Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ARGOS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
PubMed1988

A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins.

Many eukaryotic transcriptional activator proteins, including the Xenopus 5S RNA gene activator protein TFIIIA and the HeLa cell protein Sp1, have an approximately 30 amino acid repeating motif which binds to short, specific DNA sequences. Over 150 of these sequences are now known. Based on the observed distribution of amino acid residues, a series of constraints and predictions can be proposed for the structure of the motif. A compatible three-dimensional structural model has been developed by a combination of interactive model building and refinement by molecular dynamics. The model structure consists of a two-stranded beta-hairpin stabilizing a C-terminal alpha-helix by both zinc ligands and hydrophobic interactions. Four of the residue positions on the helix N-terminus and exposed face are predicted to provide base specific ligands. Further implications of the model for DNA binding are discussed.

Amino Acid Sequence↗
PubMed1990

An attempt to unify the structure of polymerases.

With the great availability of sequences from RNA- and DNA-dependent RNA and DNA polymerases, it has become possible to delineate a few highly conserved regions for various polymerase types. In this work a DNA polymerase sequence from bacteriophage SPO2 was found to be homologous to the polymerase domain of the Klenow fragment of polymerase I from Escherichia coli, which is known to be closely related to those from Staphylococcus pneumoniae, Thermus aquaticus and bacteriophages T7 and T5. The alignment of the SPO2 polymerase with the other five sequences considerably narrowed the conserved motifs in these proteins. Three of the motifs matched reasonably all the conserved motifs of another DNA polymerase type, characterized by human polymerase alpha. It is also possible to find these three motifs in monomeric DNA-dependent RNA polymerases and two of them in DNA polymerase beta and DNA terminal transferases. These latter two motifs also matched two of the four motifs recently identified in 84 RNA-dependent polymerases. From the known tertiary architecture of the Klenow fragment of E. coli pol I, a spatial arrangement can be implied for these motifs. In addition, numerous biochemical experiments suggesting a role for the motifs in a common function (dNTP binding) also support these inferences. This speculative hypothesis, attempting to unify polymerase structure at least locally, if not globally, under the pol I fold, should provide a useful model to direct mutagenesis experiments to probe template and substrate specificity in polymerases.

Amino Acid Sequence↗
PubMed1990

Determination of reliable regions in protein sequence alignments.

Judging the significance of alignments is still a major problem in sequence comparison. We present a method to delineate reliable regions within an alignment. This differs from standard approaches in that it does not attempt to attribute one significance value to the alignment as a whole, but assesses alignment quality locally. An algorithm is provided that predicts which residue pairs in an alignment are likely to be correctly matched. The predictions are evaluated by comparison with alignments taken from tertiary structural superpositions.

Algorithms↗
PubMed1992

A data bank merging related protein structures and sequences.

A data collection which merges protein structural and sequence information is described. Structural superpositions amongst proteins with similar main-chain fold were performed or collected from the literature. Sequences taken from the protein primary structure databases were associated with the multiple structural alignments providing they were at least 50% homologous in residue identity to one of the structural sequences and at least 50% of the structural sequence residues were alignable. Such restrictions allow reasonable confidence that the primary sequences share the conformation of the tertiary structural templates, except in the less conserved loop regions. Multiple structural superpositions were collected for 38 familial groups containing a total of 209 tertiary structures; 45 structures had no superposable mates and were used individually. Other information is also provided as main-chain and side-chain conformational angles, secondary structural assignments and the like. Wedding the primary and tertiary structural data resulted in an 8-fold increase of data bank sequence entries over those associated with the known three-dimensional architectures alone.

Amino Acid Sequence↗
PubMed1992

Potential of genetic algorithms in protein folding and protein engineering simulations.

Genetic algorithms are very efficient search mechanisms which mutate, recombine and select amongst tentative solutions to a problem until a near optimal one is achieved. We introduce them as a new tool to study proteins. The identification and motivation for different fitness functions is discussed. The evolution of the zinc finger sequence motif from a random start is modelled. User specified changes of the lambda repressor structure were simulated and critical sites and exchanges for mutagenesis identified. Vast conformational spaces are efficiently searched as illustrated by the ab initio folding of a model protein of a four beta strand bundle. The genetic algorithm simulation which mimicked important folding constraints as overall hydrophobic packaging and a propensity of the betaphilic residues for trans positions achieved a unique fold. Cooperativity in the beta strand regions and a length of 3-5 for the interconnecting loops was critical. Specific interaction sites were considerably less effective in driving the fold.

Algorithms↗
PubMed1993

Quantification of secondary structure prediction improvement using multiple alignments.

The use of multiple sequence alignments for secondary structure predictions is analysed. Seven different protein families, containing only sequences of known structure, were considered to provide a range of alignment and prediction conditions. Using alignments obtained by spatial superposition of main chain atoms in known tertiary protein structures allowed a mean of 8% in secondary structure prediction accuracy, when compared to those obtained from the individual sequences. Substitution of these alignments by those determined directly from an automated sequence alignment algorithm showed variations in the prediction accuracy which correlated with the quality of the multiple alignments and distance of the primary sequence. Secondary structure predictions can be reliably improved using alignments from an automatic alignment procedure with a mean increase of 6.8%, giving an overall prediction accuracy of 68.5%, if there is a minimum of 25% sequence identity between all sequences in a family.

Amino Acid Sequence↗
PubMed1994

Easy adaptation of protein structure to sequence.

An investigation into the conservation of coarse, medium and fine grain structural properties has been performed over a data set of 175 protein tertiary structures in 34 different families, each characterized by a common core fold and a library of conserved sites formed for each family. It is shown that, while the conservation of coarse and medium grain properties correlates to the structural deviation between the proteins, fine grain properties are poorly conserved except in functional sites. This flexibility in fine grain properties suggests that folding can be viewed as an optimization process whereby side chains have freedom to position themselves as best as possible given environmental conformational constraints and that given a basic framework, the local structure is able to adapt easily to sequence variation. The conserved cores of the 34 families are used to estimate a minimal core size of 35% of the fold, consistent with buried residue considerations. Finally, conservation in side chain chi 1 torsion angles is combined with structural deviation, sequence deviation and resolution to suggest a set of example structure pairs suitable for testing automatic homology modelling programs.

Hydrogen Bonding↗
PubMed1994

Conservation of amphipathic conformations in multiple protein structural alignments.

Protein amphipathic conformations, mainly alpha-helices and beta-strands, are believed to play an important role in protein folding, stability and function. The most popular method for characterizing such structures is the hydrophobic moment. We have analyzed the distribution of hydrophobic moment characteristics (peak magnitude, amphipathic indices and characteristic frequency) in a data bank containing several families of distant sequences multiply aligned by structural superposition. Sequence fragments were classified according to alpha-helix, beta-strand, non-alpha and non-beta conformations. This data bank provided an enhanced sample space compared with those previously reported in the literature. Precautions were taken to reduce over-representation of homologous sequences. Approximately 50% of all individual alpha-helices showed a hydrophobic moment peak in the expected position of the periodicity spectrum while only 38% of individual beta-strands fell in the expected range. False positives account for a surprisingly large 14 and 36% of the non-alpha and non-beta samples respectively. Conservation of hydrophobic moment characteristics and mainly the hydrophobic peak position in the expected periodicity range was examined in the multiple alignments of the distant sequences. Helices tend to conserve more frequently their hydrophobic moment than any other conformation and yet only 13% of all helical segments display such conservation in three-quarters or more of the familial sequences; the similar observation for beta-strands was even lower at 9%. Nonetheless, strongly hydrophobic positions within the structural segments were more conserved than expected.

Amino Acid Sequence↗
PubMed1994

Intramolecular cavities in globular proteins.

An analysis of internal cavities in 121 protein chains has been undertaken to improve the characterization of their occurrence, morphology and role in protein tertiary structure, including an analysis of the optimal probe size for use in their detection. A number of basic cavity characteristics were elucidated. Cavities are non-artefactual and apparently independent of the method of structure determination, resolution and refinement of the data. Overall cavity volume increases with protein size and yet constitutes only a small fraction of the total protein volume but cavities are nearly always present in proteins > 100 residues in size. They are most commonly found in the protein core. 'Empty' and solvent-containing cavities have been compared and solvated cavities found to possess a more polar surface; the two classes are also seen to exhibit different amino acid type and secondary structural preferences. In general, residues that enclose cavities do not display any extra local mobility relative to their surrounding environments. Water-containing cavities do not impose volume restrictions upon their internal solvent beyond that of bulk solvent and permit good hydrogen bonding. These results should prove useful in protein modelling and design.

Amino Acids↗
PubMed1995

Increasing thermal stability of subtilisin from mutations suggested by strongly interacting side-chain clusters.

In this paper we present for seven subtilisin structures a systematic comparison of densely packed side-group clusters (defined as an ensemble of side chains with extensive internal atomic contacts as compared with those made with the surrounding protein environment and measured relative to the maximum possible for each residue type). Spatially consistent clusters are observed at structurally equivalent positions in the proteins, as revealed by careful multiple superpositioning of the respective backbone atoms. The clusters are positioned at strategic loop-connecting sites near the protein surfaces. The residues within consistent clusters displaying extensive association show varying conservation at structurally equivalent alignment sites. Suggestions for residue substitutions, as observed over the seven tertiary structures, were taken from the cluster positions and were shown to be consistent with a number of point mutations in one of the seven structures (savinase) that result in increased thermal stability.

Amino Acid Sequence↗
PubMed1995

Detection of internal cavities in globular proteins.

We have undertaken a study of internal cavities in five protein structure groups, each containing different crystallographic structure determinations of the same protein, to understand better the nature of packing defects in protein tertiary architectures. Our results show that cavity detection and consistency of detection are highly dependent on probe and cavity size, cavity position within the globular protein and the local "quality' (r.m.s. deviation) of structural consistency within the group. The consistency of solvent placement within cavities has also been examined. We provide guidelines for estimating the likelihood of a given cavity to be an actual packing defect or to be a result of experimental error.

Animals↗
PubMed1996

Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation.

The hydrophobic part of the solvent-accessible surface of a typical monomeric globular protein consists of a single, large interconnected region formed from faces of apolar atoms and constituting approximately 60% of the solvent-accessible surface area. Therefore, the direct delineation of the hydrophobic surface patches on an atom-wise basis is impossible. Experimental data indicate that, in a two-state hydration model, a protein can be considered to be unified with its first hydration shell in its interaction with bulk water. We show that, if the surface area occupied by water molecules bound at polar protein atoms as generated by AUTOSOL is removed, only about two-thirds of the hydrophobic part of the protein surface remains accessible to bulk solvent. Moreover, the organization of the hydrophobic part of the solvent-accessible surface experiences a drastic change, such that the single interconnected hydrophobic region disintegrates into many smaller patches, i.e. the physical definition of a hydrophobic surface region as unoccupied by first hydration shell water molecules can distinguish between hydrophobic surface clusters and small interconnecting channels. It is these remaining hydrophobic surface pieces that probably play an important role in intra- and intermolecular recognition processes such as ligand binding, protein folding and protein-protein association in solution conditions. These observations have led to the development of an accurate and quick analytical technique for the automatic determination of hydrophobic surface patches of proteins. This technique is not aggravated by the limiting assumptions of the methods for generating explicit water hydration positions. Formation of the hydrophobic surface regions owing to the structure of the first hydration shell can be computationally simulated by a small radial increment in solvent-accessible polar atoms, followed by calculation of the remaining exposed hydrophobic patches. We demonstrate that a radial increase of 0.35-0.50 A resembles the effect of tightly bound water on the organization of the hydrophobic part of the solvent-accessible surface.

Algorithms↗
PubMed1996

Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence.

Existing approaches to protein secondary structure prediction from the amino acid sequence usually rely on the statistics of local residue interactions within a sliding window and the secondary structural state of the central residue. The practically achieved accuracy limit of such single residue and single sequence prediction methods is 65% in three structural stages (alpha-helix, beta-strand and coil). Further improvement in the prediction quality is likely to require exploitation of various aspects of three-dimensional protein architecture. Here we make such an attempt and present an accurate algorithm for secondary structure prediction based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence. The unique feature of our approach involves database-derived statistics on residue type occurrences in different classes of beta-bridges to delineate interacting beta-strands. The alpha-helical structures are also recognized on the basis of amino acid occurrences in hydrogen-bonded pairs (i,i + 4). The algorithm has a prediction accuracy of 68% in three structural stages, relies only on a single protein sequence as input and has the potential to be improved by 5-7% if homologous aligned sequences are also considered.

Algorithms↗
PubMed1996

Intrahelical side chain-side chain contacts: the consequences of restricted rotameric states and implications for helix engineering and design.

Intrahelical side chain-side chain (sc-sc) interactions are assumed to play a crucial role in the formation and stability of alpha-helices, yet it was found that only 37.2% of all helical residues are involved in such close contacts, assuming a specific minimum contact distance. The majority (58.0%) of these were detected between residues with amino acid sequence spacing i, i + 4. The low frequency of intrahelical sc-sc contacts with sequence separations i, i + 1 and i, i + 3, each observed with only about one-third of the i, i + 4 counts, can be directly and generally attributed to the absence of the g- conformation in helices for the dihedral angle chi 1. However, if it was assumed that each side chain may maximally make only one sc-sc contact, as most commonly observed, the percentage of contacting pairs increased relative to the maximum possible pairs for a given sequence spacing by a factor of approximately 4, e.g. from 20.9 to 81.7% for i, i + 4 contacts. Stereochemical reasons are also given for the observation that i, i + 3 contacts are composed largely of ion or polar pairs, while hydrophobic residues dominate the i, i + 4 contacts. No significantly increased density of intrahelical sc-sc contacts with increasing helix length was found. Although there were generally fewer intrahelical contacts between buried helical residues when more contacts were made to the tertiary protein environment, the number of intrahelical contacts did not increase with increasing solvent exposure of the helices. Implications for helix design and the packing of helices are discussed.

Amino Acid Sequence↗
PubMed1988

Sugar permeases of the bacterial phosphoenolpyruvate-dependent phosphotransferase system: sequence comparisons.

The amino acyl sequences of eight permeases (enzymes II and enzyme II-III pairs) of the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) have been analyzed. All systems show similar sizes, and six of these systems exhibit the same molecular weight +/- 2%. Several exhibit sequence homology. Characteristic NH2-terminal and COOH-terminal sequences were found. The NH2-terminal leader sequences are believed to function in targeting of the permeases to the membrane, whereas the characteristic COOH-terminal sequences are postulated to mediate interaction with the energy-coupling protein phospho HPr. One of the systems, the one specific for mannose, exhibits distinctive characteristics. A pair of probable phosphorylation sites was detected in each of the five most similar systems, those specific for beta-glucosides, sucrose, glucose, N-acetylglucosamine, and mannitol. One of the two equivalent phosphorylation sites (proposed phosphorylation site 1) was located approximately 80 residues from the COOH terminus of each system. The other site (proposed phosphorylation site 2) was located approximately 440 residues from the COOH termini of the glucose and N-acetylglucosamine systems, approximately 320 residues from the COOH termini of the beta-glucoside and sucrose systems, and 381 residues from the COOH terminus of the mannitol system. Intragenic rearrangement during evolutionary history may account for the different positions of phosphorylation sites 2 in the different PTS permeases. More extensive intragenic rearrangements may have given rise to entirely different positions of phosphorylation in the glucitol, mannose, and lactose systems. A single, internal amphipathic alpha-helix with characteristic features was found in each of seven of the eight enzymes II. The lactose-specific enzyme III of Staphylococcus aureus was unique in possessing a COOH-terminal amphipathic alpha-helix rich in basic amino acyl residues. Possible functions for these amphipathic segments are discussed.

Amino Acid Sequence↗
PubMed2000

Does the failure to acquire helminthic parasites predispose to Crohn's disease?

Two polarized patterns (Th1 and Th2) of cytokines regulate inflammatory responses. Each cytokine pattern inhibits production of the opposing pattern. Lymphocytes from inflamed intestine due to Crohn's disease secrete a Th1 pattern of cytokines. Crohn's disease is most prevalent in highly industrialized countries with temperate climates. It occurs rarely in tropical third world countries with poor sanitation. We propose that exposure to an environmental agent predisposes individuals to Crohn's disease. Parasitic worms (helminths) are common in tropical climates and in populations subject to crowding and poor sanitation. Children are most subject to helminthic colonization. Many helminths live within or migrate through the human gut where they interact with the mucosal immune system. The host mounts a mucosal response that includes Th2 cytokine production limiting helminthic colonization. Helminths and their eggs probably are the most potent stimulators of mucosal Th2 responses. The Th2 response provoked by parasitic worms can modulate immune reactions to unrelated parasitic, bacterial, and viral infections. Many people in developed countries now live in increasingly hygienic environments, avoiding exposure to helminths. Perhaps failure to acquire these parasites and experience mucosal Th2 conditioning predisposes to Crohn's disease, which is an overly active Th1 inflammation.

Animals↗