Atomic-detailed milestones along the folding trajectory of protein G

Details Atomic-detailed milestones along the folding trajectory of protein G Atomic-detailed milestones along the folding trajectory of protein G

2009-05-18

arxiv.org/abs/0905.2875v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the folding of proteins. Making use of a biasing algorithm, based on the principle of the ratchet-and-pawl, we have been able to calculate eight folding trajectories (to an RMSD between 1.2A and 2.5A) of the B1 domain of protein G in explicit solvent without the need of high-performance computing. The simulations show that in the denatured state there is a complex network of cause-effect relationships among contacts, which results in a rather hierarchical folding mechanism. The network displays few local and nonlocal native contacts which are cause of most of the others, in agreement with the NOE signals obtained in mildly-denatured conditions. Also nonnative contacts play an active role in the folding kinetics. The set of conformations corresponding to the transition state display phi-values with a correlation coefficient of 0.69 with the experimental ones. They are structurally quite homogeneous and topologically native-like, although some of the side chains and most of the hydrogen bonds are not in place.

Affiliated with

Also associated with

No associations

Rating

Atomic-detailed milestones along the folding trajectory of protein G does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Atomic-detailed milestones along the folding trajectory of protein G, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Atomic-detailed milestones along the folding trajectory of protein G will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-609589