Access the full text.
Sign up today, get DeepDyve free for 14 days.
MJ Frisch, GW Trucks, HB Schlegel, GE Scuseria, MA Robb, JR Cheeseman, VG Zakrzewski, JA Montgomery, RE Stratmann, JC Burant, S Dapprich, JM Millam, AD Daniels, KN Kudin, MC Strain, O Farkas, J Tomasi, V Barone, M Cossi, R Cammi, B Mennucci, C Pomelli, C Adamo, S Clifford, J Ochterski, GA Petersson, PY Ayala, Q Cui, K Morokuma, DK Malick, AD Rabuck, K Raghavachari, JB Foresman, J Cioslowski, JV Ortiz, BB Stefanov, G Liu, A Liashenko, P Piskorz, I Komaromi, R Gomperts, RL Martin, DJ Fox, T Keith, MA Al‐Laham, CY Peng, A Nanayakkara, C Gonzalez, M Chal‐lacombe, PMW Gill, B Johnson, W Chen, MW Wong, JL Andres, C Gonzalez, M Head‐Gordon, ES Replogle, JA Pople (1998)
Gaussian 98, Revision A
David Christianson (1991)
Structural biology of zinc.Advances in protein chemistry, 42
Wolfgang Maret, Bert Vallee (1998)
Thiolate ligands in metallothionein confer redox activity on zinc clusters.Proceedings of the National Academy of Sciences of the United States of America, 95 7
S. Wolfe, L. Nekludova, C. Pabo (2000)
DNA recognition by Cys2His2 zinc finger proteins.Annual review of biophysics and biomolecular structure, 29
N. Nandi, K. Bhattacharyya, B. Bagchi (2000)
Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems.Chemical reviews, 100 6
D. Sitkoff, K. Sharp, B. Honig (1994)
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent ModelsThe Journal of Physical Chemistry, 98
Gongyi Zhang, M. Kazanietz, P. Blumberg, J. Hurley (1995)
Crystal structure of the Cys2 activator-binding domain of protein kinase Cδ in complex with phorbol esterCell, 81
Thomas Simonson (2001)
Macromolecular electrostatics: continuum models and their growing pains.Current opinion in structural biology, 11 2
T. Simonson, Axel Bruenger (1994)
Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy AssessmentThe Journal of Physical Chemistry, 98
W. Richardson, C. Peng, D. Bashford, Louis Noodleman, D. Case (1997)
Incorporating solvation effects into density functional theory: Calculation of absolute aciditiesInternational Journal of Quantum Chemistry, 61
P. Kraulis (1991)
A program to produce both detailed and schematic plots of protein structures
C. Lim, D. Bashford, M. Karplus (1991)
Absolute pKa calculations with continuum dielectric methodsThe Journal of Physical Chemistry, 95
X. Barril, Jordi Muñoz, F. Luque, M. Orozco (2000)
Simplified descriptions of the topological distribution of hydrophilic/hydrophobic characteristics of moleculesPhysical Chemistry Chemical Physics, 2
I. Topol, A. Nemukhin, and Dobrogorskaya, S. Burt (2001)
Interactions of Azodicarbonamide (ADA) Species with the Model Zinc Finger Site: Theoretical Support of the Zinc Finger Domain Destruction in the HIV-1 Nucleocapsid Protein (NCp7) by ADAJournal of Physical Chemistry B, 105
Marjorie Harding (2001)
Geometry of metal-ligand interactions in proteins.Acta crystallographica. Section D, Biological crystallography, 57 Pt 3
A. Maynard, D. Covell (2001)
Reactivity of zinc finger cores: analysis of protein packing and electrostatic screening.Journal of the American Chemical Society, 123 6
N. Gresh, Walter Stewens, M. Krauss (1995)
Mono‐ and poly‐ligated complexes of Zn2+: An ab initio analysis of the metal–ligand interaction energyJournal of Computational Chemistry, 16
S Wolfe, L Nekludova, C Pabo (2000)
DNA recognition by Cys(2)‐His(2) zinc fingers, 29
M. Tissandier, K. Cowen, W. Feng, Ellen Gundlach, Michael Cohen, and Earhart, J. Coe, T. Tuttle (1998)
The Proton's Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster-Ion Solvation DataJournal of Physical Chemistry A, 102
M. Wong (1996)
Vibrational frequency prediction using density functional theoryChemical Physics Letters, 256
First Edition (1943)
An Introduction to Organic ChemistryNature, 152
Z. Dauter, Keith Wilson, L. Sieker, J. Moulis, Jacques Meyer, Elektronen Synchrotron (1996)
Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.Proceedings of the National Academy of Sciences of the United States of America, 93 17
J. Yazal, Yuanyuan Pang (1999)
Ab Initio Calculations of Proton Dissociation Energies of Zinc Ligands: Hypothesis of Imidazolate as Zinc Ligand in ProteinsJournal of Physical Chemistry B, 103
M. Nina, D. Beglov, B. Roux (1997)
Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy SimulationsJournal of Physical Chemistry B, 101
S. Miertus, E. Scrocco, J. Tomasi (1981)
Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects, 55
C. Zhan, D. Dixon (2001)
Absolute Hydration Free Energy of the Proton from First-Principles Electronic Structure CalculationsJournal of Physical Chemistry A, 105
Andrew Maynard, M. Huang, William Rice, David Covell (1998)
Reactivity of the HIV-1 nucleocapsid protein p7 zinc finger domains from the perspective of density-functional theory.Proceedings of the National Academy of Sciences of the United States of America, 95 20
R. Matthews, C. Goulding (1997)
Enzyme-catalyzed methyl transfers to thiols: the role of zinc.Current opinion in chemical biology, 1 3
A. Reed, L. Curtiss, F. Weinhold (1988)
Intermolecular interactions from a natural bond orbital, donor-acceptor viewpointChemical Reviews, 88
G. Tiraboschi, N. Gresh, C. Giessner-Prettre, L. Pedersen, D. Deerfield (2000)
Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligandsJournal of Computational Chemistry, 21
J. Jackman, K. Merz, C. Fierke (1996)
Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer.Biochemistry, 35 51
K. Flick, M. Jurica, R. Monnat, B. Stoddard (1998)
DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoINature, 394
P. Roehm, J. Berg (1999)
Selectivity of Methylation of Metal‐Bound Cysteinates and Its Consequences.ChemInform, 30
W Maret, B Vallee (1998)
Thiolate ligands confer redox activity on zinc clusters, 95
Mingjun Huang, A. Maynard, J. Turpin, L. Graham, G. Janini, D. Covell, William Rice (1998)
Anti-HIV agents that selectively target retroviral nucleocapsid protein zinc fingers without affecting cellular zinc finger proteins.Journal of medicinal chemistry, 41 9
J. Chen, Louis Noodleman, D. Case, D. Bashford (1994)
Incorporating solvation effects into density functional electronic structure calculationsThe Journal of Physical Chemistry, 98
S. Karlin, Z. Zhu (1997)
Classification of mononuclear zinc metal sites in protein structures.Proceedings of the National Academy of Sciences of the United States of America, 94 26
U. Ryde (1994)
The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculationsInternational Journal of Quantum Chemistry, 52
W. Hehre (1986)
AB INITIO Molecular Orbital Theory
and Dudev, C. Lim (2000)
Tetrahedral vs Octahedral Zinc Complexes with Ligands of Biological Interest: A DFT/CDM StudyJournal of the American Chemical Society, 122
H. Berman, Tammy Battistuz, T. Bhat, Wolfgang Bluhm, Philip Bourne, K. Burkhardt, Zukang Feng, G. Gilliland, L. Iype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. Westbrook, C. Zardecki
Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank
I. Alberts, K. Nadassy, S. Wodak (1998)
Analysis of zinc binding sites in protein crystal structuresProtein Science, 7
Kimber Clark-Baldwin, D. Tierney, Nandakumar Govindaswamy, E. Gruff, Chongwoo Kim, J. Berg, S. Koch, J. Penner‐Hahn (1998)
The Limitations of X-ray Absorption Spectroscopy for Determining the Structure of Zinc Sites in Proteins. When Is a Tetrathiolate Not a Tetrathiolate?Journal of the American Chemical Society, 120
D. Tannor, B. Marten, R. Murphy, R. Friesner, D. Sitkoff, A. Nicholls, B. Honig, M. Ringnalda, W. Goddard (1994)
Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric TheoryJournal of the American Chemical Society, 116
A. Becke (1993)
Density-functional thermochemistry. III. The role of exact exchangeJournal of Chemical Physics, 98
Jasna Klicic, R. Friesner, Shi-yi Liu, W. Guida (2002)
Accurate Prediction of Acidity Constants in Aqueous Solution via Density Functional Theory and Self-Consistent Reaction Field MethodsJournal of Physical Chemistry A, 106
T. Simonson, G. Archontis, M. Karplus (1999)
A POISSON-BOLTZMANN STUDY OF CHARGE INSERTION IN AN ENZYME ACTIVE SITE : THE EFFECT OF DIELECTRIC RELAXATIONJournal of Physical Chemistry B, 103
T. Dudev, C. Lim (2002)
Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study.Journal of the American Chemical Society, 124 23
I. Topol, J. Casas-Finet, R. Gussio, S. Burt, J. Erickson (1998)
A quantum-mechanical study of metal binding sites in zinc finger structuresJournal of Molecular Structure-theochem, 423
J. Åqvist, A. Warshel (1992)
Computer simulation of the initial proton transfer step in human carbonic anhydrase I.Journal of molecular biology, 224 1
Marjorie Harding (1999)
The geometry of metal-ligand interactions relevant to proteins.Acta crystallographica. Section D, Biological crystallography, 55 Pt 8
Yen Choo, Aaron Klug (1997)
Physical basis of a protein-DNA recognition code.Current opinion in structural biology, 7 1
K. Johnston, Gerald Bennett, and Balbuena, P. Rossky (1996)
Continuum Electrostatics Model for Ion Solvation and Relative Acidity of HCl in Supercritical WaterJournal of the American Chemical Society, 118
M. Orozco, F. Luque (2000)
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems.Chemical reviews, 100 11
P. Tummino, J. Scholten, P. Harvey, T. Holler, L. Maloney, R. Gogliotti, J. Domagala, D. Hupe (1996)
The in vitro ejection of zinc from human immunodeficiency virus (HIV) type 1 nucleocapsid protein by disulfide benzamides with cellular anti-HIV activity.Proceedings of the National Academy of Sciences of the United States of America, 93 3
U. Ryde (1995)
On the role of Glu‐68 in alcohol dehydrogenaseProtein Science, 4
K. Peariso, C. Goulding, Shan Huang, R. Matthews, J. Penner‐Hahn (1998)
Characterization of the Zinc Binding Site in Methionine Synthase Enzymes of Escherichia coli: The Role of Zinc in the Methylation of HomocysteineJournal of the American Chemical Society, 120
X. López, M. Schaefer, A. Dejaegere, M. Karplus (2002)
Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis.Journal of the American Chemical Society, 124 18
(1993)
3D search and research using the Cambridge Cristallogaphic Database
D McQuarrie (1975)
Statistical mechanics
Todor and, C. Lim (2001)
Modeling Zn2+-Cysteinate Complexes in ProteinsJournal of Physical Chemistry B, 105
J. Madura, J. Briggs, R. Wade, M. Davis, B. Luty, A. Ilin, J. Antosiewicz, M. Gilson, B. Bagheri, L. Scott, J. McCammon (1995)
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics programComputer Physics Communications, 91
Arald Jean-Charles, A. Nicholls, K. Sharp, B. Honig, A. Tempczyk, T. Hendrickson, W. Still (1991)
Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculationsJournal of the American Chemical Society, 113
D. Fabris, J. Zaia, Y. Hathout, C. Fenselau (1996)
Retention of Thiol Protons in Two Classes of Protein Zinc Ion Coordination CentersJournal of the American Chemical Society, 118
Alexander MacKerell, D. Bashford, M. Bellott, R. Dunbrack, J. Evanseck, M. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. Lau, C. Mattos, S. Michnick, T. Ngo, D. Nguyen, B. Prodhom, W. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, M. Karplus (1998)
All-atom empirical potential for molecular modeling and dynamics studies of proteins.The journal of physical chemistry. B, 102 18
Chengteh Lee, Weitao Yang, R. Parr (1988)
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.Physical review. B, Condensed matter, 37 2
D. Fabris, Y. Hathout, C. Fenselau (1999)
Investigation of Zinc Chelation in Zinc-Finger Arrays by Electrospray Mass Spectrometry.Inorganic chemistry, 38 6
K. Hasegawa, §. Ono, T. Noguchi (2002)
Ab initio density functional theory calculations and vibrational analysis of zinc-bound 4-methylimidazole as a model of a histidine ligand in metalloenzymesJournal of Physical Chemistry A, 106
V. Mohan, M. Davis, J. McCammon, B. Pettitt (1992)
Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributionsThe Journal of Physical Chemistry, 96
N. Gresh (1995)
Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computationsJournal of Computational Chemistry, 16
Lawrence Myers, Michael Terranova, A. Ferentz, Gerhard Wagner, G. Verdine (1993)
Repair of DNA methylphosphotriesters through a metalloactivated cysteine nucleophile.Science, 261 5125
and Archontis, T. Simonson (2001)
Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model.Journal of the American Chemical Society, 123 44
C. Cramer, D. Truhlar (1999)
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.Chemical reviews, 99 8
T. Simonson (1998)
DIELECTRIC CONSTANT OF CYTOCHROME C FROM SIMULATIONS IN A WATER DROPLET INCLUDING ALL ELECTROSTATIC INTERACTIONSJournal of the American Chemical Society, 120
B. Roux, T. Simonson (1999)
Implicit solvent models.Biophysical chemistry, 78 1-2
In zinc proteins, the Zn2+ cation frequently binds with a tetrahedral coordination to cysteine and histidine side chains, for example, in many DNA‐binding proteins, where it plays primarily a structural role. We examine the possibility of thiolate protonation in CysxHisyZn2+ groups, both in proteins and in solution, through a combination of theoretical calculations and database analysis. Seventy‐five percent of the thiolate‐coordinated zincs in the Cambridge Structural Database are tetrahedral, while di‐alkanethiol coordination always involves five or more ligands. Ab initio quantum calculations are performed on (ethanethiol/thiolate)3imidazole‐Zn2+ complexes in vacuum, yielding geometries and gas phase basicities. Protonating one (respectively two) thiolates increases the Zn‐S(thiol) distance by 0.4 Å (respectively 0.3 Å), providing a structural marker for protonation. The stabilities of the complexes in solution are compared by combining the gas phase basicities with continuum dielectric solvation calculations. In a continuum solvent with permittivity ε = 4, 20, or 80, one of three thiolates is predicted to be protonated at neutral pH. By extension, Cys4Zn2+ groups are expected to be protonated in the same conditions. In contrast, most Cys3His and Cys4 geometries in the Protein Data Bank (PDB) appear consistent with all‐thiolate Zn2+ coordination. This apparent discrepancy is resolved by two recent surveys of zinc protein structures, which suggest that these all‐thiolate sites are stabilized by charged and polar groups nearby in the protein, thus overcoming their intrinsic instability. However, the experimental resolution is not sufficient in all the PDB structures to rule out a thiol/thiolate mixture, and protonated thiolates may occur in some proteins not solved at high resolution or not represented in the PDB, as suggested by recent mass spectrometry experiments; this possibility should be allowed for in X‐ray structure refinement. Proteins 2002;49:37–48. © 2002 Wiley‐Liss, Inc.
Proteins: Structure Function and Bioinformatics – Wiley
Published: Jan 1, 2002
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.