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Membrane’s digest


R6G narrows BmrA conformational spectrum for a more efficient use of ATP

A Gobet, L Moissonnier, E Zarkadas, S Magnard, E Bettler, J Martin, R Terreux, G Schoehn, C Orelle, JM Jault, P Falson, V Chaptal.

bioRxiv 2024.03.15.585201;


Rhodamine6G binding on a catalytic mutant of BmrA induces cooperative ATP binding, leading to structural transitions from inward to outward facing conformations observed via cryoEM.

This asymmetric behavior, explored through structural-enzymology, demonstrates how drug binding alters the conformational spectrum of Nt-binding domains, optimizing ATP-dependent conversion to the OF-facing state and enhancing transporter activity.

Drug diffusion is rate proposed to be the rate-limiting step.


Dynamic duo: Kir6 and SUR in KATP channel structure and function.

Patton BL, Zhu P, ElSheikh A, Driggers CM, Shyng SL.

Channels (Austin). 2024 Dec;18(1):2327708.

doi: 10.1080/19336950.2024.2327708. PMID: 38489043.

KATP channels (= Kir6 and SUR subunits) regulate cellular activity by responding to changes in cellular energetics and membrane potential.

SUR subunits = part of an eight-subunit complex, modulate KATP gating through ATP binding.

Review on functional data + cryoEM structures of KATP channels


Structure of a Ca2+ bound phosphoenzyme intermediate in the inward-to-outward transition of Ca2+-ATPase 1 from Listeria monocytogenes

Sara Basse HansenRasmus Kock FlygaardMagnus KjaergaardPoul Nissen

bioRxiv 2024.03.06.583647; 


P-type Ca2+-ATPases maintain low cytosolic calcium levels and steep gradients, crucial for cellular function.

Here: single-molecule FRET studies and cryo-EM structures => mechanism of calcium transport, highlighting an irreversible step—likely calcium release—as pivotal for preventing reflux against gradients. A newly obtained cryo-EM structure of a mutant Ca2+-ATPase reveals an intermediate state, suggesting a mechanism where ADP release and cytoplasmic domain reorganization precede calcium release, crucial for the inward-to-outward transition in these transporters.


ER membrane complex (EMC): Structure, functions, and roles in diseases.

Zhu Q, Zhu X, Zhang L.

FASEB J. 2024 Mar 31;38(6):e23539.

doi: 10.1096/fj.202302266R. PMID: 38498340.

ER = crucial site for various cellular processes, including lipid and carbohydrate biosynthesis, protein folding, and membrane protein transportation. The ER membrane complex (EMC) plays a vital role in maintaining the quality control of MPs, impacting processes like protein synthesis, organelle communication, and cellular stress responses.

Disruption of EMC function has been linked to neurodevelopmental disorders and cancer => significant focus of research over the past decade, with studies aiming to elucidate its structure, function, and implications in disease pathogenesis.

Fluoride Ion Binding and Translocation in the CLCF Fluoride/Proton Antiporter: Molecular Insights from Combined Quantum-Mechanical/Molecular-Mechanical Modeling.

Chon NL, Lin H.

J Phys Chem B. 2024 Mar 21;128(11):2697-2706.

doi: 10.1021/acs.jpcb.4c00079. PMID: 38447081.

CLCF fluoride/proton antiporters facilitate the expulsion of fluoride ions from bacterial cells => fluoride resistance.

A quantum-mechanical/molecular-mechanical (QM/MM) study of an Enterococci casseliflavus CLCF homologue => key steps in the transport cycle, including the role of external gating residues in facilitating fluoride movement and subsequent acceptance of a proton by displaced residues to initiate the next cycle.


Computational design of soluble functional analogues of integral membrane proteins.

Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE.

bioRxiv [Preprint]. 2024 Mar 7:2023.05.09.540044.

doi: 10.1101/2023.05.09.540044. PMID: 38496615.

Using a deep learning approach, design of complex protein folds and soluble analogues of integral MPs, including unique topologies like those found in GPCRs, in solution.

Biophysical analyses => high thermal stability, and experimental structures confirmed remarkable design accuracy.


Multidrug efflux in Gram-negative bacteria: structural modifications in active compounds leading to efflux pump avoidance. 

Gurvic, D., Zachariae, U.

npj Antimicrob Resist 2, 6 (2024).

To understand how compounds evade Gram negative efflux pumps, authors analyzed the activity of 73,737 compounds across wild-type, efflux-deficient, and hyper-permeable strains of E. coli.

Computational investigation of the molecular features within this dataset => identification of specific chemical groups that increase the likelihood of evading efflux, emphasizing the role of efflux pumps in determining drug bioactivity in Gram-negative bacteria.


Molecular determinant deciphering of MIC-guided RND efflux substrates in E. coli

Johan Revol-Tissot, Gérard Boyer, Sandrine Alibert.

Front. Drug Discov., 08 March 2024 Sec. Anti-Infective Agents

Volume 4 – 2024 |

Study investigating molecular determinants behind reduced antibiotic activity associated with RND efflux pumps by analyzing MIC data from in vitro tests on various compounds.

By focusing on efflux-resistant Escherichia coli strains, authors identify substituents influencing the AcrAB-TolC efflux system => Structure-Activity Relationships and pharmacodynamic responses.


Structural mechanisms for VMAT2 inhibition by tetrabenazine.

Dalton MP, Cheng MH, Bahar I, Coleman JA.

Elife. 2024 Mar 22;12:RP91973.

doi: 10.7554/eLife.91973. PMID: 38517752.

The vesicular monoamine transporter 2 (VMAT2) is crucial for neurotransmitter loading into synaptic vesicles and is implicated in neuropsychiatric disorders and drug actions.

Here: cryo-EM structure of VMAT2 in complex with tetrabenazine (TBZ), revealing TBZ’s interaction at a central site, locking VMAT2 in an occluded state and elucidating non-competitive inhibition. Critical residues for gating and proton transduction are identified, along with insights into VMAT2 architecture and function.



MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.

Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R.

EMBO J. 2024 Mar 15.

doi: 10.1038/s44318-024-00063-y. PMID: 38491296.

MemPrep = method for purifying organelle membranes from yeast. Purity of membrane preparations checked by proteomics. Quantitative lipidomics => lipid composition.

This study provides a baseline for studying MP biogenesis and to the understanding the role of lipids in regulating the unfolded protein response (UPR).


Serotonin Signaling through Lipid Membranes.

Kalinichenko LS, Kornhuber J, Sinning S, Haase J, Müller CP.

ACS Chem Neurosci. 2024 Mar 18.

doi: 10.1021/acschemneuro.3c00823. PMID: 38499042.

MPs controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites.

Emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins => affects the synaptic efficacy at the synapse.

Lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse.



Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment.

Bharmoria P, Tietze AA, Mondal D, Kang TS, Kumar A, Freire MG.

Chem Rev. 2024 Mar 4.

doi: 10.1021/acs.chemrev.3c00551. PMID: 38437627.

Ionic liquids (ILs) have emerged as promising solvents for stabilizing proteins, with various approaches reported including their use as solvents, co-solvents, adjuvants, surfactants, and in aqueous biphasic systems. Analysis of published works highlights the bispecific nature of IL-protein interactions, impacting protein stability, conformational changes, and purification, with identified promising systems for future applications such as protein packaging and detergent use.



5-HT_FAsTR: a versatile, label-free, high-throughput, fluorescence-based microplate assay to quantify serotonin transport and release.

Bukowski L, Strøm ME, Andersen JL, Maesen JB, Tian L, Sinning S.

Sci Rep. 2024 Mar 19;14(1):6541.

doi: 10.1038/s41598-024-56712-z. PMID: 38504103.

The investigation of serotonin transporters have relied almost exclusively on the use of radiolabeled serotonin in heterogenous end-point assays.

Here: adaptation of the genetically encoded fluorescent biosensor, iSeroSnFR, to establish and validate ”Serotonin (5-HT) Fluorescence Assay for Transport and Release” = 5-HT_FAsTR, for functional and pharmacological studies of serotonin transport and release.

Single-molecule tethering methods for membrane proteins.

Lee D, Min D.

Methods Enzymol. 2024;694:263-284.

doi: 10.1016/bs.mie.2023.12.013. PMID: 38492954.

Development of stable single-molecule tethering methods for MPs, crucial for studying their structural dynamics using magnetic tweezers. Traditional tether complexes are prone to force-induced bond breakage, limiting their observation stability.

Here: methods (employing click chemistry, steptavidin-biotin binding, SpyCatcher-SpyTag, and SnoopCatcher-SnoopTag conjugation), offer more stable tethering.


Robust magnetic tweezers for membrane protein folding studies.

Kim S, Min D.

Methods Enzymol. 2024;694:285-301.

doi: 10.1016/bs.mie.2023.12.014. PMID: 38492955.

Single-molecule magnetic tweezers have recently been adapted for monitoring the interactions between transmembrane helices of MPs within lipid bilayers.

Here: procedures of conducting studies on membrane protein folding using a robust magnetic tweezer method (=> thousands of (un)folding transitions over hours).

=> folding pathways, folding time scales, and map of the folding energy landscapes + allow for estimating the folding speed limit of helical MPs, which serves as a link between the kinetics and barrier energies.


Sample Preparation for Electron Cryo-Microscopy of Macromolecular Machines.

Deniaud A, Kabasakal BV, Bufton JC, Schaffitzel C.

Adv Exp Med Biol. 2024;3234:173-190.

doi: 10.1007/978-3-031-52193-5_12. PMID: 38507207.

Discussion of the various widely applicable approaches to improve sample quality for structural analysis by cryo-EM.


Theoretical framework and experimental solution for the air-water interface adsorption problem in cryoEM.

Kang JS, Zhou X, Liu YT, Wang K, Zhou ZH.

Biophys Rep. 2023 Aug 31;9(4):215-229.

doi: 10.52601/bpr.2023.230008. PMID: 38516618.

CryoEM: challenges arise when samples behave differently than in negative-stain electron microscopy.

Here: a theoretical formulation is developed explaining this behavior by predicting particles migrating to the air-water interface to minimize surface energy, which can be mitigated by surfactants.


Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors.

Lutomski CA, El-Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen HY, Pagel K, Mullen C, Syka JEP, Robinson CV.

Angew Chem Weinheim Bergstr Ger. 2023 Sep 4;135(36):e202305694.

doi: 10.1002/ange.202305694. PMID: 38516403.

To address the challenge of analyzing MPs by native MS, a modified Orbitrap Eclipse Tribrid mass spectrometer coupled with an IR laser in a high-pressure linear ion trap is utilized.

=> MPs can be liberated from detergent micelles, enabling top-down MS via infrared multiphoton dissociation (IRMPD). Fragmentation patterns of MPs are analyzed, revealing successive cleavage of adjacent amino acids within TM domains. Gas-phase molecular dynamics simulations support these findings, offering insights into protein structure and fragmentation mechanisms.



Randomness french mathematician wins Abel Prize 🇫🇷🐔🍾


The winner of this years Abel mathematics prize, Michel Talagrand, developed formulae to make random processes more predictable. He showed that the contributions of many variables that influence processes such as a rivers water level often cancel each other out — making the overall result less variable, not more. Talagrand, who is retired, loves to challenge his fellow mathematicians: he keeps a list of problems on his website, offering cash to those who solve it as long as hes not too senile to understand the proofs I receive”.


‘A landmark moment: scientists use AI to design antibodies from scratch

Modified protein-design tool could make it easier to tackle challenging drug targets — but AI antibodies are still a long way from reaching the clinic.

Researchers (lead by David Baker) have used generative AI to help them make completely new antibodies for the first time.

The proof-of-principle work, is reported week in the following bioRxiv preprint:

Atomically accurate de novo design of single-domain antibodies

Nathaniel R. Bennett et al. bioRxiv 2024.03.14.585103.

Structure-guided drug discovery: back to the future.

Arrowsmith CH.

Nat Struct Mol Biol. 2024 Mar;31(3):395-396.

doi: 10.1038/s41594-024-01244-3. PMID: 38486110.

Over the past 30 years, the field of structural biology and its associated biological insights have seen amazing progress. In this Comment, Cheryl Arrowsmith recount several milestones in the field and how lessons from the past can be applied.


Snake Steak Could Be a Climate-Friendly Source of Protein

Scientific American

March 14, 2024

Pythons turn their food into meat pretty efficiently, a study finds, making them an intriguing alternative to climate-unfriendly cows.


Meet the real-life Dune sandworms

By Julian Nowogrodzki

Nature 627, 474-475 (2024)


The monstrous sandworms depicted in the movie Dune share similarities with real-life worms found on Earth. Some giant worms on Earth can grow up to 2-3 meters long and ambush prey like octopus and squid, while others have teeth for burrowing or catching prey.


Ancient viruses helped speedy nerves evolve

reference article:

Ghosh T et al. Cell. 2024. PMID: 38364788.

Some viruses can permanently insert DNA into the genetic material of invaded cells, a process that aids evolutionary processes over time.

Myelin facilitates faster transmission of electrical signals in nerves, enabling the growth of longer and thinner fibers, leading to increased brain complexity and vertebrate diversity. Remnants of an ancient viral infection play a crucial role in producing myelin, a protein essential for insulating nerve fibers in most vertebrates.


Molecular Crowding: The History and Development of a Scientific Paradigm.

Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A.

Chem Rev. 2024 Mar 11.

doi: 10.1021/acs.chemrev.3c00615. PMID: 38466779.

The concept of molecular crowding has gained acceptance since its inception in the 1980s, with broader recognition emerging in the late 1990s.

Here: review on the various aspects influenced by crowding and discussion of its evolution from colloidal and polymer physics to a biological perspective.