Constant pH Molecular Dynamics through λ-dynamics

Constant pH Molecular Dynamics through lambda-dynamics

von Eliane Briand
Kumulative Dissertation
Datum der mündl. Prüfung:2024-10-21
Erschienen:2025-02-26
Betreuer:Prof. Dr. Helmut Grubmüller
Gutachter:Prof. Dr. Ricardo Mata
Gutachter:Prof. Dr. Marina Bennati
Zum Verlinken/Zitieren: http://dx.doi.org/10.53846/goediss-11108

 

 

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Zusammenfassung

Englisch

This thesis presents a novel implementation of constant pH molecular dynamics simulations using λ-dynamics with Hamiltonian interpolation, enabled by an efficient Fast Multipole Method electrostatic solver. The accuracy of the method was validated against NMR titration data for protein test systems (cardiotoxin V, lysozyme, staphylococcal nuclease ∆PHS). New analysis tools were developed to systematically study protonation-conformation and residue-residue couplings, and applied to the test systems, revealing known as well as new protonation couplings in those proteins. The issue of convergence for residues subject to coupling is raised for constant pH simulations in general.
Keywords: biophysics; simulation; molecular dynamics; protonation; acid base; protein; constant ph; free energy
 
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