Protein folding guides disulfide bond formation

Area of Science:

• Protein folding and biophysics
• Computational chemistry and molecular dynamics
• Biochemistry and structural biology

Background:

• The Anfinsen principle states protein sequence dictates structure, but the mechanism of disulfide bond formation during folding remains unclear.
• Disulfide bonds are crucial for protein stability and function, particularly in secreted and membrane proteins.
• Understanding disulfide bond chemistry in folding is essential for protein engineering and drug design.

Purpose of the Study:

• To develop a general computational method for simulating disulfide bond formation and rupture during protein folding.
• To investigate the oxidative folding pathway of bovine pancreatic trypsin inhibitor (BPTI) as a model system.
• To elucidate the role of specific protein structures and redox conditions in guiding disulfide bond formation.

Main Methods:

• Developed a coarse-grained molecular simulation method incorporating disulfide bond chemistry.
• Simulated the oxidative folding of BPTI, analyzing folding pathways and disulfide bond formation kinetics.
• Investigated the influence of β-sheet stability and redox conditions on folding dynamics.

Main Results:

• Confirmed that BPTI folding involves multiple pathways dominated by native disulfides.
• Showed that the entropically unfavorable [14-38] disulfide bond forms after polypeptide collapse and core structuring.
• Demonstrated that subsequent folding steps involve partial unfolding and transient nonnative structures, influenced by redox state.

Conclusions:

• Specific collapsed native-like structures act as crucial guides for efficient protein folding and disulfide bond formation.
• The developed simulation method provides a general approach applicable to a wide range of single-domain proteins.
• This work clarifies a long-standing problem in protein folding, with implications for understanding enzyme-catalyzed disulfide proteins.