PubMed Health⌕ Search

Biomedical subjects

E A Larionova

Publications and source records attributed to E A Larionova.

5 recordsLinked to original sources
PubMed1999

Spatial sign-alternating charge clusters in globular proteins.

Large sign-alternating charge clusters formed by the charged side groups of amino acid residues and N- and C-terminal groups were found in the majority of considered globular proteins, namely 235 in a total of 274 protein structures, i.e. 85.8%. The clusters were determined by the criteria proposed earlier: charged groups were included in the cluster if their charged N and O atoms were located at distances between 2.4 and 7.0 A. The set of selected proteins consisted of known non-homologous protein structures from the Protein Data Bank with a resolution less than or equal to 2.5 A and pair sequence similarity less than 25%. Molecular masses of the proteins were from 5.5 to 91.5 kDa and protein chain length from 50 to 830 residues. The distribution of charged groups on the protein surface between isolated charged groups, small clusters with two and three groups, and large clusters with four or more groups were found to be approximately similar making 33, 35 and 32% of the total amount of protein charged groups, respectively. The large sign-alternating charge clusters with four or more charged groups were studied in greater detail. The amount of such clusters depends on the protein chain length. The small proteins contain 1-3 clusters while the large proteins display 4-6 or more clusters. On average, 1.5 clusters per each 100 residues were observed. In contrast with this, the size of a cluster, i.e. the number of charged groups inside a cluster, does not depend on the protein molecular mass, and large clusters are observed for proteins from a range of molecular masses. Clusters consisting of four to six charged groups occur most frequently, although extra large clusters are also often revealed. We can conclude that sign-alternating charge clusters are a common feature of the protein surface of globular protein. They are suggested to play a general functional role as a local polar factor of protein surface.

Amino Acids↗
PubMedDate not supplied

[Formation of recognition site in transcription factors: repressor of phage lambda and a murine immunoglobulin factor].

IPolar interactions between protein and the major groove of double-stranded DNA have been analyzed on the basis of a structural study of the complexes formed by two transcription factors: phage lambda repressor and murine immunoglobulin transcription factor NF kappa B-p50. Two identical molecules of these two factors form two binding sites within two different parts of a single DNA molecule. This allows one to study formation of the recognition module by comparing the binding pattern of two different parts of the DNA operator. We have shown that formation of the DNA-binding sites for the three structurally different protein domains (one in repressor and two in the immunoglobulin factor) involves polar residues selected from the largest polar cluster on the surface of the protein molecule. It was also shown that the same polar residues bind with different points of DNA sites. This result provides understanding of the recognition module adaptation to varying nucleotide sequence of the operator sites and shows the way of binding site formation.

Animals↗
PubMedDate not supplied

[Definitive role of polar residue clusters in B-DNA major groove recognition by protein factors].

The 3D structural data for a number of protein-DNA complexes were used to analyze the regions of specific contact with the major groove of B-DNA double helix. The set included seven nonhomologous complexes featuring 12 DNA-binding domains of transcription factors and regulatory factors. The protein domains differed in structure, contained different motifs in the binding region, and broadly varied in chain length, from 30 to 200 residues. Protein-DNA interaction was assessed as hydrogen bonding between polar atoms and van der Waals contacts between nonpolar atoms. The binding sites were formed mainly through polar side chain interactions. On average, the recognition site comprises seven residues, six of them polar. The contact residues nearly always belong to a largest polar cluster of the protein. Thus one can think that the protein polar residue clusters play an important role in forming the protein-DNA recognition module.

Adhesins, Bacterial↗
PubMedDate not supplied

[Principal role of large polar residue clusters of RNA-binding proteins in the formation of complexes with RNA].

Three-dimensional crystallographic data for a number of protein-RNA complexes were used to study the localization of protein binding regions at the protein surface. The set consists of ten non-homologous complexes, which include 20 independent binding sites. In most sites the contact interaction of polar residue side groups makes a significant contribution to protein binding regions. It was discovered that binding polar residues are localized essentially inside one largest cluster of polar residues at the protein surface. In fact, for fifteen regions 80.5% of polar binding residues were situated in such a large cluster. This result supports strongly a definitive role of the largest polar cluster in the recognition of the major groove of B-DNA by the protein transcription and regulatory factors, which has been recently disclosed by us. Therefore, at present one can suggest that the largest cluster of protein polar residues could play a key role in the formation of binding sites of proteins with DNA and RNA.

Animals↗