Protein structural alignment for detection of maximally conserved regions

Biophysical Chemistry

Volumn 105, Issue 2-3, 2003, Pages 595-608

  Kotlovyi, Vladimir ^a   Nichols, William Lee ^b   Ten Eyck, Lynn F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Protein structure alignment; Protein structure comparison

Indexed keywords

ELEMENT; POLYPEPTIDE; PROTEIN; PROTEIN KINASE;

ALGORITHM; ARTICLE; COMPARATIVE STUDY; MOLECULE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; TECHNIQUE;

EID: 0141448920     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(03)00069-3     Document Type: Article

References (38)

1. 1 human hemoglobin dimer. J. Mol. Biol. 270:1997;598-615.
2. Knighton D., Zheng J., Ten Eyck L.F., Ashford V., Xuong N.-h., Taylor S., Sowadski J. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science. 253:1991;407-413.
3. Knighton D., Zheng J., Ten Eyck L., Xuong N.-h., Taylor S., Sowadski J. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science. 153:1991;414-420.
4. Tsilgeny I., Grant B.D., Taylor S.S., Ten Eyck L.F. Catalytic subunit of cAMP-dependent protein kinase: Electrostatic features and peptide recognition. Biopolymers. 39:1996;353-365.
5. Tsigelny I., Greenberg J.P., Cox S., Nichols W.L., Taylor S.S., Ten Eyck L.F. 600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase. Biopolymers. 50:1999;513-524.
6. Zheng J., Knighton D.R., Xuong N.H., Taylor S.S., Sowadski J.M., Ten Eyck L.F. Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci. 2:(10):1993;1559-1573.
7. Narayana N., Cox S., Nguyen-huu X., Ten Eyck L.F., Taylor S.S. A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility. Structure. 5:(7):1997;921-935.
8. Smith C.M., Gribskov M., Shindyalov I., Taylor S.S., Ten Eyck L.F., Veretnik S., Bourne P.B. The protein kinase resource. Trends Biochem. Sci. 22:1997;444-446.
9. Knighton D.R., Pearson R.B., Sowadski J.M., Means A.R., Ten Eyck L.F., Taylor S.S., Kemp B.E. Structural basis of the intrasteric regulation of myosin light chain kinases. Science. 258:(5079):1992;130-135.
10. Nichols W.L., Rose G.D., Ten Eyck L.F., Zimm B.H. Rigid domains in proteins: An algorithmic approach to their identification. Proteins: Struct. Funct. Genet. 23:1995;38-48.
11. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Databank. Nucl. Acids Res. 28:2000;235-242.
12. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., Thornton J.M. CATH - a hierarchic classification of protein domain structures. Structure. 5:1997;1093-1108.
13. Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CH) of the optimal path. Protein Eng. 11:1998;739-747.
14. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
15. Lackner P., Koppensteiner W.A., Sippl M.J., Domingues F.S. ProSup: a refined tool for protein structure alignment. Protein Eng. 13:2000;745-752.
16. Murzin A.G., Brenner S.E., Chothia H.T.C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
17. Lo Conte L., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A. SCOP database in: refinements accommodate structural genomics. Nucl. Acids Res. 30:(2002):2002;264-267.
18. Yang A.-S., Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol. 301:2000;665-678.
19. Madej T., Gibrat J.-F., Bryant S.H. Threading a database of protein cores. Proteins: Struct. Fund. Genet. 23:1995;356-369.
20. Gibrat J.-F., Madej T., Bryant S.H. Surprising similarities in structure comparison. Curr. Opinion Struct. Biol. 6:1996;377-385.
21. Leibowitz N., Nussinov R., Wolfson H.J. MUSTA - a general, efficient, automated method for multiple structure alignment and detection of common motifs: Application to proteins. J. Comput. Biol. 8:(2):2001;93-121.
22. O'Neill B. Elementary Differential Geometry. 1997;Academic Press, San Diego.
23. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. Numerical Recipes in C. 1992;Cambridge University Press, Cambridge, UK.
24. Rackovsky S., Scheraga H.A. Differential geometry and polymer conformation I: Comparison of protein conformations. Macromolecules. 11:1978;1168-1174.
25. Chirikjian G.S., Kyatkin A.B. Engineering Applications of Non-commutative Harmonic Analysis: With Emphasis on Rotation and Motion Groups. 2000;CRC Press, Boca Raton, Florida.
26. Knuth D. The Art of Computer Programming, Vol 1. 1968;Addison-Wesley, Boston.
27. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallog. Sect. A: Found. Crystallog. Part A. 32:1976;922-923.
28. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Ada Crystallog. Sect. A: Found. Crystallog. Part A. 34:1978;827-828.
29. Murzin A.G. Sweet-tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors. J. Mol. Biol. 230:1993;689-694.
30. Somoza J.R., Jiang F., Tong L., Kang C.-H., Cho J.M., Kim S.-H. Two crystal structures of a potently sweet protein: Natural monellin at 2.75 Å resolution and single-chain monellin at 1.7 Å resolution. J. Mol. Biol. 234:1993;390-404.
31. Bode W., Engh R., Musil D., Thiele U., Huber R., Karshikov A., Brzin J., Kos J., Turk V. The 2.0 Å X-ray crystal structure of chicken egg while cystatin and its possible mode of interaction with cysteine proteinases. EMBO J. 7:1988;2593-2599.
32. Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
33. Zheng J., Knighton D.R., Ten Eyck L.F., Karlsson R., Xuong N., Taylor S.S., Sowadski J.M. Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry. 32:(9):1993;2154-2161.
34. Battistutta R., Sarno S., De Moliner E., Papinutto E., Zanotti G., Pinna L.A. The replacement of ATP by the competitive inhibitor emodin induces conformational modifications in the catalytic site of protein kinase CK2. J. Biol. Chem. 275:2000;29618-29622.
35. Kendall M.G. Rank Correlation Methods. 1970;Griffin, London.
36. Hajek J., Sidak Z. Theory of Rank Tests. 1967;Academia, Prague.
37. Myers E.W., Miller W. Optimal alignments in linear space. Comput. Appl. Biosci. 4:1988;11-17.
38. Hanks S.K., Quinn A.M., Hunter T. The protein kinase family - conserved features and deduced phylogeny of the catalytic domain. Science. 241:1988;42-52.