Kinetic characterization of the critical step in HIV-1 protease maturation
Open accessAbstract
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 amino-terminal 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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
MSM studies revealed a putative mechanism for the autocatalytic step in HIV maturation of HIV protease.
“Other MSMs studies have revealed putative mechanisms for the autocatalytic step in HIV maturation of HIV protease [64]”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [64]
Rate constants can be derived from molecular dynamics, as reported for individual reactions and for reaction networks.
“Molecular dynamics-based GARD is envisaged, among other directions, as involving network kinetics simulations, in which the rate constants are derived from molecular dynamics, as reported for individual reactions [260,265,266], as well as for reaction networks [267].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [265]
MSMs have been applied to protein folding, ligand binding, conformational change, IDP dynamics/kinetics, and ATP permeation.
“Markov state models have been applied to a wide variety of problems, spanning protein folding,402 protein-ligand binding process,403 protein conformational change,404–405 the dynamics and kinetics of IDPs,369,406–407 and ATP permeation through membrane protein channels.408”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [405]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
No citation lists for this paper
No citation lists for this paper yet — checked again daily.
References 44 · Cited by 102
Research works printed but not linked: 39
- Darke PL, et al. (1994) Dissociation and association of the HIV-1 protease dimer subunits: Equilibria and rates. Biochemistry 33(1):98-105.
- Ishima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM (2003) Solution structure of the mature HIV-1 protease monomer: Insight into the tertiary fold and stability of a precursor. J Biol Chem 278(44):43311-43319.
- Pettit SC, Everitt LE, Choudhury S, Dunn BM, Kaplan AH (2004) Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism. J Virol 78(16):8477-8485.
- Louis JM, Nashed NT, Parris KD, Kimmel AR, Jerina DM (1994) Kinetics and mechanism of autoprocessing of human immunodeficiency virus type 1 protease from an analog of the Gag-Pol polyprotein. Proc Natl Acad Sci USA 91(17):7970-7974.
- Wondrak EM, Louis JM (1996) Influence of flanking sequences on the dimer stability of human immunodeficiency virus type 1 protease. Biochemistry 35(39):12957-12962.
- Louis JM, Clore GM, Gronenborn AM (1999) Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat Struct Biol 6(9):868-875.
- Louis JM, Wondrak EM, Kimmel AR, Wingfield PT, Nashed NT (1999) Proteolytic processing of HIV-1 protease precursor, kinetics and mechanism. J Biol Chem 274(33): 23437-23442.
- Wondrak EM, Nashed NT, Haber MT, Jerina DM, Louis JM (1996) A transient precursor of the HIV-1 protease. Isolation, characterization, and kinetics of maturation. J Biol Chem 271(8):4477-4481.
- Freedberg DI, et al. (2002) Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 11(2):221-232.
- Scott WRP, Schiffer CA (2000) Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 8(12):1259-1265.
- Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA (2006) Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J 90(11):3880-3885.
- Tóth G, Borics A (2006) Flap opening mechanism of HIV-1 protease. J Mol Graph Model 24(6):465-474.
- Hornak V, Okur A, Rizzo RC, Simmerling C (2006) HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci USA 103(4): 915-920.
- Sadiq SK, De Fabritiis G (2010) Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing. Proteins 78(14):2873-2885.
- Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA (2006) Mechanism of sub- strate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol 80(7):3607-3616.
- Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2002) Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six sub- strate complexes. Structure 10(3):369-381.
- Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2000) How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol 301(5):1207-1220.
- Prabu-Jeyabalan M, et al. (2006) Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother 50(4):1518-1521.
- Tang C, Louis JM, Aniana A, Suh JY, Clore GM (2008) Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease. Nature 455(7213):693-696.
- Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9(9):646-652.
- Harvey MJ, Giupponi G, Fabritiis GD (2009) Acemd: Accelerating biomolecular dy- namics in the microsecond time scale. J Chem Theory Comput 5(6):1632-1639.
- Buch I, Harvey MJ, Giorgino T, Anderson DP, De Fabritiis G (2010) High-throughput all-atom molecular dynamics simulations using distributed computing. J Chem Inf Model 50(3):397-403.
- Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational en- sembles in biomolecular recognition. Nat Chem Biol 5(11):789-796.
- Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450(7171):913-916.
- Bowman GR, Voelz VA, Pande VS (2011) Taming the complexity of protein folding. Curr Opin Struct Biol 21(1):4-11.
- Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC (2007) Automatic discovery of metastable states for the construction of Markov models of macromolecular con- formational dynamics. J Chem Phys 126(15):155101.
- Prinz JH, et al. (2011) Markov models of molecular kinetics: Generation and valida- tion. J Chem Phys 134(17):174105.
- Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR (2009) Constructing the equi- librium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA 106(45):19011-19016.
- Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 132(5): 1526-1528.
- Buch I, Giorgino T, De Fabritiis G (2011) Complete reconstruction of an enzyme-in- hibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 108(25):10184-10189.
- Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA (1999) Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 7(9):1047-1055.
- Katoh E, et al. (2003) A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex. Protein Sci 12(7):1376-1385.
- Pietrucci F, Marinelli F, Carloni P, Laio A (2009) Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc 131(33): 11811-11818.
- Tóth G, Borics A (2006) Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases. Bio- chemistry 45(21):6606-6614.
- Hornak V, Okur A, Rizzo RC, Simmerling C (2006) HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an in- hibitor into the open state. J Am Chem Soc 128(9):2812-2813.
- Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28(1):235-242.
- Duan Y, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999-2012.
- Harvey M, De Fabritiis G (2009) An implementation of the smooth particle mesh Ewald method on GPU hardware. J Chem Theory Comput 5(9):2371-2377.
- Noé F, Horenko I, Schütte C, Smith JC (2007) Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states. J Chem Phys 126(15):155102.
- Authors
- Sadiq, S. K., Noé, F., & De Fabritiis, G.
- Affiliations
- Universitat Pompeu Fabra (ES)
- Freie Universität Berlin (DE)
- Computational Biophysics Laboratory, GRIB-IMIM, Universitat Pompeu Fabra, 08003 Barcelona, Spain; and
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-11-26
- Volume
- 109
- Issue
- 50
- Pages
- 20449-20454
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3528573
- OpenAlex
- W1981078831
- Cited by
- 102
- References
- 44
- Citations by year
- 2026: 4 · 2025: 2 · 2023: 3 · 2022: 2 · 2021: 10 · 2020: 7 · 2019: 5 · 2018: 10 · 2017: 4 · 2016: 10 · 2015: 11 · 2014: 21 · 2013: 13
- FWCI
- 5.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- European Commission
- Deutsche Forschungsgemeinschaft (825/3)
- Ministerio de Ciencia e Innovación (BIO2011/27450)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- HIV-1 protease, protease maturation, self-activation, intramolecular cleavage, polyprotein processing, conformational change, association rate constant, molecular dynamics simulation, enzyme dimerization
- MeSH terms
- Amino Acid Sequence, Enzyme Precursors, Humans, Kinetics, Models, Molecular, Protein Conformation, Protein Processing, Post-Translational, HIV-1, HIV Protease, Catalytic Domain, Protein Interaction Domains and Motifs, Protein Multimerization, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
