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Computational Characterization of Structural Dynamics and Interactions Underlying the Function of Transmembrane Domains of Integral Membrane Proteins

Principal Investigators: Christina Scharnagl (Technical University of Munich/TUM, Department of Physics E.14) and Dieter Langosch (TUM, Chair Chemistry of Biopolymers and Center for Integrated Protein Science)
HPC Platform: SuperMUC of LRZ

Introduction

Integral membrane proteins facilitate communication between the inside of the cell and its exterior. Their transmembrane domains (TMDs) perform structural and functional tasks, i.e. they drive protein/protein interactions, exhibit sequence-specific conformational dynamics on multiple size and time scales, and couple tightly to the hydrated lipid bilayer. These properties are interconnected and support a diversity of biological functions. Membrane proteins are notoriously difficult to study by experimental methods. In silico techniques like molecular dynamics (MD) simulations provide powerful tools of high spatial and temporal resolution that can effectively complement experimental methods. However, this level of detail is connected to a high demand on computational resources, only offered by high performance clusters like SuperMUC.

Results

The scientists of the Technical University of Munich (TUM) applied MD simulations to study the conformational dynamics of various TMDs in lipid bilayers and a membrane mimetic solvent. Central questions and results are summarized in Fig. 1.

Computational Characterization of Structural Dynamics and Interactions Underlying the Function of Transmembrane Domains of Integral Membrane Proteins

Fig. 1: Dynamics and interactions of single-span transmembrane domains. (A) Large-amplitude backbone motions of the TMD of wild type (WT) amyloid precursor protein (APP) and its T43I mutant, which is linked to heritable Alzheimer’s disease. The removal of a stabilizing side-chain to main-chain hydrogen bond increases helix bending around a central di-glycine hinge. (B) Bilayer restructuring around the charged N-terminus of a de novo designed highly flexible model TMD. Areas in red (blue) colour indicate increased (reduced) lipid density as compared to bulk. Shown are also snapshots of TMD-lipid arrangements from the first (a) and second shell (b). (C) Water (van der Waals spheres) linking the transmembrane helices of quiescin sulfhydryl oxidase II via hydrogen bonding to serine residues. Copyright: TUM (Germany)

In project A the researchers focus on the conformational dynamics of the TMD of the amyloid precursor protein (APP). APP is enzymatically cleaved within its TMD by γ-secretase (GSEC), forming toxic peptides regarded as molecular cause of Alzheimer's disease (AD). Finding the link between the molecular architecture of the APP TMD and cleavage is therefore of utmost importance. It seems plausible that the TMD itself is optimized for unfolding of the scissile bond. However, this expectation was challenged by experiments and MD simulations [2-4]. The achieved results suggest an entirely new model of intramembrane proteolysis [5] where reaching a cleavage-competent state requires searching a complex energy landscape by the substrate/enzyme complex (Fig. 2).

This view initiated formulation of a number of computational and experimental approaches in a collaborative research program (DFG grant FOR2290, https://www.i-proteolysis.de/). Here, the TMD dynamics of ~100 known substrates of GSEC as well as non-substrates (Gauss Collaboration project pr48ko) are compared. Knowing the key dynamical motifs for processing will help to identify new substrates and to elucidate the physiological functions of these proteases in the brain and other organs.

Computational Characterization of Structural Dynamics and Interactions Underlying the Function of Transmembrane Domains of Integral Membrane Proteins

Fig. 2: Steps determining the kinetics of substrate processing by γ-secretase. The intramembrane protease (green) is a protein complex located in the cellular membrane. Substrate TMD (red) dynamics might be involved in recognition, binding and reorganization steps funneling the enzyme/substrate complex toward the conformation conducive for cleavage. The two catalytic aspartate residues (arrows) are located in the presenilin subunit (green circles, numbers refer to the arrangement of the presenilin helices according to pdb 5FN3). MD simulations [4] revealed that extent and direction of the bending motions of the APP substrate TMD around a central di-glycine hinge are modified in mutants connected with familial Alzheimer's disease (as exemplified in Fig. 1). A model is proposed where these large-scale global modes affect exposure of the site of initial cleavage (purple spheres) and thus might determine processivity [5]. Copyright: TUM (Germany)

Project B investigated TMDs de novo designed to exhibit different conformational dynamics. The researchers want to clarify how dynamics and peptide/lipid interactions affect functional properties of the helices, such as their ability to fuse lipid membranes and to flip lipid molecules. While a detailed analysis is still ongoing, preliminary results indicate that (i) the membrane constrains helix dynamics, (ii) lipids preferentially contact peptides via electrostatic interactions of their head groups (Fig. 1 B), and (iii) peptide/lipid interaction is a two-way-process (unpublished results). The work is supported by a DFG research grant (Mechanisms of Membrane Fusion and Lipid Flip).

In project C, the TMD-TMD interaction of human quiescin sulfhydryl oxidase II, a membrane protein that aids folding of other proteins, was investigated. Atomistic simulations in a bilayer system mimicking a cellular membrane revealed how the membrane can regulate interactions between membrane helices (Fig. 1C) by providing interfacial water and/or by binding of lipid molecules to the helices [6].

Concluding Remarks

Sufficient exploration of the conformational space of protein and lipids poses a challenge in all projects. Hence, the researchers ran multiple independent copies of the simulation systems in parallel to cover aggregate times of 10-50 microseconds. This technique benefited greatly from SuperMUC's architecture and the Redisexec framework developed by the LRZ.

References:

[1] http://cbp.wzw.tum.de/index.php, http://users.physik.tu-muenchen.de/scharnagl/

[2] Pester, O., Barret, P., Hornburg, D., Hornburg, P., Pröbstle, R., Widmaier, S., Kutzner, C., Dürrbaum, M., Kapurniotu, A., Sanders, C. R., Scharnagl, C. & Langosch, D. (2013). The Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix Provides a Rationale for the Sequential Cleavage Mechanism of γ-Secretase. J. Am. Chem. Soc. 135, 1317-1329.

[3] Pester, O., Götz, A., Multhaup, G., Scharnagl, C. & Langosch, D. (2013). The Cleavage Domain of the Amyloid Precursor Protein Transmembrane Helix does not Exhibit Above-Average Backbone Dynamics. ChemBioChem 14, 1943-1948.

[4] Scharnagl, C., Pester, O., Hornburg, P., Hornburg, D., Götz, A. & Langosch, D. (2014). Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix. Biophys. J. 106, 1318-1326.

[5] Langosch, D., Scharnagl, C., Steiner, H. & Lemberg, M. K. (2015). Understanding Intramembrane Proteolysis: From Protein Dynamics to Reaction Kinetics. Trends Biochem Sci 40, 318-327.

[6] Ried, C., Scharnagl, C. & Langosch, D. (2016). Entrapment of Water at the Transmembrane Helix–Helix Interface of Quiescin Sulfhydryl Oxidase 2. Biochemistry 55, 1287–1290

Project Team:

Christina Scharnagl1*, Alexander Götz1, Dieter Langosch2*

1 Technical University Munich, Department of Physics E.14
2 Technical University Munich, Chair Chemistry of Biopolymers and Center for Integrated Protein Science (Munich)

* Principal Investigators

Scientific Contact:

Dr. Christina Scharnagl
Technische Universität München
Fakultät für Physik
Physik-Lehre Weihenstephan
Maximus-von-Imhof-Forum 4, Raum P051
D-85350 Freising (Germany)
e-mail: christina.scharnagl [at] tum.de

January 2017

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