Membrane’s digest
MP
Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E.
Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota.
Nat Commun. 2024 Jan 10;15(1):429.
doi: 10.1038/s41467-023-44426-1.
T6SS inhibits competitors through contact-dependent translocation of toxic effector proteins. The genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of the canonical membrane complex (MC) that anchor the T6SS to the cell envelope in Proteobacteria.
Here: identification of 5 genes in Bacteroides fragilis that are essential for T6SS function and encode a Bacteroidota-specific MC.
=> electron microscopy and protein-protein interaction network (and stoichiometry) underlying the assembly of the MC.
Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM.
Structural basis of prostaglandin efflux by MRP4.
Nat Struct Mol Biol. 2024 Jan 12.
doi: 10.1038/s41594-023-01176-4.
MRP4 = broadly expressed ABC transporter that is transporting prostanoids (signaling molecules derived from unsaturated fatty acids).
Here: cryoEM to determine 6 structures of ND-reconstituted MRP4 at various stages throughout its transport cycle: Substrate-bound structures of MRP4 in complex with PGE1, PGE2 and the DHEA-S, catalytically compromised MRP4 mutant bound to ATP-Mg2+.
Goel S, Feisal MR, Danmaliki GI, Liu PB, Bishop RE, Hwang PM.
Probing amino acid side chains of the integral membrane protein PagP by solution NMR: Side chain immobilization facilitates association of secondary structures.
Biochim Biophys Acta Biomembr. 2024 Jan 11:184281.
doi: 10.1016/j.bbamem.2024.184281.
ssNMR of large proteins = hampered by rapid signal decay => 1H-13C magnetization in methyl groups and/or backbone amide 1H-15N magnetization in perdeuterated environment.
Here: demonstration that biosynthetical incorporation additional 1H-12C groups that possess long-lived magnetization using cost-effective partially deuterated or unlabeled amino acid precursors added to E. coli growth media is possible. Results obtained on PagP in ”membrane-mimetic dodecylphosphocholine micelles” (hum hum, NLDR).
Gradisch R, Schlögl K, Lazzarin E, Niello M, Maier J, Mayer FP, Alves da Silva L, Skopec SMC, Blakely RD, Sitte HH, Mihovilovic MD, Stockner T.
Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors.
Nat Commun. 2024 Jan 10;15(1):417.
doi: 10.1038/s41467-023-44637-6.
Serotonin transporter (SERT) = clearance of extracellular serotonin following vesicular release (drugs used to treat neurobehavioral disorders trap SERT by blocking this transport / drugs of abuse reverse SERT directionality, causing serotonin efflux).
Here: uncovering of the coupling mechanism between the substrate and the transporter by combining MD with biochemistry.
Cooper BF, Ratkevičiūtė G, Clifton LA, Johnston H, Holyfield R, Hardy DJ, Caulton SG, Chatterton W, Sridhar P, Wotherspoon P, Hughes GW, Hall SC, Lovering AL, Knowles TJ.
An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system.
EMBO Rep. 2024 Jan 16.
doi: 10.1038/s44319-023-00014-4.
The PqiC lipoprotein a component of the putative envelope spanning Pqi lipid transport system forms an octameric toroid which stabilises the interaction between the Gram-negative OM and the remainder of the Pqi complex enabling its function.
=> PqiC assembles an octameric toroid which embeds partially into the inner leaflet.
=> The PqiC toroid receives the C-terminus of PqiB stabilising its interaction with the outer membrane.
=> The trio of Pqi proteins assemble a complex which spans cell envelope.
Molecules
Yoon S, Bae HE, Hariharan P, Nygaard A, Lan B, Woubshete M, Sadaf A, Liu X, Loland CJ, Byrne B, Guan L, Chae PS.
Rational Approach to Improve Detergent Efficacy for Membrane Protein Stabilization.
Bioconjug Chem. 2024 Jan 12.
doi: 10.1021/acs.bioconjchem.3c00507.
Synthesis of 2 sets of tandem malonate-derived glucoside (TMG) variants designed to increase the alkyl chain density in micelle interiors.
Evaluation with MPs including a GPCR, one of these TMG detergent was found to be substantially more efficient at extracting MPs and at preserving protein integrity in the long term.
=> inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study.
Methods
Marin E, Kovalev K, Poelman T, Veenstra R, Borshchevskiy V, Guskov A.
Custom Design of a Humidifier Chamber for InMeso Crystallization.
Cryst Growth Des. 2023 Dec 12;24(1):325-330.
doi: 10.1021/acs.cgd.3c01034.
Despite SP cryoEM and cryoET, certain scientific methods, such as time-resolved crystallography, still mostly rely on crystallization techniques, such as LCP or in meso crystallization.
Here: open-access blueprint for a humidity control chamber designed for LCP/in meso crystallization using a Gryphon crystallization robot.
Dobson L, Gerdán C, Tusnády S, Szekeres L, Kuffa K, Langó T, Zeke A, Tusnády GE.
UniTmp: unified resources for transmembrane proteins.
Nucleic Acids Res. 2024 Jan 5;52(D1):D572-D578.
doi: 10.1093/nar/gkad897.
UNIfied database of TransMembrane Proteins (UniTmp) = comprehensive and freely accessible resource of transmembrane protein structural information at different levels, from localization of protein segments, through the topology of the protein to the membrane-embedded 3D structure.
unified platform that merges TOPDB (Topology Data Bank of Transmembrane Proteins), TOPDOM (database of conservatively located domains and motifs in proteins), PDBTM (Protein Data Bank of Transmembrane Proteins) and HTP (Human Transmembrane Proteome).
=> can be accessed at https://www.unitmp.org.
Microbials
Veisi R, Nazarian S, Fathi J, Hadi N.
Expression and purification of TolC as a recombinant protein vaccine against Shigella flexneri and evaluation of immunogenic response in mice.
Microb Pathog. 2024 Jan 9:106539.
doi: 10.1016/j.micpath.2024.106539.
Reverse vaccinology = novel strategy that evaluate genome or proteome of the organism to find a new promising vaccine candidate.
Here: immunogenicity of a designed-recombinant antigen is evaluated through the in silico studies and animal experiments.
TolC was selected and confirmed among candidates (evaluated for TM domains, homology, conservation, antigenicity, solubility, and B- and T-cell prediction).
=> recombinant TolC protein after expression and purification, was administered to mice.
=> immunized mice depicted effective protection against Shigella. flexneri.
Miscellaneous
Organize your –80 °C freezer to save time and prevent frozen fingertips
doi: https://doi.org/10.1038/d41586-024-00031-w
Start the new year by sorting out your lab’s cold storage, to simplify purchasing, improve experiment planning and reduce the frequency of lost samples.
“We reorganized only two or three boxes at a time and kept our boxes on ice to keep everything as cold as possible.
Although this extended the entire process, it was ultimately worth it to preserve the integrity of our research materials.
We recognize that organizing the lab freezers is a massive undertaking. But organization is a gift that keeps on giving all year long. So don’t wait — resolve to get organized, stay organized and make your –80 °C freezer goals your lab’s new reality”.
‘Set it and forget it’: automated lab uses AI and robotics to improve proteins
Nature 625, 436 (2024)
doi: https://doi-org.insb.bib.cnrs.fr/10.1038/d41586-024-00093-w
References: Rapp, J. T., Bremer, B. J. & Romero, P. A. Nature Chem. Eng. https://doi-org.insb.bib.cnrs.fr/10.1038/s44286-023-00002-4 (2024).
A self-driving lab system spent half a year engineering enzymes to work at higher temperatures.
Bacteria stitch exotic building blocks into novel proteins
doi: 10.1126/science.z1y6y48
Efficient method for creating proteins with unusual amino acids opens the door to new medicines and catalysts.