Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure.
BACKGROUND
Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking.


RESULTS
Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain.


CONCLUSIONS
As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.
Lenaerts
Tom
T
SWITCH laboratory, VIB, Brussels, Belgium. tlenaert@vub.ac.be
Ferkinghoff-Borg
Jesper
J
Stricher
Francois
F
Serrano
Luis
L
Schymkowitz
Joost W H
JW
Rousseau
Frederic
F
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D009010:Monte Carlo Method; D010748:Phosphopeptides / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D051076:Proto-Oncogene Proteins c-fyn / Q000737:chemistry* / Q000378:metabolism*; D015398:Signal Transduction; D018909:src Homology Domains
D010748:Phosphopeptides; D051076:Proto-Oncogene Proteins c-fyn