Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Abstract

Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.

Fig 1

Hypothetical model for full-length E. coli GlpG dimerization. A cartoon illustration is shown in rainbow coloring with N-terminus in blue. The membrane domain of E. coli GlpG is dimeric. In this model, the dimer interface occurs through interaction of loop 1 that extends partially in the lipid bilayer (light blue). The cytoplasmic domain is separated from the membrane domain by a flexible linker. The structure of the cytoplasmic domain is from Ref. (Lazareno-Saez et al., 2013).

Fig 2

(a) Fully atomistic KcsA ion channel system (protein as yellow ribbons, lipid tails as chains, water as sticks and K⁺ and Cl⁻ ions as red and grey balls, respectively). (b) Differing multi-ion barriers for K⁺ and Na⁺. The low barrier to K⁺ outward conduction results from the ability of a K⁺ ion (red) to bind to the entrance of the selectivity filter. (c) The shift of binding site for Na⁺ (green), eliminates this process and requires a substantial amount of energy. Based on (Nimigean & Allen, 2011).

Fig 3

The transmembrane Kv1.2 voltage-gated cation channel.

Fig 4

Thermodynamic cycle used to compute free energy differences for estimating the difference in the free energy of binding of a ligand to a protein (Cycle 1) or for the relative solvation free energy difference (Cycle 2).

Fig 5

Structures of M2TM inhibitors and their binding constants. On the left side, note the excellent correlation between the FEP/MD calculations with a flexible protein and the experimental data. The image is adapted from (Gkeka et al., 2013).

Fig 6

A view of the transmembrane domain of the nicotinic acetylcholine receptor from Torpedo marmorata, with proposed coordinates for embedded cholesterol molecules. Each subunit contains four membrane-spanning helices (M1 purple, M2 green, M3 blue, M4 cyan) and three bound cholesterol molecules (yellow, orange and red). The image is based on the crystal structure PDB ID: 2BG9 from Ref. (Unwin, 2005).

Fig 7

Spontaneous re-binding of cholesterol to an intersubunit cleft in the GABA_A receptor. Two frames from a simulated MD trajectory are shown (Hénin et al., 2014). TM helices M2 (right) and M3 (left) forming the back of the pocket are shown as white cartoon, and cholesterol as orange bonds. Other specific groups are depicted as bonds using the following color code: yellow – phospholipid, orange – membrane cholesterol, green – protein amino acid residues from the back receptor subunit, and cyan – protein groups from the front receptor subunit. Data from (Hénin et al., 2014).

Fig 8

Cartoon representation of an Aβ protofilment segment (4 two-peptide layers) interacting with a lipid membrane, lateral (left) and top (right) views. The N-terminus is represented in red, the turn region in green and the C-terminus in blue. The lipid heavy atoms are represented as spheres, the headgroups are colored in yellow and the lipid tails in grey, respectively. The image is based on Ref. (Tofoleanu & Buchete, 2012b).

Fig 9

Electroporation in the cell membrane of the Gram-positive bacterium, S. aureus. Deformation of the lipid bilayer is clearly visible. Phospholipids that have been pulled in closer to the membrane core are shown in green and red, water molecules are shown in blue and the remaining lipid molecules are shown in pink (Piggot, Piñeiro & Khalid, 2012).

Fig 10

The non-bonded, normalized force distributions for three different states of CAMA, ranging from jammed (wound) to marginally jammed to relatively un-jammed (free). All three exhibit jamming signatures, namely a pronounced peak about the exponential line (dashed), though this is shifted to higher values the more apparently unjammed the peptide. Additionally, the tails of those that are less jammed are closer to the exponential line. Conformational ensembles of CAMA P6 in (b) wound state (c) linear and (d) free state. (e) Translocation of peptide CAMA – P6 through lumen of α-hemolysin. Panels b–e are adapted from Ref. (Mereuta et al., 2014).

Fig 11

Predicted structures for Aβ_1–42 monomer (transmembrane and surface structures, left), dimer (middle) and octamer (right) in contact with an implicit membrane. The molecular graphics images are adapted from Ref. (Strodel et al., 2010).

Fig 12

Left: introduction of a cytochrome domain into an amyloid fibre can change the morphology from twisted to spiral ribbons and induce systematic kinking. Centre: rigid building blocks consisting of two ellipsoids can reproduce these structures. Right: the structure depends mostly on the internal geometry of the building blocks. The molecular graphics images are based on Ref. (Forman et al., 2013).

Fig 13

Direct volume rendering of the BSI molecule 2-(biphenyl-4-sulfonyl)-1,2,3,4-tetrahydro-isoquinoline-3-carboxylic acid based on 241.760 molecular configurations in 192 metastable sets, comprising 12 chemically different groups that are distinguished by color. On the left the spatial alignment is based on a fixed substructure, on the right on Procrustes analysis.

Fig 14

Illustration of the alignment problem by aligning 150 forms of Pentane by minimizing (a) the distances between the centers of gravity of each form, furthermore, the distances between corresponding atoms summed over (b) all atoms, (c) three selected atoms, and (d) atoms in a hierarchy of sets, defined by stiff substructures and an interactively selected anchor structure.

Fig 15

Geometric molecular paths (blue) in a nano-transporter, computed by the Voronoi diagram of the atom spheres and combined with a path-dependent illumination of the molecular surface. Based on Ref. (Lindow et al., 2011).

Fig 16

Cavity dynamics in a bacteriorhodopsin monomer. From left to right: the cavities traced at time step t = 63, a channel created by the dynamics from t = 50 till t = 64, and the overall spatial cavity probability (depicted with maximum intensity projection). The images are based on Refs. (Lindow et al., 2012a; Lindow et al., 2013)

Fig 17

Temporal development of cavities in a bacteriorhodopsin monomer (for the simulation and the time steps also used in Figure 16); upper diagram: topology graph showing splits and merges of cavities; lower diagram: penetration graph depicting the cavities’ location along a user-defined axis. The image is based on Refs. (Lindow et al., 2012a; Lindow et al., 2013)

Fig 18

Visualization of microtubules (reconstructed from electron tomography data) containing about 10 billion atoms; rendered on commodity PC with subsecond framerate. The image is based on ref. (Lindow et al., 2012b).