Statistical mechanics of protein sequences

A statistical mechanical treatment of biological macromolecules is presente d that includes the sequence information as an internal coordinate. Using a path integral representation, the canonical partition function can be repr esented as a product of a polymer configurational path integral and a seque nce walk path integral. In most biological instances, the sequence composit ion influences the potential energy of intersubunit interaction. Consequent ly, the two path integrals are not separable, but rather "interact" via a s equence-dependent configurational potential. In proteins and RNA, the seque nce walk occurs in dimensions greater than three and, therefore, will be an ideal "polymer." The Markovian nature of this walk can be exploited to sho w that all the structural information is contained in the sequence. This la tter effect is a result of the dimensionality of the sequence walk and is n ot necessarily a result of biological optimization of the system. [S1063-65 1X(99)11910-X].