Biomedical subjects

A Laio

Publications and source records attributed to A Laio.

5 recordsLinked to original sources

PubMed2003

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/molecular mechanics Car-Parrinello study of key steps of the enzymatic reaction for a representative member of this family, caspase-3. The hydrolysis of the acyl-enzyme complex is described at the density functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calculations show that the attack of the hydrolytic water molecule implies an activation free energy of ca. DeltaF(A) approximately equal 19 +/- 4 kcal/mol in good agreement with experimental data and leads to a previously unrecognized gem-diol intermediate that can readily (DeltaF(A) approximately equal 5 +/- 3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well-characterized cysteine proteases (papains and cathepsins) and may help design novel transition-state analog inhibitors.

Caspase 3↗

PubMed2003

Predicting crystal structures: the Parrinello-Rahman method revisited.

By suitably adapting a recent approach [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12 562 (2002)]] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables and define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method, our approach shows no hysteresis, and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.

Journal Article↗

PubMed2000

Deciphering the folding kinetics of transmembrane helical proteins.

Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium properties and the folding kinetics of a C(alpha)-based two-helix bundle fragment (comprised of 66 aa) of bacteriorhodopsin. Various intermediates are identified and their free energy are calculated together with the free energy barrier between them. In 40% of folding trajectories, the folding rate is considerably increased by the presence of nonobligatory intermediates acting as traps. In all cases, a substantial portion of the helices is rapidly formed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our results provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.

Bacteriorhodopsins↗

PubMed2000

Physics of iron at Earth's core conditions

The bulk properties of iron at the pressure and temperature conditions of Earth's core were determined by a method that combines first-principles and classical molecular dynamic simulations. The theory indicates that (i) the iron melting temperature at inner-core boundary (ICB) pressure (330 gigapascals) is 5400 (+/-400) kelvin; (ii) liquid iron at ICB conditions is about 6% denser than Earth's outer core; and (iii) the shear modulus of solid iron close to its melting line is 140 gigapascals, consistent with the seismic value for the inner core. These results reconcile melting temperature estimates based on sound velocity shock wave data with those based on diamond anvil cell experiments.

Journal Article↗

PubMed1999

Physical origin of selectivity in ionic channels of biological membranes.

This paper shows that the selectivity properties of monovalent cation channels found in biological membranes can originate simply from geometrical properties of the inner core of the channel without any critical contribution from electrostatic interactions between the permeating ions and charged or polar groups. By using well-known techniques of statistical mechanics, such as the Langevin equations and Kramer theory of reaction rates, a theoretical equation is provided relating the permeability ratio PB/PA between ions A and B to simple physical properties, such as channel geometry, thermodynamics of ion hydration, and electrostatic interactions between the ion and charged (or polar) groups. Diffusive corrections and recrossing rates are also considered and evaluated. It is shown that the selectivity found in usual K+, gramicidin, Na+, cyclic nucleotide gated, and end plate channels can be explained also in the absence of any charged or polar group. If these groups are present, they significantly change the permeability ratio only if the ion at the selectivity filter is in van der Waals contact with them, otherwise these groups simply affect the channel conductance, lowering the free energy barrier of the same amount for the two ions, thus explaining why single channel conductance, as it is experimentally observed, can be very different in channels sharing the same selectivity sequence. The proposed theory also provides an estimate of channel minimum radius for K+, gramicidin, Na+, and cyclic nucleotide gated channels.

Biophysical Phenomena↗