Phase Transitions in Small Isotropic Bicelles

Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System

Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.

Investigation of lipid/protein interactions in trifluoroethanol-water mixtures proposes the strategy for the refolding of helical transmembrane domains

Membrane proteins are one of the keystone objects in molecular biology, but their structural studies often require an extensive search for an appropriate membrane-like environment and an efficient refolding protocol for a recombinant protein. Isotropic bicelles are a convenient membrane mimetic used in structural studies of membrane proteins. Helical membrane domains are often transferred into bicelles from trifluoroethanol-water mixtures. However, the protocols for such a refolding are empirical and the process itself is still not understood in detail. In search of the optimal refolding approaches for helical membrane proteins, we studied here how membrane proteins, lipids, and detergents interact with each other at various trifluoroethanol-water ratios. Using high-resolution NMR spectroscopy and dynamic light scattering, we determined the key states of the listed compounds in the trifluoroethanol/water mixture, found the factors that could be critical for the efficiency of refolding, and proposed several most optimal protocols. These protocols were developed on the transmembrane domain of neurotrophin receptor TrkA and tested on two model helical membrane domains-transmembrane of Toll-like receptor TLR9 and voltage-sensing domain of a potassium channel KvAP.

The architecture of transmembrane and cytoplasmic juxtamembrane regions of Toll-like receptors

Toll-like receptors (TLRs) are the important participants of the innate immune response. Their spatial organization is well studied for the ligand-binding domains, while a lot of questions remain unanswered for the membrane and cytoplasmic regions of the proteins. Here we use solution NMR spectroscopy and computer simulations to investigate the spatial structures of transmembrane and cytoplasmic juxtamembrane regions of TLR2, TLR3, TLR5, and TLR9. According to our data, all the proteins reveal the presence of a previously unreported structural element, the cytoplasmic hydrophobic juxtamembrane α-helix. As indicated by the functional tests in living cells and bioinformatic analysis, this helix is important for receptor activation and plays a role, more complicated than a linker, connecting the transmembrane and cytoplasmic parts of the proteins.

Mechanisms of membrane protein crystallization in 'bicelles'

Despite remarkable progress, mainly due to the development of LCP and ‘bicelle’ crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the “bicelle” crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of “bicelle” MP crystallization and will support rational design of crystallization.

Intrinsically disordered regions couple the ligand binding and kinase activation of Trk neurotrophin receptors

Receptor tyrosine kinases (RTKs) are key players in development and several diseases. Understanding the molecular mechanism of RTK activation by its ligand could lead to the design of new RTK inhibitors. How the extracellular domain is coupled to the intracellular kinase domain is a matter of debate. Ligand-induced dimerization and ligand-induced conformational change of pre-formed dimers are two of the most proposed models. Recently we proposed that TrkA, the RTK for nerve growth factor (NGF), is activated by rotation of the transmembrane domain (TMD) pre-formed dimers upon NGF binding. However, one of the unsolved issues is how the ligand binding is conformationally coupled to the TMD rotation if unstructured extracellular juxtamembrane (eJTM) regions separate them. Here we use nuclear magnetic resonance in bicelles and functional studies to demonstrate that eJTM regions from the Trk family are intrinsically disordered and couple the ligand-binding domains and TMDs possibly via the interaction with NGF.

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Extracellular juxtamembrane region is required for NGF binding and TrkA activation

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TrkA extracellular juxtamembrane region is unstructured and flexible

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This region couples neurotrophin-binding and transmembrane domain rotation

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The extracellular juxtamembrane region might play a role in neurotrophin recognition

Changes Experienced by Low-Concentration Lipid Bicelles as a Function of Temperature

Differential scanning calorimetry (DSC) of dipalmitoyl phosphatidylcholine (DPPC), dihexanoyl phosphatidylcholine, and dipalmitoyl phosphatidylglycerol bicelles reveals two endothermic peaks. Based on analysis of small angle neutron scattering and small angle X-ray scattering data, the two DSC peaks are associated with the melting of DPPC and a change in bicellar morphology─namely, either bicelle-to-spherical vesicle or oblate-to-spherical vesicle. The reversibility of the two structural transformations was examined by DSC and found to be consistent with the corresponding small angle scattering data. However, the peak that is not associated with the melting of DPPC does not correspond to any structural transformation for bicelles containing distearoyl phosphatidylethanolamine conjugated with polyethylene glycol. Based on complementary experimental data, we conclude that membrane flexibility, lipid miscibility, and differential solubility between the long- and short-chain lipids in water are important parameters controlling the reversibility of morphologies experienced by the bicelles.

Expression, purification and characterization of SORCS2 intracellular domain for structural studies

Neurotrophin signaling pathways are one of the major cascades in neuronal development and involved in many key processes including proliferation, differentiation, apoptosis, synaptic plasticity, axonal growth. In addition to the main classes of neurotrophin receptors, Trk and P75NTR, there are many auxiliary proteins, which can also bind neurotrophins and regulate the signaling pathways. The versatility of interactions between them could explain multiple and completely opposite biological outcomes such as cell survival or apoptosis. Membrane protein SorCS2, a vacuolar protein sorting 10 protein-domain receptor, interacts with P75NTR and controls the activity of Trk receptors. The abnormal functioning of SorCS2 is associated with neurodegenerative diseases, such as Alzheimer's and Huntington's disease. But the mechanism of SorCS2 activation and basis of the interaction with P75NTR has remained elusive. Herein, we describe two efficient approaches for the intracellular domain of the SorCS2 production employing bacterial and cell-free expression systems, as well as purification and refolding protocols. Finally, we characterized the purified protein by DLS and NMR and demonstrated that the protein sample is suitable for structural studies.

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

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.

Low- q Bicelles Are Mixed Micelles

Bicelles are used in many membrane protein studies because they are thought to be more bilayer-like than micelles. We investigated the properties of "isotropic" bicelles by small-angle neutron scattering, small-angle X-ray scattering, fluorescence anisotropy, and molecular dynamics. All data suggest that bicelles with a q value below 1 deviate from the classic bicelle that contains lipids in the core and detergent in the rim. Thus not all isotropic bicelles are bilayer-like.

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.