Membrane’s digest
MP
Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon.
Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC.
Nat Microbiol. 2024 Apr;9(4):1089-1102.
doi: 10.1038/s41564-024-01644-7. Epub 2024 Mar 27.
PMID: 38538833.
The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota.
Here: trapping of the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex => Cryo-EM analysis of purified substrate-bound T9SS translocons
Release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
Transport mechanism and pharmacology of the human GlyT1.
Wei Y, Li R, Meng Y, Hu T, Zhao J, Gao Y, Bai Q, Li N, Zhao Y.
Cell. 2024 Mar 28;187(7):1719-1732.e14.
doi: 10.1016/j.cell.2024.02.026. Epub 2024 Mar 20.
PMID: 38513663.
The glycine transporter 1 (GlyT1) = a crucial role in the regulation of inhibitory and excitatory neurotransmission by removing glycine from the synaptic cleft.
Here: cryo-EM structures of GlyT1 bound with substrate glycine and drugs ALX-5407, SSR504734, and PF-03463275 (structures captured at outward-facing, occluded, and inward-facing states).
A personal perspective of the voltage-gated potassium channel studies.
Jan LY, Jan YN.
Nat Struct Mol Biol. 2024 Mar 28.
doi: 10.1038/s41594-024-01267-w. Epub ahead of print.
PMID: 38548955.
The identification of sodium and potassium currents as underlying action potential propagation, more than 70 years ago, opened a new avenue of research into the role of ion channels.
Here: comment presenting personal perspectives of the field, from the identification of Shaker as a potential potassium channel to the mechanistic insights available to us today.
An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B.
Nat Struct Mol Biol. 2024 Mar 28.
doi: 10.1038/s41594-024-01256-z. Epub ahead of print.
PMID: 38548954.
Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family = import of oligopeptides into bacteria for nutrient uptake and to modulate the host immune response.
OppABCD = OppA: substrate-binding protein, OppB and OppC : membrane-spanning subunits, and OppD = ATPase with two NBDs.
Here: cryo-EM high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state.
Rq: there is a functionally required [4Fe-4S] cluster-binding domain in OppD.
Molecular dynamics of the human RhD and RhAG blood group proteins.
Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG.
Front Chem. 2024 Mar 19;12:1360392.
doi: 10.3389/fchem.2024.1360392.
PMID: 38566898.
Rhesus blood group antigens play an important role in transfusion medicine. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown => generated by protein modelling and molecular dynamics simulations.
Conformational changes in the Niemann-Pick type C1 protein NCR1 drive sterol translocation.
Frain KM, Dedic E, Nel L, Bohush A, Olesen E, Thaysen K, Wüstner D, Stokes DL, Pedersen BP.
Proc Natl Acad Sci U S A. 2024 Apr 9;121(15):e2315575121.
doi: 10.1073/pnas.2315575121. Epub 2024 Apr 3.
PMID: 38568972.
The Niemann-Pick type C1 is central to sterol homeostasis in eukaryotes.
The localization of S. cerevisiae NCR1 to the vacuolar membrane implies its role in sterol transport across the glycocalyx, although the existence of such a structure in fungi has been uncertain. Cryo-EM structures reveal two conformations of NCR1, termed tense and relaxed, demonstrating sterol movement through luminal domain-formed tunnels, circumventing the glycocalyx barrier.
Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants.
Pan E, Tao F, Smorodina E, Zhang S.
QRB Discov. 2024 Jan 19;5:e1.
doi: 10.1017/qrd.2024.2.
PMID: 38577032.
Structural bioinformatics study of six human ABC membrane transporters with experimentally determined cryo-electron microscopy (CryoEM) structures including ABCB7, ABCC8, ABCD1, ABCD4, ABCG1, ABCG5, and their AlphaFold2-predicted water-soluble QTY variants.
=> insight into the differences between the hydrophobic helices and hydrophilic helices => will likely further stimulate designs of water-soluble multispan TMPs and other aggregated proteins.
Titratable residues that drive RND efflux: insights from molecular simulations.
Clark R, Newman KE, Khalid S.
QRB Discovery. Published online 2024:1-25.
doi:10.1017/qrd.2024.6
RND efflux machineries are powered by proton motive force, however the proton transfer mechanism itself and indeed even its stoichiometry is still unclear.
Here: review of computational studies from the last decade that focus on elucidating the number of protons transferred per conformational cycle of the pump.
Structural analysis of resistance-nodulation cell division transporters.
Klenotic PA, Yu EW.
Microbiol Mol Biol Rev. 2024 Mar 29:e0019823.
doi: 10.1128/mmbr.00198-23. Epub ahead of print.
PMID: 38551344.
Review examining the structural basis of substrate recognition of efflux pumps and the molecular mechanisms underlying multidrug extrusion => antimicrobial resistance in bacterial pathogens.
Diverse roles of the metal binding domains and transport mechanism of copper transporting P-type ATPases.
Guo Z, Orädd F, Bågenholm V, Grønberg C, Ma JF, Ott P, Wang Y, Andersson M, Pedersen PA, Wang K, Gourdon P.
Nat Commun. 2024 Mar 27;15(1):2690.
doi: 10.1038/s41467-024-47001-4.
PMID: 38538615.
Copper transporting P-type (P1B-1-) ATPases are essential for cellular homeostasis.
Here: 4 cryo-EM structures and molecular dynamics simulations of a P1B-1-ATPase are combined to reveal that in many eukaryotes the metal binding domains (MBDs).
Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules.
Hamaguchi-Suzuki N, Adachi N, Moriya T, Yasuda S, Kawasaki M, Suzuki K, Ogasawara S, Anzai N, Senda T, Murata T.
Biochem Biophys Res Commun. 2024 Mar 28;709:149855.
doi: 10.1016/j.bbrc.2024.149855. Epub ahead of print.
PMID: 38579618.
P-gp inhibitors, such as elacridar, have been developed to circumvent the decrease in anticancer drug efficacy due to P-gp efflux.
Here: high resolution (2.5 Å) structure of the P-gp- Fab (UIC2) complex bound by three elacridar molecules (=> larger space for compound-binding sites than previously acknowledged).
Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Chi X, Chen Y, Li Y, Dai L, Zhang Y, Shen Y, Chen Y, Shi T, Yang H, Wang Z, Yan R.
Sci Adv. 2024 Mar 29;10(13):eadl3685.
doi: 10.1126/sciadv.adl3685. Epub 2024 Mar 29.
PMID: 38552027.
The solute carrier 13 (SLC13) = sodium ion-coupled anion cotransporters. They segregate into sodium ion-sulfate cotransporters (NaSs) and sodium ion-di- and-tricarboxylate cotransporters (NaDCs). NaS1 and NaDC1 regulate sulfate homeostasis and oxidative metabolism, respectively.
Here: cryoEM structures of human NaS1 (inward-facing and combined inward-facing/outward-facing conformations within a dimer both in apo and sulfate-bound states) + NaDC1’s outward-facing conformation, encompassing apo, citrate-bound, and N-(p-amylcinnamoyl) anthranilic acid (ACA) inhibitor-bound states.
=> detailed elevator mechanism driving conformational changes.
Membranes
Force-induced tail-autotomy mitochondrial fission and biogenesis of matrix-excluded mitochondrial-derived vesicles for quality control.
Liu X, Xu L, Song Y, Zhao Z, Li X, Wong CY, Chen R, Feng J, Gou Y, Qi Y, Chow HM, Yao S, Wang Y, Gao S, Liu X, Duan L.
Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2217019121.
doi: 10.1073/pnas.2217019121. Epub 2024 Mar 28.
PMID: 38547062.
Mitochondria constantly fuse and divide for mitochondrial inheritance and functions. Here: identification of a distinct type of naturally occurring fission, tail-autotomy fission, wherein a tail-like thin tubule protrudes from the mitochondrial body and disconnects, resembling autotomy.
=> separation of the matrix-excluded tubule segments into matrix-excluded mitochondrial-derived vesicles (MDVs) which recruit Parkin and LC3B, indicating the unique role of tail-autotomy fission in segregating only outer membrane components for mitophagy.
Overcoming Protein Orientation Mismatch Enables Efficient Nanoscale Light-Driven ATP Production.
Amati AM, Moning SU, Javor S, Schär S, Deutschmann S, Reymond JL, von Ballmoos C.
ACS Synth Biol. 2024 Apr 3.
doi: 10.1021/acssynbio.4c00058. Epub ahead of print.
PMID: 38569139.
ATP-producing modules energized by light-driven proton pumps are powerful tools for the bottom-up assembly of artificial cell-like systems but their maximum efficiency is prohibited by their random orientation during the reconstitution process into lipid-surrounded nanocontainers.
Here: versatile approach to uniformly orient the light-driven proton pump proteorhodopsin (pR) in liposomes.
=> uniform orientation allows for maximal rates at economical protein concentrations. The presented technology is highly customizable and not limited to light-driven proton pumps but applicable to many membrane proteins and offers a general approach to overcome orientation mismatch during membrane reconstitution.
17O Solid-State NMR Spectroscopy of Lipid Membranes.
Fu R, Ramamoorthy A.
J Phys Chem B. 2024 Apr 3.
doi: 10.1021/acs.jpcb.4c01016. Epub ahead of print.
PMID: 38568422.
Despite the limitations posed by poor sensitivity, studies have reported the unique advantages of 17O based NMR spectroscopy to study systems existing in liquid, solid, or semisolid states.
Recent studies: use of 17O NMR to study dynamic intermolecular interactions associated with some of the challenging biological systems under magic angle spinning (MAS) and aligned conditions.
Here: review on the new developments in the biological solids.
Capture of endogenous lipids in peptidiscs and effect on protein stability and activity.
Jandu RS, Yu H, Zhao Z, Le HT, Kim S, Huan T, Duong van Hoa F.
iScience. 2024 Mar 1;27(4):109382.
doi: 10.1016/j.isci.2024.109382.
PMID: 38577106.
Study of MPs in different lipid states isolated using peptidisc => observable effects on MP activity and stability. Peptidisc also enables re-incorporating specific lipids to fine-tune the protein microenvironment and assess the impact on downstream protein associations.
Molecules
High-throughput BCRP inhibitors screening system based on styrene maleic acid polymer membrane protein stabilization strategy and surface plasmon resonance biosensor.
Fang J, Shen S, Wang H, He Y, Chao L, Cao Y, Chen X, Zhu Z, Hong Z, Chai Y.
Talanta. 2024 Mar 23;274:125987.
doi: 10.1016/j.talanta.2024.125987. Epub ahead of print.
PMID: 38552478.
Novel high-throughput screening (HTS) system for BCRP inhibitors established, on the basis of SMA polymer MP stabilization strategy and SPR biosensor.
The structure, self-assembly and dynamics of lipid nanodiscs revealed by computational approaches.
Wang B, Tieleman DP.
Biophys Chem. 2024 Mar 29;309:107231.
doi: 10.1016/j.bpc.2024.107231. Epub ahead of print.
PMID: 38569455.
Review of the application of computational approaches, especially MM and MD, to characterize ND, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in ND.
Methods
Characterization of neurotransmitter inhibition for seven cathinones by a proprietary fluorescent dye method.
Persson M, Vikingsson S, Kronstrand R, Green H.
Drug Test Anal. 2024 Apr;16(4):339-347.
doi: 10.1002/dta.3547. Epub 2023 Jul 24.
PMID: 37489044.
Method measuring the inhibition of the dopamine, serotonin, and norepinephrine transporters (DAT, SERT, and NET) by stimulant drugs with use of a proprietary fluorescent dye mixture and three cell lines, each expressing a single transporter
=> semiautomated, one-pot determination of inhibition in a 384-well format.
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models.
Le VT, Malik MS, Tseng YH, Lee YC, Huang CI, Ou YY.
Comput Biol Chem. 2024 Mar 20;110:108055.
doi: 10.1016/j.compbiolchem.2024.108055. Epub ahead of print.
PMID: 38555810.
DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-window convolutional neural networks (mCNNs) for effective classification of membrane proteins into ion channels and ion transporters.
The data and source codes in this study are publicly available at the following link: https://github.com/s1129108/DeepPLM_mCNN.
Mapping of cytosol-facing organelle outer membrane proximity proteome by proximity-dependent biotinylation in living Arabidopsis cells.
Bao X, Jia H, Zhang X, Tian S, Zhao Y, Li X, Lin P, Ma C, Wang P, Song CP, Zhu X.
Plant J. 2024 Apr;118(1):7-23.
doi: 10.1111/tpj.16641. Epub 2024 Jan 23.
PMID: 38261530.
OM proximity labeling system using biotin ligase-mediated proximity biotinylation to identify the proximity proteins of the outer membranes of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells.
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?
Xie T, Huang J.
J Chem Inf Model. 2024 Apr 2.
doi: 10.1021/acs.jcim.3c01936. Epub ahead of print.
PMID: 38564295.
To investigate the performance of current protein structure prediction methods in alternative conformation prediction => data set, named IOMemP, consisting of 32 experimentally determined high-resolution IF and OF structures of 16 membrane proteins with substantial conformational changes.
Benchmarking various PSP methods against the IOMemP dataset, containing high-resolution IF and OF structures of MPs => consistent state preferences and highlights the influence of coevolution information on these preferences. AlphaFold, even without coevolution information, shows unbiased energy estimation between experimental IF and OF conformations, suggesting its potential for ACP advancement.
Microbio
Removal of Pseudomonas type IV pili by a small RNA virus.
Thongchol J, Yu Z, Harb L, Lin Y, Koch M, Theodore M, Narsaria U, Shaevitz J, Gitai Z, Wu Y, Zhang J, Zeng L.
Science. 2024 Apr 5;384(6691):eadl0635.
doi: 10.1126/science.adl0635. Epub 2024 Apr 5.
PMID: 38574145.
PP7 (= Pseudomonas phage) infects its host cell by means of a virus protein called Mat that attached to the bacterium’s type IV pilus. The pilus retracts and drags the phage to the bacterial cell surface. At the point of virus entry into the cell, the pilus is bent and snaps off, thus disabling and reducing the bacterium’s ability to infect its own host.
Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS
Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT.
bioRxiv [Preprint]. 2024 Mar 16:2024.03.16.585348.
doi: 10.1101/2024.03.16.585348.
PMID: 38559044.
Small molecule targeting essential proteins in P. aeruginosa OM were discovered, exemplified by BRD1401’s specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Further investigations revealed BRD1401’s mechanism of action involves targeting the outer membrane protein OprH, disrupting its interaction with LPS and enhancing membrane fluidity, thus highlighting the potential of whole-cell screening to unveil novel pathogen biology.
Miscellaneous
Observation of a single protein by ultrafast X-ray diffraction.
Ekeberg T, Assalauova D, Bielecki J, Boll R, Daurer BJ, Eichacker LA, Franken LE, Galli DE, Gelisio L, Gumprecht L, Gunn LH, Hajdu J, Hartmann R, Hasse D, Ignatenko A, Koliyadu J, Kulyk O, Kurta R, Kuster M, Lugmayr W, Lübke J, Mancuso AP, Mazza T, Nettelblad C, Ovcharenko Y, Rivas DE, Rose M, Samanta AK, Schmidt P, Sobolev E, Timneanu N, Usenko S, Westphal D, Wollweber T, Worbs L, Xavier PL, Yousef H, Ayyer K, Chapman HN, Sellberg JA, Seuring C, Vartanyants IA, Küpper J, Meyer M, Maia FRNC.
Light Sci Appl. 2024 Jan 12;13(1):15.
doi: 10.1038/s41377-023-01352-7. PMID: 38216563.
The concept of using ultrashort X-ray pulses to capture images of single proteins in a frozen state drove the development of XFEL, eliminating the need for crystals as signal amplifiers and enabling data collection before sample destruction. This approach was initially showcased a decade ago with the giant mimivirus.
Here: X-ray diffraction pattern from a single protein, E. coli GroEL, marks a significant milestone: feasibility of ultrafast imaging of single proteins.
A host-microbiota interactome reveals extensive transkingdom connectivity.
Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW.
Nature. 2024 Apr;628(8006):171-179.
doi: 10.1038/s41586-024-07162-0. Epub 2024 Mar 20.
PMID: 38509360.
Study of human exoproteome-microbiome interactions on a proteome scale, revealing thousands of previously unknown interactions involving hundreds of bacterial strains and host proteins. These interactions suggest underlying biological logic, such as conspecific strains sharing binding patterns and tissue-specific interactions, with implications for niche colonization, tissue remodeling, and immunomodulation, highlighting the intricate molecular-level interplay between the microbiota and human health and disease.
Bridging structural and cell biology with cryo-electron microscopy.
Nogales E, Mahamid J.
Nature. 2024 Apr;628(8006):47-56.
doi: 10.1038/s41586-024-07198-2. Epub 2024 Apr 3.
PMID: 38570716.
Here: discussion how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
mRNA drug offers hope for treating a devastating childhood disease.
Dolgin E.
Nature. 2024 Apr 3.
doi: 10.1038/d41586-024-00954-4. Epub ahead of print.
PMID: 38570656.
Drug trial results show that vaccines aren’t the only use for the mRNA technology behind the most widely used COVID-19 jabs.
Gut bacteria break down cholesterol – hinting at probiotic treatments.
Nowogrodzki J.
Nature. 2024 Apr 2.
doi: 10.1038/d41586-024-00955-3. Epub ahead of print.
PMID: 38565909.
Researchers have identified gut bacteria that can transform artery-clogging cholesterol into a more harmless form. In previous work, the authors showed that a bacterial enzyme can metabolize cholesterol into coprostanol, a lipid that is excreted instead of absorbed by the body. They have now identified gut bacteria that correlate with lower cholesterol levels in people. Whether these bacteria can directly influence blood cholesterol in people needs to be confirmed, but if they could be delivered to the right place in the gut, it might lead to new treatments.
How scientists are making the most of Reddit.
Docter-Loeb H.
Nature. 2024 Apr;628(8006):221-223.
doi: 10.1038/d41586-024-00906-y.
PMID: 38561407.
As X wanes, researchers are turning to Reddit for insights and data, and to better connect with the public.