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1. Arginine‐enveloped virus inactivation and potential mechanisms

   https://doi.org/10.1002/btpr.2931  

   Meingast, Christa; Heldt, Caryn_L (November 2019, Biotechnology Progress)

   Abstract Arginine synergistically inactivates enveloped viruses at a pH or temperature that does little harm to proteins, making it a desired process for therapeutic protein manufacturing. However, the mechanisms and optimal conditions for inactivation are not fully understood, and therefore, arginine viral inactivation is not used industrially. Optimal solution conditions for arginine viral inactivation found in the literature are high arginine concentrations (0.7–1 M), a time of 60 min, and a synergistic factor of high temperature (≥40°C), low pH (≤pH 4), or Tris buffer (5 mM). However, at optimal conditions full inactivation does not occur over all enveloped viruses. Enveloped viruses that are resistant to arginine often have increased protein stability or membrane stabilizing matrix proteins. Since arginine can interact with both proteins and lipids, interaction with either entity may be key to understanding the inactivation mechanism. Here, we propose three hypotheses for the mechanisms of arginine induced inactivation. Hypothesis 1 describes arginine‐induced viral inactivation through inhibition of vital protein function. Hypothesis 2 describes how arginine destabilizes the viral membrane. Hypothesis 3 describes arginine forming pores in the virus membrane, accompanied by further viral damage from the synergistic factor. Once the mechanisms of arginine viral inactivation are understood, further enhancement by the addition of functional groups, charges, or additives may allow the inactivation of all enveloped viruses in mild conditions. 

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2. Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils

   https://doi.org/10.1073/pnas.2015618118  

   Yang, David S.; Saeedi, Arash; Davtyan, Aram; Fathi, Mohsen; Sherman, Michael B.; Safari, Mohammad S.; Klindziuk, Alena; Barton, Michelle C.; Varadarajan, Navin; Kolomeisky, Anatoly B.; et al (March 2021, Proceedings of the National Academy of Sciences)

   The protein p53 is a crucial tumor suppressor, often called “the guardian of the genome”; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems. 

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3. Characterization of Mechanochemical Modification of Porous Silicon with Arginine

   https://doi.org/10.3390/surfaces5010007  

   DiPietro, Jacklyn A.; Kolasinski, Kurt W. (March 2022, Surfaces)

   Mechanochemistry initiated the reaction of hydrogen-terminated porous silicon (H/por-Si) powder with arginine. Samples were analyzed using Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), zeta potential, scanning electron microscopy (SEM), and photoluminescence (PL) spectroscopy. Arginine, which was physisorbed onto the surface of por-Si, blue-shifted the peak PL intensity from ~630 nm for the H/por-Si to ~565 nm for arginine-coated por-Si. Grinding for 4 h reduced >80% of the initially 2–45 µm particles to <500 nm, but was observed to quench the PL. With appropriate rinsing and centrifugation, particles in the 100 nm range were isolated. Rinsing ground powder with water was required to remove the unreacted arginine. Without rinsing, excess arginine induced the aggregation of passivated particles. However, water reacted with the freshly ground por-Si powder producing H2. A zeta potential of +42 mV was measured for arginine-terminated por-Si particles dispersed in deionized water. This positive value was consistent with termination such that NH2 groups extended away from the surface. Furthermore, this result was confirmed by FTIR spectra, which suggested that arginine was bound to silicon through the formation of a covalent Si–O bond. 

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4. Arginine Decarboxylase Is Essential for Pneumococcal Stress Responses

   https://doi.org/10.3390/pathogens10030286  

   Frances Nakamya, Mary; Ayoola, Moses B.; Shack, Leslie A.; Mohamed, Mirghani; Swiatlo, Edwin; Nanduri, Bindu (March 2021, Pathogens)

   null (Ed.)

   Polyamines such as putrescine, cadaverine, and spermidine are small cationic molecules that play significant roles in cellular processes, including bacterial stress responses and host–pathogen interactions. Streptococcus pneumoniae is an opportunistic human pathogen, which causes several diseases that account for significant morbidity and mortality worldwide. As it transits through different host niches, S. pneumoniae is exposed to and must adapt to different types of stress in the host microenvironment. We earlier reported that S. pneumoniae TIGR4, which harbors an isogenic deletion of an arginine decarboxylase (ΔspeA), an enzyme that catalyzes the synthesis of agmatine in the polyamine synthesis pathway, has a reduced capsule. Here, we report the impact of arginine decarboxylase deletion on pneumococcal stress responses. Our results show that ΔspeA is more susceptible to oxidative, nitrosative, and acid stress compared to the wild-type strain. Gene expression analysis by qRT-PCR indicates that thiol peroxidase, a scavenger of reactive oxygen species and aguA from the arginine deiminase system, could be important for peroxide stress responses in a polyamine-dependent manner. Our results also show that speA is essential for endogenous hydrogen peroxide and glutathione production in S. pneumoniae. Taken together, our findings demonstrate the critical role of arginine decarboxylase in pneumococcal stress responses that could impact adaptation and survival in the host. 

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5. The exquisite specificity of human protein arginine methyltransferase 7 (PRMT7) toward Arg-X-Arg sites

   https://doi.org/10.1371/journal.pone.0285812  

   Bondoc, Timothy J.; Lowe, Troy L.; Clarke, Steven G. (May 2023, PLOS ONE)

   Ganesan, A (Ed.)

   Mammalian protein arginine methyltransferase 7 (PRMT7) has been shown to target substrates with motifs containing two arginine residues separated by one other residue (RXR motifs). In particular, the repression domain of human histone H2B (29-RKRSR-33) has been a key substrate in determining PRMT7 activity. We show that incubating human PRMT7 and [³H]-AdoMet with full-lengthXenopus laevishistone H2B, containing the substitutions K30R and R31K (RKRSR to RRKSR), results in greatly reduced methylation activity. Using synthetic peptides, we have now focused on the enzymology behind this specificity. We show for the human and Xenopus peptide sequences 23–37 the difference in activity results from changes in the V_maxrather than the apparent binding affinity of the enzyme for the substrates. We then characterized six additional peptides containing a single arginine or a pair of arginine residues flanked by glycine and lysine residues. We have corroborated previous findings that peptides with an RXR motif have much higher activity than peptides that contain only one Arg residue. We show that these peptides have similar apparent k_mvalues but significant differences in their V_maxvalues. Finally, we have examined the effect of ionic strength on these peptides. We found the inclusion of salt had little effect on the V_maxvalue but a considerable increase in the apparent k_mvalue, suggesting that the inhibitory effect of ionic strength on PRMT7 activity occurs largely by decreasing apparent substrate-enzyme binding affinity. In summary, we find that even subtle substitutions in the RXR recognition motif can dramatically affect PRMT7 catalysis. 

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