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.

Ultrafast underdamped solvation: Agreement between computer simulation and various theories of solvation dynamics

A theoretical analysis of the three currently popular microscopic theories of solvation dynamics, namely, the dynamic mean spherical approximation (DMSA), the molecular hydrodynamic theory (MHT), and the memory function theory (MFT) is carried out. It is shown that in the underdamped limit of momentum relaxation, all three theories lead to nearly identical results when the translational motions of both the solute ion and the solvent molecules are neglected. In this limit, the theoretical prediction is in almost perfect agreement with the computer simulation results of solvation dynamics in the model Stockmayer liquid. However, the situation changes significantly in the presence of the translational motion of the solvent molecules. In this case, DMSA breaks down but the other two theories correctly predict the acceleration of solvation in agreement with the simulation results. We find that the translational motion of a light solute ion can play an important role in its own solvation. None of the existing theories describe this aspect. A generalization of the extended hydrodynamic theory is presented which, for the first time, includes the contribution of solute motion towards its own solvation dynamics. The extended theory gives excellent agreement with the simulations where solute motion is allowed. It is further shown that in the absence of translation, the memory function theory of Fried and Mukamel can be recovered from the hydrodynamic equations if the wave vector dependent dissipative kernel in the hydrodynamic description is replaced by its long wavelength value. We suggest a convenient memory kernel which is superior to the limiting forms used in earlier descriptions. We also present an alternate, quite general, statistical mechanical expression for the time dependent solvation energy of an ion. This expression has remarkable similarity with that for the translational dielectric friction on a moving ion.

Kinematic analysis and design of articulated manipulators with joint motion constraints

For an articulated manipulator with joint rotation constraints, we show that the maximum workspace is not necessarily obtained for equal link lengths but is also determined by the range and mean positions of the joint motions. We present expressions for sectional area, workspace volume, overlap volume and work area in terms of link ratios, mean positions and ranges of joint motion. We present a numerical procedure to obtain the maximum rectangular area that can be embedded in the workspace of an articulated manipulator with joint motion constraints. We demonstrate the use of analytical expressions and the numerical plots in the kinematic design of an articulated manipulator with joint rotation constraints.

Dynamic stiffness matrix of a general cable element

A computational scheme for determining the dynamic stiffness coefficients of a linear, inclined, translating and viscously/hysteretically damped cable element is outlined. Also taken into account is the coupling between inplane transverse and longitudinal forms of cable vibration. The scheme is based on conversion of the governing set of quasistatic boundary value problems into a larger equivalent set of initial value problems, which are subsequently numerically integrated in a spatial domain using marching algorithms. Numerical results which bring out the nature of the dynamic stiffness coefficients are presented. A specific example of random vibration analysis of a long span cable subjected to earthquake support motions modeled as vector gaussian random processes is also discussed. The approach presented is versatile and capable of handling many complicating effects in cable dynamics in a unified manner.

Mechanism of protonic conduction in defect pyrochlore HNbWO6.xH(2)O using MAS NMR

We have carried out H-1 Magic Angle Spinning (MAS) NMR measurements at various spinning speeds (1-12 kHz) on HNbWO(6)xH(2)O (x = 0 and 1) defect pyrochlore systems. The variation of the line width with the spinning speed in the two systems points towards the presence of motions with different time scales. We conclude that the mechanism of conduction in both the compounds are similar except that the proton hopping in hydrated form is assisted by the water of hydration.

Response, loads and stability of rotors with interconnected blades

An isolated rotor with blades interconnected through viscoelastic elements is analyzed for response, loads and stability in moment trim under forward flight conditions. A conceptual model of a multibladed rotor with rigid flap and lag motions is considered, Although the interconnecting elements are placed in the In-plane direction, considerable coupling between the flap-lag motions of the blades can occur in certain ranges of interblade element stiffness. Interblade coupling can yield significant changes in the response, loads and stability which are dependent on the interblade element and rotor parameters.

Self-consistent microscopic treatment of the effects of self-motion of the probe on ionic and dipolar solvation dynamics

A simple but self-consistent microscopic theory for the time dependent solvation energy of both ions and dipoles is presented which includes, for the first time, the details of the self-motion of the probe on its own solvation dynamics. The theory leads to several interesting predictions. The most important of them is that, for dipolar solvation, both the rotational and the translational motions of the dipolar solute probe can significantly accelerate the rate of solvation. In addition, the rotational self-motion of the solute can also give rise to an additional mechanism of nonexponentiality in solvation time correlation functions in otherwise slow liquids. A comparison between the present theoretical predictions and the recent experimental studies of Maroncelli et al. on solvation dynamics of aniline in l-propanol seems to indicate that the said experiments have missed the initial solvent response up to about 45 ps. After mapping the experimental results on the redefined time scale, the theoretical results can explain the experimental results for solvation of aniline in 1-propanol very well. For ionic solvation, the translational motion is significant for light solutes only. For example, for Li+ in water, translational motion speeds up the solvation by about 20%. The present theory demonstrates that in dipolar solvation the partial quenching of the self-motion due to the presence of specific solute-solvent interactions (such as H-bonding) may lead to a much slower solvation than that when the self-motion is present. This point has been discussed. In addition, we present the theoretical results for solvation of aniline in propylene carbonate, Here, the solvation is predicted to be complete within 15-20 ps.

Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Tunable Brownian vortex at the interface

A general kind of Brownian vortices is demonstrated by applying an external nonconservative force field to a colloidal particle bound by a conservative optical trapping force at a liquid-air interface. As the liquid medium is translated at a constant velocity with the bead trapped at the interface, the drag force near the surface provides enough rotational component to bias the particle's thermal fluctuations in a circulatory motion. The interplay between the thermal fluctuations and the advection of the bead in constituting the vortex motions is studied, and we infer that the angular velocity of the circulatory motion offers a comparative measure of the interface fluctuations.

Vortex sheet simulation of a plane �canonical� mixing layer

Discrete vortex simulations of the mixing layer carried out in the past have usually involved large induced velocity fluctuations, and thus demanded rather long time-averaging to obtain satisfactory values of Reynolds stresses and third-order moments. This difficulty has been traced here, in part, to the use of discrete vortices to model what in actuality are continuous vortex sheets. We propose here a novel two-dimensional vortex sheet technique for computing mixing layer flow in the limit of infinite Reynolds number. The method divides the vortex sheet into constant-strength linear elements, whose motions are computed using the Biot-Savart law. The downstream far-field is modelled by a steady vorticity distribution derived by application of conical similarity from the solution obtained in a finite computational domain. The boundary condition on the splitter plate is satisfied rigorously using a doublet sheet. The computed large-scale roll-up of the vortex sheet is qualitatively similar to experimentally obtained shadow-graphs of the plane turbulent mixing layer. The mean streamwise velocity profile and the growth rate agree well with experimental data. The presently computed Reynolds stresses and third-order moments are comparable with experimental and previous vortex-dynamical results, without using any external parameter (such as the vortex core-size) of the kind often used in the latter. The computed autocorrelations are qualitatively similar to experimental results along the top and bottom edges of the mixing layer, and show a well-defined periodicity along the centreline. The accuracy of the present computation is independently established by demonstrating negligibly small changes in the five invariants (including the Hamiltonian) in vortex dynamics.

Low temperature H-1 NMR relaxation studies of phase transitions in dicalcium barium propionate

The two low-temperature phase transitions in dicalcium barium propionate have been investigated by H-1 NMR relaxation (T-1,T-2,T-1 rho) studies carried out at a Larmor frequency of 300 MHz. The T-1 and T-1 rho results indicate the presence of C2H5 dynamics near these two transitions. We infer from the T-1 rho results that the slow motions of the C2H5 groups are responsible for the II-III transition.

Common underlying steering curves for motorcycles in steady turns

We study the steady turn behaviours of some light motorcycle models on circular paths, using the commercial software package ADAMS-Motorcycle. Steering torque and steering angle are obtained for several path radii and a range of steady forward speeds. For path radii much greater than motorcycle wheelbase, and for all motorcycle parameters including tyre parameters held fixed, dimensional analysis can predict the asymptotic behaviour of steering torque and angle. In particular, steering torque is a function purely of lateral acceleration plus another such function divided by path radius. Of these, the first function is numerically determined, while the second is approximated by an analytically determined constant. Similarly, the steering angle is a function purely of lateral acceleration, plus another such function divided by path radius. Of these, the first is determined numerically while the second is determined analytically. Both predictions are verified through ADAMS simulations for various tyre and geometric parameters. In summary, steady circular motions of a given motorcycle with given tyre parameters can be approximately characterised by just one curve for steering torque and one for steering angle.

Response, loads, and stability of interconnected rotor-body systems

A rotor-body system with blades interconnected through viscoelastic elements is analyzed for response, loads, and stability in propulsive trim in ground contact and under forward-flight conditions, A conceptual model of a multibladed rotor with rigid flap and lag motions, and the fuselage with rigid pitch and roll motions is considered, Although the interconnecting elements are placed in the in-plane direction, considerable coupling between the flap-lag motions of the blades can occur in certain ranges of interblade element stiffness, Interblade coupling can yield significant changes in the response, loads, and stability that are dependent on the interblade element and rotor-body parameters, Ground resonance stability investigations show that by tuning the interblade element stiffness, the ground resonance instability problem can be reduced or eliminated, The interblade elements with damping and stiffness provide an effective method to overcome the problems of ground and air resonance.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.