Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors

Assessing Protein-Protein Docking Protocols: Case Studies of G-Protein-Coupled Receptor Interactions

The interactions of G-protein-coupled receptors (GPCRs) with other proteins are critical in several cellular processes but resolving their structural dynamics remains challenging. An increasing number of GPCR complexes have been experimentally resolved but others including receptor variants are yet to be characterized, necessitating computational predictions of their interactions. Although integrative approaches with multi-scale simulations would provide rigorous estimates of their conformational dynamics, protein-protein docking remains a first tool of choice of many researchers due to the availability of open-source programs and easy to use web servers with reasonable predictive power. Protein-protein docking algorithms have limited ability to consider protein flexibility, environment effects, and entropy contributions and are usually a first step towards more integrative approaches. The two critical steps of docking: the sampling and scoring algorithms have improved considerably and their performance has been validated against experimental data. In this chapter, we provide an overview and generalized protocol of a few docking protocols using GPCRs as test cases. In particular, we demonstrate the interactions of GPCRs with extracellular protein ligands and an intracellular protein effectors (G-protein) predicted from docking approaches and test their limitations. The current chapter will help researchers critically assess docking protocols and predict experimentally testable structures of GPCR complexes.

Identification of key miRNAs regulating fat metabolism based on RNA-seq from fat-tailed sheep and F2 of wild Argali

The evolution mechanism of sheep tail fat has not yet been clear, many researches focus on this issue, yet there still many gaps to be filled in the targets and non-coding RNA regulation. In our study, the differential expression mRNAs and miRNAs were detected by RNA-seq and constructed a mRNA-miRNA network related to the lipid deposition in tail of fat-tailed sheep and F2 of Argali with domestic sheep (thin-tailed). Then 6 kinds of tissues from thin-tailed and control group were extracted for function validation of candidate genes and its regulator miRNAs. 125 differentially expressed miRNAs were identified by RNA-seq, and enrichment analysis of their target genes revealed 10 significantly enriched pathways related to lipid metabolism. In these pathways, 126 DE-miRNA target genes were also differentially expression in the same tissues in our previous transcriptomic data. In PPI network, 6 hubgenes (SCD, ACACA, GPD2, ELOVL6, ELOVL5, GPAM) were extracted using the cytoHubba application, and they may be target genes for 3 candidate DE-miRNAs (miR-320d, miR-151b, miR-6715). The validation results of RT-qPCR show: the expression trend of miR-320d is opposite to the target gene SCD, and that of miR-151b and the target gene ACACA are also opposite in 6 tissues, implying that they may have direct targeting relationships. Moreover, the expression of miR-320d in F2 tail fat was significantly higher than that in fat-tailed sheep (P < 0.05), and the expression of SCD in F2 tail fat was extremely significantly lower than that in fat-tailed sheep (P < 0.01). The expression of miR-151b in F2 tail fat and subcutaneous fat was significantly higher than that in fat-tailed sheep (P < 0.05), and the expression of ACACA in F2 subcutaneous fat was significantly lower than that in fat-tailed sheep. miR-320d may directly and negatively regulate tail fat deposition by targeting SCD, while miR-151b may indirectly and negatively regulate tail fat deposition by targeting ACACA.

Comparison of one-phase and two-phase extraction methods for porcine tissue lipidomics applying a fast and reliable tentative annotation workflow

Lipidomics has great potential for the discovery of biomarkers, elucidation of metabolic processes and identifying dysregulations in complex biological systems. Concerning biofluids like plasma or cerebrospinal fluid, several studies for the comparison of lipid extraction solvents have already been conducted. With respect to tissues, which can differ significantly in terms of dry matter content and composition, only few studies are available. The proper selection of an extraction method that covers the complexity and individuality of different tissues is challenging. The goal of this work was to provide a systematic overview on the potential of different extraction methods for a broad applicability. This study covers six different extraction procedures and four different reconstitution solvents applied to ten different porcine tissues. To get an overview of the individual lipid profiles, a workflow was developed for a fast and reliable tentative lipid annotation. Therefore, several machine learning tools were utilized, like the prediction of collision cross sections to support the tentative lipid identification in case of untargeted lipidomics. In terms of data evaluation, unsupervised (e.g. principal component analysis) and supervised (e.g. partial least square - discriminant analysis) methods were applied to visualize and subsequently interpret all generated information. Furthermore, the influence of the tissue composition on the extraction performance was investigated. It could be shown that the ten porcine tissues can be distinguished based on their lipid profile with the applied workflow and that the methyl-tert-butyl ether (MTBE) based extraction method (two-phase) showed the best overall performance for the 16 examined lipid species. With this method the highest number of features (428 in lung tissue) could be annotated. Upcoming one-phase extractions also showed a high potential concerning total number of extracted lipids. Methanol/MTBE/chloroform (MMC) extracted slightly less lipids (393 in lung and liver) than MTBE but turned out to be the best one-phase extraction method. Additionally, the numbers of extracted lipids obtained by isopropanol/water 90:10 (IPA90) (399 in stomach) and by isopropanol/methanol/chloroform (IMC) (395 in stomach) were similar to those of the modified Folch method (402 in stomach). One-phase extractions can therefore clearly be seen as preferable when a high throughput is needed.

Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs

ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features.

FRET detects lateral interaction between transmembrane domain of EGF receptor and ganglioside GM3 in lipid bilayers

Ganglioside GM3 in the plasma membranes suppresses cell growth by preventing the autophosphorylation of the epidermal growth factor receptor (EGFR). Biological studies have suggested that GM3 interacts with the transmembrane segment of EGFR. Further biophysical experiments are particularly important for quantitative evaluation of the peptide-glycolipid interplay in bilayer membranes using a simple reconstituted system. To examine these interactions in this way, we synthesized the transmembrane segment of EGFR bearing a nitrobenzoxadiazole fluorophore (NBD-TM) at the N-terminus. The affinity between EGFR and GM3 was evaluated based on Förster resonance energy transfer (FRET) between NBD-TM and ATTO594-labeled GM3 in bilayers where their non-specific interaction due to lateral proximity was subtracted by using NBD-labeled phospholipid. This method for selectively detecting the specific lipid-peptide interactions in model lipid bilayers disclosed that the lateral interaction between GM3 and the transmembrane segment of EGFR plays a certain role in disturbing the formation of active EGFR dimers.

Advances in understanding and in multi-disciplinary methodology used to assess lipid regulation of signalling cascades from the cancer cell plasma membrane

The lipid bilayer is a functional component of cells, forming a stable platform for the initiation of key biological processes, including cell signalling. There are distinct changes in the lipid composition of cell membranes during oncogenic transformation resulting in aberrant activation and inactivation of signalling transduction pathways. Studying the role of the cell membrane in cell signalling is challenging, since techniques are often limited to by timescale, resolution, sensitivity, and averaging. To overcome these limitations, combining 'computational', 'wet-lab' and 'semi-dry' approaches offers the best opportunity to resolving complex biological processes involved in membrane organisation. In this review, we highlight analytical tools that have been applied for the study of cell signalling initiation from the cancer cell membranes through computational microscopy, biological assays, and membrane biophysics. The cancer therapeutic potential of extracellular membrane-modulating agents, such as cholesterol-reducing agents is also discussed, as is the need for future collaborative inter-disciplinary research for studying the role of the cell membrane and its components in cancer therapy.

Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers

Altered lipid metabolism has been linked to cancer development and progression. Several roles have been attributed to the increased saturation and length of lipid acyl tails observed in tumors, but its effect on signaling receptors is still emerging. In this work, we have analyzed the lipid dependence of the ErbB2 growth factor receptor dimerization that plays an important role in the pathogenesis of breast cancer. We have performed coarse-grain ensemble molecular dynamics simulations to comprehensively sample the ErbB2 monomer-dimer association. Our results indicate a dynamic dimer state with a complex conformational landscape that is modulated with increasing lipid tail length. We resolve the native N-terminal "active" and C-terminal "inactive" conformations in all membrane compositions. However, the relative population of the N-terminal and C-terminal conformers is dependent on length of the saturated lipid tails. In short-tail membranes, additional non-specific dimers are observed which are reduced or absent in long-tailed bilayers. Our results indicate that the relative population as well as the structure of the dimer state is modulated by membrane composition. We have correlated these differences to local perturbations of the membrane around the receptor. Our work is an important step in characterizing ErbB dimers in healthy and diseased states and emphasize the importance of sampling lipid dynamics in understanding receptor association.

Resolving the conformational dynamics of ErbB growth factor receptor dimers

The combinatorial dimerization of the ErbB growth factor receptors (ErbB¹- ErbB⁴) are critical for their function. Here, we have characterized the conformational dynamics of ErbB transmembrane homo-dimers and hetero-dimers by using a coarse-grain simulation framework. All dimers, except ErbB^4-4 and ErbB^1-4, exhibit at least two conformations. The reported NMR structures correspond to one of these conformations, representing the N-terminal active state in ErbB^1-1 (RH2), ErbB^2-2 (RH1) and ErbB^4-4 (RH) homo-dimers and the LH dimer in ErbB^3-3 homo-dimer, validating the computational approach. Further, we predict a right-handed ErbB^3-3 dimer conformer that warrants experimental testing. The five hetero-dimers that have not yet been experimentally resolved display prominent right-handed dimers associating by the SmXXXSm motif. Our results provide insights into the constitutive signaling of ErbB⁴ after cleavage of the extracellular region. The presence of the inactive-like dimer conformers leading to symmetric kinase domains gives clues on the autoinhibition of the receptor dimers. The dimer states characterized here represent an important step towards understanding the combinatorial cross associations in the ErbB family.

Emerging Diversity in Lipid-Protein Interactions

Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid–protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid–protein interactions, and to link lipid–protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid–protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid–protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid–protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid–protein interactions.

Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations

The interaction between the secondary structure elements is the key process, determining the spatial structure and activity of a membrane protein. Transmembrane (TM) helix-helix interaction is known to be especially important for the function of so-called type I or bitopic membrane proteins. In the present work, we present the approach to study the helix-helix interaction in the TM domains of membrane proteins in various lipid environment using solution NMR spectroscopy and phospholipid bicelles. The technique is based on the ability of bicelles to form particles with the size, depending on the lipid/detergent ratio. To implement the approach, we report the experimental parameters of "ideal bicelle" models for four kinds of zwitterionic phospholipids, which can be also used in other structural studies. We show that size of bicelles and type of the rim-forming detergent do not affect substantially the spatial structure and stability of the model TM dimer. On the other hand, the effect of bilayer thickness on the free energy of the dimer is dramatic, while the structure of the protein is unchanged in various lipids with fatty chains having a length from 12 to 18 carbon atoms. The obtained data is analyzed using the computer simulations to find the physical origin of the observed effects.

Behavior of Most Widely Spread Lipids in Isotropic Bicelles

Isotropic bicelles are a widely used membrane mimetic for structural studies of membrane proteins and their transmembrane domains. Simple and cheap in preparation, they contain a patch of lipid bilayer that reproduces the native environment of membrane proteins. Despite the obvious power of bicelles in reproducing the various kinds of environments, the vast majority of structural studies employ the single lipid/detergent system. On the other hand, even if the alternative bicelle composition is used, the properties of mixtures are not characterized, and the mere presence of lipid bilayer and discoidal shape of bicelle particles is not confirmed. Here we present an extensive investigation of various bicellar mixtures and describe the behavior of bicelles with lipids other than classical DMPC, namely sphingomyelins (SM), phosphatidylethanolamines (PE), phosphatidylglycerols (PG), phosphatidylserines (PS), and cholesterol. These lipids are rarely used in modern structural biology, but can help a lot in understanding the influence of the membrane composition on the properties of both integral and peripheral membrane proteins. Additionally, the ability of diheptanoylphosphatidylcholine (DH7PC) to serve as a rim-forming agent was investigated. We followed the phase transitions as revealed by ³¹P NMR and size of particles measured by ¹H NMR diffusion as the criteria of the proper morphology and structure of bicelles. As an outcome, we state that SM exclusively, and PG/PS in mixtures with zwitterionic lipids can form small isotropic bicelles, which reproduce the key features of lipid behavior in bilayers. Mixtures, containing exclusively the anionic lipids, fail to reveal the lipid phase transition and do not follow the size predicted for the ideal bicelle particles. PE and DH7PC are the unwanted components of bicellar mixtures, and cholesterol can be added to bicelles, however, with certain precautions. In combination with our several most recent works, this study provides a practical guide for the preparation of small isotropic bicelles.