School of Science Department of Chemistry 10 Evolutionary Analysis of Hemagglutinin and Neuraminidase Mutations in Influenza Virus Supervisor: SU Haibin / CHEM Student: GUI Weishi / BCB Course: UROP 1100, Fall I have completed various tasks as part of Professor Su’s research group, which focused on the “Evolutionary Analysis of Hemagglutinin and Neuraminidase Mutations in Influenza A Virus”. Influenza A virus (IAV) is a highly pathogenic virus with a single-stranded, segmented RNA genome surrounded by a lipid envelope. Hemagglutinin (HA) and neuraminidase (NA) are crucial viral proteins that are vital to the infection process. Last semester, we discussed our findings on molecular interactions using PyMOL and outlined the progress our group has made in exploring treatment options for influenza within the field of computational chemistry. This report continues the process and focuses on fitness data analysis and relationship between the protein structure and leading mutations. Evolutionary Analysis of Hemagglutinin and Neuraminidase Mutations in Influenza Virus Supervisor: SU Haibin / CHEM Student: GUI Weishi / BCB XIONG Yule / BIBU Course: UROP 2100, Spring This paper explores the integration of molecular dynamics (MD), single-molecule FRET (smFRET), and deep mutational scanning (DMS) in influenza virus research. It introduces influenza A virus structure, emphasizing hemagglutinin (HA)’s critical role in host cell attachment and membrane fusion. DMS systematically maps genomic mutations to viral phenotypes like virulence and transmissibility, revealing functional constraints and mutational tolerance in key proteins such as HA and PB1. SmFRET visualizes conformational dynamics of HA during fusion, while MD simulations offer atomic-level insights into protein behavior and mutationinduced structural changes. Together, these techniques advance understanding of viral adaptation, immune evasion, and evolutionary limits, providing a framework for exploring influenza A virus. Evolutionary Analysis of Hemagglutinin and Neuraminidase Mutations in Influenza Virus Supervisor: SU Haibin / CHEM Student: JEON Yewon / CHEM Course: UROP 2100, Fall UROP 3100, Spring The ability of influenza viruses to adapt through mutations in hemagglutinin (HA) and related surface proteins is crucial in immune evasion, viral entry, and resistance to therapeutics. This report examines pHsensitive structural dynamics and mutations in influenza virus proteins, with insights from recent studies using high-speed atomic force microscopy (HS-AFM), constant-pH molecular dynamics (cpHMD), and classical MD simulations. The summary incorporates findings on acid-induced HA conformational changes, glycosylation-driven immune evasion, and key mutations influencing viral fitness. Additionally, a study on cap-dependent endonuclease (CEN) is included to illustrate how similar mutation-driven mechanisms can lead to antiviral resistance. This review contributes original comparative tables to highlight key residue behaviors, mutational impacts, and structure-function relationships relevant to influenza evolution and therapeutic targeting.
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