Analysis of loop boundaries using different local structure assignment methods

Protein Science

Volumn 18, Issue 9, 2009, Pages 1869-1881

  Tyagi, Manoj ^a,b,e   Bornot, Aurélie ^b,c   Offmann, Bernard ^a,d   De Brevern, Alexandre G ^b,c  

^a UNIVERSITÉ DE LA RÉUNION   (France)

^b INSERM   (France)

^c hôpital Robert Debré et Institut national de la transfusion sanguine   (France)

^d PEACCEL   (France)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Amino acids; Biochemistry; Propensities; Protein structures; Secondary structures

Indexed keywords

AMINO ACID;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATABASES, PROTEIN; METHYLTRANSFERASES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 77950542887     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.198     Document Type: Article

References (118)

1. Pauling L, Corey RB (1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 37:251-256.
2. Pauling L, Corey RB, Branson HR (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37: 205-211.
3. Hutchinson EG, Thornton JM (1993) The Greek key motif: extraction, classification and analysis. Protein Eng 6:233-245. (Pubitemid 23123763)
4. Hutchinson EG, Thornton JM (1990) HERA - a program to draw schematic diagrams of protein secondary structures. Proteins 8:203-212.
5. Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR (2004) TOPS: an enhanced database of protein structural topology. Nucleic Acids Res 32:D251-D254.
6. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
7. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
8. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242.
9. Andersen CA, Palmer AG, Brunak S, Rost B (2002) Continuum secondary structure captures protein flexibility. Structure (Camb) 10:175-184. (Pubitemid 34164596)
10. Fodje MN, Al-Karadaghi S (2002) Occurrence, conformational features and amino acid propensities for the pi-helix. Protein Eng 15:353-358.
11. Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566-579. (Pubitemid 26009520)
12. Smith D (1989) SSTRUC: A program to calculate a secondary structural summary. Department of Crystallography, Birkbeck College, University of London, Cambridge, UK.
13. Hutchinson EG, Thornton JM (1996) PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci 5:212-220.
14. Richards FM, Kundrot CE (1988) Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 3:71-84.
15. Levitt M, Greer J (1977) Automatic identification of secondary structure in globular proteins. J Mol Biol 114: 181-239.
16. Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol 5:17. (Pubitemid 41431386)
17. Labesse G, Colloc'h N, Pothier J, Mornon JP (1997) P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins. Comput Appl Biosci 13:291-295.
18. King SM, Johnson WC (1999) Assigning secondary structure from protein coordinate data. Proteins 35: 313-320. (Pubitemid 29200968)
19. Srinivasan R, Rose GD (1999) A physical basis for protein secondary structure. Proc Natl Acad Sci USA 96: 14258-14263. (Pubitemid 30000638)
20. Cubellis MV, Cailliez F, Lovell SC (2005) Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics 6 (Suppl 4):S8.
21. Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP (2005) Voro3D: 3D Voronoi tessellations applied to protein structures. Bioinformatics 21:1715-1716. (Pubitemid 40542740)
22. Dupuis F, Sadoc JF, Mornon JP (2004) Protein secondary structure assignment through Voronoi tessellation. Proteins 55:519-528. (Pubitemid 38620077)
23. Taylor T, Rivera M, Wilson G, Vaisman, II (2005) New method for protein secondary structure assignment based on a simple topological descriptor. Proteins 60: 513-524. (Pubitemid 41061643)
24. Sklenar H, Etchebest C, Lavery R (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6:46-60.
25. Majumdar I, Krishna SS, Grishin NV (2005) PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 6: 202. (Pubitemid 41372464)
26. Hosseini S, Sadeghi M, Pezeshk H, Eslahchi C, Habibi M (2005) PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms. Comput Biol Chem 32:406-411.
27. Parisien M, Major F (2005) A new catalog of protein beta-sheets. Proteins 61:545-558.
28. Kumar S, Bansal M (1996) Structural and sequence characteristics of long alpha helices in globular proteins. Biophys J 71:1574-1586. (Pubitemid 26299795)
29. Kumar S, Bansal M (1998) Geometrical and sequence characteristics of alpha-helices in globular proteins. Biophys J 75:1935-1944. (Pubitemid 28455188)
30. Bansal M, Kumar S, Velavan R (2000) HELANAL: a program to characterize helix geometry in proteins. J Biomol Struct Dyn 17:811-819. (Pubitemid 30227198)
31. Woodcock S, Mornon JP, Henrissat B (1992) Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Protein Eng 5:629-635.
32. Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP (1993) Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng 6: 377-382.
33. Fourrier L, Benros C, de Brevern AG (2004) Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics 5:58. (Pubitemid 38751278)
34. Zhang W, Dunker AK, Zhou Y (2007) Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins 71: 61-67.
35. Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339.
36. Fitzkee NC, Fleming PJ, Gong H, Panasik N, Jr, Street TO, Rose GD (2005a) Are proteins made from a limited parts list? Trends Biochem Sci 30:73-80.
37. Fitzkee NC, Fleming PJ, Rose GD (2005b) The protein coil library: a structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins 58:852-854.
38. Offmann B, Tyagi M, deBrevern AG (2007) Local Protein Structures. Curr Bioinformatics 3:165-202.
39. Rose GD, Seltzer JP (1977) A new algorithm for finding the peptide chain turns in a globular protein. J Mol Biol 113:153-164.
40. Rose GD, Gierasch LM, Smith JA (1985) Turns in peptides and proteins. Adv Protein Chem 37:1-109.
41. Hutchinson EG, Thornton JM (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci 3:2207-2216.
42. Fuchs PF, Alix AJ (2005) High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins 59:828-839.
43. Bornot A, deBrevern AG (2006) Protein beta-turn assignments. Bioinformation 1:153-155.
44. Street TO, Fitzkee NC, Perskie LL, Rose GD (2007) Physical-chemical determinants of turn conformations in globular proteins. Protein Sci 16:1720-1727.
45. Edwards MS, Sternberg JE, Thornton JM (1987) Structural and sequence patterns in the loops of beta alpha beta units. Protein Eng 1:173-181.
46. Thornton JM, Sibanda BL, Edwards MS, Barlow DJ (1988) Analysis, design and modification of loop regions in proteins. Bioessays 8:63-69.
47. Ring CS, Kneller DG, Langridge R, Cohen FE (1992) Taxonomy and conformational analysis of loops in proteins. J Mol Biol 224:685-699.
48. Wintjens RT, Rooman MJ, Wodak SJ (1996) Automatic classification and analysis of alpha alpha-turn motifs in proteins. J Mol Biol 255:235-253.
49. Boutonnet NS, Kajava AV, Rooman MJ (1998) Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins. Proteins 30: 193-212.
50. Wintjens R, Wodak SJ, Rooman M (1998) Typical interaction patterns in alphabeta and betaalpha turn motifs. Protein Eng 11:505-522. (Pubitemid 28362664)
51. Efimov AV (2008) Structural trees for proteins containing phi-motifs. Biochemistry (Mosc) 273:23-28.
52. Espadaler J, Querol E, Aviles FX, Oliva B (2006) Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics 22: 2237-2243. (Pubitemid 44390878)
53. Rekha N, Srinivasan N (2003) Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions. BMC Struct Biol 3:4.
54. Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B (2004) Classification of common functional loops of kinase super-families. Proteins 56: 539-555. (Pubitemid 38924966)
55. Srinivasan N, Bax B, Blundell TL, Parker PJ (1996) Structural aspects of the functional modules in human protein kinase-C alpha deduced from comparative analyses. Proteins 26:217-235.
56. Panchenko AR, Madej T (2004) Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins 57:539-547.
57. Panchenko AR, Madej T (2005) Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol Biol 5:10.
58. Panchenko AR, Wolf YI, Panchenko LA, Madej T (2005) Evolutionary plasticity of protein families: coupling between sequence and structure variation. Proteins 61:535-544. (Pubitemid 41547410)
59. Madej T, Panchenko AR, Chen J, Bryant SH (2007) Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins. BMC Struct Biol 7:23.
60. Wolf Y, Madej T, Babenko V, Shoemaker B, Panchenko AR (2007) Long-term trends in evolution of indels in protein sequences. BMC Evol Biol 7:19. (Pubitemid 46328646)
61. Jiang H, Blouin C (2007) Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinformatics 8: 444.
62. Huang Z, Wong CF, Wheeler RA (2008) Flexible protein-flexible ligand docking with disrupted velocity simulated annealing. Proteins 71:440-454.
63. Nabuurs SB, Wagener M, deVlieg J (2007) A flexible approach to induced fit docking. J Med Chem 50: 6507-6518
64. Wong S, Jacobson MP (2008) Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins 71:153-164.
65. Lessel U, Schomburg D (1999) Importance of anchor group positioning in protein loop prediction. Proteins 37:56-64. (Pubitemid 29408919)
66. Miyazaki S, Kuroda Y, Yokoyama S (2002) Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J Struct Funct Genomics 2:37-51. (Pubitemid 34693427)
67. Wohlfahrt G, Hangoc V, Schomburg D (2002) Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements. Proteins 47:370-378. (Pubitemid 34438686)
68. Rohl CA, Strauss CE, Chivian D, Baker D (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55:656-677. (Pubitemid 38620090)
69. Boomsma W, Hamelryck T (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics 6:159. (Pubitemid 41372506)
70. Monnigmann M, Floudas CA (2005) Protein loop structure prediction with flexible stem geometries. Proteins 61:748-762. (Pubitemid 41753146)
71. Fernandez-Fuentes N, Fiser A (2006) Saturating representation of loop conformational fragments in structure databanks. BMC Struct Biol 6:15. (Pubitemid 44438019)
72. Fernandez-Fuentes N, Oliva B, Fiser A (2006a) A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 34:2085-2097. (Pubitemid 44314206)
73. Fernandez-Fuentes N, Zhai J, Fiser A (2006b) ArchPRED: a template based loop structure prediction server. Nucleic Acids Res 34:W173-W176.
74. Zhu K, Pincus DL, Zhao S, Friesner RA (2006) Long loop prediction using the protein local optimization program. Proteins 65:438-452. (Pubitemid 44454115)
75. Kanagasabai V, Arunachalam J, Prasad PA, Gautham N (2007) Exploring the conformational space of protein loops using a mean field technique with MOLS sampling. Proteins 67:908-921. (Pubitemid 46753938)
76. Olson MA, Feig M, Brooks CL, III (2008) Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 29:820-831.
77. Prasad PA, Kanagasabai V, Arunachalam J, Gautham N (2007) Exploring conformational space using a mean field technique with MOLS sampling. J Biosci 32: 909-920. (Pubitemid 47435523)
78. Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B (2008) Loop modeling: sampling, filtering, and scoring. Proteins 70:834-843.
79. Reetz MT, Carballeira JD, Vogel A (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 45:7745-7751.
80. Hu X, Wang H, Ke H, Kuhlman B (2007) High-resolution design of a protein loop. Proc Natl Acad Sci USA 104:17668-17673.
81. Rapp CS, Strauss T, Nederveen A, Fuentes G (2007) Prediction of protein loop geometries in solution. Proteins 69:69-74. (Pubitemid 47339140)
82. Efimov AV (1991b) Structure of coiled beta-beta-hairpins and beta-beta-corners. FEBS Lett 284:288-292.
83. Efimov AV (1991a) Structure of alpha-alpha-hairpins with short connections. Protein Eng 4:245-250.
84. Rufino SD, Donate LE, Canard LH, Blundell TL (1997) Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. J Mol Biol 267:352-367.
85. Wojcik J, Mornon JP, Chomilier J (1999) New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 289:1469-1490. (Pubitemid 29296718)
86. Michalsky E, Goede A, Preissner R (2003) Loops In Proteins (LIP)-a comprehensive loop database for homology modelling. Protein Eng 16:979-985. (Pubitemid 38281748)
87. Presta LG, Rose GD (1988) Helix signals in proteins. Science 240:1632-1641.
88. Aurora R, Rose GD (1998) Helix capping. Protein Sci 7: 21-38.
89. Kruus E, Thumfort P, Tang C, Wingreen NS (2005) Gibbs sampling and helix-cap motifs. Nucleic Acids Res 33:5343-5353.
90. Wang G, Dunbrack RL, Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19:1589-1591. (Pubitemid 37038881)
91. Wang G, Dunbrack RL, Jr (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 33:W94-W98.
92. Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford H, Jr, Marquez VE, Marasco CJ, Sufrin JR, O'Gara M (1999) Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. J Mol Biol 285:2021-2034.
93. deBrevern AG (2005) New assessment of a structural alphabet. In Silico Biol 5:283-289.
94. Doig AJ, Baldwin RL (1995) N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. Protein Sci 4:1325-1336.
95. Mandel-Gutfreund Y, Zaremba SM, Gregoret LM (2001) Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands. J Mol Biol 305: 1145-1159. (Pubitemid 33027749)
96. Mandel-Gutfreund Y, Gregoret LM (2002) On the significance of alternating patterns of polar and non-polar residues in beta-strands. J Mol Biol 323:453-461. (Pubitemid 35283673)
97. Bang D, Gribenko AV, Tereshko V, Kossiakoff AA, Kent SB, Makhatadze GI (2006) Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat Chem Biol 2:139-143. (Pubitemid 44323864)
98. Rose GD (2006) Lifting the lid on helix-capping. Nat Chem Biol 2:123-124.
99. deBrevern AG, Etchebest C, Hazout S (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41:271-287.
100. Kullback S, Leibler RA (1951) On information and sufficiency. Ann Math Stat 22:79-86.
101. deBrevern AG, Benros C, Hazout S. Structural alphabet: from a local point of view to a global description of protein 3d structures. In: Yan PV, Ed. (2005a) Bioinformatics: New Research. New York: Nova Publishers, pp 127-169.
102. deBrevern AG, Camproux AC, Hazout S, Etchebest C, Tuffery P. Protein structural alphabets: beyond the secondary structure description. In: Sangadai S, Ed. (2001) Recent research developments in protein engineering. Trivandrum: Research Signpost, pp 319-331.
103. deBrevern AG, Valadie H, Hazout S, Etchebest C (2002) Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. Protein Sci 11:2871-2886.
104. deBrevern AG, Hazout S (2003) 'Hybrid protein model' for optimally defining 3D protein structure fragments. Bioinformatics 19:345-353.
105. deBrevern AG, Benros C, Gautier R, Valadie H, Hazout S, Etchebest C (2004) Local backbone structure prediction of proteins. In Silico Biol 4:381-386.
106. deBrevern AG, Wong H, Tournamille C, Colin Y, Le Van Kim C, Etchebest C (2005b) A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC). Biochim Biophys Acta 1724:288-306.
107. Benros C, deBrevern AG, Etchebest C, Hazout S (2006) Assessing a novel approach for predicting local 3D protein structures from sequence. Proteins 62:865-880.
108. deBrevern AG, Etchebest C, Benros C, Hazout S (2007) "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. J Biosci 32:51-70.
109. Etchebest C, Benros C, Bornot A, Camproux AC, deBrevern AG (2007) A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. Eur Biophys J 36:1059-1069. (Pubitemid 350045038)
110. Benros C, deBrevern AG, Hazout S (2009) Analyzing the sequence-structure relationship of a library of local structural prototypes. J Theor Biol 256:215-226.
111. Bornot A, Etchebest C, deBrevern AG (2009) A new prediction strategy for long local protein structures using an original description. Proteins 76:570-587.
112. Faure G, Bornot A, deBrevern AG (2009) Analysis of protein contacts into protein units. Biochimie 91: 876-887.
113. Lesk AM (2005) Introduction to Bioinformatics. Oxford: Oxford University Press.
114. Robson B, Garnier J (1986) Introduction to proteins and protein engineering. Amsterdam: Elsevier Press.
115. Cuff JA, Barton GJ (1999) Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34:508-519. (Pubitemid 29129701)
116. Zhang W, Dunker AK, Zhou Y (2008) Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins 71: 61-67.
117. Dovidchenko NV, Bogatyreva NS, Galzitskaya OV (2008) Prediction of loop regions in protein sequence. J Bioinform Comput Biol 6:1035-1047.
118. Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, deBrevern AG, Offmann B (2006) Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res 34:W119-W123.