Abstract
Publisher Summary This chapter examines the various aspects of ab initio protein folding using LINUS. LINUS is an ab initio method for simulating the folding of a protein on the basis of simple physical principles. The approach emphasizes the organizing role of steric exclusion and conformational entropy in guiding folding. In addition to steric interactions, which are repulsive, LINUS also includes attractive forces resulting from hydrogen bonding and hydrophobic burial. A typical LINUS simulation begins with a sequence of interest modeled as an extended polypeptide chain with all nonhydrogen atoms included. The LINUS scoring function's components include hydrogen bonding, hydrophobic contacts, and backbone torsion. The villin headpiece subdomain is a small 36-residue protein containing three short helices and a hydrophobic core. The first and second helices are joined by a six-residue loop, and the second and third helices are joined by a three-residue segment. It is found that hydrophobic collapse to the overall villin headpiece structure is seen occasionally in the ensemble of saved conformations, but it does not persist for many cycles.
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