The HIV structural protein Gag assembles to form spherical particles of radius ~70 nm. During the assembly process, the number of Gag proteins increases over several orders of magnitude, from a few at nucleation to thousands at completion. The challenge in studying protein assembly lies in the fact that current methods such as standard fluorescence or electron microscopy techniques cannot access all stages of the assembly process in a cellular context. Here, we demonstrate an approach using super-resolution fluorescence imaging that permits quantitative morphological and molecular counting analysis over a wide range of protein cluster sizes. We applied this technique to the analysis of hundreds of HIV-Gag clusters at the cellular plasma membrane, thus elucidating how different fluorescent labels can change the assembly of virions.
Keywords: Super-resolution imaging; protein assembly; protein counting; HIV-GagPage 2 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 3 Viruses represent a major class of pathogens, whose assembly in the cellular context contains important information about the complex processes governing viral infection. Viruses are nanoscale objects that assemble from small nucleation complexes to ensembles containing thousands of molecules. In the case of human immunodeficiency virus (HIV), the viral components are targeted to the plasma membrane of infected cells where they assemble and eventually form spheres ~70 nm in radius. Viral assembly is widely studied using HIV-Gag, the main structural protein of HIV, which is sufficient to drive the assembly of virus-like particles (VLPs) in the absence of other viral components 1,2 . Fluorescence imaging has been used to follow the time-dependent increase in the intensity of Gag clusters in living cells 3,4 , revealing the time scale of virion formation. Electron microscopy (EM) has elucidated the spatial arrangement of Gag in fully formed virions [5][6][7][8] . However, studying the complete assembly process requires nanoscale resolution over a large dynamic range, since the size of a cluster ranges from a few molecules to several thousand. This cannot be achieved with standard fluorescence imaging methods since they lack both the necessary resolution to determine cluster morphology, and the sensitivity to detect smaller clusters. EM-based methods in turn lack information on protein identity; thus, complexes composed of small numbers of Gag proteins are difficult to identify, precluding the first step toward quantitative analysis. As an alternative approach, super-resolution fluorescence imaging based on single molecule localization (SR) 9-11 offers nanoscale resolution of structures formed by specific proteins. Here, we use an SR-based approach to quantitatively image hundreds of forming HIV-Gag virions in different stages of cluster formation. With this inf...