Detecting structural changes in viral capsids by hydrogen exchange and mass spectrometry

Abstract

Amide hydrogen exchange and mass spectrometry have been used to study the pH-induced structural changes in the capsid of brome mosaic virus (BMV). Capsid protein was labeled in a structurally sensitive way by incubating intact viral particles in D 2 O at pH 5.4 and 7.3. Deuterium levels in the intact coat protein and its proteolytic fragments were determined by mass spectrometry. The largest deuterium increases induced by structural alteration occurred in the regions around the quasi-threefold axes, which are located at the center of the asymmetric unit. The increased levels of deuterium indicate loosening of structure in these regions. This observation confirms the previously proposed swelling model for BMV and cowpea chlorotic mottle virus (CCMV) and is consistent with the structure of swollen CCMV recently determined by cryo-electron microscopy and image reconstruction. Structural changes in the extended N-and Cterminal arms were also detected and compared with the results obtained with other swollen plant viruses. This study demonstrates that protein fragmentation/amide hydrogen exchange is a useful tool for probing structural changes in viral capsids.

Assessment of differences in the conformational flexibility of hepatitis B virus core‐antigen and e‐antigen by hydrogen deuterium exchange‐mass spectrometry

“…For each peptide, the relative deuterium uptake compared to time zero (t 5 0) was determined. [16][17][18][19][20][21][22][23], in the a2b helix, and the junction with the a3 helix (peptide [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55], and in the junction between a4b and a5 helices (peptide 104-116). Peptides were not identified for the central region of the a3 helix (residues [56][57][58][59][60][61][62][63][64][65][66][67][68] and the N-terminal half of the a5 helix (residues 121-125), hence the deuterium incorporation of these regions is unknown.…”

“…[34][35][36] The replacement of slowly exchanging amide backbone hydrogen atoms with deuterium atoms can be monitored by MS. Consequently, HDX-MS can be used to monitor the dynamic flexibility of proteins. [37][38][39][40][41] Among the wide variety of HDX-MS applications, it has been used to study a number of virus-related processes that include capsid assembly and maturation of human immunodeficiency virus (HIV) [42][43][44][45] ; maturation of bacteriophage P22 46 ; pH-induced transitions in brome mosaic virus; 47 and structural analysis of the human rhinovirus (HRV14). 48 More recently, we have used this method to monitor the dynamics of Cp149 c and its interaction with two antibodies, E1 and 3120, which have distinct binding epitopes.…”

Marine Viruses: the Beneficial Side of a Threat

“…Thus, as all viral capsids are assembled from virus-coded protein subunits, they can be modified through genetic engineering, allowing the incorporation of designed functionalities. Furthermore, the capsid of a number of viruses can be disassembled and reassembled under different conditions [57], which provide an opportunity to use viruses as nanocontainers [58].…”

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

“…HX-MS has been used to analyze protein-ligand and protein-protein interactions including viral capsid assembly [14][15][16][17] . Protein unfolding and refolding as well as temperature induced conformational changes were investigated 7,18,19 .…”