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A V Efimov

Publications and source records attributed to A V Efimov.

At least 19 recordsLinked to original sources
PubMed2001

In situ spatial organization of Potato virus A coat protein subunits as assessed by tritium bombardment.

Potato virus A (PVA) particles were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the label in the amino acids of the coat protein was determined to assess their in situ steric accessibility. This method revealed that the N-terminal 15 amino acids of the PVA coat protein and a region comprising amino acids 27 to 50 are the most accessible at the particle surface to labeling with tritium atoms. A model of the spatial arrangement of the PVA coat protein polypeptide chain within the virus particle was derived from the experimental data obtained by tritium bombardment combined with predictions of secondary-structure elements and the principles of packing alpha-helices and beta-structures in proteins. The model predicts three regions of tertiary structure: (i) the surface-exposed N-terminal region, comprising an unstructured N terminus of 8 amino acids and two beta-strands, (ii) a C-terminal region including two alpha-helices, as well as three beta-strands that form a two-layer structure called an abCd unit, and (iii) a central region comprising a bundle of four alpha-helices in a fold similar to that found in tobacco mosaic virus coat protein. This is the first model of the three-dimensional structure of a potyvirus coat protein.

Capsid↗
PubMed1999

Complementary packing of alpha-helices in proteins.

The packing of alpha-helices in proteins is restricted by both the principle of close packing and the chemical nature of side chains. As a result, (1) alpha-helical surfaces forming the interface should be complementary to each other, (2) hydrophobic stripes of the alpha-helices should fit together like pieces of a jigsaw puzzle, and (3) buried polar side chains (if there are any) should be arranged in a complementary fashion.

Models, Molecular↗
PubMed1999

Polymerization of bacteriophage T4 tail sheath protein mutants truncated at the C-termini.

Gene 18 of bacteriophage T4 encodes the contractile protein of the tail sheath. Previous work has shown that the full-length recombinant gene product (gp) 18 of 658 amino acid residues assembles in Escherichia coli cells into a long polysheath structure. However, the gp18 mutants truncated at the N-termini form insoluble aggregates similar to inclusion bodies. In this study, six plasmid vectors expressing the recombinant gp18 proteins truncated at the C-termini have been constructed. The CDelta58, CDelta129, CDelta152, C[g1]72, CDelta248, and CDelta287 proteins contain 600, 529, 506, 486, 410, and 371 residues of the full-length gp18 molecule, respectively. All the recombinant proteins were soluble and, except for the CDelta287 mutant, were assembled into polysheath-related structures. Electron microscopy of negatively stained purified proteins was performed and the resulting images were analyzed by computing their Fourier transforms. The CDelta58 and CDelta129 mutants, in addition to forming common contracted-type polysheath structures, assembled into thinner filaments that we called "noncontracted polysheaths" (NCP). The CDelta152, CDelta172, and CDelta248 proteins assembled into the NCP type only. Image processing showed that the NCP filaments significantly differ from both extended sheaths of T4 particle and polysheaths. The structure of the NCP filaments might correspond to the transitional helices postulated by Moody (J. Mol. Biol., 1973, 80, 613-636) that appeared during the process of tail contraction. Our results suggest that a short region at the C-terminus of the CDelta129 protein determines the contractile properties of the gp18 molecule. The shortest, the CDelta287 protein, does not assemble into regular structures, thus indicating that a sequence's stretch at the C-end of the CDelta248 mutant might be responsible for polymerization of gp18.

Amino Acid Sequence↗
PubMed1998

A structural tree for proteins containing S-like beta-sheets.

A structural tree for proteins and domains containing S-like beta-sheets has been constructed. An S-like beta-sheet is taken as a starting structure in modelling or as a root structure of the tree. Larger structures are obtained by a stepwise addition of beta-strands and/or alpha-helices to the root S-like beta-sheet in accordance with a restricted set of rules inferred from known principles of protein structure. Applications of the structural tree to structure comparison, protein classification and protein folding are described.

Algorithms↗
PubMed1998

Properties of recombinant bacteriophage T4 tail sheath protein and its deletion fragments.

A vector for expression of recombinant bacteriophage T4 tail sheath protein (gp18) under control of phage T7 promoter in Escherichia coli cells has been constructed. The entire length recombinant gp18 (659 amino acids) polymerizes in vivo into extended polysheaths. To study gp18 folding mechanisms, six vectors for expression of deletion mutants have been constructed. Three proteins--1N, 2N, and 3N--contain, respectively, 268, 316, and 372 amino acids of the gp18 N-tail region. The other three fragments--1C, 2C, and 3C--contain, respectively, 455, 356, and 288 amino acids of the gp18 C-tail. The fragments 1N, 2N, 1C, 2C, and 3C form insoluble aggregates during expression. However, fragment 3N accumulates in soluble form in the cellular cytoplasm and does not form polymeric structures; this has allowed an effective purification method to be developed for it. The interaction of monoclonal antibodies against recombinant gp18 with protein fragments and with phage sheath before and after contraction has been studied. The fragment 3N seems to be a stable domain of native phage sheath gp18.

Bacteriophage T4↗
PubMed1998

[Architecture of compact three alpha-helical structures].

Modeling and methodical analysis of possible compact spatial arrangements of three alpha helices bound with connections were carried out. It was suggested to describe the compact three-alpha-helical structures as combinations of alpha-helical hairpins, L-shaped structures, V-shaped structures, alpha-alpha comers, and alpha-l-alpha motifs. Practically all the structures resulting from such a modeling were shown to exist in globular proteins. Many small proteins and domains were found to consist of only these three-helical structures. This indicated that each such three-helical structure was stable by itself and capable of independent folding of its polypeptide chain into this structure.

Models, Molecular↗
PubMed1997

A structural tree for proteins containing 3beta-corners.

A structural tree for beta-proteins with predominantly orthogonal beta-sheet packing has been constructed. The 3beta-corner, a structural motif that recurs in proteins of this class, is taken as a root structure of the tree. The 3beta-corner can be represented as a triple-stranded beta-sheet folded on to itself so that its two beta-beta-hairpins are packed approximately orthogonally in different layers and the central strand bends by approximately 90 degrees in a right-handed direction when passing from one layer to the other. The larger protein structures are obtained by stepwise addition of beta-strands to the root 3beta-corner taking into account a restricted set of rules inferred from known principles of protein structure. The protein structures that can be obtained in this way are grouped into one structural class and those found in branches of the structural tree into subclasses.

Models, Chemical↗
PubMed1997

Structural trees for protein superfamilies.

Structural trees for large protein superfamilies, such as beta proteins with the aligned beta sheet packing, beta proteins with the orthogonal packing of alpha helices, two-layer and three-layer alpha/beta proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of alpha helices and/or beta strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for alpha helices to be packed in alpha-helical layers and beta strands in beta layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of alpha helices and/or beta strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold.

Animals↗
PubMed1997

[New structural motifs in alpha-helical proteins].

Four novel structural motifs were found and characterized in alpha-helical proteins. One of them consists of three alpha helices and can be represented as a combination of an alpha-alpha corner and an L-shaped structure. Its second alpha helix is a part of both one of the two alpha helices of the alpha-alpha corner and one of the two L-structure helices. The second structural motif, named the ABCD unit, consists of four alpha helices A, B, C, and D. These are consecutive in sequence and arranged in space in such a manner that the helices B, C, and D form a left-handed superhelix and the helix A is located between the helices B and D and is approximately antiparallel to them. The third motif, alpha helix-loop-alpha helix, consists of two alpha helices and a long connection. Its alpha helices are arranged in an approximately parallel manner and together with the long connection, form a left-handed alpha-1-alpha superhelix in space. The fourth structural motif considered is formed by four consecutive alpha helices. It is named the phi motif, because its overall shape is reminiscent of the Greek letter phi. Various variants of these motifs are analyzed on numerous examples of proteins with the known spatial structures.

Protein Conformation↗
PubMed1996

A structural tree for alpha-helical proteins containing alpha-alpha-corners and its application to protein classification.

A structural tree for alpha-helical proteins and domains including alpha-alpha-corners has been constructed. The alpha-alpha-corner is taken as a root structure of the tree. The larger protein structures are obtained by stepwise addition of alpha-helices to the root alpha-alpha-corner taking into account a restricted set of rules inferred from known principles of protein structure. The protein structures that can be obtained in this way are grouped into one structural class and those found in branches of the tree into subclasses.

Animals↗
PubMed1995

Structural similarity between two-layer alpha/beta and beta-proteins.

This paper demonstrates that overall folds of two-layer alpha/beta-proteins and beta-proteins with aligned beta-sheet packings have a number of common features. First of all, there are similar recurrent folding units, the so-called abcd-units, in proteins of both the classes. There are also some larger commonly occurring structures in many representatives of these classes. The fact that these proteins belong to different structural classes and have different functions supports the idea that some physical principles governing the polypeptide chain folding rather than the evolutionary divergence or functional convergence of proteins are the basis of such similarities. The analysis reported here shows that practically all the known protein structures of these classes can be obtained by stepwise addition of secondary structure element to the abcd-units taking into account three simple rules: (1) crossing of connection regions is prohibited; (2) alpha-helices should be packed into the alpha-layer and beta-strands in to the beta-layer of the growing structure; (3) beta alpha beta-units should be folded into right-handed superhelices; three consecutive beta-strands can be folded into the similar right-handed beta beta beta-superhelix if there is at least one additional beta-strand in the layer between the first and third ones. A possible selection of a conformation of a polypeptide chain segment by its protein environment is also discussed.

Models, Molecular↗
PubMed1993

Super-secondary structures involving triple-strand beta-sheets.

Triple-strand beta-sheets having up- and -down topology are widespread in proteins and occur in two forms denoted here as S-like and Z-like beta-sheets. In many cases they are included in super-secondary structures of higher order. A number of such structures is described in this paper. An important feature of these super-secondary structures is that they have a unique handedness. Another feature is that some of them only involve S-like beta-sheets and others only Z-like beta-sheets.

Protein Folding↗
PubMed1992

A novel super-secondary structure of beta-proteins. A triple-strand corner.

A novel super-secondary structure of beta-proteins, denoted here as a triple-strand corner, is considered in this paper. This structure can be represented as an antiparallel triple-strand beta-sheet folded on itself so that the two beta-beta-hairpins are packed approximately orthogonally in different layers and the central strand bends by 90 degrees in the right-handed direction when passing from one layer to the other. In all the triple-strand corners observed in proteins, the first beta-beta-hairpins are right-handed and the second ones are left-handed when viewed from the concave sides of the corners. Arrangement of other beta-strands in the proteins involving the triple-strand corners is also examined.

Hydrogen Bonding↗
PubMed1992

The organization of potato virus X coat proteins in virus particles studied by tritium planigraphy and model building.

Potato virus X particles containing the intact, undegraded Ps form of the coat protein and particles containing the in situ degraded Pf form of the coat protein, which is devoid of 19-21 amino acids from the N-terminus, were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the tritium label was studied. The tritium planigraphy revealed that the N-terminal region of the coat protein is the most accessible region for both type of PVX particles. The C-terminal region of the coat protein in the intact virus particles is almost inaccessible to the hot tritium atoms, whereas in Pf particles this region becomes available for the tritium label. A model of PVX coat protein tertiary structure was built, taking into account the predicted secondary structure of the protein, the principles of packing alpha-helices and beta-structure in globular proteins, and known biochemical, immunological, and tritium bombardment data. In the model one beta-sheet consisting of beta-strands at regions 1-12, 14-22, and 24-33 flanks the molecule and forms the outside surface of the PVX particles.

Amino Acid Sequence↗
PubMed1991

Structure of coiled beta-beta-hairpins and beta-beta-corners.

Two types of super-secondary structure, coiled beta-beta-hairpins and beta-beta-corners, are considered in this paper. A beta-beta-corner can be represented as a long beta-beta-hairpin folded orthogonally on itself so that the strands, when passing from one layer to the other, rotate in a right-handed direction about an imaginary axis. It is shown that a beta-beta-hairpin, forming a coiled coil structure or a beta-beta-corner, is right-handed when viewed from the concave side. These unique arrangements of beta-strands in the coiled beta-beta-hairpins and beta-beta-corners are of particular value in protein modelling and prediction.

Alcohol Dehydrogenase↗