Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the test case of bacteriorhodopsin.

G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 A. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.

Ab initio modeling of small, medium, and large loops in proteins.

This study presents different procedures for ab initio modeling of peptide loops of different sizes in proteins. Small loops (up to 8--12 residues) were generated by a straightforward procedure with subsequent "averaging" over all the low-energy conformers obtained. The averaged conformer fairly represents the entire set of low-energy conformers, root mean square deviation (RMSD) values being from 1.01 A for a 4-residue loop to 1.94 A for an 8-residue loop. Three-dimensional (3D) structures for several medium loops (20--30 residues) and for two large loops (54 and 61 residues) were predicted using residue-residue contact matrices divided into variable parts corresponding to the loops, and into a constant part corresponding to the known core of the protein. For each medium loop, a very limited number of sterically reasonable C(alpha) traces (from 1 to 3) was found; RMSD values ranged from 2.4 to 5.9 A. Single C(alpha) traces predicted for each of the large loops possessed RMSD values of 4.5 A. Generally, ab initio loop modeling presented in this work combines elements of computational procedures developed both for protein folding and for peptide conformational analysis.

Effects of electric field on alamethicin bound at the lipid-water interface: a molecular mechanics study.

A systematic molecular mechanics study of the alamethicin molecule was made to determine a set of low-energy conformers in vacuo and in aqueous environment. The behavior of these conformers was investigated at the phase boundary which was modeled as a plane dividing two compartments with solvation properties of water and octanol with a constant electric field applied normal to the boundary. The calculations were performed with a molecular mechanics program for calculation of stable conformations at the phase boundary utilizing the Empiric Conformational Energy Program for Peptides force field and the Hopfinger-Scheraga solvation model. 371 minimum energy conformers of alamethicin, determined in vacuo with the build-up procedure, were used as starting conformations for energy minimization in aqueous environment and at the phase boundary. Only 49 interphase-bound structures were within 12 kcal/mol of the minima which was found. No helical structures having values close to the canonical parameters for an alpha- or 3(10)-helix were found despite the presence of eight alpha-methylalanine residues which favor the formation of these helices; four helix-like structures were found, having all negative phi, psi values. All the helical conformers have very high energies in water (approximately 14 kcal/mol), but are quite stable at the phase boundary (3.7-6.8 kcal/mol above the lowest minima found). The implications of these results for proposed mechanisms for membrane-binding and voltage-dependent gating are considered.

[Analysis of the spatial structure of proteins in terms of residue-residue contacts. II. Contact affinity]. / Analiz prostranstvennoi struktury belkov v terminakh matrits ostatok-ostatochnykh kontaktov. III. Srodstvo ostatkov.

The possibility of detecting the mutual amino acid residue affinity when protein three-dimensional structures are described in terms of residue-residue contact matrices is discussed. The hypothesis of the lack of affinity between amino acid residues is examined; the values of the pertinent elements of the overall residue-residue contact matrices prove not to be statistically different from random estimates in 91%; the chance hypothesis is rejected in 9% of cases, represented as a rule by residues with charged side groups, especially oppositely charged ones.

[Conformational-functional relationships of tetragastrin analogs]. / Konformatsionno-funktsional'nye otnosheniia analogov tetragastrina.

Sets of low-energy backbone conformations of the active tetragastrin analogue Boc-Trp-Leu-Asp-Phe-NH2 and two competitive antagonists Boc-Trp-Leu psi (CH2NH)-Asp-Phe-NH2 and Boc-Trp-Leu-Asp-O-CH2-CH2-C6H5 were obtained using theoretical conformational analysis methods. Groups of the conformations were selected for the three analogues, allowing a spatial matching of Trp, Asp and Phe residues responsible for the gastrin receptor binding. Three conformations possessing the lowest energies among the geometrically similar structures of these three peptides are suggested as a model for the "receptor-bound" conformations of these analogues. Backbone spatial folding resembling an alpha-helix turn is characteristic of these conformations. The correspondence of the proposed model to the available data on structure--activity relationships for tetragastrin analogues is discussed. Orientations of the putative receptor-bound conformations in a "water--lypophylic medium" two-phase system were investigated.

[Theoretical conformational analysis of a encephalitogenic peptide molecule and a study of the structure-activity relationship in a series of its analogs]. / Teoreticheskii konformatsionnyi analiz molekuly éntsefalitogennogo peptida i issledovanie otnoshenii "struktura-aktivnost" v riadu ego analogov.

Semi-empirical energy calculations are used to determine all low-energy conformations of Trp-containing fragment 113-121 of myelin basic protein (experimental allergic encephalomyelitis inducing peptide). The computed conformations are compared with the results of physico-chemical experiments and data on biological testing of the encephalitogenic peptide analogs. The three computed structures are shown to be in a good agreement with the available experimental evidence. However, additional information is required to predict "biologically active" conformation of encephalitogenic peptide.

[Amphiphilic properties of angiotensin and its fragments]. / Amfifil'nye svoistva angiotenzina i ego fragmentov.

Many biologically active peptides are supposed to interact with specific receptors mainly due to hydrophobic forces. In order to obtain a more detailed information about the peptide molecule behavior at the "water-non-polar-phase" boundary an approach to the calculation of stable conformations on such a boundary has been developed. This approach is used for investigation of the amphiphilic properties of angiotensin and its six fragments. The results of calculations of transfer energies of these peptides from the water environment to the phase boundary are in agreement with the experimental data.

Prediction of exposure degree diagram and sites of limited proteolysis in globular proteins as an approach to computer-aided design of protein bioregulators with prolonged action.

In order to prolong the lifetime of protein bioregulators in blood it is possible to engineer analogs with protected sites of limited proteolysis. To determine the sites, primarily accessible to trypsin-like proteases, a computer procedure has been developed, including a prediction algorithm, to produce the residue diagram of a globular protein and a discriminant algorithm to determine the sites most liable to proteolysis. The accuracy of prediction of amino acid residue exposure is characterised by correlation coefficients between experimental and theoretical exposure values, the coefficients being about 0.7 as calculated for 10 globular proteins. The classification of Arg and Lys residues into two groups, susceptible or insusceptible to protease, has an error percentage of about 25.

[Prognosis of the degree of exposure of amino acid residues in globular proteins in relation to various problems of protein engineering]. / Prognozirovanie éksponirovannosti aminokislotnykh ostatkov v globuliarnykh belkakh v sviazi s nekotorymi zadachami belkovoi inzhenerii.

The algorithm was developed to predict the degree of exposure of amino acid residues in globular proteins. This algorithm combined with standard discriminant analysis methods was used for evaluation of the accessibility of Lys and Arg residues for trypsin-like proteases attack. The procedure can be useful for a computer-aided design of prolonged-action protein drug preparations.

[Calculation of stable conformations of the molecule of a serum thymic factor]. / Raschet stabil'nykh konformatsii molekuly syvorotochnogo faktora timusa.

Stable conformations of "facteur thimique sérique" (FTS) were determined by semi-empirical conformational analysis. The interpretation of the calculation results in combination with data on biological activity of the conformationally restricted FTS analogues enabled the delineation of a possible "biologically active" conformation.

[Peptides of the "middle molecule" group]. / Peptidy gruppy "srednikh molekul".

The "middle molecules", endotoxins of peptide nature appearing in biological fluids in several diseases, cause the disorder of many regulatory processes, suppress the functions of blood cells, affect the transport characteristics of cell membranes. The review covers different aspects of formation, structure and numerous biological effects of "middle molecules", including the molecular mechanism of their biological action.

[Spatial structure of a vasoactive peptide--a fibrin fragment]. / Prostranstvennaia struktura vazoaktivnogo peptida--fragmenta fibrina.

Empirical energy calculations were used to determine all low-energy conformations of vasoactive pentapeptide Ala-Arg-Pro-Ala-Lys, thereby three most stable conformations were distinguished. Biological testing of conformationally restricted analogs allowed to delineate the most probable "biologically active" conformation of the molecule.

[Theoretical conformational analysis of delta-sleep inducing peptide]. / Teoreticheskii konformatsionnyi analiz neiropeptida, indutsiruiushchego del'ta - son.

The spatial structure of o-sleep-inducing peptide has been determined by means of semi-empirical conformational analysis of its overlapping fragments. Possible intramolecular contacts in the most stable conformations are discussed. The essential role of electrostatic interactions is emphasized.

Theoretical conformational analysis of oxytocin molecule.

The total semi-empirical conformational analysis of the oxytocin molecule has been carried out. It has been revealed the two main types of stable structures of cyclic moiety backbone and the great lability of the tail. The optimal spacing of cyclic moiety side chains has been found for every backbone structure. The calculation results are in good agreement with the data of physico-chemical investigations. Among the set of stable molecule structures reported in the present study are structures with beta-turn conformation of the cyclic moiety backbone and without closer spacing of the cyclic moiety and the tail, as well as structures with closely spaced N- and C-terminal parts which, however, lack beta-turn in the cyclic moiety.