251
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Istrate AN, Tsvetkov PO, Mantsyzov AB, Kulikova AA, Kozin SA, Makarov AA, Polshakov VI. NMR solution structure of rat aβ(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease. Biophys J 2012; 102:136-43. [PMID: 22225807 DOI: 10.1016/j.bpj.2011.11.4006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/15/2011] [Accepted: 11/23/2011] [Indexed: 11/26/2022] Open
Abstract
In an attempt to reveal the mechanism of rats' resistance to Alzheimer's disease, we determined the structure of the metal-binding domain 1-16 of rat β-amyloid (rat Aβ(1-16)) in solution in the absence and presence of zinc ions. A zinc-induced dimerization of the domain was detected. The zinc coordination site was found to involve residues His-6 and His-14 of both peptide chains. We used experimental restraints obtained from analyses of NMR and isothermal titration calorimetry data to perform structure calculations. The calculations employed an explicit water environment and a simulated annealing molecular-dynamics protocol followed by quantum-mechanical/molecular-mechanical optimization. We found that the C-tails of the two polypeptide chains of the rat Aβ(1-16) dimer are oriented in opposite directions to each other, which hinders the assembly of rat Aβ dimers into oligomeric aggregates. Thus, the differences in the structure of zinc-binding sites of human and rat Aβ(1-16), their ability to form regular cross-monomer bonds, and the orientation of their hydrophobic C-tails could be responsible for the resistance of rats to Alzheimer's disease.
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Affiliation(s)
- Andrey N Istrate
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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252
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Penfold TJ, Curchod BFE, Tavernelli I, Abela R, Rothlisberger U, Chergui M. Simulations of X-ray absorption spectra: the effect of the solvent. Phys Chem Chem Phys 2012; 14:9444-50. [DOI: 10.1039/c2cp24080g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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253
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The increasing role of QM/MM in drug discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:337-62. [PMID: 22607760 DOI: 10.1016/b978-0-12-398312-1.00011-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Since its first appearance in 1976, the quantum mechanics/molecular mechanics (QM/MM) approach has mostly been used to study the chemical reactions of enzymes, which are frequently the target of drug discovery programs. In principle, a detailed understanding of the enzymatic mechanism should help researchers to design a potent enzyme inhibitor or new drug. However, QM/MM has not yet had a widespread impact on structure-based drug design. This is mostly due to its high computational cost. We expect this to change with the recent and extraordinary increases in computational power, and with the availability of more efficient algorithms for QM/MM calculations. Here, we report on some representative examples of QM/MM studies, including our own research, of pharmaceutically relevant enzymes, such as ribonuclease H and fatty acid amide hydrolase (FAAH). We aim to show how QM/MM has traditionally been used to study enzymatic catalysis. In this regard, we discuss its potential to become a routinely used drug design tool. To support this, we also discuss selected computational studies where QM/MM insights have been helpful in improving the potency of covalent inhibitors of FAAH.
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254
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Sousa SF, Fernandes PA, Ramos MJ. Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers. Phys Chem Chem Phys 2012; 14:12431-41. [DOI: 10.1039/c2cp41180f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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255
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Selvaraj S, Arul Murugan N, Ågren H. Al3+ induced planarization, conformational arrest and metallochromic shift in a pyrimidine dione dye: insight from integrated hybrid quantum–classical calculations. Phys Chem Chem Phys 2012; 14:2339-45. [DOI: 10.1039/c2cp23238c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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256
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Fox SJ, Pittock C, Fox T, Tautermann CS, Malcolm N, Skylaris CK. Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules. J Chem Phys 2011; 135:224107. [DOI: 10.1063/1.3665893] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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257
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Ihrig AC, Schiffmann C, Sebastiani D. Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups. J Chem Phys 2011; 135:214107. [DOI: 10.1063/1.3664300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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258
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Filippi C, Buda F, Guidoni L, Sinicropi A. Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches. J Chem Theory Comput 2011; 8:112-24. [PMID: 26592874 DOI: 10.1021/ct200704k] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore-protein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore.
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Affiliation(s)
- Claudia Filippi
- Faculty of Science and Technology and MESA+ Institute of Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Leonardo Guidoni
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universitá dell'Aquila, Via Campo di Pile, 67100 L'Aquila, Italy
| | - Adalgisa Sinicropi
- Dipartimento di Chimica, Universitá di Siena, Via A. De Gasperi 2, 53100 Siena, Italy
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259
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Biarnés X, Ardèvol A, Iglesias-Fernández J, Planas A, Rovira C. Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State. J Am Chem Soc 2011; 133:20301-9. [DOI: 10.1021/ja207113e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Carme Rovira
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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260
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Bernstein N, Várnai C, Solt I, Winfield SA, Payne MC, Simon I, Fuxreiter M, Csányi G. QM/MM simulation of liquid water with an adaptive quantum region. Phys Chem Chem Phys 2011; 14:646-56. [PMID: 22089416 DOI: 10.1039/c1cp22600b] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.
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Affiliation(s)
- Noam Bernstein
- Center for Computational Materials Science, Naval Research Laboratory, Washington, DC 20375, USA.
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261
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Cannuccia E, Pulci O, Sole RD, Cascella M. Optical properties of flavin mononucleotide: A QM/MM study of protein environment effects. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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262
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Tavernelli I, Curchod BF, Rothlisberger U. Nonadiabatic molecular dynamics with solvent effects: A LR-TDDFT QM/MM study of ruthenium (II) tris (bipyridine) in water. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.03.021] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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263
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Boero M. LeuRS Synthetase: A First-Principles Investigation of the Water-Mediated Editing Reaction. J Phys Chem B 2011; 115:12276-86. [DOI: 10.1021/jp2070024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-UDS, 23 rue du Loess, BP 43, F-67034 Strasbourg, France
- Research Center for Integrated Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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264
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Vassiliev S, Mahboob A, Bruce D. Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes. PHOTOSYNTHESIS RESEARCH 2011; 110:25-38. [PMID: 21964859 DOI: 10.1007/s11120-011-9689-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 09/15/2011] [Indexed: 05/26/2023]
Abstract
The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or "site." Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment-proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment-protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna-Mathews-Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.
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Affiliation(s)
- Serguei Vassiliev
- Department of Biology, Brock University, 500 Glenridge Avenue, St. Catharines, ON L2S 3A1, Canada.
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265
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Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U. Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng 2011; 109:572-82. [PMID: 21928337 DOI: 10.1002/bit.23334] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/23/2011] [Accepted: 09/06/2011] [Indexed: 11/07/2022]
Abstract
Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target compounds with high yields and turnover rates. We use integrated computational methods to generate and quantify the performance of novel biosynthetic routes that contain highly optimized catalysts. Engineering a novel reaction pathway entails addressing feasibility on multiple levels, which involves handling the complexity of large-scale biochemical networks while respecting the critical chemical phenomena at the atomistic scale. To pursue this multi-layer challenge, our strategy merges knowledge-based metabolic engineering methods with computational chemistry methods. By bridging multiple disciplines, we provide an integral computational framework that could accelerate the discovery and implementation of novel biosynthetic production routes. Using this approach, we have identified and optimized a novel biosynthetic route for the production of 3HP from pyruvate.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory of Computational Chemistry and Biochemistry, EPFL, CH-1015 Lausanne, Switzerland
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266
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Ardèvol A, Rovira C. The Molecular Mechanism of Enzymatic Glycosyl Transfer with Retention of Configuration: Evidence for a Short-Lived Oxocarbenium-Like Species. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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267
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Ardèvol A, Rovira C. The Molecular Mechanism of Enzymatic Glycosyl Transfer with Retention of Configuration: Evidence for a Short-Lived Oxocarbenium-Like Species. Angew Chem Int Ed Engl 2011; 50:10897-901. [DOI: 10.1002/anie.201104623] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Indexed: 11/10/2022]
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268
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Bovi D, Mezzetti A, Vuilleumier R, Gaigeot MP, Chazallon B, Spezia R, Guidoni L. Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin. Phys Chem Chem Phys 2011; 13:20954-64. [PMID: 21946923 DOI: 10.1039/c1cp21985e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.
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Affiliation(s)
- Daniele Bovi
- Dipartimento di Fisica, Università di Roma LA SAPIENZA, Rome, Italy
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269
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Machado MR, Dans PD, Pantano S. A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Phys Chem Chem Phys 2011; 13:18134-44. [PMID: 21927740 DOI: 10.1039/c1cp21248f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.
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270
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Rieff B, Bauer S, Mathias G, Tavan P. DFT/MM description of flavin IR spectra in BLUF domains. J Phys Chem B 2011; 115:11239-53. [PMID: 21888341 DOI: 10.1021/jp2043637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A class of photoreceptors occurring in various organisms consists of domains that are blue light sensing using flavin (BLUF). The vibrational spectra of the flavin chromophore are spectroscopically well characterized for the dark-adapted resting states and for the light-adapted signaling states of BLUF domains in solution. Here we present a theoretical analysis of such spectra by applying density functional theory (DFT) to the flavin embedded in molecular mechanics (MM) models of its protein and solvent environment. By DFT/MM we calculate flavin spectra for seven different X-ray and NMR structures of BLUF domains occurring in the transcriptional antirepressor AppA and in the blue light receptor B (BlrB) of the purple bacterium Rb. Sphaeroides as well as in the phototaxis photoreceptor Slr1694 of the cyanobacterium Synechocystis. By considering the dynamical stabilities of associated all-atom simulation models and by comparing calculated with observed vibrational spectra, we show that two of the considered structures (both AppA) are obviously erroneous and that specific features of two further crystal structures (BlrB and Slr1694) cannot represent the states of the respective BLUF domains in solution. Thereby, the conformational transitions elicited by solvation are identified. In this context we demonstrate how hydrogen bonds of varying strengths can tune in BLUF domains the C═O stretching frequencies of the flavin chromophore. Furthermore we show that the DFT/MM spectra of the flavin calculated for two different AppA BLUF conformations, which are called Trp(in) and Met(in), fit very well to the spectroscopic data observed for the dark and light states, respectively, if (i) polarized MM force fields, which are calculated by an iterative DFT/MM procedure, are employed for the flavin binding pockets and (ii) the calculated frequencies are properly scaled. Although the associated analysis indicates that the Trp(in) conformation belongs to the dark state, no clear light vs dark distinction emerges for the Met(in) conformation. In this connection, a number of methodological issues relevant for such complex computations are thoroughly discussed showing, in particular, why our current descriptions could not decide the light vs dark question for Met(in).
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Affiliation(s)
- Benjamin Rieff
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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271
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Rinkevicius Z, Murugan NA, Kongsted J, Frecuş B, Steindal AH, Ågren H. Density Functional Restricted–Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution. J Chem Theory Comput 2011; 7:3261-71. [DOI: 10.1021/ct2003572] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish e-Science Research Center (SeRC), Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Bogdan Frecuş
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Arnfinn Hykkerud Steindal
- Centre of Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Hans Ågren
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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272
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Liang X, Montoya A, Haynes BS. Local Site Selectivity and Conformational Structures in the Glycosidic Bond Scission of Cellobiose. J Phys Chem B 2011; 115:10682-91. [DOI: 10.1021/jp204199h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao Liang
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alejandro Montoya
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Brian S. Haynes
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
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273
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Fradelos G, Wesołowski TA. Importance of the Intermolecular Pauli Repulsion in Embedding Calculations for Molecular Properties: The Case of Excitation Energies for a Chromophore in Hydrogen-Bonded Environments. J Phys Chem A 2011; 115:10018-26. [DOI: 10.1021/jp203192g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgios Fradelos
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Tomasz A. Wesołowski
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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274
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Pham VT, Penfold TJ, van der Veen RM, Lima F, El Nahhas A, Johnson SL, Beaud P, Abela R, Bressler C, Tavernelli I, Milne CJ, Chergui M. Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution. J Am Chem Soc 2011; 133:12740-8. [DOI: 10.1021/ja203882y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Van-Thai Pham
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas J. Penfold
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie Et Biochimie Computationnelles, ISIC-FSB, CH-1015 Lausanne, Switzerland
| | - Renske M. van der Veen
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Frederico Lima
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Amal El Nahhas
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Steve L. Johnson
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Paul Beaud
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Rafael Abela
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Christian Bressler
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie Et Biochimie Computationnelles, ISIC-FSB, CH-1015 Lausanne, Switzerland
| | - Christopher J. Milne
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
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275
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Parker LJ, Italiano LC, Morton CJ, Hancock NC, Ascher DB, Aitken JB, Harris HH, Campomanes P, Rothlisberger U, De Luca A, Lo Bello M, Ang WH, Dyson PJ, Parker MW. Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation. Chemistry 2011; 17:7806-16. [PMID: 21681839 DOI: 10.1002/chem.201100586] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Indexed: 11/08/2022]
Abstract
Platinum-based cancer drugs, such as cisplatin, are highly effective chemotherapeutic agents used extensively for the treatment of solid tumors. However, their effectiveness is limited by drug resistance, which, in some cancers, has been associated with an overexpression of pi class glutathione S-transferase (GST P1-1), an important enzyme in the mercapturic acid detoxification pathway. Ethacraplatin (EA-CPT), a trans-Pt(IV) carboxylate complex containing ethacrynate ligands, was designed as a platinum cancer metallodrug that could also target cytosolic GST enzymes. We previously reported that EA-CPT was an excellent inhibitor of GST activity in live mammalian cells compared to either cisplatin or ethacrynic acid. In order to understand the nature of the drug-protein interactions between EA-CPT and GST P1-1, and to obtain mechanistic insights at a molecular level, structural and biochemical investigations were carried out, supported by molecular modeling analysis using quantum mechanical/molecular mechanical methods. The results suggest that EA-CPT preferentially docks at the dimer interface at GST P1-1 and subsequent interaction with the enzyme resulted in docking of the ethacrynate ligands at both active sites (in the H-sites), with the Pt moiety remaining bound at the dimer interface. The activation of the inhibitor by its target enzyme and covalent binding accounts for the strong and irreversible inhibition of enzymatic activity by the platinum complex.
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Affiliation(s)
- Lorien J Parker
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia
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276
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Liang X, Montoya A, Haynes BS. Molecular Dynamics Study of Acid-Catalyzed Hydrolysis of Dimethyl Ether in Aqueous Solution. J Phys Chem B 2011; 115:8199-206. [DOI: 10.1021/jp201951a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiao Liang
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alejandro Montoya
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Brian S. Haynes
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
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277
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Hratchian HP, Frisch MJ. Integrating steepest-descent reaction pathways for large molecules. J Chem Phys 2011; 134:204103. [DOI: 10.1063/1.3593456] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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278
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Cui G, Yang W. Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method. J Chem Phys 2011; 134:204115. [PMID: 21639432 PMCID: PMC3124537 DOI: 10.1063/1.3593390] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/04/2011] [Indexed: 11/14/2022] Open
Abstract
The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- and medium-size molecules in gas phase has currently become a routine optimization process, as it has been implemented in many electronic structure packages. However, optimization of conical intersections of small- and medium-size molecules in solution or macromolecules remains inefficient, even poorly defined, due to large number of degrees of freedom and costly evaluations of gradient difference and nonadiabatic coupling vectors. In this work, based on the sequential quantum mechanics and molecular mechanics (QM/MM) and QM/MM-minimum free energy path methods, we have designed two conical intersection optimization methods for small- and medium-size molecules in solution or macromolecules. The first one is sequential QM conical intersection optimization and MM minimization for potential energy surfaces; the second one is sequential QM conical intersection optimization and MM sampling for potential of mean force surfaces, i.e., free energy surfaces. In such methods, the region where electronic structures change remarkably is placed into the QM subsystem, while the rest of the system is placed into the MM subsystem; thus, dimensionalities of gradient difference and nonadiabatic coupling vectors are decreased due to the relatively small QM subsystem. Furthermore, in comparison with the concurrent optimization scheme, sequential QM conical intersection optimization and MM minimization or sampling reduce the number of evaluations of gradient difference and nonadiabatic coupling vectors because these vectors need to be calculated only when the QM subsystem moves, independent of the MM minimization or sampling. Taken together, costly evaluations of gradient difference and nonadiabatic coupling vectors in solution or macromolecules can be reduced significantly. Test optimizations of conical intersections of cyclopropanone and acetaldehyde in aqueous solution have been carried out successfully.
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Affiliation(s)
- Ganglong Cui
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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279
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Kumar N, Alfonso-Prieto M, Rovira C, Lodowski P, Jaworska M, Kozlowski PM. Role of the Axial Base in the Modulation of the Cob(I)alamin Electronic Properties: Insight from QM/MM, DFT, and CASSCF Calculations. J Chem Theory Comput 2011; 7:1541-51. [PMID: 26610143 DOI: 10.1021/ct200065s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum chemical computations are used to study the electronic and structural properties of the cob(I)alamin intermediate of the cobalamin-dependent methionine synthase (MetH). QM(DFT)/MM calculations on the methylcobalamin (MeCbl) binding domain of MetH reveal that the transfer of the methyl group to the substrate is associated with the displacement of the histidine axial base (His759). The axial base oscillates between a His-on form in the Me-cob(III)lamin:MetH resting state, where the Co-N(His759) distance is 2.27 Å, and a His-off form in the cob(I)alamin:MetH intermediate (2.78 Å). Furthermore, QM/MM and gas phase DFT calculations based on an unrestricted formalism show that the cob(I)alamin intermediate exhibits a complex electronic structure, intermediate between the Co(I) and Co(II)-radical corrin states. To understand this complexity, the electronic structure of Im···[Cob(I)alamin] is investigated using multireference CASSCF/QDPT2 calculations on gas phase models where the axial histidine is modeled by imidazole (Im). It is found that the correlated ground state wave function consists of a closed-shell Co(I) (d(8)) configuration and a diradical contribution, which can be described as a Co(II) (d(7))-radical corrin (π*)(1) configuration. Moreover, the contribution of these two configurations depends on the Co-NIm distance. At short Co-NIm distances (<2.5 Å), the dominant electronic configuration is the diradical state, while for longer distances it is the closed-shell state. The implications of this finding are discussed in the context of the methyl transfer reaction between the Me-H4folate substrate and cob(I)alamin.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - Mercedes Alfonso-Prieto
- Institut de Química Teòrica i Computacional (IQTCUB) and Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Institute for Computational Molecular Science, Temple University , 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Carme Rovira
- Institut de Química Teòrica i Computacional (IQTCUB) and Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA)
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia , Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia , Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
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280
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Schiffmann C, Sebastiani D. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. J Chem Theory Comput 2011; 7:1307-15. [DOI: 10.1021/ct1007108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Schiffmann
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Daniel Sebastiani
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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281
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Murugan NA, Chakrabarti S, Ågren H. Solvent dependence of structure, charge distribution, and absorption spectrum in the photochromic merocyanine-spiropyran pair. J Phys Chem B 2011; 115:4025-32. [PMID: 21417244 DOI: 10.1021/jp2004612] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP)-merocyanine (MC) pair, in chloroform and in water solvents using a combined hybrid QM/MM Car-Parrinello molecular dynamics (CP-QM/MM) and ZINDO approach. We report remarkable differences in the molecular structure and charge distribution of MC between the two solvents; the molecular structure of MC remains in neutral form in chloroform while it becomes charge-separated, zwitterionic, in water. The dipole moment of MC in water is about 50% larger than in chloroform, while the value for SP in water is in between, suggesting that the solvent is more influential than the conformation itself in deciding the dipole moment for the merocyanine-spiropyran pair. The calculations could reproduce the experimentally reported blue shift in the absorption spectra of MC when going from the nonpolar to the polar solvent, though the actual value of the absorption maximum is overestimated in chloroform solvent. We find that the CP-QM/MM approach is appropriate for structure modeling of solvatochromic and thermochromic molecules as this approach is able to capture the solvent and thermal-induced structural changes within the solute important for an accurate assessment of the properties.
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Affiliation(s)
- N Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden.
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282
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Alfonso-Prieto M, Oberhofer H, Klein ML, Rovira C, Blumberger J. Proton Transfer Drives Protein Radical Formation in Helicobacter pylori Catalase but Not in Penicillium vitale Catalase. J Am Chem Soc 2011; 133:4285-98. [DOI: 10.1021/ja1110706] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Alfonso-Prieto
- Computer Simulation & Modeling Laboratory, Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Computational Molecular Science, Temple University, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - H. Oberhofer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - M. L. Klein
- Institute for Computational Molecular Science, Temple University, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - C. Rovira
- Computer Simulation & Modeling Laboratory, Parc Científic de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - J. Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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283
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Bucher D, Pierce LCT, McCammon JA, Markwick PRL. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations. J Chem Theory Comput 2011; 7:890-897. [PMID: 21494425 PMCID: PMC3074571 DOI: 10.1021/ct100605v] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Indexed: 11/28/2022]
Abstract
We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ∼3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.
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Affiliation(s)
- Denis Bucher
- Department of Chemistry and Biochemistry, University of California , San Diego, 9500 Gilman Drive, La Jolla, California 92093- 0365, United States
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284
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König C, Neugebauer J. First-principles calculation of electronic spectra of light-harvesting complex II. Phys Chem Chem Phys 2011; 13:10475-90. [PMID: 21369568 DOI: 10.1039/c0cp02808h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a fully quantum chemical investigation of important structural and environmental effects on the site energies of chlorophyll pigments in green-plant light-harvesting complex II (LHC II). Among the tested factors are technical and structural aspects as well as effects of neighboring residues and exciton couplings in the chlorophyll network. By employing a subsystem time-dependent density functional theory (TDDFT) approach based on the frozen density embedding (FDE) method we are able to determine site energies and electronic couplings separately in a systematic way. This approach allows us to treat much larger systems in a quantum chemical way than would be feasible with a conventional density functional theory. Based on this method, we have simulated a series of mutagenesis experiments to investigate the effect of a lack of one pigment in the chlorophyll network on the excitation properties of the other pigments. From these calculations, we can conclude that conformational changes within the chlorophyll molecules, direct interactions with neighboring residues, and interactions with other chlorophyll pigments can lead to non-negligible changes in excitation energies. All of these factors are important when site energies shall be calculated with high accuracy. Moreover, the redistribution of the oscillator strengths due to exciton coupling has a large impact on the calculated absorption spectra. This indicates that modeling mutagenesis experiments requires us to consider the entire set of chlorophyll molecules in the wild type and in the mutant, rather than just considering the missing chlorophyll pigment. An analysis of the mixing of particular excitations and the coupling elements in the FDEc calculation indicates that some pigments in the chlorophyll network act as bridges which mediate the interaction between other pigments. These bridges are also supported by the calculations on the "mutants" lacking the bridging pigment.
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Affiliation(s)
- Carolin König
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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285
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Yan YA, Kühn O. Unraveling the Correlated Dynamics of the Double Hydrogen Bonds of Nucleic Acid Base Pairs in Solution. J Phys Chem B 2011; 115:5254-9. [DOI: 10.1021/jp108521g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yun-an Yan
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, D-18051 Rostock, Germany
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286
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Sushko ML, Sushko PV, Abarenkov IV, Shluger AL. QM/MM method for metal-organic interfaces. J Comput Chem 2011; 31:2955-66. [PMID: 20645296 DOI: 10.1002/jcc.21591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present a QM/MM method for modeling metal/organic interfaces, which incorporates contributions from long-range electron correlation, characteristic to metals and non-bonded interactions in organic systems. This method can be used to study structurally irregular systems. We apply the method to model finite size domains of self-assembled monolayers on the gold (111) surface and discuss the influence of boundary effects on the electrostatic and electronic properties of these systems.
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Affiliation(s)
- Maria L Sushko
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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287
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Alfonso-Prieto M, Biarnés X, Kumar M, Rovira C, Kozlowski PM. Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase. J Phys Chem B 2011; 114:12965-71. [PMID: 20853870 DOI: 10.1021/jp1043738] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The key step in the catalytic cycle of methionine synthase (MetH) is the transfer of a methyl group from the methylcobalamin (MeCbl) cofactor to homocysteine (Hcy). This mechanism has been traditionally viewed as an S(N)2-type reaction, but a different mechanism based on one-electron reduction of the cofactor (reductive cleavage) has been recently proposed. In this work, we analyze whether this mechanism is plausible from a theoretical point of view. By means of a combination of gas-phase as well as hybrid QM/MM calculations, we show that cleavage of the Co-C bond in a MeCbl···Hcy complex (Hcy = methylthiolate substrate (Me-S(-)), a structural mimic of deprotonated homocysteine) proceeds via a [Co(III)(corrin(*-))]-Me···*S-Me diradical configuration, involving electron transfer (ET) from a π*(corrin)-type state to a σ*(Co-C) one, and the methyl transfer displays an energy barrier ≤8.5 kcal/mol. This value is comparable to the one previously computed for the alternative S(N)2 reaction pathway (10.5 kcal/mol). However, the ET-based reductive cleavage pathway does not impose specific geometrical and distance constraints with respect to substrate and cofactor, as does the S(N)2 pathway. This might be advantageous from the enzymatic point of view because in that case, a methyl group can be transferred efficiently at longer distances.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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288
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Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Mikkelsen KV, Ågren H. Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution. Phys Chem Chem Phys 2011; 13:12506-16. [DOI: 10.1039/c1cp20611g] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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289
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Zhou X, Kaminski JW, Wesolowski TA. Multi-scale modelling of solvatochromic shifts from frozen-density embedding theory with non-uniform continuum model of the solvent: the coumarin 153 case. Phys Chem Chem Phys 2011; 13:10565-76. [DOI: 10.1039/c0cp02874f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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290
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Murugan NA, Kongsted J, Rinkevicius Z, Ågren H. Demystifying the solvatochromic reversal in Brooker’s merocyanine dye. Phys Chem Chem Phys 2011; 13:1290-2. [DOI: 10.1039/c0cp01014f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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291
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Böckmann M, Marx D, Peter C, Site LD, Kremer K, Doltsinis NL. Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond. Phys Chem Chem Phys 2011; 13:7604-21. [DOI: 10.1039/c0cp01661f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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292
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Fiethen SA, Staemmler V, Nair NN, Ribas-Arino J, Schreiner E, Marx D. Revealing the magnetostructural dynamics of [2Fe-2S] ferredoxins from reduced-dimensionality analysis of antiferromagnetic exchange coupling fluctuations. J Phys Chem B 2010; 114:11612-9. [PMID: 20718446 DOI: 10.1021/jp1014912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metalloproteins are biomolecular hybrids composed of an "inorganic core" embedded in a "bioorganic matrix". Cofactors typically contain transition metal clusters with complex electronic structure whereas the protein host undergoes dynamics on many length and time scales. This renders computational studies of spectroscopic properties challenging, in particular, when magnetic interactions are involved. In the present study we introduce a simplified description of the antiferromagnetic exchange coupling J in reduced dimensionality which allows one to study magnetostructural dynamics of [2Fe-2S] type iron-sulfur proteins in their oxidized form by molecular dynamics. It is demonstrated that parametrization in terms of a 2D J-surface faithfully reproduces the rigorous results both in vacuo and in Anabaena ferredoxin. In particular, we present a parametrization which relies on a spin-projected density functional approach based on two Kohn-Sham determinants corrected for self-interaction via a self-consistent linear-response Hubbard-U technique. This yields an average J for Anabaena Fd in close agreement with experimental in vitro results without any specific adjustment or fitting. The analytical J-surface can be used for [2Fe-2S] proteins in their oxidized form in general and the idea can be extended to other metalloproteins as well as to other spectroscopic properties.
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Affiliation(s)
- S Annamaria Fiethen
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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293
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Rieff B, Mathias G, Bauer S, Tavan P. Density Functional Theory Combined with Molecular Mechanics: The Infrared Spectra of Flavin in Solution†. Photochem Photobiol 2010; 87:511-23. [DOI: 10.1111/j.1751-1097.2010.00866.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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294
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Fradelos G, Wesolowski TA. The Importance of Going beyond Coulombic Potential in Embedding Calculations for Molecular Properties: The Case of Iso-G for Biliverdin in Protein-Like Environment. J Chem Theory Comput 2010; 7:213-22. [DOI: 10.1021/ct100415h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgios Fradelos
- Université de Genève, Département de Chimie Physique 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Tomasz A. Wesolowski
- Université de Genève, Département de Chimie Physique 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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295
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Götz K, Meier F, Gatti C, Burow AM, Sierka M, Sauer J, Kaupp M. Modeling environmental effects on charge density distributions in polar organometallics: validation of embedded cluster models for the methyl lithium crystal. J Comput Chem 2010; 31:2568-76. [PMID: 20740555 DOI: 10.1002/jcc.21548] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The charge density and its Laplacian at the Li-C and C-H bond critical points and other features of the electron density distribution of the methyl lithium crystal have been compared by density functional methods for (i) the isolated (LiCH(3))(4) tetramer or larger clusters, (ii) for quantum mechanically treated clusters in polarizable continuum model (PCM) surroundings, (iii) for clusters augmented by the periodic electrostatic embedded cluster model (PEECM), and for (iv) the periodic crystal. Comparisons with identical functional and basis sets indicate that both PCM and PEECM embedding of only a tetramer did not fully account for the environmental effect. In contrast, embedding of a full unit cell gave results that were essentially converged to the periodic crystal data. Effects of basis set and exchange correlation functional on the QTAIM bond descriptors are of a comparable order of magnitude as the crystal environmental effects. In this context, embedded cluster computations provide distinct advantages over explicit solid-state calculations with respect to their freedom of the choice of computational and theoretical level. This is demonstrated by embedded MP2 calculations.
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Affiliation(s)
- Kathrin Götz
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg
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296
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Barker IJ, Petersen L, Reilly PJ. Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase. J Phys Chem B 2010; 114:15389-93. [DOI: 10.1021/jp107886e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian J. Barker
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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297
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Binolfi A, Rodriguez EE, Valensin D, D'Amelio N, Ippoliti E, Obal G, Duran R, Magistrato A, Pritsch O, Zweckstetter M, Valensin G, Carloni P, Quintanar L, Griesinger C, Fernández CO. Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein. Inorg Chem 2010; 49:10668-79. [PMID: 20964419 DOI: 10.1021/ic1016752] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation of alpha-synuclein (AS) is a critical step in the etiology of Parkinson's disease (PD). A central, unresolved question in the pathophysiology of PD relates to the role of AS-metal interactions in amyloid fibril formation and neurodegeneration. Our previous works established a hierarchy in alpha-synuclein-metal ion interactions, where Cu(II) binds specifically to the protein and triggers its aggregation under conditions that might be relevant for the development of PD. Two independent, non-interacting copper-binding sites were identified at the N-terminal region of AS, with significant difference in their affinities for the metal ion. In this work we have solved unknown details related to the structural binding specificity and aggregation enhancement mediated by Cu(II). The high-resolution structural characterization of the highest affinity N-terminus AS-Cu(II) complex is reported here. Through the measurement of AS aggregation kinetics we proved conclusively that the copper-enhanced AS amyloid formation is a direct consequence of the formation of the AS-Cu(II) complex at the highest affinity binding site. The kinetic behavior was not influenced by the His residue at position 50, arguing against an active role for this residue in the structural and biological events involved in the mechanism of copper-mediated AS aggregation. These new findings are central to elucidate the mechanism through which the metal ion participates in the fibrillization of AS and represent relevant progress in the understanding of the bioinorganic chemistry of PD.
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Affiliation(s)
- Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
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298
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Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques. J Phys Chem B 2010; 114:13349-57. [DOI: 10.1021/jp1060717] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- N. Arul Murugan
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Jacob Kongsted
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Kestutis Aidas
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
| | - Hans Ågren
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. ⌀rsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen ⌀, Denmark
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299
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Bucher D, Guidoni L, Carloni P, Rothlisberger U. Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. Biophys J 2010; 98:L47-9. [PMID: 20483308 DOI: 10.1016/j.bpj.2010.01.064] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 01/11/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022] Open
Abstract
Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.
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Affiliation(s)
- Denis Bucher
- Laboratory of Computational Chemistry and Biochemistry, Swiss Federal Institute of Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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300
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Nygaard TP, Alfonso-Prieto M, Peters GH, Jensen MØ, Rovira C. Substrate Recognition in the Escherichia coli Ammonia Channel AmtB: A QM/MM Investigation. J Phys Chem B 2010; 114:11859-65. [DOI: 10.1021/jp102338h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Thomas P. Nygaard
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Günther H. Peters
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Morten Ø. Jensen
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Carme Rovira
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
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