CONFORMATIONAL ENERGY CALCULATIONS OF ENZYME‐SUBSTRATE INTERACTIONS. I. Computation of Preferred Conformations of Some Substrates of α‐Chymotrypsin

Empirical energy calculations are used to determine all low-energy conformations of the isolated α-chymotrypsin substrates N-acetyl-L-phenylalanine amide, N-acetyl-L-tyrosine amide, N-formyl-L-tyrosine amide, and N-acetyl-L-tryptophan amide. The computed conformations are in agreement with the available experimental data for L-phenylalanyl, L-tyrosyl and L-tryptophanyl side chains in proteins, and with NMR and X-ray data for these side chains in small peptides. In the following papers, certain of these low-energy substrate conformations will be shown to bind selectively to the enzyme chymotrypsin to form stable noncovalent enzyme-substrate complexes.

[1]  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.

[2]  Harold A. Scheraga,et al.  Energy Parameters in Polypeptides. I. Charge Distributions and the Hydrogen Bond , 1967 .

[3]  Harold A. Scheraga,et al.  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 , 1967 .

[4]  R. E. Marsh,et al.  The crystal structure of glycylphenylalanylglycine , 1961 .

[5]  H. Scheraga,et al.  Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M. Sundaralingam,et al.  Molecular structures of amino acids and peptides. III. The molecular structure and conformation of potassium l-tyrosine-O-sulfate dihydrate , 1971 .

[7]  E. H. Wiebenga,et al.  The crystal structure of glycyl‐l‐tyrosine hydrochloride , 1953 .

[8]  M. Tsuboi,et al.  Near Infrared Spectra of Compounds with Two Peptide Bonds and the Configuration of a Polypeptide Chain. VI. Further Evidence of the Internal Hydrogen Bonding and an Estimation of its Energy , 1957 .

[9]  J. Hamilton,et al.  Crystallographic studies of iodine-containing amino acids. I. Di-iodo-L-tyrosine dihydrate. , 1967, Acta crystallographica.

[10]  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.

[11]  Silverman Dn,et al.  Nuclear magnetic resonance studies of side-chain interactions in polyamino acids with aromatic groups. Comparison to conformational energy calculations. , 1971 .

[12]  Harold A. Scheraga,et al.  Calculations of Conformations of Polypeptides , 1968 .

[13]  R. A. Pasternak,et al.  The crystal structure of glycyl‐l‐tryptophan dihydrate , 1956 .

[14]  G. N. Ramachandran,et al.  Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins. , 2009, International journal of protein research.

[15]  M. Avignon,et al.  Une Méthode de Dosage des Isomères de Rotation des Dipeptides en Solution par Spectroscopie infrarouge , 1970 .

[16]  V. T. Ivanov,et al.  Conformational studies of peptide systems. The rotational states of the NH--CH fragment of alanine dipeptides by nuclear magnetic resonance. , 1969, Tetrahedron.

[17]  H. Scheraga,et al.  Determination of Intermolecular Potentials from Crystal Data. II. Crystal Packing with Applications to Poly(amino acids) , 1971 .

[18]  M. Marraud,et al.  Etude, par spectroscopie infra‐rouge, de la conformation de quelques composés peptidiques modèles , 1969 .

[19]  H A Scheraga,et al.  Conformational analysis of macromolecules. V. Helical structures of poly-L-aspartic acid and poly-L-glutamic acid, and related compounds. , 1968, The Journal of chemical physics.

[20]  H. Scheraga,et al.  Minimization of polypeptide energy. 8. Application of the deflation technique to a dipeptide. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

[21]  V. Sasisekharan,et al.  Studies on the conformation of amino acids X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit , 1971, Biopolymers.

[22]  S. Kang,et al.  Dipolar ion of phenylalanine: conformational analysis and electronic structure. , 1970, Journal of theoretical biology.

[23]  G. Germain,et al.  Structure cristalline de l'ester éthylique de la tyrosine , 1970 .

[24]  R. Srinivasan The crystal structure of L-tyrosine hydrohalides , 1959 .

[25]  M. Tsuboi,et al.  Near Infrared Spectra of Compounds with Two Peptide Bonds and the Configuration of a Polypeptide Chain. VII. On the Extended Forms of Polypeptide Chains , 1959 .

[26]  H. Scheraga Theoretical and experimental studies of conformations of polypeptides. , 1971, Chemical reviews.