메뉴 건너뛰기




Volumn 54, Issue 16, 2015, Pages 2683-2692

Challenges in the interpretation of protein H/D exchange data: A molecular dynamics simulation perspective

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; CRYSTAL ATOMIC STRUCTURE; GROUND STATE; HYDROGEN BONDS; PROTEINS; QUANTUM THEORY; SOLVATION; SOLVENTS;

EID: 84928652222     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b00215     Document Type: Article
Times cited : (53)

References (75)
  • 1
    • 42449151176 scopus 로고    scopus 로고
    • Protein folding and misfolding: Mechanism and principles
    • Englander, S. W., Mayne, L., and Krishna, M. M. G. (2007) Protein folding and misfolding: Mechanism and principles Q. Rev. Biophys. 40, 287-326
    • (2007) Q. Rev. Biophys. , vol.40 , pp. 287-326
    • Englander, S.W.1    Mayne, L.2    Krishna, M.M.G.3
  • 2
    • 84892698385 scopus 로고    scopus 로고
    • Ultrafast Hydrogen Exchange Reveals Specific Structural Events during the Initial Stages of Folding of Cytochrome c
    • Fazelinia, H., Xu, M., Cheng, H., and Roder, H. (2014) Ultrafast Hydrogen Exchange Reveals Specific Structural Events during the Initial Stages of Folding of Cytochrome c J. Am. Chem. Soc. 136, 733-740
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 733-740
    • Fazelinia, H.1    Xu, M.2    Cheng, H.3    Roder, H.4
  • 3
    • 80055017708 scopus 로고    scopus 로고
    • Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin
    • Ward, M. E., Shi, L., Lake, E., Krishnamurthy, S., Hutchins, H., Brown, L. S., and Ladizhansky, V. (2011) Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin J. Am. Chem. Soc. 133, 17434-17443
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 17434-17443
    • Ward, M.E.1    Shi, L.2    Lake, E.3    Krishnamurthy, S.4    Hutchins, H.5    Brown, L.S.6    Ladizhansky, V.7
  • 4
    • 79958772494 scopus 로고    scopus 로고
    • Early days of protein hydrogen exchange: 1954-1972
    • Baldwin, R. L. (2011) Early days of protein hydrogen exchange: 1954-1972 Proteins 79, 2021-2026
    • (2011) Proteins , vol.79 , pp. 2021-2026
    • Baldwin, R.L.1
  • 5
    • 84920474229 scopus 로고    scopus 로고
    • Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014
    • Pirrone, G. F., Iacob, R. E., and Engen, J. R. (2015) Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014 Anal. Chem. 87, 99-118
    • (2015) Anal. Chem. , vol.87 , pp. 99-118
    • Pirrone, G.F.1    Iacob, R.E.2    Engen, J.R.3
  • 6
    • 79951887389 scopus 로고    scopus 로고
    • Hydrogen Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
    • Konermann, L., Pan, J., and Liu, Y. (2011) Hydrogen Exchange Mass Spectrometry for Studying Protein Structure and Dynamics Chem. Soc. Rev. 40, 1224-1234
    • (2011) Chem. Soc. Rev. , vol.40 , pp. 1224-1234
    • Konermann, L.1    Pan, J.2    Liu, Y.3
  • 7
    • 84858277365 scopus 로고    scopus 로고
    • Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry - A review
    • Percy, A. J., Rey, M., Burns, K. M., and Schriemer, D. C. (2012) Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-A review Anal. Chim. Acta 721, 7-21
    • (2012) Anal. Chim. Acta , vol.721 , pp. 7-21
    • Percy, A.J.1    Rey, M.2    Burns, K.M.3    Schriemer, D.C.4
  • 8
    • 67650756766 scopus 로고    scopus 로고
    • Protein Hydrogen Exchange Measured at Single-Residue Resolution by Electron Transfer Dissociation Mass Spectrometry
    • Rand, K. D., Zehl, M., Jensen, O. N., and Jørgensen, T. J. D. (2009) Protein Hydrogen Exchange Measured at Single-Residue Resolution by Electron Transfer Dissociation Mass Spectrometry Anal. Chem. 81, 5577-5584
    • (2009) Anal. Chem. , vol.81 , pp. 5577-5584
    • Rand, K.D.1    Zehl, M.2    Jensen, O.N.3    Jørgensen, T.J.D.4
  • 10
    • 84859904015 scopus 로고    scopus 로고
    • Measuring Dynamics in Weakly Structured Regions of Proteins Using Microfluidics-Enabled Subsecond H/D Exchange Mass Spectrometry
    • Rob, T., Liuni, P., Gill, P. K., Zhu, S. L., Balachandran, N., Berti, P. J., and Wilson, D. J. (2012) Measuring Dynamics in Weakly Structured Regions of Proteins Using Microfluidics-Enabled Subsecond H/D Exchange Mass Spectrometry Anal. Chem. 84, 3771-3779
    • (2012) Anal. Chem. , vol.84 , pp. 3771-3779
    • Rob, T.1    Liuni, P.2    Gill, P.K.3    Zhu, S.L.4    Balachandran, N.5    Berti, P.J.6    Wilson, D.J.7
  • 11
    • 84878107864 scopus 로고    scopus 로고
    • Hydrogen-exchangemass spectrometry for the study of intrinsic disorder in proteins
    • Balasubramaniam, D. and Komives, E. A. (2013) Hydrogen-exchangemass spectrometry for the study of intrinsic disorder in proteins Biochim. Biophys. Acta 1834, 1202-1209
    • (2013) Biochim. Biophys. Acta , vol.1834 , pp. 1202-1209
    • Balasubramaniam, D.1    Komives, E.A.2
  • 12
    • 33750282788 scopus 로고    scopus 로고
    • Mapping protein dynamics in catalytic intermediates of the redox-driven proton pump cytochrome c oxidase
    • Busenlehner, L. S., Salomonsson, L., Brzezinski, P., and Armstrong, R. N. (2006) Mapping protein dynamics in catalytic intermediates of the redox-driven proton pump cytochrome c oxidase Proc. Natl. Acad. Sci. U. S. A. 103, 15398-15403
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 15398-15403
    • Busenlehner, L.S.1    Salomonsson, L.2    Brzezinski, P.3    Armstrong, R.N.4
  • 13
    • 84890275407 scopus 로고    scopus 로고
    • Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry
    • Wang, G., Abzalimov, R. R., Bobst, C. E., and Kaltashov, I. A. (2013) Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry Proc. Natl. Acad. Sci. U. S. A. 110, 20087-20092
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 20087-20092
    • Wang, G.1    Abzalimov, R.R.2    Bobst, C.E.3    Kaltashov, I.A.4
  • 14
    • 80053581731 scopus 로고    scopus 로고
    • Mapping Unstructured Regions and Synergistic Folding in Intrinsically Disordered Proteins with Amide H/D Exchange Mass Spectrometry
    • Keppel, T. R., Howard, B. A., and Weis, D. D. (2011) Mapping Unstructured Regions and Synergistic Folding in Intrinsically Disordered Proteins with Amide H/D Exchange Mass Spectrometry Biochemistry 50, 8722-8732
    • (2011) Biochemistry , vol.50 , pp. 8722-8732
    • Keppel, T.R.1    Howard, B.A.2    Weis, D.D.3
  • 15
    • 0000540212 scopus 로고
    • Proton Exchange in Amides: Surprises from Simple Systems
    • Perrin, C. L. (1989) Proton Exchange in Amides: Surprises from Simple Systems Acc. Chem. Res. 22, 268-275
    • (1989) Acc. Chem. Res. , vol.22 , pp. 268-275
    • Perrin, C.L.1
  • 16
    • 0032557227 scopus 로고    scopus 로고
    • pK(a) shift effects on backbone amide base-catalyzed hydrogen exchange rates in peptides
    • Fogolari, F., Esposito, G., Viglino, P., Briggs, J. M., and McCammon, J. A. (1998) pK(a) shift effects on backbone amide base-catalyzed hydrogen exchange rates in peptides J. Am. Chem. Soc. 120, 3735-3738
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 3735-3738
    • Fogolari, F.1    Esposito, G.2    Viglino, P.3    Briggs, J.M.4    McCammon, J.A.5
  • 17
    • 0015514380 scopus 로고
    • Primary Structure Effects on Peptide Hydrogen Exchange
    • Molday, R. S., Englander, S. W., and Kallen, R. G. (1972) Primary Structure Effects on Peptide Hydrogen Exchange Biochemistry 11, 150-158
    • (1972) Biochemistry , vol.11 , pp. 150-158
    • Molday, R.S.1    Englander, S.W.2    Kallen, R.G.3
  • 18
    • 84910631470 scopus 로고    scopus 로고
    • Metal-Ion-Specific Screening of Charge Effects in Protein Amide H/D Exchange and the Hofmeister Series
    • Abdolvahabi, A., Gober, J. L., Mowery, R. A., Shi, Y. H., and Shaw, B. F. (2014) Metal-Ion-Specific Screening of Charge Effects in Protein Amide H/D Exchange and the Hofmeister Series Anal. Chem. 86, 10303-10310
    • (2014) Anal. Chem. , vol.86 , pp. 10303-10310
    • Abdolvahabi, A.1    Gober, J.L.2    Mowery, R.A.3    Shi, Y.H.4    Shaw, B.F.5
  • 20
    • 84865844741 scopus 로고    scopus 로고
    • Improved Sequence Resolution by Global Analysis of Overlapped Peptides in Hydrogen/Deuterium Exchange Mass Spectrometry
    • Fajer, P. G., Bou-Assaf, G. M., and Marshall, A. G. (2012) Improved Sequence Resolution by Global Analysis of Overlapped Peptides in Hydrogen/Deuterium Exchange Mass Spectrometry J. Am. Soc. Mass Spectrom. 23, 1202-1208
    • (2012) J. Am. Soc. Mass Spectrom. , vol.23 , pp. 1202-1208
    • Fajer, P.G.1    Bou-Assaf, G.M.2    Marshall, A.G.3
  • 21
    • 35648986229 scopus 로고    scopus 로고
    • Deuterium exchange and mass spectrometry reveal the interaction differences of two synthetic modulators of RXRαLBD
    • Yan, X., Pérez, E., Leid, M., Schimerlik, M. I., de Lera, A. R., and Deinzer, M. L. (2007) Deuterium exchange and mass spectrometry reveal the interaction differences of two synthetic modulators of RXRαLBD Protein Sci. 16, 2491-2501
    • (2007) Protein Sci. , vol.16 , pp. 2491-2501
    • Yan, X.1    Pérez, E.2    Leid, M.3    Schimerlik, M.I.4    De Lera, A.R.5    Deinzer, M.L.6
  • 22
    • 0025186451 scopus 로고
    • Structural Characterisation of a Partly Folded Apomyoglobin Intermediate
    • Hughson, F. M., Wright, P. E., and Baldwin, R. L. (1990) Structural Characterisation of a Partly Folded Apomyoglobin Intermediate Science 249, 1544-1548
    • (1990) Science , vol.249 , pp. 1544-1548
    • Hughson, F.M.1    Wright, P.E.2    Baldwin, R.L.3
  • 23
    • 79955790484 scopus 로고    scopus 로고
    • Mapping the Protein-Protein Interface between a Toxin and Its Cognate Antitoxin from the Bacterial Pathogen Streptococcus pyogenes
    • Sperry, J. B., Smith, C. L., Caparon, M. G., Ellenberger, T., and Gross, M. L. (2011) Mapping the Protein-Protein Interface between a Toxin and Its Cognate Antitoxin from the Bacterial Pathogen Streptococcus pyogenes Biochemistry 50, 4038-4045
    • (2011) Biochemistry , vol.50 , pp. 4038-4045
    • Sperry, J.B.1    Smith, C.L.2    Caparon, M.G.3    Ellenberger, T.4    Gross, M.L.5
  • 26
    • 0026460815 scopus 로고
    • Hydrogen Exchange in Native and Alcohol Forms of Ubiquitin
    • Pan, Y. and Briggs, M. S. (1992) Hydrogen Exchange in Native and Alcohol Forms of Ubiquitin Biochemistry 31, 11405-11412
    • (1992) Biochemistry , vol.31 , pp. 11405-11412
    • Pan, Y.1    Briggs, M.S.2
  • 27
    • 0013994339 scopus 로고
    • Hydrogen exchange in proteins
    • Hvidt, A. and Nielsen, S. O. (1966) Hydrogen exchange in proteins Adv. Protein Chem. 21, 287-386
    • (1966) Adv. Protein Chem. , vol.21 , pp. 287-386
    • Hvidt, A.1    Nielsen, S.O.2
  • 28
    • 84886642731 scopus 로고    scopus 로고
    • Activation of ClpP Protease by ADEP Antibiotics: Insights from Hydrogen Exchange Mass Spectrometry
    • Sowole, M. A., Alexopoulos, J. A., Cheng, Y.-Q., Ortega, J., and Konermann, L. (2013) Activation of ClpP Protease by ADEP Antibiotics: Insights from Hydrogen Exchange Mass Spectrometry J. Mol. Biol. 425, 4508-4519
    • (2013) J. Mol. Biol. , vol.425 , pp. 4508-4519
    • Sowole, M.A.1    Alexopoulos, J.A.2    Cheng, Y.-Q.3    Ortega, J.4    Konermann, L.5
  • 29
    • 44949164734 scopus 로고    scopus 로고
    • A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin
    • Anderson, J. S., Hernandez, G., and LeMaster, D. M. (2008) A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin Biochemistry 47, 6178-6188
    • (2008) Biochemistry , vol.47 , pp. 6178-6188
    • Anderson, J.S.1    Hernandez, G.2    Lemaster, D.M.3
  • 30
    • 67650034385 scopus 로고    scopus 로고
    • Polarization and Polarizability Assessed by Protein Amide Acidity
    • Hernandez, G., Anderson, J. S., and LeMaster, D. M. (2009) Polarization and Polarizability Assessed by Protein Amide Acidity Biochemistry 48, 6482-6494
    • (2009) Biochemistry , vol.48 , pp. 6482-6494
    • Hernandez, G.1    Anderson, J.S.2    Lemaster, D.M.3
  • 31
    • 0344603844 scopus 로고    scopus 로고
    • The hydrogen exchange core and protein folding
    • Li, R. and Woodward, C. (1999) The hydrogen exchange core and protein folding Protein Sci. 8, 1571-1590
    • (1999) Protein Sci. , vol.8 , pp. 1571-1590
    • Li, R.1    Woodward, C.2
  • 32
    • 84872342408 scopus 로고    scopus 로고
    • Assessing the chemical accuracy of protein structures via peptide acidity
    • Anderson, J. S., Hernandez, G., and LeMaster, D. M. (2013) Assessing the chemical accuracy of protein structures via peptide acidity Biophys. Chem. 171, 63-75
    • (2013) Biophys. Chem. , vol.171 , pp. 63-75
    • Anderson, J.S.1    Hernandez, G.2    Lemaster, D.M.3
  • 34
    • 84864387458 scopus 로고    scopus 로고
    • ClpP: A structurally dynamic protease regulated by AAA+ proteins
    • Alexopoulos, J. A., Guarnéa, A., and Ortega, J. (2012) ClpP: A structurally dynamic protease regulated by AAA+ proteins J. Struct. Biol. 179, 202-210
    • (2012) J. Struct. Biol. , vol.179 , pp. 202-210
    • Alexopoulos, J.A.1    Guarnéa, A.2    Ortega, J.3
  • 37
    • 0032539561 scopus 로고    scopus 로고
    • Molecular picture of folding of a small α/β protein
    • Sheinerman, F. B. and Brooks, C. L., III. (1998) Molecular picture of folding of a small α/β protein Proc. Natl. Acad. Sci. U. S. A. 95, 1562-1567
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 1562-1567
    • Sheinerman, F.B.1    Brooks, C.L.2
  • 38
    • 0033181018 scopus 로고    scopus 로고
    • Conformational dynamics of cytochrome c: Correlation to hydrogen exchange
    • Garcia, A. E. and Hummer, G. (1999) Conformational dynamics of cytochrome c: Correlation to hydrogen exchange Proteins 36, 175-191
    • (1999) Proteins , vol.36 , pp. 175-191
    • Garcia, A.E.1    Hummer, G.2
  • 39
    • 84872145488 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments
    • Petruk, A. A., Defelipe, L. A., Limardo, R. G. R., Bucci, H., Marti, M. A., and Turjanski, A. G. (2013) Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments J. Chem. Theory Comput. 9, 658-669
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 658-669
    • Petruk, A.A.1    Defelipe, L.A.2    Limardo, R.G.R.3    Bucci, H.4    Marti, M.A.5    Turjanski, A.G.6
  • 40
    • 84873861097 scopus 로고    scopus 로고
    • Fluoroketone Inhibition of Ca2+-Independent Phospholipase A(2) through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics
    • Hsu, Y. H., Bucher, D., Cao, J., Li, S., Yang, S. W., Kokotos, G., Woods, V. L., McCammon, J. A., and Dennis, E. A. (2013) Fluoroketone Inhibition of Ca2+-Independent Phospholipase A(2) through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics J. Am. Chem. Soc. 135, 1330-1337
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 1330-1337
    • Hsu, Y.H.1    Bucher, D.2    Cao, J.3    Li, S.4    Yang, S.W.5    Kokotos, G.6    Woods, V.L.7    McCammon, J.A.8    Dennis, E.A.9
  • 41
    • 84921329442 scopus 로고    scopus 로고
    • Phosphorylation in the Catalytic Cleft Stabilizes and Attracts Domains of a Phosphohexomutase
    • Xu, J., Lee, Y. J., Beamer, L. J., and Van Doren, S. R. (2015) Phosphorylation in the Catalytic Cleft Stabilizes and Attracts Domains of a Phosphohexomutase Biophys. J. 108, 235-337
    • (2015) Biophys. J. , vol.108 , pp. 235-337
    • Xu, J.1    Lee, Y.J.2    Beamer, L.J.3    Van Doren, S.R.4
  • 42
    • 84862908883 scopus 로고    scopus 로고
    • Quantitative assessment of protein structural models by comparison of H/D exchange MS data with exchange behavior accurately predicted by DXCOREX
    • Liu, T., Pantazatos, D., Li, S., Hamuro, Y., Hilser, V. J., and Woods, V. L. (2012) Quantitative assessment of protein structural models by comparison of H/D exchange MS data with exchange behavior accurately predicted by DXCOREX J. Am. Soc. Mass Spectrom. 23, 43-56
    • (2012) J. Am. Soc. Mass Spectrom. , vol.23 , pp. 43-56
    • Liu, T.1    Pantazatos, D.2    Li, S.3    Hamuro, Y.4    Hilser, V.J.5    Woods, V.L.6
  • 43
    • 0032570266 scopus 로고    scopus 로고
    • Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model
    • Bahar, I., Wallqvist, A., Covell, D. G., and Jernigan, R. L. (1998) Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model Biochemistry 37, 1067-1075
    • (1998) Biochemistry , vol.37 , pp. 1067-1075
    • Bahar, I.1    Wallqvist, A.2    Covell, D.G.3    Jernigan, R.L.4
  • 45
    • 0023644679 scopus 로고
    • Structure of Ubiquitin Refined at 1.8 A Resolution
    • Vijay-Kumar, S., Bugg, C. E., and Cook, W. J. (1987) Structure of Ubiquitin Refined at 1.8 A Resolution J. Mol. Biol. 194, 531-544
    • (1987) J. Mol. Biol. , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 46
    • 1442355435 scopus 로고    scopus 로고
    • Quantitation of rapid proton-deuteron amide exchange using hadamard spectroscopy
    • Bougault, C., Feng, L. M., Glushka, J., Kupce, E., and Prestegard, J. H. (2004) Quantitation of rapid proton-deuteron amide exchange using hadamard spectroscopy J. Biomol. NMR 28, 385-390
    • (2004) J. Biomol. NMR , vol.28 , pp. 385-390
    • Bougault, C.1    Feng, L.M.2    Glushka, J.3    Kupce, E.4    Prestegard, J.H.5
  • 47
    • 0033566738 scopus 로고    scopus 로고
    • Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin
    • Johnson, E. C., Lazar, G. A., Desjarlais, J. R., and Handel, T. M. (1999) Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin Struct. Folding Des. 7, 967-976
    • (1999) Struct. Folding Des. , vol.7 , pp. 967-976
    • Johnson, E.C.1    Lazar, G.A.2    Desjarlais, J.R.3    Handel, T.M.4
  • 48
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    • Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 49
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen, H. J., van der Spoel, D., and van Drunen, R. (1995) GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 91, 43-56
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 43-56
    • Berendsen, H.J.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 50
    • 79959720287 scopus 로고    scopus 로고
    • How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
    • Piana, S., Lindorff-Larsen, K., and Shaw, D. E. (2011) How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization? Biophys. J. 100, L47-L49
    • (2011) Biophys. J. , vol.100 , pp. L47-L49
    • Piana, S.1    Lindorff-Larsen, K.2    Shaw, D.E.3
  • 53
    • 84892157404 scopus 로고    scopus 로고
    • Classical Electrostatics for Biomolecular Simulations
    • Cisneros, G. A., Karttunen, M., Ren, P. Y., and Sagui, C. (2014) Classical Electrostatics for Biomolecular Simulations Chem. Rev. 114, 779-814
    • (2014) Chem. Rev. , vol.114 , pp. 779-814
    • Cisneros, G.A.1    Karttunen, M.2    Ren, P.Y.3    Sagui, C.4
  • 54
    • 84907467876 scopus 로고    scopus 로고
    • Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models
    • Goyal, P., Qian, H. J., Irle, S., Lu, X. Y., Roston, D., Mori, T., Elstner, M., and Cui, Q. (2014) Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models J. Phys. Chem. B 118, 11007-11027
    • (2014) J. Phys. Chem. B , vol.118 , pp. 11007-11027
    • Goyal, P.1    Qian, H.J.2    Irle, S.3    Lu, X.Y.4    Roston, D.5    Mori, T.6    Elstner, M.7    Cui, Q.8
  • 55
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi, G., Donadio, D., and Parrinello, M. (2007) Canonical sampling through velocity rescaling J. Chem. Phys. 126, 0141011-0141017
    • (2007) J. Chem. Phys. , vol.126 , pp. 0141011-0141017
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 57
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., Henk, B., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 18, 1463-1472
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Henk, B.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 58
    • 84986440341 scopus 로고
    • SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models
    • Miyamoto, S. and Kollman, P. A. (1992) SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models J. Comput. Chem. 13, 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 60
    • 0036268465 scopus 로고    scopus 로고
    • Geometric criteria of hydrogen bonds in proteins and identification of 'bifurcated' hydrogen bonds
    • Torshin, I. Y., Weber, I. T., and Harrison, R. W. (2002) Geometric criteria of hydrogen bonds in proteins and identification of 'bifurcated' hydrogen bonds Protein Eng. 15, 359-363
    • (2002) Protein Eng. , vol.15 , pp. 359-363
    • Torshin, I.Y.1    Weber, I.T.2    Harrison, R.W.3
  • 61
    • 84986483798 scopus 로고
    • The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
    • Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., and Scharf, M. (1995) The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies J. Comput. Chem. 16, 273-284
    • (1995) J. Comput. Chem. , vol.16 , pp. 273-284
    • Eisenhaber, F.1    Lijnzaad, P.2    Argos, P.3    Sander, C.4    Scharf, M.5
  • 62
    • 0032125607 scopus 로고    scopus 로고
    • A set of van der Waals and Coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking
    • Li, A. J. and Nussinov, R. (1998) A set of van der Waals and Coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking Proteins 32, 111-127
    • (1998) Proteins , vol.32 , pp. 111-127
    • Li, A.J.1    Nussinov, R.2
  • 63
    • 84907938447 scopus 로고    scopus 로고
    • Perturbation of Long-Range Water Dynamics as the Mechanism for the Antifreeze Activity of Antifreeze Glycoprotein
    • Mallajosyula, S. S., Vanommeslaeghe, K., and MacKerell, A. D. (2014) Perturbation of Long-Range Water Dynamics as the Mechanism for the Antifreeze Activity of Antifreeze Glycoprotein J. Phys. Chem. B 118, 11696-11706
    • (2014) J. Phys. Chem. B , vol.118 , pp. 11696-11706
    • Mallajosyula, S.S.1    Vanommeslaeghe, K.2    MacKerell, A.D.3
  • 64
    • 84915782409 scopus 로고    scopus 로고
    • New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations
    • Nibali, V. C. and Havenith, M. (2014) New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations J. Am. Chem. Soc. 136, 12800-12807
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 12800-12807
    • Nibali, V.C.1    Havenith, M.2
  • 65
    • 84907921180 scopus 로고    scopus 로고
    • Local Water Dynamics around Antifreeze Protein Residues in the Presence of Osmolytes: The Importance of Hydroxyl and Disaccharide Groups
    • Krishnamoorthy, A. N., Holm, C., and Smiatek, J. (2014) Local Water Dynamics around Antifreeze Protein Residues in the Presence of Osmolytes: The Importance of Hydroxyl and Disaccharide Groups J. Phys. Chem. B 118, 11613-11621
    • (2014) J. Phys. Chem. B , vol.118 , pp. 11613-11621
    • Krishnamoorthy, A.N.1    Holm, C.2    Smiatek, J.3
  • 67
    • 84922567031 scopus 로고    scopus 로고
    • Dipolar Nanodomains in Protein Hydration Shells
    • Martin, D. R. and Matyushov, D. V. (2015) Dipolar Nanodomains in Protein Hydration Shells J. Phys. Chem. Lett. 6, 407-412
    • (2015) J. Phys. Chem. Lett. , vol.6 , pp. 407-412
    • Martin, D.R.1    Matyushov, D.V.2
  • 68
    • 84865088597 scopus 로고    scopus 로고
    • Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
    • Cino, E. A., Choy, W. Y., and Karttunen, M. (2012) Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations J. Chem. Theory Comput. 8, 2725-2740
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2725-2740
    • Cino, E.A.1    Choy, W.Y.2    Karttunen, M.3
  • 69
    • 84888332575 scopus 로고    scopus 로고
    • Complex Formation during SID and Its Effect on Proton Mobility
    • Ijaz, W., Gregg, Z., and Barnes, G. L. (2013) Complex Formation during SID and Its Effect on Proton Mobility J. Phys. Chem. Lett. 4, 3935-3939
    • (2013) J. Phys. Chem. Lett. , vol.4 , pp. 3935-3939
    • Ijaz, W.1    Gregg, Z.2    Barnes, G.L.3
  • 70
    • 84893021599 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP) - round x
    • Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T., and Tramontano, A. (2014) Critical assessment of methods of protein structure prediction (CASP)-round x Proteins 82, 1-6
    • (2014) Proteins , vol.82 , pp. 1-6
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Schwede, T.4    Tramontano, A.5
  • 71
    • 78650137058 scopus 로고    scopus 로고
    • Neutralizing Positive Charges at the Surface of a Protein Lowers Its Rate of Amide Hydrogen Exchange without Altering Its Structure or Increasing Its Thermostability
    • Shaw, B. F., Arthanari, H., Narovlyansky, M., Durazo, A., Frueh, D. P., Pollastri, M. P., Lee, A., Bilgicer, B., Gygi, S. P., Wagner, G., and Whitesides, G. M. (2010) Neutralizing Positive Charges at the Surface of a Protein Lowers Its Rate of Amide Hydrogen Exchange without Altering Its Structure or Increasing Its Thermostability J. Am. Chem. Soc. 132, 17411-17425
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 17411-17425
    • Shaw, B.F.1    Arthanari, H.2    Narovlyansky, M.3    Durazo, A.4    Frueh, D.P.5    Pollastri, M.P.6    Lee, A.7    Bilgicer, B.8    Gygi, S.P.9    Wagner, G.10    Whitesides, G.M.11
  • 72
    • 0037182850 scopus 로고    scopus 로고
    • The nature and transport mechanism of hydrated hydroxide ions in aqueous solution
    • Tuckerman, M. E., Marx, D., and Parrinello, M. (2002) The nature and transport mechanism of hydrated hydroxide ions in aqueous solution Nature 417, 925-929
    • (2002) Nature , vol.417 , pp. 925-929
    • Tuckerman, M.E.1    Marx, D.2    Parrinello, M.3
  • 73
    • 84927589222 scopus 로고    scopus 로고
    • Unveiling the Janus-Like Properties of OH
    • Crespo, Y. and Hassanali, A. (2015) Unveiling the Janus-Like Properties of OH J. Phys. Chem. Lett. 6, 272-278
    • (2015) J. Phys. Chem. Lett. , vol.6 , pp. 272-278
    • Crespo, Y.1    Hassanali, A.2
  • 74
    • 36448938198 scopus 로고    scopus 로고
    • Development of a Peptide Probe for the Occurrence of Hydrogen (1H/2H) Scrambling upon Gas-Phase Fragmentation
    • Rand, K. D. and Jørgensen, T. J. D. (2007) Development of a Peptide Probe for the Occurrence of Hydrogen (1H/2H) Scrambling upon Gas-Phase Fragmentation Anal. Chem. 79, 8686-8693
    • (2007) Anal. Chem. , vol.79 , pp. 8686-8693
    • Rand, K.D.1    Jørgensen, T.J.D.2
  • 75
    • 27344436619 scopus 로고    scopus 로고
    • Structure and properties of α-synuclein and other amyloids determined at the amino acid level
    • Del Mar, C., Greenbaum, E. A., Mayne, L., Englander, S. W., and Woods, V. L. (2005) Structure and properties of α-synuclein and other amyloids determined at the amino acid level Proc. Natl. Acad. Sci. U. S. A. 102, 15477-15482
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15477-15482
    • Del Mar, C.1    Greenbaum, E.A.2    Mayne, L.3    Englander, S.W.4    Woods, V.L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.