Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Dynamics

Background:

• The FKBP domain protein FKBP12 possesses a Trp 59 indole ring at the active site cleft.
• Crystallographic data shows a canonical orientation, but solution studies reveal dynamic behavior.

Purpose of the Study:

• To investigate the solution dynamics of the Trp 59 indole ring in FKBP12.
• To explore the energetic coupling between indole ring dynamics and other protein residues.
• To compare dynamics across different FKBP family members and variants.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy was used to study FKBP12, FKBP51, and FKBP52.
• Molecular dynamics simulations (CHARMM27) were performed on wild-type FKBP12 and its V101I variant.
• Analysis of transition matrices for sidechain and loop dynamics.

Main Results:

• A ~90° rotation of the Trp 59 indole ring occurs in 20% of FKBP12 molecules in solution.
• Homologous FK1 domains of FKBP51 and FKBP52 showed no observable indole ring flip.
• The V101I variant of FKBP12 significantly reduced the population of the perpendicular indole orientation.
• A statistical allosteric coupling of 10 kJ/mol was found between the Trp 59 sidechain and the Glu 60 sidechain dynamics.

Conclusions:

• FKBP12 exhibits significant conformational flexibility in its active site indole ring.
• This flexibility is specific to FKBP12 and not universally conserved in homologous FK1 domains.
• Allosteric coupling exists between distal residues, influencing active site dynamics.