The Beauty of Proteins

In this blog, I’ll share some captivating protein visualizations I rendered, along with the fascinating stories behind them. All these visualizations were created using ChimeraX, a powerful and user-friendly tool that makes stunning molecular visuals in just minutes.

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1. CRISPR-Cas9 Complex with DNA (PDB: 5Y36)

This visualization showcases the famous CRISPR-Cas9 complex bound to DNA. By now, you’ve likely heard about CRISPR technologies and their revolutionary role in gene editing. Here, you get a glimpse of the molecular machinery in action—a frame of this groundbreaking gene-editing tool at the molecular level.

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2. COVID-19 Spike Protein and ACE2 Receptor Binding (PDB: 6M0J)

Next is the binding of the COVID-19 spike protein to the human ACE2 receptor. This structure, solved early in the pandemic using crystallography and cryo-EM techniques, revealed the molecular mechanism of viral entry. This visualization holds special significance for medicinal chemists working to design compounds that inhibit this interaction, potentially halting viral entry and infection

The blue ribbon structure represents the SARS-CoV-2 spike protein, while the purple structure corresponds to the ACE2 receptor. The interface binding residues, which are critical for stable interactions between these two proteins, are highlighted using licorice representation or depicted as a colored surface for better clarity.

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3. E. coli Galactose Chemoreceptor Protein (PDB: 2GBP)

This protein visualization highlights the galactose chemoreceptor from Escherichia coli. It helps the bacterium detect and move toward galactose, a sugar used as a nutrient source. The protein has specific binding sites for galactose (shown as sticks with surface) and signaling molecules, enabling it to send signals to bacterial flagella, guiding the bacterium toward higher galactose concentrations and improving its survival.

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4. Myotoxin II with Varespladib (PDB: 6PWH)

This structure shows the interaction between Myotoxin II from the Bothrops moojeni snake venom and the phospholipase A2 inhibitor Varespladib (shown as sticks). Myotoxin II causes muscle damage and inflammation by breaking down membrane phospholipids. Varespladib binds to the toxin’s active site, inhibiting its activity. This visualization underscores the therapeutic potential of Varespladib in neutralizing snake venom and lays the groundwork for developing treatments against envenomation.

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5. Influenza Virus H1 Hemagglutinin (PDB: 1RU7)

The final protein is the H1 hemagglutinin from the 1934 human influenza virus. This surface protein binds to sialic acid residues on host cells, initiating infection. It plays a critical role in viral entry and immune recognition, making it a primary target for vaccine and antiviral drug development. Visualizing this protein has been pivotal in understanding influenza and designing effective interventions.

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These visualizations offer a molecular-level perspective of some of the most intriguing proteins in biology, from gene editing to viral entry and survival mechanisms. Tools like ChimeraX make it possible to render these stunning insights, bridging the gap between molecular science and visualization.