scholarly journals Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices

2021 ◽  
Author(s):  
Felix Nicolaus ◽  
Fatima Ibrahimi ◽  
Anne den Besten ◽  
Gunnar von Heijne
Keyword(s):  
Hydrophobic Interactions ◽  
Protein A ◽  
Membrane Insertion ◽  
Transmembrane Helices ◽  
Hydrophobic Residues ◽  
Electrostatic And Hydrophobic Interactions ◽  
Sequence Elements ◽  
Critical Residues ◽  
First Contact ◽  
Positively Charged

During SecYEG-mediated cotranslational insertion of membrane proteins, transmembrane helices (TMHs) first make contact with the membrane when their N-terminal end is ~45 residues away from the peptidyl transferase center. However, we recently uncovered instances where the first contact is delayed by up to ~10 residues. Here, we recapitulate these effects using a model TMH fused to two short segments from the BtuC protein: a positively charged loop and a re-entrant loop. We show that the critical residues are two Arg residues in the positively charged loop and four hydrophobic residues in the re-entrant loop. Thus, both electrostatic and hydrophobic interactions involving sequence elements that are not part of a TMH can impact the way the latter behaves during membrane insertion.

scholarly journals Structural basis for membrane insertion by the human ER membrane protein complex

Science ◽  
2020 ◽  
pp. eabb5008 ◽  
Author(s):  
Tino Pleiner ◽  
Giovani Pinton Tomaleri ◽  
Kurt Januszyk ◽  
Alison J. Inglis ◽  
Masami Hazu ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Protein Complex ◽  
Structural Basis ◽  
Membrane Insertion ◽  
Transmembrane Helices ◽  
Membrane Protein Complex ◽  
Cryo Electron Microscopy ◽  
Membrane Thinning ◽  
Positively Charged ◽  
Er Membrane

A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit ER membrane protein complex (EMC) is a conserved co- and post-translational insertase at the endoplasmic reticulum. We determined the structure of the human EMC in a lipid nanodisc to an overall resolution of 3.4 Å by cryo-electron microscopy, permitting building of a nearly complete atomic model. We used structure-guided mutagenesis to demonstrate that substrate insertion requires a methionine-rich cytosolic loop and occurs via an enclosed hydrophilic vestibule within the membrane formed by the subunits EMC3 and EMC6. We propose that the EMC uses local membrane thinning and a positively charged patch to decrease the energetic barrier for insertion into the bilayer.

scholarly journals Incorporation of short, charged peptide tags affects the temperature responsiveness of positively-charged elastin-like polypeptides

2019 ◽  
Vol 7 (34) ◽  
pp. 5245-5256 ◽  
Author(s):  
Charng-Yu Lin ◽  
Julie C. Liu
Keyword(s):  
Hydrophobic Interactions ◽  
Electrostatic And Hydrophobic Interactions ◽  
Peptide Tags ◽  
Positively Charged

Electrostatic and hydrophobic interactions between elastin-like polypeptides (ELPs) and non-ELP sequences affect the temperature responsiveness of ELP-based proteins.

Interaction of sulphone based reactive dyes with cationic surfactant: a spectroscopic and conductometric study

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Misbah Iram ◽  
Hamadia Sultana ◽  
Muhammad Usman ◽  
Bazgha Ahmad ◽  
Nadia Akram ◽  
...  
Keyword(s):  
Strong Interaction ◽  
Cetyltrimethylammonium Bromide ◽  
Hydrophobic Interactions ◽  
Reactive Dyes ◽  
Micellar System ◽  
Palisade Layer ◽  
Micellar Systems ◽  
Gibbs Energies ◽  
Electrostatic And Hydrophobic Interactions ◽  
Conductometric Study

Abstract Interaction of sulphone based reactive dyes, designated as dye-1 and dye-2, with cationic micellar system of cetyltrimethylammonium bromide (CTAB), has been investigated by spectroscopic and conductometeric measurements. Efficiency of the selected micellar systems is assessed by the values of binding constant (K b ), partition coefficient (K x ) and respective Gibbs energies. Critical micelle concentration (CMC) of surfactant, electrostatic and hydrophobic interactions as well as polarity of the medium plays significant role in this phenomenon. The negative values of Gibbs energies of binding (∆G b ) and partition (∆G p ) predicts the feasibility and spontaneity of respective processes. Similarly negative values of ∆G m and ∆H m and positive values of ∆S m , calculated from conductometeric data, further, revealed the exothermicity, spontaneity and, thus, stability of system. The results, herein, have disclosed the strong interaction between dye and surfactant molecules. The dye-2 has been observed to be solubilized to greater extent, as compared to dye 1, due to strong interaction ith hydrophiles of CTAB and accommodation of its molecules in palisade layer of micelle closer to the micelle/water interface.

scholarly journals Identification and Characterization of Novel Fc-Binding Heptapeptides from Experiments and Simulations

2018 ◽  
Author(s):  
Xiaoquan Sun ◽  
Justin Weaver ◽  
Sumith Ranil Wickramasinghe ◽  
Xianghong Qian
Keyword(s):  
Hydrophobic Interactions ◽  
Culture Media ◽  
Protein A ◽  
Md Simulations ◽  
Production Costs ◽  
Antibody Detection ◽  
Small Peptides ◽  
Affinity Ligands ◽  
Binding Behavior ◽  
Igg Isotypes

Purification of biologically-derived therapeutics is a major cost contributor to the production of this rapidly growing class of pharmaceuticals. Monoclonal antibodies comprise a large percentage of these products therefore new antibody purification tools are needed. Small peptides, as opposed to traditional antibody affinity ligands such as Protein A, may have advantages in stability and production costs. Multiple heptapeptides that demonstrate Fc binding behavior that have been identified from a combinatorial peptide library using M13 Phage Display are presented herein. Seven unique peptide sequences of diverse hydrophobicity and charge were identified. All seven peptides showed strong binding to the four major human IgG isotypes, human IgM, as well as binding to canine, rat, and mouse IgG. These seven peptides were also shown to bind human IgG4 from DMEM cell culture media with 5% FCS and 5 g/L ovalbumin present. These peptides may be useful as surface ligands for antibody detection and purification purposes. Molecular docking and classical molecular dynamics (MD) simulations were conducted to elucidate the mechanisms and energetics for the binding of these peptides to the Fc region. The binding site was found to be located between the two glycan chains inside the Fc fragment. Both hydrogen bonding and hydrophobic interactions were found to be crucial for the binding interactions. Excellent agreement for the binding strength was obtained between experimental results and simulations.

scholarly journals Rules for the self-assembly of ESCRT-III on endosomes

2021 ◽  
Author(s):  
Simon Sprenger ◽  
Simona M. Migliano ◽  
Florian Oleschko ◽  
Marvin Kobald ◽  
Michael Hess ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Interactions ◽  
The Self ◽  
Amino Acid Residues ◽  
Lateral Expansion ◽  
Endosomal Sorting ◽  
Aaa Atpase ◽  
Charged Amino Acids ◽  
Membrane Budding ◽  
Positively Charged

ABSTRACTThe endosomal sorting complexes required for transport (ESCRT) mediate various membrane remodeling processes in cells by mechanism that are incompletely understood. Here we combined genetic experiments in budding yeast with site-specific cross-linking to identify rules that govern the self-assembly of individual ESCRT-III proteins into functional ESCRT-III complexes on endosomes. Together with current structural models of ESCRT-III, our findings suggest that, once nucleated, the growing Snf7 protofilament seeds the lateral co-assembly of a Vps24 - Vps2 heterofilament. Both Vps24 and Vps2 use positively charged amino acid residues in their helices α1 to interact with negatively charged amino acids in helix α4 of Snf7 subunits of the protofilament. In the Vps24 - Vps2 heterofilament, the two subunits alternate and interact with each other using hydrophobic interactions between helices α2/α3. The co-assembly of the Vps24 - Vps2 heterofilament restricts the lateral expansion of Snf7 protofilaments and leads the immediate recruitment of the AAA-ATPase Vps4. This self-assembly process of three ESCRT-III subunits results in the formation of a Snf7 protofilament and the co-assembly of a Vps24 - Vps2 heterofilament. This sets the stage for Vps4 recruitment and the subsequent ATP-driven dynamic self-organization of ESCRT-III / Vps4 assemblies and the ensuing membrane budding and scission events.

scholarly journals The contribution of hydrophobic residues in the pore-forming region of the ryanodine receptor channel to block by large tetraalkylammonium cations and Shaker B inactivation peptides

2012 ◽  
Vol 140 (3) ◽  
pp. 325-339 ◽  
Author(s):  
Sammy A. Mason ◽  
Cedric Viero ◽  
Joanne Euden ◽  
Mark Bannister ◽  
Duncan West ◽  
...  
Keyword(s):  
Ryanodine Receptor ◽  
Hydrophobic Interactions ◽  
Structural Information ◽  
Dissociation Rate ◽  
Structural Components ◽  
Hydrophobic Residues ◽  
K Channels ◽  
New Information ◽  
Tetraalkylammonium Cations ◽  
Cytosolic Side

Although no high-resolution structural information is available for the ryanodine receptor (RyR) channel pore-forming region (PFR), molecular modeling has revealed broad structural similarities between this region and the equivalent region of K+ channels. This study predicts that, as is the case in K+ channels, RyR has a cytosolic vestibule lined with predominantly hydrophobic residues of transmembrane helices (TM10). In K+ channels, this vestibule is the binding site for blocking tetraalkylammonium (TAA) cations and Shaker B inactivation peptides (ShBPs), which are stabilized by hydrophobic interactions involving specific residues of the lining helices. We have tested the hypothesis that the cytosolic vestibule of RyR fulfils a similar role and that TAAs and ShBPs are stabilized by hydrophobic interactions with residues of TM10. Both TAAs and ShBPs block RyR from the cytosolic side of the channel. By varying the composition of TAAs and ShBPs, we demonstrate that the affinity of both species is determined by their hydrophobicity, with variations reflecting alterations in the dissociation rate of the bound blockers. We investigated the role of TM10 residues of RyR by monitoring block by TAAs and ShBPs in channels in which the hydrophobicity of individual TM10 residues was lowered by alanine substitution. Although substitutions changed the kinetics of TAA interaction, they produced no significant changes in ShBP kinetics, indicating the absence of specific hydrophobic sites of interactions between RyR and these peptides. Our investigations (a) provide significant new information on both the mechanisms and structural components of the RyR PFR involved in block by TAAs and ShBPs, (b) highlight important differences in the mechanisms and structures determining TAA and ShBP block in RyR and K+ channels, and (c) demonstrate that although the PFRs of these channels contain analogous structural components, significant differences in structure determine the distinct ion-handling properties of the two species of channel.

The red cell band 3 protein: its role in anion transport

1982 ◽  
Vol 299 (1097) ◽  
pp. 497-507 ◽  
Keyword(s):  
Binding Sites ◽  
Band 3 ◽  
Anion Transport ◽  
Anion Binding ◽  
Hydrophobic Residues ◽  
Ping Pong ◽  
Hydrophilic Residues ◽  
Aqueous Core ◽  
Positively Charged

Studies of anion transport across the red blood cell membrane fall generally into two categories: (1) those concerned with the operational characterization of the transport system, largely by kinetic analysis and inhibitor studies; and (2) those concerned with the structure of band 3, a transmembrane peptide identified as the transport protein. The kinetics are consistent with a ping-pong model in which positively charged anion-binding sites can alternate between exposure to the inside and outside compartments but can only shift one position to the other when occupied by an anion. The structural studies on band 3 indicate that only 60 % of the peptide is essential for transport. That particular portion is in the form of a dimer consisting of an assembly of membrane-crossing strands (each monomer appears to cross at least five times). The assembly presents its hydrophobic residues toward the interior of the bilayer, but its hydrophilic residues provide an aqueous core. The transport involves a small conformational change in which an anion-binding site (involving positively charged residues) can alternate between positions that are topologically in and topologically out.

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