Rapid comparison of properties on protein surface

Proteins: Structure, Function and Genetics

Volumn 73, Issue 1, 2008, Pages 1-10

  Sael, Lee ^a   La, David ^b   Li, Bin ^a   Rustamov, Raif ^b   Kihara, Daisuke ^a,b,c  

^a Purdue University   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

3D Zernike descriptor; Global local surface comparison; Protein surface physicochemical properties; Protein surface shape

Indexed keywords

GLOBIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; ELECTRIC POTENTIAL; ENZYME ACTIVE SITE; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS;

CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; SURFACE PROPERTIES;

EID: 50849126111     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22141     Document Type: Article

References (50)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
3. Mizuguchi K, Go N. Seeking significance in three-dimensional protein structure comparisons. Curr Opin Struct Biol 1995;5:377-382.
4. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
5. Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
6. Hodgkin EE, Richards WG. A semiempirical method for calculating molecular similarity. J Chem Soc-Chem Commun 1986;1342-1344.
7. Carbo R, Leyda L, Arnau M. An electron density measure of the similarity between two compounds. Int J Quantum Chem 1980;17:1185-1189.
8. Hodgkin EE, Richards WG. Molecular similarity based on electrostatic potential and electric-field. Int J Quantum Chem 1987;14:105-110.
9. Nikolova N, Jaworska J. Approaches to measure chemical similarity - a review. QSAR Comb Sci 2004;22:1006-1026.
10. Blomberg N, Gabdoulline RR, Nilges M, Wade RC. Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. Proteins 1999;37:379-387.
11. De RF, Gabdoulline RR, Menziani MC, Wade RC. Blue copper proteins: a comparative analysis of their molecular interaction properties. Protein Sci 2000;9:1439-1454.
12. De RF, Gabdoulline RR, Menziani MC, De Benedetti PG, Wade RC. Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J 2001;81:3090-3104.
13. Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC. Comparative structural and energetic analysis of WW domain-peptide interactions. J Mol Biol 2004;344:865-881.
14. Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC. Determinants of functionality in the ubiquitin conjugating enzyme family. Structure 2004;12:1563-1574.
15. Sasin JM, Godzik A, Bujnicki JM. SURF'S UP! - protein classification by surface comparisons. J Biosci 2007;32:97-100.
16. Pawlowski K, Godzik A. Surface map comparison: studying function diversity of homologous proteins. J Mol Biol 2001;309:793-806.
17. Zhang X, Bajaj C, Kwon B, Dolinsky T, Nielsen J, Baker N. Application of new multiresolution methods for the comparison of biomolecular electrostatic properties in the absence of structural similarity. Multiscale Model Simul 2006;5:1196-1213.
18. Novotni M, Klein R. 3D Zernike descriptors for content based shape retrieval. ACM Symposium on solid and physical modeling, In Proceedings of the 8th ACM Symposium on Solid Modeling and Applications, Seattle, Wash, USA, 2003. pp 216-225.
19. Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, Kihara D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins, online ahead of print; DOI: 10.1002/prot.22030.
20. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002;30:264-267.
21. Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002;321:741-765.
22. Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983;221:709-713.
23. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001;98:10037-10041.
24. Kinoshita K, Nakamura H. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics 2004;20:1329-1330.
25. Canterakis N. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. In: Proceedings of 11th Scandinavian Conference on Image Analysis, Kangerlussuaq, Greenland, 1999. pp 85-93.
26. Dym H, McKean H. Fourier series and integrals. New York: Academic Press; 1972.
27. Mak L, Grandison S, Morris RJ. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. J Mol Graph Model 2008;26:1035-1045.
28. Kapp OH, Moens L, Vanfleteren J, Trotman CN, Suzuki T, Vinogradov SN. Alignment of 700 globin sequences: extent of amino acid substitution and its correlation with variation in volume. Protein Sci 1995;4:2179-2190.
29. Aronson HE, Royer WE, Jr, Hendrickson WA. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Sci 1994;3:1706-1711.
30. Lecomte JT, Vuletich DA, Lesk AM. Structural divergence and distant relationships in proteins: evolution of the globins. Curr Opin Struct Biol 2005;15:290-301.
31. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
32. Tarricone C, Galizzi A, Coda A, Ascenzi P, Bolognesi M. Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp. Structure 1997;5:497-507.
33. Pesce A, Dewilde S, Kiger L, Milani M, Ascenzi P, Marden MC, Van Hauwaert ML, Vanfleteren J, Moens L, Bolognesi M. Very high resolution structure of a trematode hemoglobin displaying a TyrB10-TyrE7 heme distal residue pair and high oxygen affinity. J Mol Biol 2001;309:1153-1164.
34. Harutyunyan EH, Safonova TN, Kuranova IP, Popov AN, Teplyakov AV, Obmolova GV, Valnshtein BK, Dodson GG, Wilson JC. The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins. J Mol Biol 1996;264:152-161.
35. Hankeln T, Ebner B, Fuchs C, Gerlach F, Haberkamp M, Laufs TL, Roesner A, Schmidt M, Weich B, Wystub S, Saaler-Reinhardt S, Reuss S, Bolognesi M, De SD, Marden MC, Kiger L, Moens L, Dewilde S, Nevo E, Avivi A, Weber RE, Fago A, Burmester T. Neuroglobin and cytoglobin in search of their role in the vertebrate globin family. J Inorg Biochem 2005;99:110-119.
36. Lecomte JT, Vuletich DA, Lesk AM. Structural divergence and distant relationships in proteins: evolution of the globins. Curr Opin Struct Biol 2005;15:290-301.
37. Torrez M, Schultehenrich M, Livesay DR. Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces. Biophys J 2003;85:2845-2853.
38. Kinjo AR, Nishikawa K. Comparison of energy components of proteins from thermophilic and mesophilic organisms. Eur Biophys J 2001;30:378-384.
39. Xiao L, Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins. J Mol Biol 1999;289:1435-1444.
40. Spassov VZ, Karshikoff AD, Ladenstein R. Optimization of the electrostatic interactions in proteins of different functional and folding type. Protein Sci 1994;3:1556-1569.
41. Madura JD, McCammon JA. Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phosphate. J Phys Chem 1989;93:7285-7287.
42. Raychaudhuri S, Younas F, Karplus PA, Faerman CH, Ripoll DR. Backbone makes a significant contribution to the electrostatics of α/β-barrel proteins. Protein Sci 1997;6:1849-1857.
43. Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
44. Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, Ghahramani Z, Chen L, Westbrook J. The status of structural genomics defined through the analysis of current targets and structures. Pac Symp Biocomput 2004;375-386.
45. Westbrook J, Feng Z, Chen L, Yang H, Berman HM. The protein data bank and structural genomics. Nucleic Acids Res 2003;31:489-491.
46. Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005;15:275-284.
47. Kinoshita K, Nakamura H. Protein informatics towards function identification. Curr Opin Struct Biol 2003;13:396-400.
48. Li B, Turuvekere S, Agrawal M, La D, Ramani K, Kihara D. Characterization of local geometry of protein surfaces with the visibility criterion. Proteins 2007;71:670-683.
49. Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 2006;15:1550-1556.
50. Hawkins T, Kihara D. Function prediction of uncharacterized proteins. J Bioinform Comput Biol 2007;5:1-30.