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Volumn 45, Issue 1-2, 2009, Pages 171-183

Mapping the dynamics of ligand reorganization via 13CH3 and 13CH2 relaxation dispersion at natural abundance

Author keywords

Drug design; Dynamics; Ligand; Relaxation dispersion; Side chain

Indexed keywords

CARBON 13; METHYL GROUP; NEW DRUG; PEPTIDYLPROLYL ISOMERASE PIN1; PROTEIN TYROSINE PHOSPHATASE;

EID: 69249208408     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-009-9349-4     Document Type: Article
Times cited : (25)

References (44)
  • 1
    • 0029894013 scopus 로고    scopus 로고
    • Properties of known drugs. 1. Molecular frameworks
    • Bemis GW, Murcko MA (1996) Properties of known drugs. 1. Molecular frameworks. J Med Chem 39(288):7-2893
    • (1996) J Med Chem , vol.39 , Issue.288 , pp. 7-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 2
    • 0033576605 scopus 로고    scopus 로고
    • Properties of known drugs. 2. Side chains
    • Bemis GW, Murcko MA (1999) Properties of known drugs. 2. Side chains. J Med Chem 42(509):5-5099
    • (1999) J Med Chem , vol.42 , Issue.509 , pp. 5-5099
    • Bemis, G.W.1    Murcko, M.A.2
  • 3
    • 34547679071 scopus 로고    scopus 로고
    • NMR: Prediction of protein flexibility
    • Berjanskii M, Wishart DS (2006) NMR: Prediction of protein flexibility. Nat Protoc 1:683-688
    • (2006) Nat Protoc , vol.1 , pp. 683-688
    • Berjanskii, M.1    Wishart, D.S.2
  • 5
    • 33847534249 scopus 로고
    • Effects of diffusion on free precession in nuclear magnetic resonance experiments
    • Carr HY, Purcell EM (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys Rev 94:630-638
    • (1954) Phys Rev , vol.94 , pp. 630-638
    • Carr, H.Y.1    Purcell, E.M.2
  • 6
    • 0002889918 scopus 로고
    • A general two-site solution for the chemical exchange produced dependence of T2 upon the Carr-Purcell Pulse separation
    • Carver JP, Richards RE (1972) A general two-site solution for the chemical exchange produced dependence of T2 upon the Carr-Purcell Pulse separation. J Magn Reson 6:89-105
    • (1972) J Magn Reson , vol.6 , pp. 89-105
    • Carver, J.P.1    Richards, R.E.2
  • 8
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302
    • (1999) J Biomol NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 9
    • 0032473350 scopus 로고    scopus 로고
    • The mitotic peptidyl-prolyl isomerase, Pin1, interacts with Cdc25 and Plx1
    • Crenshaw DG, Yang J, Means AR, Kornbluth S (1998) The mitotic peptidyl-prolyl isomerase, Pin1, interacts with Cdc25 and Plx1. EMBO J 17:1315-1327
    • (1998) EMBO J , vol.17 , pp. 1315-1327
    • Crenshaw, D.G.1    Yang, J.2    Means, A.R.3    Kornbluth, S.4
  • 11
    • 0027308278 scopus 로고
    • Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach
    • de Dios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach. Science 260:1491-1496
    • (1993) Science , vol.260 , pp. 1491-1496
    • de Dios, A.C.1    Pearson, J.G.2    Oldfield, E.3
  • 13
    • 44949280676 scopus 로고
    • Band-selective radiofrequency pulses
    • Geen H, Freeman R (1991) Band-selective radiofrequency pulses. J Magn Reson 93:93-141
    • (1991) J Magn Reson , vol.93 , pp. 93-141
    • Geen, H.1    Freeman, R.2
  • 14
    • 0345306309 scopus 로고    scopus 로고
    • Disulfide bond isomerization in basic pancreatic trypsin inhibitor: Multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling
    • Grey MJ, Wang C, Palmer AG 3rd (2003) Disulfide bond isomerization in basic pancreatic trypsin inhibitor: Multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling. J Am Chem Soc 125:14324-14335
    • (2003) J Am Chem Soc , vol.125 , pp. 14324-14335
    • Grey, M.J.1    Wang, C.2    Palmer III, A.G.3
  • 15
    • 67650547197 scopus 로고    scopus 로고
    • Accurate measurement of methyl 13C chemical shifts by solid-state NMR for the determination of protein side chain conformation: The influenza a M2 transmembrane peptide as an example
    • Hong M, Mishanina TV, Cady SD (2009) Accurate measurement of methyl 13C chemical shifts by solid-state NMR for the determination of protein side chain conformation: The influenza a M2 transmembrane peptide as an example. J Am Chem Soc 131:7806-7816
    • (2009) J Am Chem Soc , vol.131 , pp. 7806-7816
    • Hong, M.1    Mishanina, T.V.2    Cady, S.D.3
  • 16
    • 0032871220 scopus 로고    scopus 로고
    • Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution
    • Ishima R, Torchia DA (1999) Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution. J Biomol NMR 14(36):9-372
    • (1999) J Biomol NMR , vol.14 , Issue.36 , pp. 9-372
    • Ishima, R.1    Torchia, D.A.2
  • 17
    • 5444247213 scopus 로고    scopus 로고
    • Combating susceptibility to drug resistance: Lessons from HIV-1 protease
    • King NM, Prabu-Jeyabalan M, Nalivaika EA, Schiffer CA (2004) Combating susceptibility to drug resistance: Lessons from HIV-1 protease. Chem Biol 11:1333-1338
    • (2004) Chem Biol , vol.11 , pp. 1333-1338
    • King, N.M.1    Prabu-Jeyabalan, M.2    Nalivaika, E.A.3    Schiffer, C.A.4
  • 19
    • 50249158519 scopus 로고    scopus 로고
    • 13C shifts on dihedral angle: Application to conformational analysis
    • 13C shifts on dihedral angle: Application to conformational analysis. J Am Chem Soc 130:11097-11105
    • (2008) J Am Chem Soc , vol.130 , pp. 11097-11105
    • London, R.E.1    Wingad, B.D.2    Mueller, G.A.3
  • 20
    • 0033577288 scopus 로고    scopus 로고
    • A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy
    • Loria JP, Rance M, Palmer AG 3rd (1999) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121:2331-2332
    • (1999) J Am Chem Soc , vol.121 , pp. 2331-2332
    • Loria, J.P.1    Rance, M.2    Palmer III, A.G.3
  • 21
    • 34548660854 scopus 로고    scopus 로고
    • Prolyl cis-trans isomerization as a molecular timer
    • Lu KP, Finn G, Lee TH, Nicholson LK (2007) Prolyl cis-trans isomerization as a molecular timer. Nat Chem Biol 3:619-629
    • (2007) Nat Chem Biol , vol.3 , pp. 619-629
    • Lu, K.P.1    Finn, G.2    Lee, T.H.3    Nicholson, L.K.4
  • 22
  • 23
    • 0002899752 scopus 로고
    • Modified spin-echo method for measuring nuclear relaxation times
    • Meiboom S, Gill D (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instr 29:688-691
    • (1958) Rev Sci Instr , vol.29 , pp. 688-691
    • Meiboom, S.1    Gill, D.2
  • 24
    • 0034728579 scopus 로고    scopus 로고
    • The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale
    • Millet O, Loria JP, Kroenke CD, Pons M, Palmer AGIII (2000) The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J Am Chem Soc 122:2867-2877
    • (2000) J Am Chem Soc , vol.122 , pp. 2867-2877
    • Millet, O.1    Loria, J.P.2    Kroenke, C.D.3    Pons, M.4    Palmer III, A.G.5
  • 25
    • 0000987483 scopus 로고    scopus 로고
    • An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations
    • Mulder FAA, de Graaf RA, Kaptein R, Boelens R (1998) An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations. J Magn Reson 131:351-357
    • (1998) J Magn Reson , vol.131 , pp. 351-357
    • Mulder, F.A.A.1    de Graaf, R.A.2    Kaptein, R.3    Boelens, R.4
  • 27
    • 0035819455 scopus 로고    scopus 로고
    • Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: Application to Asn and Gln residues in a cavity mutant of T4 lysozyme
    • Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE (2001b) Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: Application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 123:967-975
    • (2001) J Am Chem Soc , vol.123 , pp. 967-975
    • Mulder, F.A.1    Skrynnikov, N.R.2    Hon, B.3    Dahlquist, F.W.4    Kay, L.E.5
  • 28
    • 69249246944 scopus 로고    scopus 로고
    • Molecular basis for signal transduction in the bi-modular cell-cycle enzyme Pin1
    • Dissertation, University of Notre Dame
    • Namanja AT (2009) Molecular basis for signal transduction in the bi-modular cell-cycle enzyme Pin1. Dissertation, University of Notre Dame
    • (2009)
    • Namanja, A.T.1
  • 29
    • 33847656165 scopus 로고    scopus 로고
    • Substrate recognition reduces side-chain flexibility for conserved hydrophobic residues in human Pin1
    • Namanja AT, Peng T, Zintsmaster JS, Elson AC, Shakour MG, Peng JW (2007) Substrate recognition reduces side-chain flexibility for conserved hydrophobic residues in human Pin1. Structure 15:313-327
    • (2007) Structure , vol.15 , pp. 313-327
    • Namanja, A.T.1    Peng, T.2    Zintsmaster, J.S.3    Elson, A.C.4    Shakour, M.G.5    Peng, J.W.6
  • 30
    • 0001334658 scopus 로고    scopus 로고
    • Design principles for orally bioavailable drugs
    • Navia MA, Chaturvedi PR (1996) Design principles for orally bioavailable drugs. Drug Discov Today 1(17):9-189
    • (1996) Drug Discov Today , vol.1 , Issue.17 , pp. 9-189
    • Navia, M.A.1    Chaturvedi, P.R.2
  • 31
    • 0043234974 scopus 로고    scopus 로고
    • New probes of ligand flexibility in drug design: Transferred (13)C CSA-dipolar cross-correlated relaxation at natural abundance
    • Peng JW (2003) New probes of ligand flexibility in drug design: transferred (13)C CSA-dipolar cross-correlated relaxation at natural abundance. J Am Chem Soc 125:11116-11130
    • (2003) J Am Chem Soc , vol.125 , pp. 11116-11130
    • Peng, J.W.1
  • 33
    • 2342586724 scopus 로고    scopus 로고
    • Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
    • Perola E, Charifson PS (2004) Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding. J Med Chem 47:2499-2510
    • (2004) J Med Chem , vol.47 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 35
    • 0347610773 scopus 로고
    • Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts
    • Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492
    • (1991) J Am Chem Soc , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 36
    • 0041488802 scopus 로고    scopus 로고
    • Pharmacophore discovery-lessons learned
    • van Drie JH (2003) Pharmacophore discovery-lessons learned. Curr Pharm Des 9:1649-1664
    • (2003) Curr Pharm Des , vol.9 , pp. 1649-1664
    • van Drie, J.H.1
  • 38
    • 0033885803 scopus 로고    scopus 로고
    • Structural basis for phosphoserine-proline recognition by group IV WW domains
    • Verdecia MA, Bowman ME, Lu KP, Hunter T, Noel JP (2000) Structural basis for phosphoserine-proline recognition by group IV WW domains. Nat Struct Biol 7:639-643
    • (2000) Nat Struct Biol , vol.7 , pp. 639-643
    • Verdecia, M.A.1    Bowman, M.E.2    Lu, K.P.3    Hunter, T.4    Noel, J.P.5
  • 39
    • 41149110741 scopus 로고    scopus 로고
    • Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures
    • Vila JA, Scheraga HA (2008) Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins 71:641-654
    • (2008) Proteins , vol.71 , pp. 641-654
    • Vila, J.A.1    Scheraga, H.A.2
  • 41
    • 0028393784 scopus 로고
    • The 13C chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical-shift data
    • Wishart DS, Sykes BD (1994) The 13C chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171-180
    • (1994) J Biomol NMR , vol.4 , pp. 171-180
    • Wishart, D.S.1    Sykes, B.D.2
  • 42
    • 0037114648 scopus 로고    scopus 로고
    • Probing multiple effects on 15 N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory
    • Xu XP, Case DA (2002) Probing multiple effects on 15 N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory. Biopolymers 65:408-423
    • (2002) Biopolymers , vol.65 , pp. 408-423
    • Xu, X.P.1    Case, D.A.2
  • 44
    • 54849415462 scopus 로고    scopus 로고
    • Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance
    • Zintsmaster JS, Wilson BD, Peng JW (2008) Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance. J Am Chem Soc 130:14060-14061
    • (2008) J Am Chem Soc , vol.130 , pp. 14060-14061
    • Zintsmaster, J.S.1    Wilson, B.D.2    Peng, J.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.