Sergey V. Efimov

Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study.

A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric β-barrels.

Inversion of Population Distribution of Felodipine Conformations at Increased Concentration in Dimethyl Sulfoxide Is a Prerequisite to Crystal Nucleation

Knowledge of the preferred conformations of biologically active compounds is of the utmost importance for a better understanding of the structure-activity relationships underlying their biological activity, as well as their mechanism of action. Moreover, investigating the mechanism of nucleation from a saturated solution can facilitate the discovery and preparation of new polymorphic forms. To search regularities in the crystal nucleation of biologically active compounds (drugs) from a saturated solution, we studied the conformational preference of felodipine in dilute and saturated solution in dimethyl sulfoxide. The inversion of conformation distribution at increased concentration occurs: conformers that dominate in a dilute solution become the least abundant in the saturated one. Conformers that dominate in the saturated solution are of the same type as revealed in crystalline state by X-ray.

Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase

Abstract The elongation of single-stranded DNA repeats at the 3′-ends of chromosomes by telomerase is a key process in maintaining genome integrity in eukaryotes. Abnormal activation of telomerase leads to uncontrolled cell division, whereas its down-regulation is attributed to ageing and several pathologies related to early cell death. Telomerase function is based on the dynamic interactions of its catalytic subunit (TERT) with nucleic acids—telomerase RNA, telomeric DNA and the DNA/RNA heteroduplex. Here, we present the crystallographic and NMR structures of the N-terminal (TEN) domain of TERT from the thermotolerant yeast Hansenula polymorpha and demonstrate the structural conservation of the core motif in evolutionarily divergent organisms. We identify the TEN residues that are involved in interactions with the telomerase RNA and in the recognition of the ‘fork’ at the distal end of the DNA product/RNA template heteroduplex. We propose that the TEN domain assists telomerase biological function and is involved in restricting the size of the heteroduplex during telomere repeat synthesis.

Stereoselective PCO/POC-Rearrangement of P-C-Cage Phosphorane in the Reaction of 4,5-Dimethyl-2-(2-oxo-1,2-diphenyl)ethoxy-1,3,2-dioxaphospholane with Hexafluoroacetone.

Interaction of 4,5-dimethyl-2-(2-oxo-1,2-diphenyl)ethoxy-1,3,2-dioxaphospholane, bearing a carboxyl group in the γ-position with respect to the phosphorus atom and obtained from d,l-butanediol, with hexafluoroacetone (CCl4, -40 °C) leads to the simultaneous formation of regio- and stereoisomeric cage-like phosphoranes with phosphorus-carbon and phosphorus-oxygen bonds with a high stereoselectivity (>95%), whose structure was determined by 1D and 2D NMR spectroscopy and XRD. When stored as a solution in dichloromethane for one month, the PCO-isomer rearranges into the thermodynamically more stable POC-isomer of the cage-like phosphorane. Mild hydrolysis of the PCO/POC-isomers proceeds with a high chemoselectivity and leads to the formation of P(IV)-dioxaphospholane derivatives. Acidic hydrolysis of the POC-isomer leads to the formation of an oxirane derivative with an unexpectedly high stereoselectivity (>95%). DFT calculations (using the PBE functional) allowed us to obtain structures and energies of the initial phospholane, reaction products (PCO/POC-isomers), and an intermediate P(V)-oxaphosphirane.

NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase

Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA fragments to the ends of chromosomes. This enzyme is the focus of substantial attention, both because its structure and mechanism of action are still poorly studied, and because of its pivotal roles in aging and cellular proliferation. The use of telomerase as a potential target for the design of new anticancer drugs is also of great interest. The catalytic protein subunit of telomerase (TERT) contains an N-terminal domain (TEN) that is essential for activity and processivity. Elucidation of the structure and dynamics of TEN in solution is important for understanding the molecular mechanism of telomerase activity and for the design of new telomerase inhibitors. To approach this problem, in this study we report the 1H, 13C, and 15N chemical shift assignments of TEN from Ogataea polymorpha. Analysis of the assigned chemical shifts allowed us to identify secondary structures and protein regions potentially involved in interaction with other participants of the telomerase catalytic cycle.

Reaction of 4,5-dimethyl-2-(2-oxo-1,2-diphenylethoxy)-1,3,2-dioxaphospholane with hexafluoroacetone: formation of isomeric caged phosphoranes with phosphorus–carbon and phosphorus–oxygen bonds

Abstract4,5-Dimethyl-2-(2-oxo-1,2-diphenylethoxy)-1,3,2-dioxaphospholane bearing the carbonyl group at the γ-position to the phosphorus atom reacted with hexafluoroacetone to give regio- and stereoisomeric caged phosphoranes with phosphorus–carbon and phosphorus–oxygen bonds.

Tandem dihetero-Diels-Alder and Huisgen cycloaddition reactions. Synthesis, crystal structure and hydrolysis of the novel cage phosphoranes based on 2-(1-phenylethenyloxy)benzo-1,3,2-dioxaphosphole

The reaction of 2-(1-phenylvinyloxy)benzo-1,3,2-dioxaphosphole with hexafluoroacetone, ethyltrifluoropyruvate and chloral leads to the formation of cage phosphoranes possessing the 1-phospha-2,6,8-trioxabicyclo[3.2.1]octane framework whose structure was established by the XRD method and NMR spectroscopy. The process involves dihetero-Diels–Alder and Huisgen 1,3-dipolar cycloaddition reactions and is accompanied by the simultaneous formation of the P–C and C–C bonds. Despite the generation of three chiral carbon atoms, the stereoselectivity of the process exceeds 96%. Hydrolysis leads to the formation of functionalized aldols and phosphonates.

Chemical shift assignments and the secondary structure of the Est3 telomerase subunit in the yeast Hansenula polymorpha

Telomerase is a multisubunit ribonucleoprotein enzyme that is essential for continuous cellular proliferation. A key role of telomerase in cancer and ageing makes it a promising target for the development of cancer therapies and treatments of other age-associated diseases, since telomerase allows unlimited proliferation potential of cells in the majority of cancer types. However, the structure and molecular mechanism of telomerase action are still poorly understood. In budding yeast, telomerase consists of the catalytic subunit, the telomerase reverse transcriptase or Est2 protein, telomerase RNA (TLC1) and two regulatory subunits, Est1 and Est3. Each of the four subunits is essential for in vivo telomerase function. Est3 interacts directly with Est1 and Est2, and stimulates Est2 catalytic activity. However, the exact role of the Est3 protein in telomerase function is still unknown. Determination of the structure, dynamic and functional properties of Est3 can bring new insights into the molecular mechanism of telomerase activity. Here we report nearly complete 1H, 13C and 15N resonance assignments of Est3 from the yeast Hansenula polymorpha. Analysis of the assigned chemical shifts allowed us to identify the protein’s secondary structure and backbone dynamic properties. Structure-based sequence alignment revealed similarities in the structural organization of yeast Est3 and mammalian TPP1 proteins.