scholarly journals Hydrodynamic trapping measures the interaction between membrane-associated molecules

2018 ◽  
Author(s):  
Victoria Junghans ◽  
Jana Hladilkova ◽  
Ana Mafalda Santos ◽  
Mikael Lund ◽  
Simon J. Davis ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Interaction Potential ◽  
Liquid Flow ◽  
Lipid Membrane ◽  
Immune Cell ◽  
General Applicability ◽  
Protein Properties ◽  
Protein Distance ◽  
Protein Shape ◽  
Hydrodynamic Trapping

AbstractHow membrane proteins distribute and behave on the surface of cells is determined by the molecules’ interaction potential. However, measuring this potential, and how it varies with protein-to-protein distance, has been challenging. We here present how a method we call hydrodynamic trapping can achieve this. Our method uses the focused liquid flow from a micropipette to locally accumulate molecules protruding from a lipid membrane. The interaction potential, as well as information about the dimensions of the studied molecule, are obtained by relating the degree of accumulation to the strength of the trap. We have used this to study four representative proteins, with different height-to-width ratios and protein properties; from the globular streptavidin, to the rod-like immune cell proteins CD2, CD4 and CD45. The obtained data illustrates how protein shape, glycosylation and flexibility influence the behaviour of membrane proteins as well as underline the general applicability of the method.

scholarly journals Membrane Protein Stabilization Strategies for Structural and Functional Studies

Membranes ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 155
Author(s):  
Ekaitz Errasti-Murugarren ◽  
Paola Bartoccioni ◽  
Manuel Palacín
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Lipid Membrane ◽  
Protein Stabilization ◽  
New Drugs ◽  
Cell Physiology ◽  
Protein Preparation ◽  
Functional Studies ◽  
Membrane Protein Stability ◽  
Druggable Targets

Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.

scholarly journals Basic Residue Clusters in Intrinsically Disordered Regions of Peripheral Membrane Proteins: Modulating 2D Diffusion on Cell Membranes

Physchem ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 152-162
Author(s):  
Miquel Pons
Keyword(s):  
Membrane Proteins ◽  
Electrostatic Interactions ◽  
Lipid Membrane ◽  
Conformational Ensemble ◽  
Basic Residue ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Peripheral Membrane Proteins ◽  
Charged Residues ◽  
Disordered Regions

A large number of peripheral membrane proteins transiently interact with lipids through a combination of weak interactions. Among them, electrostatic interactions of clusters of positively charged amino acid residues with negatively charged lipids play an important role. Clusters of charged residues are often found in intrinsically disordered protein regions, which are highly abundant in the vicinity of the membrane forming what has been called the disordered boundary of the cell. Beyond contributing to the stability of the lipid-bound state, the pattern of charged residues may encode specific interactions or properties that form the basis of cell signaling. The element of this code may include, among others, the recognition, clustering, and selective release of phosphatidyl inositides, lipid-mediated protein-protein interactions changing the residence time of the peripheral membrane proteins or driving their approximation to integral membrane proteins. Boundary effects include reduction of dimensionality, protein reorientation, biassing of the conformational ensemble of disordered regions or enhanced 2D diffusion in the peri-membrane region enabled by the fuzzy character of the electrostatic interactions with an extended lipid membrane.

Solid state NMR of membrane proteins: methods and applications

2021 ◽  
Author(s):  
Vivien Yeh ◽  
Boyan B. Bonev
Keyword(s):  
Solid State ◽  
High Resolution ◽  
Membrane Proteins ◽  
Solid State Nmr ◽  
Lipid Membrane ◽  
Cell Function ◽  
Membrane Lipid ◽  
Pharmacological Intervention ◽  
Nmr Methods ◽  
Informative Approach

Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.

Crystallizationin cubo: general applicability to membrane proteins

2000 ◽  
Vol 56 (6) ◽  
pp. 781-784 ◽  
Author(s):  
Mark L. Chiu ◽  
Peter Nollert ◽  
Michèle C. Loewen ◽  
Hassan Belrhali ◽  
Eva Pebay-Peyroula ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
General Applicability

scholarly journals Methods for the solubilisation of membrane proteins: the micelle-aneous world of membrane protein solubilisation

2021 ◽  
Author(s):  
Giedre Ratkeviciute ◽  
Benjamin F. Cooper ◽  
Timothy J. Knowles
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Stability ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Modus Operandi ◽  
Membrane Mimetic ◽  
Aqueous Environments ◽  
Recent Developments

The solubilisation of membrane proteins (MPs) necessitates the overlap of two contradictory events; the extraction of MPs from their native lipid membranes and their subsequent stabilisation in aqueous environments. Whilst the current myriad of membrane mimetic systems provide a range of modus operandi, there are no golden rules for selecting the optimal pipeline for solubilisation of a specific MP hence a miscellaneous approach must be employed balancing both solubilisation efficiency and protein stability. In recent years, numerous diverse lipid membrane mimetic systems have been developed, expanding the pool of available solubilisation strategies. This review provides an overview of recent developments in the membrane mimetic field, with particular emphasis placed upon detergents, polymer-based nanodiscs and amphipols, highlighting the latest reagents to enter the toolbox of MP research.

Interfacial Behaviors of Transmembrane Peptides in Lipid Bilayer Studied by X-Ray and Neutron Reflectivity

2020 ◽  
Vol 977 ◽  
pp. 184-189
Author(s):  
Dong Jin Choi ◽  
Zeeshan Ur Rehman
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Lipid Membrane ◽  
Membrane Lipids ◽  
Solid Substrate ◽  
Neutron Reflectivity ◽  
Transmembrane Peptides ◽  
X Ray ◽  
Neutron Reflection ◽  
Membrane Spanning

Lipids and proteins can influence each other in so many different ways. Lipids may affect the structure of membrane proteins by influencing their backbone conformation, the tilt, rotation angles of their transmembrane (TM) segments, and the orientation of their side chains. The membrane-spanning parts in integral membrane proteins are predominantly hydrophobic, and most often helical. At the lipid-protein interface, the TM part of the protein and the hydrocarbon chains of the lipid molecules have to coexist to maintain the integrity of the membrane. Lipids are important components of lipid membrane are used in various experiments reported in this thesis and can act as model lipid bilayers. Once they support on solid substrate like silicon wafers, their structural properties can investigate by X-ray and neutron reflectivity and by other useful techniques. Reflectivity technique can provide detailed information such as their thickness and interaction between lipids and peptides. The thesis reports a detailed investigation of these lipids and peptides by X-ray and neutron reflection techniques

scholarly journals The Role of Phosphatidylethanolamine Adducts in Modification of the Activity of Membrane Proteins under Oxidative Stress

Molecules ◽  
2019 ◽  
Vol 24 (24) ◽  
pp. 4545 ◽  
Author(s):  
Elena E. Pohl ◽  
Olga Jovanovic
Keyword(s):  
Oxidative Stress ◽  
Membrane Proteins ◽  
Protein Function ◽  
Lipid Membrane ◽  
Membrane Lipids ◽  
Short Review ◽  
Membrane Properties ◽  
Complex Nature ◽  
Reactive Aldehydes

Reactive oxygen species (ROS) and their derivatives, reactive aldehydes (RAs), have been implicated in the pathogenesis of many diseases, including metabolic, cardiovascular, and inflammatory disease. Understanding how RAs can modify the function of membrane proteins is critical for the design of therapeutic approaches in the above-mentioned pathologies. Over the last few decades, direct interactions of RA with proteins have been extensively studied. Yet, few studies have been performed on the modifications of membrane lipids arising from the interaction of RAs with the lipid amino group that leads to the formation of adducts. It is even less well understood how various multiple adducts affect the properties of the lipid membrane and those of embedded membrane proteins. In this short review, we discuss a crucial role of phosphatidylethanolamine (PE) and PE-derived adducts as mediators of RA effects on membrane proteins. We propose potential PE-mediated mechanisms that explain the modulation of membrane properties and the functions of membrane transporters, channels, receptors, and enzymes. We aim to highlight this new area of research and to encourage a more nuanced investigation of the complex nature of the new lipid-mediated mechanism in the modification of membrane protein function under oxidative stress.

scholarly journals The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 580
Author(s):  
Irena Roterman ◽  
Katarzyna Stapor ◽  
Piotr Fabian ◽  
Leszek Konieczny
Keyword(s):  
Membrane Proteins ◽  
Lipid Membrane ◽  
Hydrophobic Interactions ◽  
Transmembrane Proteins ◽  
Soluble Proteins ◽  
Aqueous Environment ◽  
Hydrophobic Core ◽  
Hydrophobic Residues ◽  
Beta Barrel ◽  
Gauss Function

β-barrel membrane proteins have several important biological functions, including transporting water and solutes across the membrane. They are active in the highly hydrophobic environment of the lipid membrane, as opposed to soluble proteins, which function in a more polar, aqueous environment. Globular soluble proteins typically have a hydrophobic core and a polar surface that interacts favorably with water. In the fuzzy oil drop (FOD) model, this distribution is represented by the 3D Gauss function (3DG). In contrast, membrane proteins expose hydrophobic residues on the surface, and, in the case of ion channels, the polar residues face inwards towards a central pore. The distribution of hydrophobic residues in membrane proteins can be characterized by means of 1–3DG, a complementary 3D Gauss function. Such an analysis was carried out on the transmembrane proteins of bacteria, which, despite the considerable similarities of their super-secondary structure (β-barrel), have highly differentiated properties in terms of stabilization based on hydrophobic interactions. The biological activity and substrate specificity of these proteins are determined by the distribution of the polar and nonpolar amino acids. The present analysis allowed us to compare the ways in which the different proteins interact with antibiotics and helped us understand their relative importance in the development of the resistance mechanism. We showed that beta barrel membrane proteins with a hydrophobic core interact less strongly with the molecules they transport.

Engineering ancestral protein hyperstability

2016 ◽  
Vol 473 (20) ◽  
pp. 3611-3620 ◽  
Author(s):  
M. Luisa Romero-Romero ◽  
Valeria A. Risso ◽  
Sergio Martinez-Rodriguez ◽  
Beatriz Ibarra-Molero ◽  
Jose M. Sanchez-Ruiz
Keyword(s):  
Common Ancestor ◽  
A Priori ◽  
Experimental Comparison ◽  
Last Common Ancestor ◽  
Ancestral Reconstruction ◽  
Denaturation Temperature ◽  
General Applicability ◽  
Reconstruction Process ◽  
Ancestral Sequences ◽  
Protein Properties

Many experimental analyses and proposed scenarios support that ancient life was thermophilic. In congruence with this hypothesis, proteins encoded by reconstructed sequences corresponding to ancient phylogenetic nodes often display very high stability. Here, we show that such ‘reconstructed ancestral hyperstability’ can be further engineered on the basis of a straightforward approach that uses exclusively information afforded by the ancestral reconstruction process itself. Since evolution does not imply continuous progression, screening of the mutations between two evolutionarily related resurrected ancestral proteins may identify mutations that further stabilize the most stable one. To explore this approach, we have used a resurrected thioredoxin corresponding to the last common ancestor of the cyanobacterial, Deinococcus and Thermus groups (LPBCA thioredoxin), which has a denaturation temperature of ∼123°C. This high value is within the top 0.1% of the denaturation temperatures in the ProTherm database and, therefore, achieving further stabilization appears a priori as a challenging task. Nevertheless, experimental comparison with a resurrected thioredoxin corresponding to the last common ancestor of bacteria (denaturation temperature of ∼115°C) immediately identifies three mutations that increase the denaturation temperature of LPBCA thioredoxin to ∼128°C. Comparison between evolutionarily related resurrected ancestral proteins thus emerges as a simple approach to expand the capability of ancestral reconstruction to search sequence space for extreme protein properties of biotechnological interest. The fact that ancestral sequences for many phylogenetic nodes can be derived from a single alignment of modern sequences should contribute to the general applicability of this approach.

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