-
1
-
-
34548724094
-
Solvent mediated proton transfer in catalysis by carbonic anhydrase
-
Silverman D.N., and McKenna R. Solvent mediated proton transfer in catalysis by carbonic anhydrase. Acc. Chem. Res. 40 (2007) 669-675
-
(2007)
Acc. Chem. Res.
, vol.40
, pp. 669-675
-
-
Silverman, D.N.1
McKenna, R.2
-
2
-
-
33846164490
-
Low-temperature solid-state NMR spectroscopy. A strategy for the direct observation of quadrupolar nuclides of biological interest
-
Ellis P.D., and Lipton A.S. Low-temperature solid-state NMR spectroscopy. A strategy for the direct observation of quadrupolar nuclides of biological interest. Annu. Rep. NMR Spectrosc. 60 (2007) 1-38
-
(2007)
Annu. Rep. NMR Spectrosc.
, vol.60
, pp. 1-38
-
-
Ellis, P.D.1
Lipton, A.S.2
-
3
-
-
35548992252
-
Solid state NMR: new tools for insight into enzyme function
-
McDermott A., and Polenova T. Solid state NMR: new tools for insight into enzyme function. Curr. Opin. Struct. Biol. 17 (2007) 617-622
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 617-622
-
-
McDermott, A.1
Polenova, T.2
-
4
-
-
0000844092
-
The electric field gradient in noncubic metals
-
Kaufmann E.N., and Vianden R.J. The electric field gradient in noncubic metals. Rev. Mod. Phys. 51 (1979) 161-214
-
(1979)
Rev. Mod. Phys.
, vol.51
, pp. 161-214
-
-
Kaufmann, E.N.1
Vianden, R.J.2
-
5
-
-
1842637579
-
Zinc solid-state NMR spectroscopy of human carbonic anhydrase: implications for the enzymatic mechanism
-
Lipton A.S., Heck R.W., and Ellis P.D. Zinc solid-state NMR spectroscopy of human carbonic anhydrase: implications for the enzymatic mechanism. J. Am. Chem. Soc. 126 (2004) 4735-4739
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 4735-4739
-
-
Lipton, A.S.1
Heck, R.W.2
Ellis, P.D.3
-
6
-
-
34547415103
-
Modeling the metal center of Cys(4) zinc proteins
-
Lipton A.S., and Ellis P.D. Modeling the metal center of Cys(4) zinc proteins. J. Am. Chem. Soc. 129 (2007) 9192-9200
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 9192-9200
-
-
Lipton, A.S.1
Ellis, P.D.2
-
7
-
-
43249126309
-
A QM/MM approach to interpreting Zn-67 solid-state NMR data in zinc proteins
-
Lipton A.S., Heck R.W., Staeheli G.R., Valiev M., De Jong W.A., and Ellis P.D. A QM/MM approach to interpreting Zn-67 solid-state NMR data in zinc proteins. J. Am. Chem. Soc. 130 (2008) 6224-6230
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 6224-6230
-
-
Lipton, A.S.1
Heck, R.W.2
Staeheli, G.R.3
Valiev, M.4
De Jong, W.A.5
Ellis, P.D.6
-
8
-
-
52449108936
-
Residue ionization in LpxC directly observed by Zn-67 NMR spectroscopy
-
Lipton A.S., Heck R.W., Hernick M., Fierke C.A., and Ellis P.D. Residue ionization in LpxC directly observed by Zn-67 NMR spectroscopy. J. Am. Chem. Soc. 130 (2008) 12671-12679
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 12671-12679
-
-
Lipton, A.S.1
Heck, R.W.2
Hernick, M.3
Fierke, C.A.4
Ellis, P.D.5
-
9
-
-
14744270479
-
Zn-67 NMR chemical shifts and electric field gradients in zinc complexes: a quantum chemical investigation
-
Zhang Y., Mukherjee S., and Oldfield E. Zn-67 NMR chemical shifts and electric field gradients in zinc complexes: a quantum chemical investigation. J. Am. Chem. Soc. 127 (2005) 2370-2371w
-
(2005)
J. Am. Chem. Soc.
, vol.127
-
-
Zhang, Y.1
Mukherjee, S.2
Oldfield, E.3
-
10
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behavior
-
Becke A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38 (1988) 3098-3100
-
(1988)
Phys. Rev. A
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
11
-
-
0000189651
-
Density-functional thermochemistry. III. The role of exact exchange
-
Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98 (1993) 5648-5652
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
12
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee C., Yang W., and Parr R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37 (1988) 785-789
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
13
-
-
0035525888
-
2+-cysteinate complexes in proteins
-
2+-cysteinate complexes in proteins. J. Phys. Chem B 105 (2001) 10709-10714
-
(2001)
J. Phys. Chem B
, vol.105
, pp. 10709-10714
-
-
Dudev, T.1
Lim, C.2
-
14
-
-
0026463503
-
Structure of native and apo carbonic anhydrase ii and structure of some its anion-ligand complexes
-
Håkansson K., Carlsson M., Svensson L.A., and Liljas A. Structure of native and apo carbonic anhydrase ii and structure of some its anion-ligand complexes. J. Mol. Biol. 227 (1992) 1192-1204
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 1192-1204
-
-
Håkansson, K.1
Carlsson, M.2
Svensson, L.A.3
Liljas, A.4
-
15
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D.J., Bashford D., Bellott M., Dunbrack Jr. R.L., Evenseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E.I., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., and Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.J.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evenseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.I.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
16
-
-
19944408652
-
A critical evaluation of different QM/MM frontier treatments using SCC-DFTB as the QM method
-
Konig P.H., Hoffmann M., Frauenheim T., and Cui Q. A critical evaluation of different QM/MM frontier treatments using SCC-DFTB as the QM method. J. Phys. Chem. B 109 (2005) 9082-9095
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 9082-9095
-
-
Konig, P.H.1
Hoffmann, M.2
Frauenheim, T.3
Cui, Q.4
-
17
-
-
34249785686
-
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
-
Woodcock H.L., Hodoscek M., Gilbert A.T.B., Gill P.M.W., Schaefer H.F., and Brooks B.R. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J. Comput. Chem. 28 (2007) 1485-1502
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1485-1502
-
-
Woodcock, H.L.1
Hodoscek, M.2
Gilbert, A.T.B.3
Gill, P.M.W.4
Schaefer, H.F.5
Brooks, B.R.6
-
18
-
-
74649084579
-
-
Frisch, M.J. et al., and Pople, J.A., Gaussian 03, Revision B.05, Gaussian, Inc., Wallingford, CT, 2004 (2003).
-
Frisch, M.J. et al., and Pople, J.A., Gaussian 03, Revision B.05, Gaussian, Inc., Wallingford, CT, 2004 (2003).
-
-
-
-
19
-
-
43949083733
-
Free energies of chemical reactions in solution and in enzymes with ab initio Quantum Mechanics/Molecular Mechanics methods
-
Hu H., and Yang W.T. Free energies of chemical reactions in solution and in enzymes with ab initio Quantum Mechanics/Molecular Mechanics methods. Annu. Rev. Phys. Chem. 59 (2008) 573-601
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.T.2
-
20
-
-
34248224411
-
QM/MM minimum free-energy path: methodology and application to triosephosphate isomerase
-
Hu H., Lu Z.Y., and Yang W.T. QM/MM minimum free-energy path: methodology and application to triosephosphate isomerase. J. Chem. Theory Comp. 3 (2007) 390-406
-
(2007)
J. Chem. Theory Comp.
, vol.3
, pp. 390-406
-
-
Hu, H.1
Lu, Z.Y.2
Yang, W.T.3
-
21
-
-
0032190415
-
Molecular dynamics simulations of human carbonic anhydrase II: insight into experimental results and the role of solvation
-
Lu D., and Voth G.A. Molecular dynamics simulations of human carbonic anhydrase II: insight into experimental results and the role of solvation. Proteins Struct. Funct. Genet. 33 (1998) 119-134
-
(1998)
Proteins Struct. Funct. Genet.
, vol.33
, pp. 119-134
-
-
Lu, D.1
Voth, G.A.2
-
22
-
-
0033577309
-
Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II
-
Toba S., Colombo G., and Merz K.M.J. Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II. J. Am. Chem. Soc. 121 (1999) 2290-2302
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 2290-2302
-
-
Toba, S.1
Colombo, G.2
Merz, K.M.J.3
-
23
-
-
34548059996
-
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
-
Schaefer P., Riccardi D., and Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J. Chem. Phys. 123 (2005) 014905
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 014905
-
-
Schaefer, P.1
Riccardi, D.2
Cui, Q.3
-
24
-
-
33646356998
-
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes (Feature Article)
-
Riccardi D., Schaefer P., Yang Y., Yu H., Ghosh N., Prat-Resina X., Konig P., Li G., Xu D., Guo H., Elstner M., and Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes (Feature Article). J. Phys. Chem. B 110 (2006) 6458-6469
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 6458-6469
-
-
Riccardi, D.1
Schaefer, P.2
Yang, Y.3
Yu, H.4
Ghosh, N.5
Prat-Resina, X.6
Konig, P.7
Li, G.8
Xu, D.9
Guo, H.10
Elstner, M.11
Cui, Q.12
-
25
-
-
34547480925
-
a analysis for the zinc-bound water in human carbonic anhydrase II: benchmark for "multi-scale" QM/MM simulations and mechanistic implications
-
a analysis for the zinc-bound water in human carbonic anhydrase II: benchmark for "multi-scale" QM/MM simulations and mechanistic implications. J. Phys. Chem. A 111 (2007) 5703-5711
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 5703-5711
-
-
Riccardi, D.1
Cui, Q.2
-
26
-
-
31544463548
-
Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps
-
Koenig P., Ghosh N., Hoffman M., Elstner M., Tajkhorshid E., Frauenheim T., and Cui Q. Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J. Phys. Chem. A 110 (2006) 548-563
-
(2006)
J. Phys. Chem. A
, vol.110
, pp. 548-563
-
-
Koenig, P.1
Ghosh, N.2
Hoffman, M.3
Elstner, M.4
Tajkhorshid, E.5
Frauenheim, T.6
Cui, Q.7
-
28
-
-
1542779956
-
Self-Consistent-Charge Density-Functional Tight-Binding method for simulations of complex materials properties
-
Elstner M., Porezag D., Jungnickel G., Elsner J., Haugk M., Frauenheim T., Suhai S., and Seifert G. Self-Consistent-Charge Density-Functional Tight-Binding method for simulations of complex materials properties. Phys. Rev. B 58 11 (1998) 7260-7268
-
(1998)
Phys. Rev. B
, vol.58
, Issue.11
, pp. 7260-7268
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seifert, G.8
-
29
-
-
0035138648
-
A QM/MM implementation of the self consistent charge density functional tight binding (SCC-DFTB) method
-
Cui Q., Elstner M., Kaxiras E., Frauenheim T., and Karplus M. A QM/MM implementation of the self consistent charge density functional tight binding (SCC-DFTB) method. J. Phys. Chem. B 105 2 (2001) 569-585
-
(2001)
J. Phys. Chem. B
, vol.105
, Issue.2
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
30
-
-
0035249196
-
Generalized solvent boundary potential for computer simulations
-
Im W., Bernèche S., and Roux B. Generalized solvent boundary potential for computer simulations. J. Chem. Phys. 114 7 (2001) 2924-2937
-
(2001)
J. Chem. Phys.
, vol.114
, Issue.7
, pp. 2924-2937
-
-
Im, W.1
Bernèche, S.2
Roux, B.3
-
31
-
-
34547437377
-
SCC-DFTB: what is the proper degree of self-consistency?
-
Elstner M. SCC-DFTB: what is the proper degree of self-consistency?. J. Phys. Chem. A 111 (2007) 5614-5621
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 5614-5621
-
-
Elstner, M.1
-
32
-
-
19944369519
-
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
-
Nam K., Gao J.L., and York D.M. An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations. J. Chem. Theory Comp. 1 (2005) 2-13
-
(2005)
J. Chem. Theory Comp.
, vol.1
, pp. 2-13
-
-
Nam, K.1
Gao, J.L.2
York, D.M.3
-
33
-
-
0141566583
-
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis
-
Elstner M., Cui Q., Munih P., Kaxiras E., Frauenheim T., and Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. J. Comp. Chem. 24 (2003) 565
-
(2003)
J. Comp. Chem.
, vol.24
, pp. 565
-
-
Elstner, M.1
Cui, Q.2
Munih, P.3
Kaxiras, E.4
Frauenheim, T.5
Karplus, M.6
-
34
-
-
34547428921
-
Looking at Self-Consistent-Charge Density Functional Tight Binding from a semiempirical perspective
-
Otte N., Scholten M., and Thiel W. Looking at Self-Consistent-Charge Density Functional Tight Binding from a semiempirical perspective. J. Phys. Chem. A 111 (2007) 5751-5755
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 5751-5755
-
-
Otte, N.1
Scholten, M.2
Thiel, W.3
-
35
-
-
33846700979
-
Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules
-
Sattelmeyer K.W., Tirado-Rives J., and Jorgensen W.L. Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules. J. Phys. Chem. A 110 (2006) 13551-13559
-
(2006)
J. Phys. Chem. A
, vol.110
, pp. 13551-13559
-
-
Sattelmeyer, K.W.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
36
-
-
24044444942
-
Benchmark calculations of proton affinities and gas phase basicities of molecules important in the study of biological phosphoryl transfer
-
Range K., Riccardi D., Elstner M., Cui Q., and York D. Benchmark calculations of proton affinities and gas phase basicities of molecules important in the study of biological phosphoryl transfer. Phys. Chem. Chem. Phys. 7 (2005) 3070-3079
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, pp. 3070-3079
-
-
Range, K.1
Riccardi, D.2
Elstner, M.3
Cui, Q.4
York, D.5
-
37
-
-
35948946987
-
Extension of the Self-Consistent-Charge Tight-Binding-Density-Functional (SCC-DFTB) method: third order expansion of the DFT total energy and introduction of a modified effective coulomb interaction
-
Yang Y., Yu H., York D., Cui Q., and Elstner M. Extension of the Self-Consistent-Charge Tight-Binding-Density-Functional (SCC-DFTB) method: third order expansion of the DFT total energy and introduction of a modified effective coulomb interaction. J. Phys. Chem. A 111 (2007) 10861-10873
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 10861-10873
-
-
Yang, Y.1
Yu, H.2
York, D.3
Cui, Q.4
Elstner, M.5
-
38
-
-
39749169756
-
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor
-
Riccardi D., Koenig P., Guo H., and Cui Q. Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochem. 47 (2008) 2369-2378
-
(2008)
Biochem.
, vol.47
, pp. 2369-2378
-
-
Riccardi, D.1
Koenig, P.2
Guo, H.3
Cui, Q.4
-
39
-
-
60349127442
-
QM/MM methods for biomolecular systems
-
Senn H.M., and Thiel W. QM/MM methods for biomolecular systems. Angew. Chem. Int. ed. 48 (2009) 1198-1229
-
(2009)
Angew. Chem. Int. ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
40
-
-
7744225102
-
Key role of electrostatic interactions in bacteriorhodopsin proton transfer
-
Bondar A.N., Fischer S., Smith J.C., Elstner M., and Suhai S. Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J. Am. Chem. Soc. 126 (2004) 14668-14677
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 14668-14677
-
-
Bondar, A.N.1
Fischer, S.2
Smith, J.C.3
Elstner, M.4
Suhai, S.5
-
41
-
-
70349112722
-
Long-distance proton transfer with a break in the bacteriorhodopsin active site
-
Phatak P., Frahmcke J.S., Wanko M., Hoffman M., Strodel P., Smith J.C., Suhai S., Bondar A.N., and Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J. Am. Chem. Soc. 131 (2009) 7064-7078
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 7064-7078
-
-
Phatak, P.1
Frahmcke, J.S.2
Wanko, M.3
Hoffman, M.4
Strodel, P.5
Smith, J.C.6
Suhai, S.7
Bondar, A.N.8
Elstner, M.9
-
42
-
-
1642493669
-
Molecular basis of proton blockage in aquaporins
-
Cambridge, Mass. 2001
-
Chakrabarti N., Tajkhorshid E., Roux B., and Pomes R. Molecular basis of proton blockage in aquaporins. Structure 12 (2001) 65-74 Cambridge, Mass. 2001
-
(2001)
Structure
, vol.12
, pp. 65-74
-
-
Chakrabarti, N.1
Tajkhorshid, E.2
Roux, B.3
Pomes, R.4
-
43
-
-
33845595256
-
"Proton holes" in long-range proton transfer reactions in solution and enzymes: a theoretical analysis
-
Riccardi D., König P., Prat-Resina X., Yu H., Elstner M., Frauenheim T., and Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: a theoretical analysis. J. Am. Chem. Soc. 128 (2006) 16302-16311
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 16302-16311
-
-
Riccardi, D.1
König, P.2
Prat-Resina, X.3
Yu, H.4
Elstner, M.5
Frauenheim, T.6
Cui, Q.7
-
44
-
-
0002036605
-
Mémoiresur la d'ecomposition de l'eau et des corps quelle tien en dissolution à l'aide de l'électricit'e galvanique
-
Grotthus C. Mémoiresur la d'ecomposition de l'eau et des corps quelle tien en dissolution à l'aide de l'électricit'e galvanique. Ann. Chim. 58 (1806) 54
-
(1806)
Ann. Chim.
, vol.58
, pp. 54
-
-
Grotthus, C.1
-
45
-
-
50249150246
-
a of residue 66 in Staphylococal nuclease: insights from QM/MM simulations with conventional sampling
-
a of residue 66 in Staphylococal nuclease: insights from QM/MM simulations with conventional sampling. J. Phys. Chem. B 112 (2008) 8387-8397
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 8387-8397
-
-
Ghosh, N.1
Cui, Q.2
-
46
-
-
62149122220
-
Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pK(a), redox reactions and solvation free energies
-
Kamerlin S.C.L., Haranczyk M., and Warshel A. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pK(a), redox reactions and solvation free energies. J. Phys. Chem B 113 (2009) 1253-1272
-
(2009)
J. Phys. Chem B
, vol.113
, pp. 1253-1272
-
-
Kamerlin, S.C.L.1
Haranczyk, M.2
Warshel, A.3
-
47
-
-
0346433947
-
a calculations with QM/MM free energy perturbations
-
a calculations with QM/MM free energy perturbations. J. Phys. Chem. B 107 (2003) 14521-14528
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 14521-14528
-
-
Li, G.1
Cui, Q.2
-
50
-
-
33748456949
-
The barrier for proton transport in aqauporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations
-
Kato M., Pisliakov A.V., and Warshel A. The barrier for proton transport in aqauporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins Struct. Funct. Bioinform. 64 (2006) 829-844
-
(2006)
Proteins Struct. Funct. Bioinform.
, vol.64
, pp. 829-844
-
-
Kato, M.1
Pisliakov, A.V.2
Warshel, A.3
-
51
-
-
84962477148
-
Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress
-
Shurki A., and Warshel A. Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. Adv. Protein Chem. 66 (2003) 249
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 249
-
-
Shurki, A.1
Warshel, A.2
-
52
-
-
25844473576
-
a calculations in solution and proteins with QM/MM free energy perturbation simulations
-
a calculations in solution and proteins with QM/MM free energy perturbation simulations. J. Phys. Chem. B 109 (2005) 17715-17733
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 17715-17733
-
-
Riccardi, D.1
Schaefer, P.2
Cui, Q.3
-
53
-
-
3142766126
-
Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO) method
-
Pu J.Z., Gao J.L., and Truhlar D.G. Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO) method. J. Phys. Chem. A 108 (2004) 5454-5463
-
(2004)
J. Phys. Chem. A
, vol.108
, pp. 5454-5463
-
-
Pu, J.Z.1
Gao, J.L.2
Truhlar, D.G.3
-
54
-
-
33845278732
-
The catalytic mechanism of carbonic anhydrase: implications of a rate-limiting protolysis of water
-
Silverman D.N., and Lindskog S. The catalytic mechanism of carbonic anhydrase: implications of a rate-limiting protolysis of water. Acc. Chem. Res. 21 (1988) 30-36
-
(1988)
Acc. Chem. Res.
, vol.21
, pp. 30-36
-
-
Silverman, D.N.1
Lindskog, S.2
-
55
-
-
0027418070
-
Importance of the conserved active-site residues Tyr7, Glu106, and Thr199 for the catalytic function of human carbonic anhydrase II
-
Liang Z., Xue Y., Behravan G., Jonsson B., and Lindskog S. Importance of the conserved active-site residues Tyr7, Glu106, and Thr199 for the catalytic function of human carbonic anhydrase II. Eur. J. Biochem. 211 (1993) 821-827
-
(1993)
Eur. J. Biochem.
, vol.211
, pp. 821-827
-
-
Liang, Z.1
Xue, Y.2
Behravan, G.3
Jonsson, B.4
Lindskog, S.5
-
56
-
-
0027317583
-
Structural analysis of the zinc hydroxide-Thr-199-Glu-106 hydrogen-bond network in human carbonic anhydrase II
-
Xue Y., Liljas A., Jonsson B., and Lindskog S. Structural analysis of the zinc hydroxide-Thr-199-Glu-106 hydrogen-bond network in human carbonic anhydrase II. Proteins Struct. Funct. Genet. 17 (1993) 93-106
-
(1993)
Proteins Struct. Funct. Genet.
, vol.17
, pp. 93-106
-
-
Xue, Y.1
Liljas, A.2
Jonsson, B.3
Lindskog, S.4
-
57
-
-
0034832484
-
Bicarbonate as a proton donor in catalysis by Zn(II)- and Co(II)-containing carbonic anhydrases
-
Tu C., Tripp B.C., Ferry J.G., and Silverman D.N. Bicarbonate as a proton donor in catalysis by Zn(II)- and Co(II)-containing carbonic anhydrases. J. Am. Chem. Soc. 123 (2001) 5861-5866
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5861-5866
-
-
Tu, C.1
Tripp, B.C.2
Ferry, J.G.3
Silverman, D.N.4
-
58
-
-
33749189483
-
Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations?
-
Gunner M.R., Mao J., Song Y., and Kim J. Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations?. Biochim. Biophys. Acta 1757 (2006) 942-968
-
(2006)
Biochim. Biophys. Acta
, vol.1757
, pp. 942-968
-
-
Gunner, M.R.1
Mao, J.2
Song, Y.3
Kim, J.4
-
59
-
-
0000726701
-
Carbonic anhydrase: evolution of the zinc binding site by nature and by design
-
Christianson D.W., and Fierke C.A. Carbonic anhydrase: evolution of the zinc binding site by nature and by design. Acc. Chem. Res. 29 (1996) 331-339
-
(1996)
Acc. Chem. Res.
, vol.29
, pp. 331-339
-
-
Christianson, D.W.1
Fierke, C.A.2
-
60
-
-
0034640335
-
Marcus rate theory applied to enzymatic proton transfer
-
Silverman D.N. Marcus rate theory applied to enzymatic proton transfer. Biochim. Biophys. Acta 1458 (2000) 88-103
-
(2000)
Biochim. Biophys. Acta
, vol.1458
, pp. 88-103
-
-
Silverman, D.N.1
-
61
-
-
0028932267
-
Proton transfer in carbonic anhydrase measured by equilibrium isotope exchange
-
Silverman D.N. Proton transfer in carbonic anhydrase measured by equilibrium isotope exchange. Methods Enzymol. 249 (1995) 479-503
-
(1995)
Methods Enzymol.
, vol.249
, pp. 479-503
-
-
Silverman, D.N.1
-
62
-
-
33644989063
-
Computer simulation of proton solvation and transport in aqueous and biomolecular systems
-
Voth G.A. Computer simulation of proton solvation and transport in aqueous and biomolecular systems. Acc. Chem. Res. 39 (2006) 143-150
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 143-150
-
-
Voth, G.A.1
-
63
-
-
13444269025
-
Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II
-
Fisher Z., Hernandez Prada J.A., Tu C., Duda D., Yoshioka C., A.H., Govindasamy L., Silverman D.N., and McKenna R. Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II. Biochem. 44 (2005) 1097
-
(2005)
Biochem.
, vol.44
, pp. 1097
-
-
Fisher, Z.1
Hernandez Prada, J.A.2
Tu, C.3
Duda, D.4
Yoshioka, C.5
Govindasamy, L.6
Silverman, D.N.7
McKenna, R.8
-
64
-
-
67650513577
-
Elucidation of the proton transport mechanism in human carbonic anhydrase II
-
Maupin C.M., McKenna R., Silverman D.N., and Voth G.A. Elucidation of the proton transport mechanism in human carbonic anhydrase II. J. Am. Chem. Soc. 131 (2009) 7598-7608
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 7598-7608
-
-
Maupin, C.M.1
McKenna, R.2
Silverman, D.N.3
Voth, G.A.4
-
65
-
-
33947367836
-
Preferred orientations of His64 in human carbonic anhydrase II
-
Maupin C.M., and Voth G.A. Preferred orientations of His64 in human carbonic anhydrase II. Biochem. 46 (2007) 2938-2947
-
(2007)
Biochem.
, vol.46
, pp. 2938-2947
-
-
Maupin, C.M.1
Voth, G.A.2
-
66
-
-
33947684326
-
Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II
-
Fisher S.Z., Tu C., Bhatt D., Govindasamy L., Agbandje-McKenna M., McKenna R., and Silverman D.N. Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II. Biochem. 46 (2007) 3803-3813
-
(2007)
Biochem.
, vol.46
, pp. 3803-3813
-
-
Fisher, S.Z.1
Tu, C.2
Bhatt, D.3
Govindasamy, L.4
Agbandje-McKenna, M.5
McKenna, R.6
Silverman, D.N.7
-
67
-
-
0025946277
-
Conformational mobility of His-64 in the Thr-200 → Ser mutant of human carbonic anhydrase II
-
Krebs J.F., and Fierke C.A. Conformational mobility of His-64 in the Thr-200 → Ser mutant of human carbonic anhydrase II. Biochem. 30 (1991) 9153-9160
-
(1991)
Biochem.
, vol.30
, pp. 9153-9160
-
-
Krebs, J.F.1
Fierke, C.A.2
-
68
-
-
84962422584
-
Catalysis and specificity in enzymes: a study of triosephosphate isomerase (TIM) and comparison with methylglyoxal synthase (MGS)
-
Cui Q., and Karplus M. Catalysis and specificity in enzymes: a study of triosephosphate isomerase (TIM) and comparison with methylglyoxal synthase (MGS). Adv. Prot. Chem. 66 (2003) 315-372
-
(2003)
Adv. Prot. Chem.
, vol.66
, pp. 315-372
-
-
Cui, Q.1
Karplus, M.2
-
69
-
-
0346726109
-
How enzymes work: analysis by modern rate theory and computer simulations
-
Garcia-Viloca M., Gao J., Karplus M., and Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
-
(2004)
Science
, vol.303
, pp. 186-195
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
70
-
-
0026511656
-
The folding of an enzyme 1. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht A.R., Matouschek A., and Serrano L. The folding of an enzyme 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992) 771-782
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
71
-
-
0025763437
-
Enzyme catalysis - not different, just better
-
Knowles J.R. Enzyme catalysis - not different, just better. Nature 350 (1991) 121-124
-
(1991)
Nature
, vol.350
, pp. 121-124
-
-
Knowles, J.R.1
-
72
-
-
64849103999
-
a analysis of Glu 286 in cytochrome c oxidase (Rhodobacter sphaeroides): towards a consistent molecular model
-
a analysis of Glu 286 in cytochrome c oxidase (Rhodobacter sphaeroides): towards a consistent molecular model. Biochem. 47 (2009) 2468-2485
-
(2009)
Biochem.
, vol.47
, pp. 2468-2485
-
-
Ghosh, N.1
Prat-Resina, X.2
Gunner, M.R.3
Cui, Q.4
-
73
-
-
0036025446
-
Quantum mechanical methods for enzyme kinetics
-
Gao J., and Truhlar D.G. Quantum mechanical methods for enzyme kinetics. Annu. Rev. Phys. Chem. 53 (2002) 467
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 467
-
-
Gao, J.1
Truhlar, D.G.2
-
74
-
-
0037181354
-
Qm/mm studies of the triosephosphate isomerase (tim) catalyzed reactions: the effect of geometry and tunneling on proton transfer rate constants
-
Cui Q., and Karplus M. Qm/mm studies of the triosephosphate isomerase (tim) catalyzed reactions: the effect of geometry and tunneling on proton transfer rate constants. J. Am. Chem. Soc. 124 (2002) 3093
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 3093
-
-
Cui, Q.1
Karplus, M.2
-
76
-
-
0031567076
-
Molecular dynamics of an enzyme reaction: proton transfer in TIM
-
Neria E., and Karplus M. Molecular dynamics of an enzyme reaction: proton transfer in TIM. Chem. Phys. Lett. 267 (1997) 23-30
-
(1997)
Chem. Phys. Lett.
, vol.267
, pp. 23-30
-
-
Neria, E.1
Karplus, M.2
-
77
-
-
33748613208
-
Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions
-
Pu J.Z., Gao J.L., and Truhlar D.G. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem. Rev. 106 (2006) 3140-3169
-
(2006)
Chem. Rev.
, vol.106
, pp. 3140-3169
-
-
Pu, J.Z.1
Gao, J.L.2
Truhlar, D.G.3
|