[Three dimensional structure of the dimeric gene-engineered variant of green fluorescent protein EGFP-K162Q in P6(1) crystal space group].

The crystal structure of the dimeric green fluorescent protein EGFP-K162Q with C-terminal deletion MDELYK (EGFPv) has been determined in space group P6 at resolution 1.34 A. The obtained structure has been compared with that of the monomeric form of EGFP (green biomarker with enhanced photophysical properties) determined in other crystal space group P2(1)2(1)2(1) at resolution 1.50 and 1.35 A [1, 2]. Two subunits in the EGFPv structure are packed at 75 degrees with the contact surface approximately 800 A2. The dimeric structure is stabilized by six hydrogen bonds and the central hydrophobic core built of six residues. The RMSD value for Calpha atoms of 3-230 residues in the superimposed P61 and P2(1)2(1)2(1) structures is 0.55 A. The distinguishing feature of EGFPv- P6(1) structure, compared with that of EGFP-P2(1)2(1)2(1), is the noticeable difference in orientation of the Glu222 side chain and also new conformation of the loop fragment 155-159 with deviations among the Calpha atoms of superimposed structures reaching for Lys156 - 4.6 A and Lys158 - 5.5 A

[Conformational analysis of cyclic dipeptides: I].

Conformational analysis of two pairs of synthetic cyclodipeptides formed by interaction of both side chain functional groups [Formula: see text] and of the main and side chains [Formula: see text] was achieved by the method of molecular mechanics. The energetically optimal conformational states of the molecules under study were determined. It was shown that the conformational motility of cyclic system of the compounds under study depends on the relative arrangement of the amide groups and the number of atoms in the cycle.

[Conformational analysis of biologically active RGD-containing cyclopentapeptides]. / Konformatsionnyi analiz biologicheski aktivnykh RGD-soderzhashchikh tsiklopentapeptidov.

The theoretical conformational analysis of the biologically active RGD-containing pentapeptide cyclo(-Arg-Gly-Asp-Phe-DVal-), an inhibitor of laminin P1 interaction with its receptor, was performed. The space of permissible torsional angles of the backbone of the molecule was studied by the Monte Carlo method. From the large number of predicted low-energy conformers with various packings of the cyclic moiety of this pentapeptide, only those were selected that corresponded to stable structures of the model linear tripeptide Ac-Ala-Gly-Asp-NHMe. This peptide simulated the spatial possibilities of the backbones of RGD-containing fragments of laminin, vitronectin, and fibronectin. We selected several dozen structures that may be potential biologically active conformers, but only a few of them were capable of forming stable intramolecular hydrogen bonds. We assumed that a biologically active conformer of cyclo(-Arg-Gly-Asp-Phe-DVal-) can be present in significant amounts in an equilibrium mixture in solution along with other conformers without necessarily dominating among them.

[Conformational states of cyclic dipeptides with lactam bond between omega-functions of lysine and aspartic or glutamic acid residues]. / Konformatsionnye sostoianiya tsiklicheskikh dipeptidov s laktamnoi sviaz'iu mezhdu omega-funktsiiami ostatkov lizina i asparaginovoi ili glutaminovoi kisloty.

The conformations of H-Lys-Asp-OH and H-Glu-Lys-OH cyclic dipeptides were subjected to theoretical analysis by the method of atom-atom potentials with flexible geometry. Constants of spin-spin coupling of vicinal protons were calculated for the theoretical conformers of both dipeptides. CD and NMR spectra were measured for both peptides synthesized, and the calculated and experimental values of spin-spin coupling constants were compared. These coincided well for the dipeptide containing Asp residue, and we concluded that it exists in solution as one conformer. For the Glu-containing dipeptide, the existence of minor conformers, which increase the difference between experimental and theoretical spin-spin coupling constants, was shown to be possible.

[Lysine residue as an amino acid substitute for conformational constraint of Xaa-Asp fragment of biologically active peptides using side chain lactamization]. / Ostatok lizina v kachestve aminokislotnoi zameny dlia ogranicheniia konformatsionnoi podvizhnosti fragmenta Xaa-Asp biologicheski aktivnykh peptidov posredstvom laktamizatsii bokovykh tsepei.

The model cyclopeptide Ac-Lys-Asp-NHMe was used to test Lys as a possible substitute for Xaa in peptide fragment Xaa-Asp whose conformational mobility would be constrained by lactamization of the Lys and Asp side chains. By means of theoretical conformational analysis, such a lactam was shown to be capable of fixing several conformations of the peptide. Among them, 32 conformations corresponded to 8 low-energy regions of the linear peptide Ac-Ala-Asp-NHMe, which was chosen as a model for the peptide fragment Xaa-Asp. In this case, the conformational possibilities of the Xaa residue were constrained to two regions of the Phi, Psi-map, (A + G) and C according to Zimmermann-Sheraga notation.

[Automatic identification of structural gene fragments using a set of peptides]. / Avtomaticheskaia identifikatsiia fragmentov strukturnogo gena s pomoshch'iu nabora peptidov.

A computer program is designed to facilitate the identification of coding gene's fragments using a set of peptides. The program is written on Basic programming language for personal computer "Iskra-226" (USSR). To accelerate some operations, computer code commands are used. Treatment of 50 DNA fragments by means of 10 peptides takes ca. 1 h of computer time. The program outputs list coding gene's fragments and corresponding peptides. The suggested algorithm is based on our finding that the number of false identifications of a coding gene fragments may be predicted by Poisson distribution and minimized using correct criteria. The suggested method enables one to evaluate the reliability of the true identification of DNA fragments in case of mistakes in primary structure of the gene fragments or peptides.

[Statistical study of the nucleotide sequence of a prokaryotic promoter. Structural elements determining the efficacy of the transcription initiation stages]. / Statisticheskoe issledovanie nukleotidnoi posledovatel'nosti prokarioticheskogo promotora. Elementy struktury, opredeliaiushchie éffektivnost' protekaniia étapov nachala transkriptsii.

Nucleotide sequences of 188 promoter-containing DNA regions have been studied by the computer statistic analysis. Undecanucleotide NTT(G/C)TTGACA(A/T) or (G/C) X TT(G/C)A(G/C)A(A/T)TT(G/T) (recognition site) and heptanucleotide RTATATR or TATAATR (initiation site) separated by 12-19 base pairs are characteristic of a "generalized" promoter structure. Promoters can function if a minimal level of correspondence for their recognition and initiation sites to a generalized structure is attained (the correspondence function value for the whole structure is not lower than 0,61; for the most effective promoters it may be equal to 1). The transcription start is situated 3-9 base pairs after initiation site, 4-7 pairs distance being the most effective. Transcription can start from any nucleotide, preferably with A or G. The start from A is the most effective if it is contained within the CAC or CAT trinucleotides. The promoter efficiency is enhanced by some additional structural factors: the presence of an extended A-T rich region directly before the recognition site; availability of integral promoter structures or several RNA polymerase binding sites in the preceding nucleotide sequence. A characteristic feature of the promoter is the presence of either the dyadic axial symmetry elements in the initiation and recognition sites as well as in the intermediate region, or the A-T rich area in the latter.