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.

Excited state structure and dynamics of p-benzoquinone and bromanil from time-resolved resonance Raman spectra and simulation

p-Benzoquinone and its halogen substituted derivatives are known to have differing reactivities in the triplet excited state. While bromanil catalyzes the reduction of octaethylporphyrin most efficiently among the halogenated p-benzoquinones, the reaction does not take place in presence of the unsubstituted p-benzoquinone (T. Nakano and Y. Mori, Bull. Chem. Soc. Jpn., 67, 2627 (1994)). Understanding of such differences requires a detailed knowledge of the triplet state structures, normal mode compositions and excited state dynamics. In this paper, we apply a recently presented scheme (M. Puranik, S. Umapathy, J. G. Snijders, and J. Chandrasekhar, J. Chem, Phys., 115, 6106 (2001)) that combines parameters from experiment and computation in a wave packet dynamics simulation to the triplet states of p-benzoquinone and bromanil. The absorption and resonance Raman spectra of both the molecules have been simulated. The normal mode compositions and mode specific excited state displacements have been presented and compared. Time-dependent evolution of the absorption and Raman overlaps for all the observed modes has been discussed in detail. In p-benzoquinone, the initial dynamics is along the C=C stretching and C-H bending modes whereas in bromanil nearly equal displacements are observed along all the stretching coordinates.

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.

Investigation of short-time isomerization dynamics in p-nitroazobenzene from resonance Raman intensity analysis

Resonance Raman (RR) spectra are presented for p-nitroazobenzene dissolved in chloroform using 18 excitation Wavelengths, covering the region of (1)(n --> pi*) electronic transition. Raman intensities are observed for various totally symmetric fundamentals, namely, C-C, C-N, N=N, and N-O stretching vibrations, indicating that upon photoexcitation the excited-state evolution occurs along all of these vibrational coordinates. For a few fundamentals, interestingly, in p-nitroazobenzene, it is observed that the RR intensities decrease near the maxima of the resonant electronic (1)(n --> pi*) transition. This is attributed to the interference from preresonant scattering due to the strongly allowed (1)(pi --> pi*) electronic transition. The electronic absorption spectrum and the absolute Raman cross section for the nine Franck-Condon active fundamentals of p-nitroazobenzene have been successfully modeled using Heller's time-dependent formalism for Raman scattering. This employs harmonic description of the lowest energy (1)(n --> pi*) potential energy surface. The short-time isomerization dynamics is then examined from a priori knowledge of the ground-state normal mode descriptions of p-nitroazobenzene to convert the wave packet motion in dimensionless normal coordinates to internal coordinates. It is observed that within 20 fs after photoexcitation in p-nitroazobenzene, the N=N and C-N stretching vibrations undergo significant changes and the unsubstituted phenyl ring and the nitro stretching vibrations are also distorted considerably.

Model exact low-lying states and spin dynamics in ferric wheels: Fe-6 to Fe-12

Using an efficient numerical scheme that exploits spatial symmetries and spin parity, we have obtained the exact low-lying eigenstates of exchange Hamiltonians for ferric wheels up to Fe-12. The largest calculation involves the Fe-12 ring which spans a Hilbert space dimension of about 145x10(6) for the M-S=0 subspace. Our calculated gaps from the singlet ground state to the excited triplet state agree well with the experimentally measured values. Study of the static structure factor shows that the ground state is spontaneously dimerized for ferric wheels. The spin states of ferric wheels can be viewed as quantized states of a rigid rotor with the gap between the ground and first excited states defining the inverse of the moment of inertia. We have studied the quantum dynamics of Fe-10 as a representative of ferric wheels. We use the low-lying states of Fe-10 to solve exactly the time-dependent Schrodinger equation and find the magnetization of the molecule in the presence of an alternating magnetic field at zero temperature. We observe a nontrivial oscillation of the magnetization which is dependent on the amplitude of the ac field. We have also studied the torque response of Fe-12 as a function of a magnetic field, which clearly shows spin-state crossover.

Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: Decarboxylation rate, oscillations, and multiplicity

Pyruvate conversion to acetyl-CoA by the pyruvate dehydrogenase (PDH) multienzyme complex is known as a key node in affecting the metabolic fluxes of animal cell culture. However, its possible role in causing possible nonlinear dynamic behavior such as oscillations and multiplicity of animal cells has received little attention. In this work, the kinetic and dynamic behavior of PDH of eucaryotic cells has been analyzed by using both in vitro and simplified in vivo models. With the in vitro model the overall reaction rate (v(1)) of PDH is shown to be a nonlinear function of pyruvate concentration, leading to oscillations under certain conditions. All enzyme components affect v, and the nonlinearity of PDH significantly, the protein X and the core enzyme dihydrolipoamide acyltransferase (E2) being mostly predominant. By considering the synthesis rates of pyruvate and PDH components the in vitro model is expanded to emulate in vivo conditions. Analysis using the in vivo model reveals another interesting kinetic feature of the PDH system, namely, multiple steady states. Depending on the pyruvate and enzyme levels or the operation mode, either a steady state with high pyruvate decarboxylation rate or a steady state with significantly lower decarboxylation rate can be achieved under otherwise identical conditions. In general, the more efficient steady state is associated with a lower pyruvate concentration. A possible time delay in the substrate supply and enzyme synthesis can also affect the steady state to be achieved and lead's to oscillations under certain conditions. Overall, the predictions of multiplicity for the PDH system agree qualitatively well with recent experimental observations in animal cell cultures. The model analysis gives some hints for improving pyruavte metabolism in animal cell culture.

Photodissociation dynamics of CH2ICl at 222, 236, 266, 280, and-304 nm

Dynamics of I*(P-2(1/2)) formation from CH2ICl dissociation has-been investigated at five different ultraviolet excitation wavelengths, e.g., 222, 236, 266, 280, and similar to304 nm. The quantum yield of I*((2)p(1/2)) production, phi*, has been measured by monitoring nascent I(P-2(3/2)) and I* concentrations using a resonance enhanced multiphoton ionization detection scheme. The measured quantum yield as a function of excitation energy follows the same trend as that of methyl iodide except at 236 run. The photodissociation dynamics of CH2ICl also involves three upper states similar to methyl iodide, and a qualitative correlation diagram has been constructed to account for the observed quantum yield. From the difference in behavior at 236 nm, it appears that the crossing region between the two excited states ((3)Q(0) and (1)Q(1)) is located near the exit valley away from the Franck Condon excitation region. The B- and C-band transitions do not participate in the dynamics, and the perturbation of the methyl iodide states due to Cl-I interaction is relatively weak at the photolysis wavelengths employed in this investigation.

Role of length scales on microwave thawing dynamics in 2D cylinders

Microwave (MW) thawing of 2D frozen cylinders exposed to uniform plane waves from one face, is modeled using the effective heat capacity formulation with the MW power obtained from the electric field equations. Computations are illustrated for tylose (23% methyl cellulose gel) which melts over a range of temperatures giving rise to a mushy zone. Within the mushy region the dielectric properties are functions of the liquid volume fraction. The resulting coupled, time dependent non-linear equations are solved using the Galerkin finite element method with a fixed mesh. Our method efficiently captures the multiple connected thawed domains that arise due to the penetration of MWs in the sample. For a cylinder of diameter D, the two length scales that control the thawing dynamics are D/D-p and D/lambda(m), where D-p and lambda(m) are the penetration depth and wavelength of radiation in the sample respectively. For D/D-p, D/lambda(m) much less than 1 power absorption is uniform and thawing occurs almost simultaneously across the sample (Regime I). For D/D-p much greater than 1 thawing is seen to occur from the incident face, since the power decays exponentially into the sample (Regime III). At intermediate values, 0.2 < D/D-p, D/lambda(m) < 2.0 (Regime II) thawing occurs from the unexposed face at smaller diameters, from both faces at intermediate diameters and from the exposed and central regions at larger diameters. Average power absorption during thawing indicates a monotonic rise in Regime I and a monotonic decrease in Regime III. Local maxima in the average power observed for samples in Regime II are due to internal resonances within the sample. Thawing time increases monotonically with sample diameter and temperature gradients in the sample generally increase from Regime I to Regime III. (C) 2002 Elsevier Science Ltd. All rights reserved.

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.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

Nonlinear Dynamics of Beams with Stochastic Parameter Variations

The aim of this paper is to investigate the steady state response of beams under the action of random support motions. The study is of relevance in the context of earthquake response of extended land based structures such as pipelines and long span bridges, and, secondary systems such as piping networks in nuclear power plant installations. The following complicating features are accounted for in the response analysis: (a) differential support motions: this is characterized in terms of cross power spectral density functions associated with distinct support motions, (b) nonlinear support conditions, and (c) stochastically inhomogeneous stiffness and mass variations of the beam structure; questions on non-Gaussian models for these variations are considered. The method of stochastic finite elements is combined with equivalent linearization technique and Monte Carlo simulations to obtain response moments.

Synthesis, structural characterization, thermal studies and chain dynamics of poly(methacrylonitrile peroxide) by NMR spectroscopy

Poly(methacrylonitrile peroxide) (PMNP) has been synthesized from methacrylonitrile by free radical initiated oxidative polymerization and characterized by different spectroscopic methods. NMR spectroscopy confirmed the alternating copolymer structure with labile peroxy bonds in the main chain. The extreme instability of PMNP was noted from FTIR spectroscopy. Thermal degradation studies by using differential scanning calorimetry and thermogravimetry have revealed that PMNP degrades highly exothermically and the heat of degradation, 42.5 kcal mol−1, is of the same order as that reported for other vinyl polyperoxides. Mass spectral fragmentation pattern under electron impact (EI) condition has also been investigated. The mechanism of the primary exothermic degradation has been substantiated by thermochemical calculations. The chain dynamics of the polyperoxide chain has been studied by means of 13C spin–lattice relaxation times (T1) of the main chain as well as the side chain carbons. The temperature dependence of the spin–lattice relaxation times shows that the PMNP is more flexible compared to the analogous poly(styrene peroxide).

Understanding glassy dynamics from the free-energy landscape

Many interesting features of the dynamics of simple liquids near the glass transition may be understood in terms of properties of the free-energy landscape obtained from numerical studies of a model free-energy functional. Main results obtained from this approach are summarized and a list of references to relevant publications is provided. (C) 2002 Elsevier Science B.V. All rights reserved.