Mechanics of bacteriophage maturation

Abstract

Capsid maturation with large-scale subunit reorganization occurs in virtually all viruses that use a motor to package nucleic acid into preformed particles. A variety of ensemble studies indicate that the particles gain greater stability during this process, however, it is unknown which material properties of the fragile procapsids change. Using Atomic Force Microscopy-based nano-indentation, we study the development of the mechanical properties during maturation of bacteriophage HK97, a λ-like phage of which the maturationinduced morphological changes are well described. We show that mechanical stabilization and strengthening occurs in three independent ways: (i) an increase of the Young's modulus, (ii) a strong rise of the capsid's ultimate strength, and (iii) a growth of the resistance against material fatigue. The Young's modulus of immature and mature capsids, as determined from thin shell theory, fit with the values calculated using a new multiscale simulation approach. This multiscale calculation shows that the increase in Young's modulus isn't dependent on the crosslinking between capsomers. In contrast, the ultimate strength of the capsids does increase even when a limited number of cross-links are formed while full crosslinking appears to protect the shell against material fatigue. Compared to phage λ, the covalent crosslinking at the icosahedral and quasi threefold axes of HK97 yields a mechanically more robust particle than the addition of the gpD protein during maturation of phage λ. These results corroborate the expected increase in capsid stability and strength during maturation, however in an unexpected intricate way, underlining the complex structure of these self-assembling nanocontainers.AFM | elastic network model | nanoindentation | normal mode analysis | virus structural mechanics H K97 is a double stranded DNA bacteriophage infecting Escherichia coli. The capsid protein of HK97 has a subunit fold that is shared by phages λ, P22, T4, and phi29, among others, as well as the eukaryotic virus, Herpes (1). In addition, the maturation pathways of these viruses show similar morphological changes (2). HK97 provides a unique model system to study capsid maturation, as large quantities of isometric particles can be produced in an E. coli expression system. These particles are expressed without the portal and terminase proteins used for genome packaging, but can be isolated as procapsids and matured in vitro using chemical agents instead of DNA, and maturation can be trapped in various expansion states (3, 4). In vitro expansion can be effectively induced with a variety of chemical agents, including lowering the pH below 4. The particles expand from the Prohead II (P-II) form, which differs from Prohead I (P-I) by the absence of the 104AA N-terminal polypeptide (termed the Δ-domain) from each subunit (gp5). The Δ-domain is presumed to function in scaffolding capsid assembly (5, 6). The Δ-domain is cleaved by an internally packaged protease (gp4) upon assembly, allowing the particle transition to the ...

Cementing proteins provide extra mechanical stabilization to viral cages

“…This finding, together with our results, suggest that the objective of the expansion transition is not the immediate stabilization, as it appears for other phages 30 . For instance, the expanded structures of HK97 show an increment of the yield force with respect the prohead due to the crosslinking 14 . Our results are compatible with the unique observation that expansion of the lambda procapsid is fully reversible 21 , since the capsid contraction would be more difficult with a stiffer particle.…”

“…3e) indicates that the shell loses some strength during expansion. Although thin shell modelling 23 applied to lambda geometry would assign to expanded capsids a Young modulus B5 times larger than procapsids 14 , it is known that the expanded shell is fragile and easily damaged by Transmission electron microscopy (TEM) staining procedures 21 . This finding, together with our results, suggest that the objective of the expansion transition is not the immediate stabilization, as it appears for other phages 30 .…”

“…The variation of the virus shell stability is concomitant to the structural changes induced by maturation 11,12 . Atomic force microscopy (AFM) has been used to define the mechanical properties of individual viruses, and the results of these studies have been interpreted as a signature of capsid shell stability along the maturation pathway [13][14][15] . In general, while capsid expansion is not accompanied by a noticeable stiffening of the viral shell, the packed genetic material induces a major reinforcement of the virion [16][17][18] .…”

The Role of Capsid Maturation on Adenovirus Priming for Sequential Uncoating

“…Usually, mechanical strength and stiffness are considered a signature of virus stability (63)(64)(65), i.e. the harder the virus, the more resilient to aggressive conditions.…”

Modeling and simulation of the mechanical response from nanoindentation test of DNA-filled viral capsids

“…Mechanical properties of only a few viral capsids have been investigated experimentally so far. To name a few, bacteriophages λ and φ29 [1,2], plant virus CCMV [3], MVM virus [4], MLV, HIV [5,6], HSV-1 [7] and HK97 [8]. Probing viral shells with an AFM tip generally results in either reversible deformation, often observed when the applied force is below a certain value, or an irreversible capsid rupture when the applied force is above this threshold value.…”