The role of proline isomers - Rationalization and modulation of proline functional importance
Theoretical Chemistry: Molecules, Materials, Surfaces
Final Report Abstract
In this project, we used classical atomistic molecular dynamics simulations to study proline cis/trans isomerization in peptides and proteins. In particular, we developed a new method based on an enhanced sampling scheme to calculate the free-energy difference between the isomerization states of one or several proline residues. For small model peptides characteristic of an unstructured amino acid chain, excellent agreement with both experiment and another standard free-energy calculation method was found. However, for a protein featuring the proline of interest in a folded environment, the standard method was seen to be insufficient because it led to structural disruptions and free-energy values that do not agree with experimental findings. The new method, however, achieved the simulation of rapid transitions between proline isomer states while retaining the native protein structure. Calculated isomerization free energies were in very good agreement with corresponding experimental values. Furthermore, the efficiency of the method was remarkable, considering that in nature, proline isomerization occurs on time scales of 10-1000 seconds, which renders the computational investigation of the process inaccessible to brute-force atomistic simulation methods. We trace back the success of our method to the introduction of enhanced sampling in a gentle way through canonical exchange of configurations between replicas of the system with varying bias potentials rather than enforcing cis/trans transitions through high forces associated with standard harmonic bias potentials. We also showed how to derive the entire free-energy profile along the isomerizing peptide bond torsion angle based on reweighting of the configurations sampled in the different replicas of the system. This allowed to calculate the barrier heights of isomerization. We consider our method a very powerful tool to investigate the stability of proline isomer states in peptides and larger protein environments. In particular, the most recent results showed that the method is very suited to investigate the correlation of proline isomerization states in systems where multiple proline residues that can switch between the cis and trans states occur. Work is ongoing to characterize the influence of proline isomer states on the isomerization free energy of other proline residues in the same polypeptide chain and on the resulting global biomolecular conformation. We expect that new insight into the possible coupling of proline isomer states and its possible impact on biomolecular structure can be obtained.
Publications
-
Free energy calculations in biomolecular simulation: methods and examples; International virtual workshop “Computational Modeling in Chemistry, Biology and Materials – Making it Mainstream”, 24.11.2021, Cochin University of Science and Technology, India
M.M. Reif
-
Prolyl cis-trans isomerization investigated with advanced Hamiltonian Replica Exchange Molecular Dynamics; Opening Symposium of the Center for Functional Protein Assemblies, 28.9.2021, Technical University of Munich, Garching, Germany
M. Kienlein; M. Zacharias & M.M. Reif
-
Basic scripts to perform and analyze ωBP-REMD simulations
M. Kienlein
-
Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations. Structure, 31(11), 1473-1484.e6.
Kienlein, Maximilian; Zacharias, Martin & Reif, Maria M.
