The role of proline isomers - Rationalization and modulation of proline functional importance

• Applicant: Dr. Maria Reif
• Subject Area: Biophysics ; Theoretical Chemistry: Molecules, Materials, Surfaces
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 401024171

Proline cis-trans isomerization, despite its important role in protein folding and function, is poorly understood on a microscopic physico-chemical level. There are numerous experimental studies on the phenomenon, but computer-assisted approaches which are in principle able to provide the hitherto lacking detailed quantitative insight, are lagging behind. The present project seeks to close that gap by investigations using classical atomistic molecular dynamics simulations. We plan to address questions concerning the determinants of the function of certain proline residues (e.g. role in conformational coupling) and the environmental influence on these determinants (e.g. solvent, mutations or post-translational modifications). Here, various proteins for which the role of specific proline residues is experimentally known, will be investigated. Throughout, enhanced sampling methods will be used to achieve converged simulation results. A large focus will be put on a beta-hairpin model system for which extensive experimental studies on the interplay of conformational stability and proline isomerization as a function of proline-vicinal mutations have been performed. Our simulations are expected to explain the experimental findings and complement them with more detailed microscopic insight. Besides, we also plan to investigate which conditions encourage spontaneous cis-trans isomerization in a biologically relevant system for which also an extensive body of experimental information is available. We want to complement the experiment-based (structural) knowledge about the different amyloidogenicities of the trans isomers of beta-2 microglobulin and an antibody constant light domain with thermodynamic, kinetic and dynamic insight. One of the key questions to be answered here is whether the structural stabilization present in the latter due to short helical stretches but absent in the former is also reflected in different free energies of isomerization and barrier heights. The gained insight is expected to enhance our understanding of the environmental influence on and implications of proline cis-trans isomerization on an atomistic level. Ultimately, the knowledge may be used to deliberately control the isomerization which would open a plethora of opportunities concerning applications in medicine or protein engineering.

• DFG Programme: Research Grants