Molecular dynamics studies of $Ca^{2+}$ binding effects on calmodulin and determination of structure of C-terminal end of human C-Ha-ras p21 protein

Abstract

Calmodulin is a regulatory protein involved in avariety of cellular calcium-dependent signaling paths. To veryfy the effects of calcium ion(Ca$^{2+}$)binding to calmodulins, we have carried out molecular dynamics simulations at 298 K and energy minimizations for Ca$^{2+}$-bound and Ca$^{2+}$-free calmodulins. In our work, we have confirmed that the conformational transition between Ca$^{2+}$-bound and Ca$^{2+}$-free states occurs more rapidly in the N-terminal half than in the C-trmainal half. We have also shown that Ca$^{2+}$ binding to calmodulin induces the exposure of hydrophobic clefts, which enables interaction with a wide variety of enzymes, whereas the hydrophobic clefts in Ca$^{2+}$ calmodulin are packed around the central helix. Because of this packing, the binding affinity of Ca$^{2+}$-free calmodulin with various agents is reduced compared to that of Ca$^{2+}$-bound calmodulin. The packing of Ca$^{2+}$-free calmodulin is mainly achieved by helices II and III of the N-terminal half and helices V and VI of the C-terminal half. The three-dimensional structure of the carboxyl-terminal region of the human ras oncogenic protein(called p21) has been determined using HDMC(High Directional Monte Carlo) combined with MD(Molecular Dynamics) simulation. It has been well-documented that the carboxyl-terminal region of p21 is very flexible and can play an important role in transmitting a signal from the membrane attach domain. Before a several years ago, a truncated p21 containing residues 1-171-i.e, without the carboxyl terminal end- was analyzed using X-ray crystallography by Sung-Hou Kim. As based on this X-ray structure, we have carried out the theoretical calculation for 25 residues, which are corresponding to 165-189 residues of intact p21, of C-terminal end of human C-Ha-ras protein. In this calculation, the main-chain atoms of 165-169 residues have been fixed to X-ray structure, the remainder region has been allowed to move during the conformational analy...