RT Journal Article
SR Electronic
T1 Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 044586
DO 10.1101/044586
A1 R. R. Cheng
A1 O. Nordesjö
A1 R. L. Hayes
A1 H. Levine
A1 S. C. Flores
A1 J. N. Onuchic
A1 F. Morcos
YR 2016
UL http://biorxiv.org/content/early/2016/08/31/044586.abstract
AB Two-component signaling (TCS) is the primary means by which bacteria sense and respond to the environment. TCS involves two partner proteins working in tandem, which interact to perform cellular functions while limiting interactions with non-partners (i.e., “cross-talk”). We construct a Potts model for TCS that can quantitatively predict how mutating amino acid identities affect the interaction between TCS partners and non-partners. The parameters of this model are inferred directly from protein sequence data. This approach drastically reduces the computational complexity of exploring the sequence-space of TCS proteins. As a stringent test, we compare its predictions to a recent comprehensive mutational study, which characterized the functionality of 204 mutational variants of the PhoQ kinase in Escherichia coli. We find that our best predictions accurately reproduce the amino acid combinations found in experiment, which enable functional signaling with its partner PhoP. These predictions demonstrate the evolutionary pressure to preserve the interaction between TCS partners as well as prevent unwanted “crosstalk”. Further, we calculate the mutational change in the binding affinity between PhoQ and PhoP, providing an estimate to the amount of destabilization needed to disrupt TCS.