Peptide and protein folding

Abstract Ab initio peptide folding, and its role in the reductionistic approach towards the understanding of protein folding are discussed from the points of view of past, present and possible future developments. It is believed that after the initial holistic approach, we are now at a new epoch, which will be dominated by reductionism. New quantitative mathematical models will be the result of the reductionistic approach that will lead toward a new, more sophisticated holistic era.

[1]  J. W. Otvos,et al.  Raman Spectra of Amino Acids and Related Compounds. VII. Glycylglycine, Cysteine, Cystine and Other Amino Acids1 , 1950 .

[2]  Imre G. Csizmadia,et al.  Peptide models XXV. Side-chain conformational potential energy surface, E = E(χ1, χ2) of N-formyl-L-aspartic acidamide and its conjugate base N- formyl-L-aspartatamide in their γ(L) backbone conformations , 2000 .

[3]  G. Allegra,et al.  Good-and bad-solvent effect on the rotational statistics of a long chain molecule , 1998 .

[4]  Imre G. Csizmadia,et al.  Peptide Models. 3. Conformational Potential Energy Hypersurface of Formyl-l-valinamide , 1993 .

[5]  H. J. Woods,et al.  X-Ray Studies of the Structure of Hair, Wool, and Related Fibres. II. The Molecular Structure and Elastic Properties of Hair Keratin , 1934 .

[6]  A. Perczel,et al.  Prospects in computational molecular medicine: a millennial mega-project on peptide folding , 2000 .

[7]  C M Dobson,et al.  Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin. , 1989, Biochemistry.

[8]  A. Perczel,et al.  Peptide models 6. New .beta.-turn conformations from ab initio calculations confirmed by x-ray data of proteins , 1993 .

[9]  Gg Balint-Kurti,et al.  Lecture notes in Chemistry , 2000 .

[10]  R. Edelman,et al.  Clinical magnetic resonance imaging , 1990 .

[11]  J. Rivail,et al.  Peptide models 4. Topological features of molecular mechanics and ab initio 2D-ramachandran maps: Conformational data for for-Gly-NH2, for-l-Ala-NH2, Ac-l-Ala-NHMe and for-l-Val-NH2 , 1993 .

[12]  Timothy F. Havel,et al.  Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. , 1987, Journal of molecular biology.

[13]  Conmar Robinson,et al.  Atomic models. Part 1.—A new type of space filling atomic models , 1952 .

[14]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

[15]  D. Pérahia,et al.  Molecular orbital calculations on the conformation of polypeptides and proteins. V. Conformational energy maps and stereochemical rotational states of aliphatic residues , 1971, Biopolymers.

[16]  H. Scheraga,et al.  Influence of flexibility on the energy contours of dipeptide maps. , 1966, Biopolymers.

[17]  A. Perczel,et al.  Peptide models XVI. The identification of selected HCO—L—SER—NH2 conformers via a systematic grid search using ab initio potential energy surfaces , 1996 .

[18]  R. Kaptein,et al.  Nonselective three-dimensional nmr spectroscopy. The 3D NOE-HOHAHA experiment , 1988 .

[19]  D. Peters,et al.  Quantum theory of the structure and bonding in proteins: Part 16. The asparagine dipeptide , 1984 .

[20]  J. Edsall.  Raman Spectra of Amino Acids and Related Compounds. II. Guanidine and Urea Derivatives. , 1937 .

[21]  Robert L. Baldwin,et al.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.

[22]  R. Corey,et al.  Interatomic Distances and Bond Angles in the Polypeptide Chain of Proteins1,2 , 1950 .

[23]  A. Perczel,et al.  Peptide models XII Topological features of molecular mechanics and ab-initio 8D-Ramachandran maps. Conformational data for Ac-(l-Ala)4-NHMe and For-(l-Ala)4-NH2 , 1995 .

[24]  K. Bailey,et al.  The X-ray interpretation of denaturation and the structure of the seed globulins. , 1935, The Biochemical journal.

[25]  M. Tsuboi.  On Hydrogen Bonds Intimately Related with π-Electron Systems , 1952 .

[26]  J. Kendrew,et al.  Polypeptide chain configurations in crystalline proteins , 1950, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[27]  Peptide models XIII. Side-chain conformational energy surface E = E( ? 1, ? 2) of N- formyl- l- seri , 1995 .

[28]  P. Kraulis,et al.  Three-dimensional NMR spectroscopy of a protein in solution , 1988, Nature.

[29]  J. R. Downing,et al.  Infrared Absorption Studies. XI. NH-N and NH-O Bonds , 1940 .

[30]  G. Sutherland,et al.  The Infra‐Red Absorption of Carboxylic Acids in Solution I. Qualitative Features , 1938 .

[31]  G. N. Ramachandran,et al.  Stereochemical criteria for polypeptide and protein chain conformations. 3. Helical and hydrogen-bonded polypeptide chains. , 1966, Biophysical journal.

[32]  F. Momany,et al.  Ab initio studies of molecular geometries. 27. Optimized molecular structures and conformational analysis of N.alpha.-acetyl-N-methylalaninamide and comparison with peptide crystal data and empirical calculations , 1983 .

[33]  R. Hoffmann,et al.  Quantum mechanical approach to the conformational analysis of macromolecules in ground and excited states , 1969 .

[34]  M. Perutz,et al.  Structure and function of hemoglobin. , 1969, Harvey lectures.

[35]  E. J. Ambrose,et al.  New Evidence on the structure of Some Proteins from Measurements with Polarized Infra-red Radiation , 1949, Nature.

[36]  H. Scheraga,et al.  Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method , 1965 .

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

[38]  G. N. Ramachandhan.  Need for nonplanar peptide units in polypeptide chains. , 1968 .

[39]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[40]  Stefan Brode,et al.  Ab initio SCF calculations on low‐energy conformers of cyclohexaglycine , 1995, J. Comput. Chem..

[41]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[42]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[43]  S. Edwards,et al.  The Theory of Polymer Dynamics , 1986 .

[44]  B. Honig,et al.  On the formation of protein tertiary structure on a computer. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Harold A. Scheraga,et al.  Energy Parameters in Polypeptides. VI. Conformational Energy Analysis of the N‐Acetyl N′‐Methyl Amides of the Twenty Naturally Occurring Amino Acids , 1973 .

[46]  C. Anfinsen.  The Molecular Basis of Evolution , 1959, The Yale Journal of Biology and Medicine.

[47]  Peptide models XXIV: An ab initio study on N-formyl-L-prolinamide with trans peptide bond. The existence or non-existence of αL and ϵL conformations , 1999 .

[48]  D. Gruen,et al.  Infrared absorption spectra of some amino acids and their complexes. , 1948, The Journal of physical and colloid chemistry.

[49]  S. Mizushima,et al.  Intramolecular Rotation and the Structure of High Polymers. I. The Structure of Polypeptide Chain , 1948 .

[50]  F. Momany,et al.  Conformational transitions and geometry differences between low‐energy conformers of N‐acetyl‐N′‐methyl alanineamide: An ab initio study at the 4‐21G level with gradient relaxed geometries , 1984 .

[51]  D. Crowfoot.  The crystal structure of insulin I. The investigation of air-dried insulin crystals. , 1938, Proceedings of the Royal Society of London. Series A - Mathematical and Physical Sciences.

[52]  G. Raos,et al.  Macromolecular clusters in poor-solvent polymer solutions , 1997 .

[53]  L. Schäfer,et al.  Ab initio studies of structural features not easily amenable to experiment. 23. Molecular structures and conformational analysis of the dipeptide N‐acetyl‐N′‐methyl glycyl amide and the significance of local geometries for peptide structures , 1982 .

[54]  D. Cowburn,et al.  An ab initio study of intermolecular hydrogen bonding between small peptide fragments , 1986 .

[55]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[56]  J. M. Pocock,et al.  Computer Simulations of Protein Structures and Interactions , 1995 .

[57]  Frank A. Momany,et al.  Importance of correlation-gradient geometry optimization for molecular conformational analyses , 1992 .

[58]  J. Whitten,et al.  Self-consistent field studies of glycine and glycylglycine. The simplest example of a peptide bond. , 1972, Journal of the American Chemical Society.

[59]  R. Corey,et al.  The Crystal Structure of Glycine , 1939 .

[60]  G. Sutherland,et al.  The estimation of the leucine isomers in protein hydrolysates by infrared analysis. , 1948, The Biochemical journal.

[61]  D. Peters,et al.  Quantum theory of the structure and bonding in proteins. XVI: The asparagine dipeptide , 1982 .

[62]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[63]  H. Scheraga,et al.  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 , 1975 .

[64]  Paul J. Flory,et al.  The Configuration of Real Polymer Chains , 1949 .

[65]  A. Hopfinger,et al.  Theoretical evaluation of polytripeptide collagen models , 1970 .

[66]  S. Prusiner,et al.  Molecular biology and genetics of prion diseases. , 1994, Cold Spring Harbor symposia on quantitative biology.

[67]  Peptide models XXVII. An exploratory ab initio study on the 21st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe) in their γL backbone conformation , 2000 .

[68]  H. Scheraga,et al.  Energy parameters in polypeptides. IV. Semiempirical molecular orbital calculations of conformational dependence of energy and partial charge in di- and tripeptides. , 1971, The Journal of physical chemistry.

[69]  A. Perczel,et al.  Peptide Models 10. Topological features of molecular mechanics and ab initio 6D-Ramachandran maps. Conformational data for Ac-l-Ala-l-Ala-l-Ala-NHMe andFor-l-Ala-l-Ala-l-Ala-NH2 , 1994 .

[70]  M. Sternberg,et al.  On the prediction of protein structure: The significance of the root-mean-square deviation. , 1980, Journal of molecular biology.

[71]  B. Robson,et al.  Expert system for protein engineering: its application in the study of choramphenicol acetyltransferase and avian pancreatic polypeptide , 1987 .

[72]  M. Tsuboi,et al.  The Molecular Structure of N-Methylacetamide , 1950 .

[73]  Imre G. Csizmadia,et al.  Peptide models. 1. Topology of selected peptide conformational potential energy surfaces (glycine and alanine derivatives) , 1991 .

[74]  Timothy F. Havel,et al.  A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular1H−1H proximities in solution , 1984 .

[75]  Michael J. Frisch,et al.  Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: II , 1998 .

[76]  J. Edsall,et al.  Raman Spectra of Amino Acids and Related Compounds V. Deuterium Substitution in the Amino Group , 1940 .

[77]  G M Crippen,et al.  A survey of atom packing in globular proteins. , 2009, International journal of peptide and protein research.

[78]  A. M. Liquori,et al.  Van Der Waals Interaction and the Stability of Helical Polypeptide Chains , 1965, Nature.

[79]  M. Robb,et al.  Non-empirical LCAO-MO-SCF-CI calculations on organic molecules with Gaussian type functions , 1966 .

[80]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[81]  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.

[82]  M. Perutz,et al.  New X-Ray Evidence on the Configuration of Polypeptide Chains: Polypeptide Chains in Poly-γ-benzyl-L-glutamate, Keratin and Hæmoglobin , 1951, Nature.

[83]  R. Richards,et al.  237. Spectroscopic studies of the amide linkage , 1947 .

[84]  V. Sasisekharan,et al.  Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit , 1971, Biopolymers.

[85]  R. J. Boyd,et al.  Ab-initio molecular orbital study of the cis/trans conformations of the peptide bond. , 1981 .

[86]  N. Wright.  THE INFRA-RED ABSORPTION SPECTRA OF AMINO ACIDS , 1939 .

[87]  A. Khokhlov,et al.  Some problems of the statistical physics of polymer chains with volume interaction , 1978 .

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

[89]  J. Edsall.  Raman Spectra of Amino Acids and Related Compounds I. The Ionization of the Carboxyl Group , 1936 .

[90]  Johnson F. Yan,et al.  Energy parameters in polypeptides. II. Semiempirical molecular orbital calculations for model peptides , 1970 .

[91]  Lothar Schäfer,et al.  Evaluation of the dipeptide approximation in peptide modeling by ab initio geometry optimizations of oligopeptides , 1993 .

[92]  P. Flory,et al.  Statistical Mechanics of Dilute Polymer Solutions. II , 1950 .

[93]  H. Mark,et al.  Über den Aufbau des Seiden‐Fibroins , 1928 .

[94]  N. A. Kuebler,et al.  Electronic States of the Amide Group , 1967 .

[95]  A. Perczel,et al.  Peptide models VII The ending of the right-handed helices in oligopeptides [For-(Ala)n-NH2 for 2 ⩽ n ⩽ 4] and in proteins , 1995 .

[96]  A. Perczel,et al.  Peptide models. 18. Hydroxymethyl side-chain induced backbone conformational shifts of L-serine amide. All ab initio conformers of For-L-Ser-NH2 , 1996 .

[97]  S. Krimm,et al.  Ab initio force fields of glycine dipeptide in C5 and C7 conformations , 1989 .

[98]  D. Peters,et al.  Quantum theory of the structure and bonding in proteins: Part 7. The α helix and the hydrogen bonding in the tetrapeptide , 1980 .

[99]  Imre G. Csizmadia,et al.  Characteristics of Ramachandran maps of L-alanine diamides as computed by various molecular mechanics, semiempirical and ab initio MO methods.: A search for primary standard of peptide conformational stability , 1998 .

[100]  M. Huggins.  The Structure of Fibrous Proteins. , 1943 .

[101]  M. Dreyfus,et al.  Molecular orbital calculations on the conformation of polypeptides and proteins. I. Preliminary investigations and simple dipeptides. , 1970, Journal of theoretical biology.

[102]  L Wang,et al.  The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[103]  J. Edsall.  Raman Spectra of Amino Acids and Related Substances III. Ionization and Methylation of the Amino Group , 1937 .

[104]  Klevit Re,et al.  Two-dimensional 1H NMR studies of histidine-containing protein from Escherichia coli. 3. Secondary and tertiary structure as determined by NMR. , 1986 .

[105]  S. Bauer,et al.  Spectroscopic Studies of the Hydrogen Bond. II. The Shift of the O–H Vibrational Frequency in the Formation of the Hydrogen Bond , 1937 .

[106]  C. Bamford,et al.  Solubilities of the αII- and β-Forms of Synthetic Polypeptides: Evidence for an αII–β Transformation in the Amorphous Phase , 1950, Nature.

[107]  Peter A. Kollman,et al.  Quantum and molecular mechanical studies on alanyl dipeptide , 1984 .

[108]  Wolfgang Damm,et al.  Reversible peptide folding: Dependence on molecular force field used , 2000 .

[109]  A. Perczel,et al.  Peptide models 8. The use of a modified Romberg formalism for the extrapolation of molecular properties from oligomers to polymers. Polyalanine diamide in its “extended like” or (βL)n or (C5)n conformation , 1994 .

[110]  Raymond F. Borkman,et al.  AB INITIO SCF STUDIES OF THE PEPTIDES GLY-GLY, GLY-ALA, ALA-GLY, AND GLY-GLY-GLY , 1982 .

[111]  G. Sutherland,et al.  Evidence from Infra-Red Spectroscopy on the Structure of Proteins , 1949, Nature.

[112]  A. Perczel,et al.  Peptide models 5. Topological features of molecular mechanics and ab initio 4D-Ramachandran maps , 1993 .

[113]  Gustavo E. Scuseria,et al.  Geometry Optimization of Kringle 1 of Plasminogen Using the PM3 Semiempirical Method , 2000 .

[114]  A. Perczel,et al.  Peptide models XIX: Side-chain conformational energy surface and amide I vibrational frequencies of N-formyl-l-phenylalaninamide (For-Phe-NH2) in its γL or γinv or C7eq backbone conformation , 1996 .

[115]  William Thomas Astbury,et al.  X-Ray Studies of the Structure of Hair, Wool, and Related Fibres. I. General , 1932 .

[116]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

[117]  A G Császár,et al.  Ab initio characterization of building units in peptides and proteins. , 1999, Progress in biophysics and molecular biology.

[118]  A. E. Martin,et al.  Investigations of infra-red spectra-absorption of some hydroxy compounds in the region of 3μ , 1937, Proceedings of the Royal Society of London. Series A - Mathematical and Physical Sciences.

[119]  R. G. Hart,et al.  Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution , 1960, Nature.

[120]  D. Pérahia,et al.  Molecular orbital calculations on the conformation of polypeptides and proteins. IV. The conformation of the prolyl and hydroxyprolyl residues. , 1970, Journal of theoretical biology.

[121]  Charles L. Brooks,et al.  Theoretical study of blocked glycine and alanine peptide analogs , 1991 .

[122]  T. Creighton,et al.  Protein Folding , 1992 .

[123]  K. Wüthrich,et al.  Conformation of [Cd7]-metallothionein-2 from rat liver in aqueous solution determined by nuclear magnetic resonance spectroscopy. , 1991, Journal of molecular biology.

[124]  A. Perczel,et al.  Searching for the simplest structural units to describe the three-dimensional structure of proteins , 1995 .

[125]  P. V. van Duijnen,et al.  Cooperative effects in α‐helices: An ab initio molecular‐orbital study , 1982 .

[126]  L. Schäfer,et al.  Ab initio geometry refinement of some selected structures of the model dipeptide N-acetyl N'-methyl serine amide☆ , 1987 .

[127]  Ching-Hsing Yu,et al.  AB INITIO CONFORMATIONAL ANALYSIS OF THE MODEL TRIPEPTIDE N-FORMYL-L-ALANYL-L-ALANINE AMIDE , 1998 .

[128]  H A Scheraga,et al.  Low-energy structures of two dipeptides and their relationship to bend conformations. , 1974, Macromolecules.

[129]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[130]  S. Walter Englander,et al.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR , 1988, Nature.

[131]  John T. Edsall.  Raman Spectra of Amino Acids and Related Compounds. VI. Sarcosine, Ethanolamine, Choline, Betaine and Betaine Derivatives1 , 1943 .

[132]  A. Guzzo,et al.  The influence of amino-acid sequence on protein structure. , 1965, Biophysical journal.

[133]  M. Tsuboi.  On the Molecular Association in Amides as Revealed by Their Near-Infrared Absorption Spectra , 1949 .

[134]  E. J. Ambrose,et al.  Evidence of Chain Folding in a Synthetic Polypeptide and in Keratin , 1949, Nature.

[135]  G. Sutherland,et al.  INFRARED SPECTRA AND STRUCTURE OF NATURAL AND SYNTHETIC POLYPEPTIDES , 1947 .

[136]  Imre G. Csizmadia,et al.  Peptide models XV. The effect of basis set size increase and electron correlation on selected minima of the ab initio 2D-Ramachandran map of For-Gly-NH2 and For-l-Ala-NH2 , 1997 .