메뉴 건너뛰기




Volumn 50, Issue 4, 2003, Pages 552-562

Helix propensities of short peptides: Molecular dynamics versus bioinformatics

Author keywords

I sites library; Knowledge based potentials; Motifs; Protein folding; Secondary structure propensity; Structure prediction; Template effect

Indexed keywords

PEPTIDE;

EID: 0037339393     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10252     Document Type: Article
Times cited : (21)

References (47)
  • 1
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994;19:55-72.
    • (1994) Proteins , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 2
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 3
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281:565-577.
    • (1998) J Mol Biol , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 4
    • 0034604368 scopus 로고    scopus 로고
    • HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
    • Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2002;301:173-190.
    • (2002) J Mol Biol , vol.301 , pp. 173-190
    • Bystroff, C.1    Thorsson, V.2    Baker, D.3
  • 5
    • 0027174134 scopus 로고
    • Prediction of protein secondary structure by the hidden Markov model
    • Asai K, Hayamizu S, Handa K. Prediction of protein secondary structure by the hidden Markov model. Comput Appl Biosci 1993;9:141-146.
    • (1993) Comput Appl Biosci , vol.9 , pp. 141-146
    • Asai, K.1    Hayamizu, S.2    Handa, K.3
  • 6
    • 0031585987 scopus 로고    scopus 로고
    • Protein secondary structure prediction using local alignments
    • Salamov AA, Solovyev VV. Protein secondary structure prediction using local alignments. J Mol Biol 1997;268:31-36.
    • (1997) J Mol Biol , vol.268 , pp. 31-36
    • Salamov, A.A.1    Solovyev, V.V.2
  • 7
    • 0020446736 scopus 로고
    • Coiled-coils in alpha-helix-containing proteins: Analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins
    • Parry DA. Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins. Biosci Rep 1982;2:1017-1024.
    • (1982) Biosci Rep , vol.2 , pp. 1017-1024
    • Parry, D.A.1
  • 8
    • 0027165688 scopus 로고
    • Peptide models of protein folding initiation sites. I. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin
    • Waltho JP, Feher VA, Merutka G, Dyson HJ, Wright PE. Peptide models of protein folding initiation sites. I. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry 1993;32:6337-6347.
    • (1993) Biochemistry , vol.32 , pp. 6337-6347
    • Waltho, J.P.1    Feher, V.A.2    Merutka, G.3    Dyson, H.J.4    Wright, P.E.5
  • 9
    • 0343059020 scopus 로고    scopus 로고
    • Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain
    • Viguera AR, Jimenez MA, Rico M, Serrano L. Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain. J Mol Biol 1996;255:507-521.
    • (1996) J Mol Biol , vol.255 , pp. 507-521
    • Viguera, A.R.1    Jimenez, M.A.2    Rico, M.3    Serrano, L.4
  • 10
    • 0027984190 scopus 로고
    • Synthetic peptides probe folding initiation sites in platelet factor 4: Stable chain reversal found within the hydrophobic sequence LIATLKNGRKISL
    • Ilyina E, Milius R, Mayo KH. Synthetic peptides probe folding initiation sites in platelet factor 4: stable chain reversal found within the hydrophobic sequence LIATLKNGRKISL. Biochemistry 1994;33:13436-13444.
    • (1994) Biochemistry , vol.33 , pp. 13436-13444
    • Ilyina, E.1    Milius, R.2    Mayo, K.H.3
  • 12
    • 0032538302 scopus 로고    scopus 로고
    • Prediction and structural characterization of an independently folding substructure in the src SH3 domain
    • Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J Mol Biol 1998;283:293-300.
    • (1998) J Mol Biol , vol.283 , pp. 293-300
    • Yi, Q.1    Bystroff, C.2    Rajagopal, P.3    Klevit, R.E.4    Baker, D.5
  • 13
    • 0031301753 scopus 로고    scopus 로고
    • Blind predictions of local protein structure in CASP2 targets using the I-sites library
    • Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins 1997;(Suppl 1):167-171.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 167-171
    • Bystroff, C.1    Baker, D.2
  • 14
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
    • (1995) Comput Phys Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3
  • 15
    • 84986518863 scopus 로고
    • AMBER: Assisted model building with energy refinement - A general program for modeling molecules and their interactions
    • Weiner PK, Kollman PA. AMBER: assisted model building with energy refinement - a general program for modeling molecules and their interactions. J Comput Chem 1981;2:287-303.
    • (1981) J Comput Chem , vol.2 , pp. 287-303
    • Weiner, P.K.1    Kollman, P.A.2
  • 16
    • 0035135910 scopus 로고    scopus 로고
    • Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations
    • Burgi R, Daura X, Mark A, et al. Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. J Pept Res 2001;57:107-118.
    • (2001) J Pept Res , vol.57 , pp. 107-118
    • Burgi, R.1    Daura, X.2    Mark, A.3
  • 17
    • 0041140017 scopus 로고
    • Simulations of peptide conformational dynamics and thermodynamics
    • Brooks C, Case D. Simulations of peptide conformational dynamics and thermodynamics. Chem Rev 1993;93:2487-2502.
    • (1993) Chem Rev , vol.93 , pp. 2487-2502
    • Brooks, C.1    Case, D.2
  • 18
    • 0034033187 scopus 로고    scopus 로고
    • Long timescale simulations
    • Daggett V. Long timescale simulations. Curr Opin Struct Biol 2000;10:160-164.
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 160-164
    • Daggett, V.1
  • 19
    • 0035179018 scopus 로고    scopus 로고
    • Helix nucleation kinetics from molecular simulations in explicit solvent
    • Hummer G, Garcia AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins 2001;42:77-84.
    • (2001) Proteins , vol.42 , pp. 77-84
    • Hummer, G.1    Garcia, A.E.2    Garde, S.3
  • 20
    • 0034718553 scopus 로고    scopus 로고
    • Folding simulations of a three-stranded antiparallel beta-sheet peptide
    • Ferrara P, Caflisch A. Folding simulations of a three-stranded antiparallel beta-sheet peptide. Proc Natl Acad Sci USA 2000;97:10780-10785.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10780-10785
    • Ferrara, P.1    Caflisch, A.2
  • 21
    • 0030068825 scopus 로고    scopus 로고
    • Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide
    • Sieber V, Moe GR. Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide. Biochemistry 1996;35:181-188.
    • (1996) Biochemistry , vol.35 , pp. 181-188
    • Sieber, V.1    Moe, G.R.2
  • 22
    • 0030334822 scopus 로고    scopus 로고
    • Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution
    • de Alba E, Jimenez MA, Rico M, Nieto JL. Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution. Fold Des 1996;1:133-144.
    • (1996) Fold Des , vol.1 , pp. 133-144
    • De Alba, E.1    Jimenez, M.A.2    Rico, M.3    Nieto, J.L.4
  • 23
    • 0028500779 scopus 로고
    • A short linear peptide that folds into a native stable beta-hairpin in aqueous solution
    • Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol 1994;1:584-590.
    • (1994) Nat Struct Biol , vol.1 , pp. 584-590
    • Blanco, F.J.1    Rivas, G.2    Serrano, L.3
  • 24
    • 0028820601 scopus 로고
    • Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif
    • Munoz V, Serrano L. Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif. Biochemistry 1995;34:15301-15306.
    • (1995) Biochemistry , vol.34 , pp. 15301-15306
    • Munoz, V.1    Serrano, L.2
  • 25
    • 0030002295 scopus 로고    scopus 로고
    • Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues
    • Searle MS, Zerella R, Williams DH, Packman LC. Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues. Protein Eng 1996;9:559-565.
    • (1996) Protein Eng , vol.9 , pp. 559-565
    • Searle, M.S.1    Zerella, R.2    Williams, D.H.3    Packman, L.C.4
  • 26
    • 0035479690 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence-function relationship
    • Krueger BP, Kollman PA. Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship. Proteins 2001;45:4-15.
    • (2001) Proteins , vol.45 , pp. 4-15
    • Krueger, B.P.1    Kollman, P.A.2
  • 27
    • 0030914617 scopus 로고    scopus 로고
    • Comparison of database potentials and molecular mechanics force fields
    • Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997;7:194-199.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 194-199
    • Moult, J.1
  • 28
    • 0032014733 scopus 로고    scopus 로고
    • Knowledge-based potentials: Back to the roots
    • Koppensteiner WA, Sippl MJ. Knowledge-based potentials: back to the roots. Biochemistry (Mosc) 1998;63:247-252.
    • (1998) Biochemistry (Mosc) , vol.63 , pp. 247-252
    • Koppensteiner, W.A.1    Sippl, M.J.2
  • 30
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [see comments]. Science 1998;282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 31
    • 0001064488 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: Are these meaningful potentials?
    • Ben-Naim A. Statistical potentials extracted from protein structures: are these meaningful potentials? J Chem Phys 1997;107:3698-3706.
    • (1997) J Chem Phys , vol.107 , pp. 3698-3706
    • Ben-Naim, A.1
  • 32
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3;522-524.
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 34
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 36
    • 0024544755 scopus 로고
    • A fast and sensitive multiple sequence alignment algorithm
    • Vingron M, Argos P. A fast and sensitive multiple sequence alignment algorithm. Comput Appl Biosci 1989;5:115-121.
    • (1989) Comput Appl Biosci , vol.5 , pp. 115-121
    • Vingron, M.1    Argos, P.2
  • 37
    • 0029011701 scopus 로고
    • A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
    • Cornell WD, Cieplak P, Bayly CI, et al. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 1995;117:5179-5197.
    • (1995) J Am Chem Soc , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3
  • 38
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L. Particle mesh Ewald: an N. log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion with contraints: Molecular dynamics of n-alkanes
    • Ryckaert J, Ciccotti G, Berendsen H. Numerical integration of the Cartesian equations of motion with contraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.3
  • 41
    • 0032553332 scopus 로고    scopus 로고
    • Elucidating the folding problem of alpha-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters
    • Lacroix E, Viguera AR, Serrano L. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 1998;284:173-191.
    • (1998) J Mol Biol , vol.284 , pp. 173-191
    • Lacroix, E.1    Viguera, A.R.2    Serrano, L.3
  • 42
    • 0027972206 scopus 로고
    • Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A
    • Straub JE, Rashkin AB, Thirumalai D. Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A. J Am Chem Soc 1994;116:2049-2063.
    • (1994) J Am Chem Soc , vol.116 , pp. 2049-2063
    • Straub, J.E.1    Rashkin, A.B.2    Thirumalai, D.3
  • 44
    • 0035008585 scopus 로고    scopus 로고
    • Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations
    • Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H. Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations. Protein Sci 2001;10:1160-1171.
    • (2001) Protein Sci , vol.10 , pp. 1160-1171
    • Higo, J.1    Ito, N.2    Kuroda, M.3    Ono, S.4    Nakajima, N.5    Nakamura, H.6
  • 45
    • 0036467163 scopus 로고    scopus 로고
    • Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
    • Sanbonmatsu KY, Garcia AE. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins 2002;46:225-234.
    • (2002) Proteins , vol.46 , pp. 225-234
    • Sanbonmatsu, K.Y.1    Garcia, A.E.2
  • 46
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.