Biomolecules
Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…
We introduce a new measure of antigenic distance between influenza A vaccine and circulating strains. The measure correlates well with efficacies of the H3N2 influenza A component of the annual vaccine between 1971 and 2004, as do results…
We present a verified computational model of the SH3 domain transition state (TS) ensemble. This model was built for three separate SH3 domains using experimental s in all-atom protein folding simulations. While averaging over all…
PDZ (Post-synaptic density-95/discs large/zonula occludens-1) domains are relatively small (80 to 120 residues) protein binding modules central in the organization of receptor clusters and in the association of cellular proteins. Their main…
The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…
Preparations of arachidonic acid binding and non-binding proteins from bovine brain, four acidic proteins (alpha-casein, phosvitin, beta-lactoglobulin A and B), the peptide polyglutamate, and two polyanions (heparin, dextran sulfate)…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
A fully self-contained model of homochirality is presented that contains the effects of both polymerization and dissociation. The dissociation fragments are assumed to replenish the substrate from which new monomers can grow and undergo new…
In this paper the heat signaling in microtubules (MT) is investigated. It is argued that for the description of the heat signaling phenomena in MT, the hyperbolic heat transport (HHT) equation must be used. It is shown that HHT is the…
Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure,…
The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of…
Background: Hidden Markov models (HMM) are powerful machine learning tools successfully applied to problems of computational Molecular Biology. In a predictive task, the HMM is endowed with a decoding algorithm in order to assign the most…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum…
By using a mixture model for the density distribution of the three pseudobond angles formed by $C_\alpha$ atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural…
To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component…
The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…