Rewiring the specificity of two-component signal transduction systems.

By Jeffrey M. Skerker, Barrett S. Perchuk, Albert Siryaporn, Emma A. Lubin, Orr Ashenberg, M. Goulian, M. Laub. 2008

491 citations recorded by the source corpus.

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Citations in the corpus

Direct-coupling analysis of residue coevolution captures native contacts across many protein families (2011, methodology): “Simple co-variance based analysis was first applied to characterize interactions between residues belonging to partner proteins of the TCS pathways (14, 15); it was found to partially predict correct inter-protein residue contacts, but also many residue pairs which are far apart.”
Protein structure prediction from sequence variation (2012, background): “A related but actually simpler problem is that of predicting pairwise protein–protein interactions 21,47,48 .”
3D structures of membrane proteins from genomic sequencing (2012, neutral): “…generalization using pairwise sequence alignments, with a homologous pair of sequences in place of a single sequence and derivation of evolutionary couplings not within a protein but between two potentially interacting proteins (Pazos and Valencia, 2002; Skerker et al., 2008; Weigt et al., 2009).”
Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “using a global model have been successful in identifying residue interactions from evolutionary covariation, for instance between histidine kinases and response regulators (Burger & van Nimwegen, 2008; Skerker et al., 2008; Weigt et al., 2009), and this approach has only recently been generalized an”
Protein sectors: evolutionary units of three-dimensional structure (2009, background): “…proteins (Ferguson et al., 2007; Hatley et al., 2003; Kass and Horovitz, 2002; Lee et al., 2008, 2009; Peterson et al., 2004; Shulman et al., 2004; Skerker et al., 2008) and were found to be sufficient for recapitulating native folding and function in a small protein interaction module (Russ et…”
Biological Insights from Structures of Two-Component Proteins (2009, methodology): “A computational method was recently used to identify the covariant residues in large numbers of cognate HK-RR pairs (82).”
The Evolution of Two-Component Signal Transduction Systems (2012, background): “These kinases likely arose through duplication and divergence, and as noted above, the specificity of each can be converted to that of the other by just three mutations (10, 73) (Figure 5b).”
Evolution-Based Functional Decomposition of Proteins (2015, unknown): “Computed for all pairs of amino acids in the alignment, this deﬁnes a covariance matrix Alternatively, statistical dependency can be quantiﬁed by the mutual information, whose origin is similar to the relative entropy (5; 36).”
Inferring interaction partners from protein sequences using mutual information (2018, background): “Strikingly, mutating only these few 351 specificity residues has allowed to fully switch the specificity of HK-RR pairs [39].”
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information (2014, background): “Although recent stimulating work (11, 15) has demonstrated the rewiring of HK/RR signaling in vitro, our methodology could potentially afford us additional flexibility in exploring sequence space for mutations that can be used to preferentially switch the interaction of a TCS protein toward a…”
3D Protein Structure Predicted from Sequence (2011, unknown): “This suggests that residue correlation can provide information about amino acid residues that are close in structure [4,5,6,7,8,9,10,11].”
Biomolecular computing systems: principles, progress and potential (2012, background): “Studies have shown that signalling processes such as mating and osmolarity pathways in yeast 94 and two-component signalling in bacteria 89,95 can be rewired.”