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R. N. dos Santos, A. J. R. Ferrari, H. C. R. de Jesus, F. C. Gozzo, F. Morcos, L. Martínez

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The combined use of distance constraints derived from chemical cross-linking/mass spectrometry and amino acid coevolution improves the prediction of protein tertiary structures.
Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals

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In this work, we present a methodology to combine residue interaction data obtained from coevolutionary information and cross-linking/mass spectrometry distance constraints in order to identify functional states of proteins. Using a combination of structure-based models (SBM) with optimized Gaussian-like potentials, secondary structure estimation and simulated annealing molecular dynamics, we provide an automated methodology to integrate constraint data from diverse sources in order to elucidate the native conformation of full protein systems with distinct complexity and structural topologies. We show that cross-linking mass spectrometry constraints improve the structure predictions obtained from SBMs and coevolution signals, and that the constraints obtained by each method have a useful degree of complementarity that promotes enhanced fold estimates.

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