Conformational ensembles and dynamics of amphipathic aggregates and proteins examined by synergy of NMR experiments and MD simulation

The structure-function paradigm, postulating that protein structures regulate their biological functions, is based on structural biology techniques that enable protein structure determination. However, a large fraction of biomolecular systems, such as disordered proteins, cellular membranes and other amphiphilic aggregates, are beyond the scope of these methodologies. This thesis demonstrates how these disordered biomolecular systems can be characterized using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations. Cellular membranes are amphiphilic aggregates composed of phospholipids that exist in vivo in the presence of high concentrations of ions, which are essential for maintaining homeostasis and facilitating various cellular functions and signalling. However, interactions of calcium and sodium ions with lipid membranes are known to be overestimated in classical non-polarizable MD simulations, presumably because electronic polarizability is not included in these models. This thesis presents the prosECCo75 parameters for MD simulations where electronic polarization is included in the CHARMM36 force field using Electronic Continuum Correction (ECC). These parameters predict sodium and calcium binding to membranes in good agreement with NMR experiments. Furthermore, investigations of interactions between charged small molecules and membranes reveal that their binding is not generally overestimated in canonical force fields, in contrast to sodium and calcium. Moreover, the introduction of electronic polarization increases the binding strength of these molecules, exhibiting behaviour qualitatively different from that of monoatomic ions. Micelles and lipid nanodiscs are amphiphilic aggregates composed of lipids or detergents mixed with proteins or peptides. They are used, for example, as drug carriers and membrane mimetics in structural biology studies. However, their dynamic properties are often poorly understood due to the lack of straightforward methods for characterizing such systems. This thesis demonstrates how NMR experiments and MD simulations can be used to characterize the dynamics of micelles and nanodiscs in detail. Sodium Dodecyl Sulfate (SDS) micelles containing peptides, and DMPC (dimyristoyl-phosphatidylcholine) nanodiscs stabilized by 22A peptides, are used as model systems. In micelles, individual detergent molecules move independently of the embedded peptides, whereas in lipid nanodiscs, all the molecules undergo collective rotational motion. Interpreting the molecular dynamics of disordered biomolecules, such as proteins, from NMR data is challenging. Various approaches exist, yet they often rely on restrictive assumptions and require large amounts of experimental data. In this thesis, a large MD simulation dataset is used to demonstrate a linear relationship between experimentally measurable spin relaxation rates, R2, and effective correlation times τ-eff, an intuitively understandable parameter that describes the rate of protein backbone rotational dynamics. This allows for the rapid interpretation of backbone dynamics directly from experimental data without additional models. Applying this method to partially disordered proteins suggests that disordered regions rotate independently of the folded domains.

Grantor dc:publisher

University of Helsinki

Year dc:date.issued

2025

Author dc:creator

• Nencini, Ricky

• biophysics

Statement dc:rights

• This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
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Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/10138/591979

OAI record oai:identifier

https://helda.helsinki.fi/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Ahelda.helsinki.fi%3A10138%2F591979