sobolevnrm's Koehl:P [13 articles]

Abstract

Salt bridges play an important role in protein stability and protein-protein interactions.We have computed the electrostatics free energies of analogues of charged amino acid sidechains using two different implicit solvent models, the Poisson-Boltzmann (PB) model and our own Poisson-Langevin (PL) model,and compared their values to results from explicit solvent free energy calculations. A systematic difference is observed between the PB and explicit results, which we attribute to the basic assumption of PB that water density is constant.In contrast, the PL results ...

Abstract

A new continuum model is presented for computing the solvation free energies of cations in water. It combines in a single formalism based on statistical thermodynamics the Poisson model for electrostatics with the Langevin dipole model to account for nonuniform water dipole distribution around the ions. An excellent match between experimental and computed solvation free energies is obtained for 10 monovalent and divalent ions. ...

Abstract

We present an extension to the Poisson-Boltzmann model in which the solvent is modeled as an assembly of self-orienting dipoles of variable densities. Interactions between these dipoles are included implicitly using a Yukawa potential field. This model leads to a set of equations whose solutions give the dipole densities; we use the latter to study the organization of water around biomolecules. The computed water density profiles resemble those derived from molecular dynamics simulations. We also derive an excess free energy that ...

Abstract

We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra cpu cost. The solvent region is no longer modeled as a homogeneous dielectric media with free ions but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model. The model results in a variable dielectric constant epsilon(r) in the solvent region and also ...

Abstract

We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost. The solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model. The model results in a variable dielectric constant [IMG]f1.gif" ALT="Formula" BORDER="0"> in the solvent region and also in ...

Note (first note only)

December 15, 2008

Abstract

The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an approximate way using morphing' techniques, which are linear interpolations of either the Cartesian or the internal coordinates between the initial and end states, followed by energy minimization. Here we describe a web tool that implements a new method to calculate the most probable trajectory that is exact for harmonic potentials; as ...

Abstract

Electrostatics interactions play a major role in the stabilization of biomolecules: as such, they remain a major focus of theoretical and computational studies in biophysics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explicitly provide an accurate estimate of these interactions, they are usually computationally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on ...

Abstract

The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an approximate way using `morphing' techniques, which are linear interpolations of either the Cartesian or the internal coordinates between the initial and end states, followed by energy minimization. Here we describe a web tool that implements a new method to calculate the most probable trajectory that is exact for harmonic potentials; as an ...

Abstract

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized PoissonâBoltzmannâLangevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb\_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the ...

Abstract

Electrostatics plays a major role in the stabilization and function of biomolecules; as such, it remains a major focus of theoretical and computational studies of macromolecules. Electrostatic interactions are long range, and strongly dependent on the solvent and ions surrounding the biomolecule under study. During the past year, progress has been reported in the treatment of electrostatics in explicit and implicit solvent models. Interesting new developments of explicit solvent models include more efficient Ewald summation methods, as well as alternative approaches ...

Abstract

Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The ...

Abstract

The ASTRAL Compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. Partially derived from the SCOP database of protein structure domains, it includes sequences for each domain and other resources useful for studying these sequences and domain structures. The current release of ASTRAL contains 54 745 domains, more than three times as many as the initial release 4 years ago. ASTRAL has undergone major transformations in the past 2 ...

Abstract

The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (< or = 4 ...