Flaps Morph for HIV Protease

The genome of HIV codes for synthesis of a polyprotein (UniProt P04585 (POL_HV1H2)) that requires cutting by HIV protease in order to be separated into individual mature proteins required for virus maturation. Drugs that inhibit HIV protease prevent the virus from replicating, and are crucial components of anti-HIV therapies. The proteolytic active site of HIV protease is covered by two "flaps". It is believed that these flaps must open to enable substrate polyprotein to enter the active site. Drugs that inhibit HIV protease tend to "lock" the flaps closed. Mutations in HIV protease that confer resistance to inhibitor drugs often involve changes to the flaps. The active site expansion hypothesis states that mutations responsible for multi-drug resistance expand the active site cavity, thereby reducing drug affinity. There are hundreds of HIV protease crystal structures. When crystallized with bound inhibitor, the flaps have nearly always been closed. Inhibitor-free crystal structures have been classified into closed, semi-open, and wide open. As of 2017, no ligand-free crystal structure has captured a fully open conformation, defined as a distance of >13 Å between isoleucine 50's at the tips of the flaps (but see 4npt in the table below). Click the green links below to change the molecular scene. Drag to rotate. Zoom the molecule with your mouse wheel, or Shift-Drag up/down. Here is shown a morph between a closed HIV protease (1hxw) and a "wide open" protease (1tw7, ). The catalytic Asp 25's are red. (Note that "wide open" is not "fully open" -- see above.) Click the Toggle Animation Button above to start these animations if needed. flap glycines in magenta (Gly 40, 48, 49, 51, 52). in orange. (Flaps: residues 42-58.) with flaps highlighted in orange. In the case of mutant 1tw7, about 100 water molecules (not shown) reside in the active site, forming a hydrogen-bonded scaffold holding the flaps open.

spinqualitylabelsall models HIV protease: morph of flaps opening/closing (1hxw ↔ 1tw7). Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Relevant ResourcesRelevant Resources

YouTubeYouTube

• HIV protease action: Excellent half-minute video from the PDB simulating polyprotein entering protease active site between the flaps, polyprotein hydrolysis, and binding of saquinavir locking the protease closed, inactivating it.
• Mechanism and Inhibition of Aspartyl Protease Enzymes (which include HIV protease) explained by Michael Evans (Georgia Tech). Excellent detailed explanation of the catalytic mechanism and design of inhibitors.
• Wide-opening of the HIV-1 protease active site. 50 ns all-atom molecular dynamics simulation of
• Coarse-grained Brownian dynamics simulation. 2 ns simulation shows flaps opening and substrate binding.

Other External ResourcesOther External Resources

• HIV-1 Protease in the RCSB PDB Molecule of the Month.
• HIV-1 Protease in Wikipedia. Includes a link to this page.
• Discovery and development of HIV-protease inhibitors in Wikipedia.

Well-Developed, in ProteopediaWell-Developed, in Proteopedia

• Immunodeficiency virus protease includes morphs of flap movements and saquinavir binding. (HIV-1 protease redirects here.)
• Immunodeficiency virus protease 3D structures lists hundreds of crystal structures of HIV proteases.
• HIV Protease Inhibitor Resistance Profile
• Molecular Playground/HIV Protease Inhibitor includes an animated simulation of the protease inhibitor Ritonavir binding to the protease.
• Group:SMART:HIV-1 Subtype C Protease
• Protease
• Human Immunodeficiency Virus
• Journal:Acta_Cryst_D:S2059798319011355 Comparison of a retroviral protease crystallized as a monomer and a dimer.

Sandboxes in ProteopediaSandboxes in Proteopedia

• User:Tsung-Yi_Lin/Sandbox
• User:Dan_Huettner/Sandbox_1, User:Dan_Huettner/Sandbox_3
• User:David Canner/Sandbox HIV
• Sandbox 645
• Sandbox_Reserved_712
• Sandbox Reserved 955
• User:Nicole Maille/Sandbox 1

Flaps in Other ProteinsFlaps in Other Proteins

These were found by searching for "flaps" in Proteopedia.

• Sandbox 215: Omega flaps in cholesterol ester transfer protein.
• Fatty acid amide hydrolase, Sandbox_Reserved_921, Sandbox_Reserved_922

MethodsMethods

1hxw, containing the inhibitor Ritonavir, was selected in part because it is more closed than an early, unliganded wild type structure: Ile50 to Gly27 is 11.6 Å in 1hxw, vs. 16.9 Å in 3phv. (The only mutation in 1hxw is S37N.) 1tw7, with "wide open" flaps, was selected in part because its asymmetric unit contains two chains. It has many drug-resistance mutations (see table below).

The morph was generated by Proteopedia's PyMOL Morpher. 1tw7 was pre-aligned with 1hxw, aligning only residues 1-35. Alignment was done in the Jmol Java Application with the following script:

load =1hxw # "=" means load from RCSB PDB.
load append =1tw7 # add this model rather than replacing the previously loaded model.
frame all # display both models.
background white
trace only
color polymer
delay 2.0
compare {2.1} {1.1} subset {*.ca} atoms {1-35} {1-35} rotate translate 2.0 # moves model 2 to align with model 1
select 2.1 # "2.1" is the second model loaded
write 1tw7-aligned-to-1hxw.pdb

Wide-Open Drug-Free HIV Protease Crystal Structures
PDB ID	Year	Resolution; Rfree*	Asymm. Unit	Ile50 dist.†	Mutations; Comments	Wild Type
1tw7	2005	1.3 Å; WTA*	2 chains	12.25 Å	L10I, D25N, M36V, M46L, I54V, I62V, L63P, A71V, V82A, I84V, L90M	3phv
2pc0	2007	1.4 Å; BTA*	1 chain	12.2 Å	Q7K
2r8n	2008	1.2 Å; A*	1 chain	12.19 Å	Q7K, L33I, K41R, L63I
Other HIV Protease Crystal Structures With Separated Flaps
4npt	2014	1.66 Å; A*	1 chain	13.2 Å	D25N; Inhibitor is between flaps
3pj6	2011	2.25 Å; U*	1 chain	11.9 Å	V10I, D25N, D35E, I36V, M46L, T82A; Structure unreliable according to Rfree.

*R_free is categorized by FirstGlance in Jmol as A (Average), BTA (Better Than Average), U (Unreliable), WTA (Worse Than Average) at the corresponding resolution.
† Distance between the Ile50 alpha carbons in each chain. These are near the tips of the flaps, and this distance is commonly used in the literature to measure the openness of the flaps.