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H Wolfson

Publications and source records attributed to H Wolfson.

18 recordsLinked to original sources
PubMed2003

MASS: multiple structural alignment by secondary structures.

We present a novel method for multiple alignment of protein structures and detection of structural motifs. To date, only a few methods are available for addressing this task. Most of them are based on a series of pairwise comparisons. In contrast, MASS (Multiple Alignment by Secondary Structures) considers all the given structures at the same time. Exploiting the secondary structure representation aids in filtering out noisy results and in making the method highly efficient and robust. MASS disregards the sequence order of the secondary structure elements. Thus, it can find non-sequential and even non-topological structural motifs. An important novel feature of MASS is subset alignment detection: It does not require that all the input molecules be aligned. Rather, MASS is capable of detecting structural motifs shared only by a subset of the molecules. Given its high efficiency and capability of detecting subset alignments, MASS is suitable for a broad range of challenging applications: It can handle large-scale protein ensembles (on the order of tens) that may be heterogeneous, noisy, topologically unrelated and contain structures of low resolution.

Algorithms↗
PubMed2002

Lead exposure in scaffolders during refurbishment construction activity--an observational study.

The toxic effects of lead have been known for centuries. Occupational exposure to this chemical hazard has also been well documented in relation to various industry groups, including construction, where workers are recognized as being significantly exposed during refurbishment work, in particular through inhalation and ingestion of lead fumes and dust. It is easy to see how so-called 'burners', 'cutters' and 'blasters'--workers directly involved in removing old lead paint--may become exposed; the influence of personal hygiene, smoking, eating/drinking and nail biting has also been documented in the literature. We now report on one group, the scaffolders, not previously considered to be at risk. Although not directly involved in the paint removal, anecdotal and personal experience of the authors indicate that these workers, who erect and later dismantle access structures during the renovation of previously lead-painted surfaces, may take up significant amounts of lead, mainly by ingestion, to raise their personal blood lead levels (and body burden) in line with recognized 'lead workers'. Exposures of this magnitude would also bring the scaffolders involved in such refurbishment work under the Control of Lead at Work Regulations 1998. The authors make various recommendations on measures to minimize and control exposure of scaffolders to lead.

Construction Materials↗
PubMed2001

Protein folding: binding of conformationally fluctuating building blocks via population selection.

Here we review different aspects of the protein folding literature. We present a broad range of observations, showing them to be consistent with a general hierarchical protein folding model. In such a model, local relatively stable, conformationally fluctuating building blocks bind through population selection, to yield the native state. The model includes several components: (1) the fluctuating building blocks that constitute local minima along the polypeptide chain, which even if unstable still possess higher population times than all alternate conformations; (2) the landscape around the bottom of the funnels; (3) the consideration that protein folding involves intramolecular recognition; (4) similar landscapes are observed for folding and for binding, and that (5) the landscape is dynamic, changing with the conditions. The model considers protein folding to be guided by native interactions. The reviewed literature includes the effects of changing the conditions, intermediates and kinetic traps, mutations, similar topologies, fragment complementation experiments, fragments and pathways, focusing on one specific well-studied example, that of the dihydrofolate reductase, chaperones, and chaperonines, in vivo vs. in vitro folding, still using the dihydrofolate example, amyloid formation, and molecular "disorder". These are consistent with the view that binding and folding are similar events, with the differences stemming from different stabilities and hence population times.

Models, Molecular↗
PubMed2000

Conservation of polar residues as hot spots at protein interfaces.

A number of studies have addressed the question of which are the critical residues at protein-binding sites. These studies examined either a single or a few protein-protein interfaces. The most extensive study to date has been an analysis of alanine-scanning mutagenesis. However, although the total number of mutations was large, the number of protein interfaces was small, with some of the interfaces closely related. Here we show that although overall binding sites are hydrophobic, they are studded with specific, conserved polar residues at specific locations, possibly serving as energy "hot spots." Our results confirm and generalize the alanine-scanning data analysis, despite its limited size. Previously Trp, Arg, and Tyr were shown to constitute energetic hot spots. These were rationalized by their polar interactions and by their surrounding rings of hydrophobic residues. However, there was no compelling reason as to why specifically these residues were conserved. Here we show that other polar residues are similarly conserved. These conserved residues have been detected consistently in all interface families that we have examined. Our results are based on an extensive examination of residues which are in contact across protein interfaces. We utilize all clustered interface families with at least five members and with sequence similarity between the members in the range of 20-90%. There are 11 such clustered interface families, comprising a total of 97 crystal structures. Our three-dimensional superpositioning analysis of the occurrences of matched residues in each of the families identifies conserved residues at spatially similar environments. Additionally, in enzyme inhibitors, we observe that residues are more conserved at the interfaces than at other locations. On the other hand, antibody-protein interfaces have similar surface conservation as compared to their corresponding linear sequence alignment, consistent with the suggestion that evolution has optimized protein interfaces for function.

Amino Acid Sequence↗
PubMed1999

Flexible structural comparison allowing hinge-bending, swiveling motions.

We present an efficient method for flexible comparison of protein structures, allowing swiveling motions. In all currently available methodologies developed and applied to the comparisons of protein structures, the molecules are considered to be rigid objects. The method described here extends and generalizes current approaches to searches for structural similarity between molecules by viewing proteins as objects consisting of rigid parts connected by rotary joints. During the matching, the rigid subparts are allowed to be rotated with respect to each other around swiveling points in one of the molecules. This technique straightforwardly detects structural motifs having hinge(s) between their domains. Whereas other existing methods detect hinge-bent motifs by initially finding the matching rigid parts and subsequently merging these together, our method automatically detects recurring substructures, allowing full 3 dimensional rotations about their swiveling points. Yet the method is extremely fast, avoiding the time-consuming full conformational space search. Comparison of two protein structures, without a predefinition of the motif, takes only seconds to one minute on a workstation per hinge. Hence, the molecule can be scanned for many potential hinge sites, allowing practically all C(alpha) atoms to be tried as swiveling points. This algorithm provides a highly efficient, fully automated tool. Its complexity is only O(n2), where n is the number of C(alpha) atoms in the compared molecules. As in our previous methodologies, the matching is independent of the order of the amino acids in the polypeptide chain. Here we illustrate the performance of this highly powerful tool on a large number of proteins exhibiting hinge-bending domain movements. Despite the motions, known hinge-bent domains/motifs which have been assembled and classified, are correctly identified. Additional matches are detected as well. This approach has been motivated by a technique for model based recognition of articulated objects originating in computer vision and robotics.

Algorithms↗
PubMed1999

Folding funnels and conformational transitions via hinge-bending motions.

In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of "induced fit" binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels, a priori contain both the "open" and the "closed" conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes. This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield "domain swapping;" the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac repressor. Nonallosteric subunit transitions are also addressed, with some examples (aspartate receptor and BamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations.

Adenylate Kinase↗
PubMed1998

Molecular shape comparisons in searches for active sites and functional similarity.

Here we examine the reliability of surface comparisons in searches for active sites in proteins. Detection of a patch of surface on one protein which is similar to an active site in another, may suggest similarities in enzymatic mechanisms, in enzyme functions and implicate a potential target for ligand/inhibitor design. Specifically, we compare the efficacy of molecular surface comparisons with comparisons of surface atoms and of C(alpha) backbone atoms. We further investigate comparisons of specific atoms, belonging to a predefined pattern of catalytic residues versus comparisons of molecular surfaces and, separately, of surface atoms. This aspect is particularly relevant, as catalytic residues may be (partially) buried. We also explore active site comparisons versus comparisons in which the entire molecular surfaces are scanned. While here we focus on the geometrical aspect of the problem, we also investigate the effect of adding residue labels in these comparisons. Our extensive studies cover the serine proteases, containing the highly conserved triad motif, and the chorismate mutases. Since such active site comparisons entail comparisons between unconnected points in 3D space, an order-independent comparison technique is necessary. The geometric hashing algorithm is ideally suited to handling such a task. It can perform both global shape matching for the whole surfaces of large protein molecules and searching for local shape similarities for small surface motifs. Our results show that molecular surface comparisons work best when the similarity is high. As the similarity deteriorates, the number of potential solutions increases rapidly, making their ranking difficult, particularly when scanning entire molecular surfaces. Utilizing atomic coordinates directly appears more adequate under such circumstances.

Binding Sites↗
PubMed1995

A 3D sequence-independent representation of the protein data bank.

Here we address the following questions. How many structurally different entries are there in the Protein Data Bank (PDB)? How do the proteins populate the structural universe? To investigate these questions a structurally non-redundant set of representative entries was selected from the PDB. Construction of such a dataset is not trivial: (i) the considerable size of the PDB requires a large number of comparisons (there were more than 3250 structures of protein chains available in May 1994); (ii) the PDB is highly redundant, containing many structurally similar entries, not necessarily with significant sequence homology, and (iii) there is no clear-cut definition of structural similarity. The latter depend on the criteria and methods used. Here, we analyze structural similarity ignoring protein topology. To date, representative sets have been selected either by hand, by sequence comparison techniques which ignore the three-dimensional (3D) structures of the proteins or by using sequence comparisons followed by linear structural comparison (i.e. the topology, or the sequential order of the chains, is enforced in the structural comparison). Here we describe a 3D sequence-independent automated and efficient method to obtain a representative set of protein molecules from the PDB which contains all unique structures and which is structurally non-redundant. The method has two novel features. The first is the use of strictly structural criteria in the selection process without taking into account the sequence information. To this end we employ a fast structural comparison algorithm which requires on average approximately 2 s per pairwise comparison on a workstation. The second novel feature is the iterative application of a heuristic clustering algorithm that greatly reduces the number of comparisons required. We obtain a representative set of 220 chains with resolution better than 3.0 A, or 268 chains including lower resolution entries, NMR entries and models. The resulting set can serve as a basis for extensive structural classification and studies of 3D recurring motifs and of sequence-structure relationships. The clustering algorithm succeeds in classifying into the same structural family chains with no significant sequence homology, e.g. all the globins in one single group, all the trypsin-like serine proteases in another or all the immunoglobulin-like folds into a third. In addition, unexpected structural similarities of interest have been automatically detected between pairs of chains. A cluster analysis of the representative structures demonstrates the way the "structural universe' is populated.

Algorithms↗
PubMed1994

Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.

We have recently developed a fast approach to comparisons of 3-dimensional structures. Our method is unique, treating protein structures as collections of unconnected points (atoms) in space. It is completely independent of the amino acid sequence order. It is unconstrained by insertions, deletions, and chain directionality. It matches single, isolated amino acids between 2 different structures strictly by their spatial positioning regardless of their relative sequential position in the amino acid chain. It automatically detects a recurring 3D motif in protein molecules. No predefinition of the motif is required. The motif can be either in the interior of the proteins or on their surfaces. In this work, we describe an enhancement over our previously developed technique, which considerably reduces the complexity of the algorithm. This results in an extremely fast technique. A typical pairwise comparison of 2 protein molecules requires less than 3 s on a workstation. We have scanned the structural database with dozens of probes, successfully detecting structures that are similar to the probe. To illustrate the power of this method, we compare the structure of a trypsin-like serine protease against the structural database. Besides detecting homologous trypsin-like proteases, we automatically obtain 3D, sequence order-independent, active-site similarities with subtilisin-like and sulfhydryl proteases. These similarities equivalence isolated residues, not conserving the linear order of the amino acids in the chains. The active-site similarities are well known and have been detected by manually inspecting the structures in a time-consuming, laborious procedure. This is the first time such equivalences are obtained automatically from the comparison of full structures. The far-reaching advantages and the implications of our novel algorithm to studies of protein folding, to evolution, and to searches for pharmacophoric patterns are discussed.

Amino Acid Sequence↗
PubMed1993

Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition.

We describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3-D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3-D C alpha motif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understanding of protein structure and biomolecular recognition. Searches for 3-D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this method in its application to two members of the globin family and to two dehydrogenases.

Alcohol Dehydrogenase↗
PubMed1993

Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications.

We present a unique sequence-order independent approach which allows examination of three dimensional structures, searching for spatially similar substructural motifs. If the amino acids composing the motifs are contiguous in the primary chain, that is, they follow each other in the sequence, a common ancestor and a divergent evolutionary process may be implied. On the other hand, if the three-dimensional substructural motif consists of amino acids whose positions in the sequences vary between the different proteins, a convergent evolution might have taken place. Starting from different, ancient sequences, mutations may have occurred that brought about formation and conservation of a truly structural motif. Such a motif might be particularly suitable for fulfilling a specific function. Clearly, in order to be able to carry out such a task one needs a technique which allows comparisons of protein structures absolutely independent of their amino acid sequence-order. Our novel, efficient, computer vision based technique treats atoms (residues) as unconnected points in space, using strictly the atomic (either all atoms or only the C alpha atoms) coordinates. The order of the residues is completely disregarded. Detection, cataloging and analysis of "real" three-dimensional, sequence-order independent motifs in the crystallographic database is expected to be an invaluable tool for protein folding. Here we demonstrate the power of the technique by applying it to alpha/beta proteins. Our studies indicate that for some of the proteins, the "classical" structural alignments (conserving the amino acid order) are the optimal ones. Nevertheless, for others, truly spatial (out of sequential-order) amino acid equivalencing results in a better geometrical match.

Biological Evolution↗
PubMed1993

Dust from cotton manufacture: changing from static to personal sampling.

Several designs of personal samplers were tested for use to collect cotton dust. The IOM personal inhalable-dust sampler was selected because: (1) collection of the whole inhalable fraction was preferred, since all inhaled sizes are under suspicion as contributing to respiratory symptoms in cotton exposure; (2) this sampler is well characterized; and (3) it was found to be practicable in the environments examined. Gauze shields to exclude 'fly' from the personal sampler were tried, but were rejected mainly because measurement of the whole inhalable fraction by a validated sampler was felt to be more appropriate. A range of processes at a representative selection of mills was assessed by a hygiene team, and classified as 'clean' or 'dirty' in terms of present standards of control. This classification agreed well with subsequent measurements using the present method, which uses a large static sampler. A personal sampling survey then showed that in about two-thirds of 'clean' processes personal exposure of at least 80% of those employed was less than about 2-2.5 mg m-3. Only one-tenth of 'dirty' processes met this standard. Personal exposure correlates poorly with the present static method, as expected, but comparison of the results suggested that a mean background level of 0.5 mg m-3 would correspond to a median personal exposure of about 2.2 mg m-3. Side-by-side measurements by the background method differed by less than 0.15 mg m-3 on about 95% of occasions. Niven et al. (to be published) have compared the IOM head used in this study with the Manchester University sampler previously used by Cinkotai et al. [Ann. occup. Hyg. 32, 103-113 (1988)] to derive a relationship between personal exposure and prevalence of byssinotic symptoms in spinners. According to Cinkotai et al.'s results the concentrations of 2-2.5 mg m-3 discussed would correspond to a prevalence of 3-5%. However, this prevalence probably reflects higher exposures in the past.

Dust↗
PubMed1993

A computer vision based technique for 3-D sequence-independent structural comparison of proteins.

A detailed description of an efficient approach to comparison of protein structures is presented. Given the 3-D coordinate data of the structures to be compared, the system automatically identifies every region of structural similarity between the structures without prior knowledge of an initial alignment. The method uses the geometric hashing technique which was originally developed for model-based object recognition problems in the area of computer vision. It exploits a rotationally and translationally invariant representation of rigid objects, resulting in a highly efficient, fully automated tool. The method is independent of the amino acid sequence and, thus, insensitive to insertions, deletions and displacements of equivalent substructures between the molecules being compared. The method described here is general, identifies 'real' 3-D substructures and is not constrained by the order imposed by the primary chain of the amino acids. Typical structure comparison problems are examined and the results of the new method are compared with the published results from previous methods. These results, obtained without using the sequence order of the chains, confirm published structural analogies that use sequence-dependent techniques. Our results also extend previous analogies by detecting geometrically equivalent out-of-sequential-order structural elements which cannot be obtained by current techniques.

Algorithms↗
PubMed1992

An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins.

As the number of available three dimensional coordinates of proteins increases, it is now recognized that proteins from different families and topologies are constructed from independent motifs. Detection of specific structural motifs within proteins aids in understanding their role and the mechanism of their operation. To aid in identification and use of these motifs it has become necessary to develop efficient methods for systematic scanning of structural databases. To date, methods of structural protein comparison suffer from at least one of the following limitations: (1) are not fully automated (require human intervention), (2) are limited to relatively similar structures, (3) are constrained to linear alignments of the structures, (4) are sensitive to insertions, deletions or gaps in the sequences or (5) are very time consuming. We present a method to overcome the above limitations. The method discovers and ranks every piece of structural similarity between the structures compared, thus allowing the simultaneous detection of real 3-D motifs in different domains, between domains, in active sites, surfaces etc. The method uses the Geometric Hashing Paradigm which is an efficient technique originally developed for Computer Vision. The algorithm exploits the geometrical constraints of rigid objects, it is especially geared towards recognition of partial structures in rigid objects belonging to large data bases and is straightforwardly parallelizable. Computer Vision techniques are for the first time applied to molecular structure comparison, resulting in an efficient, fully automated tool. The method has been tested in a number of cases, including comparisons of the haemoglobins, immunoglobulins, serine proteinases, calcium binding proteins, DNA binding proteins and others. In all examples our results were equivalent to the published results from previous methods and in some cases additional structural information was obtained by our method.

Amino Acid Sequence↗
PubMed1977

Acetylcholine receptor metabolism in a nonfusing muscle cell line.

The development and turnover of acetylcholine receptors in a nonfusing muscle cell line has been investigated using iodinated alpha-bungarotoxin as a probe for acetylcholine receptor. logarithmically growing cells do not bind toxin, while cells that have ceased cell division bind toxin at a site which has the pharmacological characteristics of an acetylcholine receptor. These binding sites are removed from the cell surface at a rate equal to 8.9 +/- 0.5% of the total surface binding sites/h and appear at a rate equal to 8.3 +/- 1.5% of the total surface binding sites/h. Appearance of new binding sites can occur for a period of 1 1/2 h in the presence of cycloheximide, during which time 15% of the surface receptors can be replaced. There is a hidden population of receptors which is not accessible to toxin without disrupting the cell. This population amounts to 35% of the Triton-extractable receptors in the cell and is composed of two classes. One class, termed a precursor receptor, appears to move from the hidden population to the cell surface, and composes about 40% of the total hidden receptor population. The second class of hidden receptors does not appear to function as a surface precursor and is neither depleted nor enriched by any of the procedures we employed. Surface receptors and hidden receptors are distinguishable on the basis of their sedimentation coefficient about 0.5 to 0.6 S lower than surface receptors. We were unable to distinguish between precursor and non-precursor hidden receptors on the basis of cursor and nonprecursor hidden receptors on the basis of their sedimentation coefficients.

Acetylcholine↗