Modeling structural transitions from the periplasmic-open state of lactose permease and interpretations of spin label experiments

Reconciling membrane protein simulations with experimental DEER spectroscopy data

Spectroscopy experiments are crucial to study membrane proteins for which traditional structure determination methods still prove challenging. Double electron-electron resonance (DEER) spectroscopy experiments provide protein residue-pair distance distributions that are indicative of their conformational heterogeneity. Atomistic molecular dynamics (MD) simulations are another tool that have been proven to be vital to study the structural dynamics of membrane proteins such as to identify inward-open, occluded, and outward-open conformations of transporter membrane proteins, among other partially open or closed states of the protein. Yet, studies have reported that there is no direct consensus between the distributional data from DEER experiments and MD simulations, which has challenged validation of structures obtained from long-timescale simulations and using simulations to design experiments. Current coping strategies for comparisons rely on heuristics, such as mapping the nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to the choice of membranes around the protein and covalent modification of a pair of residues to nitroxide spin labels in DEER experiments. Through comparing MD simulations of two proteins, PepT_So and LeuT-both of which have been characterized using DEER experiments previously-we show that the proteins' dynamics are similar despite the choice of the detergent micelle as a membrane mimetic in DEER experiments. On the other hand, covalently modified residues show slight local differences in their dynamics and a huge divergence when the oxygen atom pair distances between spin labeled residues are measured rather than protein backbone distances. Given the computational expense associated with pairwise MTSSL labeled MD simulations, we examine the use of biased simulations to explore the conformational dynamics of the spin labels only to reveal that such simulations alter the underlying protein dynamics. Our study identifies the main cause for the mismatch between DEER experiments and MD simulations and will accelerate the development of potential mitigation strategies to improve the match.

Phylogenetic and conservation analyses of MFS transporters

Major facilitator superfamily is one of the largest superfamily of secondary transporters present across the kingdom of life. Considering the physiological and clinical importance of MFS proteins, we attempted to explore the phylogenetic and structural aspects of the superfamily. To achieve the objectives, we performed global sequence-based analyses of MFS proteins encompassing multiple taxa. Notably, phylogenetic analysis of MFS proteins resulted in the clustering of MFS proteins based on their function, rather than lineage of the respective organisms. Additionally, we employed information theoretic measures, Relative entropy (RE) and Cumulative relative entropy (CRE) to decipher fold-specific and function-specific residues, respectively, in the MFS proteins. The residues with high RE score when mapped on to the 3D-structure of MFS transporter LacY, were found to be distributed throughout the tertiary structure of the protein. On the other hand, CRE calculation was employed to contrast two subfamilies Drug H⁺ antiporter 1 and 3 (DHA1 and DHA3). The particular analysis unveiled certain differentially conserved residues in DHA1 as compared to DHA3 highlighting family-specific importance of them. Remarkably, a number of high scoring CRE residues have already established functional roles, for instance, the arginine residue present in TMH4. Altogether, the current study apart from providing an insight into the functional clustering of MFS proteins also identifies residues with established or plausible roles in the transport mechanism. Thus, the study lays a platform for future structure-function studies of these proteins.

Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H⁺ symport process. Lactose/H⁺ symport is a highly complex process that involves sugar translocation, H⁺ transfer, and large-scale protein conformational changes. The complete picture of lactose/H⁺ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition.

Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes

The all-atom CHARMM36 lipid force field (C36FF) has been tested with saturated, monounsaturated, and polyunsaturated lipids; however, it has not been validated against the 18:2 linoleoyl lipids with an unsaturated sn-1 chain. The linoleoyl lipids are common in plants and the main component of the soybean membrane. The lipid composition of soybean plasma membranes has been thoroughly characterized with experimental studies. However, there is comparatively less work done with computational modeling. Our molecular dynamics (MD) simulation results show that the pure linoleoyl lipids, 1-stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine (18:0/18:2) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (di-18:2), agree very well with the experiments, which demonstrates the accuracy of the C36FF for the computational study of soybean membranes. Based on the experimental composition, the soybean hypocotyl and root plasma membrane models are developed with each containing seven or eight types of linoleoyl phospholipids and two types of sterols (sitosterol and stigmasterol). MD simulations are performed to characterize soybean membranes, and the hydrogen bonds and clustering results demonstrate that the lipids prefer to interact with the lipids of the same/similar tail unsaturation. All the results suggest that these two soybean membrane models can be used as a basis for further research in soybean and higher plant membranes involving membrane-associated proteins.

An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations

Previous MD simulations of six phosphocholine (PC) lipid bilayers demonstrated the accuracy of the CHARMM36 force field (C36FF) for PC bilayer simulation at varied temperatures (BBA-Biomembranes, 1838 (2014): 2520-2529). In this work, we further examine the accuracy of C36FF over a wide temperature range for a broader range of lipid types such as various head groups (phosphatidic acid (PA), PC, phosphoethanolamine (PE), phosphoglycerol (PG), and phosphoserine (PS)), and tails (saturated, mono-, mixed- and poly-unsaturated acyl chains with varied chain lengths). The structural properties (surface area per lipid (SA/lip), overall bilayer thickness, hydrophobic thickness, headgroup-to-headgroup thickness, deuterium order parameter (S_CD), and spin-lattice relaxation time (T₁)) obtained from simulations agree well with nearly all available experimental data. Our analyses indicate that PS lipids have the most inter-lipid hydrogen bonds, while PG lipids have the most intra-lipid hydrogen bonds, which play the main role in their low SA/lip in PS lipids and low thicknesses in PG lipids, respectively. PS, PE, and PA lipids have the largest contact clusters with on average 5-8 lipids per cluster, while PC and PG have clusters of 4 lipids based on a cutoff distance of 6.5Å. PS lipids have much slower lipid wobble (i.e., higher correlation time) than other head groups at a given temperature as the hydrogen bonded network significantly reduces a lipid's mobility, and the rate of lipid wobble increases dramatically as temperature increases. These in-depth analyses facilitate further understanding of lipid bilayers at the atomic level.