cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.

SUMMARY: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. AVAILABILITY AND IMPLEMENTATION: This package works with Python 2.7 on MacOS and Linux. The program is freely available for download from https://github.com/ifaust83/cgheliparm. Together with the main script, the base reference files CG_X_std.lib, a number of examples and R scripts are also available from the same website. A tutorial on the use and application is also available at http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna. CONTACT: i.faustino@rug.nl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations.

Energy-coupling factor (ECF) transporters are involved in the uptake of micronutrients in bacteria. The transporters capture the substrate by high-affinity binding proteins, the so-called S-components. Here, we present the analysis of two regions of the substrate-binding pocket of the thiamine-specific S-component in Lactococcus lactis, ThiT. First, interaction of the thiazolium ring of thiamine with residues Trp34, His125 and Glu84 by π-π-stacking and cation-π is studied, and second, the part of the binding pocket that extends from the hydroxyl group. We mutated either the transported ligand (chemically) or the protein (genetically). Surprisingly, modifications in the thiazolium ring by introducing substituents with opposite electronic effects had similar effects on the binding affinity. We hypothesize that the electronic effects are superseeded by steric effects of the added substituents, which renders the study of isolated interactions difficult. Amino acid substitutions in ThiT indicate that the electrostatic interaction facilitated by residue Glu84 of ThiT and thiamine is necessary for picomolar affinity. Deazathiamine derivatives that explore the subpocket of the binding site extending from the hydroxyl group of thiamine bind with high affinity to ThiT and may be developed into selective inhibitors of thiamine transport by ECF transporters. Molecular-dynamics simulations suggest that two of these derivatives may not only bind to ThiT, but could also be transported.

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes.

Mitochondria produce most of the ATP consumed by cells through the respiratory chain in their inner membrane. This process involves protein complexes assembled into larger structures, the respiratory supercomplexes (SCs). Cardiolipin (CL), the mitochondrial signature phospholipid, is crucial for the structural and functional integrity of these SCs, but it is as yet unclear by what mechanism it operates. Our data disclose the mechanism for bulk CL in gluing SCs, steering their formation, and suggest how it may stabilize specific interfaces. We describe self-assembly molecular dynamics simulations of 9 cytochrome bc1 (CIII) dimers and 27 cytochrome c oxidase (CIV) monomers from bovine heart mitochondria embedded in a CL-containing model lipid bilayer, aimed at mimicking the crowdedness and complexity of mitochondrial membranes. The simulations reveal a large diversity of interfaces, including those of existing experimental CIII/CIV SC models and an alternative interface with CIV rotated by 180°. SC interfaces enclose 4 to 12 CLs, a ∼10 fold enrichment from the bulk. Half of these CLs glue complexes together using CL binding sites at the surface of both complexes. Free energy calculations demonstrate a larger CL binding strength, compared to other mitochondrial lipids, that is exclusive to these binding sites and results from non-additive electrostatic and van der Waals forces. This study provides a key example of the ability of lipids to selectively mediate protein-protein interactions by altering all ranges of forces, lubricate protein interfaces and act as traffic control agents steering proteins together.

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations.

In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

Parameters for Martini sterols and hopanoids based on a virtual-site description.

Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1-the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2-cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3-parameters for ergosterol were created and adapted from cholesterols; and 4-parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure.

Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels.

The respiratory chain or oxidative phosphorylation system (OxPhos) generates most of the chemical energy (ATP) used by our cells. The cytochrome c oxidase (CcO) is one of three protein complexes of OxPhos building up a proton gradient across the inner mitochondrial membrane, which is ultimately used by the ATP synthase to produce ATP. We present molecular dynamic simulations of CcO in a mimic of the mitochondrial membrane, and identify precise binding sites of cardiolipin (CL, signature phospholipid of mitochondria) on the protein surface. Two of these CL binding sites reveal pathways linking CLs to the entrance of the D and H proton channels across CcO. CLs being able to carry protons our results strongly support an involvement of CLs in the proton delivery machinery to CcO. The ubiquitous nature of CL interactions with the components of the OxPhos suggests that this delivery mechanism might extend to the other respiratory complexes.

Efficient Algorithms for Langevin and DPD Dynamics.

In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.

The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles--a small-angle neutron scattering and molecular dynamics study.

Small-angle neutron scattering and coarse-grained molecular dynamics simulations have been used to determine the structural parameters (bilayer thickness D, polar region thickness D(H), interfacial lateral area of the unit cell A(UC) and alcohol partial interfacial area A(CnOH)) of fluid dioleoylphosphatidylcholine:dioleoylphosphatidylserine (PCPS, DOPC:DOPS=24.7mol:mol) bilayers in extruded unilamellar vesicles with incorporated aliphatic alcohols (CnOH, n=8-18 is the even number of carbons in alkyl chain). External ((2))H(2)O/H(2)O contrast variation experiments revealed that D(H) decreases as a function of alkyl chain length and CnOH:PCPS molar ratio. Using measurements at single 100% ((2))H(2)O contrast we found that (i) D decreases with CnOH:PCPS molar ratio and increases with CnOH chain length (at 0.4 molar ratio); (ii) A(UC) significantly increases already in the presence of shortest CnOH studied (at 0.4 molar ratio), further increase is observed with longer CnOHs and at higher molar ratios; (iii) A(CnOH) of alcohol molecules in PCPS bilayer increases linearly with the alkyl chain length, A(CnOH) obtained for CnOHs with n≤10 corresponds to A(CnOH)≤20Å(2) - a value specific for the crystalline or solid rotator phase of alkanes. All these structural modifications induced by studied CnOHs were reproduced in MD simulations. The computational results give an accurate description of the alcohol effects at the molecular level, explaining the experimental data. The anomaly in A(CnOH) is discussed via the "umbrella" effect described for cholesterol.

Electrophoretic mobility does not always reflect the charge on an oil droplet.

Electrophoresis is widely used to determine the electrostatic potential of colloidal particles. Oil droplets in pure water show negative or positive electrophoretic mobilities depending on the pH. This is commonly attributed to the adsorption of hydroxyl or hydronium ions, resulting in a negative or positive surface charge, respectively. This explanation, however, is not in agreement with the difference in isoelectric point and point of zero charge observed in experiment. Here we present molecular dynamics simulations of oil droplets in water in the presence of an external electric field but in the absence of any ions. The simulations reproduce the negative sign and the order of magnitude of the oil droplet mobilities at the point of zero charge in experiment. The electrostatic potential in the oil with respect to the water phase, induced by anisotropic dipole orientation in the interface, is positive. Our results suggest that electrophoretic mobility does not always reflect the net charge or electrostatic potential of a suspended liquid droplet and, thus, the interpretation of electrophoresis in terms of purely continuum effects may need to be reevaluated.

Molecular dynamics simulations of mixed micelles modeling human bile.

Extensive molecular dynamics (MD) simulations of binary systems of phospholipids and bile salts, a model for human bile, have been performed. Recent progress in hardware and software development allows simulation of the spontaneous aggregation of the constituents into small mixed micelles, in agreement with experimental observations. The MD simulations reveal the structure of these micelles at atomic detail. The phospholipids are packed radially with their headgroups at the surface and the hydrophobic tails pointing toward the micellar center. The bile salts act as wedges between the phospholipid headgroups, with their hydrophilic sides exposed to the aqueous environment. The structure of the micelles strongly resembles the previously proposed radial shell model. Simulations including small fractions of cholesterol reveal how cholesterol is solubilized inside these mixed micelles without changing their overall structure.

Association behaviour of glucitol amine gemini surfactants : Self-consistent-field theory and molecular-dynamics simulations.

The association behaviour of a number of glucitol amine gemini surfactants has been investigated by means of molecular dynamics and self-consistent-field calculations. We have shown that the titratable head group of the surfactant is responsible for a micelle-to-membrane transition when changing the pH. Furthermore, the association structure of this group of surfactants is shown to be very sensitive to ionic strength. The combination of a charged head group, a spacer, and the hydrophilic glucitol side chains is responsible for the possible structural transitions in the associates as a function of ionic strength and pH.

Molecular dynamics simulation of a lipid diamond cubic phase.

This paper presents the first atomistic simulation of a cubic membrane phase. Using the molecular dynamics simulation technique both the global and the local organization of glycerolmonoolein molecules inside the diamond cubic phase are studied. Multinanosecond simulations reveal that the center of the cubic bilayer remains close to the infinite periodic minimal surface that describes the diamond geometry. We further show that the equilibrium structure of the surfactant molecules inside the cubic phase is very similar to their structure inside a simulated lamellar bilayer. The small differences arise from the packing constraints of the surfactants within the cubic phase which has an area per surfactant that increases toward the bilayer center.

Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations.

Lipid adhesion forces can be measured using several experimental techniques, but none of these techniques provide insight on the atomic level. Therefore, we performed extensive nonequilibrium molecular dynamics simulations of a phospholipid membrane in the liquid-crystalline phase out of which individual lipid molecules were pulled. In our method, as an idealization of the experimental setups, we have simply attached a harmonic spring to one of the lipid headgroup atoms. Upon retraction of the spring, the force needed to drag the lipid out of the membrane is recorded. By simulating different retraction rates, we were able to investigate the high pull rate part of the dynamical spectrum of lipid adhesion forces. We find that the adhesion force increases along the unbinding path, until the point of rupture is reached. The maximum value of the adhesion force, the rupture force, decreases as the pull rate becomes slower, and eventually enters a friction-dominated regime. The computed bond lengths depend on the rate of rupture, and show some scatter due to the nonequilibrium nature of the experiment. On average, the bond length increases from approximately 1.7 nm to 2.3 nm as the rates go down. Conformational analyses elucidate the detailed mechanism of lipid-membrane bond rupture. We present results of over 15 ns of membrane simulations. Implications for the interpretation and understanding of experimental rupture data are discussed.

Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations.

To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced, are reported. The probability density of such a pore in the membrane was obtained from the free energy of formation of the pore, which was computed from the average force needed to constrain the pore in the membrane. It was found that the free energy of a single file of water molecules spanning the bilayer is 108(+/-10) kJ/mol. From unconstrained molecular dynamic simulations it was further deduced that the nature of the pore is very transient, with a mean lifetime of a few picoseconds. The orientations of water molecules within the pore were also studied, and the spontaneous translocation of a turning defect was observed. The combined data allowed a permeability coefficient for proton permeation across the membrane to be computed, assuming that a suitable orientation of the water molecules in the pore allows protons to permeate the membrane relatively fast by means of a wirelike conductance mechanism. The computed value fits the experimental data only if it is assumed that the entry of the proton into the pore is not rate limiting.

Molecular dynamics simulation of a phospholipid membrane.

We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in future simulations. This goal being reached it is then further possible to gain insight in to those properties that are experimentally more difficult to access. The system studied is dipalmitoylphosphatidylcholine/water, consisting of 5408 atoms. Using original force field parameters the membrane turned out to approach a gel-like state. With slight changes of the parameters, the system adopted a liquid-crystalline state. Separate 80 ps runs were performed on both the gel and liquid-crystalline systems. Comparison of MD results with reliable experimental data (bilayer repeat distance, surface area per lipid, tail order parameters, atom distributions) showed that our simulations, especially the one in the liquid-crystalline phase, can serve as a realistic model for a phospholipid membrane. Further analysis of the trajectories revealed valuable information on various properties. In the liquid-crystalline phase, the interface turns out to be quite diffuse, with water molecules penetrating into the bilayer to the position of the carbonyl groups. The 10-90% width of the interface turns out to be 1.3 nm and the width of the hydrocarbon interior 3.0 nm. The headgroup dipoles are oriented at a small angle with respect to the bilayer plane. The resulting charge distribution is almost completely cancelled by the water molecules. The electron density distribution shows a large dip in the middle of the membrane. In this part the tails are more flexible. The mean life time between dihedral transitions is 20 ps. The average number of gauche angles per tail is 3.5. The occurrence of kinks is not a significant feature.