Self-assembling Peptide Detergent A6D Directly Associates with Bovine Rhodopsin and Forms Lipid-like Vesicles

2004 ◽  
Vol 845 ◽  
Author(s):  
Xiaojun Zhao ◽  
Yusuke Nagai ◽  
Shuguang Zhang
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Self Assembly ◽  
Protein Structures ◽  
Detergent Solution ◽  
Self Assembling ◽  
Bovine Rhodopsin ◽  
Hydrophobic Tail ◽  
New Type

ABSTRACTMembrane protein study critically depends on detergents, which are amphilhilic molecules containing a hydrophilic “head” and a hydrophobic “tail” to mimic biological lipid bilayers to stabilize membrane proteins. However, detergents are not fully equivalent to lipid bilayers and in fact they only partly mimic lipid bilayers function. Consequently, membrane proteins in detergent solution are more or less denatured because detergents can not effectively stabilize membrane protein structures. Therefore, it is urgent to develop new types of detergents for more effectively stabilizing membrane proteins. Previously, we have reported a new type of self-assembly peptide detergents containing a hydrophilic head composed of either a negatively charged aspartic acid or a positively charged lysine and a tail of hydrophobic amino acids of six connective alanines. This new peptide detergent has been shown to be more effective for protecting membrane protein PS I structure than that the conventional detergent does. However, what type of physical structures peptide detergent can form is unclear yet. Here we presented our AFM and DSL analysis of the peptide detergent A6D, which not only form mixed micelles with n-Octyl-beta-D-Glucoside (OG) to solubilize membrane protein rhodopsin, but also can mimic lipid bilayers to keep rhodopsin in lipid-like vesicles for its structure preservation.

Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins

2020 ◽  
Author(s):  
Jan Zaucha ◽  
Michael Heinzinger ◽  
A Kulandaisamy ◽  
Evans Kataka ◽  
Óscar Llorian Salvádor ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Protein Structures ◽  
Experimental Studies ◽  
Single Amino Acid ◽  
Evolutionary Information ◽  
Missense Variants ◽  
Current State ◽  
Aqueous Environments

Abstract Membrane proteins are unique in that they interact with lipid bilayers, making them indispensable for transporting molecules and relaying signals between and across cells. Due to the significance of the protein’s functions, mutations often have profound effects on the fitness of the host. This is apparent both from experimental studies, which implicated numerous missense variants in diseases, as well as from evolutionary signals that allow elucidating the physicochemical constraints that intermembrane and aqueous environments bring. In this review, we report on the current state of knowledge acquired on missense variants (referred to as to single amino acid variants) affecting membrane proteins as well as the insights that can be extrapolated from data already available. This includes an overview of the annotations for membrane protein variants that have been collated within databases dedicated to the topic, bioinformatics approaches that leverage evolutionary information in order to shed light on previously uncharacterized membrane protein structures or interaction interfaces, tools for predicting the effects of mutations tailored specifically towards the characteristics of membrane proteins as well as two clinically relevant case studies explaining the implications of mutated membrane proteins in cancer and cardiomyopathy.

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

scholarly journals Structures of membrane proteins

2010 ◽  
Vol 43 (1) ◽  
pp. 65-158 ◽  
Author(s):  
Kutti R. Vinothkumar ◽  
Richard Henderson
Keyword(s):  
Protein Structure ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Membrane Protein Structure ◽  
Expression Systems ◽  
Genome Sequences ◽  
Conformational Variability ◽  
Efficient Expression

AbstractIn reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class.

scholarly journals Evidence for Membrane Complex Assembly in Nanoelectrospray Generated Lipid Bilayers

2019 ◽  
Author(s):  
Matthias Wilm
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Layered Structure ◽  
Protein Complexes ◽  
Complex Assembly ◽  
Membrane Complex ◽  
Detergent Extraction ◽  
Membrane Protein Complexes

1.AbstractNanoelectrospray can be used to generate a layered structure consisting of bipolar lipids, detergent-solubilized membrane proteins, and glycerol that self-assembles upon detergent extraction into one extended layer of a protein containing membrane. This manuscript presents the first evidence that this method might allow membrane protein complexes to assemble in this process.

scholarly journals A model-free method for measuring dimerization free energies of CLC-ec1 in lipid bilayers

2018 ◽  
Vol 150 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Rahul Chadda ◽  
Lucy Cliff ◽  
Marley Brimberry ◽  
Janice L. Robertson
Keyword(s):  
Membrane Protein ◽  
Lipid Bilayers ◽  
Single Molecule ◽  
Equilibrium Constants ◽  
Correction Method ◽  
Equilibrium Studies ◽  
Model Free ◽  
Liposome Size ◽  
New Type ◽  
Protein Density

The thermodynamic reasons why membrane proteins form stable complexes inside the hydrophobic lipid bilayer remain poorly understood. This is largely because of a lack of membrane–protein systems amenable for equilibrium studies and a limited number of methods for measuring these reactions. Recently, we reported the equilibrium dimerization of the CLC-ec1 Cl−/H+ transporter in lipid bilayers (Chadda et al. 2016. eLife. https://doi.org/10.7554/eLife.17438), which provided a new type of model system for studying protein association in membranes. The measurement was conducted using the subunit-capture approach, involving passive dilution of the protein in large multilamellar vesicles, followed by single-molecule photobleaching analysis of the Poisson distribution describing protein encapsulation into extruded liposomes. To estimate the fraction of dimers (FDimer) as a function of protein density, the photobleaching distributions for the nonreactive, ideal monomer and dimer species must be known so that random co-capture probabilities can be accounted for. Previously, this was done by simulating the Poisson process of protein reconstitution into a known size distribution of liposomes composed of Escherichia coli polar lipids (EPLs). In the present study, we investigate the dependency of FDimer and ΔG° on the modeling through a comparison of different liposome size distributions (EPL versus 2:1 POPE/POPG). The results show that the estimated FDimer values are comparable, except at higher densities when liposomes become saturated with protein. We then develop empirical controls to directly measure the photobleaching distributions of the nonreactive monomer (CLC-ec1 I201W/I422W) and ideal dimer (WT CLC-ec1 cross-linked by glutaraldehyde or CLC-ec1 R230C/L249C cross-linked by a disulfide bond). The measured equilibrium constants do not depend on the correction method used, indicating the robustness of the subunit-capture approach. This strategy therefore presents a model-free way to quantify protein dimerization in lipid bilayers, offering a simplified strategy in the ongoing effort to characterize equilibrium membrane–protein reactions in membranes.

scholarly journals BRANEart: identify stability strength and weakness regions in membrane proteins

2021 ◽  
Author(s):  
Sankar Basu ◽  
Simon S. Assaf ◽  
Fabian Teheux ◽  
Marianne Rooman ◽  
Fabrizio Pucci
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Conformational Changes ◽  
Large Scale ◽  
Protein Structures ◽  
Accurate Method ◽  
Globular Proteins ◽  
Stability Properties ◽  
Overall Stability ◽  
The Stability

AbstractUnderstanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accurate method to evaluate the per-residue contributions to the overall stability of membrane proteins. It is based on an extended set of recently introduced statistical potentials derived from membrane protein structures, which better describe the stability properties of this class of proteins than standard potentials derived from globular proteins. We defined a per-residue membrane propensity index from combinations of these potentials, which can be used to identify residues which strongly contribute to the stability of the transmembrane region or which would, on the contrary, be more stable in extramembrane regions, or vice versa. Large-scale application to membrane and globular proteins sets and application to tests cases show excellent agreement with experimental data. BRANEart thus appears as a useful instrument to analyze in detail the overall stability properties of a target membrane protein, to position it relative to the lipid bilayer, and to rationally modify its biophysical characteristics and function. BRANEart can be freely accessed from http://babylone.3bio.ulb.ac.be/BRANEart.

scholarly journals Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1032
Author(s):  
Sonia Khemaissa ◽  
Sandrine Sagan ◽  
Astrid Walrant
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Hydrogen Bonds ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Noncovalent Interactions ◽  
Chemical Properties ◽  
Protein Stabilization ◽  
Physico Chemical

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.

scholarly journals High-tolerance crystalline hydrogels formed from self-assembling cyclic dipeptide

2019 ◽  
Vol 10 ◽  
pp. 1894-1901 ◽  
Author(s):  
Yongcai You ◽  
Ruirui Xing ◽  
Qianli Zou ◽  
Feng Shi ◽  
Xuehai Yan
Keyword(s):  
Self Assembly ◽  
Thermal Conditions ◽  
Great Promise ◽  
Cyclic Dipeptide ◽  
High Tolerance ◽  
Self Assembling ◽  
Structural Rigidity ◽  
High Propensity ◽  
Wide Range ◽  
New Type

Peptide-based supramolecular hydrogels, as a new type of biological nanoarchitectonic structure, hold great promise for a wide range of biomedical and nanotechnological applications, such as tissue engineering, drug delivery, and electronic and photonic energy storage. In this work, a cyclic dipeptide (CDP) cyclo-(Trp-Tyr) (C-WY), which has exceptional structural rigidity and high stability, is selected as a hydrogelator for the formation of supramolecular hydrogels. The unique hydrogen bonding in C-WY endows a high propensity for self-assembly and the resulting hydrogels are revealed to be crystalline. The crystalline hydrogels possess excellent mechanical capacity and superior tolerance to various harsh conditions, including in the presence of charged biopolymers, extreme acid/base environments, and changing thermal conditions. Such high tolerance enables the crystalline hydrogels to be applied in the complex and harsh environments of electrochemistry. In addition, this study demonstrates that the self-assembly of cyclic dipeptides results in highly robust hydrogels which can be applied for electrochemical applications such as electrochemical supercapacitors.

Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins

Nanoscale ◽  
2014 ◽  
Vol 6 (4) ◽  
pp. 2228 ◽  
Author(s):  
G. Wilhelmina de Groot ◽  
Sophie Demarche ◽  
M. Gabriella Santonicola ◽  
Louis Tiefenauer ◽  
G. Julius Vancso
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Self Assembly ◽  
Polymer Brush ◽  
The Self ◽  
Smart Polymer

Supramolecular organization of membrane proteins with anisotropic hydrophobic thickness

Soft Matter ◽  
2019 ◽  
Vol 15 (21) ◽  
pp. 4301-4310 ◽  
Author(s):  
Osman Kahraman ◽  
Christoph A. Haselwandter
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Supramolecular Organization ◽  
Membrane Compartmentalization

Azimuthal variations in membrane protein hydrophobic thickness can yield self-assembly of distinctive protein lattices and produce membrane compartmentalization.

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