bims-mimbat 2022-07-31 papers

Issue of 2022‒07‒31
five papers selected by
José Carlos de Lima-Júnior
University of California San Francisco

Membranes (Basel). 2022 Jul 20. pii: 718. [Epub ahead of print]12(7):

Protons in Gating the Kv1.2 Channel: A Calculated Set of Protonation States in Response to Polarization/Depolarization of the Channel, with the Complete Proposed Proton Path from Voltage Sensing Domain to Gate.

Alisher M Kariev, Michael E Green.

We have in the past proposed that proton motion constitutes the gating current in the potassium channel Kv1.2 and is responsible for the gating mechanism. For this to happen, there must be a proton path between the voltage-sensing domain (VSD) and the channel gate, and here we present quantum calculations that lead to a specific pair of proton paths, defined at the molecular level, with well-defined water molecule linkages, and with hydrogen bonding between residues; there is also at least one interpath crossover, where protons can switch paths. Quantum calculations on the entire 563-atom system give the complete geometry, the energy, and atomic charges. Calculations show that three specific residues (in the pdb 3Lut numbering, H418, E327, R326), and the T1 intracellular moiety, all of which have been shown experimentally to be involved in gating, would necessarily be protonated or deprotonated in the path between the VSD and the gate. Hydroxyl reorientation of serine and threonine residues are shown to provide a means of adjusting proton directions of motion. In the deprotonated state for K312, a low energy state, our calculations come close to reproducing the X-ray structure. The demonstration of the existence of a double proton path between VSD and gate supports the proposed proton gating mechanism; when combined with our earlier demonstration of proton generation in the VSD, and comparison with other systems that are known to move protons, we are close to achieving the definition of a complete gating mechanism in molecular detail. The coupling of the paths to the VSD, and to the PVPV section that essentially forms the gate, can be easily seen from the results of the calculation. The gate itself remains for further computations.

Keywords: amino acid strings; ion channel gating; proton transport paths

DOI: https://doi.org/10.3390/membranes12070718

Proc Natl Acad Sci U S A. 2022 Aug 02. 119(31): e2200727119

Molecular determinants of pH sensing in the proton-activated chloride channel.

James Osei-Owusu, Ekaterina Kots, Zheng Ruan, Ljubica Mihaljević, Kevin Hong Chen, Ami Tamhaney, Xinyu Ye, Wei Lü, Harel Weinstein, Zhaozhu Qiu.

In response to acidic pH, the widely expressed proton-activated chloride (PAC) channel opens and conducts anions across cellular membranes. By doing so, PAC plays an important role in both cellular physiology (endosome acidification) and diseases associated with tissue acidosis (acid-induced cell death). Despite the available structural information, how proton binding in the extracellular domain (ECD) leads to PAC channel opening remains largely unknown. Here, through comprehensive mutagenesis and electrophysiological studies, we identified several critical titratable residues, including two histidine residues (H130 and H131) and an aspartic acid residue (D269) at the distal end of the ECD, together with the previously characterized H98 at the transmembrane domain-ECD interface, as potential pH sensors for human PAC. Mutations of these residues resulted in significant changes in pH sensitivity. Some combined mutants also exhibited large basal PAC channel activities at neutral pH. By combining molecular dynamics simulations with structural and functional analysis, we further found that the β12 strand at the intersubunit interface and the associated "joint region" connecting the upper and lower ECDs allosterically regulate the proton-dependent PAC activation. Our studies suggest a distinct pH-sensing and gating mechanism of this new family of ion channels sensitive to acidic environment.

Keywords: PAC; TMEM206; allosteric regulation; pH sensitivity; proton-activated chloride channel

DOI: https://doi.org/10.1073/pnas.2200727119

Nature. 2022 Jul 27.

PI3K drives the de novo synthesis of coenzyme A from vitamin B5.

Christian C Dibble, Samuel A Barritt, Grace E Perry, Evan C Lien, Renee C Geck, Sarah E DuBois-Coyne, David Bartee, Thomas T Zengeya, Emily B Cohen, Min Yuan, Benjamin D Hopkins, Jordan L Meier, John G Clohessy, John M Asara, Lewis C Cantley, Alex Toker.

In response to hormones and growth factors, the class I phosphoinositide-3-kinase (PI3K) signalling network functions as a major regulator of metabolism and growth, governing cellular nutrient uptake, energy generation, reducing cofactor production and macromolecule biosynthesis1. Many of the driver mutations in cancer with the highest recurrence, including in receptor tyrosine kinases, Ras, PTEN and PI3K, pathologically activate PI3K signalling2,3. However, our understanding of the core metabolic program controlled by PI3K is almost certainly incomplete. Here, using mass-spectrometry-based metabolomics and isotope tracing, we show that PI3K signalling stimulates the de novo synthesis of one of the most pivotal metabolic cofactors: coenzyme A (CoA). CoA is the major carrier of activated acyl groups in cells4,5 and is synthesized from cysteine, ATP and the essential nutrient vitamin B5 (also known as pantothenate)6,7. We identify pantothenate kinase 2 (PANK2) and PANK4 as substrates of the PI3K effector kinase AKT8. Although PANK2 is known to catalyse the rate-determining first step of CoA synthesis, we find that the minimally characterized but highly conserved PANK49 is a rate-limiting suppressor of CoA synthesis through its metabolite phosphatase activity. Phosphorylation of PANK4 by AKT relieves this suppression. Ultimately, the PI3K-PANK4 axis regulates the abundance of acetyl-CoA and other acyl-CoAs, CoA-dependent processes such as lipid metabolism and proliferation. We propose that these regulatory mechanisms coordinate cellular CoA supplies with the demands of hormone/growth-factor-driven or oncogene-driven metabolism and growth.

DOI: https://doi.org/10.1038/s41586-022-04984-8

Adipocyte. 2022 Dec;11(1): 413-419

Towards better models for studying human adipocytes in vitro.

Fabiana Baganha, Ruby Schipper, Carolina E Hagberg.

With obesity and its comorbidities continuing to rise, we urgently need to improve our understanding of what mechanisms trigger the white adipose tissue to become dysfunctional in response to over-feeding. The recent invent of 3D culturing models has produced several noteworthy protocols for differentiating unilocular adipocytes in vitro, promising to revolutionize the obesity research field by providing more representative adipose tissue models for such mechanistic studies. In parallel, these 3D models provide important insights to how profoundly the microenvironment influences adipocyte differentiation and morphology. This commentary highlights some of the most recent 3D models, including human unilocular vascularized adipocyte spheroids (HUVASs), developed by our lab. We discuss recent developments in the field, provide further insights to the importance of the microvasculature for adipocyte maturation, and summarize what challenges remain to be solved before we can achieve a culture model that fully recapitulates all aspects of human white adipocyte biology in vitro. Taken together, the commentary highlights important recent advances regarding 3D adipocyte culturing and underlines the many advantages these models provide over traditional 2D cultures, with the aim of convincing more laboratories to switch to 3D models.

Keywords: 3D; Obesity; adipocyte; hypertrophy; in vitro model; spheroids

DOI: https://doi.org/10.1080/21623945.2022.2104514

Sci Adv. 2022 Jul 29. 8(30): eabo0696

ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy.

Cristina Olivieri, Geoffrey C Li, Yingjie Wang, Manu V S, Caitlin Walker, Jonggul Kim, Carlo Camilloni, Alfonso De Simone, Michele Vendruscolo, David A Bernlohr, Susan S Taylor, Gianluigi Veglia.

ATP-competitive inhibitors are currently the largest class of clinically approved drugs for protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic activity, preventing substrate phosphorylation. A problem with these drugs, however, is that inhibited kinases may still recognize and bind downstream substrates, acting as scaffolds or binding hubs for signaling partners. Here, using protein kinase A as a model system, we show that chemically different ATP-competitive inhibitors modulate the substrate binding cooperativity by tuning the conformational entropy of the kinase and shifting the populations of its conformationally excited states. Since we found that binding cooperativity and conformational entropy of the enzyme are correlated, we propose a new paradigm for the discovery of ATP-competitive inhibitors, which is based on their ability to modulate the allosteric coupling between nucleotide and substrate-binding sites.

DOI: https://doi.org/10.1126/sciadv.abo0696