Dynamic Allosteric Residue Coupling (darc) Spots Shed Light on Functional Changes from Sequence Variation

Defining the functional impact of protein sequence variation presents a major challenge in biology and genomics and the importance has grown dramatically as unprecedented advances in sequencing complete exomes have yielded tens of thousands of non-synonymous single nucleotide variants (nSNVs) on the human proteome. Currently there are no consistent methods to capture the mechanisms of functional changes as a result of sequence variations, particularly at non-conserved positions and in the absence of large structural changes. We present the dynamic flexibility index (dfi), a measure of residue-specific flexibility and the dynamic coupling index (dci), a technique determining coupling strength between amino acids. We apply our approach to the lactose repressor protein LacI, where substitutions at non-conserved position V52 produce progressive effects on function. dfi captures changes in flexibility in the DNA binding domain and is correlated with binding affinity. We also use dci to identify important dynamic allosteric residue coupling (darc) spots, distally located to the DNA binding domain. darc spot dfi correlates strongly with changes in repression rate as well as DNA binding affinity and shows conformational dynamics at distal sites plays an important role in LacI function.