Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations

Heparin was isolated in the beginning of the 20th century and until today remains as one of the most important drugs able to interfere with the haemostatic process. Due to the side effects produced by heparin therapy, new promising drugs have been developed, as the synthetic pentasaccharide (synthetically derived from the sequence GlcN-GlcA-GlcN-IdoA-GlcN). The anticoagulant activity of this compound is based on potentiation of antithrombin (AT) inhibitory activity upon serine proteinases of clotting cascade, a mechanism based on the conformational modification of AT. In this context, we present here a molecular dynamics (MD) study of the interaction between the synthetic pentasaccharide and AT. The obtained data correctly predicted an induced fit mechanism in AT-pentasaccharide interaction, showing a solvent-exposed P1 residue instead of a hided conformation. Also, the specific contribution of important amino acid residues to the overall process was also characterized, both in (2)S(0) and (1)C(4) conformations of IdoA residue, suggesting that there is no conformational requirement to the interaction of this residue with AT. Altogether, the results show that MD simulations could be used to characterize and quantify the interaction of synthetic compounds with AT, predicting its specific capacity to induce conformational changes in AT structure. Thus, MD simulations of heparin (and heparin-derived)-AT interactions are proposed here as a powerful tool to assist and support drug design of new antithrombotic agents.     

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

We have investigated the sampling efficiency in molecular dynamics with the PB implicit solvent when self-guiding forces are added. Compared with a high-temperature dynamics simulation, the use of self-guiding forces in room-temperature dynamics is found to be rather efficient as measured by potential energy fluctuation, gyration radius fluctuation, backbone RMSD fluctuation, number of unique clusters, and distribution of low RMSD structures over simulation time. Based on the enhanced sampling method, we have performed ab initio folding simulations of two small proteins, betabetaalpha1 and villin headpiece. The preliminary data for the folding simulations is presented. It is found that betabetaalpha1 folding proceeds by initiation of the turn and the helix. The hydrophobic collapse seems to be lagging behind or at most concurrent with the formation of the helix. The hairpin stability is weaker than the helix in our simulations. Its role in the early folding events seems to be less important than the more stable helix. In contrast, villin headpiece folding proceeds first by hydrophobic collapse. The formation of helices is later than the collapse phase, different from the betabetaalpha1 folding.     

State of the art in studying protein folding and protein structure prediction using molecular dynamics methods

This study presents an overview of the state of the art in using molecular dynamics methods to simulate protein folding and in the end game of protein structure prediction. In principle, these methods should allow the highest level of detail possible and the highest accuracy, but they are limited by both the accuracy of the force field used in the simulation and the sampling possible in the available computer time. We describe current capabilities in running the simulations longer and more efficiently.     

Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm

A highly parallel replica exchange method (REM) that couples with a newly developed molecular dynamics algorithm particle-particle particle-mesh Ewald (P3ME)/RESPA has been proposed for efficient sampling of protein folding free energy landscape. The algorithm is then applied to two separate protein systems, beta-hairpin and a designed protein Trp-cage. The all-atom OPLSAA force field with an explicit solvent model is used for both protein folding simulations. Up to 64 replicas of solvated protein systems are simulated in parallel over a wide range of temperatures. The combined trajectories in temperature and configurational space allow a replica to overcome free energy barriers present at low temperatures. These large scale simulations reveal detailed results on folding mechanisms, intermediate state structures, thermodynamic properties and the temperature dependences for both protein systems.     

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

Molecular dynamics is an important computational tool to simulate and understand biochemical processes at the atomic level. However, accurate simulation of processes such as protein folding requires a large number of both atoms and time steps. This in turn leads to huge runtime requirements. Hence, finding fast solutions is of highest importance to research. In this paper we present a new approach to accelerate molecular dynamics simulations with inexpensive commodity graphics hardware. To derive an efficient mapping onto this type of computer architecture, we have used the new Compute Unified Device Architecture programming interface to implement a new parallel algorithm. Our experimental results show that the graphics card based approach allows speedups of up to factor nineteen compared to the corresponding sequential implementation.     

Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation

Thermal stability is of great importance for industrial enzymes. Here we explored the thermal-stable mechanism of thermophilic nitrile hydratases (NHases) utilizing a molecular dynamic simulation. At a nanosecond timescale, profiles of root mean square fluctuation (RMSF) of two thermophilic NHases, 1UGQ and 1V29, under enhancing thermal stress were carried out at 300 K, 320 K, 350 K and 370 K, respectively. Results showed that the region A1 (211-231 aa) and A2 (305-316 aa) in 1UGQ, region B1 (186-192 aa) in 1V29, and most of terminal ends in both enzymes are hyper-sensitive. Salt-bridge analyses revealed that in one hand, salt-bridges contributed to maintaining the rigid structure and stable performance of the thermophilic 1UGQ and 1V29; in the other hand, salt-bridges involved in thermal sensitive regions are relatively weak and prone to be broken at elevated temperature, thereby cannot hold the stable conformation of the spatial neighborhood. In 1V29, region A1 was stabilized by a well-organized hook-hook like cluster with multiple salt-bridge interactions, region A2 was stabilized by two strong salt-bridge interactions of GLU52-ARG332 and GLU334-ARG332. In 1UGQ, the absence of a charged residue decreased its thermal sensitivity of region B1, and the formation of a small beta-sheet containing a stable salt-bridge in C-beta-terminal significantly enhanced its thermal stability. By radius of gyration calculation containing or eliminating the thermal sensitive regions, we quantified the contribution of thermal sensitive regions for thermal sensitivity of 1UGQ and 1V29. Consequently, we presented strategies to improve thermal stability of the industrialized mesophilic NHase by introducing stable salt-bridge interactions into its thermal sensitive regions.     

硅的平衡态分子动力学模拟

平衡态分子动力学模拟是研究既定系统向所期望的平衡态演化的一种方法,不仅可预测平衡态的各种性质,还为动力学加载过程提供合理的初始条件.本文主要研究Free、NVT、NVE平衡态分子动力学模拟中系统宏观量的演化过程;并讨论如何根据不同的初始条件,选择恰当的平衡态模拟方法.     

An expert protein loop refinement protocol by molecular dynamics simulations with restraints

Protein structure prediction (PSP) is a long standing problem in structural biology and bioinformatics. Within the PSP problem loop refinement is a major bottleneck. In this article we report the latest version of the CReF expert predictor system for the PSP problem with emphasis on loop refinement of the approximate 3-D structure 1ZDD_P of the Z34C mini protein predicted by CReF. We designed a loop refinement protocol based on seven molecular dynamics (MD) simulations runs at different temperatures. We found that, by letting the loop residues move freely during dynamics at 325 K and restraining the internal coordinates of the correctly predicted helical structures, while allowing them to move relative to each other, the refinement protocol was very effective in predicting an accurate loop conformation in the first 100 ps of a 1000 ps MD simulation. The quality of the predictions was confirmed by the RMSD between refined and experimental structures which varied from 0.6 to 1.3 Å. In addition, stereochemical analyses showed that 100% of all residues of the refined 1ZDD_P, including those in the loop, populates the most favorable core regions of the Ramachandran plot. Our study suggests that the proposed protocol may be suitable to refine more complex mini proteins with different classes and architectures.     

Insights into ligand selectivity in nitric oxide synthase isoforms: a molecular dynamics study

Molecular dynamics (MD) simulations were carried out for inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) isoforms complexed with substrate (L-arginine) and the iNOS specific inhibitor GW 273629, 2 for a time period of 1.2ns. The simulations were compared both within and across the isoforms. iNOS specificity of inhibitor 2 is attributed to water mediated interactions and cooperative hydrogen bond networks. Juxtaposition of the carboxylic and ammonium groups in the substrate and inhibitor serve as a modulating key in binding to the isoforms. Based on these investigations, molecules 3 and 4 were rationally designed to attain specificity among the isoforms. The capability of the designed ligands was theoretically tested through MD simulations to envisage binding patterns with both isoforms. A detailed analysis of the molecular recognition pattern shows molecule 4 to be more selective to iNOS when compared to eNOS.     

Computer simulations of protein dynamics and thermodynamics

The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton's equations are discussed. Two recent applications of these methods are examined. The first considers the rate at which molecular oxygen binds to myoglobin, an oxygen-storage protein found in muscle. The second application involves the thermodynamics of the binding of oxygen to hemoglobin, a protein that is the major component of red blood cells. The comparison of this biochemical event to one in which oxygen is bound to an unusual variant of hemoglobin illustrates many of the simulation methods commonly used in the pharmaceutical industry to aid in the drug discovery process     

Stability of C60 chains: molecular dynamics simulations

A linearly aligned structure of three C60 fullerene, interconnected by two benzorods of same size, have been investigated under heat treatment. The overall structure resembles a section of a beaded string. Nine different lengths of benzorods have been considered, and the effect on the thermal stability have been investigated by means of molecular dynamics method. It has been found that the structure is thermally stable up to elevated temperatures, and the linear alignment of the structure is persistent, up to the temperature of decomposition.     

Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models

We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (?(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ?(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.     

Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations.

Inherited forms of transmissible spongiform encephalopathy, e.g. familial Creutzfeldt-Jakob disease, Gerstmann-Str?ussler-Scheinker syndrome and fatal familial insomnia, segregate with specific point mutations of the prion protein. It has been proposed that the pathologically relevant Asp178Asn (D178N) mutation might destabilize the structure of the prion protein because of the loss of the Arg164-Asp178 salt bridge. Molecular dynamics simulations of the structured C-terminal domain of the murine prion protein and the D178N mutant were performed to investigate this hypothesis. The D178N mutant did not deviate from the NMR conformation more than the wild type on the nanosecond time scale of the simulations. In agreement with CD spectroscopy experiments, no major structural rearrangement could be observed for the D178N mutant, apart from the N-terminal elongation of helix 2. The region of structure around the disulfide bridge deviated the least from the NMR conformation and showed the smallest fluctuations in all simulations in agreement with hydrogen exchange data of the wild type prion protein. Large deviations and flexibility were observed in the segments which are ill-defined in the NMR conformation. Moreover, helix 1 showed an increased degree of mobility, especially at its N-terminal region. The dynamic behavior of the D178N mutant and its minor deviation from the folded conformation suggest that the salt bridge between Arg164 and Asp178 might not be crucial for the stability of the prion protein.     

Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

The most widely used technique to allow for parallel simulations in molecular dynamics is spatial domain decomposition, where the physical geometry is divided into boxes, one per processor. This technique can inherently produce computational load imbalance when either the spatial distribution of particles or the computational cost per particle is not uniform. This paper shows the benefits of using a hybrid MPI+OpenMP model to deal with this load imbalance. We consider LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), a prototypical molecular dynamics simulator that provides its own balancing mechanism and an OpenMP implementation for many of its modules, allowing for a hybrid setup. In this work, we extend the current OpenMP implementation of LAMMPS and optimize it and evaluate three different setups: MPI-only, MPI with the LAMMPS balance mechanism, and hybrid setup using our improved OpenMP version. This comparison is made using the five standard benchmarks included in the LAMMPS distribution plus two additional test cases. Results show that the hybrid approach can deal with load balancing problems better and more effectively (50% improvement versus MPI-only for a highly imbalanced test case) than the LAMMPS balance mechanism (only 43% improvement) and improve simulations with issues other than load imbalance.

     

MDWiZ: A platform for the automated translation of molecular dynamics simulations

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.     

Temperature-induced unfolding pathway of a type III antifreeze protein: insight from molecular dynamics simulation

Molecular dynamics simulations of the temperature-induced unfolding reaction of a cold-adapted type III antifreeze protein (AFPIII) from the Antarctic eelpout Lycodichthys dearborni have been carried out for 10 ns each at five different temperatures. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. Plots of backbone root mean square deviation (RMSD) against radius of gyration (Rg) serve as phase space trajectories. These plots also indicate that the protein unfolds without many detectable intermediates suggestive of two-state unfolding kinetics. The transition state structures are identified from essential dynamics, which utilizes a principal component analysis (PCA) on the atomic fluctuations throughout the simulation. Overall, the transition state resembles an expanded native state with the loss of the three 3₁₀ helices and disrupted C-terminal region.Our study provides insight into the structure–stability relationship of AFPIII, which may help to engineer AFPs with increased thermal stability that is more desirable than natural AFPs for some industrial and biomedical purposes.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.