Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man(9)GlcNAc(2)). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct beta sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Direct simulation of quantum dynamics in complex systems

Accurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories.

Quantum dynamics of coupled quantum-dot qubits and dephasing effects induced by detections

　

Close-coupling time-dependent quantum dynamics study of the H+HCl reaction

The paper presents a theoretical study of the dynamics of the H + HCl system on the potential energy surface (PES) of Bian and Werner (Bian, W.; Werner, H. -J., J. Chem. Phys. 2000, 112, 220). A time-dependent wave packet approach was employed to calculate state-to-state reaction probabilities for the exchanged and abstraction channels. The most recent PES for the system has been used in the calculations. Reaction probabilities have also been calculated for several values of the total angular momentum J > 0. Those have then been used to estimate cross sections and rate constants for both channels. The calculated cross sections can be compared with the results of previous quasiclassical trajectory calculations and reaction dynamics experimental on the abstraction channel. In addition, the calculated rate constants are in the reasonably good agreement with experimental measurement.

Quantum dynamics study of isotope effect for H+CH4 reaction using the SVRT model

The semirigid vibrating rotor target model is applied to study the isotope effect in reaction H + CH4-->H-2 + CH3 using time-dependent wave-packet method. The reaction probabilities for producing H-2 and HD product channels are calculated. The energy dependence of the reaction probabilities shows oscillating structures for both reaction channels. At low temperature or collision energies, the H atom abstraction is favored due to tunnelling effect. In partially deuterated CHxDy (x + y = 4), the breaking of the C-H bond is favored over that of the C-D bond in the entire energy range studied. In H + CHD3 reaction at high energies, the HD product dominates simply due to statistical factor. (C) 2003 American Institute of Physics.

Power dissipation in nanoscale conductors: classical, semi-classical and quantum dynamics

Modelling Joule heating is a difficult problem because of the need to introduce correct correlations between the motions of the ions and the electrons. In this paper we analyse three different models of current induced heating (a purely classical model, a fully quantum model and a hybrid model in which the electrons are treated quantum mechanically and the atoms are treated classically). We find that all three models allow for both heating and cooling processes in the presence of a current, and furthermore the purely classical and purely quantum models show remarkable agreement in the limit of high biases. However, the hybrid model in the Ehrenfest approximation tends to suppress heating. Analysis of the equations of motion reveals that this is a consequence of two things: the electrons are being treated as a continuous fluid and the atoms cannot undergo quantum fluctuations. A means for correcting this is suggested.

Observing time-dependent vibrational quantum dynamics in deuterium hydride molecular ions

Few-cycle laser pulses are used to "pump and probe" image the vibrational wavepacket dynamics of a HD+ molecular ion. The quantum dephasing and revival structure of the wavepacket are mapped experimentally with time-resolved photodissociation imaging. The motion of the molecule is simulated using a quantum-mechanical model predicting the observed structure. The coherence of the wavepacket is controlled by varying the duration of the intense laser pulses. By means of a Fourier transform analysis both the periodicity and relative population of the vibrational states of the excited molecular ion have been characterized.

Interaction-induced correlations and non-Markovianity of quantum dynamics

We investigate the conditions under which the trace distance between two different states of a given open system increases in time due to the interaction with an environment, therefore signaling non-Markovianity. We find that the finite-time difference in trace distance is bounded by two sharply defined quantities that are strictly linked to the occurrence of system-environment correlations created throughout their interaction and affecting the subsequent evolution of the system. This allows us to shed light on the origin of non-Markovian behaviors in quantum dynamics. We best illustrate our findings by tackling two physically relevant examples: a non-Markovian dephasing mechanism that has been the focus of a recent experimental endeavor and the open-system dynamics experienced by a spin connected to a finite-size quantum spin chain.

Electron-phonon thermalization in a scalable method for real-time quantum dynamics

We present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.