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Article

ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators

1
Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
2
Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
3
Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Alessandro Giuliani
Entropy 2021, 23(2), 170; https://doi.org/10.3390/e23020170
Received: 17 December 2020 / Revised: 21 January 2021 / Accepted: 26 January 2021 / Published: 30 January 2021
Two-component systems (TCS) are signaling machinery that consist of a histidine kinases (HK) and response regulator (RR). When an environmental change is detected, the HK phosphorylates its cognate response regulator (RR). While cognate interactions were considered orthogonal, experimental evidence shows the prevalence of crosstalk interactions between non-cognate HK–RR pairs. Currently, crosstalk interactions have been demonstrated for TCS proteins in a limited number of organisms. By providing specificity predictions across entire TCS networks for a large variety of organisms, the ELIHKSIR web server assists users in identifying interactions for TCS proteins and their mutants. To generate specificity scores, a global probabilistic model was used to identify interfacial couplings and local fields from sequence information. These couplings and local fields were then used to construct Hamiltonian scores for positions with encoded specificity, resulting in the specificity score. These methods were applied to 6676 organisms available on the ELIHKSIR web server. Due to the ability to mutate proteins and display the resulting network changes, there are nearly endless combinations of TCS networks to analyze using ELIHKSIR. The functionality of ELIHKSIR allows users to perform a variety of TCS network analyses and visualizations to support TCS research efforts. View Full-Text
Keywords: statistical inference; mutational phenotypes; interaction specificity; phosphorylation; fitness landscape; bacterial signaling statistical inference; mutational phenotypes; interaction specificity; phosphorylation; fitness landscape; bacterial signaling
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MDPI and ACS Style

Sinner, C.; Ziegler, C.; Jung, Y.H.; Jiang, X.; Morcos, F. ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators. Entropy 2021, 23, 170. https://doi.org/10.3390/e23020170

AMA Style

Sinner C, Ziegler C, Jung YH, Jiang X, Morcos F. ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators. Entropy. 2021; 23(2):170. https://doi.org/10.3390/e23020170

Chicago/Turabian Style

Sinner, Claude, Cheyenne Ziegler, Yun H. Jung, Xianli Jiang, and Faruck Morcos. 2021. "ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators" Entropy 23, no. 2: 170. https://doi.org/10.3390/e23020170

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