Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum.

The structure and the RNA-binding properties of the Lsm protein from Halobacterium salinarum have been determined. A distinctive feature of this protein is the presence of a short L4 loop connecting the β3 and β4 strands. Since bacterial Lsm proteins (also called Hfq proteins) have a short L4 loop and form hexamers, whereas archaeal Lsm proteins (SmAP) have a long L4 loop and form heptamers, it has been suggested that the length of the L4 loop may affect the quaternary structure of Lsm proteins.

Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.

Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites.

Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface.

Currently, studies of RNA/protein interactions occupy a prominent place in molecular biology and medicine. The structures of RNA-protein complexes may be determined by X-ray crystallography or NMR for further analyses. These methods are time-consuming and difficult due to the versatility and dynamics of the RNA structure.

Studying the properties of domain I of the ribosomal protein l1: incorporation into ribosome and regulation of the l1 operon expression.

L1 is a conserved protein of the large ribosomal subunit. This protein binds strongly to the specific region of the high molecular weight rRNA of the large ribosomal subunit, thus forming a conserved flexible structural element--the L1 stalk. L1 protein also regulates translation of the operon that comprises its own gene.

Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes.

We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/.

Crystallization of RNA/protein complexes.

Different complexes of ribosomal proteins with specific rRNA fragments have been crystallized and studied by our group during the last six years. There are several factors important for successful crystallization of RNA/protein complexes, among them: length and content of RNA fragments, homogeneity of RNA and protein preparations, stability of the complexes, conditions for mixing RNA and protein components before crystallization, effect of Se-Met on RNA/protein complex crystal quality. In this paper we describe findings and methodical details, which helped us to succeed in obtaining X-ray quality crystals of several RNA/protein complexes.

Further evidence on the equilibrium "pre-molten globule state": four-state guanidinium chloride-induced unfolding of carbonic anhydrase B at low temperature.

Equilibrium guanidinium chloride-induced unfolding of bovine carbonic anhydrase NB has been investigated by a combination of optical methods with size-exclusion chromatography. It has been shown that, as in the case of staphylococcal beta-lactamase, bovine carbonic anhydrase B unfolds at low temperature through two equilibrium intermediates; the molten globule and the pre-molten globule states. This pre-molten globule state has a hydrodynamic volume no more than twofold larger than that of the native state, i.