Andrew E. Torda

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

SummaryThe 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.

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.

TIME-DEPENDENT DISTANCE RESTRAINTS IN MOLECULAR-DYNAMICS SIMULATIONS

Abstract A method for enforcing nuclear Overhauser effect (NOE) distance restraints in molecular dynamics simulations is presented. Rather than model the NOE distance as static, a term is included in the force field such that the distance restraint need only be satisfied as a 〈 r −3 〉 −1/3 weighted time average over the simulation trajectory. This provides a better approximation of the physical nature of the NOE and reduces the disturbance to the force field due to the artificial term. Tests on a simple model system demonstrate the inadequacy of current methods and show the advantages of this novel approach, resulting in a more extensive search of conformational space.

Structure refinement using time-averaged J-coupling constant restraints

SummaryWe 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 procedures ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.

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 for clustering molecular dynamics configurations

Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified.

Functional analysis of the methylmalonyl-CoA epimerase from Caenorhabditis elegans.

Methylmalonyl‐CoA epimerase (MCE) is an enzyme involved in the propionyl‐CoA metabolism that is responsible for the degradation of branched amino acids and odd‐chain fatty acids. This pathway typically functions in the reversible conversion of propionyl‐CoA to succinyl‐CoA. The Caenorhabditis elegans genome contains a single gene encoding MCE (mce‐1) corresponding to a 15 kDa protein. This was expressed in Escherichia coli and the enzymatic activity was determined. Analysis of the protein expression pattern at both the tissue and subcellular level by microinjection of green fluorescent protein constructs revealed expression in the pharynx, hypodermis and, most prominently in body wall muscles. The subcellular pattern agrees with predictions of mitochondrial localization. The sequence similarity to an MCE of known structure was high enough to permit a three‐dimensional model to be built, suggesting conservation of ligand and metal binding sites. Comparison with corresponding sequences from a variety of organisms shows more than 1/6 of the sequence is completely conserved. Mutants allelic to mce‐1 showed no obvious phenotypic alterations, demonstrating that the enzyme is not essential for normal worm development under laboratory conditions. However, survival of the knockout mutants was altered when exposed to stress conditions, with mutants surprisingly showing an increased resistance to oxidative stress.

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

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 β‐sheet structures. Of the local interactions, those between residues i and i + 2 were the most important in both α‐helices and β‐strands. Some surprisingly strong correlations were discovered within β‐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. Proteins 32:175–189, 1998.

Parametrisation of time-averaged distance restraints in MD simulations

SummaryTime-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating or which grossly distort the dynamics of the system.