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PubMedDate not supplied

[Artificial proteins with a given spatial structure and biological activity].

Biologically active fragment 131-138 of human interferon alpha 2 carrying blast-transforming activity of the protein was attached to the N-terminus of the de novo protein albebetin with predetermined tertiary structure by means of genetic engineering. The chimeric protein was expressed in a wheat germ cell-free translation system and tested for compactness, stability and biological activity. According to the tests used albebetin with interferon fragment has a compact and relatively stable structure. It binds murine thymocyte receptor with high affinity and activates efficiently thymocyte blast transformation at a concentration of 10(-11) M.

Amino Acid Sequence↗
PubMed2002

Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA.

We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 A resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar alpha+beta sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit.

Amino Acid Sequence↗
PubMed2005

Consecutive ion activation for top down mass spectrometry: improved protein sequencing by nozzle-skimmer dissociation.

Mass spectra produced by nozzle-skimmer dissociation (NSD) have been little used in the past for structural characterization. NSD cannot be used on mass-separated ions (MS/MS), and for electrosprayed protein ions, previous NSD spectra showed backbone cleavages similar to those from energetic methods such as collisionally activated dissociation (CAD) or infrared multiphoton dissociation (IRMPD). However, our experimental configuration with Fourier transform (FT) MS makes possible three consecutive steps of NSD ion activation: thermal in the entrance capillary and collisional in both the nozzle-skimmer (N-S) region and the region after the skimmer before the quadrupole entrance lens (S-Q). In the high-pressure N-S region of adjustable path length, ions undergo high-frequency, low-energy collisions to rupture weak noncovalent or covalent bonds, with these "denatured" products then subjected to high-energy collisions in the low-pressure S-Q region to cleave strong backbone bonds. These NSD spectra, plus those from variable capillary thermal activation, of 8+ to 11+ ubiquitin ions electrosprayed from denatured solution show backbone cleavages between 74 of 75 amino acid pairs, vs 66 for CAD and 50 for IRMPD in the FTMS cell. Thermal activation by the inlet capillary of the newly desolvated 6+, 7+ ubiquitin ions from electrospraying the native conformer increases the NSD yield from 8% at 56 degrees C to 96% at 76 degrees C, but with little change in product branching ratios; this capillary heating has no effect on CAD or IRMPD of these ions collected in the FTMS cell. Ion desolvation with its concomitant H-bond strengthening appears to produce a transiently stable conformer whose formation can be prevented by capillary heating. The far more complex and stable noncovalent tertiary structures of large protein ions in the gas phase have made MS/MS difficult; initial inhibition of tertiary structure formation with immediate NSD ("prefolding dissociation") appears promising for the top down characterization of a 200-kDa protein.

Amino Acid Sequence↗
PubMed1987

Detection of weak sequence homology of proteins for tertiary structure prediction.

Multiple measures of similarity were employed to detect weak homologies among protein sequences (e.g., below 30% residue identity). A set of thresholds was empirically determined, by using sample proteins of known structure, so as to select only correct pairs of sequences; correct or incorrect alignment of sequences was judged by direct comparison of corresponding conformations. The empirical criterion thus set up is applicable to the prediction of a protein structure when the structure of the other protein in the pair is known. We searched all the combinations between 84 proteins of known structure and 4610 proteins stored in a sequence database, and found about 4000 pairs of sequences which satisfied the criterion. However, after excluding such pairs of proteins that belong to the same family or superfamily, the number of pairs remaining was reduced to only 19. The reliability of these data for structural prediction is discussed.

Amino Acid Sequence↗
PubMed2006

Mitochondrial protein import: convergent solutions for receptor structure.

Complex machinery has evolved to recognise and import nuclear-encoded proteins into mitochondria. Recent work now shows that the plant Tom20 mitochondrial protein import receptor has a similar tertiary structure to animal Tom20, although the proteins are evolutionarily distinct, representing an elegant example of convergent evolution.

Animals↗
PubMed2005

Scooby-domain: prediction of globular domains in protein sequence.

Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method successfully identifies sequence regions that will form a globular structure and those that are likely to be unstructured. The method does not rely on homology searches and, therefore, can identify previously unknown domains for structural elucidation. Scooby-domain is available as a Java applet at http://ibivu.cs.vu.nl/programs/scoobywww. It may be used to visualize local properties within a protein sequence, such as average hydrophobicity, secondary structure propensity and domain boundaries, as well as being a method for fast domain assignment of large sequence sets.

Hydrophobic and Hydrophilic Interactions↗
PubMed1999

Lactic acid and protein interactions: implications for the NMR visibility of lactate in biological systems.

The addition of bovine serum albumin (BSA) to a solution of lactate and alanine resulted in the disappearance of the 1H-NMR resonances from lactate but not alanine. As temperature is increased lactate becomes increasingly NMR visible and after heating above 65 degreesC and cooling to 25 degreesC lactate binding is reduced. With a concentration of 0.2 mM BSA, there was a linear relationship between NMR visible lactate versus total lactate over a range of lactate concentrations of 0.2-35 mM (slope 0.384+/-0.003) indicating that approx. 60% of the added lactate is not visible in the 1H-NMR spectrum. With a 0.1 mM BSA solution, however, the slope was markedly higher indicating that under these conditions only 25-30% of the lactate was NMR invisible. The results from this study indicate that decreased NMR visibility of lactate in proteinaceous solutions is due to non-specific binding which is dependent on the tertiary structure of the protein. This has important implications not only for the interpretation of in vivo 1H-NMR experiments but also for 13C, and 14C studies of metabolism.

Lactates↗
PubMed2005

The powerful high pressure tool for protein conformational studies.

The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2 degrees, 3 degrees and 4 degrees structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins), induces unfolding (ataxin), is a convenient tool to study enzyme dissociation (enolase), and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase). This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

Ataxin-3↗
PubMed1993

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

A program called PROTEP is described that permits the rapid comparison of pairs of three-dimensional protein structures to identify the patterns of secondary structure elements that they have in common. The representation of the protein structures as labelled graphs, where the secondary structure elements in a protein and the spatial and angular relationships between them correspond to the nodes and edges of a graph, was developed for use with an earlier program, called POSSUM, which identified subgraph isomorphisms in protein structures. PROTEP takes this representation and uses a different and more flexible approach to locating structural patterns in pairs of proteins, using a maximal common subgraph isomorphism algorithm that is based on a clique detection procedure. A range of searches is described to demonstrate that areas of common structural overlap between protein structures taken from the Protein Data Bank can be identified both effectively and efficiently.

Algorithms↗
PubMed1993

Organisation of the chicken annexin V gene and its correlation with the tertiary structure of the protein.

Chicken annexin V (anchorin CII) is a collagen binding, membrane-associated molecule with Ca2+ channel activity. Here we report on the coding sequences, promoter region, size and distribution of exons, and exon-intron junctions of the chicken annexin V gene. It is about 25 kb long and codes for 13 short exons between 50 and 581 bp length. Exon sizes and locations of splice sites are almost completely homologous to those of the human and mouse annexin II or pigeon annexin I genes, although there is only 50-60% homology in the sequence of the corresponding proteins. The four repeat structure and symmetry of the annexin V as evident from sequence and X-ray analysis studies is only partially reflected in this highly conserved exon distribution. In the first two repeats of chicken annexin V the exons correlate with protein domains containing one, two, or three alpha-helices, while in the repeats 3 and 4 exon junctions and alpha-helical domains do not correlate. The analysis of the promoter structure revealed the absence of a typical TATA-box, but a GC-rich region which may possibly promote transcription from several start sites.

Animals↗
PubMed2003

Historical review: another 50th anniversary--new periodicities in coiled coils.

In 1953, Francis Crick and Linus Pauling both proposed models of supercoiled alpha helices ('coiled coils') for the structure of keratin. These were the first attempts at modelling the tertiary structure of a protein. Crick emphasized the packing mode of the side-chains ('knobs-into-holes'), which required a periodicity of seven residues over two helical turns (7/2) and a supercoil in the opposite sense of the constituent helices. By contrast, Pauling envisaged a broader set of periodicities (4/1, 7/2, 18/5, 15/4, 11/3) and supercoils of both senses. Crick's model became canonical and the 'heptad repeat' essentially synonymous with coiled coils, but 50 years later new crystal structures and protein sequences show that the less common periodicities envisaged by Pauling also occur in coiled coils, adding a variant packing mode ('knobs-to-knobs') to the standard model. Pauling's laboratory notebooks suggest that he searched unsuccessfully for this packing mode in 1953.

Amino Acid Motifs↗
PubMed2002

NETASA: neural network based prediction of solvent accessibility.

MOTIVATION: Prediction of the tertiary structure of a protein from its amino acid sequence is one of the most important problems in molecular biology. The successful prediction of solvent accessibility will be very helpful to achieve this goal. In the present work, we have implemented a server, NETASA for predicting solvent accessibility of amino acids using our newly optimized neural network algorithm. Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction. RESULTS: Prediction in two and three state classification systems with several thresholds are provided. Our prediction method achieved the accuracy level upto 90% for training and 88% for test data sets. Three state prediction results provide a maximum 65% accuracy for training and 63% for the test data. Applicability of neural networks for ASA prediction has been confirmed with a larger data set and wider range of state thresholds. Salient differences between a linear and exponential network for ASA prediction have been analysed. AVAILABILITY: Online predictions are freely available at: http://www.netasa.org. Linux ix86 binaries of the program written for this work may be obtained by email from the corresponding author.

Algorithms↗
PubMed2006

dbPTM: an information repository of protein post-translational modification.

dbPTM is a database that compiles information on protein post-translational modifications (PTMs), such as the catalytic sites, solvent accessibility of amino acid residues, protein secondary and tertiary structures, protein domains and protein variations. The database includes all of the experimentally validated PTM sites from Swiss-Prot, PhosphoELM and O-GLYCBASE. Only a small fraction of Swiss-Prot proteins are annotated with experimentally verified PTM. Although the Swiss-Prot provides rich information about the PTM, other structural properties and functional information of proteins are also essential for elucidating protein mechanisms. The dbPTM systematically identifies three major types of protein PTM (phosphorylation, glycosylation and sulfation) sites against Swiss-Prot proteins by refining our previously developed prediction tool, KinasePhos (http://kinasephos.mbc.nctu.edu.tw/). Solvent accessibility and secondary structure of residues are also computationally predicted and are mapped to the PTM sites. The resource is now freely available at http://dbPTM.mbc.nctu.edu.tw/.

Amino Acids↗
PubMed2003

Attenuated total reflection IR spectroscopy as a tool to investigate the orientation and tertiary structure changes in fusion proteins.

Membrane fusion proceeds via a merging of two lipid bilayers and a redistribution of aqueous contents and bilayer components. It involves transition states in which the phospholipids are not arranged in bilayers and in which the monolayers are highly curved. Such transition states are energetically unfavourable since biological membranes are submitted to strong repulsive hydration electrostatic and steric barriers. Viral membrane proteins can help to overcome these barriers. Viral proteins involved in membrane fusion are membrane associated and the presence of lipids restricts drastically the potential of methods (RMN, X-ray crystallography) that have been used successfully to determine the tertiary structure of soluble proteins. We describe here how IR spectroscopy allows to solve some of the problems related to the lipid environment. The principles of the method, the experimental setup and the preparation of the samples are briefly described. A few examples illustrate how attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy can be used to gain information on the orientation and the accessibility to the water phase of the fusogenic domain of viral proteins. Recent developments suggest that the method could also be used to detect changes located in the membrane domains and to identify intermediate structural states involved in the fusion process.

Amides↗
PubMedDate not supplied

Novel stereospecificity of the L-arabinose-binding protein.

Tertiary structure refinement at 1.7 A resolution of the liganded form of L-arabinose-binding protein from Escherichia coli has revealed a novel binding site geometry which accommodates both alpha- and beta-anomers of L-arabinose. This detailed structure analysis provides new understanding of protein-sugar interaction, the process by which the binding protein minimizes the difference in the stability of the two bound sugar anomers, and the roles of periplasmic binding proteins in active transport.

Arabinose↗
PubMed2006

The influence of urea on the structure of proteins in reversed micelles.

Static fluorescence measurements from the protein Tryptophan (Trp) residues and circular dichroism (CD) spectroscopy were used to investigate changes on the tertiary and secondary structures of the protein bovine serum albumin (BSA) and the dimeric enzyme hexokinase (HK) type PII from yeast, entrapped in reversed micelles (RMs). The latter were obtained from the amphiphilic AOT (sodium bis-2-ethylhexyl sulfosuccinate) in n-hexane, at several water to surfactant ratios, W. BSA and HK were found to be anchored at the RM interface in close contact with the surfactant layer, regardless of the size of the waterpool. For BSA, such interaction promotes partial protein unfolding, according to CD data that showed a decrease in the content of helical structure from 66% in a buffer solution to 48% in the micellar moiety. When urea was present in the micelle, further loss in helical structure occurred, thus indicating that the combined effect (micellar environment and urea) altered the BSA conformation to a greater extent than did RM or urea alone. Interestingly, Trps probed the same environment in the micelle, regardless of the presence of urea, but the fluorescence was quenched to a higher extent with urea. Thus, the fluorofore emission must have been affected either by the direct interaction of urea or by indirect exchange of water structure caused by urea interacting with water and the micellar interface. Both mechanisms might be of relevance in the solvation properties nearby the Trps. For HK, an association between the enzyme and the micelle interface was indicated in the CD spectra, which exhibited a randomized structure upon interaction, whatever the RM droplet size. The urea addition to the micelle water pool did not cause further impact on the HK conformation. In addition, the influence of urea at the RM interface was not sensed by the exposed tryptophans of the enzyme, unlike the results for BSA.

Animals↗
PubMed2007

Spectroscopic study of conformational changes accompanying self-assembly of HCV core protein.

Electron microscopy and infrared and Raman spectroscopy have been used here to study the morphology, size distribution, secondary and tertiary structures of protein particles assembled from a truncated hepatitis C virus (HCV) core protein covering the first 120 aa. Particles of pure protein, having similar morphology and size distribution of those of nucleocapsids found in sera from HCV-infected patients, have been visualized for the first time. The secondary structure of these protein particles involve beta-sheet enrichment in relation to its protein monomer. Tertiary/quaternary structure has also been studied using the dynamics of H/D exchange. With this aim infrared spectra were measured as a function of H/D exchange time and subsequently analyzed by principal component analysis and two-dimensional correlation spectroscopy. Temporal dynamics of exchange for these protein particles were as follows: arginine residues exchanged first, followed by turn and unordered structures, followed by beta-sheets which may act as linkers of protein monomers.

Arginine↗