Membrane’s digest

MP

Cryo-EM structure of the human Asc-1 transporter complex.

Li Y, Guo Y, Bröer A, Dai L, Brӧer S, Yan R.

Nat Commun. 2024 Apr 8;15(1):3036.

doi: 10.1038/s41467-024-47468-1.

PMID: 38589439.

The Alanine-Serine-Cysteine transporter 1 (Asc-1 or SLC7A10) = crucial heterodimeric transporter complex with 4F2hc (SLC3A2) through a covalent disulfide bridge. This complex enables the sodium-independent transport of small neutral amino acids within the CNS.

Here: cryo-EM structures of the human Asc-1-4F2hc complex in its apo state, D-Ser bound state, and L-Ala bound state, resolved at 3.6 Å, 3.5 Å, and 3.4 Å, respectively. => structural analysis + transport assays.

Structural mechanisms of mitochondrial uncoupling protein 1 regulation in thermogenesis.

Jones SA, Ruprecht JJ, Crichton PG, Kunji ERS.

Trends Biochem Sci. 2024 Apr 1:S0968-0004(24)00071-9.

doi: 10.1016/j.tibs.2024.03.005. Epub ahead of print. PMID: 38565497.

Review on the recent cryo-EM structures of human UCP1 explaining its regulation, revealing how purine nucleotides inhibit its proton-leak activity, and how fatty acid activators enable proton flux for thermogenesis

=> molecular insights into the mechanisms underlying non-shivering thermogenesis in mammals, particularly in borwn adipose tissue.

The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195.

Rao RM, El Dhaybi I, Cadet F, Etchebest C, Diharce J.

Biochimie. 2024 Mar 16:S0300-9084(24)00067-1.

doi: 10.1016/j.biochi.2024.03.009. Epub ahead of print.

PMID: 38494108.

This study investigates the dynamics of mouse translocator protein (TSPO) using MD, focusing on the NMR structure and a homology model based on X-ray structures.

=> high protein flexibility (particularly in the NMR structure), even in the presence of the ligand PKA. The stability of the ligand differs between the NMR and homology model systems, suggesting that the NMR structure occupies a distinct conformational space within TSPO dynamics.

Translocator Protein 18 kDa (TSPO): A Promising Molecular Target for Image-Guided Surgery of Solid Cancers.

Wongso H, Kurniawan A, Setiadi Y, Kusumaningrum CE, Widyasari EM, Wibawa THA, Mahendra I, Febrian MB, Sriyani ME, Halimah I, Daruwati I, Gunawan R, Achmad A, Nugraha DH, Lesmana R, Nugraha AS.

Adv Pharm Bull. 2024 Mar;14(1):86-104.

doi: 10.34172/apb.2024.015. Epub 2023 Oct 14.

PMID: 38585455.

Review on the significance of TSPO in carcinogenesis and potential application of TSPO-targeted hybrid probes in image-guided surgery for cancer treatment. Upregulated expression of TSPO observed in several cancer types, indicating its potential as a diagnostic and prognostic marker. Recent advancements in TSPO-targeted radioligands and hybrid probes => promising opportunities for image-guided cancer surgery (small molecules, nanoparticles, and antibodies).

CyaA translocation across eukaryotic cell membranes.

Abettan A, Nguyen MH, Ladant D, Monticelli L, Chenal A.

Front Mol Biosci. 2024 Mar 22;11:1359408.

doi: 10.3389/fmolb.2024.1359408.

PMID: 38584704.

Opinion paper on the progress made so far in understanding the translocation mechanism of adenylate cyclase (CyaA) toxin, a major virulence factor produced by Bordetella pertussis. This toxin invades eukaryotic cells through a unique but poorly understood mechanism that involves a direct translocation of its N-terminal adenylate cyclase catalytic domain across the host plasma membrane.

Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity.

Marinelli F, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2024 Apr 16;121(16):e2318009121.

doi: 10.1073/pnas.2318009121. Epub 2024 Apr 8.

PMID: 38588414.

Secondary-active transporters facilitate the movement of diverse substances across cellular membranes without consuming ATP, operating against concentration gradients.

Here: computational simulations to investigate the structural mechanism of these transporters, focusing on a cardiac Na+/Ca2+ exchanger homolog.

=> complete functional cycle of the transporter, elucidating its preference for antiport rather than symport, specific exchange of Na+ and Ca2+, and the 3:1 stoichiometry.

Cryo-EM Structure of the Human Amylin 1 Receptor in Complex with CGRP and Gs Protein.

Cao J, Belousoff MJ, Danev R, Christopoulos A, Wootten D, Sexton PM.

Biochemistry. 2024 Apr 11.

doi: 10.1021/acs.biochem.4c00114. Epub ahead of print.

PMID: 38603770.

Inhibition of calcitonin gene-related peptide (CGRP) or its receptor (CGRPR) has revolutionized migraine treatment, but the role of the amylin 1 receptor (AMY1R) remains unclear.

AMY1R and CGRPR are heterodimers comprising receptor activity-modifying protein 1 (RAMP1) with the calcitonin receptor (CTR) and the calcitonin receptor-like receptor (CLR), respectively.

Structural analysis => distinct peptide organization and receptor dynamics between AMY1R-CGRP and CGRPR-CGRP complexes. Despite these variances, conserved interactions of CGRP’s C-terminus with both receptors likely contribute to cross-reactivity of nonpeptide CGRPR antagonists at AMY1R, including clinically used blockers.

Molecular Machines that Facilitate Bacterial Outer Membrane Protein Biogenesis.

Doyle MT, Bernstein HD.

Annu Rev Biochem. 2024 Apr 11.

doi: 10.1146/annurev-biochem-030122-033754. Epub ahead of print.

PMID: 38603556.

This review explores the intricate process of outer membrane protein (OMP) biogenesis in Gram-negative bacteria, discussing their translocation across the IM, their transport through the periplasmic space aided by chaperones, and their final assembly into the OM by the β-barrel assembly machine.

+  emerging concept of intermembrane supercomplex formation among molecular machines and the spatial organization of OMP insertion, suggesting a predominant localization near the cell center and the formation of supramolecular structures known as OMP islands throughout the OM.

Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F.

Karagöl A, Karagöl T, Smorodina E, Zhang S.

PLoS One. 2024 Apr 10;19(4):e0289644.

doi: 10.1371/journal.pone.0289644.

PMID: 38598436.

Structural bioinformatics analysis => study of native glutamate transporter structures and their water-soluble variants created via systematic amino acid substitutions using the QTY-code strategy.

The water-soluble variants (hydrophobic amino acids replaced with hydrophilic ones) = significant similarity to native structures despite sequence differences.

High-resolution In-situ Structures of Mammalian Mitochondrial Respiratory Supercomplexes in Reaction within Native Mitochondria

Wan Zheng, Pengxin Chai, Jiapeng Zhu, Kai Zhang

bioRxiv 2024.04.02.587796; 

doi: https://doi.org/10.1101/2024.04.02.587796

in-situ cryoEM approach of porcine mitochondria, revealing diverse respiratory supercomplex assemblies with up to 1.8-Å local resolution. These assemblies, formed by intricate protein-lipid-protein interactions, exhibit dynamic intermediates, elucidating ubiquinone/ubiquinol exchange in complex I and the Q-cycle in complex III.

=> insights into the interplay between complexes I and III in response to environmental cues.

Dissection of an ABC transporter LolCDE function analyzed by photo-crosslinking.

Tao K, Narita SI, Okada U, Murakami S, Tokuda H.

J Biochem. 2024 Mar 25;175(4):427-437.

doi: 10.1093/jb/mvad118. PMID: 38156779.

E. coli enveloppe = approximately 100 different lipoprotein species, predominantly localized to the inner leaflet of the OM. Lol system = trafficking of these lipoproteins.

Here: site-specific photo-crosslinking, to investigates the interaction between LolCDE and lipoproteins, revealing insights into their binding dynamics and the role of a LolCDE inhibitor, which promotes lipoprotein dissociation rather than inhibiting binding.

Membrane

Molecular Transportation Conversion of Membrane Tension Using a Mechanosensitive Channel in Asymmetric Lipid-Protein Vesicles.

Baba K, Kamiya K.

ACS Appl Mater Interfaces. 2024 Apr 9.

doi: 10.1021/acsami.4c02370. Epub ahead of print.

PMID: 38594642.

Study introduces asymmetric lipid-oleosin vesicles, featuring distinct lipid and oleosin monolayers, for mimicking cell membranes. These vesicles enable the reconstitution and functionality of MPs such as OmpG and facilitate vesicle fission triggered by lysoPL.

+  evaluates the transport of small molecules through MscL, highlighting the role of tension in its activation and facilitating molecule transport.

=> Overall suggest that asymmetric lipid-oleosin vesicles incorporating MscL represent promising platforms for exploring the responses of complex artificial cell models to external stimuli.

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes.

Peruzzi JA, Steinkühler J, Vu TQ, Gunnels TF, Hu VT, Lu P, Baker D, Kamat NP.

Nat Commun. 2024 Apr 11;15(1):3162.

doi: 10.1038/s41467-024-47163-1.

PMID: 38605024.

Demonstration through de novo protein design and simulations, how membrane-protein hydrophobic mismatch can be utilized to control protein integration and organization in synthetic lipid membranes, enabling the assembly of vesicles with distinct functions and applications in artificial cells, biosensors, and therapeutic nanoparticles.

Molecules

Thin adhesive oil films lead to anomalously stable mixtures of water in oil.

Nannette C, Baudry J, Chen A, Song Y, Shglabow A, Bremond N, Démoulin D, Walters J, Weitz DA, Bibette J.

Science. 2024 Apr 12;384(6692):209-213.

doi: 10.1126/science.adj6728. Epub 2024 Apr 11.

PMID: 38603504.

Report of the observation that a thin fluid film of oil separating two water droplets can lead to an adhesive interaction between the droplets. In addition, this interaction prevents their coalescence over timescales of several weeks, without the use of any surfactant or solvent.

Membrane transporters in drug development and as determinants of precision medicine.

Galetin A, Brouwer KLR, Tweedie D, Yoshida K, Sjöstedt N, Aleksunes L, Chu X, Evers R, Hafey MJ, Lai Y, Matsson P, Riselli A, Shen H, Sparreboom A, Varma MVS, Yang J, Yang X, Yee SW, Zamek-Gliszczynski MJ, Zhang L, Giacomini KM.

Nat Rev Drug Discov. 2024 Apr;23(4):255-280.

doi: 10.1038/s41573-023-00877-1. Epub 2024 Jan 24.

PMID: 38267543.

Physiologically based pharmacokinetic modeling has improved prediction of transporter-mediated drug disposition, while CryoEM has revealed structures of SLC and ABC transporters.

Here: developments, remaining questions, regulatory considerations, and future directions in transporter research.

Detergents with Scalable Properties Identify Noncanonical Lipopolysaccharide Binding to Bacterial Inner Membrane Proteins.

Urner LH, Fiorentino F, Shutin D, Sauer JB, Agasid MT, El-Baba TJ, Bolla JR, Stansfeld PJ, Robinson CV.

J Am Chem Soc. 2024 Apr 11.

doi: 10.1021/jacs.3c14358. Epub ahead of print.

PMID: 38604609.

LPS is crucial for maintaining the OM barrier in Gram-negative bacteria, often obtained with IM proteins during detergent purification. To assess whether this reflects native lipid environments, authors chemically modified detergents based on hydrophilic-lipophilic balance and packing parameter concepts.

=> qualitative differentiation of proteins copurifying with PLs and/or LPS, suggesting that LPS can influence the activity of membrane proteins not traditionally associated with outer membrane biogenesis

=> insights into membrane biology and antibiotic research through scalable detergent chemistry for streamlined protein-lipid interaction characterization.

Adamantylglycine as a high-affinity peptide label for membrane transport monitoring and regulation.

Pramod M, Alnajjar MA, Schöpper SN, Schwarzlose T, Nau WM, Hennig A.

Chem Commun (Camb). 2024 Apr 11.

doi: 10.1039/d4cc00602j. Epub ahead of print.

PMID: 38602391.

The non-canonical amino acid adamantylglycine (Ada) is introduced into peptides to allow high-affinity binding to cucurbit[7]uril (CB7). Introduction of Ada into a cell-penetrating peptide (CPP) sequence had minimal influence on the membrane transport, yet enabled up- and down-regulation of the membrane transport activity.

Methods

Plant Membrane-On-A-Chip: A Platform for Studying Plant Membrane Proteins and Lipids.

Stuebler M, Manzer ZA, Liu HY, Miller J, Richter A, Krishnan S, Selivanovitch E, Banuna B, Jander G, Reimhult E, Zipfel WR, Roeder AHK, Piñeros MA, Daniel S.

ACS Appl Mater Interfaces. 2024 Apr 9.

doi: 10.1021/acsami.3c18562. Epub ahead of print.

PMID: 38593404.

Repot of a “plant-membrane-on-a-chip,″ = supported bilayer (from membrane vesicles from protoplasts containing transgenic MPs and their native lipids) made from the plant plasma membranes of A. thaliana, N. benthamiana, or Zea mays.

=> fluorescent imaging to examine protein-protein interactions and determine the protein subunit stoichiometry of flotillins.

perspectives: studies of plant MPs, transport, biophysical processes, and protein-protein and protein-lipid interactions.

Rotary FoF1-ATP Synthase-Driven Flasklike Pentosan Colloidal Motors with ATP Synthesis and Storage.

Li Y, Liu J, Wu Y, He Q.

J Am Chem Soc. 2024 Apr 10.

doi: 10.1021/jacs.4c00334. Epub ahead of print.

PMID: 38598314.

Description of the assembly of a chloroplast-derived motor-driven colloidal structure capable of synthesizing, storing, and releasing ATP (by combining hydrothermal polymerization with chloroplast-derived proteoliposomes containing rotary FoF1-ATPase motors).

pmf => rotation of FoF1-ATPase motors, propelling the motors and enabling ATP synthesis and storage.

DeepLoc 2.1: multi-label membrane protein type prediction using protein language models.

Ødum MT, Teufel F, Thumuluri V, Almagro Armenteros JJ, Johansen AR, Winther O, Nielsen H.

Nucleic Acids Res. 2024 Apr 8:gkae237.

doi: 10.1093/nar/gkae237. Epub ahead of print.

PMID: 38587188.

DeepLoc 2.0 = a web server for the prediction of protein subcellular localization and sorting signals.

Here: DeepLoc 2.1, which additionally classifies the input proteins into the membrane protein types Transmembrane, Peripheral, Lipid-anchored and Soluble.

web server: https://services.healthtech.dtu.dk/services/DeepLoc-2.1.

Experimental and computational approaches for membrane protein insertion and topology determination.

Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I.

Methods. 2024 Apr 9:S1046-2023(24)00088-4.

doi: 10.1016/j.ymeth.2024.03.012. Epub ahead of print.

PMID: 38604415.

Review discussing molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.

Exploring GPCR conformational dynamics using single-molecule fluorescence.

Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R.

Methods. 2024 Apr 9:S1046-2023(24)00085-9.

doi: 10.1016/j.ymeth.2024.03.011. Epub ahead of print.

PMID: 38604413.

Review on state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs.

+ highlight 4 recent studies on applications of single-molecule microscopy in revealing the dynamics of GPCRs, complementary methods to verify the structural biology results.

Microbio

The twin-arginine translocation (Tat) system.

Palmer T, Berks BC.

Curr Biol. 2024 Apr 8;34(7):R267-R268.

doi: 10.1016/j.cub.2024.02.039.

PMID: 38593766.

In this Quick guide, Palmer and Berks introduce the twin-arginine translocation (Tat) systems. Tats are found in a variety of microbes and microbe-derived organelles, and are known to translocate folded substrate proteins across biological membranes.

Unravelling HetC as a peptidase-based ABC exporter driving functional cell differentiation in the cyanobacterium Nostoc PCC 7120.

Rachedi R, Risoul V, Foglino M, Aoudache Y, Lang K, Champ S, Kaplan E, Orelle C, Douzi B, Jault J-M, Latifi A.

Microbiol Spectr. 2024 Apr 2;12(4):e0405823.

doi: 10.1128/spectrum.04058-23. Epub 2024 Feb 15.

PMID: 38358282.

Peptidase-containing ABC transporters (PCAT) are involved in the maturation and export of quorum-sensing or antimicrobial peptides.

In the cyanobacterium Nostoc PCC 7120, the protein HetC is essential for the differentiation of functional heterocysts (micro-oxic and non-dividing cells specialized in atmospheric nitrogen fixation).

Here: authors show that the N-terminal part of HetC, encompassing the peptidase domain, displays a cysteine-type protease activity (catalytic residue of the ATPase domain of HetC is shown to be essential for cell differentiation).

HetC might be regulated by ppGpp to potentially facilitate the export of a signaling peptide essential for cell differentiation.

Miscellaneous

Peter Higgs: science mourns giant of particle

physics.

Castelvecchi D.

Nature. 2024 Apr 10.

doi: 10.1038/d41586-024-01069-6. Epub ahead of print.

PMID: 38605197.

The British physicist, who has died aged 94, predicted the existence of the Higgs boson in the 1960s.

Scientists discover first algae that can fix nitrogen – thanks to a tiny cell structure.

Wong C.

Nature. 2024 Apr 11.

doi: 10.1038/d41586-024-01046-z. Epub ahead of print.

PMID: 38605201.

A newly discovered ‘organelle’ that converts nitrogen gas into a useful form could pave the way for engineered plants that require less fertilizer.

Right- or left-handed? Protein in embryo cells might help decide.

Kulkarni S.

Nature. 2024 Apr;628(8007):246.

doi: 10.1038/d41586-024-00977-x.

PMID: 38565906.

Gene that codes for structural protein could determine the dominant side of the human brain.

Nanoscale scythe cuts molecular tethers using mechanical forces.

Nierengarten I.

Nature. 2024 Apr;628(8007):269-270.

doi: 10.1038/d41586-024-00909-9.

PMID: 38600266.

Nanoscale systems that release small molecules have potential therapeutic and industrial uses, but can result in low numbers of molecules reaching their target. A release system triggered by mechanical force offers a fresh approach.

Automated model building and protein identification in cryo-EM maps.

Jamali K, Käll L, Zhang R, Brown A, Kimanius D, Scheres SHW.

Nature. 2024 Apr;628(8007):450-457.

doi: 10.1038/s41586-024-07215-4. Epub 2024 Feb 26.

PMID: 38408488.

Machine-learning approach, named ModelAngelo, for automated atomic model building in cryo-EM maps.

It combines from the map with information from protein sequence and structure in a single graph neural network.