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Konstantin Korotkov

Publications and source records attributed to Konstantin Korotkov.

8 recordsLinked to original sources
PubMed2006

Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli.

DaaE is a member of the Dr adhesin family of Escherichia coli, members of which are associated with diarrhea and urinary tract infections. A receptor for Dr adhesins is the cell surface protein, decay-accelerating factor (DAF). We have carried out a functional analysis of Dr adhesins, as well as mutagenesis and crystallographic studies of DaaE, to obtain detailed molecular information about interactions of Dr adhesins with their receptors. The crystal structure of DaaE has been solved at 1.48 A resolution. Trimers of the protein are found in the crystal, as has been the case for other Dr adhesins. Naturally occurring variants and directed mutations in DaaE have been generated and analyzed for their ability to bind DAF. Mapping of the mutation sites onto the DaaE molecular structure shows that several of them contribute to a contiguous surface that is likely the primary DAF-binding site. The DAF-binding properties of purified fimbriae and adhesin proteins from mutants and variants correlated with the ability of bacteria expressing these proteins to bind to human epithelial cells in culture. DaaE, DraE, AfaE-III, and AfaE-V interact with complement control protein (CCP) domains 2-4 of DAF, and analysis of the ionic strength dependence of their binding indicates that the intermolecular interactions are highly electrostatic in nature. The adhesins AfaE-I and NfaE-2 bind to CCP-3 and CCP-4 of DAF, and electrostatic interactions contribute significantly less to these interactions. These observations are consistent with structural predictions for these Dr variants and also suggest a role for the positively charged region linking CCP-2 and CCP-3 of DAF in electrostatic Dr adhesin-DAF interactions.

Adhesins, Escherichia coli↗
PubMed2004

3,5-Substituted phenyl galactosides as leads in designing effective cholera toxin antagonists; synthesis and crystallographic studies.

With the aim of developing high-affinity mono and multivalent antagonists of cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) we are using the galactose portion of the natural receptor ganglioside GM1 as an anchoring fragment in structure-based inhibitor design efforts. In order to establish a better structure-activity relationship for guiding these studies, we designed and prepared a small focused library of twenty 3,5-substituted phenylgalactosides based on two previous leads. The compounds were tested for their ability to block CTB(5) binding to immobilized ganglioside receptor and compared to the two previous leads. The crystal structures of the most promising compounds bound to either CTB(5) or LTB(5) were then determined in order to understand the basis for affinity differences. The most potent new compound yielded a six-fold improvement over our benchmark lead m-nitrophenyl-alpha-d-galactopyranoside (MNPG), and a two-fold improvement in IC(50) over a newer MNPG derivative. These results support the notion that the m-nitrophenyl moiety of MNPG and its derivatives is an important element to retain in future optimization efforts. Additionally, a consensus binding-pocket for the alkylmorpholine or piperazine moiety present in all of the designed antagonists was established as an important area of the GM1 binding site to target in future work.

Animals↗
PubMed2004

Structural biology and structure-based inhibitor design of cholera toxin and heat-labile enterotoxin.

Structural biology studies on cholera toxin and the closely related heat-labile enterotoxin from enterotoxigenic Escherichia coli over the past decade have shed light on the mechanism of toxin action at molecular and atomic levels. Also, components of the extracellular protein secretion apparatus that translocate the toxins across the outer membrane are being investigated. At the same time, structure-based design has led to various classes of compounds targeting different toxin sites, including highly potent multivalent inhibitors that block the toxin receptor-binding process.

Bacterial Toxins↗
PubMed2004

Assessing biophysical energy transfer mechanisms in living systems: the basis of life processes.

OBJECTIVE: To explain the energetic physiologic basis for acupuncture electroconductance effects and for gas discharge visualization (GDV) assessment methods, using a quantum biophysical model of entropy and information flows. DESCRIPTION: The main reservoir of free energy in biologic processes is electron-excited states of complex molecular systems. Communities of delocalized excited pi-electrons in protein macromolecules are the basis of this energy reservoir. Specific structural-protein complexes within the mass of the skin provide channels of heightened electron conductivity, measured at acupuncture points on the surface. Stimulated impulse emissions from the skin are also developed mainly by transport of delocalized pi-electrons. Stimulated by high voltage impulses, optical emissions, with amplification in gaseous discharge, are registered by optical sensors (GDV). This quantum model supports an argument that GDV techniques provide indirect judgment about the level of energy resources at the molecular level of functioning in structural-protein complexes. Several years of GDV research have provided clinical correlations with well-accepted physiologic parameters. For example, postsurgery recovery progress is correlated with GDV parameters and GDV assessments provide independent diagnostic measures of psychophysical reserves in athletes. CONCLUSION: GDV methods for investigating human functional states, by assessing electro-optical parameters of the skin, are based on the registration of physical processes emerging from electron components of tissue conductivity.

Acupuncture Points↗
PubMed2004

A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function.

Heat shock proteins and proteases play a crucial role in cell survival under conditions of environmental stress. The heat shock protein Hsp31, produced by gene hchA at elevated temperatures in Escherichia coli, is a homodimeric protein consisting of a large A domain and a smaller P domain connected by a linker. Two catalytic triads are present per dimer, with the Cys and His contributed by the A domain and an Asp by the P domain. A new crystal Form II confirms the dimer and catalytic triad arrangement seen in the earlier crystal Form I. In addition, several loops exhibit increased flexibility compared to the previous Hsp31 dimer structure. In particular, loops D2 and D3 are intriguing because their mobility leads to the exposure of a sizable hydrophobic patch made up by surface areas of both subunits near the dimer interface. The residues creating this hydrophobic surface are completely conserved in the Hsp31 family. At the same time, access to the catalytic triad is increased. These observations lead to the hypothesis for the functioning of Hsp31 wherein loops D2 and D3 play a key role: first, at elevated temperatures, by becoming mobile and uncovering a large hydrophobic area that helps in binding to client proteins, and second, by removing the client protein from the hydrophobic patch when the temperature decreases and the loops adopt their low-temperature positions at the Hsp31 surface. The proposed mode of action of flexible loops in the functioning of Hsp31 may be a general principle employed by other chaperones.

Amino Acid Sequence↗
PubMed2003

The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad.

Heat shock proteins (Hsps) play essential protective roles under stress conditions by preventing the formation of protein aggregates and degrading misfolded proteins. EcHsp31, the yedU (hchA) gene product, is a representative member of a family of chaperones that alleviates protein misfolding by interacting with early unfolding intermediates. The 1.6-A crystal structure of the EcHsp31 dimer reveals a system of hydrophobic patches, canyons, and grooves, which may stabilize partially unfolded substrate. The presence of a well conserved, yet buried, triad in each two-domain subunit suggests a still unproven hydrolytic function of the protein. A flexible extended linker between the A and P domains may play a role in conformational flexibility and substrate binding. The alpha-beta sandwich of the EcHsp31 monomer shows structural similarity to PhPI, a protease belonging to the DJ-1 superfamily. The structure-guided sequence alignment indicates that Hsp31 homologs can be divided in three classes based on variations in the P domain that dramatically affect both oligomerization and catalytic triad formation.

Amino Acid Sequence↗
PubMed2002

Hsp31, the Escherichia coli yedU gene product, is a molecular chaperone whose activity is inhibited by ATP at high temperatures.

The Escherichia coli chromosome contains several uncharacterized heat-inducible loci that may encode novel molecular chaperones or proteases. Here we show that the 31-kDa product of the yedU gene is an efficient homodimeric molecular chaperone that is conserved in a number of pathogenic eubacteria and fungi. Heat shock protein (Hsp) 31 relies on temperature-driven conformational changes to expose structured hydrophobic domains that are likely responsible for substrate binding. Complementing the function of refolding, remodeling, and holding chaperones, Hsp 31 preferentially interacts with early unfolding intermediates and rapidly releases them in an active form after transfer to low temperatures. Although Hsp 31 does not appear to exhibit intrinsic ATPase activity, binding of ATP at high temperatures restricts the size or availability of the substrate binding site, thereby modulating chaperone activity. The possible role of ATP in coordinating the function of the cellular complement of molecular chaperones is discussed.

Amino Acid Sequence↗