Illustration of influenza nucleoproteins binding to RNA

Decoding the Flu: How Viral Proteins Interact with RNA

Rhea Morgan in Science & Nature September 2025 • 4 min read.

"Unraveling the mechanisms behind influenza A and B replication"

Influenza viruses, responsible for seasonal epidemics, rely on a complex interplay between viral proteins and RNA to replicate and spread. At the heart of this process lies the nucleoprotein (NP), a key player in ensuring viral RNA is both protected and accessible for replication and transcription.

A recent study published in Viruses delves into the intricacies of how the nucleoproteins of influenza A and B viruses (A/NP and B/NP) interact with RNA. By exploring the biochemical dynamics of these interactions, the study uncovers critical differences and similarities between the two viral strains, paving the way for innovative antiviral strategies.

Using techniques such as electron microscopy, size exclusion chromatography, and fluorescence anisotropy, researchers examined the formation of NP-RNA complexes, revealing how these interactions evolve based on RNA size, salt concentration, and specific viral proteins.

Key Players: Nucleoproteins A and B

Illustration of influenza nucleoproteins binding to RNA

The study focuses on influenza A and B viruses, both of which belong to the group of negative-strand RNA viruses (NSVs). These viruses have an RNA genome coated with nucleoprotein (NP); the nucleoprotein–RNA complex (N–RNA) is the template for both transcription and replication by the viral polymerase. NP, viral RNA (vRNA), and polymerase constitute the ribonucleoparticle (RNP).

Researchers Alice Labaronne, Christopher Swale, Alexandre Monod, Guy Schoehn, Thibaut Crépin, and Rob W. H. Ruigrok analyzed the binding affinities of A/NP and B/NP to short RNA molecules (oligonucleotides) ranging from 5 to 24 nucleotides in length. They started with monomeric proteins and observed complex formations under different conditions.

Negative Stain Electron Microscopy: Visualized the structures of NP and NP-RNA complexes.
Size Exclusion Chromatography-Multi-Angle Laser Light Scattering (SEC-MALLS): Analyzed the molecular weights and oligomeric states of the complexes.
Fluorescence Anisotropy: Measured the binding affinities between NP and RNA.

The team found that both A/NP and B/NP form oligomers with 24-nucleotide RNAs, but the specific oligomeric states differ. A/NP tends to form trimers, while B/NP can create dimers, tetramers, and larger complexes. The binding affinities of NP are similar at 50 mM NaCl, suggesting that RNAs bind to the same site. However, A/NP's affinity for 24-nt RNA decreases at higher salt concentrations (150 and 300 mM NaCl), indicating potential additional binding sites.

Future Directions: Crystallizing the Interaction

While this study provides valuable insights, the researchers emphasize the need for crystal structures of NP-RNA complexes to fully understand the interaction mechanisms. Finding the right balance between salt concentration and RNA length is crucial for crystallizing these complexes, opening doors for targeted drug development. By understanding how these viral proteins and RNA interact, we can pave the way for innovative strategies to combat influenza.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.3390/v8090247, Alternate LINK

Title: Binding Of Rna By The Nucleoproteins Of Influenza Viruses A And B

Subject: Virology

Journal: Viruses

Publisher: MDPI AG

Authors: Alice Labaronne, Christopher Swale, Alexandre Monod, Guy Schoehn, Thibaut Crépin, Rob Ruigrok

Published: 2016-09-13

Everything You Need To Know

What is the role of nucleoproteins in influenza viruses, and why are they important for viral replication?

Nucleoproteins, specifically NP, are crucial for influenza virus replication because they coat and protect the viral RNA (vRNA). The nucleoprotein-RNA complex (N–RNA) acts as the template for both transcription and replication carried out by the viral polymerase. Together, NP, vRNA, and polymerase form the ribonucleoparticle (RNP), which is essential for the virus's ability to replicate and spread. Understanding the dynamics of these interactions is vital for developing antiviral strategies. However, the article does not discuss in-depth the viral polymerase mechanism.

How do the interactions between influenza A and B nucleoproteins (A/NP and B/NP) with RNA differ, according to the research?

The research indicates that both influenza A/NP and B/NP form oligomers with 24-nucleotide RNAs, but the specific oligomeric states differ. A/NP tends to form trimers, while B/NP can create dimers, tetramers, and larger complexes. Furthermore, while both have similar binding affinities at 50 mM NaCl, A/NP's affinity for 24-nt RNA decreases at higher salt concentrations (150 and 300 mM NaCl), suggesting it has potential additional binding sites that B/NP may not. Further studies on other Influenza subtypes are needed to show the differences among all.

What methods were used to study the interactions between influenza nucleoproteins and RNA, and what kind of data did these methods provide?

Researchers utilized several techniques to study the interactions, including Negative Stain Electron Microscopy to visualize the structures of NP and NP-RNA complexes, Size Exclusion Chromatography-Multi-Angle Laser Light Scattering (SEC-MALLS) to analyze the molecular weights and oligomeric states of the complexes, and Fluorescence Anisotropy to measure the binding affinities between NP and RNA. These methods provided data on the structural formations, molecular weights, and binding strengths of the nucleoprotein-RNA complexes, enabling the characterization of these interactions. The study does not mention other methods such as NMR or X-Ray Diffraction.

What are the implications of understanding how nucleoproteins interact with RNA for the development of new antiviral drugs?

Understanding the interaction mechanisms between nucleoproteins and RNA can pave the way for innovative strategies to combat influenza. By elucidating how these viral proteins and RNA bind, researchers can identify specific targets for antiviral drugs. For example, a drug could be designed to disrupt the formation of the nucleoprotein-RNA complex, thereby inhibiting viral replication and spread. However, crystal structures of the NP-RNA complexes are still needed to fully understand these interactions and effectively target them with new drugs. Future research may explore other viral proteins that can be targeted, such as PB2.

Why is crystallizing nucleoprotein-RNA complexes important for future research, and what challenges are involved in this process?

Crystallizing nucleoprotein-RNA complexes is crucial for obtaining detailed structural information at the atomic level, which is necessary to fully understand the interaction mechanisms. The challenge lies in finding the right conditions, particularly the balance between salt concentration and RNA length, that allow the formation of stable crystals suitable for X-ray diffraction analysis. Overcoming this challenge would open doors for targeted drug development by providing a clear picture of the binding interfaces and potential drug-binding sites. The article doesn't mention specific crystallization techniques to improve the process.