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001-es BibID:	BIBFORM031436
035-os BibID:	WOS:000298552800027
Első szerző:	Bernstein, Noam
Cím:	QM/MM simulation of liquid water with an adaptive quantum region / Noam Bernstein, Csilla Várnai, Iván Solt, Steven A. Winfield, Mike C. Payne, István Simon, Mónika Fuxreiter, Gábor Csányi
Dátum:	2012
ISSN:	1463-9076
Megjegyzések:	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 angstrom) 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.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Physical chemistry chemical physics. - 14 : 2 (2012), p. 646-656. -
További szerzők:	Várnai Csilla Solt Iván Winfield, Steven Payne, Mike C. Simon István Fuxreiter Mónika (1969-) (kutató vegyész) Csányi Gábor
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031421
035-os BibID:	WOS:000265529900009 PMID:19341253
Első szerző:	Solt Iván
Cím:	Evaluating boundary dependent errors in QM/MM simulations / Iván Solt, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, Mónika Fuxreiter
Dátum:	2009
ISSN:	1520-6106
Megjegyzések:	Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 angstrom. Although computation of free energies could only be afforded until 6.0 angstrom, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	he journal of physical chemistry. B. - 113 : 17 (2009), p. 5728-5735. -
További szerzők:	Kulhánek, Petr Simon István Winfield, Steven Payne, Mike C. Csányi Gábor Fuxreiter Mónika (1969-) (kutató vegyész)
Pályázati támogatás:	K72569 OTKA
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031408
035-os BibID:	WOS:000246842300026 PMID:17497910
Első szerző:	Solt Iván
Cím:	Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+ / Iván Solt, István Simon, Attila G. Császár, Monika Fuxreiter
Dátum:	2007
ISSN:	1520-6106
Megjegyzések:	Mg(2+) and Mn(2+) ions are critical to the functioning of phosphoryl transfer enzymes, such as restriction endonucleases. Although these ions play similar roles in the chemical steps, they govern substrate specificity via modulating sequence discrimination by up to a factor of 10(5) with Mg(2+) and only up to a factor of 10 with Mn(2+). To explain whether such diversity originates in fundamental differences in the electronic structures of the nucleobase-hydrated-metal ion complexes, structures and interaction energies were determined at the density functional (DFT) and second-order Moller-Plesset (MP2) levels of theory. Although both metal ions favor identical binding sites, Mn(2+) complexes exhibit greater distortions from the ideal octahedral geometry and larger variability than the corresponding Mg(2+) systems. In inner-shell complexes, with direct contact between the metal and the nucleobase, Mg(2+) is preferred over Mn(2+) in the gas phase, due primarily to nonelectrostatic effects. The interaction energies of the two metal ions are more similar in the outer-shell complexes, likely due to reduced charge transfer between the hydrated metal ion and the base moieties. Inclusion of solvation effects can amplify the relative nucleobase preferences of Mg(2+) and Mn(2+), indicating that bulk hydration modulates the balance between electrostatic and nonelectrostatic terms. In most cases, the base substitutions in solution are facilitated more by Mn(2+) than by Mg(2+). Electrostatic properties of the environment were demonstrated to have a major influence on the nucleobase preferences of the two metal ions. Overall, quantum chemical calculations suggest that the contrasting selectivity of Mg(2+) and Mn(2+) cofactors toward nucleobases derives from the larger flexibility of the Mn(2+) complexes accompanied by the excessive polarization and charge-transfer effects as well as less favorable solvation.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	The journal of physical chemistry. B. - 111 : 22 (2007), p. 6272-6279. -
További szerzők:	Simon István Császár Attila G. (1959-) (kémikus) Fuxreiter Mónika (1969-) (kutató vegyész)
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031405
035-os BibID:	WOS:000239103800017 PMID:16761278
Első szerző:	Solt Iván
Cím:	Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP / Iván Solt, Csaba Magyar, István Simon, Peter Tompa, Monika Fuxreiter
Dátum:	2006
ISSN:	0887-3585
Megjegyzések:	Phosphorylation at Ser-133 of the kinase inducible domain of CREB (KID) triggers its binding to the KIX domain of CBP via a concomitant coil-to-helix transition. The exact role of this key event is still puzzling: it does not switch between disordered and ordered states, nor its direct interactions fully account for selectivity. Hence, we reasoned that phosphorylation may shift the conformational preferences of KID towards a binding-competent state. To this end we investigated the intrinsic structural properties of the unbound KID in phosphorylated and unphosphorylated forms by simulated annealing and molecular dynamics simulations. Although helical populations show subtle differences, phosphorylation reduces the flexibility of the turn segment connecting the two helices in the complexed structure and induces a transient structural element that corresponds to its bound conformation. It is stabilized by the pSer-133-Arg-131 interaction, which is absent from the unphosphorylated KID. Diminishing this coupling decreases the 3.1 kcal/mol contribution of pSer-133 to the binding free energy (Delta G(bind)) of the phosphorylated KID to KIX by 1.1 kcal/mol, as computed in reference to Ser-133. In a binding competent form of the S133E KID mutant, the contribution of Glu-133 to Delta G(bind) is by 1.5 kcal/mol smaller than that of pSer, suggesting that altered structural properties due to pSer -> Glu replacement impair the binding affinity. Thus, we propose that phoshorylation contributes to selectivity not merely by the direct interactions of the phosphate group with KIX, but also by promoting the formation of a transient structural element in the highly conserved turn segment.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Proteins. - 64 : 3 (2006), p. 749-757. -
További szerzők:	Magyar Csaba Simon István Tompa Péter Fuxreiter Mónika (1969-) (kutató vegyész)
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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