Molecular dynamics simulation of a 13-mer duplex DNA: a PvuII substrate

Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water are carried out under following conditions: (i) unconstrained at 300 K (230 ps); (ii) unconstrained at 283 K (500 ps); (iii) Watson-Crick basepair constrained at 283 K (1 ns); and (iv) Watson-Crick basepair constrained with ions at 283 K (1.2 ns). In all these simulation studies, the molecule was observed to be bending and maximum distortions in the double helix around was seen around the G7:C7' basepair, which is the phosphodiester bond that is cleaved by PvuII. Analysis of MD simulation with ions carried out for 1.2 ns also pointed out that the conformation of double helix alternates between a conformation close to B-form and close to A-form. It is argued that a bent non-standard conformation is recognised by the PvuII enzyme. The maximum bend occurs at the G7:C7' region, weakening the phosphodiester bond and allows His48 to get placed in such a fashion to permit the scission through a general base mechanism. The bending and distortion observed is a property of the sequence which acts as a substrate for PvuII enzyme. This is confirmed by carrying out MD studies on the Dickerson's sequence d(CGCGAATTCGCG)2 as a reference molecule, which practically does not bend or get deformed.     

Discrete molecular dynamics studies of the folding of a protein-like model

BACKGROUND: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from insensitivity to the geometrical properties of the proteins (lattice models), whereas others are computationally heavy (traditional molecular dynamics). RESULTS: We used the recently proposed approach of Zhou and Karplus to study the folding of a protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding <--> unfolding transition. In addition, we demonstrate the ability to study the core of the model protein. CONCLUSIONS: The algorithm along with the model of interresidue interactions can serve as a tool for studying the thermodynamics and kinetics of protein models.     

Effect of substrate grain size on iron-zinc reaction kinetics during hot-dip galvanizing

In the galvanizing process, it has been proposed that the grain size of the substrate steel influences the Fe-Zn alloy phase reaction kinetics and growth rate during immersion in the liquid Zn bath. Two grain sizes (nominally 15 and 85 μm) were developed in a decarburized low-carbon (0.005) steel and hot-dipped galvanized in 0.00 wt pct Al-Zn and 0.20 wt pct Al-Zn baths to study the effect of substrate grain size on Fe-Zn phase formation. Uniform attack of the substrate steel occurred in the 0.00 wt pct Al-Zn bath, since an Fe₂Al₅ inhibition layer did not form. No barrier to nucleation of the Fe-Zn phases exists in this Zn bath, and therefore, the substrate steel grain size had no significant effect on the kinetics of phase growth for the gamma, delta, and zeta phase layers. In the 0.20 wt pct Al-Zn bath, discontinuous Fe-Zn phase growth (outburst formation) occurred due to the initial formation of the Fe-Al inhibition layer. The nucleation of the Fe-Zn phases was significantly retarded in this bath for the large (85 μm) substrate grain size. Whereas outbursts were found in the 15-μm grain size substrate after 10 seconds of immersion time, it required 1200 seconds to nucleate just a few outbursts in the 85-μm substrate. These results support the mechanism that Fe-Al inhibition layer breakdown occurs along fast diffusion paths for Zn in the inhibition layer that correspond to the location of substrate steel grain boundaries where reaction with Fe can occur.     

Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A: a molecular dynamics study

A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects in the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.     

Kinetic mechanism of a partial folding reaction. 1. Properties Of the reaction and effects of denaturants

The bimolecular association rate constant (kon) and dissociation rate constant (koff) of the complex between fluorescein-labeled S-peptide analogues and folded S-protein are reported. This is the first kinetic study of a protein folding reaction in which most of the starting material is already folded and only a small part (one additional helix) becomes ordered; it provides a folding landscape with a small conformational entropy barrier, and one in which kinetic traps are unlikely. Refolding and unfolding are measured under identical strongly native conditions, and the reaction is found to be two-state at low reactant concentrations. The dissociation constant (Kd) of the complex and the properties of the transition state may be calculated from the rate constants without extrapolation. The folded complex is formed fast (kon = 1.8 x 10(7) M-1 s-1) and is very stable (Kd = 6 pM) at 10 degrees C, 10 mM MOPS, pH 6.7. Charge interactions stabilize the complex by 1.4 kcal mol-1. The charge effect enters in the refolding reaction: increasing the salt concentration reduces kon dramatically and has little effect on koff. Urea and GdmCl destabilize the complex by decreasing kon and increasing koff. The slopes (m-values) of plots of ln Kd vs [cosolvent] are 0.75 +/- 0.04 and 2.8 +/- 0.3 kcal mol-1 M-1 for urea and GdmCl, respectively. The ratio mon/(mon + moff) is 0.54 +/- 0.04 for urea and 0.57 +/- 0.1 for GdmCl, where mon is the m-value for kon and moff is the m-value for koff, indicating that more than half of the sites for interaction with either cosolvent are buried in the ensemble of structures present at the transition state.     

Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the drug-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.     

Aedes aegypti: characterization of a hemolymph polypeptide expressed during melanotic encapsulation of filarial worms

We report on the initial characterization of an 84-kDa polypeptide that is differentially expressed in Aedes aegypti during melanotic encapsulation immune reactions against filarial worms. [35S]Methionine-labeled hemolymph from mosquitoes inoculated with saline, parasites that are melanized, or parasites that are not melanized was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Results show that the level of the 84-kDa polypeptide increases considerably in those mosquitoes undergoing encapsulation reactions against parasites but remains down-regulated in those mosquitoes exposed to parasites that are not melanized or are undergoing wound healing responses (saline-inoculated). Experiments involving glycosidase treatment of hemolymph samples indicate that this polypeptide is not heavily glycosylated. Amino acid microsequencing was performed and two internal sequence fragments (15 continuous amino acids and 12 noncontinuous amino acids) were obtained. Analysis of these sequences to known sequences in a protein database did not yield any conclusive information as to the identify of the 84-kDa polypeptide. Therefore, degenerate oligonucleotide primers were designed, based on the sequence of the 15-amino-acid fragment, and used with the polymerase chain reaction (PCR) to amplify from A. aegypti genomic DNA the region between the primers. The PCR product was cloned and sequenced to verify that the nucleic acid sequence matched the known protein sequence. Screening of an A. aegypti cDNA library with this small PCR-generated clone resulted in the selection of an approximately 540-bp clone. Northern analysis with this larger cDNA clone indicates that it hybridizes to an approximately 2.0-kb message that is differentially expressed in mosquitoes undergoing melanotic encapsulation reactions against filarial worms. Furthermore, sequencing of this approximately 540-bp clone showed that it contained the 15-amino-acid sequence that had been used to design the degenerate PCR primers, indicating that an appropriate clone was selected. However, sequence analysis of this clone at the protein and nucleic acid level did not provide any conclusive answers to the identity or function of the 84-kDa polypeptide.     

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion-collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion-collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.     

Slow alpha helix formation during folding of a membrane protein

Very little is known about the folding of proteins within biological membranes. A "two-stage" model has been proposed on thermodynamic grounds for the folding of alpha helical, integral membrane proteins, the first stage of which involves formation of transmembrane alpha helices that are proposed to behave as autonomous folding domains. Here, we investigate alpha helix formation in bacteriorhodopsin and present a time-resolved circular dichroism study of the slow in vitro folding of this protein. We show that, although some of the protein's alpha helices form early, a significant part of the protein's secondary structure appears to form late in the folding process. Over 30 amino acids, equivalent to at least one of bacteriorhodopsin's seven transmembrane segments, slowly fold from disordered structures to alpha helices with an apparent rate constant of about 0.012 s-1 at pH 6 or 0.0077 s-1 at pH 8. This is a rate-limiting step in protein folding, which is dependent on the pH and the composition of the lipid bilayer.     

Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme

Molecular dynamics simulations of protein denaturation can complement and extend experimental studies of protein folding by providing atomic-level structural information about conformational transitions and any conformational states along the unfolding pathway. Previous unfolding simulations of hen egg-white lysozyme have resulted in intermediate structures with an unfolded alpha-domain and a structured beta-domain, which is inconsistent with experiment. In contrast, the beta-domain unfolded first in the two simulations presented here leaving a structured alpha-domain. Following this, intermediate states were identified that differ with respect to the packing of the helices and the elements of non-native structure adopted. The non-native structure is critical for explaining many of the experimental observations. Overall, the pooled ensemble of these intermediates is in agreement with the experimental data for the major kinetic intermediate, suggesting that the kinetic intermediate may be made up of distinct, but rapidly interconverting, partially folded conformations distinguished primarily by differences in helix packing.     

The chaperonin cycle cannot substitute for prolyl isomerase activity, but GroEL alone promotes productive folding of a cyclophilin-sensitive substrate to a cyclophilin-resistant form

The chaperonin GroEL and the peptidyl-prolyl cis-trans isomerase cyclophilin are major representatives of two distinct cellular systems that help proteins to adopt their native three-dimensional structure: molecular chaperones and folding catalysts. Little is known about whether and how these proteins cooperate in protein folding. In this study, we have examined the action of GroEL and cyclophilin on a substrate protein in two distinct prolyl isomerization states. Our results indicate that: (i) GroEL binds the same substrate in different prolyl isomerization states. (ii) GroEL-ES does not promote prolyl isomerizations, but even retards isomerizations. (iii) Cyclophilin cannot promote the correct isomerization of prolyl bonds of a GroEL-bound substrate, but acts sequentially after release of the substrate from GroEL. (iv) A denatured substrate with all-native prolyl bonds is delayed in folding by cyclophilin due to isomerization to non-native prolyl bonds; a substrate that has proceeded in folding beyond a stage where it can be bound by GroEL is still sensitive to cyclophilin. (v) If a denatured cyclophilin-sensitive substrate is first bound to GroEL, however, productive folding to a cyclophilin-resistant form can be promoted, even without GroES. We conclude that GroEL and cyclophilin act sequentially and exert complementary functions in protein folding.     

Internal union dynamics during a strike: A quasi-experimental study.

Hypothesized that union members on strike will (a) give a higher evaluation of the union and of the leadership, (b) evaluate the benefit package more highly after the strike, (c) become more militant against the employer during the strike, (d) report more willingness to participate in union activities, and (e) show more intraunion cohesion during the strike. Random samples of members of 9 local unions (3 each from Ford, General Motors, and Chrysler) were surveyed on 4 occasions: before the 1976 bargaining, during the strike at Ford, after settlement of the national contract, and 7 mo after the strike ended. Usable responses from a questionnaire totaled 1,182 (405 strikers, 777 nonstrikers). With the exception of greater intraunion cohesion during the strike, all hypotheses were confirmed. (18 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Cystic fibrosis: a disease of altered protein folding

Patch clamp technique was employed to record single Na channel currents in isolated guinea-pig ventricular myocytes. Burst mode could be elicited by step depolarization and terminates immediately after repolarization. The unitary current of burst mode was not only dependent on Na concentration in the pipettes but also on the test voltage. The open time constant increased as testing voltage becomes more positive. The results from stepwise-depolarization and ramp depolarization experiments showed that the more steps or the faster the upstroke velocity of depolarization used, the more the burst mode would occure.     

Crystal structure of a trapped phosphoenzyme during a catalytic reaction

The crystal structure of the fructose-2,6-bisphosphatase domain trapped during the reaction reveal a phosphorylated His 258, and a water molecule immobilized by the product, fructose-6-phosphate. The geometry suggests that the dephosphorylation step requires prior removal of the product for an 'associative in-line' phosphoryl transfer to the catalytic water.