Terzoli S, Tiana G. Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential.
J Phys Chem B 2020;
124:4079-4088. [PMID:
32336092 PMCID:
PMC8007105 DOI:
10.1021/acs.jpcb.0c01671]
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Abstract
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Studying the conformations
involved in the dimerization of cadherins
is highly relevant to understand the development of tissues and its
failure, which is associated with tumors and metastases. Experimental
techniques, like X-ray crystallography, can usually report only the
most stable conformations, missing minority states that could nonetheless
be important for the recognition mechanism. Computer simulations could
be a valid complement to the experimental approach. However, standard
all-atom protein models in explicit solvent are computationally too
demanding to search thoroughly the conformational space of multiple
chains composed of several hundreds of amino acids. To reach this
goal, we resorted to a coarse-grained model in implicit solvent. The
standard problem with this kind of model is to find a realistic potential
to describe its interactions. We used coevolutionary information from
cadherin alignments, corrected by a statistical potential, to build
an interaction potential, which is agnostic about the experimental
conformations of the protein. Using this model, we explored the conformational
space of multichain systems and validated the results comparing with
experimental data. We identified dimeric conformations that are sequence
specific and that can be useful to rationalize the mechanism of recognition
between cadherins.
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