Why similar protein sequences encode similar three-dimensional structures?

Theoretical Chemistry Accounts

Volumn 125, Issue 3-6, 2010, Pages 643-650

  Kaczanowski, Szymon ^a   Zielenkiewicz, Piotr ^a,b  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Evolution; Homology; Modeling; Protein; Threading

Indexed keywords

EID: 77949263661     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-009-0656-3     Document Type: Article

References (37)

1. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein Sequence and Structure, vol 5. Nat. Biomed Res Found. Washington DC, pp 345-352.
2. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89: 10915-10919.
3. Gonnet GH, Cohen MA, Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445.
4. Baussand J, Carbone A (2008) Inconsistent distances in substitution matrices can be avoided by properly handling hydrophobic residues. Evol Bioinform Online 4: 255-261.
5. Lesk AM, Chothia C (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136: 225-270.
6. Moult J (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15: 285-289.
7. Padlan EA, Love WE (1985) Refined crystal structure of deoxyhemoglobin S. II. Molecular interactions in the crystal. J Biol Chem 260: 8280-8289.
8. Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8: 641-645.
9. Koshi JM, Goldstein RA (1997) Mutation matrices and physical-chemical properties: correlations and implications. Proteins 27: 336-344.
10. Dalal S, Balasubramanian S, Regan L (1997) Protein alchemy: changing beta-sheet into alpha-helix. Nat Struct Biol 4: 548-552.
11. Chothia C (1975) Structural invariants in protein folding. Nature 254: 304-308.
12. Tanaka S, Scheraga HA (1976) Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9: 945-950.
13. Chou PY, Fasman GD (1974) Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 13: 211-222.
14. Chou PY, Fasman GD (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47: 45-148.
15. Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170.
16. Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
17. Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
18. Godzik A, Skolnick J (1992) Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA 89: 12098-12102.
19. Nishikawa K, Matsuo Y (1993) Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng 6: 811-820.
20. Jones DT, Thornton JM (1996) Potential energy functions for threading. Curr Opin Struct Biol 6: 210-216.
21. Rypniewski WR, Holden HM, Rayment I (1993) Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an X-ray analysis at 1. 8-A resolution. Biochemistry 32: 9851-9858.
22. Mauguen Y, Hartley RW, Dodson EJ, Dodson GG, Bricogne G, Chothia C, Jack A (1982) Molecular structure of a new family of ribonucleases. Nature 297: 162-164.
23. Baudet S, Janin J (1991) Crystal structure of a barnase-d(GpC) complex at 1. 9 A resolution. J Mol Biol 219: 123-132.
24. Nair SK, Calderone TL, Christianson DW, Fierke CA (1991) Altering the mouth of a hydrophobic pocket. Structure and kinetics of human carbonic anhydrase II mutants at residue Val-121. J Biol Chem 266: 17320-17325.
25. Santoro J, González C, Bruix M, Neira JL, Nieto JL, Herranz J, Rico M (1993) High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy. J Mol Biol 229: 722-734.
26. Kjeldgaard M, Jones TA (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr 1: 178-185.
27. Watanabe K, Kitamura K, Suzuki Y (1996) Analysis of the critical sites for protein thermostabilization by proline substitution in oligo-1, 6-glucosidase from Bacillus coagulans ATCC 7050 and the evolutionary consideration of proline residues. Appl Environ Microbiol 62: 2066-2073.
28. Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8: 738-748.
29. Madern D, Ebel C, Zaccai G (2000) Halophilic adaptation of enzymes. Extremophiles 4: 91-98.
30. Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R (2003) Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res 13: 1580-1588.
31. Perry RD, Fetherston JD (1997) Yersinia pestis-etiologic agent of plague. Clin Microbiol Rev 10: 35-66.
32. Altschuh D, Lesk AM, Bloomer AC, Klug A (1987) Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 193: 693-707.
33. Gobel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309-317.
34. Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci USA 91: 98-102.
35. Horner DS, Pirovano W, Pesole G (2008) Correlated substitution analysis and the prediction of amino acid structural contacts. Brief Bioinform 9: 46-56.
36. Malcolm BA, Wilson KP, Matthews BW, Kirsch JF, Wilson AC (1990) Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345: 86-89.
37. Chothia C (1992) Proteins one thousand families for the molecular biologist. Nature 357: 543-544.