Effects of long-range electrostatic forces on simulated protein folding kinetics.

Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics.

Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations.

Folding and misfolding of the collagen triple helix are studied through molecular dynamics simulations of two collagenlike peptides, [(POG)(10)](3) and [(POG)(4)POA(POG)(5)](3), which are models for wild-type and mutant collagen, respectively. To extract long time dynamics from short trajectories, we employ Markov state models. By analyzing thermodynamic and kinetic quantities calculated from the Markov state models, we examine folding mechanisms of the collagen triple helix and consequences of glycine mutations.

COMPUTING: Screen Savers of the World Unite!

Unused CPU time on desktop computers could be put to good use, if distributed computing succeeds in capturing people's imagination. In their Perspective, Shirts and Pande describe existing distributed computing projects and recent efforts to overcome parallelization problems. This vast underused resource could raise biological and other scientific computation to fundamentally new predictive levels.

Choosing weights for simulated tempering.

Simulated tempering is a method to enhance simulations of complex systems by periodically raising and lowering the temperature. Despite its advantages, simulated tempering has been overshadowed by its parallel counterpart, replica exchange (also known as parallel tempering), due to the difficulty of weight determination in simulated tempering. Here we propose a simple and fast method to obtain near-optimal weights for simulated tempering, and demonstrate its effectiveness in a molecular dynamics simulation of Ala(10) polypeptide in explicit solvent.

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.

Markovian state models (MSMs) are a convenient and efficient means to compactly describe the kinetics of a molecular system as well as a formalism for using many short simulations to predict long time scale behavior. Building a MSM consists of grouping the conformations into states and estimating the transition probabilities between these states. In a previous paper, we described an efficient method for calculating the uncertainty due to finite sampling in the mean first passage time between two states.

Protein folding under confinement: a role for solvent.

Although most experimental and theoretical studies of protein folding involve proteins in vitro, the effects of spatial confinement may complicate protein folding in vivo. In this study, we examine the folding dynamics of villin (a small fast folding protein) with explicit solvent confined to an inert nanopore. We have calculated the probability of folding before unfolding (P(fold)) under various confinement regimes.

Spectrophotometric estimation of ambroxol and cetirizine hydrochloride from tablet dosage form.

Fixed dose combination tablets containing ambroxol HCl and cetirizine HCl are clinically used as mucolytic and antiallergic. Several spectrophotometric and HPLC methods have been reported for simultaneous estimation of these drugs with other drugs. The drugs individually and in mixture obeys Beer's law over conc.

Persistent voids: a new structural metric for membrane fusion.

Motivation: Membrane fusion constitutes a key stage in cellular processes such as synaptic neurotransmission and infection by enveloped viruses. Current experimental assays for fusion have thus far been unable to resolve early fusion events in fine structural detail. We have previously used molecular dynamics simulations to develop mechanistic models of fusion by small lipid vesicles.

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

To meet the challenge of modeling the conformational dynamics of biological macromolecules over long time scales, much recent effort has been devoted to constructing stochastic kinetic models, often in the form of discrete-state Markov models, from short molecular dynamics simulations. To construct useful models that faithfully represent dynamics at the time scales of interest, it is necessary to decompose configuration space into a set of kinetically metastable states. Previous attempts to define these states have relied upon either prior knowledge of the slow degrees of freedom or on the application of conformational clustering techniques which assume that conformationally distinct clusters are also kinetically distinct.

Bayesian update method for adaptive weighted sampling.

Exploring conformational spaces is still a challenging task for simulations of complex systems. One way to enhance such a task is weighted sampling, e.g.

Genotypic characterization of Listeria spp. isolated from fresh water fish.

A total of 200 samples (muscles and viscera, 100 of each) of fresh water fish, walking catfish (Clarias batrachus) were screened for Listeria spp. All the samples were subjected to a two-step enrichment followed by plating on selective media. Confirmation of the isolates was on the basis of biochemical characters, haemolysis on blood agar and Christie, Atkins, Munch Petersen test.

Local structure formation in simulations of two small proteins.

Massively parallel all-atom, explicit solvent molecular dynamics simulations were used to explore the formation and existence of local structure in two small alpha-helical proteins, the villin headpiece and the helical fragment B of protein A. We report on the existence of transient helices and combinations of helices in the unfolded ensemble, and on the order of formation of helices, which appears to largely agree with previous experimental results. Transient local structure is observed even in the absence of overall native structure.

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.

We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods.

Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles.

With the advent of powerful synchrotron sources, solution X-ray scattering is being increasingly used to get basic information about the structure of polypeptides. The solution scattering technique essentially provides one-dimensional data, which are then interpreted in terms of a three-dimensional structure through model building. Here we calculate wide-angle solution scattering patterns for an ensemble of simulated unfolded structures of villin headpiece, which differ from the native structure by rmsd = 8.

Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion.

Lipid membrane fusion is critical to cellular transport and signaling processes such as constitutive secretion, neurotransmitter release, and infection by enveloped viruses. Here, we introduce a powerful computational methodology for simulating membrane fusion from a starting configuration designed to approximate activated prefusion assemblies from neuronal and viral fusion, producing results on a time scale and degree of mechanistic detail not previously possible to our knowledge. We use an approach to the long time scale simulation of fusion by constructing a Markovian state model with large-scale distributed computing, yielding an understanding of fusion mechanisms on time scales previously impossible to simulate to our knowledge.

One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution.

In general, finding a one-dimensional representation of the kinetics of a high-dimensional system is a great simplification for the study of complex systems. Here, we propose a method to obtain a reaction coordinate whose potential of the mean force can reproduce the commitment probability distribution from the multidimensional surface. We prove that such a relevant one-dimensional representation can be readily calculated from the equilibrium distribution of commitment probabilities, which can be obtained with simulations.

Electric fields at the active site of an enzyme: direct comparison of experiment with theory.

The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site.

Nanotube confinement denatures protein helices.

In striking contrast to simple polymer physics theory, which does not account for solvent effects, we find that physical confinement of solvated biopolymers decreases solvent entropy, which in turn leads to a reduction in the organized structural content of the polymer. Since our theory is based on a fundamental property of water-protein statistical mechanics, we expect it to have broad implications in many biological and material science contexts.

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece.

We report on the use of large-scale distributed computing simulation and novel analysis techniques for examining the dynamics of a small protein. Matters addressed include folding rate, very long time scale kinetics, ensemble properties, and interaction with water. The target system for the study, the villin headpiece, has been of great interest to experimentalists and theorists both.

Kinetic definition of protein folding transition state ensembles and reaction coordinates.

Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue betabetaalphabeta protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points along each free energy barrier. We introduced a method for determining transition states by employing the transmission probability, Ptrans, and determined which conformations were transition state ensemble members (Ptrans approximately 0.

Validation of Markov state models using Shannon's entropy.

Markov state models are kinetic models built from the dynamics of molecular simulation trajectories by grouping similar configurations into states and examining the transition probabilities between states. Here we present a procedure for validating the underlying Markov assumption in Markov state models based on information theory using Shannon's entropy. This entropy method is applied to a simple system and is compared with the previous eigenvalue method.

Kinetic computational alanine scanning: application to p53 oligomerization.

We have developed a novel computational alanine scanning approach that involves analysis of ensemble unfolding kinetics at high temperature to identify residues that are critical for the stability of a given protein. This approach has been applied to dimerization of the oligomerization domain (residues 326-355) of tumor suppressor p53. As validated by experimental results, our approach has reasonable success in identifying deleterious mutations, including mutations that have been linked to cancer.

Effect of T-2 toxin on growth, performance and haematobiochemical alterations in broilers.

Administration of dietary T-2 toxin in 120 days old broiler chicks led to significant lower body weights and increase in feed conversion ratio from 2nd week of age. There was significant reduction in haemoglobin and packed cell volume in T-2 toxicated birds at 4 ppm level only. The other hematological parameters like TEC, TLC and absolute leucocyte count did not showed any variation due to T-2 toxin in feed.

A seminoma in a monorchid guinea fowl (Numida meleagris).

A case of seminoma in a monorchid adult guinea fowl (Numida meleagris) is described. Grossly, a right enlarged testis, which was soft in consistency, and white to pale in colour with few spots of haemorrhages was observed. Histologically, the testicle revealed diffusely spread sheets of tumour cells.