AH-DB: Collecting protein structure pairs before and after binding

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Chang, Darby Tien Hao ^a   Yao, Tsung Ju ^a   Fan, Chen Yu ^a   Chiang, Chih Yun ^a   Bai, Yi Han ^a  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

COPPER ZINC SUPEROXIDE DISMUTASE; FREE RADICAL;

APO HOLO DATABASE; ARTICLE; CONFORMATIONAL TRANSITION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE ALIGNMENT; X RAY DIFFRACTION;

DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; SUPEROXIDE DISMUTASE; USER-COMPUTER INTERFACE;

EID: 84862162507     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr940     Document Type: Article

References (29)

1. Urbauer,J.L., Short,J.H., Dow,L.K. and Wand,A.J. (1995) Structural analysis of a novel interaction by calmodulin: high-affinity binding of a peptide in the absence of calcium. Biochemistry, 34, 8099-8109.
2. Kim,T.D., Ryu,H.J., Cho,H.I., Yang,C.H. and Kim,J. (2000) Thermal behavior of proteins: heat-resistant proteins and their heat-induced secondary structural changes. Biochemistry, 39, 14839-14846.
3. Michel,E.F. (2007) Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin. Biophys. J., 93, 2083-2090.
4. Dan,A., Ofran,Y. and Kliger,Y. (2010) Large scale analysis of secondary structure changes in proteins suggests a role for disorder to order transitions in nucleotide binding proteins. Proteins, 78, 236-248.
5. Goh,C.S., Milburn,D. and Gerstein,M. (2004) Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol., 14, 104-109. (Pubitemid 38258244)
6. Kim,Y., Rose,C.A., Liu,Y., Ozaki,Y., Datta,G. and Tu,A.T. (1994) Ft IR and near infared FT Raman studies of the secondary structure of insulinotropin in the solid state: α helix to b sheet conversion induced by phenol and/or by high shear force. J. Pharm. Sci., 83, 1175-1180. (Pubitemid 24247357)
7. Boden,M. and Bailey,T.L. (2006) Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics, 22, 1809.
8. Levy,Y., Hanan,E., Solomon,B. and Becker,O.M. (2001) Helix coil transition of PrP106¡V126: molecular dynamic study. Proteins, 45, 382-396. (Pubitemid 33108073)
9. Roll-Mecak,A., Cao,C., Dever,T.E. and Burley,S.K. (2000) X-ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell, 103, 781-792.
10. Henzler-Wildman,K.A., Thai,V., Lei,M., Ott,M., Wolf-Watz,M. and Fenn,T. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature, 450, 838-844. (Pubitemid 350231334)
11. Russel,D., Lasker,K., Phillips,J., Schneidman-Duhovny,D., Velazquez-Muriel,J.A. and Sali,A. (2009) The structural dynamics of macromolecular processes. Curr. Opin. Cell Biol., 21, 97-108.
12. Lange,O.F., Lakomek,N.A., Fares,C., Schroder,G.F., Walter,K.F.A., Becker,S., Meiler,J., Grubmuller,H., Griesinger,C. and de Groot,B.L. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320, 1471.
13. Bai,F., Branch,R.W., Nicolau,D.V., Pilizota,T., Steel,B.C., Maini,P.K. and Berry,R.M. (2010) Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science, 327, 685.
14. Liu,J., Perumal,N.B., Oldfield,C.J., Su,E.W., Uversky,V.N. and Dunker,A.K. (2006) Intrinsic disorder in transcription factors. Biochemistry, 45, 6873-6888. (Pubitemid 43856673)
15. Rose,P.W., Beran,B., Bi,C., Bluhm,W.F., Dimitropoulos,D., Goodsell,D.S., Prli,A., Quesada,M., Quinn,G.B. and Westbrook,J.D. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392.
16. Kim,R. and Guo,J.-T. (2009) PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. BMC Genomics, 10.
17. Meszaros,B., Simon,I. and Dosztanyi,Z. (2011) The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins. Phys. Biol., 8, 035003.
18. Gao,M. and Skolnick,J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res., 36, 3978.
19. London,N., Movshovitz-Attias,D. and Schueler-Furman,O. (2010) The structural basis of peptide-protein binding strategies. Structure, 18, 188-199.
20. Altschul,S., Madden,T., Schaffer,A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389.
21. Apweiler,R., Martin,M., O'Donovan,C., Magrane,M., Alam-Faruque,Y., Antunes,R., Barrell,D., Bely,B., Bingley,M. and Binns,D. The universal protein resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
22. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers, 22, 2577-2637.
23. Zhang,Z. (1994) Iterative point matching for registration of free-form curves and surfaces. Int J Comput Vision, 13, 119-152.
24. Theobald,D.L. and Wuttke,D.S. (2006) THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics, 22, 2171.
25. Galaleldeen,A., Strange,R.W., Whitson,L.J., Antonyuk,S.V., Narayana,N., Taylor,A.B., Schuermann,J.P., Holloway,S.P., Hasnain,S.S. and Hart,P.J. (2009) Structural and biophysical properties of metal-free pathogenic SOD1 mutants A4V and G93A. Arch. Biochem. Biophys., 492, 40-47.
26. You,Z., Cao,X., Taylor,A.B., Hart,P.J. and Levine,R.L. (2010) Characterization of a covalent polysulfane bridge in copper-zinc superoxide dismutase. Biochemistry, 49, 1191-1198.
27. Eisenberg,D., Hart,P.J., Liu,H., Pellegrini,M., Nersissian,A.M., Gralla,E.B. and Valentine,J.S. (1998) Subunit asymmetry in the three dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis. Protein Sci., 7, 545-555. (Pubitemid 28130875)
28. Fong,J.H., Shoemaker,B.A., Garbuzynskiy,S.O., Lobanov,M.Y., Galzitskaya,O.V. and Panchenko,A.R. (2009) Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. PLoS Comput. Biol., 5, e1000316.
29. Lobanov,M.Y., Shoemaker,B.A., Garbuzynskiy,S.O., Fong,J.H., Panchenko,A.R. and Galzitskaya,O.V. (2010) ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Res., 38, D283.