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Statistical thermodynamics basis of energy and residue position fluctuationsis explained for native proteins. The protein and its surroundings are treatedas a canonical system with emphasis on the effects of energy exchange betweenthe two. Fluctuations of the energy are related to fluctuations of residuepositions, which in turn are related to the connectivity matrix of the protein,thus establishing a connection between energy fluctuation pathways and proteinarchitecture. The model gives the locations of hotspots for ligand binding, andidentifies the pathways of energy conduction within the protein. Results arediscussed in terms of two sets of models, the BPTI and twelve proteins thatcontain the PDZ domain. Possible use of the model for determining functionallysimilar domains in a diverse set of proteins is pointed out.

Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations