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The structure-based approaches to computing viral fitness.

Rukmankesh Mehra1, Shivani Thakur2

  • 1Department of Chemistry, Indian Institute of Technology Bhilai, Durg, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Durg, Chhattisgarh, India.

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Viral mutations impact viral fitness by altering binding affinities to host receptors and antibodies. Understanding these evolutionary dynamics, particularly for the SARS-CoV-2 spike protein, is crucial for developing effective countermeasures.

Keywords:
ACE2 bindingAntibody bindingEvolutionFitnessModelingMutationsProtein folding stabilitySARS-CoV-2Spike proteinStructure-based approachVirus

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Area of Science:

  • Evolutionary biology
  • Structural biology
  • Virology

Background:

  • Viral mutations rapidly alter viral fitness, making viruses key models for studying evolutionary dynamics.
  • Viral entry relies on surface protein interactions, often via the receptor binding domain (RBD), with host cell receptors.
  • Antibodies generated by immune responses or vaccines compete with host receptors for binding to viral surface proteins.

Purpose of the Study:

  • To explore viral fitness by analyzing the structural impact of mutations on viral protein binding.
  • To define a molecular-level viral fitness function based on differential binding affinities.
  • To investigate these dynamics using the SARS-CoV-2 spike protein as a model.

Main Methods:

  • Utilizing computationally guided structural techniques to analyze the viral mutational landscape.
  • Examining the binding interactions of the SARS-CoV-2 spike protein's RBD with human angiotensin-converting enzyme 2 (ACE2) and antibodies.
  • Leveraging cryo-electron microscopy and biochemical data on mutations.

Main Results:

  • Viral mutations can evolve to enhance binding to host receptors while evading antibody recognition.
  • Differential binding affinities between viral proteins, host receptors, and antibodies can be quantified.
  • The SARS-CoV-2 spike protein's RBD interactions provide insights into viral fitness.

Conclusions:

  • Understanding the interplay between viral mutations, host receptors, and antibodies is essential for predicting viral evolution.
  • Structural and biophysical analyses offer a powerful approach to defining viral fitness at a molecular level.
  • This framework can inform the development of strategies to combat viral infections.