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The Range Of The Contact Interactions And The Kinetics Of The Go Models Of Proteins

Author

Listed:
  • MAREK CIEPLAK

    (Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland)

  • TRINH XUAN HOANG

    (The Abdus Salam International Center for Theoretical Physics, Strada Costriera 11, 34100 Trieste, Italy;
    INFM Via Beirut 2-4, 34014 Trieste, Italy)

Abstract

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 ofRcand 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.

Suggested Citation

  • Marek Cieplak & Trinh Xuan Hoang, 2002. "The Range Of The Contact Interactions And The Kinetics Of The Go Models Of Proteins," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 13(09), pages 1231-1242.
    • Handle: RePEc:wsi:ijmpcx:v:13:y:2002:i:09:n:s012918310200408x
    DOI: 10.1142/S012918310200408X
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