Abstract
In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.
Highlights
Since the early 1990s, many giant DNA viruses that infect eukaryotic cells have been discovered and studied [1].Examples include Paramecium bursaria Chlorella virus 1 (PBCV-1) [2,3], Chilo iridescent virus [4], Phaeocystis pouchetii virus [5], Mimivirus [6], Megavirus [7], Cafeteria roenbergensis virus [8], Faustovirus [9], Sambavirus [10], as well as non-icosahedral-shaped giant viruses [11]
Note that negatively charged residues were predominant in between the two jelly-rolls within each MCP monomer; positively charged residues were mostly located at the interface between the neighboring MCP monomers, and the rest of the positively charged residues were located on the outside edge of each jelly-roll (Figure 1e; Movie S1)
This unique feature of charge distribution of the PBCV-1 capsomer indicated that charge interactions on its side may provide strong and elegant forces to cause the biological assembly of PBCV-1 capsomers
Summary
Since the early 1990s, many giant DNA viruses that infect eukaryotic cells have been discovered and studied [1].Examples include Paramecium bursaria Chlorella virus 1 (PBCV-1) [2,3], Chilo iridescent virus [4], Phaeocystis pouchetii virus [5], Mimivirus [6], Megavirus [7], Cafeteria roenbergensis virus [8], Faustovirus [9], Sambavirus [10], as well as non-icosahedral-shaped giant viruses [11]. The size and complexity of giant viruses have challenged current structural techniques [1] and present a unique research frontier for the study of self-assembly and regulation of supramolecular assemblies on an extremely large scale. Despite their size and complexity, the protein shell (capsid) of icosahedral giant DNA viruses still assembles symmetrically from simple and similar building blocks called capsomers. 2019, 20, x FOR PEER REVIEW donut-shaped capsomers consists of six “jelly-roll” folds [15]. The “jelly-roll” fold is a wedge-shaped β-barTrheel s“tjreullyct-ruorlel”thfoaldt iiss uaswededbgye-ashllakpienddβs-boafrDreNl sAtruocrtuRrNe tAhavt iirsuusseesdinbyfeacltlinkigndsps eocfiDesNaAcroorssRNalAl three kingdvoirmusse[s1i6n]f,evctairnyginsgpeicniessizaecrforsosmalslmtharleletokignigadnotmDsN[A16]v, ivruarsyeisng[1i]n. IsnizgeiafrnotmicsomsaahlletdoragliaDnNt DANvAiruses, two jveilrluys-eros l[l1f].oIlndsgiaarnet ilcinoskaehdedtroagleDthNeAr ivniruthseesi,r tmwoajjoerllyc-arpolslidfolpdrsoatreeinlin(MkedCPto)g, eatnhder tihnethceaipr smoamjoerr is a trimecraopfsitdheprMotCeiPn ((FMigCuPr)e, 1aan,db).thTehceaspestormimereriisc acatprismomereorfs tthheenMpCaPck(Fcligouserely1tao,bc)o. vTehretsheetricimosearihcedral surfacgcaeiaponsftomtichoeerssavhtihreudensra(plFaDicgkNucArleovs1iecrl)uy.stHeosocaowsvseeevrmetbhr,leehitcohowesiarghigeadignratanlictsioucsrcafaahpceesdiodrfaftlrhoDemNvitrAhuesvc(iFarupigssuoermseae1srcss)e.smHo obawcleceutvrheaert,ierhlyogwiigs antic capsisdtifllrolamrgethlyeucnakpnsoowmne.rs so accurately is still largely unknown
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