Search results for "COMPUTATION"

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA.

2020

Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by desc…

Chapter 6 Contribution of NMR Spectroscopy to Flavour Release and Perception

2008

Abstract The control of flavouring of a food product as well as the flavour perception during consumption is a great challenge for improving food quality. However, the various ingredient composition and the different textural properties of foods can significantly affect the release of aroma compounds or sapid molecules. It is thus of major importance to determine physicochemical factors that govern diffusion and binding phenomena of these small solutes in food products. In this way, NMR spectroscopy is an efficient tool to characterize these mechanisms at a molecular scale. Diffusion rates of small solutes in aqueous, viscous and gel solutions can be extracted from relaxation or diffusion N…

Letter to the Editor: Solution structure of hypothetical protein TA1414 from Thermoplasma acidophilum

2004

Cluster and Periodic Calculations of the Ethene Protonation Reaction Catalyzed by theta-1 Zeolite: Influence of Method, Model Size, and Structural Co…

2001

The protonation of ethene by three different acid sites of theta-1 zeolite was theoretically studied to analyze the extent and relevance of the following aspects of heterogeneous catalysis: the local geometry of the Bronsted acid site in a particular zeolite, the size of the cluster used to model the catalyst, the degree of geometry relaxation around the active site, and the effects related to medium- and long-range interactions between the reaction site and its environment. It has been found that while the reaction energy is very sensitive to the local geometry of the site, the activation energy is mainly affected by the methodology used and by electrostatic effects on account of the carbo…

The structure of a native orthobunyavirus ribonucleoprotein reveals a key role for viral RNA in maintaining its helical architecture

2021

AbstractThe Bunyavirales order of RNA viruses comprises emerging pathogens for which approved preventative or therapeutic measures for human use are not available. The genome of all Bunyavirales consists of negative-sense RNA segments wrapped by the virus-encoded nucleocapsid protein (NP) to form ribonucleoproteins (RNPs). RNPs represent the active template for RNA synthesis and the form in which the genome is packaged into virions, functions that require inherent flexibility. We present a pseudo-atomic model of a native RNP purified from Bunyamwera virus (BUNV), the prototypical Bunyavirales member, based on a cryo-electron microscopy (cryo-EM) average at 13 Å resolution with subsequent fi…

Identification and characterization of DNA sequences with ars-activity from the small eukaryote Nanochlorum eucaryotum

1988

S1/2 Mechanistic insights of F1-ATPase rotation from single-molecule measurements of the power stroke

2008

Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent

2013

Human 70 kDa heat shock protein (hHsp70) is an ATP-dependent chaperone and is currently an important target for developing new drugs in cancer therapy. Knowledge of the conformations of hHsp70 is central to understand the interactions between its nucleotide-binding domain (NBD) and substrate-binding domain (SBD) and is a prerequisite to design inhibitors. The conformations of ADP-bound (or nucleotide-free) hHsp70 and ATP-bound hHsp70 was investigated by using unbiased all-atom molecular dynamics (MD) simulations of homology models of hHsp70 in explicit solvent on a timescale of .5 and 2.7 μs, respectively. The conformational heterogeneity of hHsp70 was analyzed by computing effective free-e…

Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study

2015

The elucidation of the catalytic role of LinA dehydrohalogenase in the degradation processes of hexachlorocyclohexane (HCH) isomers is extremely important to further studies on the bioremediation of HCH polluted areas. Herein, QM/MM free energy simulations are employed to provide the details of the dehydrochlorination reaction of two HCH isomers (γ and β). In particular, the role of the protonation state of one of the catalytic residues-His73-is explored. Based on our calculations, two distinct minimum free energy pathways (concerted and stepwise) were found for γ-HCH and β-HCH. The choice of the reaction channel for the dehydrochlorination reactions of γ- and β-HCH was shown to depend on t…

Biochemistry and Molecular Biology of DNA Replication in Yeast

1985

For the past two decades, the study of the mechanism of DNA replication has been focused mainly on the chromosomes of the simple prokaryotes and their viruses (1). The complexity of the eukaryotic genome and multiple levels of control during the replication of eukaryotic chromosomes have until recently prevented similar studies. In recent years, a lower eukaryote, the yeast Saccharomyces cerevisiae, has become a major focus of efforts in molecular biology. In this chapter, I will briefly review accomplishments in this area. Yeast is an ideal model system for studies on the structure and replication of the eukaryotic chromosome. Yeast cells are easy to grow and study biochemically. Genetic a…