Previous Molecular Dynamics Simulations Research Articles

Finding Dominant Reaction Pathways via Global Optimization of Action

We present a new computational approach, Action-CSA, to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing method. This approach successfully samples not only the most dominant pathway but also many other possible paths without initial guesses on reaction pathways. Pathway space is efficiently sampled by crossover operations of a set of paths and preserving the diversity of sampled pathways. The sampling ability of the approach is assessed by finding pathways for the conformational changes of alanine dipeptide and hexane. The benchmarks demonstrate that the rank order and the transition time distribution of multiple pathways identified by the new approach are in good agreement with those of long molecular dynamics simulations. We also show that the lowest action folding pathway of the mini-protein FSD-1 identified by the new approach is consistent with previous molecular dynamics simulations and experiments.

A Discrete Loop of the SERCA N-Domain Interacts with Phospholamban and Stabilizes a Compact Conformation of the SERCA Cytosolic Headpiece

The cardiac sarco/endoplasmic reticulum (ER) calcium ATPase (SERCA) and its inhibitor phospholamban (PLB) are key regulators of calcium levels in cardiac cells. In previous molecular dynamics (MD) simulations of SERCA spontaneous headpiece closure, we identified a discrete N-domain beta 5,6-loop that directs the closure of SERCA headpiece. Here we use additional MD simulations to pinpoint specific negative residues that facilitate SERCA headpiece closure. In addition, fluorescence resonance energy transfer (FRET) measurements showed that mutation of these key residues slows down calcium-dependent SERCA headpiece closure, as predicted from MD calculations. The functional significance of impaired SERCA headpiece closure was demonstrated by a 60% decrease in SERCA ATPase activity with no detectable change in calcium sensitivity. Additionally, loop mutations reduced transport of calcium as measured by a low affinity calcium sensor (R-CEPIA1er) in the ER of HEK cells. Interestingly, MD simulations of the SERCA-PLB regulatory complex model showed that PLB phosphorylation on Serine 16 stabilized a compact, ordered SERCA headpiece through an interaction with the beta 5,6-loop. Fluorescence lifetime imaging microscopy (FLIM) measurements also detected a conformational change of the SERCA-PLB regulatory complex after phosphomimetic mutation of PLB. Overall, the data suggest that this discrete loop is important for SERCA transport activity and functional regulation by PLB. This novel structural element may represent a target for modulation of SERCA activity.

Analyzing the Effects of Lipid Type on the α-Hemolysin Nanopore and 5HT3 Receptor Structure and Gating using Molecular Dynamics Simulations

Alpha-hemolysin (α-HL) is a transmembrane protein used to measure the size and charge of macromolecules. In this process, α-HL is inserted into a tethered lipid bilayer composed of 1,2-diphytanoyl-sn-glycero-3-phosphocholine (PHPC) lipids. However, all previous molecular dynamics (MD) simulations attempting to model this system have used a more common lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), to represent the PHPC-tethered bilayer. PHPC possesses highly methylated hydrophobic chains which creates a more rigid structure. The result is that simulations using POPC lipids yield channel currents at least 20% less than experimental values. MD simulations conducted with both PHPC and POPC lipids for both the full and a reduced form of the protein containing just the β-barrel indicate that PHPC lipids could more accurately describe the experimentally observed parameters. The 5-hydroxytryptamine receptor (5HT3) is the principle receptor responsible for modulating a wide range of neurological and digestive functions. Here we aim to better understand the response of the 5HT3 receptor to 5HT (serotonin) in an environment that mimics the native lipid composition. This work supports the experimental design of a field effect transistor (FET) device we are developing to measure the presence of ligands such as neurotransmitters, neuropeptides and drug molecules. To this end, MD simulations were conducted on a system composed of the Cys-loop ligand-gated ion channel protein receptor 5HT3, a 7:7:6 ratio POPC/1-stearoyl-2-docosahexaenoyl-sn-glyerco-3-phosphocholine (SDPC)/cholesterol membrane, and 5HT to determine if ligand binding causes experimentally observed protein reassembly and channel opening. This work is unique in that these simulations possess a more realistic membrane composition and that they compare the conformation of the glycosylated protein to the non-glycosylated form providing structural details of the effects of glycosylation on the binding pocket and channel pore radius.

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.

The Solvation Structure of Lithium Ions in an Ether Based Electrolyte Solution from First-Principles Molecular Dynamics.

The solvation and desolvation of the Li ion play a crucial role in the electrolytes of Li based secondary batteries, and their understanding at the microscopic level is of great importance. Oligoether (glyme) based electrolytes have attracted much attention as electrolytes used in Li based secondary batteries, such as Li-ion, Li-S, and Li-O2 batteries. However, the solvation structure of the Li ion in glyme based electrolytes has not been fully clarified yet. We present a computational study on the solvation structure of lithium ions in the mixture of triglyme and lithium bis(trifluoromethylsulfonyl)-amide (LiTFSA) by means of molecular orbital and molecular dynamics calculations based on density functional theory. We found that, in the electrolyte solution composed of the equimolar mixture of triglyme and LiTFSA, lithium ions are solvated mainly by crown-ether-like curled triglyme molecules and in direct contact with an TFSA anion. We also found the aggregate formed with Li ion and TFSA anions and/or triglyme molecule(s) is equally stable, which has not been reported in the previous classical molecular dynamics simulations, suggesting that in reality a small fraction of Li ions form aggregates and they might have a significant impact on the Li ion transport. Our results demonstrate the importance of performing electronic structure based molecular dynamics of electrolyte solution to clarify the detailed solvation structure of the Li ion.

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Thermally induced failure mechanism transition and its correlation with short-range order evolution in metallic glasses

The effect of temperature on the short-range order (SRO) structures, deformation mechanisms and failure modes of metallic glasses (MGs) is of fundamental importance for their practical applications. However, due to lack of direct structural information at the atomistic level from experiments and the absence of previous molecular dynamics (MD) simulations to reproduce experimental observations over a wide range of temperature, this issue has not been well understood. Here, by carefully constructing the atomistic models of Cu64Zr36 and Fe80W20 MGs, we are able to reproduce the major deformation modes observed experimentally, i.e. single shear banding (SB) at low temperatures, multiple shear-bandings at intermediate temperatures and homogeneous plastic flow at elevated temperatures. By examining the evolution of SRO, we find that the different failure modes exhibit distinctively different full-icosahedron (FI) evolution pathways at different temperatures. Specifically, at low temperatures, the FI concentration first deceases to a minimum, then recovers slightly, and finally comes to a plateau; at intermediate temperatures, it first decreases and then reaches a plateau; while at elevated temperatures, it decreases simply monotonically. These different pathways arise from the dynamic competition between the destruction and recovering of FI clusters. We further show that the local softening caused by the destructions of FI clusters is crucial for the formation of localized shear planes and further shear bands. Since our simulations exhibit the same trend for both MG systems, it is expected that these findings may be generic for a wide range of MGs.

Abstract 387: Cardiac Myosin-binding Protein C Structural Dynamics - a Time-resolved FRET Biosensor for Enhanced Contractility in Heart Failure Therapeutic Discovery

We have created a high-resolution time-resolved spectroscopy molecular biosensor for heart failure therapeutic discovery based on the structural dynamics of cardiac myosin-binding protein C (cMyBP-C). Drugs of interest mimic phosphorylation states of cMyBP-C, which influences myocardial contractility. β-adrenergic stimulation enhances contractility in myocardium, in part due to Protein Kinase A (PKA)-mediated phosphorylation of cMyBP-C. Recent structural and functional results have provided an understanding for how cMyBP-C physiologically regulates inotropy and lusiotropy in the heart by modulating actin-myosin interactions. Phosphorylation introduces a structural change within the regulatory M domain of cMyBP-C, leading to altered actin-myosin binding, and regulation of myocardial contraction. Previous molecular dynamics simulations suggested a specific rotation within the M domain upon phosphorylation that facilitates bending and exposes a putative binding site that is only accessible in the phosphorylated molecule. We hypothesized that these structural rearrangements in nanometer spatial orientation could be measured spectroscopically in mechanistic studies via introduction of site-directed probes within the M domain of cMyBP-C using time-resolved fluorescence resonance energy transfer (TR-FRET). Moreover, we hypothesized that this fluorescently-labeled recombinant muscle protein could be used as a TR-FRET biosensor for detecting potential drugs that alter the M domain structure in specific ways. These drugs will be particularly relevant to enhancement of myocardial contractility and represent novel therapeutics for heart failure and cardiomyopathy. Here, we engineered pairs of cysteine residues within the M domain for FRET labeling and tested the effects of phosphorylation to influence the tertiary structure and dynamics of cMyBP-C. We have characterized cMyBP-C’s molecular basis for fine-tuning contraction and our biosensor is well aligned for high-throughput spectroscopic screens for drugs that perturb structure specific to phosphorylation state. Compound discovery using this assay is applicable to development of novel cardiac disease therapies by enhancing contractility to alleviate dysfunction.

The Molecular Mechanism of Opening the Helix Bundle Crossing (HBC) Gate of a Kir Channel.

Inwardly rectifying K+ (Kir) channels, serving as natural molecular nanomachines, transport potassium ions across the plasma membrane of the cell. Along the ion permeation pathway, three relatively narrow regions (the selectivity filter (SF), the inner helix bundle crossing (HBC), and the cytosolic G loop) may serve as gates to control ion permeation. Our previous molecular dynamics simulations based on the crystal structure of a Kir3.1 chimera revealed the possible gating mechanism of the G loop gate. Here, we introduced a proline mutation in the inner helix and obtained a channel model of the open HBC gate. The open HBC gate reaches 0.6 nm in diameter, which allows partial hydrated K+ ions to pass through. During the gating process, both the transmembrane helices TM1 and TM2 cooperatively rotate in a counterclockwise direction (viewed from the extracellular side) with the aid of the phospholipid PIP2. Only when all the transmembrane helices adopt a counterclockwise rotation, the HBC gate can be stabilized in the open state. We estimate that introduction of the proline mutation decreases the energy required to open the HBC gate by about 1.4 kcal/mol (ΔΔG).

The interaction potential of NO-H2 in ground and A Rydberg state

The interaction potential for the ground and A Rydberg state of NO-H2 has been calculated using high level ab initio methods. The complex is very floppy in nature and large amplitude motions are expected to characterize its dynamics. The ground state is characterized by two very close-lying states which exhibit crossings. By analogy with other complexes the Rydberg state is characterized by much smaller well depth and larger intermolecular distance. We compare with model potentials used in previous molecular dynamics simulations of photoexcitation and relaxation and conclude on the importance of performing new studies.

Transitions of Double-Stranded DNA Between the A- and B-Forms.

The structure of double-stranded DNA (dsDNA) is sensitive to solvent conditions. In solution, B-DNA is the favored conformation under physiological conditions, while A-DNA is the form found under low water activity. The A-form is induced locally in some protein-DNA complexes, and repeated transitions between the B- and A-forms have been proposed to generate the forces used to drive dsDNA into viral capsids during genome packaging. Here, we report analyses on previous molecular dynamics (MD) simulations on B-DNA, along with new MD simulations on the transition from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI), a new metric along the A-B continuum, to quantify our results. When A-DNA is placed in an equilibrated solution at physiological ionic strength, there is no energy barrier to the transition to the B-form, which begins within about 1 ns. The transition is essentially complete within 5 ns, although occasionally a stretch of a few base pairs will remain A-like for up to ∼10 ns. A comparison of four sequences with a range of predicted A-phobicities shows that more A-phobic sequences make the transition more rapidly than less A-phobic sequences. Simulations on dsDNA with a region of roughly one turn locked in the A-form allow us to characterize the A/B junction, which has an average bend angle of 20-30°. Fluctuations in this angle occur with characteristic times of about 10 ns.

Miscibility of dl-α-tocopherol β-glucoside in DPPC monolayer at air/water and air/solid interfaces

The role of newly synthesized tocopherol glycosidic derivative in modifying molecular organization and phase transitions of phospholipid monolayer at the air/water interface has been investigated. Two-component Langmuir films of dl-α-tocopheryl β-D-glucopyranoside (BG) mixed with dipalmitoyl phosphatidylcholine (DPPC) in the whole range of mole fractions were formed at the water surface. An analysis of surface pressure versus mean molecular area (π-A) isotherms and Brewster angle microscope images showed that the presence of BG molecules changes the structure and packing of the DPPC monolayer in a BG concentration dependent manner. BG molecules incorporated into DPPC monolayer inhibit its liquid expanded to liquid condensed phase transition proportionally to the BG concentration. The monolayers were also transferred onto solid substrates and visualized using an atomic force microscope. The results obtained indicate almost complete miscibility of BG and DPPC in the monolayers at surface pressures present in the biological cell membrane (30-35·10-3 N·m-1) for a BG mole fraction as high as 0.3. This makes the monolayer less packed and more disordered, leading to an increased permeability. The results support our previous molecular dynamics simulation data.

Activity and Kinetic Characterization of Four Human CYP2D6 Polymorphisms using the Substrates Bufuralol and Dextromethorphan

Human cytochrome P450 enzymes (CYPs) are a heme‐containing enzyme superfamily that have a major role in the metabolism of drugs along with other endogenous and exogenous chemicals. Human CYP2D6 is responsible for approximately 12% of CYP‐mediated drug metabolism. There are over 100 different allelic variants of CYP2D6 with metabolic profiles ranging from poor to ultra‐rapid. Four CYP2D6 allelic variants, three with a small series of distal mutations (*34, *17‐2, *17‐3) and one possible ultra‐metabolizer (*53), were expressed and purified in E. coli to further characterize their interactions with the substrates bufuralol and dextromethorphan using HPLC with UV detection. Km and vmax values were measured for comparison between variants and the reference *1. Previous molecular dynamics simulations of these allelic variants with and without a ligand bound suggested that varied flexibility and active site accessibility altered interaction with substrates. The current metabolic and kinetic studies are compared to these molecular dynamics models to broaden the understanding of substrate interactions for CYP2D6 variants with local and distal mutations relative to the active site.Support or Funding InformationNIH 1R15‐GM086767‐02

Bounce regime of droplet collisions: A molecular dynamics study

Droplet collisions have complex dynamics, which can lead to many different regimes of outcomes. The head-on collision and bounce back regime has been observed in previous experiments but numerical simulations using macro- or mesoscale approaches have difficulties reproducing the phenomena, because the interfacial regions are not well resolved. Previous molecular dynamics (MD) simulations have not reproduced the bounce regime either but have reported the coalescence and/or shattering regimes. To scrutinize the dynamics and mechanisms of binary collisions especially the interfacial regions, head-on collision processes of two identical nano-droplets with various impact velocities both in vacuum and in an ambient of nitrogen gas are investigated by MD simulations. With the right combination of the impact velocity and ambient pressure, the head-on collision and bounce back phenomenon is successfully reproduced. The bounce phenomena are mainly attributed to the “cushion effect” of the in-between nitrogen molecules and evaporated water molecules from the two nano-droplets. The analysis has verified and also extended the current gas film theory for the bounce regime through including the effects of evaporated water molecules (vapour). Some similarities and some dissimilarities between nanoscale and macro-/meso-/microscale droplet collisions have been observed. The study provides unprecedented insight into the interfacial regions between two colliding droplets.

Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET).

Holliday Junctions are critical DNA intermediates central to double strand break repair and homologous recombination. The junctions can adopt two general forms: open and stacked-X, which are induced by protein or ion binding. In this work, fluorescence spectroscopy, metal ion luminescence and thermodynamic measurements are used to elucidate the ion binding site and the mechanism of junction conformational change. Förster resonance energy transfer measurements of end-labeled junctions monitored junction conformation and ion binding affinity, and reported higher affinities for multi-valent ions. Thermodynamic measurements provided evidence for two classes of binding sites. The higher affinity ion-binding interaction is an enthalpy driven process with an apparent stoichiometry of 2.1 ± 0.2. As revealed by Eu3+ luminescence, this binding class is homogeneous, and results in slight dehydration of the ion with one direct coordination site to the junction. Luminescence resonance energy transfer experiments confirmed the presence of two ions and indicated they are 6–7 Å apart. These findings are in good agreement with previous molecular dynamics simulations, which identified two symmetrical regions of high ion density in the center of stacked junctions. These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation.

Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering

In liquid phase chemistry dynamic solute-solvent interactions often govern the path, ultimate outcome, and efficiency of chemical reactions. These steps involve many-body movements on subpicosecond time scales and thus ultrafast structural tools capable of capturing both intramolecular electronic and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3](2+), with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering patterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited solute. By simultaneous combination of both methods only, we can extract new information about the solvation dynamic processes unfolding during the first picosecond (ps). The measured bulk solvent density increase of 0.2% indicates a dramatic change of the solvation shell around each photoexcited solute, confirming previous ab initio molecular dynamics simulations. Structural changes in the aqueous solvent associated with density and temperature changes occur with ∼1 ps time constants, characteristic for structural dynamics in water. This slower time scale of the solvent response allows us to directly observe the structure of the excited solute molecules well before the solvent contributions become dominant.

Direct observation of the velocity contribution to friction in monolayer-coated micromachines

Using a newly developed in-situ platform combined with high-speed imaging up to 200,000 frames per second, we measure friction versus velocity in a micromachined interface from 0.1 to 3000 μm/s. The steady-state friction coefficient (friction at constant velocity) of a boundary lubricant-coated interface decreases up to 300 μm/s, then increases. The friction increase is confirmed in an independent test in which velocity is increased instantaneously. Previous single asperity molecular dynamics simulations of monolayer boundary lubricants indicate that friction is independent of velocity, while experiments and simulations of periodic potentials indicate a monotonically increasing trend. We directly bridge spatial and temporal scales using rate–state constitutive laws, and attribute the decrease in friction to the decrease in asperity lifetime (a state effect), and the increase to the emerging dominance of interfacial viscosity (a rate effect).

Building Graphs to Describe Dynamics, Kinetics and Energetics in the D-Ala:D-Lac Ligase Vana

The D-Ala:D-Lac ligase VanA, plays a very important role into the resistance to vancomycin, as it allows the bacteria to replace the synthesis of D-Ala:D-Ala by the synthesis of D-Ala-D-Lac in the bacterial wall, thus making obsolete the role of vancomycin. The reaction catalyzed by VanA requires the opening of the omega-loop to let the substrates entering the active site. Previous molecular dynamics simulations have shown the spontaneous opening of omega-loop in the presence of a crystallographic disulphide bridge. Here, the conformational landscape of VanA is further explored in the absence of the bridge and by using the enhanced sampling approach temperature-accelerated molecular dynamics (TAMD). This analysis has permitted to reveal a description of the conformational space of VanA, where the internal mobility and various opening modes of omega-loop play a major role. The other important feature is the correlation of the omega-loop motion with the movements of the opposite domain. The relative mobility of these two regions is observed in the conformational space analysis and their coupling is demonstrated by the communities analysis of the protein structure. The observations made on the VanA dynamics and conformations permit to propose some residues interactions to be important for the kinetics of the omega-loop opening. Also, the various graph network analyses performed here provide a panel of methods to describe a protein function in the frame of a larger system-oriented network.

Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD) trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD) and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different charge/protonation states of ampicillin, we made available force-field parameters and static/dynamic properties derived from both Density Functional Theory and MD calculations. For the specific system investigated here, we found that: (i) the conformational statistics extracted from plain MD simulations is consistent with that obtained from REMD simulations; (ii) overall, our MD-based approach performs slightly better than any of the conformer generator tools if one takes into account both the diversity of the generated conformational set and the ability to reproduce experimentally-determined structures.

Melting properties of Pt and its transport coefficients in liquid states under high pressures

Molecular dynamics (MD) simulations of the melting and transport properties in liquid states of platinum for the pressure range (50–200 GPa) are reported. The melting curve of platinum is consistent with previous ab initio MD simulation results and the first-principles melting curve. Calculated results for the pressure dependence of fusion entropy and fusion volume show that the fusion entropy and the fusion volume decrease with increasing pressure, and the ratio of the fusion volume to fusion entropy roughly reproduces the melting slope, which has a moderate decrease along the melting line. The Arrhenius law well describes the temperature dependence of self-diffusion coefficients and viscosity under high pressure, and the diffusion activation energy decreases with increasing pressure, while the viscosity activation energy increases with increasing pressure. In addition, the entropy-scaling law, proposed by Rosenfeld under ambient pressure, still holds well for liquid Pt under high pressure conditions.