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Special Issue "Applications of Molecular Dynamics"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (15 December 2010)

Special Issue Editor

Guest Editor
Prof. Dr. Lorenz Cederbaum

Theoretische Chemie, Physikalisch-Chemisches Institut, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
Website | E-Mail

Keywords

  • molecular dynamics

Published Papers (2 papers)

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Research

Open AccessArticle Comparison of Free Energy Surfaces Calculations from Ab Initio Molecular Dynamic Simulations at the Example of Two Transition Metal Catalyzed Reactions
Int. J. Mol. Sci. 2011, 12(2), 1389-1409; doi:10.3390/ijms12021389
Received: 1 December 2010 / Revised: 4 February 2011 / Accepted: 22 February 2011 / Published: 23 February 2011
Cited by 4 | PDF Full-text (3537 KB) | HTML Full-text | XML Full-text
Abstract
We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement of a ruthenium oxoester in water and a carbon dioxide addition to a palladium complex in carbon dioxide.
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We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement of a ruthenium oxoester in water and a carbon dioxide addition to a palladium complex in carbon dioxide. For the latter reaction we also investigated the gas phase reaction in order to take solvent effects into account. We used two techniques to reconstruct the free energy surfaces: thermodynamic integration and metadynamics. Furthermore, we gave a reasonable error estimation of the computed free energy surface. We calculated a reaction barrier of ΔF = 59:5 ± 8:5 kJ mol-1 for the rearrangement of a ruthenium oxoester in water from thermodynamic integration. For the carbon dioxide addition to the palladium complex in carbon dioxide we found a ΔF = 44:9 ± 3:3 kJ mol-1 from metadynamics simulations with one collective variable. The investigation of the same reactions in the gas phase resulted in ΔF = 24:9 ± 6:7 kJ mol-1 from thermodynamic integration, in ΔF = 26:7 ± 2:3 kJ mol-1 from metadynamics simulations with one collective variable, and in ΔF = 27:1 ± 5:9 kJ mol-1 from metadynamics simulations with two collective variables. Full article
(This article belongs to the Special Issue Applications of Molecular Dynamics)
Open AccessArticle Insight into a Novel p53 Single Point Mutation (G389E) by Molecular Dynamics Simulations
Int. J. Mol. Sci. 2011, 12(1), 128-140; doi:10.3390/ijms12010128
Received: 26 November 2010 / Revised: 8 December 2010 / Accepted: 23 December 2010 / Published: 30 December 2010
Cited by 7 | PDF Full-text (3698 KB) | HTML Full-text | XML Full-text
Abstract
The majority of inactivating mutations of p53 reside in the centralcore DNA binding domain of the protein. In this computational study, we investigated the structural effects of a novel p53 mutation (G389E), identified in a patient with congenital adrenal hyperplasia, which is
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The majority of inactivating mutations of p53 reside in the central core DNA binding domain of the protein. In this computational study, we investigated the structural effects of a novel p53 mutation (G389E), identified in a patient with congenital adrenal hyperplasia, which is located within the extreme C-terminal domain (CTD) of p53, an unstructured, flexible region (residues 367–393) of major importance for the regulation of the protein. Based on the three-dimensional structure of a carboxyl-terminal peptide of p53 in complex with the S100B protein, which is involved in regulation of the tumor suppressor activity, a model of wild type (WT) and mutant extreme CTD was developed by molecular modeling and molecular dynamics simulation. It was found that the G389E amino acid replacement has negligible effects on free p53 in solution whereas it significantly affects the interactions of p53 with the S100B protein. The results suggest that the observed mutation may interfere with p53 transcription activation and provide useful information for site-directed mutagenesis experiments. Full article
(This article belongs to the Special Issue Applications of Molecular Dynamics)
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