How alkali metal ion binding alters the conformation preferences of gramicidin A: a molecular dynamics and ion mobility study

Here, we present a systematic study combing electrospray ionization-ion mobility experiments and an enhanced sampling molecular dynamics, specifically integrated tempering sampling molecular dynamics simulations (ITS-MDS), to explore the conformations of alkali metal ion (Na, K, and Cs) adducts of gramicidin A (GA) in vacuo. Folding simulation is performed to obtain inherent conformational preferences of neutral GA to provide insights about how the binding of metal ions influences the intrinsic conformations of GA. The comparison between conformations of neutral GA and alkali metal ion adducts reveals a high degree of structural similarity, especially between neutral GA and [GA + Na](+); however, the structural similarities decrease as ionic radius of the metal increases. Collision cross section (CCS) profiles for [GA + Na](+) and [GA + Cs](+) ions obtained from by ITS-MDS compare favorably with the experimental CCS, but there are significant differences from CCS profiles for [GA + K](+) ions. Such discrepancies between the calculated and measured CCS profiles for [GA + K](+) are discussed in terms of limitations in the simulation force field as well as possible size-dependent coordination of the [GA + K](+) ion complex.     

A molecular dynamics study of Lys-Trp-Lys: structure and dynamics in solution following photoexcitation

We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.     

Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study.

The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.     

Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation

A molecular dynamics (MD) simulation study has been carried out to understand the stability of the triple helical collagen models. The calculations show that the presence of the aspartic acid residue in different positions leads to the local variation in the structure. Analyses of root-mean-square deviation (RMSD), radial distribution function (RDF), puckering effect, dihedral angle variation, hydrogen bond (H-bond), and conformational changes during molecular dynamics simulation reveal that the local perturbation in the sequences, increase in chain flexibility due to removal of five membered rings in the collagen by aspartic acid, change of intermolecular H-bonding pattern, and differences in the association of water are mainly influencing the nature of stabilization of collagen by aspartic acid.     

Steered molecular dynamics simulations of Na+ permeation across the gramicidin A channel

The potential of mean forces (PMF) governing Na+ permeation through gramicidin A (gA) channels with explicit water and membrane was characterized using steered molecular dynamics (SMD) simulations. Constant-force SMD with a steering force parallel to the channel axis revealed at least seven energy wells in each monomer of the channel dimer. Except at the channel dimer interface, each energy well is associated with at least three and at most four backbone carbonyl oxygens and two water oxygens in a pseudo-hexahedral or pseudo-octahedral coordination with the Na+ ion. Repeated constant-velocity SMD by dragging a Na+ ion from each energy well in opposite directions parallel to the channel axis allowed the computation of the PMF across the gA channel, revealing a global minimum corresponding to Na+ binding sites near the entrance of gA at +/-9.3 A from the geometric center of the channel. The effect of volatile anesthetics on the PMF was also analyzed in the presence of halothane molecules. Although the accuracy of the current PMF calculation from SMD simulations is not yet sufficient to quantify the PMF difference with and without anesthetics, the comparison of the overall PMF profiles nevertheless confirms that the anesthetics cause insignificant changes to the structural makeup of the free energy wells along the channel and the overall permeation barrier. On average, the PMF appears less rugged in the outer part of the channel in the presence of anesthetics, consistent with our earlier finding that halothane interaction with anchoring residues makes the gA channel more dynamic. A causal relationship was observed between the reorientation of the coordinating backbone carbonyl oxygen and Na+ transit from one energy well to another, suggesting the possibility that even minute changes in the conformation of pore-lining residues due to dynamic motion could be sufficient to trigger the ion permeation. Because some of the carbonyl oxygens contribute to Na+ coordination in two adjacent energy wells, our SMD results reveal that the atomic picture of ion "hopping" through a gA channel actually involves a Na+ ion being carried in a relay by the coordinating oxygens from one energy well to the next. Steered molecular dynamics complements other computational approaches as an attractive means for the atomistic interpretation of experimental permeation studies.     

Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. a molecular dynamics simulation study

The effect of physiological concentrations of different chlorides on the structure of a dipalmitoyl phosphatidylcholine (DPPC) bilayer has been investigated through atomistic molecular dynamics simulations. These calculations provide support to the concept that Li+, Na+, Ca2+, Mg2+, Sr2+, Ba2+, and Ac3+, but not K+, bind to the lipid-head oxygens. Ion binding exhibits an influence on lipid order, area per lipid, orientation of the lipid head dipole, the charge distribution in the system, and therefore the electrostatic potential across the head-group region of the bilayer. These structural effects are sensitive to the specific characteristics of each cation, i.e., radius, charge, and coordination properties. These results provide evidence aimed at shedding some light into the apparent contradictions among different studies reported recently regarding the ordering effect of ions on zwitterionic phosphatidylcholine lipid bilayers.     

Si（NCO）^＋2结构与稳定性的密度泛函理论研究

使用密度泛函（DFT）方法对Si(NCO)^ 2的可能异构体进行了计算研究,在UB3LYP／6－311G（d)理论级别下得到了6种异构体的能量和振动频率,结果表明,以2个NCO基团直接与Si^ 配位形成的异体最为稳定,理论计算得到一个以2个CO分子对称方式吸附于SiN^2 两侧而形成的络合物,这个络合物是否存在需进一步证实,在UB3LYP／6－311g(D) Ez级别下,反应Si^ 2NOC→Si(NCO)^ 2的焓变为－751．94kJ/mol,说明此反应在能量上相当有利。     

Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel

The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105) is used to build a mixed all-atom and coarse-grained (AA-CG) model of the gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer and water environment. In this model, the gA peptide was described in full atomistic detail, while the lipid and water molecules were described using coarse-grained representations. The atom-CG and CG-CG interactions in the mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) simulations were performed using the resulting AA-CG model. The results from simulations of the AA-CG model compare very favorably to those from all-atom MD simulations of the entire system. Since the MS-CG method employs a general and systematic approach to obtain effective interactions from the underlying all-atom models, the present approach to rigorously develop mixed AA-CG models has the potential to be extended to many other systems.     

Complex interactions between molecular ions in solution and their effect on protein stability

Protein stability in ionic solutions depends on the delicate balance between protein-ion and ion-ion interactions. For molecular ions containing multiple charged groups, the role of ion-ion interactions is particularly important. In this study, we show how the interplay between homo- and heteroion pairing influences protein stability using polyarginine salts as a model system. For the chloride salts, protein thermostability decreases as the size of the peptide increases, indicating enhanced binding to the protein. Moreover, it indicates reduced homoion pairing between Gdm(+) and carboxylate groups that is largely responsible for aggregation suppression, rather than denaturation, in monomeric arginine solutions. However, for the sulfate salts, strong heteroion pairing between the Gdm(+) groups and the sulfate counterions compensates for the loss of homoion pairing and, in return, leads to enhanced thermostability and a dramatically reduced (up to 10-30 times) rate of protein aggregation. Molecular dynamics simulations reveal how this ion pairing enhances conformational stability and, at the same time, reduces protein association. This study provides insight into complex ion effects on protein stability and serves as an example of how these intrasolvent interactions can be leveraged to enhance protein stability.     

How ion properties determine the stability of a lipase enzyme in ionic liquids: a molecular dynamics study

The influence of eight different ionic liquid (IL) solvents on the stability of the lipase Candida antarctica lipase B (CAL-B) is investigated with molecular dynamics (MD) simulations. Considered ILs contain cations that are based either on imidazolium or guanidinium as well as nitrate, tetrafluoroborate or hexafluorophosphate anions. Partial unfolding of CAL-B is observed during high-temperature MD simulations and related changes of CAL-B regarding its radius of gyration, surface area, secondary structure, amount of solvent close to the backbone and interaction strength with the ILs are evaluated. CAL-B stability is influenced primarily by anions in the order NO(3)(-)? BF(4)(-) < PF(6)(-) of increasing stability, which agrees with experiments. Cations influence protein stability less than anions but still substantially. Long decyl side chains, polar methoxy groups and guanidinium-based cations destabilize CAL-B more than short methyl groups, other non-polar groups and imidazolium-based cations, respectively. Two distinct causes for CAL-B destabilization are identified: a destabilization of the protein surface is facilitated mostly by strong Coulomb interactions of CAL-B with anions that exhibit a localized charge and strong polarization as well as with polar cation groups. Surface instability is characterized by an unraveling of α-helices and an increase of surface area, radius of gyration and protein-IL total interaction strength of CAL-B, all of which describe a destabilization of the folded protein state. On the other hand, a destabilization of the protein core is facilitated when direct core-IL interactions are feasible. This is the case when long alkyl chains are involved or when particularly hydrophobic ILs induce major conformational changes that enable ILs direct access to the protein core. This core instability is characterized by a disintegration of β-sheets, diffusion of ions into CAL-B and increasing protein-IL van der Waals interactions. This process describes a stabilization of the unfolded protein state. Both of these processes reduce the folding free energy and thus destabilize CAL-B. The results of this work clarify the impact of ions on CAL-B stabilization. An extrapolation of the observed trends enables proposing novel ILs in which protein stability could be enhanced further.     

Influence of ions on genome packaging and ejection: a molecular dynamics study

We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na(+)), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg(2+)) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions.     

Blocking of the nicotinic acetylcholine receptor ion channel by chlorpromazine, a noncompetitive inhibitor: A molecular dynamics simulation study

A large series of pharmacological agents, distinct from the typical competitive antagonists, block in a noncompetitive manner the permeability response of the nicotinic acetylcholine receptor (nAChR) to the neurotransmitter acetylcholine. Taking the neuroleptic chlorpromazine (CPZ) as an example of such agents, the blocking mechanism of noncompetitive inhibitors to the ion channel pore of the nAChR has been explored at the atomic level using both conventional and steered molecular dynamics (MD) simulations. Repeated steered MD simulations have permitted calculation of the free energy (approximately 36 kJ/mol) of CPZ binding and identification of the optimal site in the region of the serine and leucine rings, at approximately 4 A from the pore entrance. Coulomb and the Lennard-Jones interactions between CPZ and the ion channel as well as the conformational fluctuations of CPZ were examined to assess the contribution of each to the binding of CPZ to the nAChR. The MD simulations disclose a dynamic interaction of CPZ binding to the nAChR ionic channel. The cationic ammonium head of CPZ forms strong hydrogen bonds with Glu262 (alpha), Asp268 (beta), Glu272 (beta), Ser276 (beta), Glu280 (delta), Gln271 (gamma), Glu275 (gamma), and Asn279 (gamma) nAChR residues. Finally, the conventional MD simulation of CPZ at its identified binding site demonstrates that the binding of CPZ not only blocks ion transport through the channel but also markedly inhibits the conformational transitions of the channel, necessary for nAChR to carry out its biological function.     

Diversity of the gramicidin a spatial structure: two-dimensional 1H nmr study in solution

Theoretical consideration reveals a unique relationship between NMR spectral parameters and possible types of the gramididin A spatial structure. By means of two dimensional NMR spectroscopy four distinct species were detected simultaneously in ethanol solution. Comparison of experimental data and theoretical conclusions demonstrates that species 1 and 2 are left-handed parallel double helices

differing in relative arrangement of the two polypeptide chains within the dimers, species 3 is left-handed antiparallel double helix

, and species 4 is a mirror image of species 1, i.e. right-handed parallel double helix

. The results are compared with those on spatial structures of the peptide in complex with cesium (right-handed antiparallel double helix

) and of the gramicidin A transmembrane ionchannel (N-terminal to N-terminal single-stranded dimer

).     

A molecular dynamics study of sodium chenodeoxycholate in an aqueous solution

Hydration structure and dynamics of sodium chenodeoxycholate (CDC) in water are studied by a long-time molecular dynamics calculation. Strong hydration shell around the hydrophobic region of this large solute and strong hydrogen bonds of water with both hydroxyl and carboxyl oxygen atoms have been identified. The rotation of CDC around its longitudinal axis is found to be particularly active in comparison with that around other axes of the molecule. The diffusion coefficient of CDC calculated from the slope of the mean-square displacement, 0.95 × 10⁻⁹ m²/s, is only 1/6 of that for water in the solution, 5.4 × 10⁻⁹ m²/s.     

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study.

In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5-Leu-(Aib)2-OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)s-Leu-(Aib)2-OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide. I. This leads to a significant difference in 3 [symbol: see text] (HN, HC alpha) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton-proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpreting molecular properties in the solution state by using X-ray crystallographic data.     

A molecular dynamics study of alkaline earth metal-chloride complexation in aqueous solution

The relative stability of alkaline earth metals (M2+ = Mg2+, Ca2+, Sr2+, and Ba2+) and their chloride complexes in aqueous solution is examined through molecular dynamics simulations using a flexible SPC water model with an internally consistent set of metal ion force field parameters. For each metal-chloride ion pair in aqueous solution, the free energy profile was calculated via potential of mean force simulations. The simulations provide detailed thermodynamic information regarding the relative stability of the different types of metal-chloride pairs. The free energy profiles indicate that the preference for contact ion pair formation increases with ionic radius and is closely related to the metal hydration free energies. The water residence times within the first hydration shells are in agreement with residence times reported in other computational studies. Calculated association constants suggest an increase in metal-chloride complexation with increasing cation radii that is inconsistent with experimentally observed trends. Possible explanations for this discrepancy are discussed.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.