Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding

In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift f-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our Monte Carlo Go model and the structural interpretation of experimental f-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.Comment: PNAS in pres

Principals of the theory of light reflection and absorption by low-dimensional semiconductor objects in quantizing magnetic fields at monochromatic and pulse excitations

The bases of the theory of light reflection and absorption by low-dimensional semiconductor objects (quantum wells, wires and dots) at both monochromatic and pulse irradiations and at any form of light pulses are developed. The semiconductor object may be placed in a stationary quantizing magnetic field. As an example the case of normal light incidence on a quantum well surface is considered. The width of the quantum well may be comparable to the light wave length and number of energy levels of electronic excitations is arbitrary. For Fourier-components of electric fields the integral equation (similar to the Dyson-equation) and solutions of this equation for some individual cases are obtained.Comment: 14 page

High resolution protein folding with a transferable potential

A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximately 3 Angstroms without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that a accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential (that does not require optimization to the test set) and hydrogen bonding are essential features for a realistic protein model.Comment: submitted to PNAS 2005-03-1

Electron g-Factor Anisotropy in Symmetric (110)-oriented GaAs Quantum Wells

We demonstrate by spin quantum beat spectroscopy that in undoped symmetric (110)-oriented GaAs/AlGaAs single quantum wells even a symmetric spatial envelope wavefunction gives rise to an asymmetric in-plane electron Land\'e-g-factor. The anisotropy is neither a direct consequence of the asymmetric in-plane Dresselhaus splitting nor of the asymmetric Zeeman splitting of the hole bands but is a pure higher order effect that exists as well for diamond type lattices. The measurements for various well widths are very well described within 14 x 14 band k.p theory and illustrate that the electron spin is an excellent meter variable to map out the internal -otherwise hidden- symmetries in two dimensional systems. Fourth order perturbation theory yields an analytical expression for the strength of the g-factor anisotropy, providing a qualitative understanding of the observed effects

Variation in nucleotide homology obtained by amplification, cloning and sequencing of complete S1 gene from field samples of avian infectious bronchitis virus.

Projeto/Plano de Ação: 02.09.01.030