Martin Klvana

Martin Klvana

About

16
Publications
176,683
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1,376
Citations
Introduction
Additional affiliations
June 2018 - present
Free Agent
Position
  • ...
Description
  • molecular modeling | computational chemistry | chemoinformatics | computer-aided drug design
January 2015 - May 2018
University of Maribor
Position
  • Researcher
Description
  • Molecular modeling of aflatoxin-DNA adducts
January 2014 - December 2014
National Institute of Chemistry
Position
  • Researcher
Description
  • Molecular modeling of aflatoxin-DNA adducts
Education
September 2004 - January 2010
Masaryk University
Field of study
  • Microbiology
September 1999 - June 2004
Masaryk University
Field of study
  • General Biology

Publications

Publications (16)
Article
Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze nucleotidyl-transfer reaction in base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3’OH group of the primer DNA strand, and...
Article
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalo...
Article
We carried out free-energy calculations and transient kinetic experiments for the insertion of the right (dC) and wrong (dA) nucleotides by wild-type (WT) and six mutant variants of human DNA polymerase β (Pol β). Since the mutated residues in the point-mutants, I174S, I260Q, M282L, H285D, E288K, and K289M, were not located in the Pol β catalytic s...
Article
Full-text available
Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B1 (b) differ markedly (Tm: a < g < b), but the underlying molecular origin of this experimentally observed phenomenon is yet to be identified and determined. Here, by employing explicit-solvent molecular dynamics simulations cou...
Article
Full-text available
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new...
Article
We show how a restricted reaction surface can be used to facilitate the calculation of biologically important contributions of active site geometries and dynamics to DNA polymerase fidelity. Our analysis, using human DNA polymerase beta (pol β), is performed within the framework of an electrostatic linear free energy response (EFER) model. The stru...
Thesis
Full-text available
Proteins, genes and genetic code are the most fundamental functions required for life. Among the proteins, those with catalytic functions, the so-called enzymes, are fundamentally the most important because they speed up specific and otherwise too slow chemical reactions to sustain living processes. Understanding the underlying principles of life t...
Article
Full-text available
Engineering enzymes to degrade anthropogenic compounds efficiently is challenging. We obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold higher activity than wild type toward the toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. We identified key residues in access tunnels...
Article
Full-text available
The technical formulation of hexachlorocyclohexane (HCH) mainly consists of the insecticidal γ-isomer and noninsecticidal α-, β-, and δ-isomers, among which β-HCH is the most recalcitrant and has caused serious environmental problems. A γ-HCH-utilizing bacterial strain, Sphingobium sp. MI1205, was isolated from soil which had been contaminated with...
Article
Haloalkane dehalogenase DhmA from Mycobacterium avium N85 showed poor expression and low stability when produced in Escherichia coli. Here, we present expression DhmA in newly constructed pK4RP rhodococcal expression system in a soluble and stable form. Site-directed mutagenesis was used for the identification of a catalytic pentad, which makes up...
Article
We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in t...
Article
Full-text available
Haloalkane dehalogenases are bacterial enzymes capable of carbon-halogen bond cleavage in halogenated compounds. To obtain insights into the mechanism of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), we studied the steady-state and presteady-state kinetics of the conversion of the substrates 1-chlorohexane, chlorocyclohexa...

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