Limits...
HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358.

Bichel K, Price AJ, Schaller T, Towers GJ, Freund SM, James LC - Retrovirology (2013)

Bottom Line: Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells.NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid.Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating.

View Article: PubMed Central - HTML - PubMed

Affiliation: Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

ABSTRACT

Background: Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown.

Results: Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positioned to allow single-bond resonance stabilisation of exposed capsid residue P90. NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid. In contrast, the distantly related feline lentivirus FIV can bind NUP358 but is neither isomerized by it nor requires it for infection.

Conclusion: Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating.

Show MeSH

Related in: MedlinePlus

HIV-1 CAN:NUP358Cyp complex. (a) Sequence alignment of NUP358Cyp with CypA (conserved regions are shaded and in bold). (b) Structural alignment of NUP358Cyp (yellow) from our structure with CypA (gray) from the HIV-1 CAN:CypA structure (pdb 1AK4 [23]. (c) HIV-1 CAN (green) bound to CypA (molecular surface; gray) (pdb 1AK4 [23]). (d) HIV-1 CAN (green) bound to NUP358Cyp (molecular surface; yellow). (e) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and CypA (gray). (f) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and NUP358Cyp (yellow). NUP358Cyp residues are numbered according to the equivalent CypA numbering. (g-h) Structure of CypA:Cs complex (2RMA [24]) (g) or model where NUP358Cyp has been substituted for CypA (h). Cs is in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750474&req=5

Figure 1: HIV-1 CAN:NUP358Cyp complex. (a) Sequence alignment of NUP358Cyp with CypA (conserved regions are shaded and in bold). (b) Structural alignment of NUP358Cyp (yellow) from our structure with CypA (gray) from the HIV-1 CAN:CypA structure (pdb 1AK4 [23]. (c) HIV-1 CAN (green) bound to CypA (molecular surface; gray) (pdb 1AK4 [23]). (d) HIV-1 CAN (green) bound to NUP358Cyp (molecular surface; yellow). (e) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and CypA (gray). (f) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and NUP358Cyp (yellow). NUP358Cyp residues are numbered according to the equivalent CypA numbering. (g-h) Structure of CypA:Cs complex (2RMA [24]) (g) or model where NUP358Cyp has been substituted for CypA (h). Cs is in green.

Mentions: The cyclophilin domain from human NUP358 (NUP358Cyp) shares only 65% amino acid sequence identity with CypA (Figure 1a). To determine how NUP358Cyp binds HIV-1 we solved the X-ray crystal structure of HIV-1 CAN in complex with NUP358Cyp at 1.95 Å resolution (see Additional file 1 for data collection and refinement statistics). As observed for the recently published structure of uncomplexed NUP358Cyp [21], despite the sequence variation between CypA and NUP358Cyp, the structures of the two cyclophilins are remarkably similar (Cα atoms show an r.m.s.d of 0.5 Å, Figure 1b). The slot-like binding site found in CypA is preserved in NUP358Cyp and the complex of HIV-1 CAN with NUP358Cyp has a similar quaternary arrangement to the CypA complex (Figure 1c,d). The CypA-binding loop of HIV-1 CAN projects down into NUP358Cyp and mediates almost all direct interactions. In comparison to CypA, NUP358Cyp has residues with bulkier side-chains at the capsid interface, such as K117 and D59 (A117 and G59 in CypA), resulting in a more extended active site surface. This is reflected in a larger buried surface area in the NUP358Cyp:HIV-1 CAN complex (610 Å) compared to CypA:HIV-1 CAN (420 Å). This increased surface area is consistent with the larger entropic change (and presumed greater solvent release) associated with NUP358Cyp:HIV-1 CAN versus CypA:HIV-1 CAN binding (Figure 2b) [5,6,22]. Nevertheless, almost all of the interactions in the NUP358Cyp complex are physico-chemically analogous with CypA:HIV-1 interactions. For instance, the carbonyl of I91 in CAN makes an important hydrogen bond interaction with CypA via the pyrrole ring of W121 and with NUP358Cyp via the imidazole side chain of H121 (Figure 1e,f). Sequence variation between NUP358Cyp and CypA is also accommodated because some interactions with HIV-1 CAN are made via main-chain atoms. An important hydrogen bond interaction in both NUP358Cyp and CypA occurs between the side-chain of CAN H87 and the peptide oxygen of residue 71 in the cyclophilins (Figure 1e,f). Despite the physico-chemical similarities between NUP358Cyp and CypA, there are functionally relevant structural differences. Cs inhibits capsid binding to CypA but not NUP358Cyp [6]. The large cyclic peptide drug is accommodated within the active site of CypA but superposition of the CypA-Cs complex on NUP358Cyp reveals that steric clashes preclude binding of Cs to NUP358Cyp (Figure 1g,h).


HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358.

Bichel K, Price AJ, Schaller T, Towers GJ, Freund SM, James LC - Retrovirology (2013)

HIV-1 CAN:NUP358Cyp complex. (a) Sequence alignment of NUP358Cyp with CypA (conserved regions are shaded and in bold). (b) Structural alignment of NUP358Cyp (yellow) from our structure with CypA (gray) from the HIV-1 CAN:CypA structure (pdb 1AK4 [23]. (c) HIV-1 CAN (green) bound to CypA (molecular surface; gray) (pdb 1AK4 [23]). (d) HIV-1 CAN (green) bound to NUP358Cyp (molecular surface; yellow). (e) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and CypA (gray). (f) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and NUP358Cyp (yellow). NUP358Cyp residues are numbered according to the equivalent CypA numbering. (g-h) Structure of CypA:Cs complex (2RMA [24]) (g) or model where NUP358Cyp has been substituted for CypA (h). Cs is in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750474&req=5

Figure 1: HIV-1 CAN:NUP358Cyp complex. (a) Sequence alignment of NUP358Cyp with CypA (conserved regions are shaded and in bold). (b) Structural alignment of NUP358Cyp (yellow) from our structure with CypA (gray) from the HIV-1 CAN:CypA structure (pdb 1AK4 [23]. (c) HIV-1 CAN (green) bound to CypA (molecular surface; gray) (pdb 1AK4 [23]). (d) HIV-1 CAN (green) bound to NUP358Cyp (molecular surface; yellow). (e) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and CypA (gray). (f) Detailed view of interactions between the CypA-binding loop of HIV-1 CAN (green ball-and-stick) and NUP358Cyp (yellow). NUP358Cyp residues are numbered according to the equivalent CypA numbering. (g-h) Structure of CypA:Cs complex (2RMA [24]) (g) or model where NUP358Cyp has been substituted for CypA (h). Cs is in green.
Mentions: The cyclophilin domain from human NUP358 (NUP358Cyp) shares only 65% amino acid sequence identity with CypA (Figure 1a). To determine how NUP358Cyp binds HIV-1 we solved the X-ray crystal structure of HIV-1 CAN in complex with NUP358Cyp at 1.95 Å resolution (see Additional file 1 for data collection and refinement statistics). As observed for the recently published structure of uncomplexed NUP358Cyp [21], despite the sequence variation between CypA and NUP358Cyp, the structures of the two cyclophilins are remarkably similar (Cα atoms show an r.m.s.d of 0.5 Å, Figure 1b). The slot-like binding site found in CypA is preserved in NUP358Cyp and the complex of HIV-1 CAN with NUP358Cyp has a similar quaternary arrangement to the CypA complex (Figure 1c,d). The CypA-binding loop of HIV-1 CAN projects down into NUP358Cyp and mediates almost all direct interactions. In comparison to CypA, NUP358Cyp has residues with bulkier side-chains at the capsid interface, such as K117 and D59 (A117 and G59 in CypA), resulting in a more extended active site surface. This is reflected in a larger buried surface area in the NUP358Cyp:HIV-1 CAN complex (610 Å) compared to CypA:HIV-1 CAN (420 Å). This increased surface area is consistent with the larger entropic change (and presumed greater solvent release) associated with NUP358Cyp:HIV-1 CAN versus CypA:HIV-1 CAN binding (Figure 2b) [5,6,22]. Nevertheless, almost all of the interactions in the NUP358Cyp complex are physico-chemically analogous with CypA:HIV-1 interactions. For instance, the carbonyl of I91 in CAN makes an important hydrogen bond interaction with CypA via the pyrrole ring of W121 and with NUP358Cyp via the imidazole side chain of H121 (Figure 1e,f). Sequence variation between NUP358Cyp and CypA is also accommodated because some interactions with HIV-1 CAN are made via main-chain atoms. An important hydrogen bond interaction in both NUP358Cyp and CypA occurs between the side-chain of CAN H87 and the peptide oxygen of residue 71 in the cyclophilins (Figure 1e,f). Despite the physico-chemical similarities between NUP358Cyp and CypA, there are functionally relevant structural differences. Cs inhibits capsid binding to CypA but not NUP358Cyp [6]. The large cyclic peptide drug is accommodated within the active site of CypA but superposition of the CypA-Cs complex on NUP358Cyp reveals that steric clashes preclude binding of Cs to NUP358Cyp (Figure 1g,h).

Bottom Line: Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells.NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid.Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating.

View Article: PubMed Central - HTML - PubMed

Affiliation: Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

ABSTRACT

Background: Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown.

Results: Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positioned to allow single-bond resonance stabilisation of exposed capsid residue P90. NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid. In contrast, the distantly related feline lentivirus FIV can bind NUP358 but is neither isomerized by it nor requires it for infection.

Conclusion: Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating.

Show MeSH
Related in: MedlinePlus