201
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Kozlowski D, Pilmé J, Fleurat-Lessard P. Using the unusual weak N…CO bond as a solvation probe. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.842995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- David Kozlowski
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06 and CNRS, UMR 7616, F-75005, Paris, France
| | - Paul Fleurat-Lessard
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
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202
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Bolze CS, Helbling RE, Owen RL, Pearson AR, Pompidor G, Dworkowski F, Fuchs MR, Furrer J, Golczak M, Palczewski K, Cascella M, Stocker A. Human cellular retinaldehyde-binding protein has secondary thermal 9-cis-retinal isomerase activity. J Am Chem Soc 2013; 136:137-46. [PMID: 24328211 DOI: 10.1021/ja411366w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cellular retinaldehyde-binding protein (CRALBP) chaperones 11-cis-retinal to convert opsin receptor molecules into photosensitive retinoid pigments of the eye. We report a thermal secondary isomerase activity of CRALBP when bound to 9-cis-retinal. UV/vis and (1)H NMR spectroscopy were used to characterize the product as 9,13-dicis-retinal. The X-ray structure of the CRALBP mutant R234W:9-cis-retinal complex at 1.9 Å resolution revealed a niche in the binding pocket for 9-cis-aldehyde different from that reported for 11-cis-retinal. Combined computational, kinetic, and structural data lead us to propose an isomerization mechanism catalyzed by a network of buried waters. Our findings highlight a specific role of water molecules in both CRALBP-assisted specificity toward 9-cis-retinal and its thermal isomerase activity yielding 9,13-dicis-retinal. Kinetic data from two point mutants of CRALBP support an essential role of Glu202 as the initial proton donor in this isomerization reaction.
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Affiliation(s)
- Christin S Bolze
- Department of Chemistry and Biochemistry, and ‡Graduate School for Cellular and Biomedical Sciences, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
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203
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Doemer M, Maurer P, Campomanes P, Tavernelli I, Rothlisberger U. Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin. J Chem Theory Comput 2013; 10:412-22. [PMID: 26579920 DOI: 10.1021/ct400697n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.
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Affiliation(s)
- Manuel Doemer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Patrick Maurer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Pablo Campomanes
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ivano Tavernelli
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ursula Rothlisberger
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
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204
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Bulo RE, Michel C, Fleurat-Lessard P, Sautet P. Multiscale Modeling of Chemistry in Water: Are We There Yet? J Chem Theory Comput 2013; 9:5567-77. [PMID: 26592290 DOI: 10.1021/ct4005596] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV-vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions.
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Affiliation(s)
- Rosa E Bulo
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon , Laboratoire de Chimie, 46, allée d'Italie, 69364 Lyon cedex 07, France.,Department of Theoretical Chemistry, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Carine Michel
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon , Laboratoire de Chimie, 46, allée d'Italie, 69364 Lyon cedex 07, France
| | - Paul Fleurat-Lessard
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon , Laboratoire de Chimie, 46, allée d'Italie, 69364 Lyon cedex 07, France
| | - Philippe Sautet
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon , Laboratoire de Chimie, 46, allée d'Italie, 69364 Lyon cedex 07, France
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205
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Humbert-Droz M, Zhou X, Shedge SV, Wesolowski TA. How to choose the frozen density in Frozen-Density Embedding Theory-based numerical simulations of local excitations? Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1405-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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206
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Masuda Y, Mori Y, Sakurai K. Effects of Counterion and Solvent on Proton Location and Proton Transfer Dynamics of N–H···N Hydrogen Bond of Monoprotonated 1,8-Bis(dimethylamino)naphthalene. J Phys Chem A 2013; 117:10576-87. [DOI: 10.1021/jp4061297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuichi Masuda
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yukie Mori
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kazumi Sakurai
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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207
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Tripathi R, Nair NN. Mechanism of acyl-enzyme complex formation from the Henry-Michaelis complex of class C β-lactamases with β-lactam antibiotics. J Am Chem Soc 2013; 135:14679-90. [PMID: 24010547 DOI: 10.1021/ja405319n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria that cause most of the hospital-acquired infections make use of class C β-lactamase (CBL) among other enzymes to resist a wide spectrum of modern antibiotics and pose a major public health concern. Other than the general features, details of the defensive mechanism by CBL, leading to the hydrolysis of drug molecules, remain a matter of debate, in particular the identification of the general base and role of the active site residues and substrate. In an attempt to unravel the detailed molecular mechanism, we carried out extensive hybrid quantum mechanical/molecular mechanical Car-Parrinello molecular dynamics simulation of the reaction with the aid of the metadynamics technique. On this basis, we report here the mechanism of the formation of the acyl-enzyme complex from the Henry-Michaelis complex formed by β-lactam antibiotics and CBL. We considered two β-lactam antibiotics, namely, cephalothin and aztreonam, belonging to two different subfamilies. A general mechanism for the formation of a β-lactam antibiotic-CBL acyl-enzyme complex is elicited, and the individual roles of the active site residues and substrate are probed. The general base in the acylation step has been identified as Lys67, while Tyr150 aids the protonation of the β-lactam nitrogen through either the substrate carboxylate group or a water molecule.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , 208016 Kanpur, India
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208
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Rojas-Cervellera V, Ardèvol A, Boero M, Planas A, Rovira C. Formation of a covalent glycosyl-enzyme species in a retaining glycosyltransferase. Chemistry 2013; 19:14018-23. [PMID: 24108590 DOI: 10.1002/chem.201302898] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Indexed: 01/11/2023]
Abstract
Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped (MD=molecular dynamics; QM/MM=quantum mechanics/molecular mechanics).
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Affiliation(s)
- Víctor Rojas-Cervellera
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)
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209
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Tröster P, Lorenzen K, Schwörer M, Tavan P. Polarizable water models from mixed computational and empirical optimization. J Phys Chem B 2013; 117:9486-500. [PMID: 23844727 DOI: 10.1021/jp404548k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we suggest a mixed computational and empirical approach serving to optimize the parameters of complex and polarizable molecular mechanics (PMM) models for complicated liquids. The computational part of the parameter optimization relies on hybrid calculations combining density functional theory (DFT) for a solute molecule with a PMM treatment of its solvent environment at well-defined thermodynamic conditions. As an application we have developed PMM models for water featuring ν = 3, 4, and 5 points of force action, a Gaussian inducible dipole and a Buckingham potential at the oxygen, the experimental liquid phase geometry, the experimental gas phase polarizability α(exp)(g) = 1.47 ų, and, for ν = 4 and 5, the gas phase value μ(exp)(g) = 1.855 D for the static dipole moment. The widths of the Gaussian dipoles and, for ν = 4 and 5, also the electrostatic geometries of these so-called TLνP models are derived from self-consistent DFT/PMM calculations, and the parameters of the Buckingham potentials (and the static TL3P dipole moment) are estimated from molecular dynamics (MD) simulations. The high quality of the resulting models is demonstrated for the observables targeted during optimization (potential energy per molecule, pressure, radial distribution functions) and a series of predicted properties (quadrupole moments, density at constant pressure, dielectric constant, diffusivity, viscosity, compressibility, heat capacity) at certain standard conditions. Remaining deficiencies and possible ways for their removal are discussed.
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Affiliation(s)
- Philipp Tröster
- Lehrstuhl für Biomolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
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210
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Dreyer J, Zhang C, Ippoliti E, Carloni P. Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. J Chem Theory Comput 2013; 9:3826-31. [PMID: 26584128 DOI: 10.1021/ct400374n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The membrane potential at the water/phospholipid interfaces may play a key role for proton conduction of gramicidin A (gA). Here we address this issue by Density Functional Theory-based molecular dynamics and metadynamics simulations. The calculations, performed on gA embedded in a solvated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membrane environment (about 2,000 atoms), indicate that (i) the membrane dipole potential rises at the channel mouth by ∼0.4 V. A similar value has been measured for gA embedded in a DMPC monolayer; (ii) the calculated free energy barrier is located at the channel entrance, consistent with experiments comparing gA proton conduction in different bilayers. The electronic structures of the proton ligands (water molecules and peptide units) are similar to those in the bulk solvent. Based on these results, we suggest an important role of the membrane dipole potential for the free energy barrier of proton permeation of gA. This may provide a rationale for the large increase in the rate of proton conduction under application of a transmembrane voltage, as observed experimentally. Our calculations might suggest also a role for proton desolvation for the permeation process. This role has already emerged from EVB calculations on gA embedded in a model membrane.
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Affiliation(s)
- Jens Dreyer
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Chao Zhang
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
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211
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Penfold TJ, Karlsson S, Capano G, Lima FA, Rittmann J, Reinhard M, Rittmann-Frank MH, Braem O, Baranoff E, Abela R, Tavernelli I, Rothlisberger U, Milne CJ, Chergui M. Solvent-induced luminescence quenching: static and time-resolved X-ray absorption spectroscopy of a copper(I) phenanthroline complex. J Phys Chem A 2013; 117:4591-601. [PMID: 23617226 DOI: 10.1021/jp403751m] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) ([Cu(dmp)2](+); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photoluminescence spectra in dichloromethane and acetonitrile are also presented and show a shift to longer wavelengths for the latter, which points to a stronger stabilization of the excited complex. The fine structure features of the static and transient X-ray spectra allow an unambiguous assignment of the electronic and geometric structure of the molecule in both its ground and excited (3)MLCT states. Importantly, the transient spectra are remarkably similar for both solvents, and the spectral changes can be rationalized using the optimized ground- and excited-state structures of the complex. The proposed assignment of the lifetime shortening of the excited state in donor solvents (acetonitrile) to a metal-centered exciplex is not corroborated here. Molecular dynamics simulations confirm the lack of complexation; however, in both solvents the molecules come close to the metal but undergo rapid exchange with the bulk. The shortening of the lifetime of the title complex and nine additional related complexes can be rationalized by the decrease in the (3)MLCT energy. Deviations from this trend may be explained by means of the effects of the dihedral angle between the ligand planes, the solvent, and the (3)MLCT-(1)MLCT energy gap.
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Affiliation(s)
- T J Penfold
- Laboratoire De Spectroscopie Ultrarapide, École Polytechnique Fédérale De Lausanne, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
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212
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Timko J, Kuyucak S. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. J Chem Phys 2013. [PMID: 23206041 DOI: 10.1063/1.4768247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.
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Affiliation(s)
- Jeff Timko
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia
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213
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Rovira C. The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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214
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Curchod BFE, Rothlisberger U, Tavernelli I. Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory. Chemphyschem 2013; 14:1314-40. [DOI: 10.1002/cphc.201200941] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 11/11/2022]
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215
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Valsson O, Campomanes P, Tavernelli I, Rothlisberger U, Filippi C. Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls. J Chem Theory Comput 2013; 9:2441-54. [PMID: 26583734 DOI: 10.1021/ct3010408] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore-protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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216
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217
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Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NGJ. Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Biochemistry 2013; 52:1842-4. [PMID: 23452154 PMCID: PMC3788570 DOI: 10.1021/bi400093y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fermentation-respiration switch (FrsA) protein in Vibrio vulnificus was recently reported to catalyze the cofactor-independent decarboxylation of pyruvate. We now report quantum mechanical/molecular mechenical calculations that examine the energetics of C-C bond cleavage for a pyruvate molecule bound within the putative active site of FrsA. These calculations suggest that the barrier to C-C bond cleavage in the bound substrate is 28 kcal/mol, which is similar to that estimated for the uncatalyzed decarboxylation of pyruvate in water at 25 °C. In agreement with the theoretical predictions, no pyruvate decarboxylase activity was detected for recombinant FrsA protein that could be crystallized and structurally characterized. These results suggest that the functional annotation of FrsA as a cofactor-independent pyruvate decarboxylase is incorrect.
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Affiliation(s)
- Whitney F. Kellett
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
| | - Elizabeth Brunk
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Bijoy J. Desai
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - John A. Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
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218
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Sparta M, Shirvanyants D, Ding F, Dokholyan NV, Alexandrova AN. Hybrid dynamics simulation engine for metalloproteins. Biophys J 2013; 103:767-76. [PMID: 22947938 DOI: 10.1016/j.bpj.2012.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 06/08/2012] [Accepted: 06/18/2012] [Indexed: 11/15/2022] Open
Abstract
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.
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Affiliation(s)
- Manuel Sparta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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219
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El Nahhas A, van der Veen RM, Penfold TJ, Pham VT, Lima FA, Abela R, Blanco-Rodriguez AM, Zális̆ S, Vlc̆ek A, Tavernelli I, Rothlisberger U, Milne CJ, Chergui M. X-ray Absorption Spectroscopy of Ground and Excited Rhenium–Carbonyl–Diimine Complexes: Evidence for a Two-Center Electron Transfer. J Phys Chem A 2013; 117:361-9. [DOI: 10.1021/jp3106502] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. El Nahhas
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - R. M. van der Veen
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - T. J. Penfold
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
- École Polytechnique Fédérale
de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
- SwissFEL, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - V. T. Pham
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - F. A. Lima
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - R. Abela
- SwissFEL, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - A. M. Blanco-Rodriguez
- School of Biological and Chemical
Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - S. Zális̆
- J. Heyrovský Institute
of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolej̆skova 3, Prague, Czech Republic
| | - A. Vlc̆ek
- J. Heyrovský Institute
of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolej̆skova 3, Prague, Czech Republic
- School of Biological and Chemical
Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - I. Tavernelli
- École Polytechnique Fédérale
de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - U. Rothlisberger
- École Polytechnique Fédérale
de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - C. J. Milne
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - M. Chergui
- École Polytechnique Fédérale
de Lausanne, Laboratoire de spectroscopie ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
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220
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Murugan NA, Olsen JMH, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe. J Phys Chem Lett 2013; 4:70-77. [PMID: 26291214 DOI: 10.1021/jz3018557] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils. We study the fibril-environment-induced structural and spectral changes of THT at each binding site and compare the results to the fibril-free situation in aqueous solution. All binding sites are found to show a similar effect with respect to the conformational changes of THT; in the presence of the fibril, its molecular geometry tends to become planarized. However, depending on the dielectric nature of the specific binding site, a red shift, blue shift, or no shift in the absorption spectra of THT is predicted. Interestingly, the experimentally measured red shift in the spectra is seen only when THT binds to one of the core or surface-binding sites. It is found that the dielectric nature of the microenvironment in the fibril is strongly nonhomogeneous.
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Affiliation(s)
- N Arul Murugan
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Jógvan Magnus Haugaard Olsen
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Zilvinas Rinkevicius
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Kestutis Aidas
- §Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Sauletekio al. 9, LT-10222 Vilnius, Lithuania
| | - Hans Ågren
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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221
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Mennucci B. Modeling environment effects on spectroscopies through QM/classical models. Phys Chem Chem Phys 2013; 15:6583-94. [DOI: 10.1039/c3cp44417a] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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222
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Gonçalves MB, Dreyer J, Lupieri P, Barrera-Patiño C, Ippoliti E, Webb MR, Corrie JET, Carloni P. Structural prediction of a rhodamine-based biosensor and comparison with biophysical data. Phys Chem Chem Phys 2013; 15:2177-83. [DOI: 10.1039/c2cp42396k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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223
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Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U. Photodynamics of Lys+-Trp protein motifs: Hydrogen bonds ensure photostability. Faraday Discuss 2013; 163:189-203; discussion 243-75. [DOI: 10.1039/c3fd00037k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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224
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Weiss AKH, Hofer TS. Exploiting the capabilities of quantum chemical simulations to characterise the hydration of molecular compounds. RSC Adv 2013. [DOI: 10.1039/c2ra21873a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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225
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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226
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Selvaraj ARK, Murugan NA, Ågren H. Solvent Polarity-Induced Conformational Unlocking of Asparagine. J Phys Chem A 2012; 116:11702-8. [DOI: 10.1021/jp307715n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ananda Rama Krishnan Selvaraj
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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227
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Sieffert N, Bühl M, Gaigeot MP, Morrison CA. Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations. J Chem Theory Comput 2012; 9:106-18. [DOI: 10.1021/ct300784x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nicolas Sieffert
- Université Joseph Fourier Grenoble I, CNRS UMR-5250 Département de Chimie Moléculaire, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Michael Bühl
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Marie-Pierre Gaigeot
- Université d’Evry val d’Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Carole A. Morrison
- EaStCHEM School of Chemistry, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh, EH9 3JJ, United Kingdom
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228
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Tanzi L, Ramondo F, Guidoni L. Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation. J Phys Chem A 2012; 116:10160-71. [DOI: 10.1021/jp3045059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luana Tanzi
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Fabio Ramondo
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical
and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100
L’Aquila, Italy
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229
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Thompson AJ, Dabin J, Iglesias-Fernández J, Ardèvol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ. The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew Chem Int Ed Engl 2012; 51:10997-1001. [DOI: 10.1002/anie.201205338] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/10/2022]
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230
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Thompson AJ, Dabin J, Iglesias-Fernández J, Ardèvol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ. The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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231
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Penfold TJ, Milne CJ, Tavernelli I, Chergui M. Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies. PURE APPL CHEM 2012. [DOI: 10.1351/pac-con-12-04-02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.
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Affiliation(s)
- Thomas J. Penfold
- 1Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - Christopher J. Milne
- 2Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- 1Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie et Biochimie Computationnelles, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
| | - Majed Chergui
- 2Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, Switzerland
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232
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Phatak P, Sumner I, Iyengar SS. Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events. J Phys Chem B 2012; 116:10145-64. [PMID: 22838384 PMCID: PMC3558621 DOI: 10.1021/jp3015047] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process.
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Affiliation(s)
- Prasad Phatak
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
| | - Isaiah Sumner
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN-47405
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233
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Ribas-Arino J, Marx D. Covalent mechanochemistry: theoretical concepts and computational tools with applications to molecular nanomechanics. Chem Rev 2012; 112:5412-87. [PMID: 22909336 DOI: 10.1021/cr200399q] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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234
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Bankura A, Chandra A. Hydroxide ion can move faster than an excess proton through one-dimensional water chains in hydrophobic narrow pores. J Phys Chem B 2012; 116:9744-57. [PMID: 22793519 DOI: 10.1021/jp301466e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon nanotubes (CNT) are known to provide a hydrophobic, confined environment for water where its structure and dynamics can be very different from those of bulk water. In particular, narrow CNTs of the type (6,6) allow only a single one-dimensional (1D) chain of water molecules inside them, thus providing an idealized scenario to study motion in 1D along water chains. In the present study, we have investigated structural and dynamic behavior of water and also of an excess proton and hydroxide ion in water-filled narrow CNTs by means of ab initio molecular dynamics and combined quantum-classical simulations. The main focus of the present work is on the molecular mechanism and kinetics of hydronium and hydroxide ion migration along 1D water chains of different lengths in confinement. It is found that the hydrogen-bonded structures of water and the excess proton and hydroxide ion in CNTs can be very different from those in bulk, and these altered solvation structures play critical roles in determining the proton-transfer (PT) rates along water chains. For the present 1D chain systems, the hydroxide ion is found to migrate at a slightly faster rate than the excess proton, unlike their relative mobilities in bulk water. This faster migration of the hydroxide ion is found not only in CNTs with periodicity along the tube axis but also in isolated CNTs where the excess proton and the hydroxide ion are allowed to move under the influence of an electric field of an oppositely charged ion. The roles of rotational jumps and hydrogen-bond fluctuations in the PT events are discussed. In addition, the significance of hydrogen-bonding defects on the dynamics of an excess proton and hydroxide ion is also discussed for varying chain lengths.
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Affiliation(s)
- Arindam Bankura
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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235
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: Application to zwitterionic glycine in aqueous solution. J Chem Phys 2012; 137:024501. [DOI: 10.1063/1.4732307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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236
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Silva DL, Murugan NA, Kongsted J, Rinkevicius Z, Canuto S, Ågren H. The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution. J Phys Chem B 2012; 116:8169-81. [PMID: 22694126 DOI: 10.1021/jp3032034] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.
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Affiliation(s)
- Daniel L Silva
- Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05314-970 São Paulo, SP, Brazil.
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237
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Nguyen TH, Arnesano F, Scintilla S, Rossetti G, Ippoliti E, Carloni P, Natile G. Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. J Chem Theory Comput 2012; 8:2912-20. [DOI: 10.1021/ct300167m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Trung Hai Nguyen
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Fabio Arnesano
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Simone Scintilla
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Statistical and Biological Physics Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,
I-34136 Trieste, Italy
| | - Giovanni Natile
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
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238
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Brunk E, Arey JS, Rothlisberger U. Role of environment for catalysis of the DNA repair enzyme MutY. J Am Chem Soc 2012; 134:8608-16. [PMID: 22537339 DOI: 10.1021/ja301714j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. Our findings suggest that the entire reaction is an energetically neutral process, in which the first step is rate determining, requiring protonation of adenine (N(7)) to initiate cleavage, and the second step is strongly exothermic, involving hydrolysis of an oxacarbenium ion intermediate. Although water molecules are catalytically active in both steps, the first step requires an entirely different level of solvent organization compared to the second. Needed to secure protonation at N(7), a long-term solvation pattern is established which facilitates the involvement of three out of the five structured water molecules in the active site. This persistent arrangement coordinates the catalytically active water molecules into prime positions to assist the proton transfer: (i) a water molecule frequently bridges the catalytic residues and (ii) the bridging water molecule is assisted by 1-2 other 'supporting' water molecules. To maintain this configuration, MutY, surprisingly, uses hydrophobic residues in combination with hydrophilic residues to tune the microenvironment into a 'water trap'. Hydrophilic residues prolong solvent residence times by maintaining hydrogen-bonding networks, whereas the hydrophobic residues constrain the positioning of the catalytic water molecules that assist the proton-transfer event. In this way, the enzyme uses both entropic and enthalpic considerations to guide the water-assisted reaction.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, Switzerland
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239
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Biological applications of hybrid quantum mechanics/molecular mechanics calculation. J Biomed Biotechnol 2012; 2012:236157. [PMID: 22536015 PMCID: PMC3321478 DOI: 10.1155/2012/236157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 10/27/2011] [Accepted: 11/11/2011] [Indexed: 12/17/2022] Open
Abstract
Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs) and molecular mechanics (MMs) calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD) simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the misaminoacylated tRNA(Leu), and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.
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240
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Fritsch S, Poblete S, Junghans C, Ciccotti G, Delle Site L, Kremer K. Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. PHYSICAL REVIEW LETTERS 2012; 108:170602. [PMID: 22680848 DOI: 10.1103/physrevlett.108.170602] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Indexed: 05/04/2023]
Abstract
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.
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Affiliation(s)
- S Fritsch
- Max Planck Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany
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241
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Abolfath RM, Biswas PK, Rajnarayanam R, Brabec T, Kodym R, Papiez L. Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution. J Phys Chem A 2012; 116:3940-5. [PMID: 22397677 PMCID: PMC3356683 DOI: 10.1021/jp300258n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here.
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Affiliation(s)
- Ramin M Abolfath
- School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, Texas 75080, USA.
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242
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Tripathi R, Nair NN. Thermodynamic and Kinetic Stabilities of Active Site Protonation States of Class C β-Lactamase. J Phys Chem B 2012; 116:4741-53. [DOI: 10.1021/jp212186q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
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243
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The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics. Arch Biochem Biophys 2012; 525:121-30. [PMID: 22516655 DOI: 10.1016/j.abb.2012.04.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/31/2012] [Accepted: 04/04/2012] [Indexed: 11/21/2022]
Abstract
Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide to water and oxygen (2H(2)O(2) → 2H(2)O+O(2)) with high efficiency. The enzyme is first oxidized to a high-valent iron intermediate, known as Compound I (Cpd I, Por(·+)-Fe(IV)=O) which, at difference from other hydroperoxidases, is reduced back to the resting state by further reacting with H(2)O(2). The normal catalase activity is reduced if Cpd I is consumed in a competing side reaction, forming a species named Cpd I*. In recent years, Density Functional Theory (DFT) methods have unraveled the electronic configuration of these high-valent iron species, helping to assign the intermediates trapped in the crystal structures of oxidized catalases. It has been demonstrated that the a priori assumption that the H(+)/H(-) type of mechanism for Cpd I reduction leads to the generation of singlet oxygen is not justified. Moreover, it has been shown by ab initio metadynamics simulations that two pathways are operative for Cpd I reduction: a His-mediated mechanism (described as H·/H(+) + e(-)) in which the distal His acts as an acid-base catalyst and a direct mechanism (described as H·/H·) in which the distal His does not play a direct role. Independently of the mechanism, the reaction proceeds by two one-electron transfers rather than one two-electron transfer, as previously assumed. Electron transfer to Cpd I, regardless of whether the electron is exogenous or endogenous, facilitates protonation of the oxoferryl group, to the point that formation of Cpd I* may be controlled by the easiness of protonation of reduced Cpd I.
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244
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Lorenzen K, Schwörer M, Tröster P, Mates S, Tavan P. Optimizing the Accuracy and Efficiency of Fast Hierarchical Multipole Expansions for MD Simulations. J Chem Theory Comput 2012; 8:3628-36. [PMID: 26593008 DOI: 10.1021/ct300080n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Based on p'th order Cartesian Taylor expansions of Coulomb interactions and on hierarchical decompositions of macromolecular simulation systems into hierarchies of nested, structure-adapted, and adaptively formed clusters of increasing size, fast multipole methods are constructed for rapid and accurate calculations of electrostatic interactions. These so-called SAMMp algorithms are formulated through totally symmetric and traceless tensors describing the multipole moments and the coefficients of local Taylor expansions. Simple recursions for the efficient evaluation and shifting of multipole moments are given. The required tensors are explicitly given up to order p = 4. The SAMMp algorithms are shown to guarantee the reaction principle. For systems with periodic boundaries, a reaction field (RF) correction is applied, which introduces at distances beyond the "minimum image convention" boundary a dielectric continuum surrounding each cluster at the top level of coarse graining. The correctness of the present SAMMp implementation is demonstrated by analyzing the scaling of the residuals and by checking the numerical accuracy of the reaction principle for a pair of distant molecular ions in vacuum. Molecular dynamics simulations of pure water and aqueous solutions containing artificial ions, which are enclosed by periodic boundaries, demonstrate the stability and low-noise behavior of SAMMp/RF.
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Affiliation(s)
- Konstantin Lorenzen
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität , Oettingenstrasse 67, 80538 München, Germany
| | - Magnus Schwörer
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität , Oettingenstrasse 67, 80538 München, Germany
| | - Philipp Tröster
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität , Oettingenstrasse 67, 80538 München, Germany
| | - Simon Mates
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität , Oettingenstrasse 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität , Oettingenstrasse 67, 80538 München, Germany
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245
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Wigginton KR, Menin L, Sigstam T, Gannon G, Cascella M, Hamidane HB, Tsybin YO, Waridel P, Kohn T. UV radiation induces genome-mediated, site-specific cleavage in viral proteins. Chembiochem 2012; 13:837-45. [PMID: 22416020 DOI: 10.1002/cbic.201100601] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Indexed: 11/07/2022]
Abstract
Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes site-specific virus protein cleavage upon UV irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and protein damage was characterized with ESI- and MALDI-based FT-ICR, Orbitrap, and TOF mass spectroscopy. Top-down mass spectrometry of the products identified the backbone cleavage site as Cys46-Ser47 in the virus capsid protein, a location of viral genome-protein interaction. The presence of viral RNA was essential to inducing backbone cleavage. The similar bacteriophage GA did not exhibit site-specific protein cleavage. Based on the major protein fragments identified by accurate mass analysis, a cleavage mechanism is proposed by radical formation. The mechanism involves initial oxidation of the Cys46 side chain followed by hydrogen atom abstraction from Ser47 C(α). Computational protein QM/MM studies confirmed the initial steps of the radical mechanism. Collectively, this study describes a rare incidence of genome-induced protein cleavage without the addition of sensitizers.
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Affiliation(s)
- Krista Rule Wigginton
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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246
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Ferrer S, Ruiz-Pernía J, Martí S, Moliner V, Tuñón I, Bertrán J, Andrés J. Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 85:81-142. [PMID: 21920322 DOI: 10.1016/b978-0-12-386485-7.00003-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic active site can be optimized to improve the transition state analogues (TSA) and to enhance the catalytic activity, even improve the active site to favor a desired direction of some promiscuous enzymes. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are described. The interplay between enzyme design, molecular simulations, and experiments will be presented to emphasize the interdisciplinary nature of this research field. This text highlights the recent advances and examples selected from our laboratory are shown, of how the applications of these tools are a first attempt to de novo design of protein active sites. Identification of neutral/advantageous/deleterious mutation platforms can be exploited to penetrate some of Nature's closely guarded secrets of chemical reactivity. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. The first part describes briefly how the molecular modeling is carried out. Then, we discuss the requirements of hybrid quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) simulations, analyzing what are the basis of these theoretical methodologies, how we can use them with a view to its application in the study of enzyme catalysis, and what are the best methodologies for assessing its catalytic potential. In the second part, we focus on some selected examples, taking as a common guide the chorismate to prephenate rearrangement, studying the corresponding molecular mechanism in vacuo, in solution and in an enzyme environment. In addition, examples involving catalytic antibodies (CAs) and promiscuous enzymes will be presented. Finally, a special emphasis is made to provide some hints about the logical evolution that can be anticipated in this research field. Moreover, it helps in understanding the open directions in this area of knowledge and highlights the importance of computational approaches in discovering specific drugs and the impact on the rational design of tailor-made enzymes.
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Affiliation(s)
- Silvia Ferrer
- Departamento de Química Física y Analítica, Universitat Jaume I, Castellón, Spain
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247
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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248
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Vargiu AV, Magistrato A. Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study. Inorg Chem 2012; 51:2046-57. [DOI: 10.1021/ic201659v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Attilio V. Vargiu
- CNR-IOM, Unità Operativa
di Supporto SLACS, c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato,
Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos,
National
Simulation Center, c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste,
Italy
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249
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Garrec J, Patel C, Rothlisberger U, Dumont E. Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations. J Am Chem Soc 2012; 134:2111-9. [DOI: 10.1021/ja2084042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Chandan Patel
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
| | - Ursula Rothlisberger
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Elise Dumont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
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250
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Bucher D, Sandala GM, Durbeej B, Radom L, Smith DM. The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions. J Am Chem Soc 2012; 134:1591-9. [DOI: 10.1021/ja207809b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Bucher
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Bo Durbeej
- Division of Computational
Physics, IFM Theory and Modelling, Linköping University, SE-581 83 Linköping, Sweden
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Computer-Chemie-Centrum, University of Erlangen-Nürnberg, 91052 Erlangen, Germany
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