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PubMed1969

Kinetics of incorporation of structural proteins into Sindbis virions.

The morphogenesis of Sindbis virus was studied by determining the kinetics with which newly synthesized nucleocapsid and envelope proteins appeared in virions released into the extracellular medium. Assembly of the nucleocapsid was more rapid than modification of the cellular membrane by the addition of the viral envelope protein. However, both viral structural proteins were efficiently incorporated into virions; a 0.5-hr pulse-labeling period resulted in the release of maximally labeled virus during the next hour. When protein synthesis was inhibited, release of virus soon declined even though large amounts of both viral structural proteins were present within the cell and ribonucleic acid replication was unaffected.

Animals↗
PubMed2001

Protein structure prediction.

The prediction of protein structure, based primarily on sequence and structure homology, has become an increasingly important activity. Homology models have become more accurate and their range of applicability has increased. Progress has come, in part, from the flood of sequence and structure information that has appeared over the past few years, and also from improvements in analysis tools. These include profile methods for sequence searches, the use of three-dimensional structure information in sequence alignment and new homology modeling tools, specifically in the prediction of loop and side-chain conformations. There have also been important advances in understanding the physical chemical basis of protein stability and the corresponding use of physical chemical potential functions to identify correctly folded from incorrectly folded protein conformations.

Animals↗
PubMed1999

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.

Animals↗
PubMed1994

Sequence divergence analysis for the prediction of seven-helix membrane protein structures: II. A 3-D model of human rhodopsin.

A three-dimensional (3-D) model of the transmembrane domain of human rhodopsin was predicted from the sequence divergence analysis of 42 sequences of rhodopsins and visual pigments without a template. The prediction steps include multiple sequence alignment, calculation of a variability profile of the aligned sequences, use of the variability profile to identify the boundaries of transmembrane regions, their secondary structure and packing shape in a helix bundle, prediction of side-chain conformations and structure refinement. The identification of the retinal binding site was assisted by its known covalent linkage with K296. The structural features of the predicted 3-D model are in good agreement with a low resolution electron density map of bovine rhodopsin and with residues in contact with retinal as determined experimentally.

Amino Acid Sequence↗
PubMed1985

mRNA sequence of three respiratory syncytial virus genes encoding two nonstructural proteins and a 22K structural protein.

An mRNA sequence of two human respiratory syncytial viral nonstructural protein genes and of a gene for a 22,000-molecular-weight (22K) protein was obtained by cDNA cloning and DNA sequencing. Sequences corresponding to the 5' ends of the respective transcripts were deduced directly by primer extension and dideoxy nucleotide sequencing of the mRNAs. The availability of a bicistronic clone (pRSC6) confirmed the gene order for this portion of the genome. Contrary to other unsegmented negative-stranded RNA viruses, a 19-nucleotide intercistronic sequence was present between the NS1 and NS2 genes. The translation of cloned viral sequences in the bicistronic and monocistronic clones (pRSNS1 and pRSNS2) revealed two moderately hydrophobic proteins of 15,568 and 14,703 daltons. Their similarity in molecular size explained our earlier inability to resolve these proteins. A DNA sequence of an additional recombinant plasmid (pRSA2) revealed a long open reading frame encoding a 22,156-dalton protein containing 194 amino acids. It was relatively basic and moderately hydrophobic. A protein of this size was readily translated in vitro from a viral mRNA hybrid selected by this plasmid and corresponded to an unglycosylated 22K protein seen in purified extracellular virus but not associated with detergent- and salt-resistant cores. A second open reading frame of 90 amino acids partially overlapping with the C terminus of the 22K protein was also present within this sequence. This was reminiscent of the viral matrix protein gene which was previously shown by us to contain two overlapping reading frames. The finding of three additional viral transcripts encoding at least three identifiable proteins in human respiratory syncytial virus was a novel departure from the usual genetic organization of paramyxoviruses. The 5' ends of all three transcripts had a 5'NGGGCAAAU sequence that is common to all viral transcripts analyzed so far. Although there was no obvious homology immediately upstream of the polyadenylate tail, an AGUUA (AGUAA in the case of NS2) was present between 1 and 4 nucleotides upstream of the polyadenylate end of NS1 and 22K protein mRNAs.

Amino Acid Sequence↗
PubMed2006

Delineation of protein structure classes from multivariate analysis of protein Raman optical activity data.

Vibrational Raman optical activity (ROA), measured as a small difference in the intensity of Raman scattering from chiral molecules in right and left-circularly polarized incident light, or as the intensity of a small circularly polarized component in the scattered light, is a powerful probe of the aqueous solution structure of proteins. On account of the large number of structure-sensitive bands in protein ROA spectra, multivariate analysis techniques such as non-linear mapping (NLM) are especially favourable for determining structural relationships between different proteins. Here NLM is used to map a dataset of 80 polypeptide, protein and virus ROA spectra, considered as points in a multidimensional space with axes representing the digitized wavenumbers, into readily visualizable two and three-dimensional spaces in which points close to or distant from each other, respectively, represent similar or dissimilar structures. Discrete clusters are observed which correspond to the seven structure classes all alpha, mainly alpha, alphabeta, mainly beta, all beta, mainly disordered/irregular and all disordered/irregular. The average standardised ROA spectra of the proteins falling within each structure class have distinct features characteristic of each class. A distinct cluster containing the wheat protein A-gliadin and the plant viruses potato virus X, narcissus mosaic virus, papaya mosaic virus and tobacco rattle virus, all of which appear in the mainly alpha cluster in the two-dimensional representation, becomes clearly separated in the direction of increasing disorder in the three-dimensional representation. This suggests that the corresponding five proteins, none of which to date has yielded high-resolution X-ray structures, consist mainly of alpha-helix and disordered structure with little or no beta-sheet. This combination of structural elements may have functional significance, such as facilitating disorder-to-order transitions (and vice versa) and suppressing aggregation, in these proteins and also in sequences within other proteins. The use of ROA to identify proteins containing significant amounts of disordered structure will, inter alia, be valuable in structural genomics/proteomics since disordered regions often inhibit crystallization.

Animals↗
PubMedDate not supplied

[Lambdoid phage structural proteins and antigens].

The composition of structural proteins of lambdoid phages such as lambda, phi 80 434 divided by molecular weights was determined by means of SDS-disc-electrophoresis in a 15% polyacrylamide gel. The proteins of the same phages were divided by isoelectric points using an isoelectric focusing in a 5,25% polyacrylamide gel with 8 M urea and a gradient pH 7.0--3.5. The both methods brought out a composition character of the virion proteins and illustrated the high degree of similarity among the structural proteins of phages lambda and 434 and a far less similarity among the proteins lambda and phi 80. The antigenic composition of the lambdoid phage was determined and the basic antigenes were identified on one-dimensional and two-dimensional immunoelectrophoregrams. The appreciable immunochemical affinity of basic antigenes of the lambda and 434, but a partial affinity of the phages lambda and phi 80 were found. The basic protein of the head pE proved to be immunochemically similar for all three phages.

Antigens, Viral↗
PubMed2003

Changes in plasma membrane protein structure after photodynamic action in freshly isolated rat pancreatic acini. An FTIR study.

Photodynamic action of a plasma membrane-specific photosensitizer sulphonated aluminium phthalocyanine (SALPC) has been found to regulate cellular signalling pathways. The present study aimed to investigate whether SALPC photodynamic action modulates the structure of plasma membrane proteins, and as control, of model proteins. To check the photodynamic effect, intrinsic fluorescence of model proteins bovine serum albumin (BSA), phospholipase A2 (PLA2), and calmodulin were monitored continuously during photodynamic action (SALPC 1 microM, light 14,000 1x at > 580 nm). Significant decrease in fluorescence intensity was observed in BSA and PLA2, whereas the fluorescence of calmodulin was not affected. Confirming a major change in protein structure, difference IR spectrum revealed a significant downward deflection after photodynamic action in both BSA and in pancreatic acinar cells, whereas SALPC alone or light illumination alone resulted in no major deflection. Quantitative FTIR analysis indicated that in BSA, photodynamic action decreased the content of alpha-helix, increased the content of beta-turn and random structures, whereas beta-sheet remained the same; in freshly isolated rat pancreatic acini, photodynamic action decreased the content of alpha-helix and beta-sheet, increased the content of 1-turn and random structures. Taken together the fact that under the present experimental conditions SALPC mainly localized at the plasma membrane, it is concluded that SALPC photodynamic action directly modulates plasma membrane protein structure.

Animals↗
PubMed1993

Genomic organization of the structural proteins of borna disease virus revealed by a cDNA clone encoding the 38-kDa protein.

Borna disease is a rare neurological disease of sheep and horses. The etiological agent, borna disease virus (BDV), has been shown to be an RNA virus but has not been characterized sufficiently to assign it to a virus family. Previous studies have shown that three BDV-specific proteins of 14, 24 and 38 to 39 kDa are found in infected animals and cell culture (Ludwig et al., 1988, Prog. Med. Virol. 35, 107-151). cDNA clones have been isolated that encode the 14- and 24-kDa proteins; using the nucleotide sequences from these clones additional cDNAs were isolated that contained a large open reading frame (ORF) corresponding to the 38-kDa protein. Monoclonal antibodies against the BDV 38- to 39-kDa protein recognized the protein product of the large ORF. The relative gene order of the three BDV proteins (5' 38, 14, and 24 kDa 3') can be deduced from cDNAs which include portions of both the 24- and 38-kDa ORFs. The abundance of these proteins in BDV-infected animals and cultured cells suggests that these proteins are structural components of the virus. Previously all BDV-specific mRNAs (10.5, 3.6, 2.1, and 0.85 kb) were thought to be organized as overlapping 3' coterminal RNAs. Oligonucleotide probes made to the nucleotide sequence of the cDNA that encodes the 38-kDa protein identified an additional BDV-specific mRNA of 1.4 kb. This 1.4-kb mRNA species partially overlaps with the 2.1-kb RNA but is not 3' coterminal.

Amino Acid Sequence↗
PubMed2003

EVA: Evaluation of protein structure prediction servers.

EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods. EVA currently assesses servers for secondary structure prediction, contact prediction, comparative protein structure modelling and threading/fold recognition. Every day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent to the servers and their predictions are collected. The predictions are then compared to the experimental structures once a week; the results are published on the EVA web pages. Over time, EVA has accumulated prediction results for a large number of proteins, ranging from hundreds to thousands, depending on the prediction method. This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods.

Automation↗
PubMed2002

Protein structure prediction in 2002.

Central issues concerning protein structure prediction have been highlighted by the recently published summary of the fourth community-wide protein structure prediction experiment (CASP4). Although sequence/structure alignment remains the bottleneck in comparative modeling, there has been substantial progress in fully automated remote homolog detection and in de novo structure prediction. Significant further progress will probably require improvements in high-resolution modeling.

Models, Molecular↗
PubMed2001

Cloning of rainbow trout egg envelope proteins: members of a unique group of structural proteins.

All vertebrate eggs are surrounded by an extracellular envelope that protects the egg and is vital for a successful fertilization. The terminology and functions of the egg envelope vary in different vertebrate groups, but the envelope itself is consistently composed of a few major proteins that are deposited around the oocyte during oocyte growth. Here, we describe the deduced amino acid sequences and tissue expression patterns of the three major egg envelope proteins for rainbow trout (Oncorhynchus mykiss). All three vitelline envelope proteins (VEPs) are expressed in the livers of both male and female fish, with higher expression in females. In addition, VEPgamma mRNA is also detected in the female gonads. To our knowledge, this is the first time that expression of a VEP protein gene has been demonstrated to occur in more than one organ. Sequence comparison reveals that all three VEP proteins share distinct homology with their amphibian, avian, and mammalian counterparts. Whereas mammalian zona pellucida protein 3 isoforms contain two conserved serines needed for sperm binding, these are not conserved in teleost species, in which sperm entry is restricted to the micropyle. Besides the difference in VEPgamma sperm-binding function, the high sequence homology suggests that the egg envelope proteins from these distinct vertebrate groups share a common ancestry and form a unique group of structural proteins.

Amino Acid Sequence↗
PubMed1991

Proteins specified by swine transmissible gastroenteritis virus: identification of non-structural proteins by two-dimensional electrophoresis.

Four virus-induced non-structural proteins with apparent molecular weights of 11-14 kilodaltons (kDa) were identified by two-dimensional electrophoresis in cells infected by TGEV. Differences in the number of non-structural proteins were observed among virulent and attenuated TGEV strains as well as with two antigenically related feline and canine coronaviruses.

Animals↗
PubMed1993

An approach to systematic detection of protein structural motifs.

A procedure to detect similar local structures of proteins from C alpha coordinates is presented. First, the conformations of seven-residue peptide segments are approximated by a limited number of representatives, each of which is assigned a symbol. Thus, the overall conformation of a protein is represented by a symbol string. The comparison of these symbol strings using a sequence alignment technique then gives pairs of similar local structures. These pairs are considered candidates of structural motifs. The application of the procedure to the analysis of 93 proteins gave 858 pairs of similar local structures, which included several well-known structural motifs such as the nucleotide-binding beta alpha beta-unit and the calcium-binding EF hand. The characterization of amino acid patterns of similar local structures given by the procedure should be useful for the development of protein structure prediction based on the acquisition of empirical rules from a large-scale database.

Algorithms↗
PubMed1997

Sisyphus and prediction of protein structure.

The problem of predicting protein structure from the sequence remains fundamentally unsolved despite more than three decades of intensive research effort. However, new and promising methods in three-dimensional (3D), 2D and 1D prediction have reopened the field. Mean-force-potentials derived from the protein databases can distinguish between correct and incorrect models (3D). Inter-residue contacts (2D) can be detected by analysis of correlated mutations, albeit with low accuracy. Secondary structure, solvent accessibility and transmembrane helices (1D) can be predicted with significantly improved accuracy using multiple sequence alignments. Some of these new prediction methods have proven accurate and reliable enough to be useful in genome analysis, and in experimental structure determination. Moreover, the new generation of theoretical methods is increasingly influencing experiments in molecular biology.

Computers↗
PubMedDate not supplied

[Surface potential energy of peptides and conformation of amino acid residues in proteins. Preliminary results of processing using databank protein structures].

The fact of enzymatic synthesis of a protein polypeptide chain have been mentioned. The potential energy surfaces of peptides have been analysed. Based on the obtained results and characteristic peculiarity of the enzymatic reactions have been concluded that the non-glycine residues in a three-dimensional (3-D) protein structure most likely should be in the negative conformations. The analysis of the amino acid residue conformations have been performed on the 185 3-D protein structures obtained by the X-ray crystallography at high resolution. It has been shown that the changes in the protein surrounding environment, in crystalline forms and functional state of protein, bindings of the ligands and inhibitors do not lead to the changes in the polarity of non-glycine residues conformational angles phi, and in the polarity of the conformational angles omega of all residues. Based on the results, 81 independent protein structures have been selected. The preliminary results of analysis of glycine and non-glycine residue conformations occurring in these structures have been presented.

Amino Acids↗
PubMed1997

Correlation between side chain mobility and conformation in protein structures.

Thermal factors of protein atoms as determined by X-ray crystallographic techniques show a tendency to be larger in side chains with unfavourable local conformations rather than in those displaying conformational energy minima. It follows that side chain atoms are more mobile if they are in a non-rotameric configuration and that the stereochemistry of protein structures cannot be fully assessed or simulated without consideration of thermal factors that monitor flexibility in various regions of the protein. The observations should also prove useful in protein folding and design.

Amino Acids↗