Related papers: Understanding conserved amino acids in proteins
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…