Constructing a useful tool for characterizing amino acid conformers by means of quantum chemical and graph theory indices

Computers and Chemistry

Volumn 26, Issue 6, 2002, Pages 667-682

  Cárdenas, Constanza ^a,b   Obregón, Mateo ^a   Llanos, Eugenio José ^a,b   Machado, Eduardo ^a   Bohórquez, Hugo Javier ^a   Villaveces, Jose Luis ^b   Patarroyo, Manuel Elkin ^a,b  

^a FUNDACIÓN INSTITUTO DE INMUNOLOGÍA DE COLOMBIA FIDIC   (Colombia)

^b UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

Author keywords

Backbone conformers; Correlation between amino acid conformers; Molecular similarity; Secondary structure; Side chain conformers; Theoretically derived indices

Indexed keywords

AMINO ACIDS; GRAPH THEORY; MATHEMATICAL MODELS; MOLECULAR STRUCTURE;

MOLECULAR SIMILARITY;

CONFORMATIONS;

AMINO ACID; PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; CLUSTER ANALYSIS; PROTEIN SECONDARY STRUCTURE; STATISTICAL MODEL;

AMINO ACIDS; CLUSTER ANALYSIS; MODELS, CHEMICAL; MODELS, STATISTICAL; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0036827274     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(02)00052-9     Document Type: Article

References (63)

1. Basu D., Williams C.-B., Allen P.-M. In vivo antagonism of a T cell response by an endogenously expressed ligand. Proc. Natl. Acad. Sci. USA. 95:1998;14332-14336.
2. Bermúdez C., Daza E.-E., Andrade E. Characterization and comparison of Escherichia coli transfer RNAs by graph theory based on secondary structure. J. Theor. Biol. 197:1999;193-205.
3. Bernstein F.-C., Koetzle T.-F., Williams G.-J.-B., Meyer E.-F.-J., Brice M.-D., Rogers J.-R., Kennard O., Shimanouch T., Tasumi M. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
4. Creamer T.-P., Rose G.-D. Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl. Acad. Sci. USA. 89:1992;5937-5941.
5. Császár A.-G., Perczel A. Ab initio characterization of building units in peptides and proteins. Prog. Biophys. Mol. Biol. 71:1999;243-309.
6. Dayhoff, M.-O., Schwartz, R.-M., Orcutt, B.-C., 1978. Atlas of Protein Sequence and Structure. National Biomedic Research Foundation, pp. 345-348.
7. Espinosa G., Yaffe D., Cohen Y., Arenas A., Giralt F. Neural network based quantitative structural property relations (QSPRs) for predicting boiling points of aliphatic hydrocarbons. J. Chem. Inf. Comput. Sci. 40:2000;859-879.
8. Everitt, B., 1977. Cluster analysis, Social Science Research Council, London.
9. Frisch, M.-J., Trucks, G.-W., Schlegel, H.-B., Gill, P.-M.-W., Johnson, B.-G., Robb, M.-A., Cheesemtm, J.-R., Keith, T., Petersson, G.-A., Montgomery, J.A., Raghavachari, K., Al-Laham, M.-A., Zakrzewski, V.-G., Ortiz, J.-V., Foresrnan, J.-B., Cioslowski, I., Stefanov, B.-B., Nanayakkara, A., Challacombe, M., Peng, C.-Y, Ayala, P.-Y., Chen, W., Wong, M.-W., Andres, J.-L., Replogle, E.-S., Gomperts, R., Martin, R.-L., Fox, D.-J., Binkley, J.-S., Defrees, D.-J., Baker, J., Stewart, J.-P., Head-Gordon, M., Gonzalez, C., Pople, J.-A., 1995. GAUSSIAN-94, revision D.4. Gaussian Inc., Pittsburg PA.
10. Fukui K., Oono T., Cabaniols J.-P., Nkao K., Hirokawa K., Inayoshi A., Sanui T., Kanellopoulos J., Iwata E., Noda M., Katsuki M., Kourilsky P., Sasazuki T. Diversity of T cell repertoire shaped by a single peptide ligand is critically affected by its amino acid residue at a T cell receptor contact. Proc. Natl. Acad. Sci. USA. 97:2000;13760-13765.
11. Hall L.-H., Kier L.-B. The molecular connectivity chi indexes and kappa shape indexes in structure-property modeling. Lipkowitz K.-B., Boyd D.-B. Reviews in Computational Chemistry. 2:1997;367-412 VCH Publishers, New York.
12. Hall L.-H., Kier L.-B. The nature of structure-activity relationships and their relation to molecular connectivity. Eur. J. Med. Chem.-Chimica Therapeutica. 4:1997;307-312.
13. Jameson, S.-C., 1998. T cell receptor antagonism in vivo, at last. Proc. Natl. Acad. Sci. USA 95, 14001-1400.
14. Jameson S.-C., Bevan M.-J. T cell receptor antagonists and partial agonists. Immunity. 2:1995;1-11.
15. Karelson M., Lobanov V.-S. Quantum chemical descriptors in QSAR/QSPR studies. Chem. Rev. 96:1996;1027-1043.
16. Kawashima S., Kanehisha M. AAIndex: amino acid index data base. Nucl. Acid Res. 28:2000;374.
17. Kawashima S., Ogata H., Kanehisha M. AAIndex: amino acid index data base. Nucl. Acid Res. 27:1999;368-369.
18. Kersh G.-A., Miley M.-J., Nelson C.-A., Grakoui A., Horvath S., Donermeyer D.-L., Kappler J., Allen P.-M., Fremont D.-H. Structural and functional consequences of altering a peptide MHC anchor residue. J. Immunol. 166:2001;3345-3354.
19. Kidera A., Konishi Y., Oka M., Ooi T., Scheraga H.-A. Structural analysis of the physical properties of the 20 naturally occurring amino acids. J. Prot. Chern. 4:1985;23-55.
20. Kidera A., Konishi Y., Ooi T., Scheraga H.-A. Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids. J. Prot. Chem. 4:1985;265-297.
21. Kier L.-B., Hall L.-H. Derivation and significance of valence molecular connectivity. J. Pharm. Sci. 70:1981;583-589.
22. Kier L.-B., Hall L.-H. Molecular Connectivity in Structure-Activity Analysis. 1981;Wiley Research Studies Press, New York.
23. Kier L.-B., Hall L.-H. Intermolecular accessibility: the meaning of molecular connectivity. J. Chem. Inf. Comput. Sci. 40:2000;792-795.
24. Laskowski R.-A., MacArthur M.-W., Moss D.-S., Thornton J.-M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:1993;283-291.
25. Lee K.-H., Xie D., Freire E., Amzel L.-M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. PROTEINS: Struct. Funct. Genet. 20:1994;68-84.
26. López R., Urquiza M., Curtidor H., Caminos J.-E., Mora H., Puentes A., Patarrayo M.-E. Plasmodium falciparum: red blood cell binding studies of peptides derived from histidine-rich KAHRP-I, HRP-II and HRP-III proteins. Acta Trop. 75:2000;349-359.
27. Lucic B., Lukovits I., Nikolić S., Trinajstić N. Distance-related indexes in the quantitative structure-property relationship modeling. J. Chem. Inf. Comput. Sci. 41:2001;527-535.
28. Mandloi M., Sikarwar A., Sapre N.-S., Karmarkar S., Khadikar P.-V. A comparative QSAR study using wiener, szeged, and molecular connectivity indices. J. Chem. Inf. Comput. Sci. 40:2000;57-62.
29. Michener C.-D., Sokal R.-R. A quantitative approach to a problem in classification. Evolution. 11:1957;130.
30. Mishra R.-K., Garcia-Domenech R., Galvez J. Getting discriminant functions of antibacterial activity from physicochemical and topological parameters. J. Chem. Inf. Comput. Sci. 41:2001;387-393.
31. Morris A.-L., MacArthur W., Hutchinson E.-G., Thornton J.-M. Stereochemical quality of protein coordinates. PROTEINS: Struct. Func. Genet. 12:1992;345-364.
32. Nakai K., Kidera A., Kanehisha M. Cluster analysis of amino acid indices for prediction of protein structure and function. Prot. Eng. 2:1988;93-100.
33. Niño V.-M., Daza E.-E., Tello M. A criteria to classify biological activity of benzimidazoles from a model of structural similarity. J. Chem. Inf. Comput. Sci. 41:2001;495-504.
34. Nishimura Y., Chen Y.-Z., Kanai T., Yokomizo H., Matsuoka T., Matsushita S. Modification of human T-cell responses by altered peptide ligands: a new approach to antigen-specific modification. Intern. Med. 37:1998;804-817.
35. Oblak M., Randic M., Solmajer T. Quantitative structure-activity relationship of flavonoid analogues. 3. Inhibition of p56lck protein tyrosine kinase. J. Chem. Inf. Comput. Sci. 40:2000;994-1001.
36. Ocampo M., Urquiza M., Guzmán F., Rodríguez L.-E., Suárez J.-E., Curtidor H., Rosas J., Díaz M., Patarroyo M.-E. Two MSA-2 peptides that bind to human red blood cells are relevant to Plasmodium falciparum merozoite invasion. J. Pept. Res. 55:2000;216-223.
37. Palma R.D., Sacerdoti G., Abbate G.-F., Martucci P., Mazzarella G. Use of altered peptide ligands to modulate immune responses as a possible immunotherapy for allergies. Allergy. 2000;56-59.
38. Ponce A.-M., Blanco S.-E., Molina A.-S., García-Domenech R., Gálvez J. Study of the action of flavonoids on xanthine-oxidase by molecular topology. J. Chem. Inf. Comput. Sci. 40:2000;1039-1045.
39. Puentes A., García J., Vera R., López R., Urquiza M., Vanegas M., Salazar L.-M., Patarroyo M.-E. Serine repeat antigen peptides which bind specifically to red blood cells. Parasitol. Int. 49:2000;105-117.
40. Ramachandran G.-N., Ramakrisnan C., Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:1963;95-99.
41. Randic M. On characterization of molecular branching. J. Am. Chem. Soc. 97:1975;6609-6615.
42. Randic M., Basak S.-C. On use of the variable connectivity index 1 f in QSAR: toxicity of aliphatic ethers. J. Chem. Inf. Comput. Sci. 41:2001;614-618.
43. Randic M., Zupan J. On interpretation of well-known topological indices. J. Chem. Inf. Comput. Sci. 41:2001;550-560.
44. Rodríguez L.-E., Urquiza M., Ocampo M., Suárez J.-E., Curtidor H., Guzmán F., Vargas L.-E., Triviños M., Rosas M., Patarroyo M.-E. Plasmodium falciparum EBA-175 kDa protein peptides which bind to human red blood cells. Parasitology. 120:2000;225-235.
45. Rohlf, F.-J., 1992. Numerical Taxonomy and Multivariate Analysis System (NTSYS).
46. Rohlf F.-J., Sokal R.-R. Comparing numerical taxonomic studies. Syst. Zool. 17:1981;459-490.
47. Rohrbaugh R.-H., Jurs P.-C. Descriptions of molecular shape applied in studies of structure/activity and structure/property relationships. Anal. Chim. Acta. 199:1987;99-109.
48. Schrauber H., Eisenhaber F., Argos P. Rotamers: to be or not to be? an analysis of amino acid side chain conformations in globular proteins. J. Mol. Biol. 230:1993;592-612.
49. Schuh R.-T., Farris J.-S. Methods for investigating taxonomic congruence and their applicattion to the leptopodomorpha. Syst. Zool. 30:1981;331-351.
50. Schweitzer R.-C., Morris J.-B. Improved quantitative structure property relationships for the prediction of dielectric constants for a set of diverse compounds by subletting of the data set. J. Chem. Inf. Comput. Sci. 40:2000;1253-1261.
51. Sebzda E., Mariathasan S., Ohteki T., Jones R., Bachman M.-F., Ohashi P. Selection of the T cell repertoire. Annu. Rev. Immunol. 17:1999;829-874.
52. Semichem, 1995. CODESSA: Comprehensive Descriptors for Structural and Statistical Analysis, Semichem and the University of Florida.
53. Stahura F.-L., Godden J.-W., Xue L., Bajorath J. Distinguishing between natural products and synthetic molecules by descriptor shannon entropy analysis and binary QSAR calculations. J. Chem. Inf. Comput. Sci. 40:2000;1245-1252.
54. Stanfel L.-E. A new approach to clustering amino acids. J. Theor. Biol. 183:1996;195-205.
55. Suárez J.-E., Urquiza M., Curtidor H., Rodríguez L.-E., Ocampo M., Torres E., Guzmán F., Patarroyo M.-E. A GBP 130 derived peptide from Plasmodium falciparum binds to human erythrocytes and inhibits merozoite invasion in vitro. Mem. Inst. Oswaldo Cruz. 95:2000;495-501.
56. Tommii K., Kanehisha M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Prot. Eng. 9:1996;27-36.
57. Tuppurainen K. Frontier orbital energies, hydrophobicity and steric factors as physical QSAR descriptors of molecular mutagenicity. A review with a case study: MX compounds. Chemosphere. 38:1999;3015-3030.
58. Urquiza M., Rodríguez L.-E., Suárez J.-E., Guzmán F., Ocampo M., Curtidor H., Segura C., Trujillo E., Patarroyo M.-E. Identification of Plasmodium falciparum MSP-1 peptides able to bind to human red blood cells. Parasite Immunol. 18:1996;515-526.
59. Urquiza M., Suárez J.-E., Cárdenas C., López R., Puentes A., Chávez F., Calvo J.-C., Patarroyo M.-E. Plasmodium falciparum AMA-1 erythrocyte binding peptides implicate AMA-1 as erythrocyte binding protein. Vaccine. 19:2000;508-513.
60. Vera R., Marín V., García J., Urquiza M., Torres E., Trujillo M., Rosas J., Patarroyo M.-E. Amino terminal peptides of the ring infected erythrocyte surface antigen of Plasmodium falciparum bind specifically to erythrocytes. Vaccine. 18:2000;1289-1293.
61. Wiener H. Structural determination of paraffin boiling point. J. Am. Chem. Soc. 69:1947;17-20.
62. Williams C.-B., Vidal K., Donermeyer D., Peterson D.-A., White J.-M., Allen P.-M. In vivo expression of a TCR antagonist: T cells escape central tolerance but are antagonized in the peripher. J. Immunol. 161:1998;128-137.
63. Xue L., Bajorath J. Molecular descriptors for effective classification of biologically active compounds based on principal component analysis identified by a genetic algorithm. J. Chem. Inf. Comput. Sci. 40:2000;801-809.