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Bound Na(+) is a Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation.

Ikuo Kurisaki^1,2, Masayoshi Takayanagi^1,2, Masataka Nagaoka^1,2

¹Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.

The Journal of Physical Chemistry. B

|May 11, 2016

Summary

Sodium ions (Na(+)) binding negatively impacts thrombin-substrate interactions, reducing substrate access to the active site. This finding explains thrombin

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Area of Science:

Biochemistry and Molecular Biology
Enzymology
Protein Dynamics

Background:

Thrombin is a key enzyme in blood coagulation and a model for sodium-activated allosteric enzymes.
Previous studies suggested sodium ion (Na(+)) binding enhances thrombin-substrate interactions, but this remains debated due to subtle structural changes and potential steric hindrance.

Purpose of the Study:

To investigate the precise effect of Na(+) binding on the thrombin-substrate association reaction using computational simulations.
To resolve the controversy regarding Na(+)'s role in modulating thrombin's enzymatic activity.

Main Methods:

Employed extensive molecular dynamics (MD) simulations, performing 210 independent simulations for both apo (Na(+)-free) and holo (Na(+)-bound) thrombin systems.
Analyzed substrate access trajectories to the primary substrate binding pocket (S1-pocket).

Main Results:

Observed a significant 3-fold reduction in substrate access to the S1-pocket upon Na(+) binding.
MD simulations indicated that Na(+) binding hinders substrate access and retention within the S1-pocket.
Concluded that bound Na(+) acts as a negative effector in thrombin-substrate complex formation.

Conclusions:

Sodium ions negatively influence thrombin's stereospecific substrate binding.
This inhibitory effect of Na(+) explains thrombin's relatively low Na(+) binding affinity, which is crucial for minimizing detrimental impacts on substrate binding.