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Volumn 83, Issue 6, 2014, Pages 631-642

Probing the origin of structural stability of single and double stapled p53 peptide analogs bound to MDM2

Author keywords

conformation population; contact map; end to end distance; native contact; potential of mean forces; stapled peptide; WaterMap

Indexed keywords

ALKENE; HYDROCARBON; PEPTIDE DERIVATIVE; PROTEIN MDM2; PROTEIN P53; MOLECULAR PROBE; PROTEIN BINDING;

EID: 84896286645     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12284     Document Type: Article
Times cited : (16)

References (45)
  • 1
    • 77956400377 scopus 로고    scopus 로고
    • The tumor suppressor p53: From structures to drug discovery
    • Joerger A.C., Fersht A.R., (2010) The tumor suppressor p53: from structures to drug discovery. Cold Spring Harb Perspect Biol; 2: a000919.
    • (2010) Cold Spring Harb Perspect Biol , vol.2
    • Joerger, A.C.1    Fersht, A.R.2
  • 2
    • 37549040575 scopus 로고    scopus 로고
    • The challenge of drugging undruggable targets in cancer: Lessons learned from targeting BCL-2 family members
    • Verdine G.L., Walensky L.D., (2007) The challenge of drugging undruggable targets in cancer: lessons learned from targeting BCL-2 family members. Clin Cancer Res; 13: 7264-7270.
    • (2007) Clin Cancer Res , vol.13 , pp. 7264-7270
    • Verdine, G.L.1    Walensky, L.D.2
  • 5
    • 0034697649 scopus 로고    scopus 로고
    • An all-hydrocarbon cross-linking system for enhancing the helicity and metabolic stability of peptides
    • Schafmeister C.E., Po J., Verdine G.L., (2000) An all-hydrocarbon cross-linking system for enhancing the helicity and metabolic stability of peptides. J Am Chem Soc; 122: 5891-5892.
    • (2000) J Am Chem Soc , vol.122 , pp. 5891-5892
    • Schafmeister, C.E.1    Po, J.2    Verdine, G.L.3
  • 6
    • 3543098742 scopus 로고    scopus 로고
    • Helical beta-peptide inhibitors of the p53-hDM2 interaction
    • Kritzer J.A., Lear J.D., Hodsdon M.E., Schepartz A., (2004) Helical beta-peptide inhibitors of the p53-hDM2 interaction. J Am Chem Soc; 126: 9468-9469.
    • (2004) J Am Chem Soc , vol.126 , pp. 9468-9469
    • Kritzer, J.A.1    Lear, J.D.2    Hodsdon, M.E.3    Schepartz, A.4
  • 9
    • 84880529288 scopus 로고    scopus 로고
    • Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments
    • Madhavi S.G., Adzhigirey M., Day T., Annabhimoju R., Sherman W., (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des; 27: 221-234.
    • (2013) J Comput Aided Mol des , vol.27 , pp. 221-234
    • Madhavi, S.G.1    Adzhigirey, M.2    Day, T.3    Annabhimoju, R.4    Sherman, W.5
  • 11
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen W.L., Maxwell D.S., Tirado-Rives J., (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc; 118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 12
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski G.A., Friesner R.A., Tirado-Rives J., Jorgensen W.L., (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B; 105: 6474-6487.
    • (2001) J Phys Chem B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 14
    • 36449003554 scopus 로고
    • Constant-pressure molecular-dynamics algorithms
    • Martyna G.J., Tobias D.J., Klein M.L., (1994) Constant-pressure molecular-dynamics algorithms. J Chem Phys; 101: 4177-4189.
    • (1994) J Chem Phys , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 15
    • 0001538909 scopus 로고
    • Canonical dynamics - Equilibrium phase-space distributions
    • Hoover W.G., (1985) Canonical dynamics-equilibrium phase-space distributions. Phys Rev A; 31: 1695-1697.
    • (1985) Phys Rev A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 16
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y., Okamoto Y., (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett; 314: 141-151.
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 17
    • 0000504254 scopus 로고
    • A multiple-time-step molecular dynamics algorithm for macromolecules
    • Humphreys D.D., Friesner R.A., Berne B.J., (1994) A multiple-time-step molecular dynamics algorithm for macromolecules. J Phys Chem; 98: 6885-6892.
    • (1994) J Phys Chem , vol.98 , pp. 6885-6892
    • Humphreys, D.D.1    Friesner, R.A.2    Berne, B.J.3
  • 18
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li H., Robertson A.D., Jensen J.H., (2005) Very fast empirical prediction and rationalization of protein pKa values. Proteins: Struct, Funct, Bioinf; 61: 704-721.
    • (2005) Proteins: Struct, Funct, Bioinf , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 19
    • 57349090665 scopus 로고    scopus 로고
    • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    • Bas D.C., Rogers D.M., Jensen J.H., (2008) Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins: Struct, Funct, Bioinf; 73: 765-783.
    • (2008) Proteins: Struct, Funct, Bioinf , vol.73 , pp. 765-783
    • Bas, D.C.1    Rogers, D.M.2    Jensen, J.H.3
  • 20
    • 79951476387 scopus 로고    scopus 로고
    • PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions
    • Olsson M.H.M., Søndergaard C.R., Rostkowski M., Jensen J.H., (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput; 7: 525-537.
    • (2011) J Chem Theory Comput , vol.7 , pp. 525-537
    • Olsson, M.H.M.1    Søndergaard, C.R.2    Rostkowski, M.3    Jensen, J.H.4
  • 21
    • 79960258119 scopus 로고    scopus 로고
    • Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values
    • Søndergaard C.R., Olsson M.H.M., Rostkowski M., Jensen J.H., (2011) Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J Chem Theory Comput; 7: 2284-2295.
    • (2011) J Chem Theory Comput , vol.7 , pp. 2284-2295
    • Søndergaard, C.R.1    Olsson, M.H.M.2    Rostkowski, M.3    Jensen, J.H.4
  • 22
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    • Abel R., Young T., Farid R., Berne B.J., Friesner R.A., (2008) Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc; 130: 2817-2831.
    • (2008) J Am Chem Soc , vol.130 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friesner, R.A.5
  • 23
    • 79952161696 scopus 로고    scopus 로고
    • Ligand binding to protein-binding pockets with wet and dry regions
    • Wang L., Berne B.J., Friesner R.A., (2011) Ligand binding to protein-binding pockets with wet and dry regions. Proc Natl Acad Sci U S A; 108: 1326-1330.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 1326-1330
    • Wang, L.1    Berne, B.J.2    Friesner, R.A.3
  • 24
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig R.W., (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys; 22: 1420-1426.
    • (1954) J Chem Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 25
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood J.G., (1935) Statistical mechanics of fluid mixtures. J Chem Phys; 3: 300-313.
    • (1935) J Chem Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 26
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B., (1995) The calculation of the potential of mean force using computer simulations. Comput Phys Commun; 91: 275-282.
    • (1995) Comput Phys Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 27
    • 0035277126 scopus 로고    scopus 로고
    • Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations
    • Souaille M., Roux B., (2001) Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput Phys Commun; 135: 40-57.
    • (2001) Comput Phys Commun , vol.135 , pp. 40-57
    • Souaille, M.1    Roux, B.2
  • 28
    • 17444366185 scopus 로고    scopus 로고
    • Temperature weighted histogram analysis method, replica exchange, and transition paths
    • Gallicchio E., Andrec M., Felts A.K., Levy R.M., (2005) Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B; 109: 6722-6731.
    • (2005) J Phys Chem B , vol.109 , pp. 6722-6731
    • Gallicchio, E.1    Andrec, M.2    Felts, A.K.3    Levy, R.M.4
  • 29
    • 0037442915 scopus 로고    scopus 로고
    • Potentials of mean force between ionizable amino acid side chains in water
    • Masunov A., Lazaridis T., (2003) Potentials of mean force between ionizable amino acid side chains in water. J Am Chem Soc; 125: 1722-1730.
    • (2003) J Am Chem Soc , vol.125 , pp. 1722-1730
    • Masunov, A.1    Lazaridis, T.2
  • 30
    • 34547267323 scopus 로고    scopus 로고
    • Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface
    • Sun Y., Dominy B.N., Latour R.A., (2007) Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. J Comput Chem; 28: 1883-1892.
    • (2007) J Comput Chem , vol.28 , pp. 1883-1892
    • Sun, Y.1    Dominy, B.N.2    Latour, R.A.3
  • 31
    • 77449088300 scopus 로고    scopus 로고
    • Probing the α-helical structural stability of stapled p53 peptides: Molecular dynamics simulations and analysis
    • Guo Z., Mohanty U., Noehre J., Sawyer T.K., Sherman W., Krilov G., (2010) Probing the α-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis. Chem Biol Drug Des; 75: 348-359.
    • (2010) Chem Biol Drug des , vol.75 , pp. 348-359
    • Guo, Z.1    Mohanty, U.2    Noehre, J.3    Sawyer, T.K.4    Sherman, W.5    Krilov, G.6
  • 32
    • 33845597265 scopus 로고    scopus 로고
    • N-methylation of N(alpha)-acylated, fully C(alpha)-methylated, linear, folded peptides: Synthetic and conformational aspects
    • Moretto A., Crisma M., Kaptein B., Broxterman Q.B., Toniolo C., (2006) N-methylation of N(alpha)-acylated, fully C(alpha)-methylated, linear, folded peptides: synthetic and conformational aspects. Biopolymers; 84: 553-565.
    • (2006) Biopolymers , vol.84 , pp. 553-565
    • Moretto, A.1    Crisma, M.2    Kaptein, B.3    Broxterman, Q.B.4    Toniolo, C.5
  • 34
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal-structures - Quasi-chemical approximation
    • Miyazawa S., Jernigan R.L., (1985) Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules; 18: 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 35
    • 33749047118 scopus 로고    scopus 로고
    • A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
    • Hamacher K., Hubsch A., McCammon J.A., (2006) A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys; 124: 164907.
    • (2006) J Chem Phys , vol.124 , pp. 164907
    • Hamacher, K.1    Hubsch, A.2    McCammon, J.A.3
  • 36
    • 77954133901 scopus 로고    scopus 로고
    • Introduction of all-hydrocarbon i, i + 3 staples into alpha-helices via ring-closing olefin metathesis
    • Kim Y.W., Kutchukian P.S., Verdine G.L., (2010) Introduction of all-hydrocarbon i, i + 3 staples into alpha-helices via ring-closing olefin metathesis. Org Lett; 12: 3046-3049.
    • (2010) Org Lett , vol.12 , pp. 3046-3049
    • Kim, Y.W.1    Kutchukian, P.S.2    Verdine, G.L.3
  • 42
    • 84874834874 scopus 로고    scopus 로고
    • Evaluation of hydration free energy by level-set variational implicit-solvent model with coulomb-field approximation
    • Guo Z., Li B., Dzubiella J., Cheng L.T., McCammon J.A., Che J., (2013) Evaluation of hydration free energy by level-set variational implicit-solvent model with coulomb-field approximation. J Chem Theory Comput; 9: 1778-1787.
    • (2013) J Chem Theory Comput , vol.9 , pp. 1778-1787
    • Guo, Z.1    Li, B.2    Dzubiella, J.3    Cheng, L.T.4    McCammon, J.A.5    Che, J.6
  • 43
    • 39149130730 scopus 로고    scopus 로고
    • Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors
    • Giannetti A.M., Koch B.D., Browner M.F., (2008) Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J Med Chem; 51: 574-580.
    • (2008) J Med Chem , vol.51 , pp. 574-580
    • Giannetti, A.M.1    Koch, B.D.2    Browner, M.F.3
  • 44
    • 0141887118 scopus 로고    scopus 로고
    • Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution
    • Rajamani R., Naidoo K.J., Gao J., (2003) Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. J Comput Chem; 24: 1775-1781.
    • (2003) J Comput Chem , vol.24 , pp. 1775-1781
    • Rajamani, R.1    Naidoo, K.J.2    Gao, J.3
  • 45
    • 0344121638 scopus 로고    scopus 로고
    • The filling potential method: A method for estimating the free energy surface for protein-ligand docking
    • Fukunishi Y., Mikami Y., Nakamura H., (2003) The filling potential method: a method for estimating the free energy surface for protein-ligand docking. J Phys Chem B; 107: 13201-13210.
    • (2003) J Phys Chem B , vol.107 , pp. 13201-13210
    • Fukunishi, Y.1    Mikami, Y.2    Nakamura, H.3


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