Biomolecules
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein…
Phi-values are experimental measures of the effects of mutations on the folding kinetics of a protein. A central question is which structural information Phi-values contain about the transition state of folding. Traditionally, a Phi-value…
We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the structural change, we propose a…
The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this…
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
PCR (Polymerase Chain Reaction), a method which replicates a selected sequence of DNA, has revolutionized the study of genomic material, but mathematical study of the process has been limited to simple deterministic models or descriptions…
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an…
The folding rates of two-state proteins have been found to correlate with simple measures of native-state topology. The most prominent among these measures is the relative contact order (CO), which is the average CO or 'localness' of all…
According to the 'old view', proteins fold along well-defined sequential pathways, whereas the 'new view' sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also…
In a seminal paper Caspar and Klug established a theory that provides a family of polyhedra as blueprints for the structural organisation of viral capsids. In particular, they encode the locations of the proteins in the shells that…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
By considering the energy cost of messages carried by proteins as proportional to their information content we found experimental proof that proteins from all living organisms tend to have their estimated semantic content of information per…