bims-cemest 2025-05-18 papers

J Cell Sci. 2025 May 01. pii: jcs263757. [Epub ahead of print]138(9):

Quality control of un-imported mitochondrial proteins at a glance.

Megan Balzarini, John Kim, Hilla Weidberg.

Mitochondria are metabolic hubs that are essential for cellular homeostasis. Most mitochondrial proteins are translated in the cytosol and imported into the organelle. However, import machineries can become overwhelmed or disrupted by physiological demands, mitochondrial damage or diseases, such as metabolic and neurodegenerative disorders. Impaired import affects mitochondrial function and causes un-imported pre-proteins to accumulate not only in the cytosol but also in other compartments, including the endoplasmic reticulum and nucleus. Quality control pathways have evolved to mitigate the accumulation of these mistargeted proteins and prevent proteotoxicity. In this Cell Science at a Glance article and the accompanying poster, we summarize the fate of un-imported mitochondrial proteins and the compartment-specific quality control pathways that regulate them.

Keywords: Mitochondrial protein import; Mitochondrial stress; Protein quality control

DOI: https://doi.org/10.1242/jcs.263757

Nucleic Acids Res. 2025 May 10. pii: gkaf428. [Epub ahead of print]53(9):

Specific branches of the proteostasis network regulate the toxicity associated with mistranslation.

Donovan W McDonald, Rebecca N Dib, Christopher De Luca, Ashmi Shah, Martin L Duennwald.

All cellular functions rely on accurate protein biosynthesis. Yet, many variants of transfer RNA (tRNA) genes that induce amino acid misincorporation are found in human genomes. Mistranslation induces pleiotropic effects on proteostasis, ranging from protein misfolding to impaired protein biosynthesis and degradation. We employ Saccharomyces cerevisiae (budding yeast), a genetically and biochemically tractable model that facilitates quantitative analysis of how specific proteostasis pathways interact with mistranslating tRNAs. We tested two mistranslating tRNASer variants, one inducing proline to serine (P > S), the other arginine to serine (R > S) misincorporation. We found that P > S misincorporation impairs cellular fitness and sensitizes cells to protein misfolding to a greater extent than R > S misincorporation. Of note, we also show that, even though both tRNA variants induce misincorporation of serine, they result in the accumulation of misfolded proteins by distinct mechanisms. Specifically, R > S misincorporation reduces that association of Hsp70 with misfolded proteins, while P > S misincorporation impairs the degradation of nascent polypeptides. Our findings reveal that different mistranslating tRNASer variants impair specific branches of proteostasis and thus compromise cellular fitness by distinct mechanisms.

DOI: https://doi.org/10.1093/nar/gkaf428

Isr J Chem. 2024 Dec;pii: e202300125. [Epub ahead of print]64(12):

Pharmacologic Targeting of PDIA1 Inhibits NLRP3 Inflammasome Assembly and Activation.

Jessica D Rosarda, Caroline R Stanton, Emily B Chen, Michael J Bollong, R Luke Wiseman.

The NLRP3 inflammasome is a cytosolic protein complex that regulates innate immune signaling in response to diverse pathogenic insults through the proteolytic processing and secretion of pro-inflammatory cytokines such as IL-1β. Hyperactivation of NLRP3 inflammasome signaling is implicated in the onset and pathogenesis of numerous diseases, motivating the discovery of new strategies to suppress NLRP3 inflammasome activity. We sought to define the potential for the proteostasis regulator AA147 to inhibit the assembly and activation of the NLRP3 inflammasome. AA147 is a pro-drug that is metabolically converted to a reactive metabolite at the endoplasmic reticulum (ER) membrane to covalently modify ER-localized proteins such as protein disulfide isomerases (PDIs). We show that AA147 inhibits NLRP3 inflammasome activity in monocytes and monocyte-derived macrophages through a mechanism involving impaired assembly of the active inflammasome complex. This inhibition is mediated through AA147-dependent covalent modification of PDIA1. Genetic depletion or treatment with other highly selective PDIA1 inhibitors similarly blocks NLRP3 inflammasome assembly and activation. Our results identify PDIA1 as a potential therapeutic target to mitigate NLRP3 inflammasome-mediated pro-inflammatory signaling implicated in etiologically diverse diseases.

Keywords: NLRP3; inflammasome; inhibitor; innate immunity; protein disulfide isomerase; small molecule

DOI: https://doi.org/10.1002/ijch.202300125

Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2425061122

Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants.

Christopher N Woods, Maria K Janowska, Lindsey D Ulmer, Jasleen Kaur Sidhu, Natalie L Stone, Ellie I James, Miklos Guttman, Matthew F Bush, Rachel E Klevit.

Found from bacteria to humans, small heat shock proteins (sHSPs) are the least understood protein chaperones. HSPB5 (or αB-crystallin) is among the most widely expressed of the 10 human sHSPs, including in muscle, brain, and eye lens where it is constitutively present at high levels. A high content of disorder in HSPB5 has stymied efforts to uncover how its structure gives rise to function. To uncover its mechanisms of action, we compared human HSPB5 and two disease-associated mutants, R120G and D109H. Expecting to learn how the mutations lead to loss of function, we found instead that the mutants are constitutively activated chaperones while wild-type HSPB5 can transition reversibly between nonactivated (low activity) and activated (high activity) states in response to changing conditions. Techniques that provide information regarding interactions and accessibility of disordered regions revealed that the disordered N-terminal regions (NTR) that are required for chaperone activity exist in a complicated interaction network within HSPB5 oligomers and are sequestered from solvent in nonactivated states. Either mutation or an activating pH change causes rearrangements in the network that expose parts of the NTR, making them more available to bind an aggregating client. Although beneficial in the short-term, failure of the mutants to adopt a state with lower activity and lower NTR accessibility leads to increased coaggregation propensity and, presumably, early cataract. The results support a model where chaperone activity and solubility are modulated through the quasi-ordered NTR and its multiple competing interactions.

Keywords: protein aggregation; protein chaperones; small heat shock proteins

DOI: https://doi.org/10.1073/pnas.2425061122

Biophys Rev. 2025 Apr;17(2): 247-257

Protein folding: basic statistical physics models and computational multipopulation genetic algorithms.

Luis Olivares-Quiroz, Marcos Angel Gonzalez Olvera.

In this work, we present a brief and concise review about the main features of protein folding which is one of the central research questions at the interface of physics, molecular biology, and computational sciences. We describe the physical foundations of the protein folding phenomenon itself and how it arises as both a free energy minimization process combined with a hydrophobic collapse of the enzyme molten globule due to inter and intramolecular forces among amino acid residues themselves and water molecules. We cover briefly some basic statistical physics-based models to predict the thermodynamic properties of the protein folding transition. Then, we focus our attention on the implementation of computational algorithms designed to minimize energy functions in polypeptides.

Keywords: Energy minimization; Genetic algorithms; Hydrophobic collapse; Protein folding; Statistical physics

DOI: https://doi.org/10.1007/s12551-025-01281-2