scholarly journals 7-Transmembrane Helical (7TMH) Proteins: Pseudo-Symmetry and Conformational Plasticity

2018 ◽  
Author(s):  
Philippe Youkharibache ◽  
Alexander Tran ◽  
Ravinder Abrol
Keyword(s):  
Transmembrane Helix ◽  
Magic Number ◽  
Evolutionary Process ◽  
Transmembrane Helices ◽  
Sequence Structure ◽  
Protein Superfamilies ◽  
Evolution Path ◽  
Conformational Plasticity ◽  
Intragenic Duplication ◽  
Fold Formation

AbstractMembrane proteins sharing 7 transmembrane helices (7-TMH) dominate the polytopic TMH proteome. They cannot be grouped under a monolithic fold or superfold, however, a parallel structural analysis of folds around that magic number of 7-TMH in distinct 6/7/8-TMH protein superfamilies (SWEET, PnuC, TRIC, FocA, Aquaporin, GPCRs, AND MFS), reveals a common homology, not in their structural fold, but in their systematic pseudo-symmetric construction. Our analysis leads to guiding principles of intragenic duplication and pseudo-symmetric assembly of ancestral 3 or 4 Transmembrane Helix (3/4-TMH) protodomains/protofolds. A parallel deconstruction and reconstruction of these domains provides a structural and mechanistic framework for the evolution path of current pseudo-symmetrical transmembrane helical (TMH) proteins. It highlights the conformational plasticity inherent to fold formation itself. The sequence/structure analysis of different 6/7/8-TMH superfamilies provides a unifying theme of their evolutionary process involving the intragenic duplication of protodomains with varying degrees of sequence and fold divergence under conformational and functional constraints.

scholarly journals Point Mutations in Transmembrane Helices 2 and 3 of ExbB and TolQ Affect Their Activities in Escherichia coli K-12

2004 ◽  
Vol 186 (13) ◽  
pp. 4402-4406 ◽  
Author(s):  
Volkmar Braun ◽  
Christina Herrmann
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Transmembrane Helix ◽  
Point Mutations ◽  
Transmembrane Helices ◽  
The Third ◽  
Form Part ◽  
K 12

ABSTRACT Replacement of glutamate 176, the only charged amino acid in the third transmembrane helix of ExbB, with alanine (E176A) abolished ExbB activity in all determined ExbB-dependent functions of Escherichia coli. Combination of the mutations T148A in the second transmembrane helix and T181A in the third transmembrane helix, proposed to form part of a proton pathway through ExbB, also resulted in inactive ExbB. E176 and T148 are strictly conserved in ExbB and TolQ proteins, and T181 is almost strictly conserved in ExbB, TolQ, and MotA.

scholarly journals FOLDING ELASTIC TRANSMEMBRANE HELICES TO FIT IN A LOW-RESOLUTION IMAGE BY ELECTRON MICROSCOPY

2011 ◽  
Vol 09 (supp01) ◽  
pp. 37-50 ◽  
Author(s):  
YUTAKA UENO ◽  
KAZUNORI KAWASAKI ◽  
OSAMU SAITO ◽  
MASAFUMI ARAI ◽  
MAKIKO SUWA
Keyword(s):  
Membrane Proteins ◽  
Structure Prediction ◽  
Molecular Model ◽  
Imaging Techniques ◽  
Transmembrane Helix ◽  
Prediction Method ◽  
Molecular Shape ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Low Resolution

Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.

Substrate processing in intramembrane proteolysis by γ-secretase – the role of protein dynamics

2017 ◽  
Vol 398 (4) ◽  
pp. 441-453 ◽  
Author(s):  
Dieter Langosch ◽  
Harald Steiner
Keyword(s):  
Transmembrane Helix ◽  
Peptide Bond ◽  
Common Denominator ◽  
Transmembrane Helices ◽  
Intramembrane Proteases ◽  
Bond Scission ◽  
Catalytic Sites ◽  
Substrate Processing

Abstract Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.

scholarly journals Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates

2017 ◽  
Vol 28 (15) ◽  
pp. 2076-2090 ◽  
Author(s):  
Christopher J. Guerriero ◽  
Karl-Richard Reutter ◽  
Andrew A. Augustine ◽  
G. Michael Preston ◽  
Kurt F. Weiberth ◽  
...  
Keyword(s):  
Molecular Chaperones ◽  
Transmembrane Helix ◽  
Integral Membrane Proteins ◽  
Membrane Insertion ◽  
Transmembrane Helices ◽  
Vitro Assay ◽  
Dual Pass ◽  
Erad Pathway ◽  
Insight Into

Integral membrane proteins fold inefficiently and are susceptible to turnover via the endoplasmic reticulum–associated degradation (ERAD) pathway. During ERAD, misfolded proteins are recognized by molecular chaperones, polyubiquitinated, and retrotranslocated to the cytoplasm for proteasomal degradation. Although many aspects of this pathway are defined, how transmembrane helices (TMHs) are removed from the membrane and into the cytoplasm before degradation is poorly understood. In this study, we asked whether the hydrophobic character of a TMH acts as an energetic barrier to retrotranslocation. To this end, we designed a dual-pass model ERAD substrate, Chimera A*, which contains the cytoplasmic misfolded domain from a characterized ERAD substrate, Sterile 6* (Ste6p*). We found that the degradation requirements for Chimera A* and Ste6p* are similar, but Chimera A* was retrotranslocated more efficiently than Ste6p* in an in vitro assay in which retrotranslocation can be quantified. We then constructed a series of Chimera A* variants containing synthetic TMHs with a range of ΔG values for membrane insertion. TMH hydrophobicity correlated inversely with retrotranslocation efficiency, and in all cases, retrotranslocation remained Cdc48p dependent. These findings provide insight into the energetic restrictions on the retrotranslocation reaction, as well as a new computational approach to predict retrotranslocation efficiency.

scholarly journals Sampling the conformational space of the catalytic subunit of human γ-secretase

2015 ◽  
Author(s):  
Xiao-chen Bai ◽  
Eeson Rajendra ◽  
Guanghui Yang ◽  
Yigong Shi ◽  
Sjors Scheres
Keyword(s):  
Secondary Structure ◽  
Transmembrane Domain ◽  
Transmembrane Helix ◽  
Butyl Ester ◽  
Catalytic Subunit ◽  
Conformational Space ◽  
Transmembrane Helices ◽  
Classification Procedure ◽  
Previous Sample ◽  
Molecular Plasticity

Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of γ-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we introduce an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of γ-secretase. In addition, we present a γ-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain.

scholarly journals A selective transmembrane recognition mechanism by a membrane-anchored ubiquitin ligase adaptor

2020 ◽  
Vol 220 (1) ◽  
Author(s):  
Felichi Mae Arines ◽  
Aaron Jeremy Hamlin ◽  
Xi Yang ◽  
Yun-Yu Jennifer Liu ◽  
Ming Li
Keyword(s):  
Conformational Changes ◽  
Transmembrane Helix ◽  
Environmental Cues ◽  
Transmembrane Helices ◽  
Recognition Mechanism ◽  
Show Evidence ◽  
Transmembrane Regions ◽  
Underlying Mechanisms ◽  
Open Question

While it is well-known that E3 ubiquitin ligases can selectively ubiquitinate membrane proteins in response to specific environmental cues, the underlying mechanisms for the selectivity are poorly understood. In particular, the role of transmembrane regions, if any, in target recognition remains an open question. Here, we describe how Ssh4, a yeast E3 ligase adaptor, recognizes the PQ-loop lysine transporter Ypq1 only after lysine starvation. We show evidence of an interaction between two transmembrane helices of Ypq1 (TM5 and TM7) and the single transmembrane helix of Ssh4. This interaction is regulated by the conserved PQ motif. Strikingly, recent structural studies of the PQ-loop family have suggested that TM5 and TM7 undergo major conformational changes during substrate transport, implying that transport-associated conformational changes may determine the selectivity. These findings thus provide critical information concerning the regulatory mechanism through which transmembrane domains can be specifically recognized in response to changing environmental conditions.

scholarly journals Insights into substrate-mediated assembly of the chloroplast TAT receptor complex

2020 ◽  
Author(s):  
Qianqian Ma ◽  
Christopher Paul New ◽  
Carole Dabney-Smith
Keyword(s):  
Structural Model ◽  
Substrate Recognition ◽  
Transmembrane Helix ◽  
Complex Function ◽  
Transmembrane Helices ◽  
Translocation Event ◽  
Active Substrate ◽  
Tat System ◽  
Folded Proteins ◽  
Transport Complex

AbstractThe Twin Arginine Transport (TAT) system translocates fully folded proteins across the thylakoid membrane in the chloroplast (cp) and the cytoplasmic membrane of bacteria. In chloroplasts, cpTAT transport is achieved by three components: Tha4, Hcf106, and cpTatC. Hcf106 and cpTatC function as the substrate recognition/binding complex while Tha4 is thought to play a significant role in forming the translocation pore. Recent studies challenged this idea by suggesting that cpTatC-Hcf106-Tha4 function together in the active translocase. Here, we have mapped the inter-subunit contacts of cpTatC-Hcf106 during the resting state and built a cpTatC-Hcf106 structural model based on our crosslinking data. In addition, we have identified a substrate-mediated reorganization of cpTatC-Hcf106 contact sites during active substrate translocation. The proximity of Tha4 to the cpTatC-Hcf106 complex was also identified. Our data suggest a model for cpTAT function in which the transmembrane helices of Hcf106 and Tha4 may each contact the fifth transmembrane helix of cpTatC while the insertion of the substrate signal peptide may rearrange the cpTatC-Hcf106-Tha4 complex and initiate the translocation event.One sentence summaryProtein subunits of the thylakoidal twin arginine transport complex function together during substrate recognition and translocase assembly.

scholarly journals Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating

2014 ◽  
Vol 289 (44) ◽  
pp. 30590-30601 ◽  
Author(s):  
Kazuhiro Abe ◽  
Kazutoshi Tani ◽  
Yoshinori Fujiyoshi
Keyword(s):  
Molecular Conformation ◽  
Transmembrane Helix ◽  
Transmembrane Helices ◽  
Competitive Antagonist ◽  
Molecular Conformations ◽  
Systematic Comparison ◽  
Azimuthal Position ◽  
Cryo Electron Microscopy ◽  
Open Conformation ◽  
P Type

Gastric H+,K+-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K+-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H+,K+-ATPase is consistent with that observed in sarcoplasmic reticulum Ca2+-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general.

Alpha-periodicity analysis of small multidrug resistance (SMR) efflux transporters

1998 ◽  
Vol 76 (5) ◽  
pp. 791-797 ◽  
Author(s):  
Robert A Edwards ◽  
Raymond J Turner
Keyword(s):  
Amino Acids ◽  
Multidrug Resistance ◽  
Transmembrane Helix ◽  
Power Spectra ◽  
Substitution Matrix ◽  
Transmembrane Helices ◽  
Homologous Proteins ◽  
Small Multidrug Resistance ◽  
Amino Acid Properties ◽  
Periodicity Analysis

Proteins in the small multidrug resistance (SMR) family of transport proteins are about 110 amino acids in length and are predicted to have four transmembrane helices. This family is divided into a two groups, one of which we have referred to as small multidrug pumps (Smp) and confer resistance to a wide variety of quaternary ammonium compounds through a proton-drug efflux antiport mechanism. Members of the second group within this family have, as yet, not had their substrate profile characterized and are referred to as Sug proteins. Alpha-periodicity analysis was conducted on a set of six homologous proteins of the SMR family consisting of three established Smp and three Sug proteins. Several amino acid properties were used in the analysis including hydropathy, variability, and a substitution matrix for lipid exposed amino acids. The scanning window was varied between 8 and 14 residues and the alpha-periodicity was calculated from the peaks in the Fourier transform power spectra in the region between 3.0 and 4.3 residues/turn. This analysis adds to the hydropathy analysis to give a more confident prediction of which residues are within the lipid bilayer for each of the four transmembrane helices. Information was also obtained that allowed for the identification of zones within each transmembrane helix that face the interior of the helical bundle on one side and are lipid exposed on the other face.Key words: modeling, SMR, QAC, multidrug resistance, transporter, hydrophopathy, periodicity, amphipathicity.

scholarly journals Visualization of lipid bilayer in the crystals by solvent contrast modulation

2014 ◽  
Vol 70 (a1) ◽  
pp. C1498-C1498
Author(s):  
Yoshiyuki Norimatsu ◽  
Junko Tsueda ◽  
Ayami Hirata ◽  
Shiho Iwasawa ◽  
Chikashi Toyoshima
Keyword(s):  
Lipid Bilayer ◽  
Electron Density ◽  
Lipid Bilayers ◽  
Transmembrane Helix ◽  
Real Space ◽  
New Method ◽  
Imaging Plate ◽  
Salt Bridges ◽  
Transmembrane Helices ◽  
X Ray

A new method of X-ray solvent contrast modulation was developed to visualize lipid bilayers in crystals of membrane proteins at a high enough resolution to resolve individual phospholipids molecules (~3.5 Å ). Visualization of lipid bilayer has been escaping from conventional crystallographic methods due to its extreme flexibility, and our knowledge on the behavior of lipid bilayer is still very much limited. Here we applied the new method of X-ray solvent contrast modulation to crystals of Ca2+-ATPase in 4 different physiological states. As phospholipids have to be added to make crystals of Ca2+-ATPase, it is expected that lipid bilayers are present in the crystals. Moreover, transmembrane helices of Ca2+-ATPase rearrange drastically during the reaction cycle and some of them show substantial movements perpendicular to the bilayer plane. Thus these crystals provide a rare opportunity to directly visualize phospholipids interacting with a membrane protein in different conformations. Complete diffraction data covering from 200 to 3.2 Å resolution were collected at BL41XU, Spring-8, using an R-Axis V imaging plate detector for crystals soaked in solvent of different electron density. A new concept "solvent exchange probability", which should be 1 in the bulk solvent, 0 inside the protein and an intermediate at interface, was introduced and used as a restraint for real space phase improvement. The electron density maps thus obtained clearly show that: (i) Phospholipid molecules surrounding the protein are fixed apparently by Arg/Lys-phosphate salt bridges or Trp-carbonyl hydrogen bonds and follow the movements of transmembrane helices. Movements of as large as 12 Å are allowed. (ii) If the movement of a transmembrane helix exceeds this limit, associated phospholipids change the partners for fixation or change the orientation of the entire protein molecule.

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