生物大分子
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
Evidence is presented suggesting, for the first time, that the protein foldability metric sigma=(T_theta - T_f)/T_theta, where T_theta and T_f are, respectively, the collapse and folding transition temperatures, could be used also to…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…
Mouse prion protein PrP106-126 is a peptide corresponding to the residues 107-127 of human prion protein. It has been shown that PrP106-126 can reproduce the main neuropathological features of prionrelated transmissible spongiform…
In this paper the heat transport in microtubules (MT) is investigated. When the dimension of the structure is of the order of the de Broglie wave length the transport phenomena must be analyzed within quantum mechanics. In this paper we…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
This paper was withdrawn by the authors.
The aim of this article is to present a developed method that decomposes the autofluorescence spectrum into the spectra of naturally occurring biochemical components of biotissue. It requires knowledge of detailed spectrum behaviour of…
Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure can be acquired already during translation. We carried out a comprehensive statistical analysis of some average…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of the missing tRNA genes are embedded in others. We argue from bioinformatic evidence that position specific intron splicing is the key behind co-location of these…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
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…
Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
We discuss recent progress towards the establishment of important structure-property-function relationships in eumelanins - key functional bio-macromolecular systems responsible for photo-protection and immune response in humans, and…
The distribution of inequivalent geometries occurring during self-assembly of the major capsid protein in thermodynamic equilibrium is determined based on a master equation approach. These results are implemented to characterize the…
A formalism is developed which allows to determine the locations of all local symmetry axes of three-dimensional particles with overall icosahedral symmetry. It relies on the fact that the root system of the non-crystallographic Coxeter…