A physics-based, coarse-grained model with orientation-dependent hydrogen bond potential for investigating protein folding

PHYS 422

Eng Hui Yap, enghui@berkeley.edu, Department of Bioengineering, UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, CA 94720, Nicolas Lux Fawzi, fawzin@berkeley.edu, UCSF / UC Berkeley Joint Graduate Group in Bioengineering, UC Berkeley, Berkeley, CA 94720, and Teresa Head-Gordon, TLHead-Gordon@lbl.gov, Department of Bioengineering and UCSF/UCB Joint Graduate Group in Bioengineering, University of California, Berkeley, Berkeley, CA 94720.
We present a reformulation of our sequence-based α-carbon model to introduce a fourth bead type, new dihedral angle potentials, and a potential of mean force hydrogen bonding term that encourages the cooperative formation of protein-like secondary structures. The orientational-dependent hydrogen bonding term is based on a similar potential developed by Ben-Naim and later adopted by Silverstein and co-workers in the study of a simple 2D model of water. Our model now incorporates a mean field estimate of the orientation dependent properties that give rise to specific hydrogen bond pairing to stabilize α-helices and β-sheets. We illustrate the new potential using folding studies of proteins L and G and preliminary results on two immunology proteins IM7 and IM9. The model shows greater folding cooperativity and improvements in designability of new proteins.

Poster Session
7:30 PM-10:00 PM, Wednesday, 13 September 2006 Moscone Center -- Hall D, Poster

8:00 PM-10:00 PM, Monday, 11 September 2006 Moscone Center -- Hall D, Sci-Mix

Division of Physical Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006