Role of Secondary Motifs in Fast Folding Polymers A Dynamical Variational Principle.pdfVIP

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle 1 1 2 Amos Maritan , Cristian Micheletti and Jayanth R. Banavar (1) International School for Advanced Studies (S.I.S.S.A.) - INFM, Via Beirut 2-4, 34014 Trieste, Italy and 0 0 the Abdus Salam International Centre for Theoretical Physics. 0 (2) Department of Physics and Center for Materials Physics, 104 Davey Laboratory, The Pennsylvania State University, 2 University Park, Pennsylvania 16802 (February 6, 2008) b e A fascinating and open question challenging biochemistry, physics and even geometry is the presence F of highly regular motifs such as α-helices in the folded state of biopolymers and proteins. Stimulating 8 explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational ] principle for selection in conformation space based on the requirement that the backbone of the h native state of biologically viable polymers be rapidly accessible from the denatured state. The c e variational principle is shown to result in the emergence of helical order in compact structures. m A fundamental problem in every day life is that of merable ones with a given compactness. Earlier studi