Recent Submissions

  • SphereCon-a method for precise estimation of residue relative solvent accessible area from limited structural information.

    Gress, Alexander; Kalinina, Olga V; HIPS, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Universitätscampus E8.1 66123 Saarbrücken, Germany. (Oxford Academic, 2020-03-10)
    Motivation: In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results: We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates.
  • Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes.

    Levitsky, Lev I; Kliuchnikova, Anna A; Kuznetsova, Ksenia G; Karpov, Dmitry S; Ivanov, Mark V; Pyatnitskiy, Mikhail A; Kalinina, Olga V; Gorshkov, Mikhail V; Moshkovskii, Sergei A; HIPS, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Universitätscampus E8.1 66123 Saarbrücken, Germany. (Wiley-Blackwell, 2019-10-01)
    Proteogenomics is based on the use of customized genome or RNA sequencing databases for interrogation of shotgun proteomics data in search for proteome-level evidence of genome variations or RNA editing. In this work, we identified the products of adenosine-to-inosine RNA editing in human and murine brain proteomes using publicly available brain proteome LC-MS/MS datasets and an RNA editome database compiled from several sources. After filtering of false-positive results, 20 and 37 sites of editing in proteins belonging to 14 and 32 genes were identified for murine and human brain proteomes, respectively. Eight sites of editing identified with high spectral counts overlapped between human and mouse brain samples. Some of these sites were previously reported using orthogonal methods, such as NMDA glutamate receptors, CYFIP2, coatomer alpha, etc. Also, differential editing between neurons and microglia was demonstrated in this work for some of the proteins from primary murine brain cell cultures. Because many edited sites are still not characterized functionally at the protein level, our results provide a necessary background for their further analysis in normal and diseased cells and tissues using targeted proteomic approaches.