Kinetics and thermodynamics of type VIII -turn formation: a CD, NMR and microsecond explicit molecular dynamics study of the GDNP tetrapeptide

¹ Université Paris 7
² Utrecht University
³ Università degli Studi della Basilicata, Potenza
⁴ Université de Reims Champagne-Ardenne

^* To whom correspondence should be addressed. E-mail: a.m.j.j.bonvin{at}chem.uu.nl.

Submitted on September 12, 2005
Revised on October 12, 2005
Accepted on 12 January 2006

	Abstract

We report a experimental and theoretical study on type VIII b-turn using a designed peptide of sequence GDNP. CD and NMR studies reveal that this peptide exists in equilibrium between type VIII b-turn and extended conformations. Extensive MD simulations give a description of the free energy landscape of the peptide in which we retrieve the same two main conformations suggested by the experiments. The free energy difference between the two conformational states is very small and the transition between them occurs within a few kT at 300 K on a nanosecond time scale. The equilibrium is mainly driven by entropic contribution, which favours extended conformations over b-turns. This confirms other theoretical studies showing that b-turns are marginally stable in water solution because of the larger entropy of the extended state unless some stabilizing interactions exist. Our observations may be extended to any type of b-turn and have important consequences for protein folding. A comparison of our MD and CD results also suggests a possible type VIII b-turn CD signature indicated by one main band at 200 nm, close to that of random coil, and a fairly large shoulder at 220 nm. Last, our results clearly show that the XXXP motif can only fold into a type VIII b-turn, which is consistent with its fairly strong propensity for this type of turn. This important finding may help for peptide design and is in line with recent studies on bioactive elastin peptides.

Key Words: GDNP, b-turns, kinetics, molecular dynamics, thermodynamics, type VIII