Conformal Regime Research Articles

Molecular dynamics simulation of glycoprotein-glycans of immunoglobulin G and Immunoglobulin M

Glycoprotein-glycans have recently been implicated to play a variety of functional roles. The same glycan chain have been found complexed with proteins of diverse functions. In this article two such glycan chains found attached to Fc regions of immunoglobulin G and immunoglobulin M have been studied. An extensive simulated annealing procedure have been adopted to arrive at a low-energy minimum of the two oligosaccharides. Molecular dynamics simulations have been performed to study the flexibility of the glycosidic linkages. It was found that both glycan chains can undergo conformational transitions and adopt folded and extended conformations. The two beta (1-2) linkages of complex-type glycan had been found to prefer different conformational regime and the terminal fucose linked to the GlcNAc residue drastically modifies the GlcNAc beta (1-4) GlcNAc linkage conformation. In the high-mannose type glycan chain alpha (1-3) linkages can induce flexibility in addition to the alpha (1-6) linkages. The results have been compared with recent experimental nmr and fluorescence energy transfer data.

NMR Studies of Drugs: Antipyrine and Analogs. I. Use of Achiral and Chiral Lanthanide Shift Reagents to Examine Hindered Rotation.

The 200 MHz 1H NMR spectra of the analgesic, antipyrine, 1, have been studied in CDC13 solution at ambient temperatures with the achiral lanthanide shift reagent (LSR) tris (6, 6, 7, 7, 8, 8, 8-heptafluoro-2, 2-dimethyl-3, 5-octanedionato) europium (III), Eu(FOD)3, 2, and with the chiral LSR, tris[3-(heptafluoropropylhydroxymethylene)-(+)-camphorato]europium(III), Eu(HFC)3, 3., Lanthanide-induced shift (LIS) magnitudes and broadening of selected signals are consistent with predominant LSR binding at the carbonyl oxygen with either 2 or 3. Of the different possible conformational regimes for the N-phenyl group of 1, our results appear to rule out a slow exchange limit (SEL) system with the N-phenyl coplanar with the heterocyclic ring. Perpendicular rings in an SEL regime can not be ruled out. A rapidly-rotating N-phenyl (fast exchange limit, FEL system) would also be consistent with observed results. Accurate chemical shifts for the aryl protons (overlapped in the 200 MHz spectrum of unshifted 1) are determined from spectra with added LSR by extrapolation to zero molar ratios of [LSR]:[1]. Relative slopes in the plots of chemical shift versus [LSR]:[1] molar ratios are calculated for each proton signal of 1.

Non-linear integral equation and excited-states scaling functions in the sine-Gordon model

The NLIE (the non-linear integral equation equivalent to the Bethe ansatz equations for finite size) is generalized to excited states, that is states with holes and complex roots over the antiferromagnetic ground state. We consider the sine-Gordon/massive Thirring model (sG/mT) in a periodic box of length L using the light-cone approach, in which the sG/mT model is obtained as the continuum limit of an inhomogeneous six-vertex model. This NLIE is an useful starting point to compute the spectrum of excited states both analytically in the large L (perturbative) and small L (conformal) regimes as well as numerically. We derive the conformal weights of the Bethe states with holes and non-string complex roots (close and wide roots) in the UV limit. These weights agree with the Coulomb gas description, yielding a UV conformal spectrum related by duality to the IR conformal spectrum of the six-vertex model.

Electronic excitation transfer in chains modulated by conformational dynamic disorder

Electronic excitations along sites that undergo spatial and temporal fluctuations due to conformational chain motion have been studied in the picture of the stochastic master equation by means of the dynamic Monte Carlo (DMC) and the cumulant expansion (CE) approach. An incoherent site-to-site hopping which is adiabatic relative to the changes of conformational site coordinates has been assumed. The elementary act of conformational change has been considered to be fast, whereas the electronic transfer during the time period of the conformational event has been assumed to be negligibly small. The time evolution of electronic intersite coupling is thus controlled by chromophore sites that, in particular, correspond to the conformational minima of the potential energy landscape. The generalized equations of motion adapted for both the DMC and the CE analysis have been reduced to formulate donor site excitation probabilities 〈Piexc(t)〉 and donor excitation survival functions 〈PD(t)〉 for a simplified chain. In this polymer model, (i) specific nearest-neighbor electronic coupling occurs with two distinct transfer rates W1 and W2 corresponding to two different spatial arrangements of the pendant sites in the pair and (ii) transitions between two definite conformational states occur both in the correlated and in the uncorrelated regime. For short chains and a moderate number of sites in the rotational dyads the whole range from the dynamic to the static limit in the interplay between excitation transfer and correlated conformational motion has been calculated by the DMC method. By means of the cumulant technique well-behaved solutions could be obtained only in the fast conformational transition regime which allows a direct comparison with the DMC results. For longer chains up to 100 sites, in the limit case of uncorrelated conformational motion, preliminary cumulant approaches have been given which, for very rapid conformational rates, agree well with the dynamic effective medium approximation (DEMA) solutions.

Unified approach to Thermodynamic Bethe Ansatz and finite size corrections for lattice models and field theories

We present a unified approach to the Thermodynamic Bethe Ansatz (TBA) for magnetic chains and field theories that includes the finite size (and zero-temperature) calculations for lattice BA models. In all cases, the free energy follows by quadratures from the solution of a single nonlinear integral equation (NLIE) (a system of NLIE appears for nested BA). We derive the NLIE for: (a) the six-vertex model with twisted boundary conditions, (b) the XXZ chain in an external magnetic field h z and (c) the massive Thirring sine-Gordon model (mT-sG) in a periodic box of size β ≡ T -1 using the light-cone approach. This NLIE is solved by iteration in one regime (high T in the XXZ chain and low T in the sG-mT model). In the opposite (conformal) regime, the leading behaviors are obtained in closed form. Higher corrections can be derived from the Riemann-Hilbert form of the NLIE that we present.

The conformational effects of quaternary centres

Quaternary centres impose a particularly simple conformational regime on adjacent acyclic bonds; this is shown by force field calculations on alkanes and confirmed by crystal structure database studies on quaternary ammonium ions; possible implications are considered.