Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

Adam Liwo and Cezary Czaplewski

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
Faculty of Chemistry, University of Gdask, ul. Sobieskiego 18, 80-952 Gdask, Poland

 

Jarosaw Pillardy and Harold A. Scheraga

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301

 

(Received 21 March 2001; accepted 15 May 2001)

A general method to derive site-site or united-residue potentials is presented. The basic principle of the method is the separation of the degrees of freedom of a system into the primary and secondary ones. The primary degrees of freedom describe the basic features of the system, while the secondary ones are averaged over when calculating the potential of mean force, which is hereafter referred to as the restricted free energy (RFE) function. The RFE can be factored into one-, two-, and multibody terms, using the cluster-cumulant expansion of Kubo. These factors can be assigned the functional forms of the corresponding lowest-order nonzero generalized cumulants, which can, in most cases, be evaluated analytically, after making some simplifying assumptions. This procedure to derive coarse-grain force fields is very valuable when applied to multibody terms, whose functional forms are hard to deduce in another way (e.g., from structural databases). After the functional forms have been derived, they can be parametrized based on the RFE surfaces of model systems obtained from all-atom models or on the statistics derived from structural databases. The approach has been applied to our united-residue force field for proteins. Analytical expressions were derived for the multibody terms pertaining to the correlation between local and electrostatic interactions within the polypeptide backbone; these expressions correspond to up to sixth-order terms in the cumulant expansion of the RFE. These expressions were subsequently parametrized by fitting to the RFEs of selected peptide fragments, calculated with the empirical conformational energy program for peptides force field. The new multibody terms enable not only the heretofore predictable -helical segments, but also regular -sheets, to form as the lowest-energy structures, as assessed by test calculations on a model helical protein A, as well as a model 20-residue polypeptide (betanova); the latter was not possible without introducing these new terms. ©2001 American Institute of Physics.