CAPS-DB: A structural classification of helix-capping motifs

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Segura, Joan ^a   Oliva, Baldomero ^b   Fernandez Fuentes, Narcis ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; CAPS DB DATABASE; CARBOXY TERMINAL SEQUENCE; CLUSTER ANALYSIS; DATA PROCESSING; GEOMETRY; HYDROGEN BOND; INFORMATION RETRIEVAL; PRIORITY JOURNAL; PROTEIN CAPING; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEOMICS; SEQUENCE ALIGNMENT;

ALGORITHMS; AMINO ACID MOTIFS; CLUSTER ANALYSIS; DATABASES, PROTEIN; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; USER-COMPUTER INTERFACE;

EID: 84862168663     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr879     Document Type: Article

References (32)

1. Presta,L.G. and Rose,G.D. (1988) Helix signals in proteins. Science, 240, 1632-1641.
2. Richardson,J.S. and Richardson,D.C. (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science, 240, 1648-1652.
3. Milner-White,E., Ross,B.M., Ismail,R., Belhadj-Mostefa,K. and Poet,R. (1988) One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. J. Mol. Biol., 204, 777-782.
4. Aurora,R., Srinivasan,R. and Rose,G.D. (1994) Rules for alpha-helix termination by glycine. Science, 264, 1126-1130. (Pubitemid 2080614)
5. Stickle,D.F., Presta,L.G., Dill,K.A. and Rose,G.D. (1992) Hydrogen bonding in globular proteins. J. Mol. Biol., 226, 1143-1159.
6. Seale,J.W., Srinivasan,R. and Rose,G.D. (1994) Sequence determinants of the capping box, a stabilizing motif at the N-termini of alpha-helices. Protein Sci., 3, 1741-1745. (Pubitemid 24356598)
7. Munoz,V., Blanco,F.J. and Serrano,L. (1995) The hydrophobic-staple motif and a role for loop-residues in alpha-helix stability and protein folding. Nat. Struct. Biol., 2, 380-385.
8. Dasgupta,S. and Bell,J.A. (1993) Design of helix ends. Amino acid preferences, hydrogen bonding and electrostatic interactions. Int. J. Pept. Protein Res., 41, 499-511. (Pubitemid 23144745)
9. Harper,E.T. and Rose,G.D. (1993) Helix stop signals in proteins and peptides: the capping box. Biochemistry, 32, 7605-7609. (Pubitemid 23240801)
10. Aurora,R. and Rose,G.D. (1998) Helix capping. Protein Sci., 7, 21-38. (Pubitemid 28133743)
11. Tripet,B. and Hodges,R.S. (2002) Helix capping interactions stabilize the N-terminus of the kinesin neck coiled-coil. J. Struct. Biol., 137, 220-235. (Pubitemid 35430436)
12. Bang,D., Gribenko,A.V., Tereshko,V., Kossiakoff,A.A., Kent,S.B. and Makhatadze,G.I. (2006) Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat. Chem. Biol., 2, 139-143. (Pubitemid 44323864)
13. Ermolenko,D.N., Thomas,S.T., Aurora,R., Gronenborn,A.M. and Makhatadze,G.I. (2002) Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices. J. Mol. Biol., 322, 123-135. (Pubitemid 36132674)
14. Makhatadze,G.I. (2005) Thermodynamics of alpha-helix formation. Adv. Protein Chem., 72, 199-226.
15. Thomas,S.T., Loladze,V.V. and Makhatadze,G.I. (2001) Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices. Proc. Natl Acad. Sci. USA, 98, 10670-10675. (Pubitemid 32878679)
16. Thomas,S.T. and Makhatadze,G.I. (2000) Contribution of the 30/36 hydrophobic contact at the C-terminus of the alpha-helix to the stability of the ubiquitin molecule. Biochemistry, 39, 10275-10283. (Pubitemid 30663050)
17. Rezvanpour,A., Phillips,J.M. and Shaw,G.S. (2009) Design of high-affinity S100-target hybrid proteins. Protein Sci., 18, 2528-2536.
18. Koscielska-Kasprzak,K., Cierpicki,T. and Otlewski,J. (2003) Importance of alpha-helix N-capping motif in stabilization of betabetaalpha fold. Protein Sci., 12, 1283-1289. (Pubitemid 36597515)
19. Iovino,M., Falconi,M., Petruzzelli,R. and Desideri,A. (2001) Role of the helix capping in the stability of the mouse prion (180-213) segment: investigation through molecular dynamics simulations. J. Biomol. Struct. Dyn., 19, 237-246. (Pubitemid 33035240)
20. Narayana,N., Phillips,N.B., Hua,Q.X., Jia,W. and Weiss,M.A. (2006) Diabetes mellitus due to misfolding of a beta-cell transcription factor: stereospecific frustration of a Schellman motif in HNF-1alpha. J. Mol. Biol., 362, 414-429. (Pubitemid 44307151)
21. Oliva,B., Bates,P.A., Querol,E., Aviles,F.X. and Sternberg,M.J. (1997) An automated classification of the structure of protein loops. J. Mol. Biol., 266, 814.
22. Fernandez-Fuentes,N., Oliva,B. and Fiser,A. (2006) A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res., 34, 2085-2097. (Pubitemid 44314206)
23. Everitt,B. (1974) Cluster Analysis, Chapt. 3. Heineman Educational Books Ltd, London.
24. Berman,H.M., Battistuz,T., Bhat,T.N., Bluhm,W.F., Bourne,P.E., Burkhardt,K., Feng,Z., Gilliland,G.L., Iype,L., Jain,S. et al. (2002) The Protein Data Bank. Acta Crystallogr. D. Biol. Crystallogr., 58, 899-907. (Pubitemid 34653017)
25. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403.
26. Wang,G. and Dunbrack,R.L. Jr (2003) PISCES: a protein sequence culling server. Bioinformatics, 19, 1589-1591. (Pubitemid 37038881)
27. Holm,L. and Sander,C. (1991) Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J. Mol. Biol., 218, 183.
28. Krivov,G.G., Shapovalov,M.V. and Dunbrack,R.L. Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
29. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
30. Sobolev,V., Sorokine,A., Prilusky,J., Abola,E.E. and Edelman,M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332. (Pubitemid 29213759)
31. Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weigths. J. Mol. Biol., 243, 574-578.
32. Pei,J. and Grishin,N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712. (Pubitemid 32851378)