (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. Journal of Physical Chemistry B 111, 260–285.CrossRefGoogle ScholarPubMed
Liwo, A., Khalili, M. & Scheraga, H. A. (2005). Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America 102, 2362–2367.CrossRefGoogle ScholarPubMed
Liwo, A., Lee, J., Ripoll, D. R., Pillardy, J. & Scheraga, H. A. (1999a). Protein structure prediction by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America 96, 5482–5485.CrossRefGoogle ScholarPubMed
Liwo, A., Oldziej, S., Czaplewski, C., Kleinerman, D. S., Blood, P. & Scheraga, H. A. (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. Journal of Chemical Theory and Computation 6, 890–909.CrossRefGoogle ScholarPubMed
Liwo, A., Oldziej, S., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1997a). 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. Journal of Computational Chemistry 18, 849–873.3.0.CO;2-R>CrossRefGoogle Scholar
Liwo, A., Pillardy, J., Czaplewski, C., Lee, J., Ripoll, D. R., Groth, M., Rodziewicz-Motowidlo, S., Kaźmierkiewicz, R., Wawak, R. J., Oldziej, S. & Scheraga, H. A., (2000). UNRES – a united-residue force field for energy-based prediction of protein structure-origin and significance of multibody terms, RECOMB 2000. In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (eds. Shamir, R., Miyano, S., Istrail, S., Pevzner, P. & Waterman, M.), pp. 193–200, Tokyo, Japan, New York: ACM.CrossRefGoogle Scholar
Liwo, A., Pillardy, J., Kaźmierkiewicz, R., Wawak, R. J., Groth, M., Czaplewski, C., Oldziej, S. & Scheraga, H. A. (1999b). Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods. Theoretical Chemistry Accounts 101, 16–20.CrossRefGoogle Scholar
Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S., Oldziej, S. & Scheraga, H. A. (1997b). 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. Journal of Computational Chemistry 18, 874–887.3.0.CO;2-O>CrossRefGoogle Scholar
Lorand, L. (1951). ‘Fibrino-Peptide’: New Aspects of the Fibrinogen–Fibrin Transformation. Nature 167, 992–993.CrossRefGoogle ScholarPubMed
Lu, W. & Ziff, E. B. (2005). PICK1 interacts with ABP/GRIP to regulate AMPA receptor trafficking. Neuron 47, 407–421.CrossRefGoogle ScholarPubMed
Maciejczyk, M., Spasic, A., Liwo, A. & Scheraga, H. A. (2010). Coarse-grained model of nucleic acid bases. Journal of Computational Chemistry 31, 1644–1655.CrossRefGoogle ScholarPubMed
Makowski, M., Liwo, A. & Scheraga, H. A. (2011). Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. Journal of Physical Chemistry B 115, 6130–6137.CrossRefGoogle ScholarPubMed
Mandelkern, L., Krigbaum, W. R., Scheraga, H. A. & Flory, P. J. (1952). Sedimentation behavior of flexible chain molecules: polyisobutylene. Journal of Chemical Physics 20, 1392–1397.CrossRefGoogle Scholar
Martin, O. A., Arnautova, Y. A., Icazatti, A. A., Scheraga, H. A. & Vila, J. A. (2013). Physics-based method to validate and repair flaws in protein structures. Proceedings of the National Academy of Science of the United States of America 110, 16826–16831.CrossRefGoogle ScholarPubMed
Martin, O. A., Vila, J. A. & Scheraga, H. A. (2012). CheShift-2: graphic validation of protein structures. Bioinformatics 28, 1538–1539.CrossRefGoogle ScholarPubMed
Matheson, R. R. JR & Scheraga, H. A. (1978). A method for predicting nucleation sites for protein folding based on hydrophobic contacts. Macromolecules 11, 819–829.CrossRefGoogle Scholar
Matheson, R. R. JR & Scheraga, H. A. (1979). Steps in the pathway of the thermal unfolding of ribonuclease A. A nonspecific surface-labeling study. Biochemistry 12, 2437–2445.CrossRefGoogle Scholar
Meadows, D. H., Jardetzky, O., Epand, R. M., Ruterjans, H. H. & Scheraga, H. A. (1968). Assignment of the histidine peaks in the nuclear magnetic resonance spectrum of ribonuclease. Proceedings of the National Academy of Science of the United States of America 60, 766–772.CrossRefGoogle ScholarPubMed
Meadows, D. H., Markley, J. L., Cohen, J. S. & Jardetzky, O. (1967). Nuclear magnetic resonance studies of the structure and binding sites of enzymes. I. Histidine residues. Proceedings of the National Academy of Science of the United States of America 58, 1307–1313.CrossRefGoogle ScholarPubMed
Miller, M. H. & Scheraga, H. A. (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). Journal of Polymer Science: Polymer Symposia, 54, p. 171–200.Google Scholar
Mirau, P. A. & Bovey, F. A. (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, vol. 31, 206.Google Scholar
Momany, F. A., Mcguire, R. F., Burgess, A. W. & Scheraga, H. A. (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. Journal of Physical Chemistry 79, 2361–2381.CrossRefGoogle Scholar
Montelione, G. T., Wüthrich, K., Burgess, A. W., Nice, E. C., Wagner, G., Gibson, K. D. & Scheraga, H. A. (1992). Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. Biochemistry 31, 236–249.CrossRefGoogle ScholarPubMed
Nanias, M., Czaplewski, C. & Scheraga, H. A. (2006). Replica exchange and multicanonical algorithms with the coarse-grained united-residue (UNRES) force field. Journal of Chemical Theory and Computation 2, 513–528.CrossRefGoogle Scholar
Navon, A., Ittah, V., Laity, J. H. & Scheraga, H. A., Hass, E. & Gussakovsky, E. E. (2001). Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A. Biochemistry 40, 93–104.CrossRefGoogle ScholarPubMed
Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S. & Scheraga, H. A. (1992). Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. Journal of Physical Chemistry 96, 6472–6484.CrossRefGoogle Scholar
Némethy, G., Pottle, M. S. & Scheraga, H. A. (1983). Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. Journal of Physical Chemistry 87, 1883–1887.CrossRefGoogle Scholar
Némethy, G. & Scheraga, H. A. (1962a). The structure of water and hydrophobic bonding in proteins. I. A model for the thermodynamic properties of liquid water. Journal of Chemical Physics 36, 3382–3400.CrossRefGoogle Scholar
Némethy, G. & Scheraga, H. A. (1962b). The structure of water and hydrophobic bonding in proteins. II. A model for the thermodynamic properties of aqueous solutions of hydrocarbons. Journal of Chemical Physics 36, 3401–3417.CrossRefGoogle Scholar
Némethy, G. & Scheraga, H. A. (1962c). The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. Journal of Chemical Physics 66, 1773–1789.CrossRefGoogle Scholar
Némethy, G. & Scheraga, H. A. (1965). Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers 3, 155–184.CrossRefGoogle Scholar
Némethy, G. & Scheraga, H. A. (1977). Protein folding. Quarterly Review of Biophysics 10, 239–352.CrossRefGoogle ScholarPubMed
Némethy, G. & Scheraga, H. A. (1979). A possible folding pathway of bovine pancreatic RNase. Proceedings of the National Academy of Sciences of the United States of America 76, 6050–6054.CrossRefGoogle ScholarPubMed
Némethy, G., Steinberg, I. Z. & Scheraga, H. A. (1963). The influence of water structure and of hydrophobic interactions on the strength of side-chain hydrogen bonds in proteins. Biopolymers 1, 43–69.CrossRefGoogle Scholar
Neurath, H. & Saum, A. M. (1939). The denaturation of serum albumin. Diffusion and viscosity measurements in the presence of urea. Journal of Biological Chemistry 128, 347–362.CrossRefGoogle Scholar
Ni, F., Konishi, Y., Bullock, L. D., Rivetna, M. N. & Scheraga, H. A. (1989c). 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, 3106–3119.CrossRefGoogle Scholar
Ni, F., Konishi, Y., Frazier, R. B., Scheraga, H. A. & Lord, S. T. (1989a). High resolution NMR studies of fibrinogen like peptides in solution: interaction of thrombin with residues 1–23 of the Aα chain of human fibrinogen. Biochemistry 28, 3082–3094.CrossRefGoogle Scholar
Ni, F., Meinwald, Y. C., Vasquez, M. & Scheraga, H. A. (1989b). High-resolution NMR studies of fibrinogen-like peptides in solution: structure of a thrombin-bound peptide corresponding to residues 7-16 of the Aα chain of human fibrinogen. Biochemistry 28, 3094–3105.CrossRefGoogle Scholar
Nishikawa, K. & Scheraga, H. A. (1976). Geometrical criteria for formation of coiled-coil structures of polypeptide chains. Macromolecules 9, 395–407.CrossRefGoogle ScholarPubMed
Niu, G. C. C., Go, N. & Scheraga, H. A. (1973). Calculation of the conformation of the pentapeptide cyclo(glycylglycyl-glycylprolylprolyl). III. Treatment of a flexible molecule. Macromolecules 6, 91–99. Erratum: ibid, 6, 796.CrossRefGoogle Scholar
Oldziej, S., Liwo, A., Czaplewski, C., Pillardy, J. & Scheraga, H. A. (2004). Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins. Journal of Physical Chemistry B 108, 16934–16949.CrossRefGoogle Scholar
Ooi, T., Scott, R. A., Vanderkooi, G. & Scheraga, H. A. (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. Journal of Chemical Physics 46, 4410–4426.CrossRefGoogle ScholarPubMed
Owicki, J. C., & Scheraga, H. A. (1977). Monte Carlo calculations in the isothermal-isobaric ensemble. 2. Dilute aqueous solution of methane. Journal of the American Chemical Society 99, 7413–7418.CrossRefGoogle Scholar
Pauling, L., Corey, R. B. & Bransom, H. R. (1951). The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences of the United States of America 37, 205–211.CrossRefGoogle ScholarPubMed
Petkova, A. T., Yau, W. M. & Tycko, R. (2006). Experimental constraints on quaternary structure in Alzheimer's amyloid fibrils. Biochemistry 45, 498–512.CrossRefGoogle Scholar
Piela, L., Kostrowicki, J. & Scheraga, H. A. (1989). On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method. Journal of Physical Chemistry 93, 3339–3346.CrossRefGoogle Scholar
Pillardy, J., Czaplewski, C., Liwo, A., Lee, J., Ripoll, D. R., Kazmierkiewicz, R., Oldziej, S., Wedemeyer, W. J., Gibson, K. D., Arnautova, Y. A., Saunders, J., Ye, Y. J. & Scheraga, H. A. (2001). Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America 98, 2329–2333.CrossRefGoogle ScholarPubMed
Pillardy, J., Czaplewski, C., Wedemeyer, W. J. & Scheraga, H. A. (2000). Conformation-Family Monte Carlo (CFMC): an efficient computational method for identifying the low-energy states of a macromolecule. Helvetica Chimica Acta 83, 2214–2230.3.0.CO;2-E>CrossRefGoogle Scholar
Pincus, M. R. & Scheraga, H. A. (1979). Conformational energy calculations of enzyme-substrate and enzyme-inhibitor complexes of lysozyme. 2. Calculation of the structures of complexes with a flexible enzyme. Macromolecules 12, 633–644.CrossRefGoogle Scholar
Pincus, M. R., & Scheraga, H. A. (1981). Theoretical calculations on enzyme-substrate complexes: the basis of molecular recognition and catalysis. Accounts of Chemical Research 14, 299–306.CrossRefGoogle Scholar
Platzer, K. E. B., Ananthanarayanan, V. S., Andreatta, R. H. & Scheraga, H. A. (1972a). Helix-coil stability constants for the naturally occurring amino acids in water. IV. Alanine parameters from random poly(hydroxypropyl-glutamine-co-L-alanine). Macromolecules 5, 177–187.CrossRefGoogle Scholar
Platzer, K. E. B., Momany, F. A. & Scheraga, H. A. (1972b). Conformational energy calculations of enzyme–substrate interactions. I. Computation of preferred conformations of some substrates of α–chymotrypsin. International Journal of Peptide and Protein Research 4, 187–200.CrossRefGoogle Scholar
Platzer, K. E. B., Momany, F. A. & Scheraga, H. A. (1972c). Conformational energy calculations of enzyme–substrate interactions. II. Computation of the binding energy for substrates in the active site of α-chymotrypsin. International Journal of Peptide and Protein Research 4, 201–219.CrossRefGoogle Scholar
Poland, D. C. & Scheraga, H. A. (1965a). Statistical mechanics of non-covalent bonds in polyamino acids. I. Hydrogen bonding of solutes in water, and the binding of water to polypeptides. Biopolymers 3, 275–419. (1965a); 3, 593.CrossRefGoogle Scholar
Poland, D. C. & Scheraga, H. A. (1965b). Hydrophobic bonding and micelle stability. Journal of Physical Chemistry 69, 2431–2442.CrossRefGoogle Scholar
Poland, D. C. & Scheraga, H. A. (1966a). Hydrophobic bonding and micelle stability; the influence of ionic head groups. Journal of Colloid and Interface Science 21, 273–283.CrossRefGoogle Scholar
Poland, D. & Scheraga, H. A. (1966b). Phase transitions in one dimension, and the helix-coil transition in polyamino acids. Journal of Chemical Physics 45, 1456–1463.CrossRefGoogle ScholarPubMed
Poland, D. & Scheraga, H. A. (1966c). Occurrence of a phase transition in nucleic acid models. Journal of Chemical Physics 45, 1464–1469.CrossRefGoogle ScholarPubMed
Poland, D. & Scheraga, H. A. (1966d). Kinetics of the helix–coil transition in polyamino acids. Journal of Chemical Physics 45, 2071–2090.CrossRefGoogle ScholarPubMed
Poland, D. & Scheraga, H. A. (1969). The equilibrium unwinding in finite chains of DNA. Physiological Chemistry and Physics 1, 389–446.Google Scholar
Poland, D. & Scheraga, H. A. (1970). Theory of Helix–Coil Transitions in Biopolymers. New York: Academic Press.Google Scholar
Poland, D., Vournakis, J. N. & Scheraga, H. A. (1966). Cooperative interactions in single–strand oligomers of adenylic acid. Biopolymers 4, 223–235.CrossRefGoogle ScholarPubMed
Rhee, Y. M. & Pande, V. S. (2003). Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Journal of Biophysics 84, 775–786.CrossRefGoogle ScholarPubMed
Riehm, J. P., Broomfield, C. A. & Scheraga, H. A. (1965). The abnormal carboxyl groups of ribonuclease. II. Positions in the amino acid sequence. Biochemistry 4, 760–771.CrossRefGoogle Scholar
Ripoll, D. R. & Scheraga, H. A. (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, 1283–1303.CrossRefGoogle Scholar
Ripoll, D. R. & Scheraga, H. A. (1989). The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method; tests on encephalin. Journal of Protein Chemistry 8, 263–287.CrossRefGoogle Scholar
Ripoll, D. R., Liwo, A. & Scheraga, H. A. (1998). New Developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin. Biopolymers, 46, 117–126.3.0.CO;2-P>CrossRefGoogle ScholarPubMed
Rojas, A. V., Liwo, A., Browne, D. & Scheraga, H. A. (2010). Mechanism of fiber assembly; treatment of Αβ-peptide aggregation with a coarse-grained united-residue force field. Journal of Molecular Biology 404, 537–552.CrossRefGoogle Scholar
Rojas, A. V., Liwo, A. & Scheraga, H. A. (2007). Molecular dynamics with the united-residue (UNRES) force field. Ab initio folding simulations of multi-chain proteins. Journal of Physical Chemistry B 111, 293–309.CrossRefGoogle Scholar
Rojas, A. V., Liwo, A. & Scheraga, H. A. (2011). A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ 1–28). Journal of Physical Chemistry B 115, 12978–12983.CrossRefGoogle Scholar
Roterman, I. K., Lambert, M. H., Gibson, K. D. & Scheraga, H. A. (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. Journal of Biomolecular Structure and Dynamics 7, 421–453.CrossRefGoogle ScholarPubMed
Rothwarf, D. M., Li, Y. J. & Scheraga, H. A. (1998). Regeneration of bovine pancreatic ribonuclease A. Identification of two nativelike three-disulfide intermediates involved in separate pathways. Biochemistry 37, 3760–3766.CrossRefGoogle ScholarPubMed
Ryle, A. P., Sanger, F., Smith, L. F. & Kitai, R. (1955). The disulfide bonds of insulin. Biochemistry 60, 541–556.Google ScholarPubMed
Scheraga, H. A. (1955). Non-Newtonian viscosity of solutions of ellipsoidal particles. Journal of Chemical Physics 23, 1526–1532.CrossRefGoogle Scholar
Scheraga, H. A. (1957). Tyrosyl-carboxylate ion hydrogen bonding in ribonuclease. Biochemistry Biophysics Acta 23, 196–197.CrossRefGoogle ScholarPubMed
Scheraga, H. A. (1961). Protein Structure. New York: Academic Press.Google Scholar
Scheraga, H. A. (1967). Structural studies of pancreatic ribonuclease. Federation Proceedings 26, 1380–1387.Google ScholarPubMed
Scheraga, H. A. (1968). Calculations of conformations of polypeptides. Advances in Physical Organic Chemistry 6, 103–184.Google Scholar
Scheraga, H. A. (1969a). Calculation of conformations of polypeptides from amino acid sequence, Nobel Symposium 11, on Symmetry and Function of Biological Systems at the Macromolecular Level, (eds. Engstrom, A. & Strandberg, B.), pp. 43–78. Stockholm: Almqvist and Wiksell.Google Scholar
Scheraga, H. A. (1969b). Calculation of polypeptide conformation. The Harvey Lectures 63, 99–138.Google ScholarPubMed
Scheraga, H. A. (1971). Theoretical and experimental studies of conformations of polypeptides. Chemical Reviews 71, 195–217.CrossRefGoogle ScholarPubMed
Scheraga, H. A. (1973). On the dominance of short-range interactions in polypeptides and proteins. Pure and Applied Chemistry 36, 1–8.CrossRefGoogle Scholar
Scheraga, H. A. (1979). Interactions in aqueous solution. Accounts of Chemical Research 12, 7–14.CrossRefGoogle Scholar
Scheraga, H. A. (1984). Protein structure and function, from a colloidal to a molecular view. Carlsberg Research Communications 49, 1–55.CrossRefGoogle Scholar
Scheraga, H. A. (1998). Theory of hydrophobic interactions. Journal of Biomolecular Structure and Dynamics 16, 447–460.CrossRefGoogle ScholarPubMed
Scheraga, H. A. (2004). The thrombin–fibrinogen interaction. Biophysical Chemistry 112, 117–130.CrossRefGoogle ScholarPubMed
Scheraga, H. A. (2011a). Respice, Adspice, and Prospice. Annual Review of Biophysics 40, 1–39.CrossRefGoogle ScholarPubMed
Scheraga, H. A. (2011b). Ribonucleases as models for understanding protein folding. In Ribonucleases (ed. Nicholson, A. W.), In Nucleic Acids and Molecular Biology, (ed. Bujnicki, J.), pp. 367–397. Springer, Berlin.CrossRefGoogle Scholar
Scheraga, H. A. (2013). Simulations of the folding of proteins: A historical perspective. In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, from Bioinformatics to Molecular Quantum Mechanics (ed. Liwo, A.), pp. 1–23. Springer-Verlag, Berlin, Heidelberg, Ch. 1.Google Scholar
Scheraga, H. A. & Backus, J. K. (1951). Flow birefringence in solutions of n-hexadecyltrimethylammonium bromide. Journal of the American Chemical Society 73, 5108–5112.CrossRefGoogle Scholar
Scheraga, H. A. & Backus, J. K. (1952). Flow birefringence in arrested clotting systems. Journal of the American Chemical Society 74, 1979–1983.CrossRefGoogle Scholar
Scheraga, H. A., Edsall, J. T. & Gadd, J. O. JR (1951). Double refraction of flow: numerical evaluation of extinction angle and birefringence as a function of velocity gradient. Journal of Chemical Physics 19, 1101–1108.CrossRefGoogle Scholar
Scheraga, H. A., Konishi, Y. & Ooi, T. (1984). Multiple pathways for regenerating ribonuclease A. Advances in Biophysics 18, 21–41.CrossRefGoogle ScholarPubMed
Scheraga, H. A., Konishi, Y., Rothwarf, D. M. & Mui, P. W. (1987). Toward an understanding of the folding of ribonuclease A. Proceedings of the National Academy of Sciences of the United States of America 84, 5740–5744.CrossRefGoogle ScholarPubMed
Scheraga, H. A. & Laskowski, M. JR (1957). The fibrinogen-fibrin conversion. Advanced Protein Chemistry 12, 1–131.CrossRefGoogle Scholar
Scheraga, H. A. & Mandelkern, L. (1953). Consideration of the hydrodynamic properties of proteins. Journal of the American Chemical Society 75, 179–184.CrossRefGoogle Scholar
Scheraga, H. A. & Némethy, G. (1991). Calculated structures and stabilities of fibrous macromolecules. In Molecules in Natural Science and Medicine - an Encomium for Linus Pauling (eds. Maksic, Z. B. & Maksic, M. E.), pp. 141–176. Chichester: Ellis Horwood.Google Scholar
Scheraga, H. A., Némethy, G. & Steinberg, I. Z. (1962). The contribution of hydrophobic bonds to the thermal stability of protein conformations. Journal of Biological Chemistry 237, 2506–2508.CrossRefGoogle Scholar
Scheraga, H. A., Pillardy, J., Liwo, A., Lee, J., Czaplewski, C., Ripoll, D. R., Wedemeyer, W. J. & Arnautova, Y. A. (2002a). Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. Journal of Computational Chemistry 23, 28–34.CrossRefGoogle ScholarPubMed
Scheraga, H. A. & Rackovsky, S. (2014). Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. Proceedings of the National Academy of Sciences of the United States of America 111, 5225–5229.CrossRefGoogle ScholarPubMed
Scheraga, H. A., Vila, J. A. & Ripoll, D. R. (2002b). Helix–coil transitions re-visited. Biophysical Chemistry 101–102, 255–265.CrossRefGoogle ScholarPubMed
Schmid, F. X. (1986). Fast-folding and slow-folding forms of unfolded proteins. Methods in Enzymology 131, 70–82.CrossRefGoogle ScholarPubMed
Schneider, H., Kresheck, G. C. & Scheraga, H. A. (1965). Thermodynamic parameters of hydrophobic bond formation in a model system. Journal of Physical Chemistry 69, 1310–1324.CrossRefGoogle Scholar
Schrier, E. E., Pottle, M. & Scheraga, H. A. (1964). The influence of hydrogen and hydrophobic bonds on the stability of the carboxylic acid dimers in aqueous solution. Journal of the American Chemical Society 86, 3444–3449.CrossRefGoogle Scholar
Senet, P., Maisuradze, G. G., Foulie, C., Delarue, P. & Scheraga, H. A. (2008). How main-chains of proteins explore the free-energy landscape in native states. Proceedings of the National Academy of Sciences of the United States of America 105, 19708–19713.CrossRefGoogle ScholarPubMed
Sheng, M. & Sala, C. (2001). PDZ domains and the organization of supramolecular complexes. Annual Review of Neuroscience 24, 1–29.CrossRefGoogle ScholarPubMed
Siegel, B. M., Mernan, J. P. & Scheraga, H. A. (1953). The configuration of native and partially polymerized fibrinogen. Biochemistry Biophysics Acta 11, 329–336.CrossRefGoogle Scholar
Sieradzan, A. K., Hansmann, U. H. E., Scheraga, H. A. & Liwo, A. (2012a). Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. Journal of Chemical Theory and Computation 8, 4746–4757.CrossRefGoogle Scholar
Sieradzan, A. K., Scheraga, H. A. & Liwo, A. (2012b). Determination of the potentials of mean force for stretching of Cα…Cα virtual bonds in polypeptides from the ab initio energy surfaces of terminally-blocked N-methylacetamide and N-pyrrolidylacetamide. In From Computational Biophysics to Systems Biology (CBSB11) (eds. Carloni, P., Hansmann, U. H. E., Lippert, T., Meinke, J. H., Mohanty, S., Nadler, W. and Zimmermann, O.), vol. 8, pp. 191–195. Forschungszentrum Jülich.Google Scholar
Smith-Gill, S. J., Rupley, J. A., Pincus, M. R., Carty, R. P. & Scheraga, H. A. (1984). Experimental identification of a theoretically predicted “left-sided” binding mode for (GlcNAc)6 in the active site of lysozyme. Biochemistry 23, 993–997.CrossRefGoogle ScholarPubMed
Staudinger, J., Zhou, J., Burgess, R., Elledge, S. J. & Olson, E. N. (1995). PICK1: a perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system. Journal of Cellular Biology 128, 263–271.CrossRefGoogle ScholarPubMed
Steinberg, I. Z. & Scheraga, H. A. (1963). Entropy changes accompanying association reactions of proteins. Journal of Biological Chemistry 238, 172–181.CrossRefGoogle ScholarPubMed
Sturtevant, J. M., Laskowski, M. JR, Donnelly, T. H. & Scheraga, H. A. (1955). Equilibria in the fibrinogen fibrin conversion. III. Heats of polymerization and clotting of fibrin monomer. Journal of the American Chemical Society 77, 6168–6172.CrossRefGoogle Scholar
Sumner, J. B. (1933). The chemical nature of enzymes. Science 78, 335.CrossRefGoogle ScholarPubMed
Sumner, J. B., Gralén, N. & Eriksson-Quensel, I. B. (1938). The molecular weights of urease, canavalin, concanavalin A and concanavalin B. Science 87, 395–396.CrossRefGoogle ScholarPubMed
Sun, T., Lin, F. H., Cambell, R. L., Allingham, J. S. & Davies, P. L. (2014). An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters. Science 343, 795–798.CrossRefGoogle ScholarPubMed
Takei, K., Slepnev, V. I., Haucke, V. & De Camilli, P. (1999). Functional partnership between amphiphysin and dynamin in clathrin-mediated endocytosis. Nature Cell Biology 1, 33–39.CrossRefGoogle ScholarPubMed
Tanaka, S. & Scheraga, H. A. (1977). Hypothesis about the mechanism of protein folding. Macromolecules 10, 291–304.CrossRefGoogle ScholarPubMed
Tanford, C., Hauenstein, J. D. & Rands, D. G. (1955). Phenolic hydroxyl ionization in proteins. II. Ribonuclease. Journal of the American Chemical Society 77, 6409–6413.CrossRefGoogle Scholar
Telford, J. N., Nagy, J. A., Hatcher, P. A. & Scheraga, H. A. (1980). Location of peptide fragments in the fibrinogen molecule by immunoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America 77, 2372–2376.CrossRefGoogle ScholarPubMed
Tycko, R. (2006). Molecular structure of amyloid fibrils: insights from solid-state NMR. Quarterly Review of Biophysics 39, 1–55.CrossRefGoogle ScholarPubMed
Vila, J. A., Arnautova, Y. A., Martin, O. A. & Scheraga, H. A. (2009a). Quantum-mechanics-derived 13Cα chemical shift server (Che Shift) for protein structure validation. Proceedings of the National Academy of Sciences of the United States of America 106, 16972–16977.CrossRefGoogle Scholar
Vila, J. A., Arnautova, Y. A., Vorobjev, Y. & Scheraga, H. A. (2011). Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proceedings of the National Academy of Sciences of the United States of America 108, 5602–5607.CrossRefGoogle ScholarPubMed
Vila, J. A., Baldoni, H. A. & Scheraga, H. A. (2009b). Performance of density functional models to reproduce observed 13Cα chemical shifts of proteins in solution. Journal of Computational Chemistry 30, 884–892.CrossRefGoogle ScholarPubMed
Vila, J. A., Ripoll, D. R. & Scheraga, H. A. (2003). Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proceedings of the National Academy of Sciences of the United States of America 100, 14812–14816.CrossRefGoogle Scholar
Vila, J. A. & Scheraga, H. A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of 13Cα chemical shifts. Accounts of Chemical Research 42, 1545–1553.CrossRefGoogle ScholarPubMed
Vila, J. A., Villegas, M. E., Baldoni, H. A. & Scheraga, H. A. (2007). Predicting 13Cα chemical shifts for validation of protein structures. Journal of Biomolecular NMR 38, 221–235.CrossRefGoogle ScholarPubMed
Von Dreele, P. H., Lotan, N., Ananthanarayanan, V. S., Andreatta, R. H., Poland, D. & Scheraga, H. A. (1971a). Helix-coil stability constants for the naturally occurring amino acids in water. II. Characterization of the host polymers and application of the host-guest technique to random poly(hydroxyproplyglutamine-co-hydroxybutylglutamine). Macromolecules 4, 408–417.CrossRefGoogle Scholar
Von Dreele, P. H., Poland, D. & Scheraga, H. A. (1971b). Helix-coil stability constants for the naturally occurring amino acids in water. I. Properties of copolymers and approximate theories. Macromolecules 4, 396–407.CrossRefGoogle Scholar
Von Stackelberg, M. & Meuthem, B. (1958). Feste gashydrate Vii. Hydrate wasserlöslicher äther. Zeitschrift Elektrochemistry 62, 130–131.Google Scholar
Von Stackelberg, M. & Müller, H. R. (1954). Feste gashydrate II. Strukur und raumchemi. Zeitschrift Elektrochemistry 58, 25–39.Google Scholar
Vournakis, J. N., Poland, D. & Scheraga, H. A. (1967). Anti-cooperative interactions in single-strand oligomers of deoxyriboadenylic acid. Biopolymers 5, 403–422.CrossRefGoogle ScholarPubMed
Vournakis, J. N., Scheraga, H. A., Rushizky, G. W. & Sober, H. A. (1966). Neighbor–neighbor interactions in single–strand polynucleotides; optical rotatory dispersion studies of the ribonucleotide ApApCp. Biopolymers 4, 33–41.CrossRefGoogle Scholar
Wako, H. & Scheraga, H. A. (1982a). Distance-constraint approach to protein folding. I. Statistical analysis of protein conformations in terms of distances between residues. Journal of Protein Chemistry 1, 5–45.CrossRefGoogle Scholar
Wako, H. & Scheraga, H. A. (1982b). Distance-constraint approach to protein folding. II. Prediction of three-dimensional structure of bovine pancreatic trypsin inhibitor. Journal of Protein Chemistry 1, 85–117.CrossRefGoogle Scholar
Wales, D. J. & Scheraga, H. A. (1999). Global optimization of clusters, crystals and biomolecules. Science 285, 1368–1372.CrossRefGoogle ScholarPubMed
Warme, P. K., Momany, F. A., Rumball, S. V., Tuttle, R. W. & Scheraga, H. A. (1974). Computation of structures of homologous proteins; α-lactalbumin from lysozyme. Biochemistry 13, 768–782.CrossRefGoogle ScholarPubMed
Wlodawer, A. & Sjölin, L. (1983). Structure of ribonuclease A. Results of joint neutron and x-ray refinement at 2.0-Å resolution. Biochemistry 22, 2720–2728.CrossRefGoogle Scholar
Wojcik, J., Altmann, K. H., & Scheraga, H. A. (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, 121–134.CrossRefGoogle Scholar
Woody, R. W., Friedman, M. E., Scheraga, H. A. (1966). Structural studies of ribonuclease. XXII. Location of the third buried tyrosyl residue in ribonuclease. Biochemistry 5, 2034–2042.CrossRefGoogle ScholarPubMed
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. Wiley Interscience.CrossRefGoogle Scholar
Xu, X. & Scheraga, H. A. (1998). Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40–95] disulfide bond. Biochemistry 37, 7561–7571.CrossRefGoogle ScholarPubMed
Xu, X., Rothwarf, D. M. & Scheraga, H. A. (1996). Nonrandom distribution of the one-disulfide intermediates in the regeneration of ribonuclease A. Biochemistry 35, 6406–6417.CrossRefGoogle ScholarPubMed
Yan, J. F., Momany, F. A. & Scheraga, H. A. (1970). Conformational analysis of macromolecules. VI. Helical Structures of o-, m-, and p-chlorobenzyl Esters of Poly-L-Aspartic Acid. Journal of the American Chemical Society 92, 1109–1115.CrossRefGoogle Scholar
Yan, J. F., Vanderkooi, G. & Scheraga, H. A. (1968). Conformational analysis of macromolecules. V. Helical structures of poly–L–aspartic acid and poly-L-glutamic acid, and related compounds. Journal of Chemical Physics 49, 2713–2726.CrossRefGoogle ScholarPubMed
Yin, Y., Sieradzan, A. K., Liwo, A., He, Y. & Scheraga, H. A. (2015) Physics-based potentials for coarse-grained modeling of protein-DNA interactions. Journal of Chemical Theory and Computation, in press.CrossRefGoogle ScholarPubMed
Zeng, Y., Montrichok, A. & Zocchi, G. (2004). Bubble nucleation and cooperativity in DNA melting. Journal of Molecular Biology 339, 67–75.CrossRefGoogle ScholarPubMed
Zimm, B. H. & Bragg, J. K. (1959). Theory of the phase transition between helix and random coil in polypeptide chains. Journal of Chemical Physics 31, 526–535.CrossRefGoogle Scholar