A MOLECULAR DYNAMICS STUDY OF THE HEAT SHOCK PROTEIN Hsp70

Abstract

Heat shock protein Hsp70 is a chaperon which helps folding of other proteins. It consists of two domains: a nucleotide binding domain where ATP or ADP binds and a substrate binding domain where the protein to be folded binds [1]. In the presence of ATP, the substrate affinity of Hsp70 is low. Binding of a substrate triggers ATP hydrolysis. In ADP bound form, the substrate affinity is high [1]. The allosteric communication between the two domains is mediated by a linker. The ATPase activity is pH dependent, the optimum pH being around 7.5 [2]. This study aims at understanding the role of the linker in triggering the ATP hydrolysis and the origin of the pH dependence of the reaction using molecular dynamics simulations. It is experimentally known that an Hsp70 construct containing only the nucleotide binding domain and the linker has the same ATPase rate as the full length Hsp70. Hence, in order to reduce the computational cost, simulations have been made on a truncated Hsp70 structure. Several simulations with different nucleotide states (ATP bound, ADP bound or nucleotide free) and with different starting geometries have been carried out in order to determine possible positions of the linker and its effect on the active site arrangement. Moreover, pKa values of some important residues inside or near the active site [3, 4] have been calculated via thermodynamic integration simulations. Thermodynamic integration simulations indicate that Asp194 and Asp201 have elevated pKa values, suggesting that these residues may be protonated at pH 7.5. Asp8 and Glu171 have lower pKa values, hence are probably unprotonated. Simulations with different protonation states of Asp194 and Asp201 have been carried out. It has been observed that the protonation states of these residues affect the conformational behavior of Hsp70.