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Thermodynamically–Weighted Conformational Ensemble of Cyclic RGD Peptidomimetics from NOE Data

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Department of Chemistry, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
Center of Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, 20133 Milano, Italy
Cite this: J. Phys. Chem. B 2016, 120, 29, 7098–7107
Publication Date (Web):July 7, 2016
https://doi.org/10.1021/acs.jpcb.6b04941
Copyright © 2016 American Chemical Society
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Abstract

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In the case of flexible molecules, the standard approach of transforming NOE intensities into spatial restraints and of building conformational models minimizing these restraints greatly neglects the richness of molecular conformations. Making use of NOE intensities measured in triplicate and of an iterative molecular–dynamics scheme, we optimized a force field to generate a set of conformations whose ensemble is compatible with the experimental data, and is weighted according to the Boltzmann distribution. This scheme is applied to two cyclic peptidomimetic ligands of integrins. Their difference in binding affinity is recapitulated in terms of their difference in conformational fluctuations.

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