Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

Area of Science:

• Computational chemistry and biophysics.
• Polymer dynamics and statistical mechanics.

Background:

• The hybrid basis approach (HBA) has shown effectiveness in studying polymer dynamics for flexible synthetic polymers.
• The HBA combines long time sorting and maximum correlation approximation for efficient computation.
• Its applicability to more complex systems like proteins with varying stiffness and longer persistence lengths requires investigation.

Purpose of the Study:

• To evaluate the efficacy of the HBA for polymers with diverse monomers and structural complexities, exemplified by a transthyretin peptide fragment.
• To investigate the local and global dynamics of this peptide in an explicit water environment using molecular dynamics simulations and HBA.
• To assess the HBA's capability in capturing dynamics beyond flexible synthetic polymers.

Main Methods:

• Classical molecular dynamics simulations of a transthyretin peptide fragment in explicit water.
• Application of the hybrid basis approach (HBA) using diffusion theory.
• Calculation of dynamic properties from both simulation outcomes and HBA-based diffusion theory.

Main Results:

• The HBA demonstrates efficacy in describing the dynamics of a complex peptide system, extending its utility beyond simpler polymers.
• Explicit solvent molecular dynamics simulations provide equilibrium averages for HBA calculations.
• The mode-coupling approach within HBA successfully captures both long-range and local dynamics.

Conclusions:

• The HBA is a versatile and computationally convenient method for studying the dynamics of complex molecular systems, including protein fragments.
• The study confirms the HBA's ability to handle polymers with varied monomer types and structural characteristics.
• This work validates the HBA's predictive power for both local and global dynamics in realistic biological environments.