Membrane’s digest 

MP

Among the recombinant TSPOs, the BcTSPO.

Issop L, Duma L, Finet S, Lequin O, Lacapère JJ. 

Biochimie. 2024 Jan 25:S0300-9084(24)00029-4. 

doi: 10.1016/j.biochi.2024.01.011. 

Overexpression of recombinant Bacillus cereus TSPO (BcTSPO) in E. coli => recovery with a bound hemin both in bacterial membrane and inclusion bodies.

BcTSPO purified in SDS from IB = structured + can bind various ligands (NMR experiments suggest that different aa of the binding cavity are involved). 

PPIX binds to the cavity of BcTSPO => question of the role of TSPO in heme biosynthesis.

Exploring the K+ binding site and its coupling to transport in the neurotransmitter:sodium symporter LeuT. 

Schmidt SG, Nygaard A, Mindell JA, Loland CJ.

Elife. 2024 Jan 25;12:RP87985. 

doi: 10.7554/eLife.87985. 

The neurotransmitter:sodium symporters (NSSs) are secondary active transporters that couple the reuptake of substrate to the symport of one or two sodium ions. 

LeuT (= bacterial NSS homologue) could serve as a model protein for the exploration of K+ binding in NSS proteins. 

Here: impact of K+ on substrate affinity and transport as well as on LeuT conformational equilibrium states (radioligand binding assays and FRET) 

=> K+ binding to LeuT modulates substrate transport and that the K+ affinity.

Probing the pH Sensitivity of OprM: Insights into Metastable States and Semi-Open Conformation.

Roy RK, Patra N. 

J Phys Chem B. 2024 Jan 25;128(3):622-634. 

doi: 10.1021/acs.jpcb.3c05384. 

Analysis of OprM pore opening using MD => metastable states in between open and closed states. 

=> Upon mutation of R376, the energy barrier for the conversion of the close to open conformation decreases. 

=> constant pH MD  was performed to capture the effect of pH in both conformations: pH-responsive conformational states characteristics.

Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance.

Behera DU, Gaur M, Sahoo M, Subudhi E, Subudhi BB. 

RSC Med Chem. 2023 Oct 28;15(1):127-138. 

doi: 10.1039/d3md00483j. 

Molecular docking to identify inhibitor and substrate hits for the AcrB binding pocket + MIC evaluation of the efflux inhibition in combination with colistin + checkerboard assay to demonstrate synergism + Time-kill assay. 

=> argatroban = bacterial efflux inhibitor.

Residues within the LptC transmembrane helix are critical for Escherichia coli LptB2 FG ATPase regulation. 

Cina NP, Frank DW, Klug CS.

Protein Sci. 2024 Feb;33(2):e4879. 

doi: 10.1002/pro.4879. 

7 LPS transport (Lpt) proteins => movement of LPS to the OM.

LptB2 FG (IM component of the Lpt bridge) = type VI ABC transporter

 => driving force for LPS extraction from the IM and subsequent transport across a stable protein bridge to the outer leaflet of the OM. 

LptC = periplasmic protein anchored to the IM by a single TM helix. LptC regulates the ATPase activity of LptB2 FG. 

Here: effects of LptC mutations in vivo in unbiased alanine screen + functional effects of these mutations by nanoDSF and SDSL-EPR in combination with in vitro ATPase assay. 

=> specific residues in the TM helix of LptC destabilize the LptB2 FGC complex and regulate the ATPase activity of LptB.

Methods

Atomic force microscope kymograph analysis: A case study of two membrane proteins. 

Weaver DR, Schaefer KG, King GM.

Methods. 2024 Jan 27:S1046-2023(24)00032-X. 

doi: 10.1016/j.ymeth.2024.01.013. 

Kymograph used by AFM community to boost temporal resolution: well suited for revealing protein dynamics at the single molecule level in near-native conditions. 

Here: conformational dynamics of difficult-to-study sparse distributions of MPs, comparing AFM kymograph analysis for SecDF (conformational dynamics primarily in direction normal to the membrane surface) and Pgp (combination of lateral dynamics and vertical motion).

=> kymograph analysis is largely robust to lateral drift, however if there is significant azimuthal maximum height dependence, the rotational drift can potentially produce artifactual transitions. 

Measuring the height is generally superior to measurement of width.

The blobulator: a webtool for identification and visual exploration of hydrophobic modularity in protein sequences. 

Pitman C, Santiago-McRae E, Lohia R, Bassi K, Joseph TT, Hansen MEB, Brannigan G.

bioRxiv [Preprint]. 2024 Jan 22:2024.01.15.575761. 

doi: 10.1101/2024.01.15.575761. 

”the blobulator”: web interface to detect intrinsic modularity in any protein sequence based on hydrophobicity. 

Case studies: a globular protein, two orthologous MPs, and an IDP.

The blobulator GUI can be found at www.blobulator.branniganlab.org.

Streamlined Biotinylation, Enrichment and Analysis for Enhanced Plasma Membrane Protein Identification Using TurboID and TurboID-Start Biotin Ligases. 

Sarihan M, Kasap M, Akpinar G.

J Membr Biol. 2024 Jan 30. 

doi: 10.1007/s00232-023-00303-y. 

The hydrophobic nature and low expression levels of Plasma membrane proteins (PMPs) => challenges for conventional enrichment methods. 

Here: novel TurboID-based enrichment approach for PMPs (reduction in non-specific biotinylation events => improved PMP enrichment and assessment of the subcellular proteome associated with the plasma membrane).

Proton Logic Gate Based on a Gramicidin-ATP Synthase Integrated Biotransducer. 

Chen Y, Méhes G, Liu B, Gao L, Cui M, Lin C, Hirono-Hara Y, Hara KY, Mitome N, Miyake T.

ACS Appl Mater Interfaces. 2024 Jan 31. 

doi: 10.1021/acsami.3c15251. 

Development of a hybrid biotransducer composed of ATP synthase and gramicidin A (gA), controlled by a sulfonated polyaniline (SPA) conducting polymer layer deposited on a microelectrode, and to simulate a model circuit that integrates bidirectional biological signal transmission through supported lipid bilayers (SLBs). 

Proton transport across the gA channel controlled by applying voltage to the SPA or introducing calcium ions (inhibitor) and EDTA molecules (inhibitor remover). 

=> the proton current is controlled by the flux of ADP and calcium ions. 

XOR logic gate as an enzymatic logic system where the output proton current is controlled by Input A (ATP synthase) and Input B (calcium ions), making use of the unidirectional and bidirectional transmission of protons in ATP synthase and gA, respectively.

😮🤩🤯

Microbio

Escherichia coli CadB is capable of promiscuously transporting muropeptides and contributing to peptidoglycan recycling. 

Simpson BW, Gilmore MC, McLean AB, Cava F, Trent MS. 

J Bacteriol. 2024 Jan 25;206(1):e0036923. 

doi: 10.1128/jb.00369-23. Epub 2024 Jan 3. 

E. coli has dedicated pathways to recycle almost all cell wall fragments they produce. AmpG and Opp are two known recycling transporters. 

Here: identification of a 3rd transporter, CadB.

The EcoCyc Database. 

Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J, Paulsen I.

EcoSal Plus. 2023 Dec 12;11(1):eesp00022023. 

doi: 10.1128/ecosalplus.esp-0002-2023. 

EcoCyc = bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. 

Long-term goal = description of the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts.

Includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway + information on the regulation of gene expression, gene essentiality, and nutrient conditions.

Also contains tools for the analysis of high-throughput data sets + steady-state metabolic flux model generated from each new version of EcoCyc and can be executed online (prediction of metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions). 

Discovery of a structural class of antibiotics with explainable deep learning. 

Wong, F., Zheng, E.J., Valeri, J.A. et al. 

Nature 626, 177–185 (2024). https://doi-org.insb.bib.cnrs.fr/10.1038/s41586-023-06887-8

An explainable deep learning model using a chemical substructure-based approach for the exploration of chemical compound libraries identified structural classes of compounds with antibiotic activity and low toxicity.

Killer prey: Ecology reverses bacterial predation.

Vasse M, Fiegna F, Kriesel B, Velicer GJ. 

PLoS Biol. 2024 Jan 23;22(1):e3002454. 

doi: 10.1371/journal.pbio.3002454. 

The temperature at which prey grow before interacting with a bacterial predator can determine the very direction of predation, reversing predator and prey identities. This suggests that the sign of lethal microbial antagonisms may often change across abiotic gradients in natural microbial communities.

The benefits of not tidying up labs (just kidding !!! don’t try this in our lab ;-D): the discovery was made because the researchers left the prey on the bench for 24 hours at room temperature instead of the usual 32°C… because there was simply no room left in the incubator !

podcasted in the following (in french):

https://www.radiofrance.fr/franceculture/podcasts/avec-sciences/des-bacteries-changent-de-camp-et-passent-de-proies-a-predateurs-4961846

Miscellaneous

Communities in structural biology.

Winn MD.

Nat Struct Mol Biol. 2024 Jan;31(1):6-7. 

doi: 10.1038/s41594-023-01197-z. PMID: 38253661.

Collaboration is key to modern science, with major advances using multiple complementary approaches and dependent on sophisticated infrastructure. Yet science is also highly personal, as each person carves out a reputation and career. How does this work out in reality, and how can communities be built to benefit science and scientists?

A very interesting comment on the evolution of academic science in the context of technological breakthroughs and social media. Part of NSMB’s 30th anniversary edition.

Forget lung, breast or prostate cancer: why tumour naming needs to change

Nature 626, 26-29 (2024)

doi: https://doi-org.insb.bib.cnrs.fr/10.1038/d41586-024-00216-3

The conventional way of classifying metastatic cancers according to their organ of origin is denying people access to drugs that could help them.

Blood pressure pulsations modulate central neuronal activity via mechanosensitive ion channels.

Luna Jammal Salameh et al.,

Science383,eadk8511(2024).

DOI:10.1126/science.adk8511

Spontaneous slow oscillations have been described in the rat olfactory bulb local field potential, even in the absence of respiration. Jammal Salameh et al. discovered a subpopulation of neurons within the olfactory bulb that can directly sense cardiovascular pressure pulsations. The modulation of their excitability is transduced by mechanosensitive ion channels.

Directed evolution of enzymatic silicon-carbon bond cleavage in siloxanes.

Nicholas S. Sarai et al., 

Science 383, 438-443 (2024).

DOI:10.1126/science.adi5554

Using directed evolution, scientists have created the first enzyme known to break a silicon-carbon bond. The finding could be a preliminary step toward biodegrading volatile methyl siloxanes—chemicals that are made by the megaton each year.