Biomolecules
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate…
We address the controversial hot question concerning the validity of the loose-coupling versus the lever-arm models in the actomyosin dynamics by re-interpreting and extending the washboard potential model proposed by some of us in a…
The three-dimensional structures of two common repeat motifs Val$^1$-Pro$^2$-Gly$^3$-Val$^4$-Gly$^5$ and Val$^1$-Gly$^2$-Val$^3$-Pro$^4$-Gly$^5$-Val$^6$-Gly$^7$-Val$^8$-Pro$^9$ of tropoelastin are investigated by using the multicanonical…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the…
In this perspective we address the question: why are proteins seemingly so hard to crystallize? We suggest that this is because of evolutionary negative design, i.e. proteins have evolved not to crystallize, because crystallization, as with…
Using the model for the processive movement of a dimeric kinesin we proposed before, we study the dynamics of a number of mutant homodimeric and heterodimeric kinesins that were constructed by Kaseda et al. (Kaseda, K., Higuchi, H. and…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
The stability and conservation properties of a recently proposed polymerization model are studied. The achiral (racemic) solution is linearly unstable once the relevant control parameter (here the fidelity of the catalyst) exceeds a…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
We describe a faster and more accurate algorithm for computing the statistical mechanics of DNA denaturation according to the Poland-Scheraga type. Nearest neighbor thermodynamics is included in a complete and general way. The algorithm…
ZSPA-1 is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA-1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the…
We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic…
Using a Brownian dynamics simulation, we numerically studied the interaction of DNA with histone and proposed an octamer-rotation model to describe the process of nucleosome formation. Nucleosome disruption under stretching was also…
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted…