An efficient algorithm to perform local concerted movements of a chain molecule

Area of Science:

• Computational chemistry
• Molecular dynamics
• Biophysics

Background:

• Efficient manipulation of local chain molecule portions is crucial for molecular simulations.
• Existing methods for concerted rotation have limitations in flexibility and applicability.

Purpose of the Study:

• To propose and validate a novel numerical strategy for generalized concerted rotation moves.
• To enhance the efficiency of sampling and refinement in molecular simulations.

Main Methods:

• Utilizing Denavit-Hartenberg parameters for chain description.
• Generalizing concerted rotation by opening and closing chain portions in tangent and orthogonal spaces.
• Enforcing detailed balance in Monte Carlo simulations without Jacobian reweighting.

Main Results:

• Demonstrated efficient exploration of configuration manifolds for protein fragments and cyclic molecules.
• Showcased the "local backbone volume" metric reproducing protein mobility profiles.
• Successfully refined protein fragments with varying secondary structures.

Conclusions:

• The proposed methodology offers a valuable tool for exploration and sampling in biomolecular simulations.
• The approach simplifies detailed balance enforcement and allows tuning of degree-of-freedom fluctuations.