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Nedjoua D, Krallafa AM. Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus. Comput Biol Chem 2018; 74:86-93. [PMID: 29567490 DOI: 10.1016/j.compbiolchem.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/28/2017] [Accepted: 03/07/2018] [Indexed: 11/18/2022]
Abstract
Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC.
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Affiliation(s)
- Drici Nedjoua
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
| | - Abdelghani Mohamed Krallafa
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
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2
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Affiliation(s)
- Zhuoqin Yu
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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3
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El Khoury L, Naseem-Khan S, Kwapien K, Hobaika Z, Maroun RG, Piquemal JP, Gresh N. Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions. J Comput Chem 2017; 38:1897-1920. [DOI: 10.1002/jcc.24830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/18/2017] [Accepted: 04/03/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
| | - Karolina Kwapien
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
- Institut Charles-Gerhardt, UMR 5253, CNRS-UM2-UM1-ENSM; Montpellier France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Richard G. Maroun
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
- Institut Universitaire de France; Paris Cedex 05 75231 France
- Department of Biomedical Engineering; The University of Texas at Austin; Texas 78712
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
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4
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Sponer J, Berger I, Spačková N, Leszczynski J, Hobza P. Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations. J Biomol Struct Dyn 2016; 17 Suppl 1:1-24. [PMID: 22607400 DOI: 10.1080/07391102.2000.10506597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.
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Affiliation(s)
- J Sponer
- a J. Heyrovský Institute of Physical Chemistiy, Academy of Sciences of the Czech Republic , Dolejškova 3 , 182 23 , Prague , Czech Republic
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5
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Gresh N, El Hage K, Perahia D, Piquemal JP, Berthomieu C, Berthomieu D. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters. J Comput Chem 2014; 35:2096-106. [DOI: 10.1002/jcc.23724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/09/2014] [Accepted: 08/12/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Nohad Gresh
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
| | - Krystel El Hage
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
- Unité de Biochimie, Université Saint-Joseph; Beirut Lebanon
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA); UMR 8113, Ecole Normale Supérieure France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités; UPMC, UMR7616 CNRS Paris France
| | - Catherine Berthomieu
- CEA, DSV, IBEB, Laboratoire des Interactions Protéine-Métal; Saint-Paul-lez-Durance France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale; Saint-Paul-lez-Durance France
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS-UM2-UM1-ENSCM; 8 rue de l'Ecole Normale 34296 Montpellier Cedex 5 France
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6
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Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput 2012; 8:1314-1324. [PMID: 22754403 PMCID: PMC3383645 DOI: 10.1021/ct200812y] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.
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Affiliation(s)
- Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
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Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins 2011; 79:203-20. [PMID: 21058398 DOI: 10.1002/prot.22873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926-2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K(i) value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
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8
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Synthesis and evaluation of non-hydrolyzable D-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-D-mannose as a new strong inhibitor of phosphomannose isomerases. Bioorg Med Chem 2009; 17:7100-7. [PMID: 19783448 DOI: 10.1016/j.bmc.2009.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/28/2009] [Accepted: 09/03/2009] [Indexed: 11/23/2022]
Abstract
Non-hydrolyzable d-mannose 6-phosphate analogues in which the phosphate group was replaced by a phosphonomethyl, a dicarboxymethyl, or a carboxymethyl group were synthesized and kinetically evaluated as substrate analogues acting as potential inhibitors of type I phosphomannose isomerases (PMIs) from Saccharomyces cerevisiae and Escherichia coli. While 6-deoxy-6-phosphonomethyl-d-mannose and 6-deoxy-6-carboxymethyl-D-mannose did not inhibit the enzymes significantly, 6-deoxy-6-dicarboxymethyl-D-mannose appeared as a new strong competitive inhibitor of both S. cerevisiae and E. coli PMIs with K(m)/K(i) ratios of 28 and 8, respectively. We thus report the first malonate-based inhibitor of an aldose-ketose isomerase to date. Phosphonomethyl mimics of the 1,2-cis-enediolate high-energy intermediate postulated for the isomerization reaction catalyzed by PMIs were also synthesized but behave as poor inhibitors of PMIs. A polarizable molecular mechanics (SIBFA) study was performed on the complexes of d-mannose 6-phosphate and two of its analogues with PMI from Candida albicans, an enzyme involved in yeast infection homologous to S. cerevisiae and E. coli PMIs. It shows that effective binding to the catalytic site occurs with retention of the Zn(II)-bound water molecule. Thus the binding of the hydroxyl group on C1 of the ligand to Zn(II) should be water-mediated. The kinetic study reported here also suggests the dianionic character of the phosphate surrogate as a likely essential parameter for strong binding of the inhibitor to the enzyme active site.
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9
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Monovich LG, Tommasi RA, Fujimoto RA, Blancuzzi V, Clark K, Cornell WD, Doti R, Doughty J, Fang J, Farley D, Fitt J, Ganu V, Goldberg R, Goldstein R, Lavoie S, Kulathila R, Macchia W, Parker DT, Melton R, O'Byrne E, Pastor G, Pellas T, Quadros E, Reel N, Roland DM, Sakane Y, Singh H, Skiles J, Somers J, Toscano K, Wigg A, Zhou S, Zhu L, Shieh WC, Xue S, McQuire LW. Discovery of potent, selective, and orally active carboxylic acid based inhibitors of matrix metalloproteinase-13. J Med Chem 2009; 52:3523-38. [PMID: 19422229 DOI: 10.1021/jm801394m] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The matrix metalloproteinase enzyme MMP-13 plays a key role in the degradation of type II collagen in cartilage and bone in osteoarthritis (OA). An effective MMP-13 inhibitor would therefore be a novel disease modifying therapy for the treatment of arthritis. Our efforts have resulted in the discovery of a series of carboxylic acid inhibitors of MMP-13 that do not significantly inhibit the related MMP-1 (collagenase-1) or tumor necrosis factor-alpha (TNF-alpha) converting enzyme (TACE). It has previously been suggested (but not proven) that inhibition of the latter two enzymes could lead to side effects. A promising carboxylic acid lead 9 was identified and a convergent synthesis developed. This paper describes the optimization of 9 and the identification of a compound 24f for further development. Compound 24f is a subnanomolar inhibitor of MMP-13 (IC(50) value 0.5 nM and K(i) of 0.19 nM) having no activity against MMP-1 or TACE (IC(50) of >10000 nM). Furthermore, in a rat model of MMP-13-induced cartilage degradation, 24f significantly reduced proteoglycan release following oral dosing at 30 mg/kg (75% inhibition, p < 0.05) and at 10 mg/kg (40% inhibition, p < 0.05).
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Affiliation(s)
- Lauren G Monovich
- Arthritis and Bone Metabolism Research, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
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10
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Šramko M, Garaj V, Remko M. Thermodynamics of binding of angiotensin-converting enzyme inhibitors to enzyme active site model. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Zabardasti A, Kakanejadifard A, Amani S, Salehnassaje M. Thermodynamics of Zinc(II) Complexes with N′ 1, N′ 2-Dihydroxy- N1, N2-dipyridin-2-ylethanediamidediimide in the Gas Phase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 281] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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13
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Dudev T, Lim C. Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study. J Am Chem Soc 2007; 128:10541-8. [PMID: 16895422 DOI: 10.1021/ja063111s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many of the essential metalloproteins are located in the cell, whose cytoplasmic fluid contains several small inorganic anions, such as Cl-, NO2-, NO3-, H2PO4-, and SO4(2-), that play an indispensable role in determining the cell's volume, regulating the cell's pH, signal transduction, muscle contraction, as well as cell growth and metabolism. However, the physical principles governing the competition between these abundant, intracellular anions and protein or nucleic acid residues in binding to cytoplasmic metal cations such as Na+, K+, Mg2+, and Ca2+ are not well understood; hence, we have delineated the physicochemical basis for this competition using density functional theory in conjunction with the continuum dielectric method. The results show that the metal cation can bind to its target protein against a high background concentration of inorganic anions because (i) desolvating a negatively charged Asp/Glu carboxylate in a protein cavity costs much less than desolvating an inorganic anion in aqueous solution and (ii) the metal-binding site acts as a polydentate ligand that uses all its ligating entities to bind the metal cation either directly or indirectly. The results also show that the absolute hydration free energy of the "alien" anion as well as the net charge and relative solvent exposure of the metal-binding protein cavity are the key factors governing the competition between protein and inorganic ligands for a given cytoplasmic metal cation. Increasing the net negative charge of the protein cavity, while decreasing the number of available amide groups for metal binding, protects the metal-bound ligands from being dislodged by cellular anions, thus revealing a "protective" role for carboxylate groups in a protein cavity, in addition to their role in high affinity metal-binding.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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14
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Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2007; 28:938-57. [PMID: 17253648 DOI: 10.1002/jcc.20586] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.
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Affiliation(s)
- Celine Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Université Paris-Sud XI, 15 rue Georges Clémenceau, 91405 Orsay, France
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15
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Jain T, Jayaram B. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes. Proteins 2007; 67:1167-78. [PMID: 17380508 DOI: 10.1002/prot.21332] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Zinc is one of the most important metal ions found in proteins performing specific functions associated with life processes. Coordination geometry of the zinc ion in the active site of the metalloprotein-ligand complexes poses a challenge in determining ligand binding affinities accurately in structure-based drug design. We report here an all atom force field based computational protocol for estimating rapidly the binding affinities of zinc containing metalloprotein-ligand complexes, considering electrostatics, van der Waals, hydrophobicity, and loss in conformational entropy of protein side chains upon ligand binding along with a nonbonded approach to model the interactions of the zinc ion with all the other atoms of the complex. We examined the sensitivity of the binding affinity predictions to the choice of Lennard-Jones parameters, partial atomic charges, and dielectric treatments adopted for system preparation and scoring. The highest correlation obtained was R2 = 0.77 (r = 0.88) for the predicted binding affinity against the experiment on a heterogenous dataset of 90 zinc containing metalloprotein-ligand complexes consisting of five unique protein targets. Model validation and parameter analysis studies underscore the robustness and predictive ability of the scoring function. The high correlation obtained suggests the potential applicability of the methodology in designing novel ligands for zinc-metalloproteins. The scoring function has been web enabled for free access at www.scfbio-iitd.res.in/software/drugdesign/bapplz.jsp as BAPPL-Z server (Binding Affinity Prediction of Protein-Ligand complexes containing Zinc metal ions).
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Affiliation(s)
- Tarun Jain
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
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16
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Pye CC, Corbeil CR, Rudolph WW. An ab initio investigation of zinc chloro complexes. Phys Chem Chem Phys 2006; 8:5428-36. [PMID: 17119651 DOI: 10.1039/b610084h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of geometry, frequency, and energy calculations of chloroaquazinc(II) complexes were carried out at up to the MP2/6-31+G* level. A thorough examination of all species up to and including hexacoordinate species, and with up to six chlorides, was carried out. The structures of the complexes are compared with experimental data where available. The solution chemistry of zinc(II) in the presence of chloride is discussed, and Raman spectra of zinc perchlorate with increasing amount of chloride are presented.
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Affiliation(s)
- Cory C Pye
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
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17
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Oliveira FG, Sant'Anna CMR, Caffarena ER, Dardenne LE, Barreiro EJ. Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors. Bioorg Med Chem 2006; 14:6001-11. [PMID: 16843671 DOI: 10.1016/j.bmc.2006.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 05/10/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
In the present work, several computational methodologies were combined to develop a model for the prediction of PDE4B inhibitors' activity. The adequacy of applying the ligand docking approach, keeping the enzyme rigid, to the study of a series of PDE4 inhibitors was confirmed by a previous molecular dynamics analysis of the complete enzyme. An exhaustive docking procedure was performed to identify the most probable binding modes of the ligands to the enzyme, including the active site metal ions and the surrounding structural water molecules. The enzyme-inhibitor interaction enthalpies, refined by using the semiempirical molecular orbital approach, were combined with calculated solvation free energies and entropy considerations in an empirical free energy model that enabled the calculation of binding free energies that correlated very well with experimentally derived binding free energies. Our results indicate that both the inclusion of the structural water molecules close to the ions in the binding site and the use of a free energy model with a quadratic dependency on the ligand free energy of solvation are important aspects to be considered for molecular docking investigations involving the PDE4 enzyme family.
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Affiliation(s)
- Fernanda G Oliveira
- LASSBio, Laboratório de Avaliação e Síntese de Substãncias Bioativas, Faculdade de Farmácia and Instituto de Química, Universidade Federal do Rio de Janeiro, PO Box 68006, Rio de Janeiro, RJ 21944-910, Brazil
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Antony J, Piquemal JP, Gresh N. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. J Comput Chem 2005; 26:1131-47. [PMID: 15937993 DOI: 10.1002/jcc.20245] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.
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Affiliation(s)
- Jens Antony
- Freie Universität Berlin, FB Mathematik und Informatik, Institut für Mathematik II, AG Biocomputing, Arnimallee 2-6, D-14195 Berlin, Germany
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19
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Gresh N, Piquemal JP, Krauss M. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem 2005; 26:1113-30. [PMID: 15934064 DOI: 10.1002/jcc.20244] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, FRE 2718 CNRS, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France.
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20
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Patel S, Mackerell AD, Brooks CL. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 2005; 25:1504-14. [PMID: 15224394 DOI: 10.1002/jcc.20077] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P-FQ potential. The proteins include 1FSV, 1ENH, 1PGB, 1VII, 1H8K, and 1CRN, representing both helical and beta-sheet secondary structural elements. Constant pressure and temperature (NPT) molecular dynamics simulations are performed on time scales of several nanoseconds, the longest simulations yet reported using explicitly polarizable all-atom empirical potentials (for both solvent and protein) in the condensed phase. In terms of structure, the FQ force field allows deviations from native structure up to 2.5 A (with a range of 1.0 to 2.5 A). This is commensurate to the performance of the CHARMM22 nonpolarizable model and other currently existing polarizable models. Importantly, secondary structural elements maintain native structure in general to within 1 A (both helix and beta-strands), again in good agreement with the nonpolarizable case. In qualitative agreement with QM/MM ab initio dynamics on crambin (Liu et al. Proteins 2001, 44, 484), there is a sequence dependence of average condensed phase atomic charge for all proteins, a dependence one would anticipate considering the differing chemical environments around individual atoms; this is a subtle quantum mechanical feature captured in the FQ model but absent in current state-of-the-art nonpolarizable models. Furthermore, there is a mutual polarization of solvent and protein in the condensed phase. Solvent dipole moment distributions within the first and second solvation shells around the protein display a shift towards higher dipole moments (increases on the order of 0.2-0.3 Debye) relative to the bulk; protein polarization is manifested via the enhanced condensed phase charges of typical polar atoms such as backbone carbonyl oxygens, amide nitrogens, and amide hydrogens. Finally, to enlarge the sample set of proteins, gas-phase minimizations and 1 ps constant temperature simulations are performed on various-sized proteins to compare to earlier work by Kaminsky et al. (J Comp Chem 2002, 23, 1515). The present work establishes the feasibility of applying a fully polarizable force field for protein simulations and demonstrates the approach employed in extending the CHARMM force field to include these effects.
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Affiliation(s)
- Sandeep Patel
- Department of Molecular Biology (TPC-6), The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla California 92037, USA
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21
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OHNO T, OHISA N. Studies on Textural and Chemical Changes in Aged Rice Grains. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2005. [DOI: 10.3136/fstr.11.385] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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Gresh N, Kafafi SA, Truchon JF, Salahub DR. Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study. J Comput Chem 2004; 25:823-34. [PMID: 15011254 DOI: 10.1002/jcc.20012] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, deltaE(conf), of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components of the energy and the particular impact of the polarization energy component on deltaE(conf). We perform comparisons with respect to single-point HF, DFT, LMP2, and MP2 computations done at the SIBFA-derived energy minima. Such comparisons are made first for the 10 conformers derived from phi/psi torsional angle energy-minimization (the rigid rotor approach), and, in a second step, after allowing additional relaxation of the C(alpha) centered valence angles. In both series of energy-minimization, the SIBFA deltaE(conf) compared best with the LMP2 results using the 6-311G** basis set, the rms being 1.3 kcal/mol. In the absence of the polarization component, the rms is 3.5 kcal/mol. In both series of minimizations, the magnitudes of deltaE(conf), computed as differences with respect to the most stable conformer taken as energy zero, decrease along the series: HF > DFT > LMP2 > SIBFA > MP2, indicative of increasing stabilization of the most highly folded conformers.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, FRE 2718 CNRS, Université René-Descartes, IFR Biomédicale, 45, Rue des Saints-Pères, 75006 Paris, France.
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23
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Gresh N, Shi GB. Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation. J Comput Chem 2004; 25:160-8. [PMID: 14648615 DOI: 10.1002/jcc.10312] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog-enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université René-Descartes, 4, Avenue de l'Observatoire, 75006, Paris, France.
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24
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Roux C, Lee JH, Jeffery CJ, Salmon L. Inhibition of Type I and Type II Phosphomannose Isomerases by the Reaction Intermediate Analogue 5-Phospho-d-Arabinonohydroxamic Acid Supports a Catalytic Role for the Metal Cofactor. Biochemistry 2004; 43:2926-34. [PMID: 15005628 DOI: 10.1021/bi035688h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The phosphomannose isomerases (PMI) comprise three families of proteins: type I, type II, and type III PMIs. Members of all three families catalyze the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P) but share little or no sequence identity. Because (1) PMIs are essential for the survival of several microorganisms, including yeasts and bacteria, and (2) the PMI enzymes from several pathogens do not share significant sequence identity to the human protein, PMIs have been considered as potential therapeutic targets. Elucidation of the catalytic and regulatory mechanisms of the different types of PMIs is strongly needed for rational species-specific drug design. To date, inhibition and crystallographic studies of all PMIs are still largely unexplored. As part of our research program on aldose-ketose isomerases, we report in this paper the evaluation of two new inhibitors of type I and type II PMIs from baker's yeast and Pseudomonas aeruginosa, respectively. We found that 5-phospho-D-arabinonohydroxamic acid (5PAH), which is the most potent inhibitor of phosphoglucose isomerase (PGI), is by far the best inhibitor ever reported of both type I and type II PMI-catalyzed isomerization of M6P to F6P. 5PAH, which has an inhibition constant at least 3 orders of magnitude smaller than that of previously reported PMI inhibitors, may be the first high-energy intermediate analogue inhibitor of the enzymes. We also tested the related molecule 5-phospho-D-arabinonate (5PAA), which is a strong competitive inhibitor of PGI, and found that it does not inhibit either PMI. All together, our results are consistent with a catalytic role for the metal cofactor in PMI activity.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8124, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Université Paris-Sud XI, 91405 Orsay, France
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25
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Dardenne LE, Werneck AS, de Oliveira Neto M, Bisch PM. Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair. Proteins 2003; 52:236-53. [PMID: 12833547 DOI: 10.1002/prot.10368] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25((-))...His159((+)) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG-->(His159)-ND1 direction; (ii) the electrostatic profile has a saddle-point character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E(SG-->ND1) attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator.
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Affiliation(s)
- Laurent E Dardenne
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro-UFRJ, CCS, Bloco G, Ilha do Fundão, 21949-900 Rio de Janeiro, RJ, Brazil
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26
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Gresh N, Šponer JE, Špačková N, Leszczynski J, Šponer J. Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA. J Phys Chem B 2003. [DOI: 10.1021/jp022659s] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Judit E. Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Nad'a Špačková
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jerzy Leszczynski
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jiři Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
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27
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Smiesko M, Remko M. Coordination and thermodynamics of stable Zn(II) complexes in the gas phase. J Biomol Struct Dyn 2003; 20:759-70. [PMID: 12744706 DOI: 10.1080/07391102.2003.10506893] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Ab initio molecular orbital methods in combination with DFT calculations were used to study the structural and thermodynamic properties of 17 complexes containing zinc cation and four first-shell ligands as models of active site of metalloenzymes (e.g. angiotensin converting enzyme, thermolysin). The geometry of the complexes was relaxed by complete optimization by ab initio molecular orbital methods at Hertree-Fock level with 3-21G* basis set. Following single point calculation with tight SCF criteria at the B3LYP level with 6-311+G(2d,p) basis set was used to calculate accurate interaction enthalpies. The structure and thermodynamics of optimized complexes are discussed from the point of view of their biological importance.
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Affiliation(s)
- Martin Smiesko
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia.
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28
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Burda JV, Šponer J, Hrabáková J, Zeizinger M, Leszczynski J. The Influence of N7Guanine Modifications on the Strength of Watson−Crick Base Pairing and Guanine N1Acidity: Comparison of Gas-Phase and Condensed-Phase Trends. J Phys Chem B 2003. [DOI: 10.1021/jp027850g] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Gresh N, Derreumaux P. Generating Conformations for Two Zinc-Binding Sites of HIV-1 Nucleocapsid Protein from Random Conformations by a Hierarchical Procedure and Polarizable Force Field. J Phys Chem B 2003. [DOI: 10.1021/jp022527z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire, CNRS FRE 2463 4, Avenue de l'Observatoire, 75006 Paris, France, and Information Génétique et Structurale, CNRS-UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Philippe Derreumaux
- Laboratoire de Pharmacochimie Moléculaire, CNRS FRE 2463 4, Avenue de l'Observatoire, 75006 Paris, France, and Information Génétique et Structurale, CNRS-UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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30
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Rulíšek L, Havlas Z. Theoretical Studies of Metal Ion Selectivity. 3. A Theoretical Design of the Most Specific Combinations of Functional Groups Representing Amino Acid Side Chains for the Selected Metal Ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+). J Phys Chem B 2003. [DOI: 10.1021/jp026951b] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
| | - Zdeněk Havlas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
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31
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Rulíšek L, Šponer J. Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects. J Phys Chem B 2003. [DOI: 10.1021/jp027058f] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lubomír Rulíšek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
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32
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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33
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Gresh N, Policar C, Giessner-Prettre C. Modeling Copper(I) Complexes: SIBFA Molecular Mechanics versus ab Initio Energetics and Geometrical Arrangements. J Phys Chem A 2002. [DOI: 10.1021/jp0106146] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Gresh
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Policar
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Giessner-Prettre
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
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Krauss M, Gilson HSR, Gresh N. Structure of the First-Shell Active Site in Metallolactamase: Effect of Water Ligands. J Phys Chem B 2001. [DOI: 10.1021/jp012099h] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Comparison of DFT, Møller–Plesset, and coupled cluster calculations of the proton dissociation energies of imidazole and N -methylacetamide in the presence of zinc(II). ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00405-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Tiraboschi G, Fournié-Zaluski MC, Roques BP, Gresh N. Intramolecular chelation of Zn2+by α- and β-mercaptocarboxamides. A parallelab initioand polarizable molecular mechanics investigation. Assessment of the role of multipole transferability. J Comput Chem 2001. [DOI: 10.1002/jcc.1064] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water--or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics of molecular recognition. First introduced more than 20 years ago, polarizable force fields seek to account for appropriate variations in charge distribution with dielectric environment. Over the past five years, an accelerated pace of development of such force fields has taken place on systems ranging from liquid water to metalloenzymes. Noteworthy progress has been made in better understanding the capabilities and limitations of polarizable models for water and in the formulation and utilization of complete specifically parameterized polarizable force fields for peptides and proteins.
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Affiliation(s)
- T A Halgren
- Schrödinger Inc, 1 Exchange Place, Suite 604, Jersey City, NJ 07302, USA.
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Guo H, Gresh N, Roques BP, Salahub DR. Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics. J Phys Chem B 2000. [DOI: 10.1021/jp0012247] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong Guo
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Nohad Gresh
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Bernard P. Roques
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Dennis R. Salahub
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
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El Yazal J, Roe RR, Pang YP. Zinc's Affect on Proton Transfer between Imidazole and Acetate Predicted by ab Initio Calculations. J Phys Chem B 2000. [DOI: 10.1021/jp994283x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jamal El Yazal
- Mayo Clinic Cancer Center, Tumor Biology Program, Department of Molecular Pharmacology and Experimental Therapeutics, Molecular Neuroscience Program, and Mayo Foundation for Medical Education and Research, 200 First Street SW, Rochester, Minnesota 55905
| | - Rachel R. Roe
- Mayo Clinic Cancer Center, Tumor Biology Program, Department of Molecular Pharmacology and Experimental Therapeutics, Molecular Neuroscience Program, and Mayo Foundation for Medical Education and Research, 200 First Street SW, Rochester, Minnesota 55905
| | - Yuan-Ping Pang
- Mayo Clinic Cancer Center, Tumor Biology Program, Department of Molecular Pharmacology and Experimental Therapeutics, Molecular Neuroscience Program, and Mayo Foundation for Medical Education and Research, 200 First Street SW, Rochester, Minnesota 55905
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Terp GE, Christensen IT, Jørgensen FS. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes. J Biomol Struct Dyn 2000; 17:933-46. [PMID: 10949161 DOI: 10.1080/07391102.2000.10506582] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural differences between the eight enzyme-substrate complexes were studied with particular emphasis on the active site, and possible sites for obtaining selectivity among the MMP's are discussed. Differences in the P1' pocket are well-documented and have been extensively exploited in inhibitor design. The present work indicates that selectivity could be further improved by considering the P2 pocket as well.
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Affiliation(s)
- G E Terp
- Royal Danish School of Pharmacy, Department of Medicinal Chemistry, Copenhagen, Denmark
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41
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Rogalewicz F, Ohanessian G, Gresh N. Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase:ab initio and SIBFA molecular mechanics calculations. J Comput Chem 2000. [DOI: 10.1002/1096-987x(200008)21:11<963::aid-jcc6>3.0.co;2-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tiraboschi G, Gresh N, Giessner-Prettre C, Pedersen LG, Deerfield DW. Parallelab 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 ligands. J Comput Chem 2000. [DOI: 10.1002/1096-987x(200009)21:12<1011::aid-jcc1>3.0.co;2-b] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gresh N, Šponer J. Complexes of Pentahydrated Zn2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations. J Phys Chem B 1999. [DOI: 10.1021/jp9921351] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Unité de Pharmacochimie Moléculaire et Structurale, U266 INSERM, UMR 8600 CNRS, U.F.R. des Sciences Pharmaceutiques et Biologiques, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Jırí Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Tiraboschi G, Roques BP, Gresh N. Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(199910)20:13<1379::aid-jcc5>3.0.co;2-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Gresh N, Guo H, Salahub DR, Roques BP, Kafafi SA. Critical Role of Anisotropy for the Dimerization Energies of Two Protein−Protein Recognition Motifs: cis-N-Methylacetamide versus a β-Sheet Conformer of Alanine Dipeptide. A Joint ab Initio, Density Functional Theory, and Molecular Mechanics Investigation. J Am Chem Soc 1999. [DOI: 10.1021/ja9742489] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Hong Guo
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Dennis R. Salahub
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Bernard P. Roques
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Sherif A. Kafafi
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
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Dumas F, Fressigné C, Langlet J, Giessner-Prettre C. Theoretical Investigations of the Influence of Pressure on the Selectivity of the Michael Addition of Diphenylmethaneamine to Stereogenic Crotonates. J Org Chem 1999; 64:4725-4732. [PMID: 11674545 DOI: 10.1021/jo9825308] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SIBFA (sum of interactions between fragments ab initio computed) molecular mechanics systematics has been modified to take into account the effect of pressure on intra- and intermolecular energies. The van der Waals radii are related to the pressure, using Bridgman results on the variation of crystal volume, on one hand, and the relation between the volume of an atom and its van der Waals radius on the other. This procedure produces a decrease of the volume of the systems considered. The modified systematics is used for the study of the conformation at 1 atm and 15 kbar of two stereogenic crotonates and of the complexes formed by these two molecules with the diphenylmethaneamine and the three solvent molecules present in the experiment. The results obtained show that in the case of NMECC 1a the diastereoselectivity induced by high pressure and by the presence of methanol proceeds from an important stabilization of the pro-R reactive complex in which the crotonate has a stacked-transoid conformation. This stabilization is mainly due to intermolecular interactions. In the case of the second crotonate considered, NMCC 1b, our results indicate that pressure induces a stabilization of the pro-R and pro-S complexes having the axial conformation for which the reaction exhibits little diastereoselectivity in qualitative agreement with experimental data. This study tends to show that it is possible to account theoretically for the influence of pressure on molecular conformation and/or complex structure, using a molecular mechanics method that is able to take into account the variation of volumes of the different entities present in the system studied.
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Affiliation(s)
- F. Dumas
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France, and Centre Régional Universitaire de Spectroscopie UPRESA 6014 CNRS, IRCOF, Université de Rouen, 76821 Mont St Aignan Cedex, France
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Computational Approaches to the Studies of the Interactions of Nucleic Acid Bases. COMPUTATIONAL MOLECULAR BIOLOGY 1999. [DOI: 10.1016/s1380-7323(99)80078-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gresh N, Parisel O, Giessner-Prettre C. Electronic distribution influence on molecular mechanics results. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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