Investigation of contact interactions of (001) MgO: molecular dynamics simulations studies

2002 ◽  
Vol 12 (3) ◽  
pp. 593-601 ◽  
Author(s):  
C. W. Yong ◽  
W. Smith ◽  
K. Kendall
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Contact Interactions ◽  
Dynamics Simulations

scholarly journals THE RANGE OF THE CONTACT INTERACTIONS AND THE KINETICS OF THE GO MODELS OF PROTEINS

2002 ◽  
Vol 13 (09) ◽  
pp. 1231-1242 ◽  
Author(s):  
MAREK CIEPLAK ◽  
TRINH XUAN HOANG
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Contact Interactions ◽  
Residue Contact ◽  
Cutoff Distance ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Van Der Waals Radii

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue–residue contact interactions are selected based on a cutoff distance, Rc. The folding times strongly depend on the value of Rc and nonmonotonically. This indicates a need for a physically determined set of native contacts. One may accomplish it by considering the van der Waals radii of the residual atoms and checking if the atoms overlap. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding.

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