Q:
What is the main difference between surface- and interior-critical residues?

A:
Allosteric surface residues play regulatory roles that are fundamentally distinct from those of allosteric residues within the interior. While surface residues may often constitute the sources or sinks of allosteric signals, interior residues act to transmit such signals. Thus, different approaches are needed for identifying these two classes of residues. Surface-critical residues are identified by finding pockets such that the occlusion of such pockets is likely to interfere with large-scale protein motions (see Documentation for details; see also Ming and Wall, 2005; Mitternacht and Berezovsky, 2011). Interior-critical residues are identified by finding information-flow bottlenecks within the protein structure (see Documentation and main paper for details; see also del Sol et al, 2006; Ghosh et al, 2008; Rousseau et al, 2005).

del Sol, A., Fujihashi, H., Amoros, D., and Nussinov, R. (2006). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2(1).

Ghosh, A., and Vishveshwara, S. (2008). Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes. Biochemistry. 47, 11398-11407.

Ming, Dengming, and Michael E. Wall. “Quantifying allosteric effects in proteins.” Proteins: Structure, Function, and Bioinformatics 59.4 (2005): 697-707.

Mitternacht, S. and Berezovsky, I.N. (2011). Binding leverage as a molecular basis for allosteric regulation. PLoS Comput. Biol. 7, e1002148.

Rousseau, F. and Schymkowitz, J. (2005). A systems biology perspective on protein structural dynamics and signal transduction. Curr. Opin. Struct. Biol. 15, 23–30.