Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12−Thr-Pro-(Ala)10−NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr- (Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.

Proton NMR study of molecular dynamics in ammonium tribromo stannate (NH4SnBr3)

The proton second moment M2 and spin-lattice relaxation time T1 have been measured in ammonium tribromo stannate (NH4SnBr3) in the temperature range 77–300 K, to determine the ammonium dynamics. The continuous wave signal is strong and narrow at 77 and 300 K but has revealed an interesting intensity anomaly between 210 and 125 K. T1 shows a maximum (13 s) around 220 K. No minimum in the T1 vs 1000/T plot was observed down to 77 K. M2 and T1 results are interpreted in terms of NH+4 ion dynamics. The activation energy Ea for NH+4 ion reorientation is estimated to be 1.4 kcal mol−1.

Sorbate properties and cage-to-cage diffusion of argon in NaCaA: a molecular dynamics study

Detailed molecular dynamics simulations of argon in zeolite NaCaA are reported. Thermodynamic, structural, and dynamical properties of the sorbate as a function of temperature have been obtained. The properties calculated include various site-site radial distribution functions, different energy distribution functions, selfdiffusion coefficients, the power spectra, and properties relating to cage-to-cage diffusion. The results suggest that sorbate is delocalized above 300 K. Both modes of cage-to-cage diffusion-the surface-mediated and centralized diffusion-are associated with negative barrier heights. Surprisingly, rate of cage-to-cage diffusion is associated with negative and positive activation energies below and above 500 K. The observed differences in the behavior of the rate of cage-to-cage diffusion between Xe-NaY and Ar-NaCaA systems and the nature of the potential energy surface are discussed. Presence of sorbatezeolite interactions results in significant enhancement in the rate of cage-to-cage diffusion and rate of cage visits. It is shown that properties dependent on the long-time behavior such as the diffusion coefficient and the rate of cages visited exhibit the expected Arrhenius dependence on temperature.

A Molecular Dynamics Study of Atomic Correlations in Glassy BzS3t

Glassy B&, the parent compound of the superionic conductor LiI-Li&B& has been studied by the molecular dynamics technique using a new potential model. The results suggest that the glass is made up of local units of four-membered B2S2 rings bridged by sulfur atoms, leading to a chainlike structure. Various pair correlation functions have been analyzed, and the B2Sz rings have been found to be planar. The calculated neutron structure factor shows a peak at 1.4 A-' which has been attributed to B-B correlations at 5.6 A. The glass transition temperature of the simulated system has been calculated to be around 800 K.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

1H NMR study of molecular dynamics and phase transition in (NH4)2ZnBr4

The proton second moment (M2) and spin-lattice relaxation time (T1) have been measured in (NH4)2ZnBr4 in the range 77-300 K. The room-temperature spectrum shows a structure which disappears around 243 K. The signal is strong and narrow even at 77 K. Proton T1 shows a maximum at 263 K, caused by spin rotation interaction and decreases with decreasing temperature till 235 K, where it shows a sudden increase. Below 235 K, again it decreases and shows a slope change around 216.5 K (reported Tc). From 216.5 K, T1 decreases continuously without exhibiting any minimum down to 77 K. The narrow line at 77 K, and absence of a T1 minimum down to 77 K indicate the possibility of quantum mechanical tunnelling in this system. Motional parameters such as activation energy and pre-exponential factor have been evaluated for the reorientational motion of the NH+4 ion.

Effect of the valine-threonine constraint on the dynamics of the proline helix — A molecular dynamics study

Proline residues in helices play an important role in the structure of proteins. The proline residue introduces a kink in the helix which varies from about 5-degrees to 50-degrees. The presence of other residues such as threonine or valine near the proline region can influence the flexibility exhibited by the kinked helix, which can have an important biological role. In the present paper, the constraint introduced by threonine and valine on a proline helix is investigated by molecular dynamics studies. The systems considered am (1) a poly-alanine helix with threonine-proline residues (TP) and (2) a poly-alanine helix with valine-threonine-proline residues (VTP), in the middle. Molecular dynamics simulations are carried out on these two systems for 500 ps. The results are analyzed in terms of structural transitions, bend-related parameters and sidechain orientations.

Molecular Dynamics Investigation of Structure and Transport in the K2O-2SiO2 System Using a Partial Charge Based Model Potential

Potassium disilicate glass and melt have been investigated by using a new partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygenrich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Molecular Dynamics Simulations of Orientational Relaxation in Dipolar Lattice: Lack of Diffusive Decay for Second and Higher Rank Correlation Functions

Extensive molecular dynamics simulations have been carried out to calculate the orientational correlation functions Cl(t), G(t) = [4n/(21 + l)]Ci=-l (Y*lm(sZ(0)) Ylm(Q(t))) (where Y,,(Q) are the spherical harmonics) of point dipoles in a cubic lattice. The decay of Cl(t) is found to be strikingly different from higher l-correlation functions-the latter do not exhibit diffusive dynamics even in the long time. Both the cumulant expansion expression of Lynden-Bell and the conventional memory function equation provide very good description of the Cl(t) in the short time but fail to reproduce the observed slow, long time decay of c1 (t) .

Molecular dynamics Investigation of structure and transport in the K2O-2SiO2 system using a partial charge based model potential

Potassium disilicate glass and melt have been investigated by using anew partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygen-rich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Sorbate properties of xenon in cloverite: A molecular dynamics study

Molecular dynamics calculations on xenon adsorbed in the cubic cavity of cloverite, a gallophosphate, is presented. Guest-host radial distribution functions, guest-host energy distribution functions, power spectra, and diffusion coefficients for xenon are reported at 397, 494, and 716 K. Results suggest that xenon is highly mobile at 700 K. A shift in the peak position of the power spectra toward lower frequency is observed with increase in temperature. (C) 1994 Academic Press, Inc.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Molecular dynamics investigation of sorption of argon in NaCaA zeolite

A molecular dynamics calculation of argon in NaCaA zeolite at 393 K and 1 atom per cage is reported. Equilibrium properties such as guest-host interaction energy, guest-guest dimerization and bonding energy, various guest-host and guest-guest radial distribution functions and dynamical properties such as the mean-square displacement, power spectra and diffusion coefficient have been obtained.

Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates

2',3'-cyclic nucleotides are intermediates and substrates of Ribonuclease (RNase)-catalysed reactions. The characterization of the equilibrium conformation as well as the flexibility inherent in these molecules helps in understanding the enzymatic action of RNases. The present study explores parameters like phase angle, glycosydic torsion angle and hydrogen bond to find possible interrelationship between them through Molecular Dynamics (MD) simulations on 3'-GMP, 3'-UMP, A>p, G>p, U>p, C>p, GpA>p and UpA>p. Interesting results of the effect of cyclisation and other constraints such as hydrogen bond between certain groups on the equilibrium ribose conformation have emerged from this study.