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Biomedical subjects

A E Torda

Publications and source records attributed to A E Torda.

At least 19 recordsLinked to original sources
PubMed1999

Enhanced protein fold recognition using secondary structure information from NMR.

NMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determination. In the absence of an X-ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial secondary structure data and threading a sequence through a library of candidate folds. Using a literature test set, the threading method alone has only a one-third chance of producing a correct answer among the top ten guesses. With realistic secondary structure information, one can expect a 60-80% chance of finding a homologous structure. The method has then been applied to examples with published estimates of secondary structure. This implementation is completely independent of sequence homology, and sequences are optimally aligned to candidate structures with gaps and insertions allowed. Unlike work using predicted secondary structure, we test the effect of differing amounts of relatively reliable data.

Algorithms↗
PubMed1998

The dependence of amino acid pair correlations on structural environment.

A statistical analysis was performed to determine to what extent an amino acid determines the identity of its neighbors and to what extent this is determined by the structural environment. Log-linear analysis was used to discriminate chance occurrence from statistically meaningful correlations. The classification of structures was arbitrary, but was also tested for significance. A list of statistically significant interaction types was selected and then ranked according to apparent importance for applications such as protein design. This showed that, in general, nonlocal, through-space interactions were more important than those between residues near in the protein sequence. The highest ranked nonlocal interactions involved residues in beta-sheet structures. Of the local interactions, those between residues i and i + 2 were the most important in both alpha-helices and beta-strands. Some surprisingly strong correlations were discovered within beta-sheets between residues and sites sequentially near to their bridging partners. The results have a clear bearing on protein engineering studies, but also have implications for the construction of knowledge-based force fields.

Amino Acids↗
PubMed1998

Protein fold recognition without Boltzmann statistics or explicit physical basis.

We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.

Algorithms↗
PubMed1997

Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations.

The immunodominant region on the circumsporozoite surface (CS) protein of the malaria parasite Plasmodium falciparum contains 37 repeated copies of a asparagine-alanine-asparagine-proline (NANP) motif NMR studies of linear synthetic peptides containing one, two or three repeat units provided evidence for nascent type I beta-turns within the NPNA cadence in aqueous solution. The beta-turns could be stabilised upon substituting proline for alpha-methylproline (p(Me)) in the dodecamer (NP(Me)NA)3, without loss of the ability to elicit antibodies cross-reactive with P. falciparum sporozoites. In this work, four 4 ns MD simulations of the dodecapeptide Acetyl-(NP(Me)NA)3, in water, using NOE distance restraints, using 3J-coupling constant restraints, using both these restraints and without restraints, were carried out to determine the conformations of this peptide in aqueous solution. An unrestrained MD simulation of the unmethylated Ac-(NPNA)3 peptide in water was also carried out to investigate the effect of the additional methyl groups on the structure and dynamics of the peptide. The application of NOE distance restraints and 3J-coupling constant restraints leads to contradictory results, probably due to different averaging time scales inherent to the measurement of these data, which exceed the 100 ps averaging applied in the simulations. The additional methyl groups lead to more compact structures, which display enhanced local fluctuations. The central tetrapeptide adopts a type I beta-turn, while the outer motifs display more conformational variability. The three motifs in the methylated dodecamer peptide, however, adopt frequently in the distance restrained MD simulation a compact structure such that the outer motifs appear to form a hydrophobic core by stacking of their two proline rings. This arrangement also suggests how a peptide containing multiple tandemly linked copies of a stable beta-turn NPNA motif might adopt a folded stem-like structure, which conceivably may be of biological relevance in the native CS protein.

Animals↗
PubMed1997

Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.

We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics.

Algorithms↗
PubMed1997

Perspectives in protein-fold recognition.

Fold recognition force fields based on statistics from native structures have become commonplace. New, nonphysical force fields based on optimizing parameters rather than reflecting Boltzmann statistics may offer improvement in force-field performance for threading and other applications. Improvements in sequence-to-structure alignments will also be essential for improved fold recognition.

Algorithms↗
PubMed1995

Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.

Time-averaging restraints in molecular dynamics simulations were introduced to account for the averaging implicit in spectroscopic data. Space- or molecule-averaging restraints have been used to overcome the fact that not all molecular conformations can be visited during the finite time of a simulation of a single molecule. In this work we address the issue of using the correct Boltzmann weighting for each member of an ensemble, both in time and in space. It is shown that the molecular- or space-averaging method is simple in theory, but requires a priori knowledge of the behaviour of a system. This is illustrated using a five-atom model system and the small cycle peptide analogue somatostatin. When different molecular conformers that are separated by energy barriers insurmountable on the time scale of a simulation contribute significantly to a measured NOE intensity, the use of space- or molecule-averaged distance restraints yields a more appropriate description of the measured data than conventional single-molecule refinement with or without application of time averaging.

Algorithms↗
PubMed1994

A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.

Chymotrypsin inhibitor 2 (CI-2) is one of the growing family of proteins for which well-defined solution and crystal structures have been published and for which small, but distinct differences between these were found. It presents an ideal case to address the question of whether a structural difference is physically real or due to the simplifying approximations with respect to averaging that are used in the conventional methods for structure refinement. NOE distance and 3J coupling constant restrained molecular dynamics simulations were performed using conventional and time-averaged restraints, both in vacuo and in aqueous solution, and the trajectories were compared with structural properties of published structures. The time-averaged restrained molecular dynamics simulations sampled more conformations at various times and visited states consistent with both previously published solution and crystal structures. It was found that the difference between these structures is due to the refinement methodology used. Application of time-averaged restraints in structure refinement yields a physically different picture of the molecular mobility.

Computer Simulation↗
PubMed1994

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.

Algorithms↗
PubMed1993

A structure refinement method based on molecular dynamics in four spatial dimensions.

We have developed a method for structure refinement based on molecular dynamics in four spatial dimensions (4D-MD). The method was applied with success to the structure refinement of Cyclosporin A (CPA) and the lac-repressor headpiece (LAC) using atom-atom distance restraints derived from NMR data, two cases where conventional MD refinement methods failed. In the case of CPA we were able to refine seven out of nine substantially different structures, while conventional MD only refines three structures. Previously, it had appeared to be impossible to refine a given LAC structure with conventional MD methods, manual modifications were necessary in order to fulfil all the distance restraints. In this study we show that LAC can be refined without manual interference and using only 5000 steps (10 ps) of 4D-MD. The latter result is particularly interesting because it indicates that this method may be a very useful tool when modelling loops in proteins.

Amino Acid Sequence↗
PubMed1993

Structure refinement using time-averaged J-coupling constant restraints.

We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.

Amino Acid Sequence↗
PubMed1991

On deriving spatial protein structure from NMR or X-ray diffraction data.

During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments generate a set of interproton distance constraints, which is subsequently used to generate spatial structures that satisfy the experimental data. Correspondingly, crystallographic least-squares and molecular dynamics refinement is routinely applied to obtain a protein structure that is compatible with the observed structure factor amplitudes. The quality of the structure obtained will depend on the number and quality of the experimental data and on the searching power of the refinement method and protocol. The potential energy annealing conformational search (PEACS) algorithm is shown to be an improvement over standard molecular dynamics search methods. The use of time-dependent distance or structure factor restraints in molecular dynamics refinement yields a much better representation of experimental information than the fixed, static restraints which have generally been used until now. Conventional structure refinement methods lead to a too static and rigid picture of a protein in solution or in the crystalline state.

Algorithms↗
PubMed1990

Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

A penalty function is introduced into molecular dynamics simulations that improves on current methods for enforcing nuclear magnetic resonance-based distance restraints. Rather than treating nuclear Overhauser effects as static distance bounds, they are considered as quantities that must be satisfied on average over the course of a simulation trajectory. The efficacy of the method is demonstrated on the previously determined structure of tendamistat. The molecular dynamics simulations show that the time-averaged constraints increase the mobility allowed to molecules, produce better agreement with distance bounds, improve searching properties and give a better estimate of the conformational space occupied by the molecule in solution.

Magnetic Resonance Spectroscopy↗
PubMed1989

Proton nmr relaxation study of the dynamics of anthopleurin-A in solution.

Spin-spin and spin-lattice 1H-nmr relaxation times of the sea anemone polypeptide anthopleurin-A were measured at frequencies of 200, 300, 400, and 500 MHz. Relaxation times were fitted iteratively by least squares regression to the isotropic tumbling model, Woessner's model for anisotropic motion, and Lipari and Szabo's "model-independent" model. Data for aromatic and aliphatic methine protons could not be fitted satisfactority using the isotropic model. Good fits were obtained, however, using the model-independent approach, indicating that high-frequency internal motions of the polypeptide backbone were significant. In addition, a range of tau c values from 2.2 to 3.2 ns was obtained for various methine protons, suggesting that overall rotational reorientation of the molecule was anisotropic. Methyl group relaxation data were fitted satisfactorily by Woessner's model. Some assessment has been made of the effect of experimental errors on the quality of fit to the data, as well as of the contribution of experimental values at certain frequencies to definition of the spectral density function.

Animals↗
PubMed1988

Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics.

The solution conformation of the cardiac stimulatory sea anemone polypeptide anthopleurin-A has been characterised using distance geometry and restrained molecular dynamics calculations. A set of 253 approximate interproton distance restraints and 14 peptide backbone torsion angle restraints derived from two-dimensional 1H-NMR spectra at 500 MHz were used as input for these calculations. 13 structures generated by either metric matrix or variable target function distance geometry calculations were refined using energy minimisation and restrained molecular dynamics. The resulting structures contain a region of twisted antiparellel beta-sheet to which two separate regions of unordered chain are linked by three disulphide bonds. Two loops, one including Pro-41 and the other encompassing residues 10-18, are poorly defined by the NOE data.

Animals↗
PubMed1987

Amide proton exchange rates in cardioactive sea anemone polypeptides.

Amide hydrogen exchange rates have been measured using high-resolution 1H nuclear magnetic resonance (NMR) spectroscopy at 300 MHz for three homologous cardioactive polypeptides, anthopleurin-A from Anthopleura xanthogrammica and Anemonia sulcata toxins I and II. There are approximately 15 slowly exchanging hydrogens in each polypeptide, but the slowest exchange rates are found in ATX II, with ATX I and AP-A having rates similar to one another. The exchange rates correlate with the thermal stability of these molecules, but not with the potency and species specificity of their biological activities. The data for AP-A are interpreted in terms of a recent structural model for this polypeptide.

Amides↗