Nucleotide-dependent conformational states of actin

Area of Science:

• Biochemistry
• Molecular Biology
• Biophysics

Background:

• Actin's conformational flexibility is crucial for its function.
• The DNase-I binding (DB) loop and nucleotide binding cleft are key regulatory sites.
• Understanding nucleotide-dependent conformational changes is vital for deciphering actin dynamics.

Purpose of the Study:

• To investigate how bound nucleotides (ATP, ADP-Pi, ADP) affect actin's conformational free-energy landscape.
• To determine the nucleotide-dependent folding of the DB loop in monomeric and trimeric actin.
• To analyze the opening and closing dynamics of the actin nucleotide binding cleft.

Main Methods:

• All-atom molecular dynamics (MD) simulations.
• Metadynamics algorithm for enhanced sampling of conformational changes.
• Calculation of free-energy profiles for DB loop folding and cleft opening/closing.

Main Results:

• In ADP-bound monomeric actin, the DB loop exists in a balance of folded and unfolded states, explaining crystallization challenges.
• In ADP-bound actin trimers, the DB loop is stabilized in a folded state.
• The nucleotide binding cleft favors a closed conformation with ATP and ADP-Pi, but an open conformation with ADP.

Conclusions:

• Nucleotide state dictates actin's conformational landscape, influencing DB loop stability and cleft conformation.
• A mechanism of allosteric interaction between the nucleotide binding cleft and DB loop is proposed.
• The actin nucleotide binding cleft width directly modulates the folding free-energy barrier of the DB loop.