Relaxation to native conformation of a bond-fluctuating protein chain with hydrophobic and polar nodes.
The conformation and dynamics of a protein chain with hydrophobic and polar nodes are examined by the bond-fluctuation model using Monte Carlo simulations on a cubic lattice. The minimal (nearest neighbor) interaction leads to standard (self-avoiding walk) conformation, i.e., the scaling of the radius of gyration R(g) with the molecular weight N R(g) proportional, variant Ngamma with gamma approximately 3/5 . Specific interactions with longer range and higher strength are needed to approach the native globular conformations with gamma<3/5 . Relaxation into the globular ground state shows a weak power-law decay, i.e., R(g) proportional, variant t(-alpha) , alpha approximately 0.06-0.12 .
Bjursell
Johan
J
George Mason University, MS 5C3, Fairfax, Virginia 22030-4444, USA.
Pandey
R B
RB
D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009038:Motion; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D055672:Static Electricity; D013329:Structure-Activity Relationship
D011506:Proteins