Insight into the molecular mechanism about lowered dihydrofolate binding affinity to dihydrofolate reductase-like 1 ...

Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To address this question, we studied the binding of DHF to DHFRL1 and DHFR by using molecular dynamics simulation. Moreover, to investigate the role the 24th residue of DHFR/DHFRL1 plays in DHF binding, R24W DHFRL1 mutant was also studied. The van der Waals interaction are more crucial for the total DHF binding energies, while the difference between the DHF binding energies of human DHFR and DHFRL1 can be attributed to the electrostatic interaction and the polar desolvation free energy.More specifically, lower DHF affinity to DHFRL1 can be mainly attributed to the reduction of net electrostatic interactions of residues Arg32 and Gln35 of DHFRL1 with DHF as being affected by Arg24. The side chain of Arg24 in DHFRL1 can extend deeply into the binding sites of DHF and NADPH, and disturb the DHF binding by steric effect, which rarely happens in human DHFR and R24W DHFRL1 mutant. Additionally, the conformation of loop I in DHFRL1 was also studied in this work. Interestingly, the loop conformation resemble to normal closed state of Escherichia coli DHFR other than the closed state of human DHFR. We hope this work will be useful to understand the general characteristics of DHFRL1.