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At least 19 recordsLinked to original sources
PubMed1975

Fish rhabdoviruses: comparative study of protein structure.

Proteins from four fish rhabdoviruses have been studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The viruses were: trout viral hemorrhagic septicemia (VHS), infectious hematopoietic necrosis virus (IHN), spring viremia virus of carp (SVC), and the pike fry rhabdovirus (PFR). For the two salmonid viruses (VHS-IHN), gel electrophoresis indicated the proteins, with molecular weights estimated to be 190,000, 80,000, 38,000, 25,000, and 19,000, respectively. The electrophoretic profile of the two other viruses (SVC-PFR) revealed four major proteins with molecular weights of 190,000 80,000 42,000 and 21,000, respectively. In this case a minor component with 50,000 daltons was found. For each virus only one protein was found to be glycosylated, i.e., the one with a molecular weight of 80,000. A major protein (molecular weight between 38,000 and 42,000) was found to be associated with the nucleocapsid. All these results revealed marked similarities in protein structure between the four fish rhabdoviruses and the previously well-characterized members of rhabdovirus group. However, one can distinguish two groups of viruses: the first one is composed of salmonid viruses (VHS and IHN) with a protein structure comparable to that of rabies virus and potato yellow dwarf virus; the second one is composed of carp and pike viruses, having a protein structure very similar to that of vesicular stomatitis virus.

Animals↗
PubMed1992

IPSA-Inductive Protein Structure Analysis.

The Inductive Structure Protein Analysis (IPSA) project presents a new method for investigating protein structure. IPSA includes the creation of a new database which was designed specifically for the analysis of protein structure by statistics and machine learning. The Protein Representation Language (PRL) database includes explicit and symbolic representations of geometrical, topological and chemophysical information about secondary structures and the relationships between secondary structures. The IPSA methodology consists of: the use of PRL information to produce a new database of examples of secondary structures which associate together (examples of possible super-secondary structures); then the use of a variety of clustering techniques to produce a consensus clustering of these examples (super-secondary structures); these super-secondary structures are finally examined to uncover any biological features of significance. We have applied this method to find simple super-secondary structures consisting of pairs of alpha-helices. We found four well-defined super-secondary structures, one formed exclusively by long range interactions, and another in association with an additional element of secondary structure (alpha t alpha-motif). Examinations were carried out using homologous pairs and conformational fits which confirm our clustering.

Cluster Analysis↗
PubMed1992

[A structural protein study of the influenza A (H1N1) virus by polyacrylamide gel electrophoresis].

Influenza is an acute respiratory disease typically appearing as an epidemic. Three immunological types of the influenza virus are known: A, B and C. Continually, antigen changes occur, especially in type A. Therefore, a comparative study was carried out on 4 influenza A(H1N1) virus strains in relation to protein structure (surface antigens), by using polyacrylamide gel electrophoresis by the modified Laemmli method. The objective was to compare the structural proteins of the A/Havana/1292/78 (H1N1) national strain with the proteins of 3 international pattern strains. In all the cases, 6 bands were detected by densitometry. In the 4 strains studied the most abundant protein was M. Great differences between the Cuban strain and the 3 international patterns were not seen.

Antigens, Viral↗
PubMed1992

A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding.

An automated method for the optimal placement of polar hydrogens in a protein structure is described. This method treats the polar, side chain hydrogens of lysine, serine, threonine, and tyrosine and the amino terminus of a protein. The program, called NETWORK, divides the potential hydrogen-bonding pairs of a protein into groups of interacting donors and acceptors. A search is conducted on each of the local groups to find an arrangement which forms the most hydrogen bonds. If two or more arrangements have the same number of hydrogen bonds, the arrangement with the shortest set of hydrogen bonds is selected. The polar hydrogens of the histidyl side chain are specifically treated, and the ionization state of this residue is allowed to change, if this change results in additional hydrogen bonds for the local group. The program will accept Protein Data Bank as well as Biosym-format coordinate files. Input and output routines can be easily modified to accept other coordinate file formats. The predictions from this method are compared to known hydrogen positions for bovine pancreatic trypsin inhibitor, insulin, RNase-A, and trypsin for which the neutron diffraction structures have been determined. The usefulness of this program is further demonstrated by a comparison of molecular dynamics simulations for the enzyme cytochrome P-450cam with and without using NETWORK.

Animals↗
PubMed1991

Mammalian reoviruses contain a myristoylated structural protein.

The structural protein mu 1 of mammalian reoviruses was noted to have a potential N-myristoylation sequence at the amino terminus of its deduced amino acid sequence. Virions labeled with [3H]myristic acid were used to demonstrate that mu 1 is modified by an amide-linked myristoyl group. A myristoylated peptide having a relative molecular weight (Mr) of approximately 4,000 was also shown to be a structural component of virions and was concluded to represent the 4.2-kDa amino-terminal fragment of mu 1 which is generated by the same proteolytic cleavage that yields the carboxy-terminal fragment and major outer capsid protein mu 1C. The myristoylated 4,000-Mr peptide was found to be present in reovirus intermediate subviral particles but to be absent from cores, indicating that it is a component of the outer capsid. A distinct large myristoylated fragment of the intact mu 1 protein was also identified in intermediate subviral particles, but no myristoylated mu-region proteins were identified in cores, consistent with the location of mu 1 in the outer capsid. Similarities between amino-terminal regions of the reovirus mu 1 protein and the poliovirus capsid polyprotein were noted. By analogy with other viruses that contain N-myristoylated structural proteins (particularly picornaviruses), we suggest that the myristoyl group attached to mu 1 and its amino-terminal fragments has an essential role in the assembly and structure of the reovirus outer capsid and in the process of reovirus entry into cells.

Amino Acid Sequence↗
PubMed1976

Structural proteins in the myofilaments and regulation of contraction in vertebrate smooth muscle.

The contractile systems of vertebrate smooth and striated muscles are compared. Smooth muscles contain relatively large amounts of actin and tropomyosin organized into thin filaments, and smaller amounts of myosin in the form of thick filaments. The protein contents are consistent with observed thin:thick filament ratios of about 15-18:1 in smooth compared to 2:1 in striated muscle. The basic characteristics of both types of contractile proteins are similar; but there are a variety of quantitative differences in protein structures, enzymatic activities and filament stabilities. Biochemical and X-ray diffraction data generally support recent ultrastructural evidence concerning the organization of the myofilaments in smooth muscle, although a basic contractile unit comparable to the sarcomere in striated muscle has not been discerned. Myofilament interactions and contraction in smooth muscle are controlled by changes in the Ca2+ concentration. Recent evidence suggests the Ca2+-binding regulatory site is associated with the myosin in vertebrate smooth muscle (as in a variety of invertebrate muscles), rather than with troponin which is the regulatory protein associated with the thin filament in vertebrate striated muscle.

Actomyosin↗
PubMed1991

Brave new proteins: what evolution reveals about protein structure.

Synthetic proteins provide important information about the principles of protein structure. They illuminate the processes of natural protein evaluation, but are not limited by these processes. Here, we review studies of several mutant proteins and discuss the general principles that can be derived from them.

Animals↗
PubMed1990

The expert system approach to predicting protein structure.

Prediction of protein structure is an open-ended problem. Since an approach from first principles cannot be taken in reasonable computer time, short-cuts using further data are necessary. Such data include information about the specific protein in question, and information in databases which are about proteins in general. Is it possible to write a general, flexible 'superalgorithm' which would suit most circumstances? If so, it would seem likely to overcome one of the most understated but nonetheless greatest difficulties associated with molecular modelling and computer-aided drug design--reproducibility. To this end, a 'polymorphic programming environment' has been developed which represents both an expert system and a high-level language for theoretical chemists and molecular biologists. This language is GLOBAL (Ball et al., 1990). In a series of earlier studies, and more recently by means of GLOBAL itself, the nature of reproducibility and its rather surprising limits have been explored, and in general the current status and future potential of protein modelling have been examined.

Expert Systems↗
PubMed1990

Protein structure and function at low temperatures.

Proteins represent the major components in the living cell that provide the whole repertoire of constituents of cellular organization and metabolism. In the process of evolution, adaptation to extreme conditions mainly referred to temperature, pH and low water activity. With respect to life at low temperatures, effects on protein structure, protein stability and protein folding need consideration. The sequences and topologies of proteins from psychrophilic, mesophilic and thermophilic organisms are found to be highly homologous. Commonly, adaptive changes refer to multiple alterations of the amino acid sequence, which presently cannot be correlated with specific changes of structure and stability; so far it has not been possible to attribute specific increments in the free energy of stabilization to well-defined amino-acid exchanges in an unambiguous way. The stability of proteins is limited at high and low temperatures. Their expression and self-organization may be accomplished under conditions strongly deviating from optimum growth conditions. Molecular adaptation to extremes of temperature seems to be accompanied by a flattening of the temperature profile of the free energy of stabilization. In principle, the free energy of stabilization of proteins is small compared to the total molecular energy. As a consequence, molecular adaptation to extremes of physical conditions only requires marginal alterations of the intermolecular interactions and packing density. Careful statistical and structural analyses indicate that altering the number of ion pairs and hydrophobic interactions allows the flexibility of proteins to be adjusted so that full catalytic function is maintained at varying temperatures.

Drug Stability↗
PubMed1992

The muscle-derived lens of a squid bioluminescent organ is biochemically convergent with the ocular lens. Evidence for recruitment of aldehyde dehydrogenase as a predominant structural protein.

Many of the structural proteins of ocular lenses, commonly referred to as crystallins, are identical to specific enzymes or the result of a recent gene duplication (Piatigorsky, J., and Wistow, G. (1991) Science 252, 1078-1079). One such enzyme, aldehyde dehydrogenase (ALDH), has been recruited as a lens crystallin in certain mammals (Wistow, G., and Kim, H. (1991) J. Mol. Evol. 32, 262-269) and cephalopods (Tomarev, S., Zinovieva, R., and Piatigorsky, J. (1991) J. Biol. Chem. 266, 24226-24231). We report here that a transparent tissue, derived from muscle but functioning as a lens in the light-emitting organ of a squid, Euprymna scolopes, shows striking biochemical convergence with the epidermally derived ocular lenses of some mammals and cephalopods. In the light organ lens of E. scolopes, an ALDH-like protein is the predominant molecular component. The typical muscle-specific proteins are replaced as the dominant species by a protein composed of 54-kDa subunits. This protein, which we designate as L-crystallin, constitutes approximately 70% of the total soluble protein of the light organ lens. The amino acid sequences of three peptides of L-crystallin (approximately 9% of the total protein) showed 54.5% sequence identity with human cytosolic ALDH. Using polyclonal antiserum made against L-crystallin, we found that it is present in low abundance in other tissues of the squid, including muscle and the ocular lens. This polyclonal antiserum also cross-reacted with the ALDH-like crystallins found in the ocular lenses of certain mammals and cephalopods. L-Crystallin showed no ALDH activity, which is similar to several other enzyme/crystallins, including ALDH/eta-crystallin (Wistow, G., and Kim, H. (1991) J. Mol. Evol. 32, 262-269). The characteristics of this muscle-derived lens are evidence that a common biochemical basis underlies transparency and that certain proteins may possess properties that promote their selection as lens structural proteins.

Aldehyde Dehydrogenase↗
PubMed1977

Analysis of intracellular feline leukemia virus proteins II. Generation of feline leukemia virus structural proteins from precursor polypeptides.

The synthesis and processing of feline leukemia virus (FeLV) polypeptides were studied in a chronically infected feline thymus tumor cell line, F-422, which produces the Rickard strain of FeLV. Immune precipitation with antiserum to FeLV p30 and subsequent sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to isolate intracellular FeLV p30 and possible precursor polypeptides. SDS-PAGE of immune precipitates from cells pulse-labeled for 2.5 min with [35S]methionin revealed the presence of a 60,000-dalton precursor polypeptide (Pp60) as well as a 30,000-dalton polypeptide. When cells were grown in the presence of the proline analogue L-azetidine-2-carboxylic acid, a 70,000-dalton precursor polypeptide (Pp70) was found in addition to Pp60 after a 2.5-min pulse. The cleavage of Pp60 could be partially inhibited by the general protease inhibitor phenyl methyl sulfonyl fluoride (PMSF). This partial inhibition was found to occur only if PMSF was present during pulse-labeling. Intracellular Pp70 and Pp60 and FeLV virion p70, p30, p15, p11, and p10 were subjected to tryptic peptide analysis. The results of this tryptic peptide analysis demonstrated that intracellular Pp70 and virion p70 were identical and that both contained the tryptic peptides of FeLV p30, p15, p11, and p10. Pp60 contained the tryptic peptides of FeLV P30, P15, and P10, but lacked the tryptic peptides of P11. The results of pactamycin gene ordering experiments indicated that the small structural proteins of FeLV are ordered p11-p15-p10-p30. The data indicate that the small structural proteins of FeLV are synthesized as part of a 70,000-dalton precursor. A cleavage scheme for the generation of FeLV p70, p30, p15, p11, and p10 from precursor polypeptides is proposed.

Azetidinecarboxylic Acid↗
PubMed1976

Structure and synthesis of a lipid-containing bacteriophage. Purification, chemical composition, and partial sequences of the structural proteins.

The four structural proteins of the lipid-containing bacteriophage PM2 have been purified by dissociation of the virus in the presence of acetic acid followed by a combination of gel filtration and ion-exchange chromatography in the presence of sodium dodecylsulfate and guanidine hydrochloride. Amino acid analyses of each of the proteins were performed and correlated with the properties and functions of the proteins. Protein I has the highest polarity and is the only water-soluble protein. Protein II has a rather high polarity and hydrophobicity index and probably interacts electrostatically and hydrophobically with the bilayer. Proteins III and IV have low polarities and possess the solubility properties of proteolipids. At least protein III and perhaps also protein IV may interact with the bilayer. No fatty acids are covalently linked to these proteins. Tryptic fingerprints showed that proteins I and II contain a high proportion of hydrophobic peptides, but especially protein I also contains a large number of hydrophilic peptides. Proteins III and IV have relatively few hydrophobic peptides despite their relatively high hydrophobicity. Protein IV has two distinct regions, as shown by partial sequence studies. Basic amino acids at the N-terminus would serve for interaction with the viral DNA, the following hydrophobic sequence might interact with protein III or with the bilayer.

Amino Acid Sequence↗
PubMed2026

Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures.

Pairwise sequence comparisons are at the center of molecular evolutionary analyses. However, viral pairwise comparisons are challenging because extreme mutation rates and evolutionary pressure cause genomes to diverge rapidly, limiting detectable sequence similarity to fewer than 3% of virus pairs. To overcome these limitations, we compared viruses based on structural similarity, using predicted protein structures from ColabFold and Foldseek to define protein fold clusters. We represented each virus genome by its protein structural content. Pairwise similarities between viruses were then quantified using the Jaccard index based on the presence or absence of protein fold clusters. Using a recently established viral protein fold database, we compared all pairs of eukaryotic viruses in RefSeq. This approach increased the proportion of comparable viral genome pairs from 2.4% to 16.5%. Using this protein-fold representation of viruses, we were able to accurately predict viral families with an average sensitivity of 85.9%. Investigation of viral families showing limited sensitivity with this approach uncovered a laterally transferred structural cluster (Rep/NS1) broadly shared across diverse viral families and found in the avian lineage of adenoviruses. Sequence homology suggests that this Rep was acquired from Parvoviridae, but the protein is mutant in the ATPase active site, indicating possible exaptation toward a purely DNA-binding function. In Gammapapillomaviruses, several E4 clusters were associated with human tropism. In summary, by representing viruses with structural protein clusters, we can classify highly divergent viruses, trace lateral gene transfer, and uncover features associated with viral host range.

Humans↗
PubMed1992

Intracellular transport of rubella virus structural proteins expressed from cloned cDNA.

The structural proteins of rubella virus consist of a nucleocapsid protein (C) and two membrane-embedded spike glycoproteins (E1 and E2). Since many reports have suggested that rubella virus buds intracellularly, we have examined the intracellular transport of the structural proteins in the absence of virion formation, particularly whether the membrane glycoproteins are retained inside the cell or are transported to the cell surface. We have expressed the structural proteins from cloned cDNA either alone or in different combinations, have examined the intracellular location of the proteins by immunofluorescence and using biochemical methods, and have looked for plasma membrane-localized E1 or E2 using a cell surface biotinylation assay. The C protein was found in the Golgi complex when expressed with E2 and E1; without the membrane glycoproteins, C appeared to remain in the endoplasmic reticulum (ER). When expressed alone, E1 was retained in a pre-Golgi compartment, and was not detected at the cell surface in any cell line. When E2 was expressed alone a small fraction could be detected at the cell surface, but the majority was retained intracellularly, apparently in the ER and the Golgi. Both proteins were transported to the surface when they were expressed together, albeit with low efficiencies in all cell lines. These data suggest that, although neither glycoprotein carries a dominant intracellular retention signal, E2 and E1 are largely retained in the Golgi even when present as a transport-competent heterodimer.

Amino Acid Sequence↗
PubMed1991

High level expression of the major core protein VP7 and the non-structural protein NS3 of bluetongue virus in yeast: use of expressed VP7 as a diagnostic, group-reactive antigen in a blocking ELISA.

The major core protein VP7 and a non-structural protein NS3 of bluetongue virus serotype 1 have been synthesized from recombinant plasmids using both an in vitro transcription/translation system and a yeast expression system. Bluetongue virus genes were transcribed under the control of the bacteriophage SP6 promoter and the regulatable yeast metallothionein promoter. An indirect ELISA showed that expression of NS3 in yeast was inducible with 1 mM CuSO4 and VP7 synthesis was constitutive but could be further induced. The preferred procedure for antigen extraction from yeast was sonication for VP7 and SDS/NaOH treatment for NS3. Yeast-expressed VP7 antigen and a monoclonal antibody were used in a blocking ELISA to distinguish sera raised against bluetongue virus serotypes from those generated to viruses of the epizootic haemorrhagic disease serogroup.

Antigens, Viral↗