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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Receptor-binding loops in alphacoronavirus adaptation and evolution.

Alan H M Wong1, Aidan C A Tomlinson1, Dongxia Zhou2

  • 1Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.

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Human coronavirus (HCoV-229E) evolves through changes in receptor-binding loops. These loop variations alter virus affinity for aminopeptidase N (APN) and antibody binding, driving viral adaptation.

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Area of Science:

  • Virology
  • Structural Biology
  • Evolutionary Biology

Background:

  • RNA viruses exhibit high mutation rates, facilitating adaptation.
  • The precise mechanisms by which viral mutations enhance fitness remain incompletely understood.
  • Human coronavirus 229E (HCoV-229E) is an important human pathogen.

Purpose of the Study:

  • To elucidate the structural basis of HCoV-229E receptor recognition.
  • To understand the role of specific viral domains in adaptation and evolution.
  • To investigate the relationship between receptor-binding loop variation and viral fitness.

Main Methods:

  • X-ray crystallography was used to determine the structure of the HCoV-229E receptor-binding domain (RBD) in complex with its receptor, aminopeptidase N (APN).
  • Phylogenetic analysis was employed to study the evolutionary history of HCoV-229E receptor-binding loop variations.
  • Binding assays were performed to assess the affinity of different viral variants for APN and neutralizing antibodies.

Main Results:

  • The X-ray crystal structure revealed that three extended loops within the RBD are critical for APN binding.
  • Phylogenetic analysis identified six distinct RBD classes based on natural loop variations, with viruses from these classes successively dominating the human population over 50 years.
  • These RBD classes exhibited differential affinities for APN and varying susceptibility to HCoV-229E neutralizing antibodies.

Conclusions:

  • Extended loops are the primary determinants of receptor binding in HCoV-229E.
  • Variation in these loops drives the adaptation and evolution of alphacoronaviruses.
  • This study provides a structural and evolutionary model for HCoV-229E adaptation via loop-receptor interactions.