The arginine-rich RNA binding motif is found in a wide variety of proteins, including several viral regulatory proteins. Although related at the primary sequence level, arginine-rich domains from different proteins adopt different conformations depending on the RNA site recognized, and in some cases fold only in the context of RNA. Here we show that the RNA binding domain of the Jembrana disease virus (JDV) Tat protein is able to recognize two different TAR RNA sites, from human and bovine immunodeficiency viruses (HIV and BIV, respectively), adopting different conformations in the two RNA contexts and using different amino acids for recognition. In addition to the conformational differences, the JDV domain requires the cyclin T1 protein for high-affinity binding to HIV TAR, but not to BIV TAR. The "chameleon-like" behavior of the JDV Tat RNA binding domain reinforces the concept that RNA molecules can provide structural scaffolds for protein folding, and suggests mechanisms for evolving distinct RNA binding specificities from a single multifunctional domain.

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Background: Single domain variable regions of shark antibodies (V-NARs) are promising biotherapeutic candidates. Results: A V-NAR specific for human serum albumin was humanized, and its crystal structure in complex with the antigen was solved, revealing an unusual recognition mode. Conclusion: Humanization preserved antigen binding properties and activity of the parental shark antibody. Significance: A structural framework for humanization of shark antibodies was established.

Globally accessible preventive and therapeutic molecules against SARS-CoV-2 are urgently needed. DARPin molecules are an emerging class of novel therapeutics based on naturally occurring repeat proteins (∼15 kDa in size) and can be rapidly produced in bacteria in large quantities. Here, we report the identification of 380 DARPin molecules specifically targeting the SARS-CoV-2 spike protein selected from a naïve library of 1012 DARPin molecules. Using extensive biophysical and biochemical characterization, (pseudo)virus neutralization assays and cryo-EM analysis, 11 mono-DARPin molecules targeting either the receptor binding domain (RBD), the S1 N-terminal-domain (NTD) or the S2 domain of the SARS-CoV-2 spike protein were chosen. Based on these 11 mono-DARPin molecules, 31 anti-SARS-CoV-2 multi-DARPin molecules were constructed which can broadly be grouped into 2 types; multi-paratopic RBD-neutralizing DARPin molecules and multi-mode DARPin molecules targeting simultaneously RBD, NTD and the S2 domain. Each of these multi-DARPin molecules acts by binding with 3 DARPin modules to the SARS-CoV-2 spike protein, leading to potent inhibition of SARS-CoV-2 infection down to 1 ng/ml (12 pM) and potentially providing protection against viral escape mutations. Additionally, 2 DARPin modules binding serum albumin, conferring an expected half-life of about 3 weeks in humans, were included in the multi-DARPin molecules. The protective efficacy of one multi-DARPin molecule was studied in a Golden Syrian hamster SARS-CoV-2 infection model, resulting in a significant reduction in viral load and pathogenesis. In conclusion, the multi-DARPin molecules reported here display very high antiviral potency, high-production yield, and a long systemic half-life, and thereby have the potential for single-dose use for prevention and treatment of COVID-19.

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with potential resistance to existing drugs emphasizes the need for new therapeutic modalities with broad variant activity. Here we show that ensovibep, a trispecific DARPin (designed ankyrin repeat protein) clinical candidate, can engage the three units of the spike protein trimer of SARS-CoV-2 and inhibit ACE2 binding with high potency, as revealed by cryo-electron microscopy analysis. The cooperative binding together with the complementarity of the three DARPin modules enable ensovibep to inhibit frequent SARS-CoV-2 variants, including Omicron sublineages BA.1 and BA.2. In Roborovski dwarf hamsters infected with SARS-CoV-2, ensovibep reduced fatality similarly to a standard-of-care monoclonal antibody (mAb) cocktail. When used as a single agent in viral passaging experiments in vitro, ensovibep reduced the emergence of escape mutations in a similar fashion to the same mAb cocktail. These results support further clinical evaluation of ensovibep as a broad variant alternative to existing targeted therapies for Coronavirus Disease 2019 (COVID-19).

An arginine-rich peptide from the Jembrana disease virus (JDV) Tat protein is a structural ''chameleon'' that binds bovine immunodeficiency virus (BIV) or HIV TAR RNAs in two different binding modes, with an affinity for BIV TAR even higher than the cognate BIV peptide. We determined the NMR structure of the JDV Tat-BIV TAR high-affinity complex and found that the C-terminal tyrosine in JDV Tat forms a network of inter-and intramolecular hydrogen bonding and stacking interactions that simultaneously stabilize the ␤-hairpin conformation of the peptide and a base triple in the RNA. A neighboring histidine also appears to help stabilize the peptide conformation. Induced fit binding is recurrent in protein-protein and protein-nucleic acid interactions, and the JDV Tat complex demonstrates how high affinity can be achieved not only by optimization of the binding interface but also by inducing new intramolecular contacts that stabilize each binding partner. Comparison to the cognate BIV Tat peptide-TAR complex shows how such a costabilization mechanism can evolve with only small changes to the peptide sequence. In addition, the bound structure of BIV TAR in the chameleon peptide complex is strikingly similar to the bound conformation of HIV TAR, suggesting new strategies for the development of HIV TAR binding molecules.NMR ͉ RNA structure ͉ RNA-binding domain T he ability of macromolecules to interact with high affinity and specificity is often accompanied by conformational changes in the binding partners (1-4). Flexibility of one or both molecules can contribute to optimization of the binding surfaces and allow binding to multiple partners (5, 6). Numerous examples of conformational adaptability have been observed in protein-protein and protein-nucleic acid interactions, including Ig proteins, which can accommodate a remarkably wide range of binding partners, and the ribosome, where induced-fit binding helps direct its ordered assembly (7-9).In RNA-protein interactions, the arginine-rich motif (ARM) has served as a model system for examining structural mechanisms that underlie induced fit binding (10-12). Studies of ARM peptide-RNA complexes, including the Tat ARM-TAR RNA interactions of several lentiviruses, have shown that the unbound ARMs generally are unfolded and can adopt a variety of conformations upon RNA binding, often with a concomitant change in RNA structure. In the case of HIV Tat, a relatively weak binding ARM peptide remains in an extended conformational when bound to HIV TAR but causes a large conformational change in the RNA, inducing stacking between the two helical stems and formation of a U-A:U base triple (13-23). In the case of bovine immunodeficiency virus (BIV) Tat, a conformational change in BIV TAR also is observed upon binding, but the cognate ARM peptide undergoes a large conformational rearrangement, forming a ␤-hairpin structure that facilitates high-affinity binding through a large set of specific contacts to the RNA (24-29). Despite the striking difference in binding modes of these two...

LOX‐1 is a scavenger receptor that functions as the primary receptor for oxidized low‐density lipoprotein (OxLDL) in endothelial cells. The binding of OxLDL to LOX‐1 is believed to lead to endothelial activation, dysfunction, and injury, which constitute early atherogenic events. Because of its potential pathological role in atherosclerosis, LOX‐1 has been proposed as a therapeutic target for the treatment of this disease. In order to antagonize the ligand‐binding function of cell surface LOX‐1, we generated a series of recombinant human LOX‐1–crystallizable fragment (Fc) fusion proteins and subsequently characterized their biochemical properties and ligand‐binding activities in vitro. Consistent with the notion that oligomerization of cell surface LOX‐1 is required for high‐avidity binding of ligands, we found that LOX‐1–Fc fusion protein containing four ligand‐binding domains per Fc dimer, but not the one containing two ligand‐binding domains, exhibited ligand‐binding activity. Optimal ligand‐binding activity could be achieved via crosslinking of LOX‐1–Fc fusion proteins with a polyclonal antibody against Fc. The crosslinked LOX‐1–Fc protein also effectively inhibited the binding and internalization of OxLDL by cell surface LOX‐1. These findings demonstrate that functional oligomerization is required for recombinant LOX‐1–Fc to function as an effective antagonist. Structured digital abstract http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-7213199: LOX1 (uniprotkb:http://www.ebi.uniprot.org/entry/P78380) and LOX1 (uniprotkb:http://www.ebi.uniprot.org/entry/P78380) physically interact (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0914) by molecular sieving (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0071)