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Volumn 56, Issue 2, 2013, Pages 238-248

Rapid and accurate evaluation of the binding energies and the individual N-H⋯O=C, N-H⋯N, C-H⋯O=C, and C-H⋯N interaction energies for hydrogen-bonded peptide-base complexes

Author keywords

dipole dipole interaction; hydrogen bond; individual hydrogen bonding energy; peptide base complexes; total binding energy

Indexed keywords

AB INITIO CALCULATIONS; ATTRACTIVE INTERACTIONS; DIPOLE DIPOLE INTERACTIONS; INDIVIDUAL HYDROGEN BONDING ENERGY; PEPTIDE-BASE COMPLEXES; REPULSIVE INTERACTION ENERGY; REPULSIVE INTERACTIONS; SUPRAMOLECULAR ASSEMBLIES;

EID: 84879784855     PISSN: 16747291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-012-4715-6     Document Type: Article
Times cited : (8)

References (36)
  • 1
    • 0000965687 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
    • 10.1021/cr9800255 1:CAS:528:DyaK1MXmsFarurY%3D
    • Hobza P, Šponer J. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chem Rev, 1999, 99(11): 3247-3276
    • (1999) Chem Rev , vol.99 , Issue.11 , pp. 3247-3276
    • Hobza, P.1    Šponer, J.2
  • 2
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Šponer J, Leszczynski J, Hobza P. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers, 2002, 61(1): 3-31
    • (2002) Biopolymers , vol.61 , Issue.1 , pp. 3-31
    • Šponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 3
    • 38749109655 scopus 로고    scopus 로고
    • Detection and evaluation of hydrogen bond strength in nucleic acid base pairs
    • 10.1021/jp075992a 1:CAS:528:DC%2BD2sXhsVehurjE
    • Mohajeri A, Nobandegani FF. Detection and evaluation of hydrogen bond strength in nucleic acid base pairs. J Phys Chem A, 2008, 112(2): 281-295
    • (2008) J Phys Chem A , vol.112 , Issue.2 , pp. 281-295
    • Mohajeri, A.1    Nobandegani, F.F.2
  • 4
    • 34247897078 scopus 로고    scopus 로고
    • The origins of femtomolar protein-ligand binding: Hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site
    • 10.1021/ja066950n 1:CAS:528:DC%2BD2sXjvFCitLc%3D
    • DeChancie J, Houk KN. The origins of femtomolar protein-ligand binding: Hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site. J Am Chem Soc, 2007, 129(17): 5419-5429
    • (2007) J Am Chem Soc , vol.129 , Issue.17 , pp. 5419-5429
    • Dechancie, J.1    Houk, K.N.2
  • 5
    • 0038682661 scopus 로고    scopus 로고
    • H-bonding cooperativity and energetics of α-helix formation of five 17-amino acid peptides
    • 10.1021/ja035302q 1:CAS:528:DC%2BD3sXksF2ku7w%3D
    • Wieczorek R, Dannenberg JJ. H-bonding cooperativity and energetics of α-helix formation of five 17-amino acid peptides. J Am Chem Soc, 2003, 125(27): 8124-8129
    • (2003) J Am Chem Soc , vol.125 , Issue.27 , pp. 8124-8129
    • Wieczorek, R.1    Dannenberg, J.J.2
  • 7
    • 7444232597 scopus 로고    scopus 로고
    • 15N three-bond and other scalar J-couplings in cooperative peptide models. A density functional theory study
    • 10.1021/ja0492788 1:CAS:528:DC%2BD2cXotFGhu7c%3D
    • 15N three-bond and other scalar J-couplings in cooperative peptide models. A density functional theory study. J Am Chem Soc, 2004, 126(43): 14190-14197
    • (2004) J Am Chem Soc , vol.126 , Issue.43 , pp. 14190-14197
    • Salvador, P.1    Kobko, N.2    Wieczorek, R.3    Dannenberg, J.J.4
  • 8
    • 77950813968 scopus 로고    scopus 로고
    • Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding
    • 10.1021/ja909575j 1:CAS:528:DC%2BC3cXjs1Wku78%3D
    • Tong Y, Mei Y, Li YL, Ji CG, Zhang JZH. Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding. J Am Chem Soc, 2010, 132(14): 5137-5142
    • (2010) J Am Chem Soc , vol.132 , Issue.14 , pp. 5137-5142
    • Tong, Y.1    Mei, Y.2    Li, Y.L.3    Ji, C.G.4    Zhang, J.Z.H.5
  • 9
    • 26444598454 scopus 로고    scopus 로고
    • Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
    • 10.1002/prot.20607 1:CAS:528:DC%2BD2MXhtFSrsbfI
    • Lejeune D, Delsaux N, Charloteaux B, Thomas A, Brasseur R. Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. Prot Struct Funct Bioinfor, 2005, 61(2): 258-271
    • (2005) Prot Struct Funct Bioinfor , vol.61 , Issue.2 , pp. 258-271
    • Lejeune, D.1    Delsaux, N.2    Charloteaux, B.3    Thomas, A.4    Brasseur, R.5
  • 10
    • 0000127073 scopus 로고
    • Sequence-specific recognition of double helical nucleic acids by proteins
    • 10.1073/pnas.73.3.804 1:CAS:528:DyaE28XhsVKgsL8%3D
    • Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Nat Acad Sci USA, 1976, 73(3): 804-808
    • (1976) Proc Nat Acad Sci USA , vol.73 , Issue.3 , pp. 804-808
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 11
    • 0037418657 scopus 로고    scopus 로고
    • Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains
    • 10.1016/S0022-2836(03)00091-3 1:CAS:528:DC%2BD3sXitlWgs7g%3D
    • Cheng AC, Chen WW, Fuhrmann CN, Frankel AD. Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains. J Mol Biol, 2003, 327(4): 781-796
    • (2003) J Mol Biol , vol.327 , Issue.4 , pp. 781-796
    • Cheng, A.C.1    Chen, W.W.2    Fuhrmann, C.N.3    Frankel, A.D.4
  • 12
    • 0347087296 scopus 로고    scopus 로고
    • Ab initio interaction energies of hydrogen-bonded amino acid side chain-nucleic acid base interactions
    • 10.1021/ja037264g 1:CAS:528:DC%2BD3sXpvFGlurk%3D
    • Cheng AC, Frankel AD. Ab initio interaction energies of hydrogen-bonded amino acid side chain-nucleic acid base interactions. J Am Chem Soc, 2004, 126(2): 434-435
    • (2004) J Am Chem Soc , vol.126 , Issue.2 , pp. 434-435
    • Cheng, A.C.1    Frankel, A.D.2
  • 13
    • 26444619105 scopus 로고    scopus 로고
    • Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes
    • 1:CAS:528:DC%2BD3sXps1ehtrc%3D
    • Jeong E, Kim H, Lee SW, Han K. Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Mol Cells, 2003, 16(2): 161-167
    • (2003) Mol Cells , vol.16 , Issue.2 , pp. 161-167
    • Jeong, E.1    Kim, H.2    Lee, S.W.3    Han, K.4
  • 14
    • 84962360703 scopus 로고    scopus 로고
    • Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil
    • 10.1021/jp066902p 1:CAS:528:DC%2BD2sXpsVWqtQ%3D%3D
    • Hunter KC, Millen AL, Wetmore SD. Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil. J Phys Chem B, 2007, 111(7): 1858-1871
    • (2007) J Phys Chem B , vol.111 , Issue.7 , pp. 1858-1871
    • Hunter, K.C.1    Millen, A.L.2    Wetmore, S.D.3
  • 15
    • 0034300441 scopus 로고    scopus 로고
    • A road map for the calculation of molecular binding energies
    • 10.1021/jp001507z 1:CAS:528:DC%2BD3cXmsVCnuro%3D
    • Dunning TH Jr. A road map for the calculation of molecular binding energies. J Phys Chem A, 2000, 104(40): 9062-9080
    • (2000) J Phys Chem A , vol.104 , Issue.40 , pp. 9062-9080
    • Dunning, Jr.T.H.1
  • 16
    • 4043137165 scopus 로고    scopus 로고
    • Accurate interaction energies of hydrogen-bonded nucleic acid base pairs
    • 10.1021/ja048436s
    • Šponer J, Jurečka P, Hobza P. Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J Am Chem Soc, 2004, 126(32): 10142-10151
    • (2004) J Am Chem Soc , vol.126 , Issue.32 , pp. 10142-10151
    • Šponer, J.1    Jurečka, P.2    Hobza, P.3
  • 17
    • 20844449600 scopus 로고    scopus 로고
    • On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level
    • 10.1063/1.1906205
    • Dabkowska I, Jurečka P, Hobza P. On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level. J Chem Phys, 2005, 122(20): 204322
    • (2005) J Chem Phys , vol.122 , Issue.20 , pp. 204322
    • Dabkowska, I.1    Jurečka, P.2    Hobza, P.3
  • 18
    • 77950154377 scopus 로고    scopus 로고
    • On the structure and geometry of biomolecular binding motifs(hydrogen-bonding, stacking, X-H.π): WFT and DFT calculations
    • 10.1021/ct900376r 1:CAS:528:DC%2BD1MXhsFeksbfM
    • Riley KE, Pitoňák M, Černý J, Hobza P. On the structure and geometry of biomolecular binding motifs(hydrogen-bonding, stacking, X-H.π): WFT and DFT calculations. J Chem Theory Comput, 2010, 6(1): 66-80
    • (2010) J Chem Theory Comput , vol.6 , Issue.1 , pp. 66-80
    • Riley, K.E.1    Pitoňák, M.2    Černý, J.3    Hobza, P.4
  • 19
    • 33846999347 scopus 로고    scopus 로고
    • Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: Complete basis set calculations at the MP2 and CCSD(T) levels
    • 10.1021/jp0661692 1:CAS:528:DC%2BD28XhtlKjsrnJ
    • Rejnek J, Hobza P. Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels. J Phys Chem B, 2007, 111(3): 641-645
    • (2007) J Phys Chem B , vol.111 , Issue.3 , pp. 641-645
    • Rejnek, J.1    Hobza, P.2
  • 20
    • 0035942888 scopus 로고    scopus 로고
    • Strength of the N-H.O=C and C-H.O=C bonds in formamide and N-methylacetamide dimmers
    • 10.1021/jp003888m 1:CAS:528:DC%2BD3MXjtVGhtr8%3D
    • Vargas R, Garza J, Friesner RA, Stern H, Hay BP, Dixon DA. Strength of the N-H.O=C and C-H.O=C bonds in formamide and N-methylacetamide dimmers. J Phys Chem A, 2001, 105(20): 4963-4968
    • (2001) J Phys Chem A , vol.105 , Issue.20 , pp. 4963-4968
    • Vargas, R.1    Garza, J.2    Friesner, R.A.3    Stern, H.4    Hay, B.P.5    Dixon, D.A.6
  • 21
    • 0042378707 scopus 로고    scopus 로고
    • Cooperative hydrogen-bonding in adenine-thymine and guanine-cytosine base pairs. Density functional theory and møller-plesset molecular orbital study
    • 10.1021/jp0344646 1:CAS:528:DC%2BD3sXlslKnu74%3D
    • Asensio A, Kobko N, Dannenberg JJ. Cooperative hydrogen-bonding in adenine-thymine and guanine-cytosine base pairs. Density functional theory and møller-plesset molecular orbital study. J Phys Chem A, 2003, 107(33): 6441-6443
    • (2003) J Phys Chem A , vol.107 , Issue.33 , pp. 6441-6443
    • Asensio, A.1    Kobko, N.2    Dannenberg, J.J.3
  • 22
    • 84961978617 scopus 로고    scopus 로고
    • Relative strengths of NH.O and CH.O hydrogen bonds between polypeptide chain segments
    • 10.1021/jp053416d 1:CAS:528:DC%2BD2MXmvVWnsro%3D
    • Scheiner S. Relative strengths of NH.O and CH.O hydrogen bonds between polypeptide chain segments. J Phys Chem B, 2005, 109(33): 16132-16141
    • (2005) J Phys Chem B , vol.109 , Issue.33 , pp. 16132-16141
    • Scheiner, S.1
  • 23
    • 33749682240 scopus 로고    scopus 로고
    • Contributions of NH.O and CH.O hydrogen bonds to the stability of β-sheets in proteins
    • 10.1021/jp063225q 1:CAS:528:DC%2BD28XosVyltrw%3D
    • Scheiner S. Contributions of NH.O and CH.O hydrogen bonds to the stability of β-sheets in proteins. J Phys Chem B, 2006, 110(37): 18670-18679
    • (2006) J Phys Chem B , vol.110 , Issue.37 , pp. 18670-18679
    • Scheiner, S.1
  • 24
    • 33644586876 scopus 로고    scopus 로고
    • Probing the competition between secondary structures and local preferences in gas phase isolated peptide backbones
    • 10.1039/b516245a 1:CAS:528:DC%2BD28Xhs12nt78%3D
    • Chin W, Piuzzi F, Dimicoli I, Mons M. Probing the competition between secondary structures and local preferences in gas phase isolated peptide backbones. Phys Chem Chem Phys, 2006, 8(9): 1033-1048
    • (2006) Phys Chem Chem Phys , vol.8 , Issue.9 , pp. 1033-1048
    • Chin, W.1    Piuzzi, F.2    Dimicoli, I.3    Mons, M.4
  • 25
    • 70349898420 scopus 로고    scopus 로고
    • An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides
    • 10.1002/jcc.21266 1:CAS:528:DC%2BD1MXhtF2ltb7O
    • Sun CL, Jiang XN, Wang CS. An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides. J Comput Chem, 2009, 30(15): 2567-2575
    • (2009) J Comput Chem , vol.30 , Issue.15 , pp. 2567-2575
    • Sun, C.L.1    Jiang, X.N.2    Wang, C.S.3
  • 26
    • 79951996465 scopus 로고    scopus 로고
    • Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase
    • 10.1002/jcc.21680 1:CAS:528:DC%2BC3MXitleisr4%3D
    • Li Y, Jiang XN, Wang CS. Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase. J Comput Chem, 2011, 32(5): 953-966
    • (2011) J Comput Chem , vol.32 , Issue.5 , pp. 953-966
    • Li, Y.1    Jiang, X.N.2    Wang, C.S.3
  • 27
    • 79960619107 scopus 로고    scopus 로고
    • Rapid evaluation of the binding energies between peptide amide and DNA base
    • 10.1002/jcc.21856 1:CAS:528:DC%2BC3MXotVCnur4%3D
    • Li Y, Wang CS. Rapid evaluation of the binding energies between peptide amide and DNA base. J Comput Chem, 2011, 32(13): 2765-2772
    • (2011) J Comput Chem , vol.32 , Issue.13 , pp. 2765-2772
    • Li, Y.1    Wang, C.S.2
  • 28
    • 77953041320 scopus 로고    scopus 로고
    • Investigation on the individual contributions of N-H.O=C and C-H.O=C interactions to the binding energies of β-sheet models
    • Wang CS, Sun CL. Investigation on the individual contributions of N-H.O=C and C-H.O=C interactions to the binding energies of β-sheet models. J Comput Chem, 2010, 31(5): 1036-1044
    • (2010) J Comput Chem , vol.31 , Issue.5 , pp. 1036-1044
    • Wang, C.S.1    Sun, C.L.2
  • 29
    • 77449154965 scopus 로고    scopus 로고
    • Rapid prediction of the hydrogen bond cooperativity in N-methylacetamide chains
    • 10.1002/cphc.200900591 1:CAS:528:DC%2BD1MXhsFKgurrL
    • Jiang XN, Wang CS. Rapid prediction of the hydrogen bond cooperativity in N-methylacetamide chains. ChemPhysChem, 2009, 10(18): 3330-3336
    • (2009) ChemPhysChem , vol.10 , Issue.18 , pp. 3330-3336
    • Jiang, X.N.1    Wang, C.S.2
  • 30
    • 77950878169 scopus 로고    scopus 로고
    • A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides, acetamides, and N-methylformamides
    • 1:CAS:528:DC%2BC3cXktFGmsbo%3D
    • Jiang XN, Sun CL, Wang CS. A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides, acetamides, and N-methylformamides. J Comput Chem, 2010, 31(7): 1410-1420
    • (2010) J Comput Chem , vol.31 , Issue.7 , pp. 1410-1420
    • Jiang, X.N.1    Sun, C.L.2    Wang, C.S.3
  • 31
    • 84890021933 scopus 로고
    • The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors
    • 10.1080/00268977000101561 1:CAS:528:DC%2BD2sXht1alt7fM
    • Boys SF, Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys, 1970, 19(4): 553-566
    • (1970) Mol Phys , vol.19 , Issue.4 , pp. 553-566
    • Boys, S.F.1    Bernardi, F.2
  • 32
    • 30244527819 scopus 로고    scopus 로고
    • How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers
    • 10.1063/1.472902 1:CAS:528:DyaK2sXhtVCmuw%3D%3D
    • Simon S, Duran M, Dannenberg JJ. How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers. J Chem Phys, 1996, 105(24): 11024-11031
    • (1996) J Chem Phys , vol.105 , Issue.24 , pp. 11024-11031
    • Simon, S.1    Duran, M.2    Dannenberg, J.J.3
  • 35
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA field for proteins via comparison with accurate quantum chemical calculations on peptides
    • 10.1021/jp003919d
    • Kaminsky GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B, 2001, 105(28): 6474-6487
    • (2001) J Phys Chem B , vol.105 , Issue.28 , pp. 6474-6487
    • Kaminsky, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4


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