Related papers: Putting Proteins back into Water
We investigate the temperature dependence of thermodynamic (density, isobaric heat capacity), dynamical (self-diffusion coefficient, shear viscosity), and dielectric properties of several water models, the commonly employed TIP3P water…
The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Water is a ubiquitous liquid with unique physico-chemical properties, whose nature has shaped our planet and life as we know it. Water in restricted geometries has different properties than in bulk. Confinement can prevent low-temperature…
Establishing a description for confinement is not something simple. In order to try to understand a little about this phenomenon, we will explore the thermodynamics of models that try to describe it in terms of propagators with violation of…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
Twenty years ago Poole et al. (Nature 360, 324, 1992) suggested that the anomalous properties of supercooled water may be caused by a critical point that terminates a line of liquid-liquid separation of lower-density and higher-density…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
We consider a new model which consists of a DNA together with a RNA. Here we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model we use methods of statistical mechanics,…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…