Biomolecules
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
A generalized autocatalytic model for chiral polymerization is investigated in detail. Apart from enantiomeric cross-inhibition, the model allows for the autogenic (non-catalytic) formation of left and right-handed monomers from a substrate…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
Mechanical characterization of protein molecules has played a role on gaining insight into the biological functions of proteins, since some proteins perform the mechanical function. Here, we present the mesoscopic model of biological…
The interaction cutoff contribution to the ruggedness of protein-protein energy landscape (the artificial ruggedness) is studied in terms of relative energy fluctuations for 1/r^n potentials based on a simplistic model of a protein complex.…
The paper shows how the diffusive movement of ions through a channel protein can be described as a chemical reaction over an arbitrary shaped potential barrier. The result is simple and intuitive but without approximation beyond the…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
We assess the reliability of the recently developed approach denominated Dominant Reaction Pathways (DRP) by studying the folding of a 16-residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in…
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
TThe paper had many errors.
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can…
The low-frequency Raman spectra of Na-and Cs-DNA water solutions have been studied to determine the mode of counterion vibrations with respect to phosphate groups of the DNA double helix. The obtained spectra are characterized by the water…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach,…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…