Position-specific propensities of amino acids in the -strand

BMC Structural Biology

Volumn 10, Issue , 2010, Pages

  Bhattacharjee, Nicholus ^a   Biswas, Parbati ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BETA AMINO ACID; AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; HYDROPHOBICITY; PERIODICITY; PHYSICAL CHEMISTRY; PROTEIN STRUCTURE; CHEMICAL PHENOMENA; CHEMISTRY; GENETICS; POSITION WEIGHT MATRIX; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE;

AMINO ACIDS; DATABASES, PROTEIN; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; POSITION-SPECIFIC SCORING MATRICES; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 77957144851     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-10-29     Document Type: Article

References (66)

1. Free energy determinants of secondary structure formation: I. -Helices. AS Yang B Honig, J Mol Biol 1995 252 351 365 10.1006/jmbi.1995.0502 7563056
2. Flexibility of -Helices: Results of a Statistical Analysis of Database Protein Structures. EG Emberly R Mukhopadhyay NS Wingreen C Tang, J Mol Biol 2003 327 229 237 10.1016/S0022-2836(03)00097-4 12614621
3. Conformation of twisted -sheets in proteins. CJ Chothia, J Mol Biol 1973 75 295 302 10.1016/0022-2836(73)90022-3 4728692
4. Free energy determinants of secondary structure formation. II. Antiparallel -sheets. AS Yang B Honig, J Mol Biol 1995 252 366 376 10.1006/jmbi.1995.0503 7563057
5. Flexibility of -sheets: Principal component analysis of database protein structures. EG Emberly R Mukhopadhyay C Tang NS Wingreen, Proteins 2004 55 91 98 10.1002/prot.10618 14997543
6. Strcture-based conformational preferences of amino acids. P Koehl M Levitt, Proc Natl Acad Sci USA 1999 96 12524 12529 10.1073/pnas.96.22.12524 10535955
7. Conformational Parameters for Amino Acids in Helical, -Sheet, and Random Coil Regions Calculated from Proteins. PY Chou GD Fasman, Biochemistry 1974 13 211 222 10.1021/bi00699a001 4358939
8. A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. SN Malkov MV Zivkovic MV Beljanski MB Hall SD Zaric, J Mol Model 2008 14 769 775 10.1007/s00894-008-0313-0 18504624
9. Protein structure prediction and structural genomics. D Baker A Sali, Science 2001 294 93 96 10.1126/science.1065659 11588250 (Pubitemid 32952955)
10. Ab initio protein structure prediction. C Hardin TV Pogorelov Z Luthey-Schulten, Curr Opin Struct Biol 2002 12 1756 181 10.1016/S0959-440X(02) 00306-8 (Pubitemid 34327476)
11. Predicting protein three-dimensional structure. J Moult, Curr Opin Biotechnol 1999 10 583 588 10.1016/S0958-1669(99)00037-3 10600698
12. Review: protein secondary structure prediction continues to rise. B Rost, J Struct Biol 2001 134 204 218 10.1006/jsbi.2001.4336 11551180
13. Protein structure prediction in 2002. J Schonbrun WJ Wedemeyer D Baker, Curr Opin Struct Biol 2002 12 348 354 10.1016/S0959-440X(02)00336-6 12127454
14. Amino acid distribution in protein secondary structures. P Argos J Palau, Int J Prot Pept Res 1982 19 380 393 10.1111/j.1399-3011.1982.tb02619.x
15. Amino acid preferences for specific locations at the ends of -helices. JS Richardson DC Richardson, Science 1988 240 1648 1652 10.1126/science.3381086 3381086
16. Dissecting -Helices: Position-Specific Analysis of -Helices in Globular Proteins. S Kumar M Bansal, Proteins 1998 31 460 476 10.1002/(SICI)1097- 0134(19980601)31:4<460::AID-PROT12>3.0.CO;2-D 9626705
17. Helix signals in proteins. LG Presta GD Rose, Science 1988 240 1632 1641 10.1126/science.2837824 2837824
18. Position dependence of non-polar amino acid intrinsic helical propensities. M Petukhov V Munoz N Yumoto S Yoshikawa L Serrano, J Mol Biol 1998 278 279 289 10.1006/jmbi.1998.1682 9571050
19. Position dependence of amino acid intrinsic helical propensities. II. Non-charged polar residues: Ser, Thr, Asn, and Gln. M Petukhov K Uegaki N Yumoto S Yoshikawa L Serrano, Protein Sci 1999 8 2144 2150 10.1110/ps.8.10.2144 10548060
20. Side chain structures in the first turn of the -helix. S Penel E Hughes AJ Doig, J Mol Biol 1999 287 127 143 10.1006/jmbi.1998.2549 10074412
21. Amino acid intrinsic -helix dependence at several positions of C terminus. M Petukhov K Uegaki N Yumoto L Serrano, Protein Sci 2002 11 766 777 10.1110/ps.2610102 11910021
22. Effect of the N1 residue on the stability of the -helix for all 20 amino acids. DAE Cochran S Penel AJ Doig, Protein Sci 2001 10 463 470 10.1110/ps.31001 11344315
23. Side improved prediction of N-termini of -helices using empirical information. CL Wilson AJ Boardma PE Doig SJ Hubbard, Proteins 2004 57 322 330 10.1002/prot.20218 15340919
24. Effect of the N2 residue on the stability of the -helix for all 20 amino acids. DAE Cochran AJ Doig, Protein Sci 2001 10 1305 1311 10.1110/ps.50701 11420432
25. Amino acid pairing at the N- and C-termini of helical segments in proteins. NA Fonseca R Camacho AL Magalhaes, Proteins 2008 70 188 196 10.1002/prot.21525 17654550
26. Capping and -helix stability. L Serrano AR Fersht, Nature 1989 342 296 299 10.1038/342296a0 2812029
27. Effect of alanine versus glycine in -helices on protein stability. L Serrano JL Neira J Sancho AR Fersht, Nature 1992 256 453 456 10.1038/356453a0
28. The role of neutral histidine at the N-cap position. JTJ Lecomte CD Moore, J Am Chem Soc 1991 113 9663 9665 10.1021/ja00025a037
29. Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of 6 amino acid substitutions at Thr 59. JA Bell WJ Becktel C Sauer WA Baase BW Matthews, Biochemistry 1992 31 3590 3596 10.1021/bi00129a006 1567817
30. Helix capping propensities in peptides parallel thoes in proteins. A Chakrabartty AJ Doig RL Baldwin, Proc Natl Acad Sci USA 1993 90 11332 11336 10.1073/pnas.90.23.11332 8248248
31. Stabilisation of -helical structures in short peptides via end capping. B Farood EJ Feliciano KP Nambiar, Proc Natl Acad Sci USA 1993 90 838 842 10.1073/pnas.90.3.838 8430094
32. Capping interactions in isolated -helices:Position-dependent substitution effects and structure of a serine-capped helix. PC Lyu DE Wemmer HX Zhou RJ Pinker NR Kallenbach, Biochemistry 1993 32 421 425 10.1021/bi00053a006 8422351
33. Stabilisation of -helix in C-terminal fragments of neuropeptide-Y. N Yumoto S Murase T Hattori H Yamamoto Y Tatsu S Yoshikawa, Biochem Biophys Res Commun 1993 196 1490 1495 10.1006/bbrc.1993.2420 8250906
34. Determination of free energies of N-capping in -helices by modification of Lifson-Roig helix-coil theory to include N- and C-capping. AJ Doig A Chakrabartty TM Kingler RL Baldwin, Biochemistry 1994 33 3396 3403 10.1021/bi00177a033 8136377
35. N- and C-capping preferences for all 20 amino acids in helical peptides. AJ Doig RL Baldwin, Protein Sci 1995 4 2247 2251 10.1002/pro.5560041101 8563620
36. Factors that affect the stabilisation of -helices in short peptides by a capping box. M Petukhov N Yumoto S Murase R Onmura S Yashikawa, Biochemistry 1996 35 387 397 10.1021/bi9513766 8555208
37. Rules for -helix termination by glycine. R Aurora R Srinivasan GD Rose, Science 1994 264 1126 1130 10.1126/science.8178170 8178170
38. Structural basis of amino acid -helix propensity. M Blader XJ Zhang BW Matthews, Science 1993 260 1637 1640 10.1126/science.8503008 8503008
39. Relative helix-forming tendencies of nonpolar amino acids. S Padmanabhan S Marquesee T Ridgeway TM Laue RL Baldwin, Nature 1990 344 268 270 10.1038/344268a0 2314462
40. Amino Acid Propensities are Position-dependent Throughout the Length of -Helices. DE Engel WF DeGrado, J Mol Biol 2004 337 1195 1205 10.1016/j.jmb.2004.02.004 15046987
41. Strcture-based conformational preferences of amino acids. P Koehl M Levitt, Proc Natl Acad Sci USA 1999 96 12524 12529 10.1073/pnas.96.22.12524 10535955
42. Intrinsic Secondary Structure Propensities of the Amino Acids, Using Statistical - Matrices: Comparison With Experimental Scales. V Munoz L Serrano, Proteins 1994 20 301 311 10.1002/prot.340200403 7731949
43. Hydrogen bond strength and -sheet propensities: the role of a side chain blocking effect. Y Bai SW Englander, Proteins 1994 18 262 266 10.1002/prot.340180307 8202467
44. Role of electrostatic screening in determining protein main chain conformational preferences. F Avbelj J Moult, Biochemistry 1995 34 755 764 10.1021/bi00003a008 7827034
45. Intrinsic -sheet propensities result from van der Waals interactions between side chains and the local backbone. AG Street SL Mayo, Proc Natl Acad Sci USA 1999 96 9074 9076 10.1073/pnas.96.16.9074 10430897
46. Mean curvature as a major determinant of -sheet propensity. E Koh T Kim HS Cho, Bioinformatics 2006 22 297 302 10.1093/bioinformatics/bti775 16287940
47. Beta-sheet propensity and its correlation with parameters based on conformation. D Pal P Chakrabarti, Acta Crystallogr D, Biol Crystallogr 2000 56 589 594 10.1107/S090744490000367X (Pubitemid 30324822)
48. -Sheet capping: Signals that initiate and terminate-sheet formation. F FarzadFard N Gharaei H Pezeshk S Marashi, J Struct Biol 2008 161 101 110 10.1016/j.jsb.2007.09.024 18006332
49. Enlarged representative set of protein structures. U Hobohm C Sander, Protein Sci 1994 3 522 524 10.1002/pro.5560030317 8019422
50. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. W Kabsch C Sander, Biopolymers 1983 22 2577 2637 10.1002/bip.360221211 6667333
51. On the Significance of Alternating Patterns of Polar and Non-polar Residues in Beta-strands. Y Mandel-Gutfreund LM Gregoret, J Mol Biol 2002 323 453 461 10.1016/S0022-2836(02)00973-7 12381301
52. Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures. M Duan M Huang C Ma L Li Y Zhou, Protein Sci 2008 17 1505 1512 10.1110/ps.035691.108 18519808
53. Local Hydrophobicity Stabilizes Secondary Structures in Proteins. MI Kanehisa TY Tsong, Biopolymers 1980 19 1617 1628 10.1002/bip.1980.360190906 7426680
54. C Tanford, The Hydrophobic Effect Wiley, New York 2 1979
55. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. HJ H SR S MTJ Record, J Mol Biol 1989 209 801 816 10.1016/0022-2836(89)90608-6 2585510
56. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. WC Wimley TP Creamer SH White, Biochemistry 1996 35 5109 5124 10.1021/bi9600153 8611495
57. Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of -sheet formation in proteins. H Zhu W Braun, Protein Sci 1999 8 326 342 10048326
58. Ranking the factors that contribute to protein -sheet folding. M Parisien F Major, Proteins 2007 68 824 829 10.1002/prot.21475 17523189
59. Estimation of the number of -helical and -strand segments in proteins using circular dichroism spectroscopy. N Sreerama SY Venyaminov RW Woody, Protein Sci 1999 8 370 380 10048330
60. Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. MW West MH Hecht, Protein Sci 1995 4 2032 2039 10.1002/pro.5560041008 8535239
61. TE Creighton, Proteins:Structure and Molecular Properties W. H. Freeman and Company 2 1984
62. Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. H Xiong BL Buckwalter HM Shieh MH Hecht, Proc Natl Acad Sci USA 1995 92 6349 6353 10.1073/pnas.92.14.6349 7603994
63. Amino Acid Pairing Preferences in Parallel -Sheets in Proteins. HM Fooks ACR Martin DN Woolfson RB Sessions EG Hutchinson, J Mol Biol 2006 356 32 44 10.1016/j.jmb.2005.11.008 16337654
64. SCOP: a structural classification of proteins database for the investigation of sequences and structures. AG Murzin SE Brenner H T C Chothia, J Mol Biol 1995 247 536 540 7723011
65. Prediction of secondary structure of proteins by means of hydrophobicity profiles. H Cid M Bunster E Arriagada M Campos, FEBS Lett 1982 150 247 254 10.1016/0014-5793(82)81344-6
66. Computer-Based Redesign of a Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo Sheet Design. X Hu H Wang H Ke B Kuhlman, Structure 2008 16 1799 1805 10.1016/j.str.2008.09.013 19081056