A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems

Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three‐dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent.

[1]  P. Y. Chou,et al.  Conformational studies on copolymers of hydroxypropyl-L-glutamine and L-leucine. Circular dichroism studies. , 1972, Biochemistry.

[2]  Lawrence B. Evans,et al.  Thermodynamic representation of phase equilibria of mixed‐solvent electrolyte systems , 1986 .

[3]  Georg E. Schulz,et al.  Principles of Protein Structure , 1979 .

[4]  George B. Benedek,et al.  Phenomenological theory of equilibrium thermodynamic properties and phase separation of micellar solutions , 1986 .

[5]  J. Hermans.  Experimental free energy and enthalpy of formation of the alpha-helix. , 1966, The Journal of physical chemistry.

[6]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[7]  H. Scheraga,et al.  Helix-Coil Stability for the Naturally Occurring Amino Acids in Water. VIII. Valine Parameters from Random Poly(hydroxypropylglutamine-co-L-valine) and Poly(hydroxybutylglutamine-co-L-valine) , 1973 .

[8]  H. Scheraga,et al.  Helix--coil stability constants for the naturally occurring amino acids in water. X. Tyrosine parameters from random poly(hydroxypropylglutamine-co-L-tyrosine). , 1972, Macromolecules.

[9]  L. Pauling,et al.  The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[10]  H. Scheraga,et al.  Conformational studies of poly‐L‐alanine in water , 1968, Biopolymers.

[11]  H. Scheraga,et al.  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 , 1984, Biopolymers.

[12]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[13]  H. Scheraga,et al.  Helix‐coil stability constants for the naturally occurring amino acids in water. XII. Asparagine parameters from random poly(hydroxybutylglutamine‐co‐L‐asparagine) , 1977, Biopolymers.

[14]  Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 18. Tryptophan Parameters from Random Poly[(hydroxypropyl)glutamine-co-L-tryptophan] , 1980 .

[15]  C. D. Barry,et al.  Comparison of predicted and experimentally determined secondary structure of adenyl kinase , 1974, Nature.

[16]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[17]  D Eisenberg,et al.  Hydrophobicity and amphiphilicity in protein structure , 1986, Journal of cellular biochemistry.

[18]  H. Scheraga.  Use of random copolymers to determine the helix-coil stability constants of the naturally occurring amino acids , 1978 .

[19]  J. King,et al.  Deciphering the Rules of Protein Folding , 1989 .

[20]  M. Huggins.  Solutions of Long Chain Compounds , 1941 .

[21]  J. Prausnitz,et al.  LOCAL COMPOSITIONS IN THERMODYNAMIC EXCESS FUNCTIONS FOR LIQUID MIXTURES , 1968 .

[22]  E. Blout,et al.  A new technique for producing oriented synthetic polypeptides: Some initial results , 1963 .

[23]  Herbert I. Britt,et al.  Local composition model for excess Gibbs energy of electrolyte systems. Part I: Single solvent, single completely dissociated electrolyte systems , 1982 .

[24]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[25]  Helix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine] , 1981 .

[26]  G. Allegua.  The calculation of average functions of local conformations for a non-interacting copolymer system with neighbor interactions , 1967 .

[27]  M. Huggins.  Some Properties of Solutions of Long-chain Compounds. , 1942 .

[28]  Aage Fredenslund,et al.  Group‐contribution estimation of activity coefficients in nonideal liquid mixtures , 1975 .

[29]  Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 17. Threonine Parameters from Random Poly(hydroxylbutylglutamine-co-L-threonine) , 1978 .

[30]  Isidor Kirshenbaum,et al.  The Vapor Pressure and Heat of Vaporization of N15 , 1941 .

[31]  D. Davies,et al.  A CORRELATION BETWEEN AMINO ACID COMPOSITION AND PROTEIN STRUCTURE. , 1964, Journal of molecular biology.

[32]  Lawrence B. Evans,et al.  A local composition model for the excess Gibbs energy of aqueous electrolyte systems , 1986 .

[33]  H. Scheraga,et al.  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) , 1990 .

[34]  T. Alan Hatton,et al.  Amino acids in AOT reversed micelles. 2. The hydrophobic effect and hydrogen bonding as driving forces for interfacial solubilization , 1990 .

[35]  J. S. Rowlinson,et al.  Molecular Thermodynamics of Fluid-Phase Equilibria , 1969 .

[36]  P M Cullis,et al.  Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.

[37]  Harold A. Scheraga,et al.  Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly[(hydroxybutyl)glutamine-co-L-histidine] , 1984 .

[38]  O. Ptitsyn,et al.  Thermodynamic parameters of helix‐coil transition in polypeptide chains I. Poly‐(L‐glutamic acid) , 1971, Biopolymers.

[39]  V. Lim.  Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. , 1974, Journal of molecular biology.

[40]  H. Scheraga,et al.  Helix‐coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamine‐CO‐L‐proline) , 1990, Biopolymers.

[41]  C. Chothia.  The nature of the accessible and buried surfaces in proteins. , 1976, Journal of molecular biology.

[42]  J. Richardson,et al.  Principles and Patterns of Protein Conformation , 1989 .

[43]  P. S. Kim,et al.  Intermediates in the folding reactions of small proteins. , 1990, Annual review of biochemistry.

[44]  A. Ben-Naim.  Solvent effects on protein association and protein folding , 1990, Biopolymers.

[45]  G. Fasman,et al.  The conformational transitions of uncharged poly-L-lysine. Alpha helix-random coil-beta structure. , 1967, Biochemistry.

[46]  J M Prausnitz.  Molecular Thermodynamics for Chemical Process Design , 1979, Science.

[47]  A. Holtzer,et al.  The stability of the polyglutamic acid alpha helix. , 1968, Journal of the American Chemical Society.

[48]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[49]  Chau‐Chyun Chen,et al.  Phase Partitioning of Biomolecules: Solubilities of Amino Acids , 1989 .

[50]  H. Scheraga,et al.  Helix–coil stability constants for the naturally occurring amino acids in water. XXI. Glutamine parameters from random poly(hydroxypropylglutamine‐co‐L‐glutamine) and poly(hydroxybutylglutamine‐co‐L‐glutamine) , 1982 .

[51]  M. Sternberg,et al.  Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. , 1987, Journal of molecular biology.

[52]  G. Schulz,et al.  Three-dimensional structure of adenyl kinase , 1974, Nature.

[53]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[54]  Gunnar von Heijne,et al.  Trans‐membrane Translocation of Proteins , 1979 .

[55]  E. R. Blout,et al.  THE DEPENDENCE OF THE CONFORMATIONS OF SYNTHETIC POLYPEPTIDES ON AMINO ACID COMPOSITION1,2 , 1960 .

[56]  C Chothia,et al.  Conformation of acetylcholine at muscarinic nerve receptors: crystal and molecular structure of 2-trimethylammoniummethyl-5-methyl furan iodide (5-methylfurmethide iodide). , 1976, Journal of molecular biology.

[57]  H. Scheraga,et al.  Helix‐coil stability constants for the naturally occuring amino acids in water. XIV. Methionine parameters from random poly(hydroxypropylglutamine,L‐Methionine) , 1977, Biopolymers.

[58]  Douglas Poland,et al.  Theory of helix-coil transitions in biopolymers , 1970 .

[59]  P. Y. Chou,et al.  Prediction of protein conformation. , 1974, Biochemistry.

[60]  P. Flory.  Thermodynamics of High Polymer Solutions , 1941 .

[61]  E. Peggion,et al.  Ultraviolet Rotatory Properties of Synthetic Polypeptides in Solution. II. The Behavior of Poly(1-benzyl-L-histidine) in Trifluoroethanol in the Presence of Different Acids , 1971 .

[62]  H. Scheraga,et al.  Helix-coil stability constants for the naturally occurring amino acids in water. IX. Glutamic acid parameters from random poly(hydroxybutylglutamine-co-L-glutamic acid). , 1975, Macromolecules.

[63]  J. Janin,et al.  Surface and inside volumes in globular proteins , 1979, Nature.

[64]  S. Lifson.  Theory of the helix–coil transition in DNA considered as a copolymer , 1963 .

[65]  H. Scheraga,et al.  Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. VI. Leucine Parameters from Random Poly(hydroxypropylglutamine-co-L-leucine) and Poly(hydroxybutylglutamine-co-L-leucine) , 1972 .