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001-es BibID:	BIBFORM031423
Első szerző:	Mones, Letif
Cím:	The energy gap as a universal reaction coordinate for the simulation of chemical reactions / Letif Mones, Petr Kulhánek, István Simon, Alessandro Laio, Monika Fuxreiter
Dátum:	2009
ISSN:	1520-6106
Megjegyzések:	The selection of a proper reaction coordinate is a major bottleneck in simulations of chemical reactions in complex systems. Increasing the number of variables that are used to bias the reaction largely affects the convergence and leads to an unbearable increase in computational price. This problem can be overcome by employing a complex reaction coordinate that depends on many geometrical variables of the system, such as the energy gap (EGAP) in the empirical valence bond (EVB) method. EGAP depends on all of the coordinates of the system, and its robustness has been demonstrated for a variety of enzymatic reactions. In this work, we demonstrate that EGAP, derived from a classical representation, can be used as a reaction coordinate in systems described with any quantum chemistry Hamiltonian. Benefits of using EGAP as a reaction coordinate as compared to a traditional geometrical variable are illustrated in the case of a symmetric nucleophilic substitution reaction in water solution. EGAP is shown to provide a significantly more efficient sampling and allows a better localization of the transition state as compared to a geometrical reaction coordinate.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	The Journal of Physical Chemistry. B. - 113 : 22 (2009), p. 7867-7873. -
További szerzők:	Kulhánek, Petr Simon István Laio, Alessandro Fuxreiter Mónika (1969-) (kutató vegyész)
Pályázati támogatás:	K72569 OTKA
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031412
035-os BibID:	PMID:18020376 WOS:000251547700018
Első szerző:	Mones, Letif
Cím:	Probing the two-metal ion mechanism in the restriction endonuclease BamHI / Letif Mones, Petr Kulhánek, Jan Florián, István Simon, Monika Fuxreiter
Dátum:	2007
ISSN:	0006-2960
Megjegyzések:	The choreography of restriction endonuclease catalysis is a long-standing paradigm in molecular biology. Bivalent metal ions are required almost for all PD..D/ExK type enzymes, but the number of cofactors essential for the DNA backbone scission remained ambiguous. On the basis of crystal structures and biochemical data for various restriction enzymes, three models have been developed that assign critical roles for one, two, or three metal ions during the phosphodiester hydrolysis. To resolve this apparent controversy, we investigated the mechanism of BamHI catalysis using quantum mechanical/molecular mechanical simulation techniques and determined the activation barriers of three possible pathways that involve a Glu-113 or a neighboring water molecule as a general base or an external nucleophile that penetrated from bulk solution. The extrinsic mechanism was found to be the most favorable with an activation free energy of 23.4 kcal/mol, in reasonable agreement with the experimental data. On the basis of the effect of the individual metal ions on the activation barrier, metal ion A was concluded to be pivotal for the reaction, while the enzyme lacking metal ion B still has moderate efficiency. Thus, we propose that the catalytic scheme of BamHI does not involve a general base for nucleophile generation and requires one obligatory metal ion for catalysis that stabilizes the attacking nucleophile and coordinates it throughout the nucleophilic attack. Such a model may also explain the variation in the number of metal ions in the crystal structures and thus could serve as a framework for a unified catalytic scheme of type II restriction endonucleases.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban külföldön készült közlemény
Megjelenés:	Biochemistry. - 46 : 50 (2007), p. 14514-14523. -
További szerzők:	Kulhánek, Petr Florián, Jan Simon István Fuxreiter Mónika (1969-) (kutató vegyész)
Pályázati támogatás:	T049073 OTKA F046164 OTKA
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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