Impact of increased membrane realism on conformational sampling of proteins

Abstract

The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) is heavily dependent on the lipid composition. While the field is pushing towards implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein function or if it matters over long timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma with more than 10 different lipid species membrane is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or -independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ~1 kcal/mol. The free energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.

Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes

“…54 PMp represents membranes of mung bean hypocotyl 19 that have a more complex lipid mixture than previously modeled plant PMs containing up to 10 lipid types. 28,51 The lipid composition of PMf is similar to that of the previously modeled yeast PM, 48 although half of sterol molecules is substituted by an inositol-containing SL, mannosyl-inositol-phosphoryl-ceramide (MIPC) based on the work of Hechtberger et al 79 The lipid distribution in all three PM systems is asymmetric and similar to experimental data in that the majority of SLs are Journal of Chemical Information and Modeling pubs.acs.org/jcim Article in the outer leaflets, and 80% of PE, PA, PI, and almost all PS are in the cytosolic leaflet. 80 Importantly, these three PM systems significantly differ in the content and distribution of PC lipids, SLs, and sterols (Figure S2).…”

“…It has been demonstrated that using realistic membrane complexity is essential for reproducing the energetics of conformational transitions in membrane proteins. 28 During the last 35 years, molecular simulations of lipid membranes have substantially evolved from studies of singlecomponent bilayers 29 to modeling realistic cellular membranes with various lipid types. 30 The progress became rapid with the development of accurate force fields, programs to simulate membrane models, and tools to preassemble lipids in a bilayer.…”

“…36 This required developments of tools for easy building of membranes with complex lipid compositions 31,32 and improvements to computational approaches. 37 For example, all-atom MD simulations of membranes with nativelike lipid composition have been performed for the outer 38−41 and inner membranes of Gram-negative bacteria, 42−45 cell membrane of Gram-positive bacteria, 46 archaebacterial membranes, 47 PM and organelle membranes of yeast, 48−50 and PM of plants, 28,51 among others. These membrane systems usually included up to 600 lipids of 4−10 lipid types that were simulated on the nano-to microsecond (ns−μs) time scale.…”

Elevator-type Mechanism of the Cyanobacterial Bicarbonate Transporter

“…In addition to portraying a realistic molecular environment, the increased membrane complexity may also affect thermodynamics barriers across the conformational landscape. 35 To this end, we constructed a lipid membrane based on previously characterized compositions determined for cyanobacteria (Figure 2A). 47, 48 Notably, the cyanobacteria plasma membrane is comprised of mainly glycolipids.…”

“…25,26 Recent efforts in Markov state modeling have characterized the conformational heterogeneity of proteins of key interest to the plant biology community including phytohormone receptors, [27][28][29] and circadian clock photoreceptors. [30][31][32] Several membrane transporters have also been investigated using these methodologies including sugar transporters (SWEETs and SemiSWEETs), [33][34][35] bacterial nitrate transporters, 36 human neurotransmitter 26,37 and peptide transporters. 38 However, these transporters follow either the rocker-switch or rocking bundle mechanisms of alternate-access to facilitate the substrate transport.…”