Structure of Adeno-Associated Virus Type 4

Padron, Eric; Bowman, Valorie D.; Kaludov, Nikola; Govindasamy, Lakshmanan; Levy, Hazel C.; Nick, Phillip; McKenna, Robert; Muzyczka, Nicholas; Chiorini, John A.; Baker, Timothy S.; Agbandje‐McKenna, Mavis

doi:10.1128/jvi.79.8.5047-5058.2005

Cited by 92 publications

(98 citation statements)

References 72 publications

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“…Identification and alignment of the capsid genes from the mouse tissues was done using Clustal X (32). A 3D homology model of the VP3 structure of AAVM41 was generated from the coordinates of the crystal structures of AAV1, AAV7, and AAV8 (17) and a homology model of AAV6 (33), the parental viruses, using the Coot program (34). After superimposition of these template coordinates, the chimeric M41 VP3 structural model was generated by manual cutting and pasting of the appropriate amino acid sequences from each serotype and regularization of the model geometry.…”

Section: Methodsmentioning

confidence: 99%

A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection

Yang

Jiang

Drouin

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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To engineer gene vectors that target striated muscles after systemic delivery, we constructed a random library of adeno-associated virus (AAV) by shuffling the capsid genes of AAV serotypes 1 to 9, and screened for muscle-targeting capsids by direct in vivo panning after tail vein injection in mice. After 2 rounds of in vivo selection, a capsid gene named M41 was retrieved mainly based on its high frequency in the muscle and low frequency in the liver. Structural analyses revealed that the AAVM41 capsid is a recombinant of AAV1, 6, 7, and 8 with a mosaic capsid surface and a conserved capsid interior. AAVM41 was then subjected to a sideby-side comparison to AAV9, the most robust AAV for systemic heart and muscle gene delivery; to AAV6, a parental AAV with strong muscle tropism. After i.v. delivery of reporter genes, AAVM41 was found more efficient than AAV6 in the heart and muscle, and was similar to AAV9 in the heart but weaker in the muscle. In fact, the myocardium showed the highest gene expression among all tissues tested in mice and hamsters after systemic AAVM41 delivery. However, gene transfer in non-muscle tissues, mainly the liver, was dramatically reduced. AAVM41 was further tested in a genetic cardiomyopathy hamster model and achieved efficient long-term ␦-sarcoglycan gene expression and rescue of cardiac functions. Thus, direct in vivo panning of capsid libraries is a simple tool for the de-targeting and retargeting of viral vector tissue tropisms facilitated by acquisition of desirable sequences and properties.

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Section: Methodsmentioning

confidence: 99%

A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection

Yang

Jiang

Drouin

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

187

164

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“…The structures of AAV1 to AAV5 and AAV8 have been determined by X-ray crystallography and/or cryo-electron microscopy and image reconstruction (cryo-EM) (23,36,47,52,66,73; unpublished data), and preliminary characterization of crystals has also been reported for AAV1, AAV5, AAV7, and AAV9 (15,45,46,55). The capsid VP structures contain a conserved eight-stranded (␤B to ␤I) ␤-barrel core and large loop regions between the strands that form the capsid surface.…”

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confidence: 99%

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Govindasamy

Gurda

et al. 2010

J Virol

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The three-dimensional structure of adeno-associated virus (AAV) serotype 6 (AAV6) was determined using cryo-electron microscopy and image reconstruction and using X-ray crystallography to 9.7-and 3.0-Å resolution, respectively. The AAV6 capsid contains a highly conserved, eight-stranded (␤B to ␤I) ␤-barrel core and large loop regions between the strands which form the capsid surface, as observed in other AAV structures. The loops show conformational variation compared to other AAVs, consistent with previous reports that amino acids in these loop regions are involved in differentiating AAV receptor binding, transduction efficiency, and antigenicity properties. Toward structure-function annotation of AAV6 with respect to its unique dual glycan receptor (heparan sulfate and sialic acid) utilization for cellular recognition, and its enhanced lung epithelial transduction compared to other AAVs, the capsid structure was compared to that of AAV1, which binds sialic acid and differs from AAV6 in only 6 out of 736 amino acids. Five of these residues are located at or close to the icosahedral 3-fold axis of the capsid, thereby identifying this region as imparting important functions, such as receptor attachment and transduction phenotype. Two of the five observed amino acids are located in the capsid interior, suggesting that differential AAV infection properties are also controlled by postentry intracellular events. Density ordered inside the capsid, under the 3-fold axis in a previously reported, conserved AAV DNA binding pocket, was modeled as a nucleotide and a base, further implicating this capsid region in AAV genome recognition and/or stabilization.

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“…Structures determined for AAVs show capsids assembled from the common VP3 region (20)(21)(22)(23)(24)(25)(26)(27)(28)(29). There is currently no experimentally determined structure for VP1u or the overlapping VP1/ VP2 N terminus.…”

mentioning

confidence: 99%

“…There is currently no experimentally determined structure for VP1u or the overlapping VP1/ VP2 N terminus. Low-resolution density globules located inside the capsid under the icosahedral 2-fold axes have been interpreted as the VP1u (25,28). The VP3 topology contains a core eightstranded (␤B to ␤I) ␤-barrel motif and large loop insertions between the ␤-strands which form the surface of the capsid.…”

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confidence: 99%

Structural Insights into Adeno-Associated Virus Serotype 5

Govindasamy

DiMattia

Gurda

et al. 2013

J Virol

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The adeno-associated viruses (AAVs) display differential cell binding, transduction, and antigenic characteristics specified by their capsid viral protein (VP) composition. Toward structure-function annotation, the crystal structure of AAV5, one of the most sequence diverse AAV serotypes, was determined to 3.45-Å resolution. The AAV5 VP and capsid conserve topological features previously described for other AAVs but uniquely differ in the surface-exposed HI loop between ␤H and ␤I of the core ␤-barrel motif and have pronounced conformational differences in two of the AAV surface variable regions (VRs), VR-IV and VR-VII. The HI loop is structurally conserved in other AAVs despite amino acid differences but is smaller in AAV5 due to an amino acid deletion. This HI loop is adjacent to VR-VII, which is largest in AAV5. The VR-IV, which forms the larger outermost finger-like loop contributing to the protrusions surrounding the icosahedral 3-fold axes of the AAVs, is shorter in AAV5, creating a smoother capsid surface topology. The HI loop plays a role in AAV capsid assembly and genome packaging, and VR-IV and VR-VII are associated with transduction and antigenic differences, respectively, between the AAVs. A comparison of interior capsid surface charge and volume of AAV5 to AAV2 and AAV4 showed a higher propensity of acidic residues but similar volumes, consistent with comparable DNA packaging capacities. This structure provided a three-dimensional (3D) template for functional annotation of the AAV5 capsid with respect to regions that confer assembly efficiency, dictate cellular transduction phenotypes, and control antigenicity. R ecombinant adeno-associated viruses (rAAVs) are promising viral vectors for gene delivery applications (1, 2). These viruses belong to the single-stranded DNA (ssDNA)-packaging Parvoviridae and genus Dependovirus. Hundreds of AAV genotypes have been sequenced from several mammalian species, and to date 12 serotypes (AAV1 to AAV12) have been defined for the human and nonhuman primate isolates (3-15). The 12 serotypes are classified into eight genetic groups, clades A to F and clonal isolates AAV4 and AAV5, based on antigenic reactivity and sequence similarity (15). The groups are represented by AAV1 to AAV9, with AAV1 and AAV6 belonging to the same clade A because of their high sequence similarity and antigenic cross-reactivity. The representative members share ϳ55 to 99% sequence identity, with AAV4 and AAV5 being the most divergent from each other and from the other members.The linear ssDNA AAV genome, ϳ4.7 kb in length, contains two genes: cap, which encodes the capsid viral proteins (VPs; VP1, ϳ87 kDa; VP2, ϳ73 kDa; VP3, ϳ62 kDa) and rep, which encodes the replication proteins necessary for genome replication and genome packaging. Inverted terminal repeats (ITRs) at the end of the AAV genome, 145 bp in length, are the only essential active sequence required to function as (i) the origin for DNA replication, (ii) the packaging signal, and (iii) integration sites (16)(17)(18)(19). Recombina...

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Structure of Adeno-Associated Virus Type 4

Cited by 92 publications

References 72 publications

A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection

A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Structural Insights into Adeno-Associated Virus Serotype 5

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