메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Computing H/D-Exchange rates of single residues from data of proteolytic fragments

Author keywords

[No Author keywords available]

Indexed keywords

HIGH SPATIAL RESOLUTION; HIGH-RESOLUTION MASS ANALYSIS; HYDROGEN/DEUTERIUM EXCHANGE; PROTEIN CONFORMATION; PROTEOLYTIC FRAGMENTS; SOLVENT ACCESSIBILITY; SPATIAL RESOLUTION; WILD-TYPE PROTEINS;

EID: 77955407833     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-424     Document Type: Article
Times cited : (38)

References (30)
  • 1
    • 39649103425 scopus 로고    scopus 로고
    • Molecular Dynamics of Hydrogen Bonds in Protein-D2O: The Solvent Isotope Effect
    • 10.1021/jp0771668, 18193847
    • Sheu SY, Schlag EW, Selzle HL, Yang DY. Molecular Dynamics of Hydrogen Bonds in Protein-D2O: The Solvent Isotope Effect. J Phys Chem A 2008, 112:797-802. 10.1021/jp0771668, 18193847.
    • (2008) J Phys Chem A , vol.112 , pp. 797-802
    • Sheu, S.Y.1    Schlag, E.W.2    Selzle, H.L.3    Yang, D.Y.4
  • 2
    • 12244285932 scopus 로고    scopus 로고
    • Chemical Cross-Linking and High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Interaction Analysis: Application to a Calmodulin/Target Peptide Complex
    • Kalkhof S, Ihling C, Mechtler K, Sinz A. Chemical Cross-Linking and High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Interaction Analysis: Application to a Calmodulin/Target Peptide Complex. Analytical Chemistry 2004, 77(2):495-503.
    • (2004) Analytical Chemistry , vol.77 , Issue.2 , pp. 495-503
    • Kalkhof, S.1    Ihling, C.2    Mechtler, K.3    Sinz, A.4
  • 3
    • 0032994428 scopus 로고    scopus 로고
    • Chemistry for the analysis of proteinprotein interactions: Rapid and efficient cross-linking triggered by long wavelength light
    • 10.1073/pnas.96.11.6020, 26828, 10339534
    • Fancy DA, Kodadek T. Chemistry for the analysis of proteinprotein interactions: Rapid and efficient cross-linking triggered by long wavelength light. Proc Natl Acad Sci USA 1999, 96:6020-6024. 10.1073/pnas.96.11.6020, 26828, 10339534.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 6020-6024
    • Fancy, D.A.1    Kodadek, T.2
  • 4
    • 0005227479 scopus 로고    scopus 로고
    • Identification of the Sites of Hydroxyl Radical Reaction with Peptides by Hydrogen/Deuterium Exchange: Pr evalence of Reactions with the Side Chains
    • 10.1021/bi991569j, 10677225
    • Goshe M, Chen Y, Anderson V. Identification of the Sites of Hydroxyl Radical Reaction with Peptides by Hydrogen/Deuterium Exchange: Pr evalence of Reactions with the Side Chains. Biochemistry 2000, 39(7):1761-1770. 10.1021/bi991569j, 10677225.
    • (2000) Biochemistry , vol.39 , Issue.7 , pp. 1761-1770
    • Goshe, M.1    Chen, Y.2    Anderson, V.3
  • 5
    • 0033522982 scopus 로고    scopus 로고
    • Mapping the ribosomal RNA neighborhood of protein L11 by directed hydroxyl radical probing
    • 10.1006/jmbi.1999.2706, 10366501
    • Holmberg L, Noller HF. Mapping the ribosomal RNA neighborhood of protein L11 by directed hydroxyl radical probing. J Mol Biol 1999, 289(2):223-233. 10.1006/jmbi.1999.2706, 10366501.
    • (1999) J Mol Biol , vol.289 , Issue.2 , pp. 223-233
    • Holmberg, L.1    Noller, H.F.2
  • 6
    • 0842283944 scopus 로고    scopus 로고
    • Analysis of Protein Solvent Accessible Surfaces by Photochemical Oxidation and Mass Spectrometry
    • 10.1021/ac0302004, 14750862
    • Sharp J, Becker J, Hettich R. Analysis of Protein Solvent Accessible Surfaces by Photochemical Oxidation and Mass Spectrometry. Analytical Chemistry 2004, 76(3):672-683. 10.1021/ac0302004, 14750862.
    • (2004) Analytical Chemistry , vol.76 , Issue.3 , pp. 672-683
    • Sharp, J.1    Becker, J.2    Hettich, R.3
  • 7
    • 0037039335 scopus 로고    scopus 로고
    • Mapping Protein-Protein Interactions in Solution by NMR Spectroscopy
    • 10.1021/bi011870b, 11771996
    • Zuiderweg E. Mapping Protein-Protein Interactions in Solution by NMR Spectroscopy. Biochemistry 2002, 41:1-7. 10.1021/bi011870b, 11771996.
    • (2002) Biochemistry , vol.41 , pp. 1-7
    • Zuiderweg, E.1
  • 8
    • 0037076525 scopus 로고    scopus 로고
    • Probing the Topology of the Glycine Receptor by Chemical Modification Coupled to Mass Spectrometry
    • 10.1021/bi015895m, 11994009
    • Leite J, Cascio M. Probing the Topology of the Glycine Receptor by Chemical Modification Coupled to Mass Spectrometry. Biochemistry 2002, 41(19):6140-6148. 10.1021/bi015895m, 11994009.
    • (2002) Biochemistry , vol.41 , Issue.19 , pp. 6140-6148
    • Leite, J.1    Cascio, M.2
  • 9
    • 32344436397 scopus 로고    scopus 로고
    • Identification of Subunit-Subunit Interactions in Bacteriophage P22 Procapsids by Chemical Cross-linking and Mass Spectrometry
    • 10.1021/pr050356f, 16457603
    • Kang S, Hawkridge A, Johnson K, Muddiman D, Prevelige P. Identification of Subunit-Subunit Interactions in Bacteriophage P22 Procapsids by Chemical Cross-linking and Mass Spectrometry. Journal of Proteome Research 2006, 5(2):370-377. 10.1021/pr050356f, 16457603.
    • (2006) Journal of Proteome Research , vol.5 , Issue.2 , pp. 370-377
    • Kang, S.1    Hawkridge, A.2    Johnson, K.3    Muddiman, D.4    Prevelige, P.5
  • 10
    • 0037146801 scopus 로고    scopus 로고
    • Mapping of protein:protein contact surfaces by hydrogen/deuterium exchange, followed by on-line high-performance liquid chromatography-electrospray ionization fourier-transform ion-cyclotron-resonance mass analysis
    • 10.1016/S0021-9673(02)01357-2, 12489858
    • Lam T, Lanman J, Emmett M, Hendrickson C, Prevelige P. Mapping of protein:protein contact surfaces by hydrogen/deuterium exchange, followed by on-line high-performance liquid chromatography-electrospray ionization fourier-transform ion-cyclotron-resonance mass analysis. Journal of Chromatography A 2002, 982:85-95. 10.1016/S0021-9673(02)01357-2, 12489858.
    • (2002) Journal of Chromatography A , vol.982 , pp. 85-95
    • Lam, T.1    Lanman, J.2    Emmett, M.3    Hendrickson, C.4    Prevelige, P.5
  • 11
    • 0027529263 scopus 로고
    • Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation
    • 10.1002/pro.5560020404, 2142359, 8390883
    • Zhang Z, Smith DL. Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 1993, 2(4):522-531. 10.1002/pro.5560020404, 2142359, 8390883.
    • (1993) Protein Sci , vol.2 , Issue.4 , pp. 522-531
    • Zhang, Z.1    Smith, D.L.2
  • 15
    • 0031172203 scopus 로고    scopus 로고
    • Enhancement of the Effective Resolution of Mass Spectra of High Mass Biomolecules by Maximum Entropy-Based Deconvolution to Eliminate the Isotopic Natural Abundance Distribution
    • Zhang Z, Guan S, Marshall AG. Enhancement of the Effective Resolution of Mass Spectra of High Mass Biomolecules by Maximum Entropy-Based Deconvolution to Eliminate the Isotopic Natural Abundance Distribution. Journal of American Society of Mass Spectrometry 1997, 8:659-670.
    • (1997) Journal of American Society of Mass Spectrometry , vol.8 , pp. 659-670
    • Zhang, Z.1    Guan, S.2    Marshall, A.G.3
  • 16
    • 0031912073 scopus 로고    scopus 로고
    • Determinants of protein hydrogen exchange studied in equine cytochrome c
    • 10.1002/pro.5560070323, 2143952, 9541406
    • Milne JS, Mayne L, Roder H, Wand AJ, Englander SW. Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Sci 1998, 7(3):739-745. 10.1002/pro.5560070323, 2143952, 9541406.
    • (1998) Protein Sci , vol.7 , Issue.3 , pp. 739-745
    • Milne, J.S.1    Mayne, L.2    Roder, H.3    Wand, A.J.4    Englander, S.W.5
  • 17
    • 84874652195 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC
    • The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC. , http://www.pymol.org
  • 18
    • 84888275170 scopus 로고    scopus 로고
    • SCIL (Symbolic Constraints for Integer Linear Programming)
    • SCIL (Symbolic Constraints for Integer Linear Programming). 2004, , http://www.mpi-sb.mpg.de/SCIL
    • (2004)
  • 20
    • 77955451628 scopus 로고    scopus 로고
    • für Informationstechnik Berlin KZZ
    • für Informationstechnik Berlin KZZ Solving Constraint Integer Programs 2009, für Informationstechnik Berlin KZZ., http://scip.zib.de/
    • (2009) Solving Constraint Integer Programs
  • 21
    • 69249204145 scopus 로고    scopus 로고
    • ILOG-CPLEX 10.0
    • ILOG-CPLEX 10.0. 2007, , http://www.ilog.com
    • (2007)
  • 22
    • 84888280311 scopus 로고    scopus 로고
    • SoPlex (Sequential object-oriented simplex class library)
    • SoPlex (Sequential object-oriented simplex class library). 2004, , http://www.zib.de/Optimization/Software/Soplex
    • (2004)
  • 23
    • 0004180332 scopus 로고    scopus 로고
    • Wiley-interscience series in discrete mathematics and optimization, New York: Wiley & Sons
    • Wolsey LA. Integer programming 1998, Wiley-interscience series in discrete mathematics and optimization, New York: Wiley & Sons.
    • (1998) Integer programming
    • Wolsey, L.A.1
  • 24
    • 34250461535 scopus 로고
    • The traveling salesman problem and minimum spanning trees: Part II
    • Held M, Karp R. The traveling salesman problem and minimum spanning trees: Part II. Mathematical Programming 1971, 1:6-25.
    • (1971) Mathematical Programming , vol.1 , pp. 6-25
    • Held, M.1    Karp, R.2
  • 26
    • 0015514380 scopus 로고
    • Primary structure effects on peptide group hydrogen exchange
    • 10.1021/bi00752a003, 5061873
    • Molday RS, Englander SW, Kallen RG. Primary structure effects on peptide group hydrogen exchange. Biochemistry 1972, 11(2):150-158. 10.1021/bi00752a003, 5061873.
    • (1972) Biochemistry , vol.11 , Issue.2 , pp. 150-158
    • Molday, R.S.1    Englander, S.W.2    Kallen, R.G.3
  • 27
    • 0027250665 scopus 로고
    • Primary structure effects on peptide group hydrogen exchange
    • 10.1002/prot.340170110, 8234246
    • Bai Y, Milne JS, Mayne L, Englander SW. Primary structure effects on peptide group hydrogen exchange. Proteins 1993, 17:75-86. 10.1002/prot.340170110, 8234246.
    • (1993) Proteins , vol.17 , pp. 75-86
    • Bai, Y.1    Milne, J.S.2    Mayne, L.3    Englander, S.W.4
  • 28
    • 33749490463 scopus 로고    scopus 로고
    • Supercritical Fluid Chromatography Reduction of Hydrogen/Deuterium Back Exchange in Solution-Phase Hydrogen/Deuterium Exchange with Mass Spectrometric Analysis
    • 10.1021/ac060693n, 17007536
    • Emmett MR, Kazazic S, Marshall AG, Chen W, Shi SDH, Bolanos B, Greig MJ. Supercritical Fluid Chromatography Reduction of Hydrogen/Deuterium Back Exchange in Solution-Phase Hydrogen/Deuterium Exchange with Mass Spectrometric Analysis. Analytical Chemistry 2006, 78(19):7058-7060. 10.1021/ac060693n, 17007536.
    • (2006) Analytical Chemistry , vol.78 , Issue.19 , pp. 7058-7060
    • Emmett, M.R.1    Kazazic, S.2    Marshall, A.G.3    Chen, W.4    Shi, S.D.H.5    Bolanos, B.6    Greig, M.J.7
  • 29
    • 60649094922 scopus 로고    scopus 로고
    • Fast Reversed-Phase Liquid Chromatography to Reduce Back Exchange and Increase Throughput in H/D Exchange Monitored by FT-ICR Mass Spectrometry
    • 10.1016/j.jasms.2008.11.010, 2673454, 19095461
    • Zhang HM, Bou-Assaf GM, Emmett MR, Marshall AG. Fast Reversed-Phase Liquid Chromatography to Reduce Back Exchange and Increase Throughput in H/D Exchange Monitored by FT-ICR Mass Spectrometry. Journal of the American Society for Mass Spectrometry 2009, 20(3):520-524. 10.1016/j.jasms.2008.11.010, 2673454, 19095461.
    • (2009) Journal of the American Society for Mass Spectrometry , vol.20 , Issue.3 , pp. 520-524
    • Zhang, H.M.1    Bou-Assaf, G.M.2    Emmett, M.R.3    Marshall, A.G.4
  • 30
    • 57449107282 scopus 로고    scopus 로고
    • Enhanced Digestion Efficiency, Peptide Ionization Efficiency, and Sequence Resolution for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
    • 10.1021/ac801417d, 2784605, 19551977
    • Zhang HM, Kazazic S, Schaub TM, Tipton JD, Emmett MR, Marshall AG. Enhanced Digestion Efficiency, Peptide Ionization Efficiency, and Sequence Resolution for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2008, 80(23):9034-41. 10.1021/ac801417d, 2784605, 19551977.
    • (2008) Anal Chem , vol.80 , Issue.23 , pp. 9034-9041
    • Zhang, H.M.1    Kazazic, S.2    Schaub, T.M.3    Tipton, J.D.4    Emmett, M.R.5    Marshall, A.G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.