Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

Area of Science:

• Biochemistry
• Structural Biology
• Enymology

Background:

• Human triosephosphate isomerase (HsTIM) deficiency is a genetic disorder often caused by the E104D mutation.
• This mutation reduces enzyme thermostability by affecting a large water cluster in the inter-subunit interface.
• The structural basis linking this water cluster to thermolability remains unclear.

Purpose of the Study:

• To investigate the structural role of the water cluster in the inter-subunit interface of HsTIM.
• To elucidate the mechanism by which the E104D mutation-induced water cluster affects enzyme thermostability and function.

Main Methods:

• Comparative structural analysis of wild-type and E104D mutant HsTIM.
• Analysis of water molecule distribution and conservation in the dimer interface.
• Molecular dynamics simulations to assess protein flexibility and dynamics.

Main Results:

• An atypical "wet-core-dry-rim" water topology was identified in the HsTIM dimer interface, with 16 water molecules conserved in non-archaeal TIMs.
• The E104D mutation did not significantly alter overall protein structure but increased flexibility in the water-rich interface region.
• Molecular dynamics simulations showed increased root-mean-square deviation in the water cluster region of the mutant, correlating with thermolability.

Conclusions:

• A large cluster of water molecules buried within protein interfaces can be structurally fragile and functionally significant.
• This water cluster in HsTIM is crucial for maintaining quaternary structure and enzyme stability.
• The E104D mutation destabilizes HsTIM by increasing the flexibility of this water cluster, leading to enzyme deficiency.