Barnase-Barstar: from first encounter to final complex.

Area of Science:

• Biochemistry
• Computational Biology
• Molecular Biophysics

Background:

• Transient protein complex formation is crucial for cellular functions.
• The precise mechanisms and energy landscapes of protein association, including energy barriers, remain incompletely understood.
• Computational methods offer atomistic insights into these complex processes.

Purpose of the Study:

• To investigate the atomistic details of protein-protein association using computational simulations.
• To elucidate the role of electrostatics and mutations in the Barnase-Barstar complex formation.
• To determine the energy landscape and identify energy barriers during complexation.

Main Methods:

• Constraint biased Molecular Dynamics simulations were employed.
• Simulations covered the reaction coordinate from diffusion to the bound state for wild-type and mutant Barnase-Barstar complexes.
• Analysis included structural characterization and Potential of Mean Force (PMF) calculations.

Main Results:

• Two distinct protein association patterns were identified, driven by charged contact points near the binding site.
• Electrostatic interactions and mutations modulate the prevalence of these association patterns.
• A single dominant energy barrier was found around 0.3 nm, corresponding to desolvation, with its height influenced by electrostatics.

Conclusions:

• Protein association is not a single pathway but involves distinct patterns influenced by electrostatics.
• Electrostatic forces significantly impact the energy barrier height during complex formation but not its position.
• Computational simulations provide valuable insights into the energetics and mechanisms of protein complex assembly.