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Biomedical subjects

Ursula Rothlisberger

Publications and source records attributed to Ursula Rothlisberger.

22 records · Page 2Linked to original sources

Accelerating rare reactive events by means of a finite electronic temperature.

The range of chemical problems that are directly accessible to first-principles molecular dynamics simulations based on density functional theory is extended with a novel method apt to accelerate rare reactive events. The introduction of a finite electronic temperature within the Mermin formalism leads to a lowering of chemical activation barriers and thus to an exponential enhancement of the rate at which these reactions are observed during a first-principles molecular dynamics simulation. The method presented here makes direct use of the intrinsic chemical information encoded in the electronic structure, and is therefore able to lower selectively chemically relevant activation energies even in systems where many competing low-energy pathways for conformational transitions or diffusive motions are present. The performance of this new approach is demonstrated for a series of prototypical chemical reactions in gas and in condensed phase. A typical acceleration that can be achieved is, for example, a factor of 10(5) for the cis-trans isomerization of peroxynitrous acid in aqueous solution at room temperature.

Journal Article↗

The role and perspective of ab initio molecular dynamics in the study of biological systems.

Ab initio molecular dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing number of applications to biochemical systems. Here we describe the principles on which ab initio MD is based. We focus on the most popular implementation, based on density functional theory and plane wave basis set. By a survey of recent applications, we show that despite the current limitations of size and time scale, ab initio MD (and hybrid ab initio MD/MM approaches) can play an important role for the modeling of biological systems. Finally, we provide a perspective for the advancement of methodological approaches which may further expand the scope of ab initio MD in biomolecular modeling.

Animals↗

Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations.

The emergence of drug-resistant variants is a serious side effect associated with acquired immune deficiency syndrome therapies based on inhibition of human immunodeficiency virus type 1 protease (HIV-1 PR). In these variants, compensatory mutations, usually located far from the active site, are able to affect the enzymatic activity via molecular mechanisms that have been related to differences in the conformational flexibility, although the detailed mechanistic aspects have not been clarified so far. Here, we perform multinanosecond molecular dynamics simulations on L63P HIV-1 PR, corresponding to the wild type, and one of its most frequently occurring compensatory mutations, M46I, complexed with the substrate and an enzymatic intermediate. The quality of the calculations is established by comparison with the available nuclear magnetic resonance data. Our calculations indicate that the dynamical fluctuations of the mutated enzyme differ from those in the wild type. These differences in the dynamic properties of the adducts with the substrate and with the gem-diol intermediate might be directly related to variations in the enzymatic activity and therefore offer an explanation of the observed changes in catalytic rate between wild type and mutated enzyme. We anticipate that this "flexibility-assisted" mechanism might be effective in the vast majority of compensatory mutations, which do not change the electrostatic properties of the enzyme.

Drug Resistance, Viral↗