Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Thrombin is crucial for antithrombotic and chemotherapeutic drug development.
• The physiological and pathological roles of thrombin's light chain are not fully understood.
• Disease-associated single deletion of Lysine 9 (ΔK9) in the light chain warrants further investigation.

Purpose of the Study:

• To investigate the structural and functional impacts of the LYS9 deletion in thrombin's light chain.
• To elucidate the mechanisms underlying the LYS9 deletion-associated bleeding disorder.
• To explore the allosteric effects of the light chain on thrombin function.

Main Methods:

• Utilized 10 μs molecular dynamics simulations.
• Applied supervised and unsupervised machine learning methodologies.
• Conducted traditional structural analyses and decision tree learning on hydrogen bonding features.

Main Results:

• LYS9 deletion significantly perturbs thrombin's conformational ensemble.
• The deletion destabilizes the catalytic cleft and regulatory regions, inducing nanosecond-scale motions.
• Distinct Na+ ion binding modes were observed for wild-type and ΔK9 mutant thrombin.
• Seven critical hydrogen bonding interactions were identified as key differentiators between wild-type and mutant thrombin.

Conclusions:

• LYS9 deletion has significant localized and long-range allosteric effects on thrombin.
• The light chain plays a critical role as an allosteric effector in thrombin.
• These findings provide quantitative insights into the LYS9 deletion-associated bleeding disorder.