메뉴 건너뛰기




Volumn 61, Issue 3, 2005, Pages 545-558

A new catalog of protein β-sheets

Author keywords

annotation; sheet; Energy; H bonding motifs; Helix; X ray crystal structures

Indexed keywords

PROTEIN;

EID: 27544511313     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20677     Document Type: Article
Times cited : (17)

References (57)
  • 1
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
    • Chou PY, Fasman GD. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 2
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • Gamier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
    • (1978) J Mol Biol , vol.120 , pp. 97-120
    • Gamier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 3
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002;47:228-235.
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 4
    • 0141523251 scopus 로고    scopus 로고
    • Beta edge strands in protein structure prediction and aggregation
    • Siepen JA, Radford SE, Westhead DR. Beta edge strands in protein structure prediction and aggregation. Protein Sci 2003;12: 2348-2359.
    • (2003) Protein Sci , vol.12 , pp. 2348-2359
    • Siepen, J.A.1    Radford, S.E.2    Westhead, D.R.3
  • 5
    • 0000095892 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
    • Liwo A, Oldziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comp Chem 1997;18:849-873.
    • (1997) J Comp Chem , vol.18 , pp. 849-873
    • Liwo, A.1    Oldziej, S.2    Pincus, M.R.3    Wawak, R.J.4    Rackovsky, S.5    Scheraga, H.A.6
  • 6
    • 0000095890 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of local interactions and determination of the weights of energy terms by Z-score optimization
    • Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Oldziej S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of local interactions and determination of the weights of energy terms by Z-score optimization. J Comp Chem 1997;18:874-887.
    • (1997) J Comp Chem , vol.18 , pp. 874-887
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Oldziej, S.5    Scheraga, H.A.6
  • 7
    • 0001181898 scopus 로고    scopus 로고
    • United-residue force field for off-lattice protein-structure simulations; III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
    • Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein-structure simulations; III. origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comp Chem 1998;19:259-276.
    • (1998) J Comp Chem , vol.19 , pp. 259-276
    • Liwo, A.1    Kazmierkiewicz, R.2    Czaplewski, C.3    Groth, M.4    Oldziej, S.5    Wawak, R.J.6    Rackovsky, S.7    Pincus, M.R.8    Scheraga, H.A.9
  • 8
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 9
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 10
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using ROSETTA
    • Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999;Suppl 3:171-176.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 13
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 14
    • 0000573263 scopus 로고
    • Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
    • Pauling L, Corey RB. Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets. Proc Natl Acad Sci USA 1951;37:729-740.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 729-740
    • Pauling, L.1    Corey, R.B.2
  • 15
    • 76549252207 scopus 로고
    • The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain
    • Pauling L, Corey RB, Branson HR. The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951;37:205-211.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 205-211
    • Pauling, L.1    Corey, R.B.2    Branson, H.R.3
  • 16
    • 0013852463 scopus 로고
    • Structure of hen egg-white lysozyme. Ax three-dimensional fourier synthesis at 2 angstrom resolution
    • Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR. Structure of hen egg-white lysozyme. Ax three-dimensional fourier synthesis at 2 angstrom resolution. Nature 1965;206:757-761.
    • (1965) Nature , vol.206 , pp. 757-761
    • Blake, C.C.1    Koenig, D.F.2    Mair, G.A.3    North, A.C.4    Phillips, D.C.5    Sarma, V.R.6
  • 17
    • 0023927904 scopus 로고
    • Identification of structural motifs from protein coordinate data: Secondary structure and first-level super secondary structure
    • Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level super secondary structure. Proteins 1988;3:71-84.
    • (1988) Proteins , vol.3 , pp. 71-84
    • Richards, F.M.1    Kundrot, C.E.2
  • 18
    • 0030998184 scopus 로고    scopus 로고
    • P-SEA: A new efficient assignment of secondary structure from c alpha trace of proteins
    • Labesse G, Colloc'h N, Pothier J, Mornon JP. P-SEA: a new efficient assignment of secondary structure from c alpha trace of proteins. Comput Appl Biosci 1997;13:291-295.
    • (1997) Comput Appl Biosci , vol.13 , pp. 291-295
    • Labesse, G.1    Colloc'h, N.2    Pothier, J.3    Mornon, J.P.4
  • 19
    • 0033562619 scopus 로고    scopus 로고
    • Assigning secondary structure from protein coordinate data
    • King SM, Johnson WC. Assigning secondary structure from protein coordinate data. Proteins 1999;35:313-320.
    • (1999) Proteins , vol.35 , pp. 313-320
    • King, S.M.1    Johnson, W.C.2
  • 20
    • 0035958742 scopus 로고    scopus 로고
    • Defining linear segments in protein structure
    • Taylor WR. Defining linear segments in protein structure. J Mol Biol 2001;310:1135-1150.
    • (2001) J Mol Biol , vol.310 , pp. 1135-1150
    • Taylor, W.R.1
  • 21
    • 2442596233 scopus 로고    scopus 로고
    • Protein secondary structure assignment through Voronoi tessellation
    • Dupuis F, Sadoc JF, Mornon JP. Protein secondary structure assignment through Voronoi tessellation. Proteins 2004;55:519-528.
    • (2004) Proteins , vol.55 , pp. 519-528
    • Dupuis, F.1    Sadoc, J.F.2    Mornon, J.P.3
  • 22
    • 0024821134 scopus 로고
    • Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis
    • Sklenar H, Etchebest C, Lavery R. Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989;6:46-60.
    • (1989) Proteins , vol.6 , pp. 46-60
    • Sklenar, H.1    Etchebest, C.2    Lavery, R.3
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 24
  • 25
    • 0042622443 scopus 로고    scopus 로고
    • DSSPcont: Continuous secondary structure assignments for proteins
    • Carter P, Andersen CAF, Rost B. DSSPcont: continuous secondary structure assignments for proteins. Nucl Acids Res 2003;31:3293-3295.
    • (2003) Nucl Acids Res , vol.31 , pp. 3293-3295
    • Carter, P.1    Andersen, C.A.F.2    Rost, B.3
  • 26
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 27
    • 1442300068 scopus 로고    scopus 로고
    • Flexibility of beta-sheets: Principal component analysis of database protein structures
    • Emberly EG, Mukhopadhyay R, Tang C, Wingreen NS. Flexibility of beta-sheets: principal component analysis of database protein structures. Proteins 2004;55:91-98.
    • (2004) Proteins , vol.55 , pp. 91-98
    • Emberly, E.G.1    Mukhopadhyay, R.2    Tang, C.3    Wingreen, N.S.4
  • 29
    • 0036296028 scopus 로고    scopus 로고
    • Twist and shear in beta-sheets and beta-ribbons
    • Ho BK, Curmi PM. Twist and shear in beta-sheets and beta-ribbons. J Mol Biol 2002;317:291-308.
    • (2002) J Mol Biol , vol.317 , pp. 291-308
    • Ho, B.K.1    Curmi, P.M.2
  • 30
    • 0027207221 scopus 로고
    • Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
    • Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP. Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Prot Eng 1993;6:377-382.
    • (1993) Prot Eng , vol.6 , pp. 377-382
    • Colloc'h, N.1    Etchebest, C.2    Thoreau, E.3    Henrissat, B.4    Mornon, J.P.5
  • 31
    • 0033529861 scopus 로고    scopus 로고
    • Intrinsic beta-sheet propensities result from van der waals interactions between side chains and the local backbone
    • Street AG, Mayo SL. Intrinsic beta-sheet propensities result from van der waals interactions between side chains and the local backbone. Proc Natl Acad Sci USA 1999;96:9074-9076.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9074-9076
    • Street, A.G.1    Mayo, S.L.2
  • 32
    • 0018543443 scopus 로고
    • Antiparallel and parallel β-strands differ in amino acid residue preferences
    • Lifson S, Sander C. Antiparallel and parallel β-strands differ in amino acid residue preferences. Nature 1979;282:109-111.
    • (1979) Nature , vol.282 , pp. 109-111
    • Lifson, S.1    Sander, C.2
  • 33
    • 0019317336 scopus 로고
    • Specific recognition in the tertiary structure of beta-sheets of proteins
    • Lifson S, Sander C. Specific recognition in the tertiary structure of beta-sheets of proteins. J Mol Biol 1980;139:627-639.
    • (1980) J Mol Biol , vol.139 , pp. 627-639
    • Lifson, S.1    Sander, C.2
  • 34
    • 0029048210 scopus 로고
    • Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the coulombic interactions
    • Maccallum PH, Poet R, Milner-White EJ. Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the coulombic interactions. J Mol Biol 1995;248:361-373.
    • (1995) J Mol Biol , vol.248 , pp. 361-373
    • Maccallum, P.H.1    Poet, R.2    Milner-White, E.J.3
  • 35
    • 0029078444 scopus 로고
    • Coulombic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands
    • Maccallum PH, Poet R, Milner-White EJ. Coulombic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands. J Mol Biol 1995;248:374-384.
    • (1995) J Mol Biol , vol.248 , pp. 374-384
    • Maccallum, P.H.1    Poet, R.2    Milner-White, E.J.3
  • 36
    • 33845554708 scopus 로고
    • Crystallographic evidence for the existence of C-H⋯O, C-H⋯N, and C-H⋯Cl hydrogen bonds
    • Taylor R, Kennard O. Crystallographic evidence for the existence of C-H⋯O, C-H⋯N, and C-H⋯Cl hydrogen bonds. J Am Chem Soc 1982;104:5063-5070.
    • (1982) J Am Chem Soc , vol.104 , pp. 5063-5070
    • Taylor, R.1    Kennard, O.2
  • 37
    • 0025875873 scopus 로고
    • Occurrence of bifurcated three-center hydrogen bonds in proteins
    • Preissner R, Egner U, Saenger W. Occurrence of bifurcated three-center hydrogen bonds in proteins. FEBS Lett 1991;288:192-196.
    • (1991) FEBS Lett , vol.288 , pp. 192-196
    • Preissner, R.1    Egner, U.2    Saenger, W.3
  • 38
    • 0028978764 scopus 로고
    • The occurrence of C-H⋯O hydrogen bonds in proteins
    • Derewenda ZS, Lee L, Derewenda U. The occurrence of C-H⋯O hydrogen bonds in proteins. J Mol Biol 1995;252:248-262.
    • (1995) J Mol Biol , vol.252 , pp. 248-262
    • Derewenda, Z.S.1    Lee, L.2    Derewenda, U.3
  • 39
    • 0034679011 scopus 로고    scopus 로고
    • How strong is the Calpha-H⋯O=C hydrogen bond?
    • Vargas R, Garza J, Dixon DA, Hay BP. How strong is the Calpha-H⋯O=C hydrogen bond? J Am Chem Soc 2000;122: 4750-4755.
    • (2000) J Am Chem Soc , vol.122 , pp. 4750-4755
    • Vargas, R.1    Garza, J.2    Dixon, D.A.3    Hay, B.P.4
  • 40
    • 0035979146 scopus 로고    scopus 로고
    • The Calpha-H⋯O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
    • Senes A, Ubarretxena-Belandia I, Engelman DM. The Calpha-H⋯O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci USA 2001;98:9056-9061.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 9056-9061
    • Senes, A.1    Ubarretxena-Belandia, I.2    Engelman, D.M.3
  • 41
    • 76549238253 scopus 로고
    • The pleated sheet, a new layer configuration of polypeptide chains
    • Pauling L, Corey RB. The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 1951;37:251-256.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 251-256
    • Pauling, L.1    Corey, R.B.2
  • 42
    • 0024566942 scopus 로고
    • New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
    • Boobbyer DN, Goodford PJ, McWhinnie PM, Wade RC. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem 1989;32:1083-1094.
    • (1989) J Med Chem , vol.32 , pp. 1083-1094
    • Boobbyer, D.N.1    Goodford, P.J.2    McWhinnie, P.M.3    Wade, R.C.4
  • 43
    • 0016399124 scopus 로고
    • Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals
    • Hagler AT, Huler E, Lifson S. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J Am Chem Soc 1974;96:5319-5327.
    • (1974) J Am Chem Soc , vol.96 , pp. 5319-5327
    • Hagler, A.T.1    Huler, E.2    Lifson, S.3
  • 44
    • 0016399126 scopus 로고
    • Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties
    • Hagler AT, Lifson S. Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties. J Am Chem Soc 1974;96:5327-5335.
    • (1974) J Am Chem Soc , vol.96 , pp. 5327-5335
    • Hagler, A.T.1    Lifson, S.2
  • 45
    • 0037022563 scopus 로고    scopus 로고
    • Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation
    • Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 2002;99:2754-2759.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 2754-2759
    • Richardson, J.S.1    Richardson, D.C.2
  • 47
    • 0029150955 scopus 로고
    • Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets
    • Yang AS, Honig B. Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets. J Mol Biol 1995;252: 366-376.
    • (1995) J Mol Biol , vol.252 , pp. 366-376
    • Yang, A.S.1    Honig, B.2
  • 48
    • 0028960071 scopus 로고
    • Role of electrostatic screening in determining protein main chain conformational preferences
    • Avbelj F, Moult J. Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 1995;34:755-764.
    • (1995) Biochemistry , vol.34 , pp. 755-764
    • Avbelj, F.1    Moult, J.2
  • 49
    • 0017701604 scopus 로고
    • Automatic identification of secondary structure in globular proteins
    • Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol 1977;114:181-239.
    • (1977) J Mol Biol , vol.114 , pp. 181-239
    • Levitt, M.1    Greer, J.2
  • 50
  • 52
    • 0027092678 scopus 로고
    • Selection of a representative set of structures from the Brookhaven Protein Data Bank
    • Hobohm U, Scharf M, Schneider R, Sander C. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci 1992;1:409-417.
    • (1992) Protein Sci , vol.1 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 53
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack Jr RL. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 54
  • 55
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. Molscript: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallog 1991;24: 946-950.
    • (1991) J Appl Crystallog , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 56
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
    • (1997) Methods Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 57
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comp Graph Stat 1996;5(3):299-314.
    • (1996) J Comp Graph Stat , vol.5 , Issue.3 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.