Biomolecules
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Rubisco, probably the most abundant protein in the biosphere, performs an essential part in the process of carbon fixation through photosynthesis thus facilitating life on earth. Despite the significant effect that Rubisco has on the…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
We review the existing mathematical models which describe physicochemical mechanisms capable of producing a symmetry-breaking transition to a state in which one chirality dominates the other. A new model is proposed, with the aim of…
The approach for calculation of the mode intensities of DNA conformational vibrations in the Raman spectra is developed. It is based on the valence-optic theory and the model for description of conformational vibrations of DNA with…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations, have been developed during the last…
Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable non-racemic steady states of nonequilibrium chemical systems have been discussed as…
We consider nucleation of amyloid fibrils in the case when the process occurs by the mechanism of direct polymerization of practically fully extended protein segments, i.e. beta-strands, into beta-sheets. Applying the classical nucleation…
Under favourable conditions, many proteins can assemble into macroscopically large aggregate's, Parkinson's and other neurological and systemic diseases. The overall process of protein aggregation is characterized by initial lag time during…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…
With the aid of quantum mechanical calculations we investigate the electronic structure of the full length (FL) potassium channel protein, FL-KcsA, in its closed conformation, and the electronic structure of the ClC chloride channel. The…
Starting from the hypothesis that the tubulin dimer is a conformationally bistable molecule - fluctuating between a curved and a straight configuration at room temperature - we develop a model for polymorphic dynamics of the microtubule…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
We investigated the role of peptide folding stability in peptide immunogenicity. It was the aim of this thesis to implement a stability criterion based on energy computations using an AMBER force field, and to test the implementation with a…
Cancer is a proliferation disease affecting a genetically unstable cell population, in which molecular alterations can be somatically inherited by genetic, epigenetic or extragenetic transmission processes, leading to a cooperation of…