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At least 919 records · Page 51Linked to original sources
PubMed1996

Visualization of the onset of distortion-product otoacoustic emissions, and measurement of their latency.

This paper describes a method for visualization of the onset of distortion-product otoacoustic emission (DPOAE) waveforms in the time domain. The DPOAE waveforms are obtained using ensemble averaging of samples of microphone output. A rectangular sample window is used, and the primary tones are turned on within the sample window. The phases of the primary tones (f1 and f2) are varied systematically between samples in such a way that the primary tones, and all DPOAEs (e.g., 2f2-f1, 3f1-2f2, 2f1), except the DPOAE of interest (e.g., 2f1-f2), are cancelled in the ensemble average. Visualization of the DPOAE onset allows measurement of the onset latency (OSL) of the DPOAE. These direct measurements of OSL are compared to phase-gradient latencies (PGLs) in the same ears determined by measuring the phase change of the DPOAE as a function of DPOAE frequency. The direct measures of OSL vary from > 10 to < 1 ms, decrease with increasing frequency and increasing stimulus level, and are shorter in rabbits than humans. The direct measures of OSL are, in general, quantitatively similar to PGL estimates, but there are exceptions. Visualization of DPOAE onset also allows quantification of DPOAE rise times, and reveals phase and amplitude changes of the DPOAE that occur several milliseconds after onset in rabbits and humans. It is proposed that the phase and amplitude changes result from vector summation of multiple components of the DPOAE signal, each with a different latency.

Acoustic Stimulation↗
PubMed2006

Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides.

Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely indicative of kinks in the full-length protein. This minireview focuses on methods and protocols for NMR structure calculation and analysis of peptide structures under conditions of conformational sampling. The methods outlined allow the identification and analysis of structured peptides containing break points owing to conformational sampling and the differentiation between oligomerization and ensemble-averaged observation of multiple peptide conformations.

Mathematics↗
PubMed1996

Molecular physiology and pharmacology of HERG. Single-channel currents and block by dofetilide.

BACKGROUND: The human ether-a-go-go-related gene (HERG) is one locus for the hereditary long-QT syndrome. A hypothesis is that HERG produces the repolarizing cardiac potassium current IKr with the consequence that mutations in HERG prolong the QT interval by reducing IKr. The elementary properties of HERG are unknown, and as a test of the hypothesis that HERG produces IKr, we compared their elementary properties. METHODS AND RESULTS: We injected HERG cRNA into Xenopus oocytes and measured currents from single channels or current variance from the noise produced by ensembles of channels recorded from macro patches. Single-channel conductance was dependent on the extracellular potassium concentration ([K]o). At physiological [K]o, it was 2 picosiemens (pS), and at 100 mmol/L [K]o, it was 10 pS. Openings occurred in bursts with a mean duration of 26 ms at -100 mV. Mean open time was 3.2 ms and closed times were 1.0 and 26 ms. In excised macro patches, HERG currents were blocked by the class III antiarrhythmic drug dofetilide, with an IC50 of 35 nmol/L. Dofetilide block was slow and greatly attenuated at positive potentials at which HERG rectifies. CONCLUSIONS: The microscopic physiology of HERG and IKr is similar, consistent with HERG being an important component of IKr. The pharmacology is also similar; dofetilide appears to primarily block activated channels and has a much lower affinity for closed and inactivated channels.

Animals↗
PubMed2004

A comparison of methods for modeling quantitative structure-activity relationships.

A large number of methods are available for modeling quantitative structure-activity relationships (QSAR). We examine the predictive accuracy of several methods applied to data sets of inhibitors for angiotensin converting enzyme, acetylcholinesterase, benzodiazepine receptor, cyclooxygenase-2, dihydrofolate reductase, glycogen phosphorylase b, thermolysin, and thrombin. Descriptors calculated with CoMFA, CoMSIA, EVA, HQSAR, and traditional 2D and 2.5D descriptors were used for developing models with partial least squares (PLS). In addition, the genetic function approximation algorithm, genetic PLS, and back-propagation neural networks were used for deriving models from 2.5D descriptors (i.e., 2D descriptors and 3D descriptors calculated from CORINA structures and Gasteiger-Marsili charges). Predictive accuracy was assessed using designed test sets. It was found that HQSAR generally performs as well as CoMFA and CoMSIA; other descriptor sets performed less well. When 2.5D descriptors were used, only neural network ensembles were found to be similarly or more predictive than PLS models. In addition, we show that many cross-validation procedures yield similar estimates of the interpolative accuracy of methods. However, the lack of correspondence between cross-validated and test set predictive accuracy for four sets underscores the benefit of using designed test sets.

Algorithms↗
PubMed2002

On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces.

Lactoferrin (Lf) is a non-heme, iron binding protein present in many physiological fluids of vertebrates where its main role is the microbicidal activity. It has been isolated by different methods, including dye-affinity chromatography. Red HE-3B is one of the most common triazinic dyes applied in protein purification, but scant knowledge is available on structural details and on the energetics of its interaction with proteins. In this work we present a computational approach useful for identifying possible binding sites for Red HE-3B in apo and holo forms of Lfs from human and bovine source. A new geometrical description of Red HE-3B is introduced which greatly simplifies the conformational analysis. This approach proved to be of particular advantage for addressing conformational ensembles of highly flexible molecules. Predictions from this analysis were correlated with experimentally observed dye-binding sites, as mapped by protection from proteolysis in Red HE-3B/Lf complexes. This method could bear relevance for the screening of possible dye-binding sites in proteins whose structure is known and as a potential tool for the design of engineered protein variants which could be purified by dye-affinity chromatography.

Amino Acid Sequence↗
PubMedDate not supplied

Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry.

The "protein-folding problem" refers to the question of how and why a denatured polypeptide chain can spontaneously fold into a compact and highly ordered conformation. The classical description of this process in terms of reaction pathways has been complemented by models that describe folding as a biased conformational diffusion on a multidimensional energy landscape. The identification and characterization of short-lived intermediates provide important insights into the mechanism of folding. Pulsed hydrogen/deuterium exchange (HDX) methods are among the most powerful tools for studying the properties of kinetic intermediates. Analysis of pulse-labeled proteins by mass spectrometry (MS) provides information that is complementary to that obtained in nuclear magnetic resonance (NMR) studies; NMR data represent an average of entire protein ensembles, whereas MS can detect co-existing protein species. MS-based pulse-labeling experiments can distinguish between folding scenarios that involve parallel pathways, and those where folding is channeled through obligatory intermediates. The proteolytic digestion/MS technique provides spatially resolved information on the HDX pattern of folding intermediates. This method is especially important for proteins that are too large to be studied by NMR. Although traditional pulsed HDX protocols are based on quench-flow techniques, it is also possible to use electrospray (ESI) MS to analyze the reaction mixture on-line and "quasi-instantaneously" after labeling. This approach allows short-lived protein conformations to be studied by their HDX level, their ESI charge-state distribution, and their ligand-binding state. Covalent labeling of free cysteinyl residues provides an alternative approach to pulsed HDX experiments. Another promising development is the use of synchrotron X-rays to induce oxidation at specific sites within a protein for studying their solvent accessibility during folding.

Animals↗
PubMed1991

Alignment methods for averaging of high-resolution cardiac signals: a comparative study of performance.

Accurate signal estimation by means of coherent averaging techniques needs temporal alignment methods. A known low-pass filtering effect is yielded when alignment errors are present. This is very critical in the estimation of low-level high-frequency potentials in high-resolution ECG analysis. A comparative study of the performance of three alignment methods (the double-level method, a new time-delay estimation method based on normalized integrals, and matched filtering) is presented in this paper. A real signal and additive random noise for several signal-to-noise ratios (SNR's) are selected to make an ensemble of computer-simulated beats. The relation between the standard deviation of temporal misalignment versus SNR is discussed. A second study with real ECG signals is also presented. Several morphologies of QRS and P waves are tested. The results are in agreement with the computer simulation study. Nevertheless, the power spectrum of the noise process can affect the results. Matched filter estimation has been tested in the presence of power line interference (50 Hz), with poor results. An application of the three alignment methods as a function of the SNR is proposed. The new time-delay estimation method has been observed to be robust, even in the presence of nonwhite noise.

Computer Simulation↗
PubMed1996

The value of medical history and physical examination in diagnosing sacroiliac joint pain.

STUDY DESIGN: This prospective study evaluated the diagnostic utility of historically accepted sacroiliac joint tests. A multidisciplinary expert panel recommended 12 of the "best" sacroiliac joint tests to be evaluated against a criterion standard of unequivocal gain relief after an intra-articular injection of local anesthetic into the sacroiliac joint. OBJECTIVES: To identify a single sacroiliac joint test or ensemble of test that are sufficiently useful in diagnosing sacroiliac joint disorders to be clinically valuable. SUMMARY OF BACKGROUND DATA: No previous research has been done to evaluate any physical test of sacroiliac joint pain against an accepted criterion standard. METHODS: Historical data was obtained, and the 12 tests were performed by two examiners on 85 patients who subsequently underwent sacroiliac joint blocks. Ninety percent or more relief was considered a positive response, and less then 90% relief was considered a negative response. RESULTS: There were 45 positive and 40 negative responses. No historical feature, none of the 12 sacroiliac joint tests, and no ensemble of these 12 tests demonstrated worthwhile diagnostic value. CONCLUSION: Sacroiliac joint pain is resistant to identification by the historical and physical examination data from tests evaluated in this study.

Adolescent↗
PubMed2003

A simple procedure to weight empirical potentials in a fitness function so as to optimize its performance in ab initio protein-folding problem.

In an approach to the protein folding problem by a Genetic Algorithm, the fitness function plays a critical role. Empirical potentials are generally used to build the fitness function, and they must be weighted to obtain a valuable one. The weights are generally found by the comparison with a set of misfolded structures (decoys), but a dependence of the obtained fitness generally arises on the used decoys. Here we describe a general procedure to find out, from a given set of potentials, their better linear combination that could either identify the wild structure or prove their powerlessness. We use topological considerations over the hyperspace of the potentials, and a multiple linear inequalities solver. The iterated method flows through the following steps: it determines a direction in the hyperspace of the potentials, which identifies the native structure as a vertex among a set of misfolded decoys. A multiple linear inequalities solver obtains the direction. A Genetic Algorithm, tailored to the specific problem, uses the fitness function defined by this direction and generally reaches a new structure better than the experimental one, which is added to the ensemble. The decoys so generated are not dependent on a deterministic criterion. This iterative procedure can be stopped either by identifying an effective fitness function or by proving the impossibility of its achievement. In order to test the method under the hardest conditions, we choose numerous and heterogeneous quantities as components of the fitness function. This method could be a useful tool for the scientific community in order to test any fitness proposed and to recognize the most important components on which it is built.

Algorithms↗
PubMed2005

Overcoming the slowing down of flat-histogram Monte Carlo simulations: cluster updates and optimized broad-histogram ensembles.

We study the performance of Monte Carlo simulations that sample a broad histogram in energy by determining the mean first-passage time to span the entire energy space of d-dimensional ferromagnetic Ising/Potts models. We first show that flat-histogram Monte Carlo methods with single-spin flip updates such as the Wang-Landau algorithm or the multicanonical method perform suboptimally in comparison to an unbiased Markovian random walk in energy space. For the d = 1, 2, 3 Ising model, the mean first-passage time tau scales with the number of spins N = L(d) as tau proportional N2L(z). The exponent z is found to decrease as the dimensionality d is increased. In the mean-field limit of infinite dimensions we find that z vanishes up to logarithmic corrections. We then demonstrate how the slowdown characterized by z > 0 for finite d can be overcome by two complementary approaches--cluster dynamics in connection with Wang-Landau sampling and the recently developed ensemble optimization technique. Both approaches are found to improve the random walk in energy space so that tau proportional N2 up to logarithmic corrections for the d = 1, 2 Ising model.

Journal Article↗
PubMed2003

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model.

The accuracy of model selection from decoy ensembles of protein loop conformations was explored by comparing the performance of the Samudrala-Moult all-atom statistical potential (RAPDF) and the AMBER molecular mechanics force field, including the Generalized Born/surface area solvation model. Large ensembles of consistent loop conformations, represented at atomic detail with idealized geometry, were generated for a large test set of protein loops of 2 to 12 residues long by a novel ab initio method called RAPPER that relies on fine-grained residue-specific phi/psi propensity tables for conformational sampling. Ranking the conformers on the basis of RAPDF scores resulted in selected conformers that had an average global, non-superimposed RMSD for all heavy mainchain atoms ranging from 1.2 A for 4-mers to 2.9 A for 8-mers to 6.2 A for 12-mers. After filtering on the basis of anchor geometry and RAPDF scores, ranking by energy minimization of the AMBER/GBSA potential energy function selected conformers that had global RMSD values of 0.5 A for 4-mers, 2.3 A for 8-mers, and 5.0 A for 12-mers. Minimized fragments had, on average, consistently lower RMSD values (by 0.1 A) than their initial conformations. The importance of the Generalized Born solvation energy term is reflected by the observation that the average RMSD accuracy for all loop lengths was worse when this term is omitted. There are, however, still many cases where the AMBER gas-phase minimization selected conformers of lower RMSD than the AMBER/GBSA minimization. The AMBER/GBSA energy function had better correlation with RMSD to native than the RAPDF. When the ensembles were supplemented with conformations extracted from experimental structures, a dramatic improvement in selection accuracy was observed at longer lengths (average RMSD of 1.3 A for 8-mers) when scoring with the AMBER/GBSA force field. This work provides the basis for a promising hybrid approach of ab initio and knowledge-based methods for loop modeling.

Algorithms↗
PubMed1995

An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.

A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of the data sets. The method, based on the clustering of similar structures, has been tested in the homology model building of the structure of Sox-5, a sequence-specific DNA-binding protein belonging to the high mobility group (HMG) nuclear proteins family. Sox (SRY box) genes are the autosomal genes related to the sex-determining SRY, Y chromosomal gene. The Sox-5 protein, encoded by one of the SRY-related genes, displays a 29% sequence identity with the HMG1 B-box domain whose structure, determined previously by NMR, has been used in our study to predict the structure of Sox-5. Two independent ensembles of HMG1 structures, each represented by closely related coordinate sets, were used. Nine representative structures for HMG1 were subsequently selected as starting points for the modelling of Sox-5. The model of the protein shows close similarity to the HMG1 fold, with differences at the secondary structure level located mainly in alpha-helices 1 and 3. A left-handed, three residue per turn polyproline II helix, forming a conserved polyproline II/alpha-helix supersecondary motif, was identified in the N-terminal region of Sox-5 and other HMG boxes.

Algorithms↗
PubMed1993

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.

Algorithms↗
PubMed2004

Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry.

A novel method for characterization of the simultaneous reductive unfolding pathways of five isoforms of bovine pancreatic ribonuclease B (RNase B) is demonstrated. The results indicate that each isoform unfolds reductively through two three-disulfide-containing structured intermediates before proceeding to the fully reduced form, as in the reductive unfolding pathways of the A variant lacking the carbohydrate chain. The rates of reduction of bovine pancreatic ribonuclease A (RNase A) and RNase B and the formation and consumption of their reductive intermediates are identical, indicating that the unfolding events necessary to expose disulfide bonds for reduction are not affected by the oligosaccharide. The method utilizes top-down mass spectrometry and a naturally occurring tag on the protein, viz. the carbohydrate moiety, to obtain unfolding information of an ensemble of protein isoforms and is a generally applicable methodological advance for conducting folding studies on mixtures of different proteins.

Animals↗
PubMed2005

Protein folding and the organization of the protein topology universe.

The mechanism by which proteins fold to their native states has been the focus of intense research in recent years. The rate-limiting event in the folding reaction is the formation of a conformation in a set known as the transition-state ensemble. The structural features present within such ensembles have now been analysed for a series of proteins using data from a combination of biochemical and biophysical experiments together with computer-simulation methods. These studies show that the topology of the transition state is determined by a set of interactions involving a small number of key residues and, in addition, that the topology of the transition state is closer to that of the native state than to that of any other fold in the protein universe. Here, we review the evidence for these conclusions and suggest a molecular mechanism that rationalizes these findings by presenting a view of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose an explanation for the overwhelming importance of topology in the transition states for protein folding.

Animals↗
PubMed1998

Hydration properties of xylitol: computer simulation.

We present a molecular dynamics simulation of xylitol in SPC/E water using classical Gibbs ensemble molecular dynamics simulation. The simulation is done both with and without periodic charge update, and no qualitative difference in the results obtained by both methods is found. The analysis of the radial and angular distribution functions, the water-water hydrogen bond distributions, and water residence times allow the conclusion that there is a relatively strong hydration of xylitol. This polyol adopts a single linear conformation and, from the point of view of the hydration dynamics, it should be classified as positively hydrated.

Carbohydrate Conformation↗
PubMed2006

Phi-value analysis of apo-azurin folding: comparison between experiment and theory.

Pseudomonas aeruginosa azurin is a 128-residue beta-sandwich metalloprotein; in vitro kinetic experiments have shown that it folds in a two-state reaction. Here, we used a variational free energy functional to calculate the characteristics of the transition state ensemble (TSE) for folding of the apo-form of P. aeruginosa azurin and investigate how it responds to thermal and mutational changes. The variational method directly yields predicted chevron plots for wild-type and mutant apo-forms of azurin. In parallel, we performed in vitro kinetic-folding experiments on the same set of azurin variants using chemical perturbation. Like the wild-type protein, all apo-variants fold in apparent two-state reactions both in calculations and in stopped-flow mixing experiments. Comparisons of phi (phi) values determined from the experimental and theoretical chevron parameters reveal an excellent agreement for most positions, indicating a polarized, highly structured TSE for folding of P. aeruginosa apo-azurin. We also demonstrate that careful analysis of side-chain interactions is necessary for appropriate theoretical description of core mutants.

Amino Acid Substitution↗