生物大分子
We used statistical thermodynamics of conformational fluctuations and the elements of algebraic graph theory together with data from 2000 protein crystal structures, and showed that folded native proteins with harmonic interactions exhibit…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Superparamagnetism of tryptophan implying the presence of magnetic domain is reported. The observation helps us to conceive assembly of proteins as a physical lattice gas with multidimensional Ising character, each lattice points assuming…
Caffeine (CAF) is one of the most widely and regularly consumed biologically active substances. We use computer simulation approach to the study of CAF activity by searching for its possible complexes with biopolymer fragments. The…
The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use…
Methods for patterning biomolecules on a substrate at the single molecule level have been studied as a route to sensors with single-molecular sensitivity or as a way to probe biological phenomena at the single-molecule level. However, the…
Developing an accurate scoring function is essential for successfully predicting protein structures. In this study, we developed a statistical potential function, called OPUS-Beta, for energetically evaluating beta-sheet contact pattern…
Biopolymers are characterized by heterogeneous interactions, and usually perform their biological tasks forming contacts within domains of limited size. Combining polymer theory with a replica approach, we study the scaling properties of…
For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous…
In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement…
Antibiotic-resistant bacterial infection becomes one of the most serious risks to public health care today. However, discouragingly, the development of new antibiotics has been little progressed over the last decade. There is an urgent need…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
Folding of Ubiquitin (Ub) is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained Self-Organized-Polymer model with side chains. The calculated radius of gyration, showing dramatic variations…
In this paper we propose a wet lab algorithm for prediction of radiation fog by DNA computing. The concept of DNA computing is essentially exploited for generating the classifier algorithm in the wet lab. The classifier is based on a new…
Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role…