GONCEARENCO Alexander

Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions

Published date : 26 Oct 2015

NBDB database describes proteinmotifs, elementary functional loops (EFLs) that are involved in binding

type
Journal Paper
journal
Nucleic Acids Research, 2015, doi: 10.1093/nar/gkv1124
Impact Factor
9.112

Protein function from its emergence to diversity in contemporary proteins

Published date : 09 Jun 2015

The goal of this work is to learn from nature the rules that govern evolution and the design of protein function. The fundamental laws of physics lie in the foundation of the protein structure and all stages of the protein evolution, determining optimal sizes and shapes at different levels of structural hierarchy. We looked back into the very onset of the protein evolution with a goal to find elementary functions (EFs) that came from the prebiotic world and served as building blocks of the first enzymes.

type
Journal Paper
journal
Physical Biology, Vol. 12, No. 4, 2015, doi:10.1088/1478-3975/12/4/045002
Impact Factor
2.536

The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins

Published date : 12 Dec 2014

Background: Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding of selective forces and their compositional determinants, the very nature of underlying mutational biases remains unclear.

type
Journal Paper
journal
Biology Direct 2014 Mar;42(5):2879-92. doi: 10.1093/nar/gkt1336
Impact Factor
4.04

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

Published date : 25 Dec 2013

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels.

type
Journal Paper
journal
Nucleic Acids Research, 2013, Pg 1–14, doi:10.1093/nar/gkt1336
Impact Factor
8.276

SPACER: server for predicting allosteric communication and effects of regulation

Published date : 13 Jun 2013

The SPACER server provides an interactive framework for exploring allosteric communication in proteins with different sizes, degrees of oligomerization and function. SPACER uses recently developed theoretical concepts based on the thermodynamic view of allostery. It proposes easily tractable and meaningful measures that allow users to analyze the effect of ligand binding on the intrinsic protein dynamics. The server shows potential allosteric sites and allows users to explore communication between the regulatory and functional sites.

type
Journal Paper
journal
Nuclei Acids Research 2013, Jul 1;41(W1):W266-W272, doi: 10.1093/nar/gkt460