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Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins 2021; 90:96-109. [PMID: 34312913 PMCID: PMC9290662 DOI: 10.1002/prot.26189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.
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Affiliation(s)
- Heike I Rösner
- BRIC, University of Copenhagen, Copenhagen N, Denmark.,Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Martina Caldarini
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy
| | - Gregory Potel
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Daniel Malmodin
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Maria A Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Ricardo A Broglia
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Niels Bohr Institutet, University of Copenhagen, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Guido Tiana
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Center for Complexity and Biosystems, Università degli Studi di Milano, Milan, Italy
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Rösner HI, Caldarini M, Prestel A, Vanoni MA, Broglia RA, Aliverti A, Tiana G, Kragelund BB. Cold Denaturation of the HIV-1 Protease Monomer. Biochemistry 2017; 56:1029-1032. [DOI: 10.1021/acs.biochem.6b01141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heike I. Rösner
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
- Biotech
Research and Innovation Centre (BRIC), Faculty of Health and Medical
Sciences, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martina Caldarini
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Andreas Prestel
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maria A. Vanoni
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Ricardo A. Broglia
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
- Niels Bohr Institute, Blegdamsvej
17, 2100 Copenhagen Ø, Denmark
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
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Borkar AN, Rout MK, Hosur RV. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study. PLoS One 2011; 6:e19830. [PMID: 21738569 PMCID: PMC3126794 DOI: 10.1371/journal.pone.0019830] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/18/2011] [Indexed: 11/22/2022] Open
Abstract
Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR) was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH) solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.
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Affiliation(s)
- Aditi Narendra Borkar
- Institute of Bioinformatics and Biotechnology, University of Pune, Ganeshkhind, Pune, India
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Manoj Kumar Rout
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Ramakrishna V. Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Kalina, Santa Cruz Mumbai, India
- * E-mail:
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Bonomi M, Barducci A, Gervasio FL, Parrinello M. Multiple routes and milestones in the folding of HIV-1 protease monomer. PLoS One 2010; 5:e13208. [PMID: 20967249 PMCID: PMC2954147 DOI: 10.1371/journal.pone.0013208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/11/2010] [Indexed: 11/25/2022] Open
Abstract
Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIV–1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIV–1 protease.
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Affiliation(s)
- Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Switzerland.
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Kumar D, Paul S, Hosur RV. BEST-HNN and 2D-(HN)NH experiments for rapid backbone assignment in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:111-117. [PMID: 20236846 DOI: 10.1016/j.jmr.2010.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 02/07/2010] [Accepted: 02/15/2010] [Indexed: 05/28/2023]
Abstract
HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H(N), (15)N) assignment in ((13)C, (15)N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times (T(2)) are short. We show here that BEST modification Schanda et al. (2006) [2] increases the sensitivity per unit time by more than a factor of 2.0 and thus substantially increases the speed of data collection; good 3D data can be collected in 8-10h. Next, we present a simple method for amino-acid type identification based on simple 2D versions of the HNN experiment, labeled here as 2D-(HN)NH. Each of these experiments which produce anchor points for Gly, Ala, Ser/Thr residues, can be recorded in less than an hour. These enable rapid data acquisition, rapid analysis, and consequently rapid assignment of backbone (H(N), (15)N) resonances. The 2D-(HN)NH experiment does not involve aliphatic/aromatic protons and hence can be applied to deuterated protein samples as well, which is an additional advantage. The experiments have been demonstrated with human ubiquitin (76 aa) and acetic-acid denatured HIV-1 protease (99 aa), as representatives of folded and unfolded protein systems, respectively.
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Affiliation(s)
- Dinesh Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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