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Mutational fitness landscape of human influenza H3N2 neuraminidase.

Cell reports | 2023

Influenza neuraminidase (NA) has received increasing attention as an effective vaccine target. However, its mutational tolerance is not well characterized. Here, the fitness effects of >6,000 mutations in human H3N2 NA are probed using deep mutational scanning. Our result shows that while its antigenic regions have high mutational tolerance, there are solvent-exposed regions with low mutational tolerance. We also find that protein stability is a major determinant of NA mutational fitness. The deep mutational scanning result correlates well with mutational fitness inferred from natural sequences using a protein language model, substantiating the relevance of our findings to the natural evolution of circulating strains. Additional analysis further suggests that human H3N2 NA is far from running out of mutations despite already evolving for >50 years. Overall, this study advances our understanding of the evolutionary potential of NA and the underlying biophysical constraints, which in turn provide insights into NA-based vaccine design.

Pubmed ID: 36640354 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


ATCC (tool)

RRID:SCR_001672

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

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ClinicalTrials.gov (tool)

RRID:SCR_002309

Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.

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Amplicon (tool)

RRID:SCR_003294

Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

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FoldX (tool)

RRID:SCR_008522

A computer algorithm that provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FOLDEF has been tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins . FoldX uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FoldX have been weighted using empirical data obtained from protein engineering experiments.

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New England Biolabs (tool)

RRID:SCR_013517

An Antibody supplier

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Coot (tool)

RRID:SCR_014222

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

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Phenix (tool)

RRID:SCR_014224

A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab.

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MolProbity (tool)

RRID:SCR_014226

A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.

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autoPROC (tool)

RRID:SCR_015748

Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.

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MDCK-SIAT1 (tool)

RRID:CVCL_Z936

Cell line MDCK-SIAT1 is a Spontaneously immortalized cell line with a species of origin Canis lupus familiaris (Dog)

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HEK293T (tool)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

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Ig, k light chain (antibody)

RRID:AB_397315

This monoclonal targets Ig, κ light chain

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