Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing

Sadiq, S. Kashif; Fabritiis, Gianni De

doi:10.1002/prot.22806

Cited by 64 publications

(104 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This agrees well with previous calculations and experimental measurements of the relaxation rate of fast-flap conformational opening, which exhibits a small kinetic barrier (k flap ≈ 0.1 ns −1 ) (10,15,33,34). Even though self-association via both flap opening and lateral threading was observed, it is difficult to attribute any event solely to either one or the other mechanism.…”

Section: Resultssupporting

confidence: 91%

“…Here, a wide-open conformation corresponds to λ x < −20 Å. Only a few trajectories transiently exhibited wide-opening, consistent with the experimentally observed 100-μs relaxation timescale (33) and with previous simulations of the mature protease (15). This also places a lower limit of ∼100 μs on the wide-opening relaxation time for an immature protease.…”

Section: Resultssupporting

confidence: 89%

“…A wide-open flap conformation in the free enzyme has been characterized previously (14,15). Here, a wide-open conformation corresponds to λ x < −20 Å.…”

Section: Resultsmentioning

confidence: 92%

“…The existence of conformational ensembles in free enzyme is well established (24,25). We have shown previously that several conformations in HIV-1 protease preexist in apo form (15).…”

mentioning

confidence: 93%

“…Access to this site is modulated by a pair of flexible β-hairpin flaps (Fig. 1C) that must first open to allow entry and then close (10)(11)(12)(13)(14)(15) to make substrate cleavage viable through a structurally conserved recognition pattern (16)(17)(18)(19). Recent advances in paramagnetic relaxation enhancement (PRE) (20) reveal transient N-terminal contacts within the active site, but a complete structural characterization of this transient process in full atomic detail remains an outstanding challenge and is the aim of this work.…”

mentioning

confidence: 99%

See 4 more Smart Citations

Kinetic characterization of the critical step in HIV-1 protease maturation

Sadiq

Noé

Fabritiis

2012

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

Self Cite

114

View full text Add to dashboard Cite

HIV maturation requires multiple cleavage of long polyprotein chains into functional proteins that include the viral protease itself. Initial cleavage by the protease dimer occurs from within these precursors, and yet only a single protease monomer is embedded in each polyprotein chain. Self-activation has been proposed to start from a partially dimerized protease formed from monomers of different chains binding its own N termini by self-association to the active site, but a complete structural understanding of this critical step in HIV maturation is missing. Here, we captured the critical self-association of immature HIV-1 protease to its extended aminoterminal recognition motif using large-scale molecular dynamics simulations, thus confirming the postulated intramolecular mechanism in atomic detail. We show that self-association to a catalytically viable state requires structural cooperativity of the flexible β-hairpin "flap" regions of the enzyme and that the major transition pathway is first via self-association in the semiopen/open enzyme states, followed by enzyme conformational transition into a catalytically viable closed state. Furthermore, partial N-terminal threading can play a role in self-association, whereas wide opening of the flaps in concert with self-association is not observed. We estimate the association rate constant (k on ) to be on the order of ∼1 × 10 4 s −1 , suggesting that N-terminal self-association is not the rate-limiting step in the process. The shown mechanism also provides an interesting example of molecular conformational transitions along the association pathway.conformational kinetics | Markov state model | high-throughput molecular dynamics H IV, along with all retroviruses, achieves infectious maturation of nascent virus particles through cleavage of polyprotein precursors by the viral protease. In particular, the GagPol chains contain several covalently linked proteins including the protease itself (Fig. 1A). Thus, maturation of the virus is initiated by autocatalysis of viral protease initially embedded in GagPol precursors. HIV-1 protease is functional only in dimeric form (1, 2) because activity of monomeric protease precursor is three orders of magnitude less than the mature dimer (3), and yet only a single monomer is embedded within each precursor. Two individual monomers in different GagPol chains must, therefore, come together to form an embedded dimeric protease, which ultimately cleaves itself into a mature form (Fig. 1B).Experiments indicate initial cleavage by a precursor protease still embedded in the GagPol chain occurs through an intramolecular, concentration-independent mechanism with the precursor protease cleaving its own terminus (4) and critically modulated by the N-terminal region (5-8). Mutations that block N-terminal cleavage result in severe loss of efficiency in catalytic activity. Cleavage at the protease (PR), reverse transcriptase (RT) junction at the C-terminal end of the protease by the precursor protease occurs via an intermolecular, concentrat...

show abstract

Section: Resultssupporting

confidence: 91%

Section: Resultssupporting

confidence: 89%

“…A wide-open flap conformation in the free enzyme has been characterized previously (14,15). Here, a wide-open conformation corresponds to λ x < −20 Å.…”

Section: Resultsmentioning

confidence: 92%

“…The existence of conformational ensembles in free enzyme is well established (24,25). We have shown previously that several conformations in HIV-1 protease preexist in apo form (15).…”

mentioning

confidence: 93%

mentioning

confidence: 99%

See 3 more Smart Citations

Kinetic characterization of the critical step in HIV-1 protease maturation

Sadiq

Noé

Fabritiis

2012

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

Self Cite

114

View full text Add to dashboard Cite

show abstract

Mercury Detoxification by Bacteria: Simulations of Transcription Activation and MercuryCarbon Bond Cleavage

Guo

Parks

Johs

et al. 2011

Modeling of Molecular Properties

View full text Add to dashboard Cite

Identifying binding hot spots on protein surfaces by mixed‐solvent molecular dynamics: HIV‐1 protease as a test case

et al. 2015

View full text Add to dashboard Cite

Mixed-solvent molecular dynamics (MixMD) simulations use full protein flexibility and competition between water and small organic probes to achieve accurate hot-spot mapping on protein surfaces. In this study, we improved MixMD using HIV-1 protease as the test case. We used three probe-water solutions (acetonitrile-water, isopropanol-water, and pyrimidine-water), first at 50% w/w concentration and later at 5% v/v. Paradoxically, better mapping was achieved by using fewer probes; 5% simulations gave a superior signal-to-noise ratio and far fewer spurious hot spots than 50% MixMD. Furthermore, very intense and well-defined probe occupancies were observed in the catalytic site and potential allosteric sites that have been confirmed experimentally. The Eye site, an allosteric site underneath the flap of HIV-1 protease, has been confirmed by the presence of a 5-nitroindole fragment in a crystal structure. MixMD also mapped two additional hot spots: the Exo site (between the Gly16-Gly17 and Cys67-Gly68 loops) and the Face site (between Glu21-Ala22 and Val84-Ile85 loops). The Exo site was observed to overlap with crystallographic additives such as acetate and DMSO that are present in different crystal forms of the protein. Analysis of crystal structures of HIV-1 protease in different symmetry groups has shown that some surface sites are common interfaces for crystal contacts, which means they are surfaces that are relatively easy to desolvate and complement with organic molecules. MixMD should identify these sites; in fact, their occupancy values help establish a solid cut-off where “druggable” sites are required to have higher occupancies than the crystal-packing faces.

show abstract

Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing

Cited by 64 publications

References 61 publications

Kinetic characterization of the critical step in HIV-1 protease maturation

Kinetic characterization of the critical step in HIV-1 protease maturation

Mercury Detoxification by Bacteria: Simulations of Transcription Activation and MercuryCarbon Bond Cleavage

Identifying binding hot spots on protein surfaces by mixed‐solvent molecular dynamics: HIV‐1 protease as a test case

Contact Info

Product

Resources

About