Allostery in Its Many Disguises: From Theory to Applications.

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts

Experimental and theoretical study of intermolecular interactions in solution

Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Recent Research Developments in Protein Engineering

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A Comparison Between the PISA Model and the RAM Theory: their Abilities to Reproduce Internal Energy as Calculated by Monte Carlo Simulations

We present a comparative analysis of the PISA and RAM models using Monte Carlo (MC) simulations as references. The PISA and RAM models have in common a factorization of the pair distribution into an angular and a radial part. For the angular part both the PISA and RAM models use a Boltzmann weighting. First, we show that this factorization itself and the Boltzmann weighting are satisfactory approximations in a wide range of density and temperature conditions. Indeed, the Boltzmann weighting yields very good average energies (angular average). The chief approximation of the PISA method consists of taking a Heaviside step function for the distribution of the centres of mass. In the RAM theory the distribution of the centres of mass in the molecular fluid is supposed to be the same as the distribution of a spherically symmetric reference fluid. The RAM hypothesis and the PISA approximation are tested and discussed for several molecular liquids (nitrogen, bromine, carbon tetrachloride, benzene, and cis- and trans-decalin). We show that the RAM theory is unable to give a reliable radial distribution function except for systems studied under favourable conditions (nitrogen and bromine at high temperature). The agreement between MC and RAM radial distribution functions is particularly poor for highly non-spherical molecules like trans-decalin. The quality of the PISA approximation of the radial distribution function is also discussed in terms of molecular shape. Finally, we show that the more sophisticated RAM theory does not necessarily yield better internal energies than the simplest but very efficient PISA model. © 1990 Taylor & Francis Group, LLC.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Pisa: A new model for the estimation of intermolecular interaction energies in the liquid state

We propose a new model for the estimation of intermolecular interaction energies in the liquid state. This model, which we call PISA, is especially devoted to the calculation of the London‐Pauli contribution. The model has been tested on a large ensemble of pure liquids and the results compare well with those obtained by molecular dynamics and Monte‐Carlo simulations. The advantages of PISA are its simplicity and rapidity. Copyright © 1988 Wiley‐VCH Verlag GmbH & Co. KGaA, WeinheimSCOPUS: ar.jinfo:eu-repo/semantics/publishe

The importance of quadrupolar interactions in molecular recognition processes involving a phenyl group

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Study of NMR Relaxation of Xenon- 131 in Quadrupolar Solvents

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