Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

A molecular dynamics study of chloride capture from water by the tetraprotonated cryptand SC24 is presented. The system under study consisted of a cryptand molecule, chloride ion, and 319 water molecules. Calculations were performed for 19 distances between the cryptand and the chloride. For each distance a trajectory of at least 60 ps was obtained. Two anion binding sites of comparable energy were found. The chloride can bind either inside the cryptand cavity or more loosely outside of the ligand. The binding sites are separated by an energy barrier of 20 kcal/mol. Chloride movement toward the cryptand is accompanied by stepwise dehydration of the anion. The energy loss due to this dehydration is offset by the electrostatic attraction between the anion and the ligand and by an increase in favorable water-water interactions. The most striking feature of chloride capture is a rapid cooperative change in the conformation of the cryptand when the Cl- starts to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, so that they point toward the chloride. The shift provides electrostatic stabilization, which compensates for the loss of the remaining three water molecules from the hydration shell of the anion. The N-H bonds remain directed toward the anion during its further movement into the ligand and guide chloride into a stable position inside the cryptand cavity. The flexibility of the receptor, the stepwise dehydration of an ionic substrate, and the characteristic balance between different energy components in the system all may be features of ion binding common to a wide range of abiotic and biological ionophores.     

A molecular dynamics study of the interaction of oleate and dodecylammonium chloride surfactants with complex aluminosilicate minerals

Surface characteristics of complex aluminosilicate minerals like spodumene [LiAl(SiO(3))(2)], jadeite [NaAl(SiO(3))(2)], feldspar [KAlSi(3)O(8)], and muscovite [K(2)Al(4)(Al(2)Si(6)O(20))(OH)(4)]) are modeled. Surface energies are computed for the cleavage planes of these minerals. Adsorption mechanisms of anionic chemisorbing type oleate and cationic physisorbing type dodecylammonium chloride molecules on two different crystal planes, that is (110) and (001), of spodumene and jadeite are studied in terms of the surface-surfactant interaction energies computed using molecular dynamics (MD) simulations. The conclusions drawn from purely theoretical computations match remarkably well with our experimental results.     

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K(+) ions in water over the 0.001-2 kbar range. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. It also provides a microscopic picture in terms of the pore network in liquid water.     

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study

Urea and GdmCl are widely used to denature proteins at high concentrations. Here, we used MD simulations to study the denaturation mechanisms of helical peptide in different concentrations of GdmCl and urea. It was found that the helical structure of the peptide in water simulation is disappeared after 5 ns while the helicity of the peptide is disappeared after 70 ns in 2 M urea and 25 ns in 1 M GdmCl. Surprisingly, this result shows that the helical structure in low concentration of denaturants is remained more with respect to that solvated in water. The present work strongly suggests that urea interact more preferentially to non-polar and aromatic side chains in 2 M urea; therefore, hydrophobic residues are in more favorable environment in 2 M urea. Our results also reveal that the hydrogen bonds between urea and the backbone is the dominant mechanism by which the peptide is destabilized in high concentration of urea. In 1 M and 2 M GdmCl, GdmCl molecules tend to engage in transient stacking interactions with aromatics and hydrophobic planar side chains that lead to displacement of water from the hydration surface, providing more favorable environment for them. This shows that accumulation of GdmCl around hydrophobic surfaces in 1 M and 2 M GdmCl solutions prevents proper solvation of the peptide at the beginning. In high GdmCl concentrations, water solvate the peptide better than 1 M and 2 M GdmCl. Therefore, our results strongly suggest that hydrogen bonds between water and the peptide are important factors in the destabilization of peptide in GdmCl solutions.     

A spectroelectrochemical study of the reduction of a Schiff base cryptand

The electrochemical reduction of a bicyclic hexaimino Schiff base cryptand 1 (N[(CH2)2N-CH-meta-C6H4-CH=N(CH2)2]3N) and that of one of its strands 2 ((CH3)2CH-N=CH-meta-C6H4-CH=N-CH(CH3)2) has been studied by visible and near infrared in-situ spectroelectrochemical techniques. These results are in good agreement with those obtained using alkali metals, but in this case the effect of the formation of ion pairs is minimized through the use of tetrabutylammonium cations. It is confirmed that 1- and 1= have the same visible and near IR spectrum. The spectrum of the products of the electrochemical reduction of 2 is similar to those of 1- or 1=.     

Ab initio molecular dynamics of liquid 1,3-dimethylimidazolium chloride

Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.     

A noncanonical binding site of linezolid revealed via molecular dynamics simulations

Linezolid, an antibiotic of oxazolidinone family, is a translation inhibitor. The mechanism of its action that consists in preventing the binding of aminoacyl-tRNA to the A-site of the large subunit of a ribosome was embraced on the basis of the X-ray structural analysis of the linezolid complexes with vacant bacterial ribosomes. However, the known structures of the linezolid complexes with bacterial ribosomes poorly explain the linezolid selectivity in suppression of protein biosynthesis, depending on the amino acid sequence of the nascent peptide. In the present study the most probable structure of the linezolid complex with a E. coli ribosome in the A,A/P,P-state that is in line with the results of biochemical studies of linezolid action has been obtained by molecular dynamics simulation methods.     

Structural basis of specific binding between Aurora A and TPX2 by molecular dynamics simulations

In the present study, the impacts of G198N and W128F mutations on the recognition between Aurora A and targeting protein of Xenopus kinesin-like protein 2 (TPX2) were investigated using molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis. The predicted binding free energy of the wild-type complex is more favorable than those of three mutants, indicating that both single and double mutations are unfavorable for the Aurora A and TPX2 binding. It is also observed that the mutations alternate the binding pattern between Aurora A and TPX2, especially the downstream of TPX2. An intramolecular hydrogen bond between the atom OD of Asp11(TPX2) and the atom HE1 of Trp34(TPX2) disappear in three mutants and thus lead to the instability of the secondary structure of TPX2. The combination of different molecular modeling techniques is an efficient way to understand how mutation has impacts on the protein-protein binding and our work gives valuable information for the future design of specific peptide inhibitors for Aurora A.     

A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine

Molecular dynamics simulations have been used to investigate the ternary complex formed between chicken liver dihydrofolate reductase, a phenyl triazine inhibitor, and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The solvent was represented by a sphere of water molecules encompassing the system. We report the results of quantum mechanical calculations of the rotational barrier in the pyrophosphate link and the barrier to inversion of the triazine ring. AMBER parameters for NADPH and the triazine are provided. Over the course of a 300-ps molecular dynamics simulation of the ternary complex in water, the triazine inhibitor maintains the same hydrogen bonding and hydrophobic interactions with the enzyme that are observed in the X-ray crystal structure. Despite the low calculated barrier to inversion of the triazine ring, a single puckered conformation is observed throughout the simulation. It is proposed that this is primarily due to interactions with Phe34, which maintains an approximately parallel orientation to the triazine ring. The nicotinamide portion of NADPH maintains the interactions observed in the crystal structure, but more conformational change is observed at the adenine end together with associated changes in the protein. Two conformations for the sidechain of Tyr31 are present in the X-ray structure. The main simulation reported here corresponds to the conformation characterized by (χ₁ = ? 161°, χ₂ = ? 103°). A separate simulation was also performed in which the sidechain of Tyr31 was initially set to the other conformation present in the crystal structure (χ₁ = 139°, χ₂ = ?99°). During this simulation, χ₁ of this sidechain gradually changed until it occupied the region characterized by χ₁ = ?160°, thereby suggesting that this is the preferred conformation for this residue. The simulation required 200 ps to reach structural equilibrium (as measured by the root mean square, rms, deviation from the initial crystal structure), thus reinforcing the view that simulations of at least several hundreds of picoseconds are desirable when studying such systems. © 1995 John Wiley & Sons, Inc.     

A molecular dynamics study of water near silicate surfaces

We have conducted a molecular dynamics simulation of water between uncharged silicate surfaces in order to understand, on a molecular basis, the structural and dynamical properties of vicinal water (i.e., the water between the surfaces). The results of our preliminary simulation indicate that the vicinal water differs substantially from pure bulk water in the transient orientation of molecular dipole moments and rate of relaxation of these moments. In contrast, no significant long-range differences between the radial distribution functions or hydrogen bonding patterns of vicinal and bulk water are evident.     

Kinetics of surface enrichment: A molecular dynamics study

We use molecular dynamics to study the kinetics of surface enrichment (SE) in a stable homogeneous mixture (AB), placed in contact with a surface which preferentially attracts A. The SE profiles show a characteristic double-exponential behavior with two length scales: ξ(-), which rapidly saturates to its equilibrium value, and ξ(+), which diverges as a power-law with time (ξ(+)～t(θ)). We find that hydrodynamic effects result in a crossover of the growth exponent from θ?0.5 to θ?1.0. There is also a corresponding crossover in the growth dynamics of the SE layer thickness.     

A molecular dynamics study of water between Lennard-Jones walls

An MD simulation of 216 ST2 water molecules between 12-6 Lennard-Jones walls has been performed which extend over 20 ps at an average temperature of 287 K. The oxygen atom density profile is reported the influence of the walls on the orientation of the water molecules on the self-diffusion coefficient have been investigated The results are compared with those from MC and MD simulations of similar systems.     

A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation

Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein-solvent and solvent-solvent hydrogen bonding have been analyzed and compared to the ones in trehalose-water and sucrose-water systems (Proteins 2005, 59, 291-302). Results help in rationalizing, at a molecular level, the effects of homologues disaccharides on protein structure/dynamics experimentally observed. Furthermore, the effectiveness of disaccharides in bioprotection in terms of peculiar protein-matrix coupling is also discussed.     

A molecular dynamics simulation study of nanoscale liquid threads

The properties of liquid threads in angular direction are studied. On the basis of Gibbs theory, a thermodynamic model is constructed and a formula of surface of tension is derived. For the determination of surface tension, different methods are presented. We investigate seven different systems (the numbers of molecules N are 1600, 2240, 2880, 3360, 4000, 4800, and 5280) by molecular dynamics simulations. We analyze the surface tension obtained by various routes, then whether the classical Laplace equation is applicable in nanoscale can be determined. The results obtained by molecular dynamics simulations support that surface tension is dependent on the dividing surface curvature.     

氯化钠对朊病毒结构稳定性影响的分子动力学研究

朊病毒疾病是由正常构象的PrPC转化为致病构象的PrPSc引起的一类可传染的蛋白质构象病.采用分子动力学模拟的方法研究了0～500mmol/L的NaCl溶液体系对人朊病毒构象影响并深入探讨了其分子机制.研究发现NaCl可以降低朊病毒的结构稳定性,并引起其α-螺旋含量的急剧降低.进一步的研究表明高浓度NaCl溶液体系能够显著破坏朊病毒螺旋1内部的重要盐桥Asp144-Arg148和Asp147-Arg151,同时明显降低其主要氢键Arg151 N:Asp147 O,Tyr150 N:Glu146 O,Tyr149 N:Tyr145 O和Arg148 N:Asp144 O的稳定性,并诱导朊病毒的疏水核心发生明显扩张,促使朊病毒整体稳定性的下降,这些可能是NaCl促进朊病毒构象转换的重要原因.     

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.