Identifying Distinct Structural Features of the SARS-CoV-2 Spike Protein Fusion Domain Essential for Membrane Interaction

Abstract

The SARS-CoV-2 spike protein is the primary antigenic determinant of the virus and has been studied extensively, yet the process of membrane fusion remains poorly understood. The fusion domain (FD) of viral glycoproteins is well established as facilitating the initiation of membrane fusion. An improved understanding of the structural plasticity associated with these highly conserved regions aids in our knowledge of the molecular mechanisms that drive viral fusion. Within the spike protein, the FD of SARS-CoV-2 exists immediately following S2′ cleavage at the N-terminus of the S2 domain. Here we have shown that following the introduction of a membrane at pH 7.4, the FD undergoes a transition from a random coil to a more structurally well-defined postfusion state. Furthermore, we have classified the domain into two distinct regions, a fusion peptide (FP, S 816 –G 838 ) and a fusion loop (FL, D 839 –F 855 ). The FP forms a helix–turn–helix motif upon association with a membrane, and the favorable entropy gained during this transition from a random coil is likely the driving force behind membrane insertion. Membrane depth experiments then revealed the FP is found inserted within the membrane below the lipid headgroups, while the interaction of the FL with the membrane is shallower in nature. Thus, we propose a structural model relevant to fusion at the plasma membrane in which the FP inserts itself just below the phospholipid headgroups and the FL lays upon the lipid membrane surface.

Lassa virus glycoprotein complex review: insights into its unique fusion machinery

“…However, in the case of LASV and the arenavirus family, both an NFP and IFL are present and create a fusion domain that initiates fusion by targeting the host cell membrane [ 157 , 173 , 174 ]. Thus far, the only other class one fusion protein with this characteristic are coronaviruses, potentially contributing to their remarkable infectivity [ 83–88 ].…”

“…Moreover, another unique feature of LASV is that the fusion peptide contains two distinct components: an N-terminal fusion peptide (NFP), similar to HIV and influenza, and an internal fusion loop (IFL) with a disulfide bond, similar to EBOV. The only other class one fusion protein shown to have both an NFP and IFL are coronaviruses [ 83–88 ]. The unusual retention of SSP also has intriguing roles in GPC synthesis and maturation as well as fusion activity [ 74 , 75 , 89–91 ].…”

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

“…Despite the addition of these sequences, few PPIs are found explaining a limited interactome or many PPIs are missing ( Latysheva et al, 2016 ). This method is usually combined with other methods such as machine learning methods ( De Braekeleer, Douet-Guilbert and De Braekeleer, 2014 ; Birtles and Lee, 2021 ). The accuracy values, therefore, take several methods and are not specific to the domain fusion method.…”

Carbohydrate Ligands for COVID-19 Spike Proteins

“…The densely glycosylated spike (S) protein of SARS-CoV-2, a trimeric class I fusion protein with a metastable prefusion conformation [2,3], docks to enter host cells. When binding to a host-cell receptor, the S1 subunit triggers a dramatic structural rearrangement to fuse the viral membrane with the host-cell membrane, leading to receptor-dependent endocytosis [4,5].…”