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R A Goldstein

Publications and source records attributed to R A Goldstein.

At least 37 records · Page 2Linked to original sources
PubMed1997

Evolution of model proteins on a foldability landscape.

We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process.

Biopolymers↗
PubMed1997

Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information.

We demonstrate the applicability of our previously developed Bayesian probabilistic approach for predicting residue solvent accessibility to the problem of predicting secondary structure. Using only single-sequence data, this method achieves a three-state accuracy of 67% over a database of 473 non-homologous proteins. This approach is more amenable to inspection and less likely to overlearn specifics of a dataset than "black box" methods such as neural networks. It is also conceptually simpler and less computationally costly. We also introduce a novel method for representing and incorporating multiple-sequence alignment information within the prediction algorithm, achieving 72% accuracy over a dataset of 304 non-homologous proteins. This is accomplished by creating a statistical model of the evolutionarily derived correlations between patterns of amino acid substitution and local protein structure. This model consists of parameter vectors, termed "substitution schemata," which probabilistically encode the structure-based heterogeneity in the distributions of amino acid substitutions found in alignments of homologous proteins. The model is optimized for structure prediction by maximizing the mutual information between the set of schemata and the database of secondary structures. Unlike "expert heuristic" methods, this approach has been demonstrated to work well over large datasets. Unlike the opaque neural network algorithms, this approach is physicochemically intelligible. Moreover, the model optimization procedure, the formalism for predicting one-dimensional structural features and our previously developed method for tertiary structure recognition all share a common Bayesian probabilistic basis. This consistency starkly contrasts with the hybrid and ad hoc nature of methods that have dominated this field in recent years.

Algorithms↗
PubMed1997

Protein heteronuclear NMR assignments using mean-field simulated annealing.

A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic resonance experiments is described. Connectivity data obtained from HNC alpha, HN(CO)C alpha, HN(C alpha)H alpha, and H alpha (C alpha CO)NH and spin-system identification data obtained from CP-(H)CCH-TOCSY and CP-(H)C(C alpha CO)NH-TOCSY were used to perform sequence-specific assignments using a mean-field formalism and simulated annealing. This mean-field method reports the resonance assignments in a probabilistic fashion, displaying the certainty of assignments in an unambiguous and quantitative manner. This technique was applied to the NMR data of the 172-residue peptide-binding domain of the E. coli heat-shock protein, DnaK. The method is demonstrated to be robust to significant amounts of missing, spurious, noisy, extraneous, and erroneous data.

Computer Simulation↗
PubMed1996

Why are some proteins structures so common?

Many biological proteins are observed to fold into one of a limited number of structural motifs. By considering the requirements imposed on proteins by their need to fold rapidly, and the ease with which such requirements can be fulfilled as a function of the native structure, we can explain why certain structures are repeatedly observed among proteins with negligible sequence similarity. This work has implications for the understanding of protein sequence structure relationships as well as protein evolution.

Evolution, Molecular↗
PubMed1996

Constructing amino acid residue substitution classes maximally indicative of local protein structure.

Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition.

Amino Acid Sequence↗
PubMed1996

Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes.

We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions-comparable to the highest accuracies reported in the literature to date-are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins.

Amino Acid Sequence↗
PubMed1996

Probabilistic reconstruction of ancestral protein sequences.

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.

Amino Acid Sequence↗
PubMed1996

Airborne pollutants and the immune system.

The effects of airborne pollutants on the immune system have been most widely studied in the respiratory tract. Entry may occur as a volatile gas (ozone, benzene), as liquid droplets (sulfuric acid, nitrogen dioxide), or as particulate matter (diesel exhaust, aromatic hydrocarbons). The subsequent interaction with the immune system may result in local and systemic responses, and studies have shown examples of disease occurring from both overactive immune responses and immunosuppression. For the most part, airborne pollutants (small molecular weight chemicals) have to be coupled with other substances (proteins or conjugates) before they can be recognized by the immune system and exert their effects. Fortunately, this encounter rarely causes immunologically mediated human disorders. The following briefly reviews some of the disorders that may occur. Immunologically nonspecific inflammation of the lung can occur after inhalation of ozone in anyone given sufficient dose and time of exposure. Immunologically specific cell-mediated (T lymphocyte) reactions appear to predominate in chronic beryllium disease, which results in a granulomatous form of lung disease. Beryllium alone does not appear to be antigenic but requires chemical linkage with a larger molecule. Mercury-induced autoimmune disease (immune system attacks self-antigens) affecting kidneys and lungs has been demonstrated in animal models (changes similar to those seen in people with Goodpasture's syndrome). Immunosuppression can be demonstrated after exposure to polycyclic aromatic hydrocarbons (2,3,7,8-tetrachlorodibenzo-p-dioxin). Hypersensitivity (or allergic) reactions can occur after exposure to toluene diisocyanate (occupational asthma). In summary, airborne pollutants may cause a wide spectrum of immunologically mediated disorders. There is clearly an underlying genetic basis for the susceptibility to immunologic disease resulting from exposure to pollutants, but knowledge in this area is rudimentary at present. Studies have been impeded by lack of appropriate in vitro models, as well as difficulties in identifying the biologically active substance.

Air Pollutants↗
PubMed1996

Health hazards to humans associated with domestic pets.

Allergy to pets, particularly when manifested as asthma, is an important health hazard. The health impact of severe clinical disease associated with allergy to pets can be minimized by avoidance of pets. Many individuals with milder disease keep their pets and obtain medications for relief of their allergy symptoms. Bird fancier's disease can result in profound deterioration of pulmonary function, and requires avoidance of bird exposure. Animal bites are the commonest health hazard of domestic pets and result in tissue damage and infection risk. Bites are treated by cleaning the wound, and appropriate use of antibiotics and tetanus prophylaxis. Diverse infectious diseases are transmitted to humans by their pets; these diseases are particularly dangerous to immunocompromised individuals. The infectious diseases can be partly prevented by avoiding ill animals and by washing of hands following exposure to pets or pet-derived secretions. They can be treated by appropriate antibiotics and/or specific immune globulins and/or vaccines.

Animals↗
PubMed1996

Correlating structure-dependent mutation matrices with physical-chemical properties.

We have investigated how structure-dependent mutation matrices derived in previous work correlate with various physical-chemical properties of the 20 naturally occurring amino acids. Among the properties we investigated were delta G of transfer from water to octanol and cyclohexane, alpha helical and beta sheet propensity, size, and charge. We found that the delta G of transfer to octanol had a high correlation with matrices for all categories of residues, especially the matrices for buried and exposed positions. This result suggests that octanol is a good model for understanding both the changes in stability resulting from substitutions of buried residues and changes in foldability resulting from varying exposed residues. We also found the correlations of the matrices with size and charge varied with the local environment, and that neither alpha helical nor beta sheet propensity had high correlations with most matrices. Thus, conservation of size and charge appear to be important in specific environments, and conservation of alpha helix and beta sheet propensity do not seem to be key factors.

Amino Acids↗
PubMed1995

Optimal local propensities for model proteins.

Lattice models of proteins were used to examine the role of local propensities in stabilizing the native state of a protein, using techniques drawn from spin-glass theory to characterize the free-energy landscapes. In the strong evolutionary limit, optimal conditions for folding are achieved when the contributions from local interactions to the stability of the native state is small. Further increasing the local interactions rapidly decreases the foldability.

Models, Chemical↗
PubMed1995

Context-dependent optimal substitution matrices.

Substitution matrices are a key tool in important applications such as identifying sequence homologies, creating sequence alignments and more recently using evolutionary patterns for the prediction of protein structure. We have derived a novel approach to the derivation of these matrices that utilizes not only multiple sequence alignments, but also the associated evolutionary trees. The key to our method is the use of a Bayesian formalism to calculate the probability that a given substitution matrix fits the tree structures and multiple sequence alignment data. Using this procedure, we can determine optimal substitution matrices for various local environments, depending on parameters such as secondary structure and surface accessibility.

Evolution, Molecular↗
PubMed1994

NIH conference. Asthma.

Asthma is characterized by inflammation, reversible airway obstruction, and increased airway responsiveness to various stimuli. It has received wide public attention in recent years because of increasing morbidity and deaths, particularly among black persons. The important role of inflammation in the immunopathogenesis of asthma has led to a newer therapeutic approach directed at interrupting this inflammatory process. Among immune regulatory pathways involved in asthma pathogenesis, two lymphokines appear to be particularly important in controlling IgE production. Interleukin-4 is required for IgE production; without it, IgE production is inhibited. Interferon-gamma can diminish cell priming for interleukin-4 production. Thus, the interplay of these two cytokines will determine whether cells that can make interleukin-4 will be produced and, therefore, whether IgE will be produced in response to allergic stimuli. Further, in response to appropriate stimuli, mast cells and eosinophils are attracted to airways and release cytokines, lipid mediators, and preformed substances that cause inflammation. Modern asthma treatment is directed at interrupting this inflammatory process and places a much greater emphasis on use of anti-inflammatory agents, such as aerosolized or parenteral corticosteroids, and on non-steroidal anti-inflammatory agents, such as cromolyn sodium and nedocromil sodium. Research advances without therapeutic application, however, limit success. Projects such as the National Institute of Allergy and Infectious Diseases' National Cooperative Inner-City Asthma Study, which is directed toward underserved populations, are intended to identify more clearly the factors responsible for increasing morbidity and to develop appropriate therapeutic interventions.

Asthma↗
PubMed1993

Three-dimensional model for the hormone binding domains of steroid receptors.

We have used a motif-based structural search method to identify structural homologs of the hormone binding domains of the nuclear receptors from among a set of known protein structures and have found the closest similarity with members of the subtilisin-like serine proteases. These proteins consist of an open twisted sheet of parallel beta-strands flanked on both sides by alpha-helices. The alignment with the protease scaffold was refined by using multiple sequence prealignment of different sets of nuclear receptors, and alternative model structures were screened by considering their consistency with the results of biochemical experiments defining the ligand binding pocket. In the most favored model, nearly all of the residues thought to be involved in ligand binding map to a pocket of appropriate dimensions where the subtilisin-like proteases have their active site. The three-dimensional model that we propose for the hormone binding domains of the nuclear receptors provides a framework for the design of experiments to further investigate nuclear receptor structure and function.

Amino Acid Sequence↗
PubMed1992

Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set.

Amino Acids↗
PubMed1992

Optimal protein-folding codes from spin-glass theory.

Protein-folding codes embodied in sequence-dependent energy functions can be optimized using spin-glass theory. Optimal folding codes for associative-memory Hamiltonians based on aligned sequences are deduced. A screening method based on these codes correctly recognizes protein structures in the "twilight zone" of sequence identity in the overwhelming majority of cases. Simulated annealing for the optimally encoded Hamiltonian generally leads to qualitatively correct structures.

Bence Jones Protein↗