Dihedral-angle information entropy as a gauge of secondary structure propensity

¹ Georgia Institute of Technology

^* To whom correspondence should be addressed. E-mail: hernandez{at}gatech.edu.

Submitted on May 16, 2006
Revised on July 31, 2006
Accepted on 29 August 2006

	Abstract

Protein structural information can be uncovered using an information-theory-based entropy and auxiliary functions by taking advantage of high-quality correlation plots between the dihedral angles about a residue and those between sequential residues. A standard information entropy for a primary sequence has been defined using the values of the probabilities of the most likely dihedral angles allong the sequence. The distribution of entropy differences relative to the standard for each protein in a reference set ---a sublibrary of the PDB at the 90% sequence redundancy level--- appears to be nearly Gaussian. It gives rise to an auxiliary checking function whose value signals the extent to which the dihedral angle propensities differ from typical structures. Such deviations can arise either because of incorrect dihedral angle assignments or secondary structural propensities that are atypical of the structures in the reference set. This auxiliary checking function can be readily calculated at the public website, http://www.d2check.gatech.edu. Its utility is demonstrated here in an analysis displaying differences between experimentally and theoretically derived structures, and in the analysis of structures derived by homology modeling. A comparison of the new measure, D₂Check, to other checking functions based on backbone conformation--namely, PROCHECK and WHAT_CHECK--is also provided.

Key Words: Ramachandran plot, phi-psi dihedral-angle distributions, protein structure validation, tosion angles