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1. Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein

   https://doi.org/10.1021/acs.macromol.9b02715  

   Wonderly, William R.; Cristiani, Thomas R.; Cunha, Keila C.; Degen, George D.; Shea, Joan-Emma; Waite, J. Herbert (August 2020, Macromolecules)

   Ensembles of amino acid side chains often dominate the interfacial interactions of intrinsically disordered proteins; however, backbone contributions are far from negligible. Using a combination of nanoscale force measurements and molecular dynamics simulations, we demonstrated with analogous mussel-mimetic adhesive peptides and peptoids both 34 residues long that highly divergent adhesive/cohesive outcomes can be achieved on mica surfaces by altering backbone chemistry only. The Phe, Tyr, and Dopa containing peptoid variants used in this study deposited as dehydrated and incompressible films that facilitated analysis of peptoid side chain contributions to adhesion and cohesion. For example, whereas Phe and Dopa peptoids exhibited similar cohesion, Dopa peptoids were ∼3 times more adhesive than Phe peptoids on mica. Compared with the peptides, Phe peptoid achieved only ∼20% of Phe containing peptide adhesion, but the Dopa peptoids were >2-fold more adhesive than the Dopa peptides. Cation−π interactions accounted for some but not all of the cohesive interactions. Our results were corroborated by molecular dynamics simulations and highlight the importance of backbone chemistry and the potential of peptoids or peptoid/peptide hybrids as wet adhesives and primers. 

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2. Interactions of SARS-CoV-2 and MERS-CoV fusion peptides measured using single-molecule force methods

   https://doi.org/10.1016/j.bpj.2023.01.016  

   Qiu, Cindy; Whittaker, Gary R; Gellman, Samuel H; Daniel, Susan; Abbott, Nicholas L (February 2023, Biophysical Journal)

   We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide sequences within coronavirus (CoV) spike proteins. Within the fusion peptides of SARS-CoV-2 and MERS-CoV, a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. While a non-polar triad (LLF) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9s, respectively). Here we explore if single molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask if sequence variations between FP1 from SARS-2 and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 ± 0.03 nN versus 0.68 ± 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single residue diversity in viral fusion peptides, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts. 

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3. Type III secretion system effector proteins are mechanically labile

   https://doi.org/10.1073/pnas.2019566118  

   LeBlanc, Marc-André; Fink, Morgan R.; Perkins, Thomas T.; Sousa, Marcelo C. (March 2021, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins—such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)—impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ( Δ G unfold 0 ) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published Δ G unfold 0 for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force ( F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δ x ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust ( F unfold > 80 pN) and brittle (Δ x ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion. 

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4. Ion exchange and bioregeneration by partial nitritation/anammox for mainstream municipal wastewater treatment

   Chero-Osorio, Sheyla; Steele, Lanica; Carson, Valerie; Bhattacharjee, Ananda S; Wang, Meng; Kuhn, John; Ergas, Sarina J (July 2025, Bioresource technology)

   Conventional biological nitrogen removal (BNR) processes for mainstream municipal wastewater (MMW) treatment have high energy and chemical costs. Partial nitritation/anammox (PN/A) has the potential to reduce the carbon footprint of BNR; however, its implementation for MMW treatment has been limited by the low ammonium and high organic matter concentrations in MMW, which prevent suppression nitrite oxidizing bacteria (NOB) and heterotrophic denitrifiers. In this study, after organic carbon diversion, ammonium was separated from MMW in a novel bench-scale sequencing batch biofilm reactor (SBBR) containing chabazite, a natural zeolite mineral with a high ammonium ion exchange (IX) capacity. After breakthrough, chabazite was bioregenerated by PN/A biofilms. Recirculation was applied from the bottom to the top of the column to create an aerobic zone (top) for ammonia-oxidizing microorganisms (AOM) and an anoxic zone (bottom) for anammox bacteria. Rapid IX-PN/A SBBR startup was observed after inoculation with PN/A enrichments. The time required for bioregeneration decreased with increasing recirculation rate, with high total inorganic nitrogen (TIN) removal efficiency (81 %) and ammonium removal rate (0.11 g N/L/day) achieved at recirculation velocity of 1.43 m/h. The core microbiome of the IX-PN/A SBBR contained a high abundance of bacteria of the phylum Pseudomonadota (15.27–20.62 %), Patescibacteria (12.38–20.05 %), Chloroflexota (9.36–14.23 %), and Planctomycetota (7.55–12.82 %), while quantitative PCR showed the highest ammonia monooxygenase (amoA, 2.0 × 102) and anammox copy numbers (amx, 1.0 × 104) in the top layers. The single-stage IX-PN/A SBBR achieved stable BNR for >two years without chemical inputs, media replacement or brine waste production. 

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5. Intra-axonal Nanomagnetic Forces Differentially Impact hTau40 Transport Dynamics in Primary Cortical and Hippocampal Neurons

   https://doi.org/10.1021/acsnano.4c14767  

   Landis, Mackenna K; Kunze, Anja (March 2025, ACS Nano)

   A crucial aspect of neural engineering is the ability to manipulate proteins that are substantially involved in axonal outgrowth and maintenance. Previous work in this field has shown that applying low-magnitude (piconewton) forces to early stage neurons can result in altered distributions of critical structural proteins, such as the microtubule-associated protein Tau. Uncovering the mechanisms of Tau redistribution could provide a tool for manipulating dysregulated forms of the protein. This study examined how the transport of Tau responded to intra-axonal nanomagnetic forces (NMFs) in primary cortical and hippocampal neurons. High magnification, live cell fluorescent imaging was employed to visualize the transport of both full-length human Tau (hTau40) and amine-terminated, starch-coated fluorescent magnetic nanoparticles (afMNPs) to observe how these cell-internal forces could impact the transport of hTau40 within the axon. Here, we found that afMNPs acted by pulling on hTau40 puncta under NMF application, especially within cortical cells, where afMNPs were more likely to be found within the axon. Forces greater than 1 pN enabled differentiated transport speeds and displacement of hTau40 based on relative force direction. This data indicates that NMF can be utilized to engineer hTau40 transport, even in cells at later stages of maturation. 

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