Search PubMed⌕ Search

Biomedical subjects

M Levitt

Publications and source records attributed to M Levitt.

At least 55 records · Page 3Linked to original sources
PubMed1998

Genetic screening and ethics: European perspectives.

Analysis and comparison of genetic screening programs shows that the extent of development of programs varies widely across Europe. Regional variations are due not only to genetic disease patterns but also reflect the novelty of genetic services. In most countries, the focus for genetic screening programs has been pregnant women and newborn children. Newborn children are screened only for disorders which are treatable. Prenatal screening when provided is for conditions for which termination may be offered. The only population screening programs for adults are those for thalassaemia carrier status in Cyprus, Greece and Italy. Social responses to genetic screening range from acceptance to hostility. There is a fundamental tension between individual and community in the debates in various European countries about implementation of screening programs. Opposition to genetic screening is frequently expressed in terms of arguments about "eugenics" with insufficient regard to the meaning of the term and its implications. Only a few countries have introduced explicit legislation on genetic screening. Legislation to address discrimination may provide more safeguards than legislation protecting genetic information itself.

Adult↗
PubMed1998

Production and elimination of sulfur-containing gases in the rat colon.

Highly toxic sulfur-containing gases have been pathogenetically implicated in ulcerative colitis. Utilizing a rat model, we studied the production and elimination of sulfur-containing gases within the unperturbed colon. The major sulfur-containing gases were hydrogen sulfide (H2S), methanethiol, and dimethyl sulfide with cecal accumulation rates of 2.6, 0.096, and 0.046 microliter/min, respectively. The dependence of H2S production on dietary components was demonstrated via a sixfold reduction with fasting and a fivefold increase with carrageenan (a nonabsorbable, sulfur compound) feeding. Zinc acetate reduced cecal H2S by fivefold, indicating the importance of H2S binding by divalent cations. During passage from the cecum to the rectum, > 90% of the sulfur gases were absorbed or metabolized. An H2 35S turnover of 97%/min was observed in the isolated cecum. Thus mucosal exposure is > 10 times the measured accumulation rate. Cecal mucosal tissue very rapidly metabolized H2S and methanethiol via a nonmethylating reaction.

Animals↗
PubMed1997

A structural census of the current population of protein sequences.

We examine the occurrence of the approximately 300 known protein folds in different groups of organisms. To do this, we characterize a large fraction of the currently known protein sequences ( approximately 140,000) in structural terms, by matching them to known structures via sequence comparison (or by secondary-structure class prediction for those without structural homologues). Overall, we find that an appreciable fraction of the known folds are present in each of the major groups of organisms (e.g., bacteria and eukaryotes share 156 of 275 folds), and most of the common folds are associated with many families of nonhomologous sequences (i.e., >10 sequence families for each common fold). However, different groups of organisms have characteristically distinct distributions of folds. So, for instance, some of the most common folds in vertebrates, such as globins or zinc fingers, are rare or absent in bacteria. Many of these differences in fold usage are biologically reasonable, such as the folds of metabolic enzymes being common in bacteria and those associated with extracellular transport and communication being common in animals. They also have important implications for database-based methods for fold recognition, suggesting that an unknown sequence from a plant is more likely to have a certain fold (e.g., a TIM barrel) than an unknown sequence from an animal.

Amino Acid Sequence↗
PubMed1997

Factors affecting the ability of energy functions to discriminate correct from incorrect folds.

Eighteen low and medium resolution empirical energy functions were tested for their ability to distinguish correct from incorrect folds from three test sets of decoy protein conformations. The energy functions included 13 pairwise potentials of mean force, covering a wide range of functional forms and methods of parameterization, four potentials that attempt to detect properly formed hydrophobic cores, and one environment-based potential. the first of the three test sets consists of large ensembles of plausible conformations for eight small proteins, all of which have correct native secondary structure and are reasonably compact. The second is the set of all subconformations in a database of known protein structures applied to the sequences in that database (ungapped threading). The third is a set of ensembles of 1000 conformations each for seven small proteins taken from molecular dynamics simulations at 298 K and 498 K. Our results show that there are functions effective for each challenge set; moreover, success in one test is no guarantee of success in another. We examine the factors that seem to be important for accurate discrimination of correct structures in each of the test sets, and note that extremely simple functions are often as effective as more complex functions.

Chemical Phenomena↗
PubMed1997

A retrospective analysis of CASP2 threading predictions.

Analysis of CASP2 protein threading results shows that the success rate of structure predictions varies widely among prediction targets. We set "critical" thresholds in fold recognition specificity and threading model accuracy at the points where "incorrect" CASP2 predictions just outnumber "correct" predictions. Using these thresholds we find that correct predictions were made for all of those targets and for only those targets where more than 50% of target residues may be superimposed on previously known structures. Three-fourths of these correct predictions were furthermore made for targets with greater than 12% residue identity in structural alignment, where characteristic sequence motifs are also present. Based on these observations we suggest that the sustained performance of threading methods is best characterized by counting the numbers of correct predictions for targets of increasing "difficulty." We suggest that target difficulty may be assigned, once the true structure of the target is known, according to the fraction of residues superimposable onto previously known structures and the fraction of identical residues in those structural alignments.

Models, Molecular↗
PubMed1997

Competitive assessment of protein fold recognition and alignment accuracy.

The predictions made for fold recognition and modeling accuracy at the 1996 Critical Assessment of Structure Prediction meeting (CASP2) were assessed to discover which groups did best. With 32 groups making a total of 369 predictions, it was necessary to use simple criteria for distinguishing between the entries. By focusing on the predictors' ability to use the sequence of the unknown target structure to recognize the target fold from a database of known folds and also on the quality of the model judged by the accuracy of the predicted alignment, it is easy to determine the best predictions for a given target. Assessing overall performance of the predictors on all the targets is much more difficult and use was made of weighted averages of fold recognition and alignment accuracy with and without normalization for target difficulty. By plotting these results in two dimensions the winning groups stand out, allowing readers to focus their attention on the most promising methods. When the present results are compared with the results of the earlier CASP1 meeting, held in 1994, it is clear that threading predictions have progressed dramatically. For this assessor, the strongest lesson learned is that subjectivity is pervasive and affects us all. It is abundantly clear that the blind predictions made at CASP are essential if progress is to be made in predicting protein structure.

Models, Molecular↗
PubMed1997

Simulating the minimum core for hydrophobic collapse in globular proteins.

To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding.

Alkenes↗
PubMed1997

An Eastern Cooperative Oncology Group phase I trial of all-trans-retinoic acid and interferon-alpha: E2Y92.

The Eastern Cooperative Oncology Group conducted a Phase I trial to determine the maximally tolerated doses of combination therapy with alpha interferon (IFN-alpha) and all-trans-retinoic acid (tRA). Fifty patients with incurable malignancies received IFN-alpha administered subcutaneously three times weekly, and tRA administered by mouth at bedtime. Doses were escalated between patient groups, starting at tRA dose level of 45 mg/m2 and 3 million units of IFN-alpha. Major, dose-limiting toxicities were attributable to either the tRA (rash, chelitis) or IFN (constitutional symptoms), and were observed only at tRA dose levels of 224 mg/m2 and 291 mg/m2, or 6 million units of IFN-alpha. The maximally tolerated dose level of 172.5 mg/m2 of tRA and 3 million units of IFN-alpha was well-tolerated, with no grade 3 or 4 toxicities attributable to therapy. One patient at the third dose level (75 mg/m2 of tRA and 3 million units of IFN-alpha) developed acute hepatic and renal failure and a metabolic encephalopathy of unclear etiology. We conclude that tRA and IFN-alpha may be safely administered together at the maximally tolerated dose of tRA as a single agent without unexpected side effects. The recommended doses of IFN-alpha and tRA for Phase II trials are 3 million units of IFN-alpha and 172.5 mg/m2 of tRA.

Adult↗
PubMed1997

Protein folding: the endgame.

The last stage of protein folding, the "endgame," involves the ordering of amino acid side-chains into a well defined and closely packed configuration. We review a number of topics related to this process. We first describe how the observed packing in protein crystal structures is measured. Such measurements show that the protein interior is packed exceptionally tightly, more so than the protein surface or surrounding solvent and even more efficiently than crystals of simple organic molecules. In vitro protein folding experiments also show that the protein is close-packed in solution and that the tight packing and intercalation of side-chains is a final and essential step in the folding pathway. These experimental observations, in turn, suggest that a folded protein structure can be described as a kind of three-dimensional jigsaw puzzle and that predicting side-chain packing is possible in the sense of solving this puzzle. The major difficulty that must be overcome in predicting side-chain packing is a combinatorial "explosion" in the number of possible configurations. There has been much recent progress towards overcoming this problem, and we survey a variety of the approaches. These approaches differ principally in whether they use ab initio (physical) or more knowledge-based methods, how they divide up and search conformational space, and how they evaluate candidate configurations (using scoring functions). The accuracy of side-chain prediction depends crucially on the (assumed) positioning of the main-chain. Methods for predicting main-chain conformation are, in a sense, not as developed as that for side-chains. We conclude by surveying these methods. As with side-chain prediction, there are a great variety of approaches, which differ in how they divide up and search space and in how they score candidate conformations.

Animals↗
PubMed1997

Insights into human colonic physiology obtained from the study of flatus composition.

To better understand the physiology of colonic gas production, each flatus passage of 16 subjects over a 4-h period was analyzed by gas chromatography for N2, O2, H2, CO2, CH4, and for odoriferous sulfur-containing gases. Appreciable intraindividual and enormous interindividual variability was observed, indicating that each gas passage reflected the interaction of highly variable liberation and/or removal mechanisms. The predominant flatus gas was CO2, H2, and N2 in seven, six, and three subjects, respectively. Gases produced intraluminally (H2, CO2, and CH4) comprised approximately 74% of flatus, and rapid CO2 and H2 productions were responsible for high passage rates. A positive correlation between flatus H2 and CO2 suggested that CO2, like H2, mainly was a bacterial product. Whereas methanogens and H2S-producing bacteria usually are mutually exclusive in feces, CH4 and H2S did not negatively correlate, indicating coexistence of both organisms in the colon. We conclude that analysis of flatus composition provides a novel means of assessing colonic physiology, particularly ongoing bacterial metabolism throughout the unperturbed colon.

Adolescent↗
PubMed1997

Packing as a structural basis of protein stability: understanding mutant properties from wildtype structure.

Modeling of protein core mutations using sidechain packing can forecast their effects on stability. We have assessed the structural basis of this approach, by evaluating the accuracy of our 1991 model of a three-site mutant of lambda repressor (V36L/M40L/V47I), against the recently reported crystal structure. The three mutated residues matched the crystal structure to within 0.89A (1.11A for sidechain atoms), giving fairly accurate sidechain placement and packing (81-99th percentile rank in coordinate accuracy). However, the model used different sidechain torsional angles than seen in the crystal structure at residues 36 and 40, apparently to compensate for the backbone shifts present in the actual mutant structure, but not accounted for in our modeling method. To understand the structural basis of stability across a set of lambda repressor core mutants, we have analyzed the mutant models, revealing several simple packing effects: V36I, predicted to be stabilized by filling a hydrophobic cavity; M40V, destabilized by a steric clash with the unusual structural demands of a helix-turn transition. These effects illustrate how mutant stability can often be understood directly from scrutiny of wildtype structure. Simply adding the calculated energies of neighboring point mutations predicts the stability effect of the combined mutant relatively well, with little apparent cooperativity, yielding simple rules for each site's amino acid preferences. Our treatment of core packing indicates that it can permit a large fraction of sequences to fit the native fold, as observed experimentally, far more than indicated by rotamer hard-sphere models.

Amino Acid Sequence↗
PubMed1996

Energy functions that discriminate X-ray and near native folds from well-constructed decoys.

This study generates ensembles of decoy or test structures for eight small proteins with a variety of different folds. Between 35,000 and 200,000 decoys were generated for each protein using our four-state off-lattice model together with a novel relaxation method. These give compact self-avoiding conformations each constrained to have native secondary structure. Ensembles of these decoy conformations were used to test the ability of several types of empirical contact, surface area and distance-dependent energy functions to distinguish between correct and incorrect conformations. These tests have shown that none of the functions is able to distinguish consistently either the X-ray conformation or the near-native conformations from others which are incorrect. Certain combinations of two of these energy functions were able, however, consistently to identify X-ray structures from amongst the decoy conformations. These same combinations are better also at identifying near-native conformations, consistently finding them with a hundred-fold higher frequency than chance. The fact that these combination energy functions perform better than generally accepted energy functions suggests their future use in folding simulations and perhaps threading predictions.

Crystallography, X-Ray↗
PubMed1996

From structure to sequence and back again.

With a simple lattice model and sequence design algorithm, we can design sequences to fit arbitrary compact globular structures. We judged the success of the design algorithm by performing exhaustive conformational searches to determine if a designed sequence's lowest energy conformation matched the target for which it was designed. Designed sequences tend to be much better optimized for their targets than a natural sequence is optimized for its lowest energy model conformation. We examined the effect of varying the number of available amino acid types on the success of the design method. It was more difficult but not impossible to successfully design discriminating sequences using fewer amino acid types.

Algorithms↗