Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy

Toshimasa Yamazaki, Andrew P. Hinck, Yun Xing Wang, Linda K. Nicholson, Dennis A. Torchia, Paul Wingfield, Stephen J. Stahl, Joshua D. Kaufman, Chong Hwan Chang, Peter J. Domaille, Patrick Y S Lam

Research output: Contribution to journalArticle

68 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)495-506
Number of pages12
JournalProtein Science
Volume5
Issue number3
StatePublished - Mar 1996
Externally publishedYes

Fingerprint

Nuclear magnetic resonance spectroscopy
Urea
Peptide Hydrolases
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Biomolecular Nuclear Magnetic Resonance
HIV Protease Inhibitors
Autolysis
Stereochemistry
Geometry
Hinges
Simulated annealing
X-Rays
X rays
Atoms
Substrates
Human immunodeficiency virus 1 p16 protease
Proteins

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

Yamazaki, T., Hinck, A. P., Wang, Y. X., Nicholson, L. K., Torchia, D. A., Wingfield, P., ... Lam, P. Y. S. (1996). Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. Protein Science, 5(3), 495-506.

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 journalArticle

Yamazaki, T, Hinck, AP, Wang, YX, Nicholson, LK, Torchia, DA, Wingfield, P, Stahl, SJ, Kaufman, JD, Chang, CH, Domaille, PJ & Lam, PYS 1996, 'Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy', Protein Science, vol. 5, no. 3, pp. 495-506.
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. / Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. In: Protein Science. 1996 ; Vol. 5, No. 3. pp. 495-506.
@article{5ce2a423284440b8b605b5563ad0b6c5,
title = "Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy",
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 {\AA} or 5°, respectively. Neglecting residues in disordered loops, the RMS deviation (RMSD) for backbone atoms in the family of structures was 0.60 {\AA} 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-{\AA} 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 {\AA}. 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.",
keywords = "comparison to crystal structure, cyclic urea inhibitor, HIV-1 protease, NMR, protease inhibitor, protein flexibility, protein structure",
author = "Toshimasa Yamazaki and Hinck, {Andrew P.} and Wang, {Yun Xing} and Nicholson, {Linda K.} and Torchia, {Dennis A.} and Paul Wingfield and Stahl, {Stephen J.} and Kaufman, {Joshua D.} and Chang, {Chong Hwan} and Domaille, {Peter J.} and Lam, {Patrick Y S}",
year = "1996",
month = "3",
language = "English (US)",
volume = "5",
pages = "495--506",
journal = "Protein Science",
issn = "0961-8368",
publisher = "Cold Spring Harbor Laboratory Press",
number = "3",

}

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 -