Molecular Modeling Studies on Amphotericin B and its Complex with Phospholipid,

Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-to-tail dimeric structure and lipid - amphotericin B complex demonstrate interesting features of the flexibilities within the molecule and define the optimal interactions for the formation of a stable dimeric structure and complex with phospholipid.

Dynamics of zeolite cage and its effect on the diffusion properties of sorbate: persistence of diffusion anomaly in NaA zeolite

Recent computer simulations on zeolites Y and A have found that the diffusion coefficient and the rate of intercage diffusion exhibit, apart from a linear dependence on the reciprocal of the square of the sorbate diameter, an anomalous peak as sorbate diameter approaches the window diameter. Here we report molecular dynamics simulations of zeolite NaA incorporating framework flexibility as a function of sorbate diameter in order to verify the existence of anomalous diffusion. Results suggest persistence of anomalous diffusion or ring effect. This suggests that the anomalous behavior is a general effect characteristic of zeolites Y and A. The barrier for diffusion across the eight-ring window is seen to be negative and is found to decrease with sorbate size. The effect of sorbate on the cage motion has also been investigated. Results suggest that the window expands during intercage migration only if the sorbate size is comparable to the window diameter. Flexible cage simulations yield a higher value for the diffusion coefficient and also the rate of intercage diffusion. This increase has been shown to be due to an increase in the intercage diffusions via the centralized diffusion mode rather than the surface-mediated mode. It is shown that this increase arises from an increase in the single particle density distribution in the region near the cage center.

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Translational and rotational motion in molecular liquids: A computer simulation study of Lennard-Jones ellipsoids

In order to understand the translational and rotational motion in dense molecular liquids, detailed molecular dynamics simulations of Lennard-Jones ellipsoids have been carried out for three different values of the aspect ratio kappa. For ellipsoids with an aspect ratio equal to 2, the product of the translational diffusion coefficient (D-T) and the average orientational correlation time of the l-th rank harmonics (tau(lR)), converges to a nearly constant value at high density. Surprisingly, this density independent value of D-T tau(lR) is within 5% of the hydrodynamic prediction with the slip boundary condition. This is despite the fact that both D-T and tau(lR) themselves change nearly by an order of magnitude in the density range considered, and the rotational correlation function itself is strongly nonexponential. For small aspect ratios (kappa less than or equal to 1.5), the rotational correlation function remains largely Gaussian even at a very large density, while for a large aspect ratio (kappa greater than or equal to 3), the transition to the nematic liquid-crystalline phase precludes the hydrodynamic regime. Thus, the rotational dynamics of ellipsoids show great sensitivity to the aspect ratio. At low density, tau(lR) goes through a minimum value, indicating the role of interactions in enhancing the rate of orientational relaxation. (C) 1997 American Institute of Physics. [S0021-9606(97)50142-5].

Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein

Eosinophil Cationic Protein (ECP) is a member of RNase A superfamily which carries out the obligatory catalytic role of cleaving RNA. It is involved in a variety of biological functions. Molecular dynamics simulations followed by essential dynamics analysis on this protein are carried out with the goal of gaining insights into the dynamical properties at atomic level. The top essential modes contribute to subspaces and to the transition phase. Further, the sidechain-sidechain/sidechain-mainchain hydrogen bond clusters are analyzed in the top modes, and compared with those of crystal structure. The role of residues identified by these methods is discussed in the context of concerted motion, structure and stability of the protein.

Hydrogen-bond dynamics near a micellar surface: Origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

Slow orientational dynamics of water molecules at a micellar surface

The dynamics of water molecules near an aqueous micellar interface is studied in an atomistic molecular dynamics simulation of cesium pentadecafluorooctanoate (CsPFO) in water. The dipolar orientational time correlation function (tcf) and the translational diffusion of the water molecules are investigated. Results show that both the reorientational and the translational motion of water molecules near the micelle are restricted. In particular, the orientational tcf exhibits a very slow component in the long time which is slower than its bulk value by 2 orders of magnitude. This slow decay seems to be related to the slow decay often observed in experiments. The origin of the slow decay is analyzed.

Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.

Identity, energetics, dynamics and environment of interfacial water molecules in a micellar solution

The structure and energetics of interfacial water molecules in the aqueous micelle of cesium perfluorooctanoate have been investigated, using large-scale atomistic molecular dynamics simulations, with the primary objective of classifying them. The simulations show that the water molecules at the interface fall into two broad classes: bound and free, present in a ratio of 9:1. The bound water molecules can be further categorized on the basis of the number of hydrogen bonds (one or two) that they form with the surfactant headgroups. The hydrogen bonds of the doubly hydrogen-bonded species are found to be, on the average, slightly weaker than those in the singly bonded species. The environment around interfacial water molecules is more ordered than that in the bulk. The surface water molecules have substantially lower potential energy, because of interaction with the micelle. In particular, both forms of bound water have energies that are lower by �2.5-4.0 kcal/ mol. Entropy is found to play an important role in determining the relative concentration of the species.

Size-dependent and strain rate effects in quantum dot nanostructures with molecular dynamic simulations

Size and strain rate effects are among several factors which play an important role in determining the response of nanostructures, such as their deformations, to the mechanical loadings. The mechanical deformations in nanostructure systems at finite temperatures are intrinsically dynamic processes. Most of the recent works in this context have been focused on nanowires [1, 2], but very little attention has been paid to such low dimensional nanostructures as quantum dots (QDs). In this contribution, molecular dynamics (MD) simulations with an embedded atom potential method(EAM) are carried out to analyse the size and strain rate effects in the silicon (Si) QDs, as an example. We consider various geometries of QDs such as spherical, cylindrical and cubic. We choose Si QDs as an example due to their major applications in solar cells and biosensing. The analysis has also been focused on the variation in the deformation mechanisms with the size and strain rate for Si QD embedded in a matrix of SiO2 [3] (other cases include SiN and SiC matrices).It is observed that the mechanical properties are the functions of the QD size, shape and strain rate as it is in the case for nanowires [2]. We also present the comparative study resulted from the application of different EAM potentials in particular, the Stillinger-Weber (SW) potential, the Tersoff potentials and the environment-dependent interatomic potential (EDIP) [1]. Finally, based on the stabilized structural properties we compute electronic bandstructures of our nanostructures using an envelope function approach and its finite element implementation.

An ultra-stable Cu nanowire under thermo-mechanical loading: A molecular dynamic study

We report on the formation of a stable Body-Centered Heptahedral (BCH) crystalline nanobridge structure of diameter ~ 1nm under high strain rate tensile loading to a <100> Cu nanowire. Extensive Molecular Dynamics (MD) simulations are performed. Six different cross-sectional dimensions of Cu nanowires are analyzed, i.e. 0.3615 x 0.3615 nm2, 0.723 x 0.723 nm2, 1.0845 x 1.0845 nm2, 1.446 x 1.446 nm2, 1.8075 x 1.8075 nm2, and 2.169 x 2.169 nm2. The strain rates used in the present simulations are 1 x 109 s-1, 1 x 108 s-1, and 1 x 107 s-1. We have shown that the length of the nanobridge can be characterized by larger plastic strain. A large plastic deformation is an indication that the structure is highly stable. The BCH nanobridge structure also shows enhanced mechanical properties such as higher fracture toughness and higher failure strain. The effect of temperature, strain rate and size of the nanowire on the formation of BCH structure is also explained in details. We also show that the initial orientation of the nanowires play an important role on the formation of BCH crystalline structure. Results indicate that proper tailoring of temperature and strain rate during processing or in the device can lead to very long BCH nanobridge structure of Cu with enhanced mechanical properties, which may find potential application for nano-scale electronic circuits.

Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape

We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid.

Relaxation and jump dynamics of water at the mica interface

The orientational relaxation dynamics of water confined between mica surfaces is investigated using molecular dynamics simulations. The study illustrates the wide heterogeneity that exists in the dynamics of water adjacent to a strongly hydrophilic surface such as mica. Analysis of the survival probabilities in different layers is carried out by normalizing the corresponding relaxation times with bulk water layers of similar thickness. A 10-fold increase in the survival times is observed for water directly in contact with the mica surface and a non-monotonic variation in the survival times is observed moving away from the mica surface to the bulk-like interior. The orientational relaxation time is highest for water in the contact layer, decreasing monotonically away from the surface. In all cases the ratio of the relaxation times of the 1st and 2nd rank Legendre polynomials of the HH bond vector is found to lie between 1.5 and 1.9 indicating that the reorientational relaxation in the different water layers is governed by jump dynamics. The orientational dynamics of water in the contact layer is particularly novel and is found to undergo distinct two-dimensional hydrogen bond jump reorientational dynamics with an average waiting time of 4.97 ps. The waiting time distribution is found to possess a long tail extending beyond 15 ps. Unlike previously observed jump dynamics in bulk water and other surfaces, jump events in the mica contact layer occur between hydrogen bonds formed by the water molecule and acceptor oxygens on the mica surface. Despite slowing down of the water orientational relaxation near the surface, life-times of water in the hydration shell of the K ion are comparable to that observed in bulk salt solutions. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4717710]

Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations

The discrepancy between the X-ray and NMR structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase in relation to the functionally important plasticity of the molecule led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures appears to confirm this correlation. In consonance with the reported results of the investigations in cellular compartments and aqueous solution, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important in function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. Selvaraj M, Ahmad R, Varshney U and Vijayan M 2012 Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J. Biosci. 37 953-963] DOI 10.1007/s12038-012-9276-5