Abstract
The three-dimensional solution structure of the HIV-1 protease homodimer, MW 22.2 kDa, complexed to a potent, cyclic urea-based inhibitor, DMP323, is reported. This is the first solution structure of an HIV protease/inhibitor complex that has been elucidated. Multidimensional heteronuclear NMR spectra were used to assemble more than 4,200 distance and angle constraints. Using the constraints, together with a hybrid distance geometry/simulated annealing protocol, an ensemble of 28 NMR structures was calculated having no distance or angle violations greater than 0.3 Å or 5°, respectively. Neglecting residues in disordered loops, the RMS deviation (RMSD) for backbone atoms in the family of structures was 0.60 Å relative to the average structure. The individual NMR structures had excellent covalent geometry and stereochemistry, as did the restrained minimized average structure. The latter structure is similar to the 1.8-Å X-ray structure of the protease/DMP323 complex (Chang CH et al., 1995, Protein Science, submitted); the pairwise backbone RMSD calculated for the two structures is 1.22 Å. As expected, the mismatch between the structures is greatest in the loops that are disordered and/or flexible. The flexibility of residues 37-42 and 50-51 may be important in facilitating substrate binding and product release, because these residues make up the respective hinges and tips of the protease flaps. Flexibility of residues 4-8 may play a role in protease regulation by facilitating autolysis.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 495-506 |
| Number of pages | 12 |
| Journal | Protein Science |
| Volume | 5 |
| Issue number | 3 |
| State | Published - Mar 1996 |
| Externally published | Yes |
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Keywords
- comparison to crystal structure
- cyclic urea inhibitor
- HIV-1 protease
- NMR
- protease inhibitor
- protein flexibility
- protein structure
ASJC Scopus subject areas
- Biochemistry
Cite this
Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. / Yamazaki, Toshimasa; Hinck, Andrew P.; Wang, Yun Xing; Nicholson, Linda K.; Torchia, Dennis A.; Wingfield, Paul; Stahl, Stephen J.; Kaufman, Joshua D.; Chang, Chong Hwan; Domaille, Peter J.; Lam, Patrick Y S.
In: Protein Science, Vol. 5, No. 3, 03.1996, p. 495-506.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy
AU - Yamazaki, Toshimasa
AU - Hinck, Andrew P.
AU - Wang, Yun Xing
AU - Nicholson, Linda K.
AU - Torchia, Dennis A.
AU - Wingfield, Paul
AU - Stahl, Stephen J.
AU - Kaufman, Joshua D.
AU - Chang, Chong Hwan
AU - Domaille, Peter J.
AU - Lam, Patrick Y S
PY - 1996/3
Y1 - 1996/3
N2 - The three-dimensional solution structure of the HIV-1 protease homodimer, MW 22.2 kDa, complexed to a potent, cyclic urea-based inhibitor, DMP323, is reported. This is the first solution structure of an HIV protease/inhibitor complex that has been elucidated. Multidimensional heteronuclear NMR spectra were used to assemble more than 4,200 distance and angle constraints. Using the constraints, together with a hybrid distance geometry/simulated annealing protocol, an ensemble of 28 NMR structures was calculated having no distance or angle violations greater than 0.3 Å or 5°, respectively. Neglecting residues in disordered loops, the RMS deviation (RMSD) for backbone atoms in the family of structures was 0.60 Å relative to the average structure. The individual NMR structures had excellent covalent geometry and stereochemistry, as did the restrained minimized average structure. The latter structure is similar to the 1.8-Å X-ray structure of the protease/DMP323 complex (Chang CH et al., 1995, Protein Science, submitted); the pairwise backbone RMSD calculated for the two structures is 1.22 Å. As expected, the mismatch between the structures is greatest in the loops that are disordered and/or flexible. The flexibility of residues 37-42 and 50-51 may be important in facilitating substrate binding and product release, because these residues make up the respective hinges and tips of the protease flaps. Flexibility of residues 4-8 may play a role in protease regulation by facilitating autolysis.
AB - The three-dimensional solution structure of the HIV-1 protease homodimer, MW 22.2 kDa, complexed to a potent, cyclic urea-based inhibitor, DMP323, is reported. This is the first solution structure of an HIV protease/inhibitor complex that has been elucidated. Multidimensional heteronuclear NMR spectra were used to assemble more than 4,200 distance and angle constraints. Using the constraints, together with a hybrid distance geometry/simulated annealing protocol, an ensemble of 28 NMR structures was calculated having no distance or angle violations greater than 0.3 Å or 5°, respectively. Neglecting residues in disordered loops, the RMS deviation (RMSD) for backbone atoms in the family of structures was 0.60 Å relative to the average structure. The individual NMR structures had excellent covalent geometry and stereochemistry, as did the restrained minimized average structure. The latter structure is similar to the 1.8-Å X-ray structure of the protease/DMP323 complex (Chang CH et al., 1995, Protein Science, submitted); the pairwise backbone RMSD calculated for the two structures is 1.22 Å. As expected, the mismatch between the structures is greatest in the loops that are disordered and/or flexible. The flexibility of residues 37-42 and 50-51 may be important in facilitating substrate binding and product release, because these residues make up the respective hinges and tips of the protease flaps. Flexibility of residues 4-8 may play a role in protease regulation by facilitating autolysis.
KW - comparison to crystal structure
KW - cyclic urea inhibitor
KW - HIV-1 protease
KW - NMR
KW - protease inhibitor
KW - protein flexibility
KW - protein structure
UR - http://www.scopus.com/inward/record.url?scp=9044228016&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=9044228016&partnerID=8YFLogxK
M3 - Article
C2 - 8868486
AN - SCOPUS:9044228016
VL - 5
SP - 495
EP - 506
JO - Protein Science
JF - Protein Science
SN - 0961-8368
IS - 3
ER -