1
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Tran TT, Fanucci GE. Natural Polymorphisms D60E and I62V Stabilize a Closed Conformation in HIV-1 Protease in the Absence of an Inhibitor or Substrate. Viruses 2024; 16:236. [PMID: 38400012 PMCID: PMC10892587 DOI: 10.3390/v16020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
HIV infection remains a global health issue plagued by drug resistance and virological failure. Natural polymorphisms (NPs) contained within several African and Brazilian protease (PR) variants have been shown to induce a conformational landscape of more closed conformations compared to the sequence of subtype B prevalent in North America and Western Europe. Here we demonstrate through experimental pulsed EPR distance measurements and molecular dynamic (MD) simulations that the two common NPs D60E and I62V found within subtypes F and H can induce a closed conformation when introduced into HIV-1PR subtype B. Specifically, D60E alters the conformation in subtype B through the formation of a salt bridge with residue K43 contained within the nexus between the flap and hinge region of the HIV-1 PR fold. On the other hand, I62V modulates the packing of the hydrophobic cluster of the cantilever and fulcrum, also resulting in a more closed conformation.
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Affiliation(s)
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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2
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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3
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Gamble Jarvi A, Bogetti X, Singewald K, Ghosh S, Saxena S. Going the dHis-tance: Site-Directed Cu 2+ Labeling of Proteins and Nucleic Acids. Acc Chem Res 2021; 54:1481-1491. [PMID: 33476119 DOI: 10.1021/acs.accounts.0c00761] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Account, we showcase site-directed Cu2+ labeling in proteins and DNA, which has opened new avenues for the measurement of the structure and dynamics of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the spin label is assembled in situ from natural amino acid residues and a metal complex and requires no post-expression synthetic modification or purification procedures. The labeling scheme exploits a double histidine (dHis) motif, which utilizes endogenous or site-specifically mutated histidine residues to coordinate a Cu2+ complex. Pulsed EPR measurements on such Cu2+-labeled proteins potentially yield distance distributions that are up to 5 times narrower than the common protein spin label-the approach, thus, overcomes the inherent limitation of the current technology, which relies on a spin label with a highly flexible side chain. This labeling scheme provides a straightforward method that elucidates biophysical information that is costly, complicated, or simply inaccessible by traditional EPR labels. Examples include the direct measurement of protein backbone dynamics at β-sheet sites, which are largely inaccessible through traditional spin labels, and rigid Cu2+-Cu2+ distance measurements that enable higher precision in the analysis of protein conformations, conformational changes, interactions with other biomolecules, and the relative orientations of two labeled protein subunits. Likewise, a Cu2+ label has been developed for use in DNA, which is small, is nucleotide independent, and is positioned within the DNA helix. The placement of the Cu2+ label directly reports on the biologically relevant backbone distance. Additionally, for both of these labeling techniques, we have developed models for interpretation of the EPR distance information, primarily utilizing molecular dynamics (MD) simulations. Initial results using force fields developed for both protein and DNA labels have agreed with experimental results, which has been a major bottleneck for traditional spin labels. Looking ahead, we anticipate new combinations of MD and EPR to further our understanding of protein and DNA conformational changes, as well as working synergistically to investigate protein-DNA interactions.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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4
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Darunavir-Resistant HIV-1 Protease Constructs Uphold a Conformational Selection Hypothesis for Drug Resistance. Viruses 2020; 12:v12111275. [PMID: 33171603 PMCID: PMC7695139 DOI: 10.3390/v12111275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/24/2023] Open
Abstract
Multidrug resistance continues to be a barrier to the effectiveness of highly active antiretroviral therapy in the treatment of human immunodeficiency virus 1 (HIV-1) infection. Darunavir (DRV) is a highly potent protease inhibitor (PI) that is oftentimes effective when drug resistance has emerged against first-generation inhibitors. Resistance to darunavir does evolve and requires 10–20 amino acid substitutions. The conformational landscapes of six highly characterized HIV-1 protease (PR) constructs that harbor up to 19 DRV-associated mutations were characterized by distance measurements with pulsed electron double resonance (PELDOR) paramagnetic resonance spectroscopy, namely double electron–electron resonance (DEER). The results show that the accumulated substitutions alter the conformational landscape compared to PI-naïve protease where the semi-open conformation is destabilized as the dominant population with open-like states becoming prevalent in many cases. A linear correlation is found between values of the DRV inhibition parameter Ki and the open-like to closed-state population ratio determined from DEER. The nearly 50% decrease in occupancy of the semi-open conformation is associated with reduced enzymatic activity, characterized previously in the literature.
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5
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Ahsan M, Pindi C, Senapati S. Electrostatics Plays a Crucial Role in HIV-1 Protease Substrate Binding, Drugs Fail to Take Advantage. Biochemistry 2020; 59:3316-3331. [PMID: 32822154 DOI: 10.1021/acs.biochem.0c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease (HIVPR) is an important drug target for combating AIDS. This enzyme is an aspartyl protease that is functionally active in its dimeric form. Nuclear magnetic resonance reports have convincingly shown that a pseudosymmetry exists at the HIVPR active site, where only one of the two aspartates remains protonated over the pH range of 2.5-7.0. To date, all HIVPR-targeted drug design strategies focused on maximizing the size-shape complementarity and van der Waals interactions of the small molecule drugs with the deprotonated, symmetric active site envelope of crystallized HIVPR. However, these strategies were ineffective with the emergence of drug resistant protease variants, primarily due to the steric clashes at the active site. In this study, we traced a specificity in the substrate binding motif that emerges primarily from the asymmetrical electrostatic potential present in the protease active site due to the uneven protonation. Our detailed results from atomistic molecular dynamics simulations show that while such a specific mode of substrate binding involves significant electrostatic interactions, none of the existing drugs or inhibitors could utilize this electrostatic hot spot. As the electrostatic is long-range interaction, it can provide sufficient binding strength without the necessity of increasing the bulkiness of the inhibitors. We propose that introducing the electrostatic component along with optimal fitting at the binding pocket could pave the way for promising designs that might be more effective against both wild type and HIVPR resistant variants.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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6
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Tran TT, Liu Z, Fanucci GE. Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study. Biochem Biophys Res Commun 2020; 532:219-224. [PMID: 32863004 DOI: 10.1016/j.bbrc.2020.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 02/02/2023]
Abstract
HIV infection is a global health epidemic with current FDA-approved HIV-1 Protease inhibitors (PIs) designed against subtype B protease, yet they are used in HIV treatment world-wide regardless of patient HIV classification. In this study, double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy was utilized to gain insights in how natural polymorphisms in several African and Brazilian protease (PR) variants affect the conformational landscape both in the absence and presence of inhibitors. Findings show that Subtypes F and H HIV-1 PR adopt a primarily closed conformation in the unbound state with two secondary mutations, D60E and I62V, postulated to be responsible for the increased probability for closed conformation. In contrast, subtype D, CRF_AG, and CRF_BF HIV-1 PR adopt a primarily semi-open conformation, as observed for PI-naïve-subtype B when unbound by substrate or inhibitor. The impact that inhibitor binding has on shifting the conformational land scape of these variants is also characterized, where analysis provides classification of inhibitor induced shifts away from the semi-open state into weak, moderate and strong effects. The findings are compared to those for prior studies of inhibitor induced conformational shifts in PI-naïve Subtype B, C and CRF_AE.
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Affiliation(s)
- Trang T Tran
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA.
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7
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Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:365-374. [PMID: 31243634 PMCID: PMC6941145 DOI: 10.1007/s10858-019-00260-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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8
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Maphumulo SI, Halder AK, Govender T, Maseko S, Maguire GEM, Honarparvar B, Kruger HG. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study. Chem Biol Drug Des 2018; 92:1899-1913. [PMID: 30003668 DOI: 10.1111/cbdd.13364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
HIV-1 protease (HIV PR) is considered as one of the most attractive targets for the treatment of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease inhibitors (PIs) is a crucial ongoing research field. Recently, our research group evaluated the binding affinities of different FDA approved PIs against the South African HIV-1 subtype C (C-SA) protease (PR). The CSA-HIV PR displayed weaker binding affinity for most of the clinical PIs compared to HIV-1 B subtype for West and Central Europe, the Americas. In the current work, the flap dynamics of four different systems of HIV-1 C-SA PR complexed to FDA approved second generation PIs and its impact on binding was explored over the molecular dynamic trajectories. It was observed that the interactions of the selected drugs with the binding site residues of the protease may not be the major contributor for affinity towards PIs. Various post-MD analyses were performed, also entropic contributions, solvation free energies and hydrophobic core formation interactions were studied to assess how the flap dynamics of C-SA PR which is affected by such factors. From these contributions, large van der Waals interactions and low solvation free energies were found to be major factors for the higher activity of ATV against C-SA HIV PR. Furthermore, a comparatively stable hydrophobic core may be responsible for higher stability of the PR flaps of the ATV complex. The outcome of this study provides significant guidance to how the flap dynamics of C-SA PR is affected by various factors as a result of the binding affinity of various protease inhibitors. It will also assist with the design of potent inhibitors against C-SA HIV PR that apart from binding in the active site of PR can interacts with the flaps to prevent opening of the flaps resulting in inactivation of the protease.
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Affiliation(s)
- Siyabonga I Maphumulo
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Amit K Halder
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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9
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McGillewie L, Ramesh M, Soliman ME. Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases. Protein J 2017; 36:385-396. [PMID: 28762197 DOI: 10.1007/s10930-017-9735-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Aspartic proteases are a class of hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer's. The flap region of aspartic proteases is a characteristic unique structural feature of these enzymes; and found to have a profound impact on protein overall structure, function and dynamics. Flap dynamics also plays a crucial role in drug binding and drug resistance. Therefore, understanding the structure and dynamic behavior of this flap regions is crucial in the design of potent and selective inhibitors against aspartic proteases. Defining metrics that can describe the flap motion/dynamics has been a challenging topic in literature. This review is the first attempt to compile comprehensive information on sequence, structure, motion and metrics used to assess the dynamics of the flap region of different aspartic proteases in "one pot". We believe that this review would be of critical importance to the researchers from different scientific domains.
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Affiliation(s)
- Lara McGillewie
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa
| | - Muthusamy Ramesh
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa
| | - Mahmoud E Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa.
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10
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Meir A, Abdelhai A, Moskovitz Y, Ruthstein S. EPR Spectroscopy Targets Structural Changes in the E. coli Membrane Fusion CusB upon Cu(I) Binding. Biophys J 2017. [PMID: 28636907 DOI: 10.1016/j.bpj.2017.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacterial cells have developed sophisticated systems to deal with the toxicity of metal ions. Escherichia coli CusCFBA is a complex efflux system, responsible for transferring Cu(I) and Ag(I) ions; this system, located in the periplasm, involves four proteins, CusA, CusB, CusC, and CusF. CusA, CusB, and CusC are connected to one another in an oligomerization ratio of 3:6:3 CusA/CusB/CusC to form the CusCBA periplasm membrane transporter. CusB is an adaptor protein that connects the two membrane proteins CusA (inner membrane) and CusC (outer membrane). CusF is a metallochaperone that transfers Cu(I) and Ag(I) to the CusCBA transporter from the periplasm. The crystal structures of CusB, CusC, CusF, and the CusBA complex have been resolved, shedding some light on the efflux mechanism underlying this intriguing system. However, since CusB is an adaptor protein, its role in operating this system is significant, and should be understood in detail. Here, we utilize EPR spectroscopy to target the conformational changes that take place in the full CusB protein upon binding Cu(I). We reveal that CusB is a dimer in solution, and that the orientation of one molecule with respect to the other molecule changes upon Cu(I) coordination, resulting in a more compact CusB structure. These structural and topological changes upon Cu(I) binding probably play the role of a switch for opening the channel and transferring metal ions from CusB to CusC and out of the cell.
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Affiliation(s)
- Aviv Meir
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Ahmad Abdelhai
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Yoni Moskovitz
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel.
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11
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Levy AR, Turgeman M, Gevorkyan-Aiapetov L, Ruthstein S. The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations. Protein Sci 2017; 26:1609-1618. [PMID: 28543811 DOI: 10.1002/pro.3197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/15/2017] [Indexed: 01/20/2023]
Abstract
Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution. Electron paramagnetic resonance (EPR) spectroscopy has recently emerged as a powerful tool for resolving biological reactions and mechanisms in solution. When coupled with computational methods, EPR with site-directed spin labeling and nanoscale distance measurements can provide structural information on a protein or protein complex in solution. We use these methods to show that Atox1 can accommodate at least four different conformations in the apo state (unbound to copper), and two different conformations in the holo state (bound to copper). We also demonstrate that the structure of Atox1 in the holo form is more compact than in the apo form. Our data provide insight regarding the structural mechanisms through which Atox1 can fulfill its dual role of copper binding and transfer.
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Affiliation(s)
- Ariel R Levy
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Meital Turgeman
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Lada Gevorkyan-Aiapetov
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Sharon Ruthstein
- The Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan, 5290002, Israel
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12
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Yu Y, Wang J, Chen Z, Wang G, Shao Q, Shi J, Zhu W. Structural insights into HIV-1 protease flap opening processes and key intermediates. RSC Adv 2017. [DOI: 10.1039/c7ra09691g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The study provided an integrated view of the transition pathway of the flap opening of HIV-1 protease using MD simulation.
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Affiliation(s)
- Yuqi Yu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Jinan Wang
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Zhaoqiang Chen
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Guimin Wang
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Jiye Shi
- UCB Biopharma SPRL
- Chemin du Foriest
- Belgium
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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13
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Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution. J Biol Chem 2016; 291:22741-22756. [PMID: 27576689 DOI: 10.1074/jbc.m116.747568] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multidrug resistance to current Food and Drug Administration-approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug pressure-selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impacts of the hinge-region natural polymorphism at residue 35, glutamate to aspartate (E35D), alone and in conjunction with residue 57, arginine to lysine (R57K), are characterized with the goal of understanding how altered salt bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt bridge interactions between residues 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D and R57K), x-ray structures reveal an altered network of interactions that replace the salt bridge thus stabilizing the structural integrity between the flap and hinge regions. Despite the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge-region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and the conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.
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Affiliation(s)
- Zhanglong Liu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Lingna Hu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Linh Pham
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Katye M Poole
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Yan Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Brian P Mahon
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Wenxing Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Kunhua Li
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Nathan E Goldfarb
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Robert McKenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
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14
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Costa MGS, Batista PR, Bisch PM, Perahia D. Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes. J Chem Theory Comput 2016; 11:2755-67. [PMID: 26575568 DOI: 10.1021/acs.jctc.5b00003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteins are found in solution as ensembles of conformations in dynamic equilibrium. Exploration of functional motions occurring on micro- to millisecond time scales by molecular dynamics (MD) simulations still remains computationally challenging. Alternatively, normal mode (NM) analysis is a well-suited method to characterize intrinsic slow collective motions, often associated with protein function, but the absence of anharmonic effects preclude a proper characterization of conformational distributions in a multidimensional NM space. Using both methods jointly appears to be an attractive approach that allows an extended sampling of the conformational space. In line with this view, the MDeNM (molecular dynamics with excited normal modes) method presented here consists of multiple-replica short MD simulations in which motions described by a given subset of low-frequency NMs are kinetically excited. This is achieved by adding additional atomic velocities along several randomly determined linear combinations of NM vectors, thus allowing an efficient coupling between slow and fast motions. The relatively high-energy conformations generated with MDeNM are further relaxed with standard MD simulations, enabling free energy landscapes to be determined. Two widely studied proteins were selected as examples: hen egg lysozyme and HIV-1 protease. In both cases, MDeNM provides a larger extent of sampling in a few nanoseconds, outperforming long standard MD simulations. A high degree of correlation with motions inferred from experimental sources (X-ray, EPR, and NMR) and with free energy estimations obtained by metadynamics was observed. Finally, the large sets of conformations obtained with MDeNM can be used to better characterize relevant dynamical populations, allowing for a better interpretation of experimental data such as SAXS curves and NMR spectra.
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Affiliation(s)
- Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz , 21040-360, Rio de Janeiro, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21949-901 Rio de Janeiro, Brazil.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique , 61, F-94235 Cachan, France
| | - Paulo R Batista
- Programa de Computação Científica, Fundação Oswaldo Cruz , 21040-360, Rio de Janeiro, Brazil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21949-901 Rio de Janeiro, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique , 61, F-94235 Cachan, France
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15
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Appadurai R, Senapati S. Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity. Biochemistry 2016; 55:1529-40. [PMID: 26892689 DOI: 10.1021/acs.biochem.5b00946] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8-21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies.
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Affiliation(s)
- Rajeswari Appadurai
- BJM School of Biosciences and Department of Biotechnology, Indian Institution of Technology Madras , Chennai 600 036, India
| | - Sanjib Senapati
- BJM School of Biosciences and Department of Biotechnology, Indian Institution of Technology Madras , Chennai 600 036, India
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16
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Liu Z, Casey TM, Blackburn ME, Huang X, Pham L, de Vera IMS, Carter JD, Kear-Scott JL, Veloro AM, Galiano L, Fanucci GE. Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts. Phys Chem Chem Phys 2016; 18:5819-31. [PMID: 26489725 PMCID: PMC4758878 DOI: 10.1039/c5cp04556h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The conformational landscape of HIV-1 protease (PR) can be experimentally characterized by pulsed-EPR double electron-electron resonance (DEER). For this characterization, nitroxide spin labels are attached to an engineered cysteine residue in the flap region of HIV-1 PR. DEER distance measurements from spin-labels contained within each flap of the homodimer provide a detailed description of the conformational sampling of apo-enzyme as well as induced conformational shifts as a function of inhibitor binding. The distance distribution profiles are further interpreted in terms of a conformational ensemble scheme that consists of four unique states termed "curled/tucked", "closed", "semi-open" and "wide-open" conformations. Reported here are the DEER results for a drug-resistant variant clinical isolate sequence, V6, in the presence of FDA approved protease inhibitors (PIs) as well as a non-hydrolyzable substrate mimic, CaP2. Results are interpreted in the context of the current understanding of the relationship between conformational sampling, drug resistance, and kinetic efficiency of HIV-1PR as derived from previous DEER and kinetic data for a series of HIV-1PR constructs that contain drug-pressure selected mutations or natural polymorphisms. Specifically, these collective results support the notion that inhibitor-induced closure of the flaps correlates with inhibitor efficiency and drug resistance. This body of work also suggests DEER as a tool for studying conformational sampling in flexible enzymes as it relates to function.
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Affiliation(s)
- Zhanglong Liu
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Thomas M Casey
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Mandy E Blackburn
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Xi Huang
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Linh Pham
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Ian Mitchelle S de Vera
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jeffrey D Carter
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jamie L Kear-Scott
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Angelo M Veloro
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Luis Galiano
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
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17
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Casey TM, Fanucci GE. Spin labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease. Methods Enzymol 2015; 564:153-87. [PMID: 26477251 DOI: 10.1016/bs.mie.2015.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An understanding of macromolecular conformational equilibrium in biological systems is oftentimes essential to understand function, dysfunction, and disease. For the past few years, our lab has been utilizing site-directed spin labeling (SDSL), coupled with electron paramagnetic resonance (EPR) spectroscopy, to characterize the conformational ensemble and ligand-induced conformational shifts of HIV-1 protease (HIV-1PR). The biomedical importance of characterizing the fractional occupancy of states within the conformational ensemble critically impacts our hypothesis of a conformational selection mechanism of drug-resistance evolution in HIV-1PR. The purpose of the following chapter is to give a timeline perspective of our SDSL EPR approach to characterizing conformational sampling of HIV-1PR. We provide detailed instructions for the procedure utilized in analyzing distance profiles for HIV-1PR obtained from pulsed electron-electron double resonance (PELDOR). Specifically, we employ a version of PELDOR known as double electron-electron resonance (DEER). Data are processed with the software package "DeerAnalysis" (http://www.epr.ethz.ch/software), which implements Tikhonov regularization (TKR), to generate a distance profile from electron spin-echo amplitude modulations. We assign meaning to resultant distance profiles based upon a conformational sampling model, which is described herein. The TKR distance profiles are reconstructed with a linear combination of Gaussian functions, which is then statistically analyzed. In general, DEER has proven powerful for observing structural ensembles in proteins and, more recently, nucleic acids. Our goal is to present our advances in order to aid readers in similar applications.
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Affiliation(s)
- Thomas M Casey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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18
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Kumalo HM, Bhakat S, Soliman ME. Investigation of flap flexibility of β-secretase using molecular dynamic simulations. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1064831] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hezekiel M. Kumalo
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Soumendranath Bhakat
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Biophysical Chemistry, Lund University, P.O. Box 124, SE, 22100 Lund, Sweden
| | - Mahmoud E. Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
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19
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Karubiu W, Bhakat S, McGillewie L, Soliman MES. Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics. MOLECULAR BIOSYSTEMS 2015; 11:1061-6. [DOI: 10.1039/c4mb00631c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, for the first time, we report the flap opening and closing in Plasmepsin proteases – plasmepsin II (PlmII) was used as a prototype model.
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Affiliation(s)
- Wilson Karubiu
- School of Health Sciences
- University of KwaZulu-Natal
- Durban-4000
- South Africa
| | | | - Lara McGillewie
- School of Health Sciences
- University of KwaZulu-Natal
- Durban-4000
- South Africa
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20
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Naicker P, Stoychev S, Dirr HW, Sayed Y. Amide hydrogen exchange in HIV-1 subtype B and C proteases - insights into reduced drug susceptibility and dimer stability. FEBS J 2014; 281:5395-410. [DOI: 10.1111/febs.13084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/29/2014] [Accepted: 09/29/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Previn Naicker
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Stoyan Stoychev
- Council for Scientific and Industrial Research; Biosciences; Pretoria South Africa
| | - Heini W. Dirr
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
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21
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Carter JD, Mathias JD, Gomez EF, Ran Y, Xu F, Galiano L, Tran NQ, D'Amore PW, Wright CS, Chakravorty DK, Fanucci GE. Characterizing solution surface loop conformational flexibility of the GM2 activator protein. J Phys Chem B 2014; 118:10607-17. [PMID: 25127419 PMCID: PMC4161144 DOI: 10.1021/jp505938t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
GM2AP
has a β-cup topology with numerous X-ray structures
showing multiple conformations for some of the surface loops, revealing
conformational flexibility that may be related to function, where
function is defined as either membrane binding associated with ligand
binding and extraction or interaction with other proteins. Here, site-directed
spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy
and molecular dynamic (MD) simulations are used to characterize the
mobility and conformational flexibility of various structural regions
of GM2AP. A series of 10 single cysteine amino acid substitutions
were generated, and the constructs were chemically modified with the
methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes
were obtained and subsequently simulated using the microscopic order
macroscopic disorder (MOMD) program. Line shapes for sites that have
multiple conformations in the X-ray structures required two spectral
components, whereas spectra of the remaining sites were adequately
fit with single-component parameters. For spin labeled sites L126C
and I66C, spectra were acquired as a function of temperature, and
simulations provided for the determination of thermodynamic parameters
associated with conformational change. Binding to GM2 ligand did not
alter the conformational flexibility of the loops, as evaluated by
EPR and NMR spectroscopies. These results confirm that the conformational
flexibility observed in the surface loops of GM2AP crystals is present
in solution and that the exchange is slow on the EPR time scale (>ns).
Furthermore, MD simulation results are presented and agree well with
the conformational heterogeneity revealed by SDSL.
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Affiliation(s)
- Jeffery D Carter
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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22
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Carter JD, Gonzales EG, Huang X, Smith AN, de Vera IMS, D'Amore PW, Rocca JR, Goodenow MM, Dunn BM, Fanucci GE. Effects of PRE and POST therapy drug-pressure selected mutations on HIV-1 protease conformational sampling. FEBS Lett 2014; 588:3123-8. [PMID: 24983495 DOI: 10.1016/j.febslet.2014.06.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 01/11/2023]
Abstract
Conformational sampling of pre- and post-therapy subtype B HIV-1 protease sequences derived from a pediatric subject infected via maternal transmission with HIV-1 were characterized by double electron-electron resonance spectroscopy. The conformational ensemble of the PRE construct resembles native-like inhibitor bound states. In contrast, the POST construct, which contains accumulated drug-pressure selected mutations, has a predominantly semi-open conformational ensemble, with increased populations of open-like states. The single point mutant L63P, which is contained in PRE and POST, has decreased dynamics, particularly in the flap region, and also displays a closed-like conformation of inhibitor-bound states. These findings support our hypothesis that secondary mutations accumulate in HIV-1 protease to shift conformational sampling to stabilize open-like conformations, while maintaining the predominant semi-open conformation for activity.
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Affiliation(s)
- Jeffrey D Carter
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Estrella G Gonzales
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xi Huang
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Adam N Smith
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | | | - Peter W D'Amore
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - James R Rocca
- Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Maureen M Goodenow
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610-3633, USA
| | - Ben M Dunn
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610-0245, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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23
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Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N. Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 2014; 10:3438-3448. [PMID: 25136270 PMCID: PMC4132871 DOI: 10.1021/ct4010454] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Indexed: 12/22/2022]
Abstract
![]()
Under the selective pressure of therapy,
HIV-1 protease mutants
resistant to inhibitors evolve to confer drug resistance. Such mutations
can impact both the dynamics and structures of the bound and unbound
forms of the enzyme. Flap+ is a multidrug-resistant variant of HIV-1
protease with a combination of primary and secondary resistance mutations
(L10I, G48V, I54V, V82A) and a strikingly altered thermodynamic profile
for darunavir (DRV) binding relative to the wild-type protease. We
elucidated the impact of these mutations on protein dynamics in the
DRV-bound state using molecular dynamics simulations and NMR relaxation
experiments. Both methods concur in that the conformational ensemble
and dynamics of protease are impacted by the drug resistance mutations
in Flap+ variant. Surprisingly this change in ensemble dynamics is
different from that observed in the unliganded form of the same variant
(Cai, Y. et al. J. Chem. Theory Comput.2012, 8, 3452–3462). Our comparative
analysis of both inhibitor-free and bound states presents a comprehensive
picture of the altered dynamics in drug-resistant mutant HIV-1 protease
and underlies the importance of incorporating dynamic analysis of
the whole system, including the unliganded state, into revealing drug
resistance mechanisms.
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Affiliation(s)
- Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Wazo Myint
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3 , 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Janet L Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3 , 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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24
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Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B 2013; 117:6625-34. [PMID: 23638941 DOI: 10.1021/jp400797y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple time scales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than 3 orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model-free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions. Using simulations of HIV-1 protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
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25
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de Vera IMS, Smith AN, Dancel MCA, Huang X, Dunn BM, Fanucci GE. Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease. Biochemistry 2013; 52:3278-88. [PMID: 23566104 DOI: 10.1021/bi400109d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enzyme targets in rapidly replicating systems, such as retroviruses, commonly respond to drug-selective pressure with mutations arising in the active site pocket that limit inhibitor effectiveness by introducing steric hindrance or by eliminating essential molecular interactions. However, these primary mutations are disposed to compromising pathogenic fitness. Emerging secondary mutations, which are often found outside of the binding cavity, may or can restore fitness while maintaining drug resistance. The accumulated drug pressure selected mutations could have an indirect effect in the development of resistance, such as altering protein flexibility or the dynamics of protein-ligand interactions. Here, we show that accumulation of mutations in a drug-resistant HIV-1 protease (HIV-1 PR) variant, D30N/M36I/A71V, changes the fractional occupancy of the equilibrium conformational sampling ensemble. Correlations are made among populations of the conformational states, namely, closed-like, semiopen, and open-like, with inhibition constants, as well as kinetic parameters. Mutations that stabilize a closed-like conformation correlate with enzymes of lowered activity and with higher affinity for inhibitors, which is corroborated by a further increase in the fractional occupancy of the closed state upon addition of inhibitor or substrate-mimic. Cross-resistance is found to correlate with combinations of mutations that increase the population of the open-like conformations at the expense of the closed-like state while retaining native-like occupancy of the semiopen population. These correlations suggest that at least three states are required in the conformational sampling model to establish the emergence of drug resistance in HIV-1 PR. More importantly, these results shed light on a possible mechanism whereby mutations combine to impart drug resistance while maintaining catalytic activity.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Chemistry, P.O. Box 117200, University of Florida , Gainesville, Florida 32611-7200, United States
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26
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Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD. Small molecule regulation of protein conformation by binding in the Flap of HIV protease. ACS Chem Biol 2013; 8:1223-31. [PMID: 23540839 DOI: 10.1021/cb300611p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the Tm of apo-PR by 3.5-5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.
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Affiliation(s)
- Theresa Tiefenbrunn
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Stefano Forli
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Michael M. Baksh
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Max W. Chang
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Meaghan Happer
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Ying-Chuan Lin
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Alexander L. Perryman
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Jin-Kyu Rhee
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Bruce E. Torbett
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Arthur J. Olson
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - John H. Elder
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - M. G. Finn
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - C. David Stout
- Deparatment
of Integrative Structural and Computational Biology, ‡Department of Chemistry, §Department of Molecular
and Experimental Medicine, ∥Department of Immunology and Microbial Science, The Scripps Research Institute, 10550
N. Torrey Pines Rd., La Jolla, California 92037, United States
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27
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How conformational changes can affect catalysis, inhibition and drug resistance of enzymes with induced-fit binding mechanism such as the HIV-1 protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:867-73. [PMID: 23376188 DOI: 10.1016/j.bbapap.2013.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 11/21/2022]
Abstract
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor molecules. These conformational changes have been suggested to follow an induced-fit mechanism in which the molecules first bind in the open conformation in those cases where binding in the closed conformation appears to be sterically obstructed such as for the HIV-1 protease. In this article, we present a general model for the catalysis and inhibition of enzymes with induced-fit binding mechanism. We derive general expressions that specify how the overall catalytic rate of the enzymes depends on the rates for binding, for the conformational changes, and for the chemical reaction. Based on these expressions, we analyze the effect of mutations that mainly shift the conformational equilibrium on catalysis and inhibition. If the overall catalytic rate is limited by product unbinding, we find that mutations that destabilize the closed conformation relative to the open conformation increase the catalytic rate in the presence of inhibitors by a factor exp(ΔΔGC/RT) where ΔΔGC is the mutation-induced shift of the free-energy difference between the conformations. This increase in the catalytic rate due to changes in the conformational equilibrium is independent of the inhibitor molecule and, thus, may help to understand how non-active-site mutations can contribute to the multi-drug-resistance that has been observed for the HIV-1 protease. A comparison to experimental data for the non-active-site mutation L90M of the HIV-1 protease indicates that the mutation slightly destabilizes the closed conformation of the enzyme. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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28
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Huang X, de Vera IMS, Veloro AM, Blackburn ME, Kear JL, Carter JD, Rocca JR, Simmerling C, Dunn BM, Fanucci GE. Inhibitor-induced conformational shifts and ligand-exchange dynamics for HIV-1 protease measured by pulsed EPR and NMR spectroscopy. J Phys Chem B 2012; 116:14235-44. [PMID: 23167829 PMCID: PMC3709468 DOI: 10.1021/jp308207h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double electron-electron resonance (DEER) spectroscopy was utilized to investigate shifts in conformational sampling induced by nine FDA-approved protease inhibitors (PIs) and a nonhydrolyzable substrate mimic for human immunodeficiency virus type 1 protease (HIV-1 PR) subtype B, subtype C, and CRF_01 A/E. The ligand-bound subtype C protease has broader DEER distance profiles, but trends for inhibitor-induced conformational shifts are comparable to those previously reported for subtype B. Ritonavir, one of the strong-binding inhibitors for subtypes B and C, induces less of the closed conformation in CRF_01 A/E. (1)H-(15)N heteronuclear single-quantum coherence (HSQC) spectra were acquired for each protease construct titrated with the same set of inhibitors. NMR (1)H-(15)N HSQC titration data show that inhibitor residence time in the protein binding pocket, inferred from resonance exchange broadening, shifting or splitting correlates with the degree of ligand-induced flap closure measured by DEER spectroscopy. These parallel results show that the ligand-induced conformational shifts resulting from protein-ligand interactions characterized by DEER spectroscopy of HIV-1 PR obtained at the cryogenic temperature are consistent with more physiological solution protein-ligand interactions observed by solution NMR spectroscopy.
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Affiliation(s)
- Xi Huang
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | | | - Angelo M. Veloro
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Mandy E. Blackburn
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Jamie L. Kear
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Jeffery D. Carter
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - James R. Rocca
- Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
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29
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Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA. Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput 2012; 8:3452-3462. [PMID: 23144597 PMCID: PMC3491577 DOI: 10.1021/ct300076y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the rapidly evolving disease of HIV drug resistance readily emerges, nullifying the effectiveness of therapy. Drug resistance has been extensively studied in HIV-1 protease where resistance occurs when the balance between enzyme inhibition and substrate recognition and turn-over is perturbed to favor catalytic activity. Mutations which confer drug resistance can impact the dynamics and structure of both the bound and unbound forms of the enzyme. Flap+ is a multi-drug-resistant variant of HIV-1 protease with a combination of mutations at the edge of the active site, within the active site, and in the flaps (L10I, G48V, I54V, V82A). The impact of these mutations on the dynamics in the unliganded form in comparison with the wild-type protease was elucidated with Molecular Dynamic simulations and NMR relaxation experiments. The comparative analyses from both methods concur in showing that the enzyme's dynamics are impacted by the drug resistance mutations in Flap+ protease. These alterations in the enzyme dynamics, particularly within the flaps, likely modulate the balance between substrate turn-over and drug binding, thereby conferring drug resistance.
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Affiliation(s)
- Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Wazo Myint
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
- Co-Corresponding authors: Celia A. Schiffer Phone: (508) 856-8008. Rieko Ishima Phone: (412) 648-9056
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Co-Corresponding authors: Celia A. Schiffer Phone: (508) 856-8008. Rieko Ishima Phone: (412) 648-9056
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30
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Lemmon G, Kaufmann K, Meiler J. Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand. Chem Biol Drug Des 2012; 79:888-96. [PMID: 22321894 DOI: 10.1111/j.1747-0285.2012.01356.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Predicting HIV-1 protease/inhibitor binding affinity as the difference between the free energy of the inhibitor bound and unbound state remains difficult as the unbound state exists as an ensemble of conformations with various degrees of flap opening. We improve computational prediction of protease/inhibitor affinity by invoking the hypothesis that the free energy of the unbound state while difficult to predict is less sensitive to mutation. Thereby the HIV-1 protease/inhibitor binding affinity can be approximated with the free energy of the bound state alone. Bound state free energy can be predicted from comparative models of HIV-1 protease mutant/inhibitor complexes. Absolute binding energies are predicted with R = 0.71 and SE = 5.91 kJ/mol. Changes in binding free energy upon mutation can be predicted with R = 0.85 and SE = 4.49 kJ/mol. Resistance mutations that lower inhibitor binding affinity can thereby be recognized early in HIV-1 protease inhibitor development.
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Affiliation(s)
- Gordon Lemmon
- Department of Chemistry, Center for Structural Biology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
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31
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Mittal S, Cai Y, Nalam MNL, Bolon DNA, Schiffer CA. Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J Am Chem Soc 2012; 134:4163-8. [PMID: 22295904 DOI: 10.1021/ja2095766] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human immunodeficiency virus Type-1 (HIV-1) protease is crucial for viral maturation and infectivity. Studies of protease dynamics suggest that the rearrangement of the hydrophobic core is essential for enzyme activity. Many mutations in the hydrophobic core are also associated with drug resistance and may modulate the core flexibility. To test the role of flexibility in protease activity, pairs of cysteines were introduced at the interfaces of flexible regions remote from the active site. Disulfide bond formation was confirmed by crystal structures and by alkylation of free cysteines and mass spectrometry. Oxidized and reduced crystal structures of these variants show the overall structure of the protease is retained. However, cross-linking the cysteines led to drastic loss in enzyme activity, which was regained upon reducing the disulfide cross-links. Molecular dynamics simulations showed that altered dynamics propagated throughout the enzyme from the engineered disulfide. Thus, altered flexibility within the hydrophobic core can modulate HIV-1 protease activity, supporting the hypothesis that drug resistant mutations distal from the active site can alter the balance between substrate turnover and inhibitor binding by modulating enzyme activity.
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Affiliation(s)
- Seema Mittal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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32
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Limiting assumptions in structure-based design: binding entropy. J Comput Aided Mol Des 2012; 26:3-8. [PMID: 22212342 DOI: 10.1007/s10822-011-9494-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 01/08/2023]
Abstract
In order to deal with the complexity of biological systems at the atomic level, limiting assumptions are often made which do not reflect the reality of the system under study. One example is the assumption that the entropy of binding of the macromolecule is not influenced significantly by the different ligands. Recent experimental data on ligands binding to HIV-1 protease challenge this assumption.
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33
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Batista PR, Pandey G, Pascutti PG, Bisch PM, Perahia D, Robert CH. Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening. J Chem Theory Comput 2011; 7:2348-52. [PMID: 26606609 DOI: 10.1021/ct200237u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Describing biological macromolecular energetics from computer simulations can pose major challenges, and often necessitates enhanced conformational sampling. We describe the calculation of conformational free-energy profiles along carefully chosen collective coordinates: "consensus" normal modes, developed recently as robust alternatives to conventional normal modes. In an application to the HIV-1 protease, we obtain efficient sampling of significant flap opening movements governing inhibitor binding from relatively short simulations, in close correspondence with experimental results.
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Affiliation(s)
- Paulo R Batista
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Gaurav Pandey
- Indian Institute of Technology , Roorkee, 247667, India.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France
| | - Pedro G Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - David Perahia
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Charles H Robert
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico Chimique, Université Paris Diderot, Sorbonne Paris Cité , 75005 Paris, France
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34
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Karthik S, Senapati S. Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle. Proteins 2011; 79:1830-40. [PMID: 21465560 DOI: 10.1002/prot.23008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/13/2011] [Accepted: 01/17/2011] [Indexed: 11/07/2022]
Abstract
The flexibility of HIV-1 protease flaps is known to be essential for the enzymatic activity. Here we attempt to capture a multitude of conformations of the free and substrate-bound HIV-1 protease that differ drastically in their flap arrangements. The substrate binding process suggests the opening of active site gate in conjunction with a reversal of flap tip ordering, from the native semiopen state. The reversed-flap, open-gated enzyme readily transforms to a closed conformation after proper placement of the substrate into the binding cleft. After substrate processing, the closed state protease which possessed opposite flap ordering relative to the semiopen state, encounters another flap reversal via a second open conformation that facilitates the evolution of native semiopen state of correct flap ordering. The complicated transitional pathway, comprising of many high and low energy states, is explored by combining standard and activated molecular dynamics (MD) simulation techniques. The study not only complements the existing findings from X-ray, NMR, EPR, and MD studies but also provides a wealth of detailed information that could help the structure-based drug design process.
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Affiliation(s)
- Suresh Karthik
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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35
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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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36
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Perryman AL, Zhang Q, Soutter HH, Rosenfeld R, McRee DE, Olson AJ, Elder JE, Stout CD. Fragment-based screen against HIV protease. Chem Biol Drug Des 2010; 75:257-68. [PMID: 20659109 DOI: 10.1111/j.1747-0285.2009.00943.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.
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Affiliation(s)
- Alexander L Perryman
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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37
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Kear JL, Blackburn ME, Veloro AM, Dunn BM, Fanucci GE. Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility. J Am Chem Soc 2010; 131:14650-1. [PMID: 19788299 DOI: 10.1021/ja907088a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease plays a fundamental role in the maturation and life cycle of the retrovirus HIV-1, as it functions in regulating post-translational processing of the viral polyproteins gag and gag-pol; thus, it is a key target of AIDS antiviral therapy. Accessibility of substrate to the active site is mediated by two flaps, which must undergo a large conformational change from an open to a closed conformation during substrate binding and catalysis. The electron paramagnetic resonance (EPR) method of site-directed spin labeling (SDSL) with double electron-electron resonance (DEER) spectroscopy was utilized to monitor the conformations of the flaps in apo HIV-1 protease (HIV-1PR), subtypes B, C, and F, CRF01_A/E, and patient isolates V6 and MDR 769. The distance distribution profiles obtained from analysis of the dipolar modulated echo curves were reconstructed to yield a set of Gaussian-shaped populations, which provide an analysis of the flap conformations sampled. The relative percentages of each conformer population described as "tucked/curled", "closed", "semi-open", and "wide-open" were determined and compared for various constructs. The results and analyses show that sequence variations among subtypes, CRFs, and patient isolates of apo HIV-1PR alter the average flap conformation in a way that can be understood as inducing shifts in the relative populations, or conformational sampling, of the previously described four conformations for HIV-1PR.
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Affiliation(s)
- Jamie L Kear
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, Florida 32611-7200, USA
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38
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Qin S, Minh DL, McCammon JA, Zhou HX. Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease. J Phys Chem Lett 2010; 1:107-110. [PMID: 20228897 PMCID: PMC2837415 DOI: 10.1021/jz900023w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 11/03/2009] [Indexed: 05/06/2023]
Abstract
The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida
32306
| | - David
D. L. Minh
- Departments of Chemistry and
Biochemistry and of Pharmacology, Center for Theoretical Biological
Physics, and Howard Hughes Medical Institute, University of California
at San Diego, La Jolla, California 92093-0365
| | - J. Andrew McCammon
- Departments of Chemistry and
Biochemistry and of Pharmacology, Center for Theoretical Biological
Physics, and Howard Hughes Medical Institute, University of California
at San Diego, La Jolla, California 92093-0365
| | - Huan-Xiang Zhou
- Department of Physics and Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida
32306
- To whom correspondence should be
addressed. Phone: (850) 645-1336. Fax: (850) 644-7244. E-mail:
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39
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Blackburn ME, Veloro AM, Fanucci GE. Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy. Biochemistry 2009; 48:8765-7. [PMID: 19691291 DOI: 10.1021/bi901201q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Double electron-electron resonance (DEER), a pulsed electron paramagnetic resonance (EPR) spectroscopy technique, was utilized to characterize conformational population shifts in HIV-1 protease (HIV-1PR) upon interaction with various inhibitors. Distances between spin-labeled sites in the flap region of HIV-1PR were determined, and detailed analyses provide population percentages for the ensemble flap conformations upon interaction with inhibitor or substrate. Comparisons are made between the percentage of the closed conformer seen with DEER and enzymatic inhibition constants, thermodynamic dissociation constants, and the number of hydrogen bonds identified in crystallographic complexes.
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Affiliation(s)
- Mandy E Blackburn
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, Florida 32611-7200, USA
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40
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Galiano L, Blackburn ME, Veloro AM, Bonora M, Fanucci GE. Solute effects on spin labels at an aqueous-exposed site in the flap region of HIV-1 protease. J Phys Chem B 2009; 113:1673-80. [PMID: 19146430 DOI: 10.1021/jp8057788] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of solutes on spin-label mobility and protein conformation have been investigated with X-band continuous-wave and pulsed electron paramagnetic resonance (EPR) spectroscopy for spin labels attached to an aqueous-exposed site in the beta-hairpin flap region of HIV-1 protease. Specifically, we examined the effects of glycerol, sucrose, PEG3000, and Ficoll400 for four commonly used nitroxide spin labels and found that the largest perturbations to the EPR line shapes occur for solutions containing PEG3000 and glycerol. From comparisons of the spectral line shapes and distance distribution profiles of spin-labeled HIV-1 protease with and without inhibitor, it was concluded that solutes such as glycerol and PEG3000 alter the line shapes of the spin label in the beta-hairpin flaps of HIV-1 PR by modulation of spin-label mobility through changes in preferential interactions with the solutes. It is noteworthy that the high osmolality of the 40% glycerol solution did not alter the conformation of the flaps as determined from pulsed EPR distance measurements.
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Affiliation(s)
- Luis Galiano
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, USA
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41
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Galiano L, Ding F, Veloro AM, Blackburn ME, Simmerling C, Fanucci GE. Drug pressure selected mutations in HIV-1 protease alter flap conformations. J Am Chem Soc 2009; 131:430-1. [PMID: 19140783 DOI: 10.1021/ja807531v] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The flap conformations of two drug-resistant HIV-1 protease constructs were characterized by molecular dynamic (MD) simulations and distance measurements with pulsed electron paramagnetic resonance (EPR) spectroscopy. MD simulations accurately regenerate the experimentally determined distance profiles and provide structural interpretations of the EPR data. The combined analyses show that the average conformation of the flaps, the range of flap opening and closing, and the flexibility of the flaps differ markedly in HIV-1PR as multiple mutations arise in response to antiviral therapy, providing structural insights into the mechanism of inhibitor resistance.
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Affiliation(s)
- Luis Galiano
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, USA
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42
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Torbeev VY, Raghuraman H, Mandal K, Senapati S, Perozo E, Kent SBH. Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy. J Am Chem Soc 2009; 131:884-5. [PMID: 19117390 DOI: 10.1021/ja806526z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unliganded form of nitroxide spin-labeled HIV-1 protease and three different complexes with inhibitors were studied by pulse-EPR spectroscopy to determine "interflap" distance distributions in solution. In the unliganded enzyme, we observed a rather broad distribution with three maxima corresponding to three flap conformers; the principal form is a "semiopen/semiopen" conformer. In the complexes with inhibitors, the dominant conformer is an asymmetric "closed/semiopen" form. Moreover, the distance distribution profile is significantly varied among the different inhibitors, which mimic different species on the reaction coordinate for enzyme catalyzed proteolysis.
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Affiliation(s)
- Vladimir Yu Torbeev
- Institute for Biophysical Dynamics, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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43
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Stone K, Townsend J, Sarver J, Sapienza P, Saxena S, Jen-Jacobson L. Electron Spin Resonance Shows Common Structural Features for Different Classes ofEcoRI-DNA Complexes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803588] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Clore GM. Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement. MOLECULAR BIOSYSTEMS 2008; 4:1058-69. [PMID: 18931781 PMCID: PMC2807640 DOI: 10.1039/b810232e] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many biological macromolecular interactions proceed via lowly-populated, highly transient species that arise from rare excursions between the minimum free energy configuration and other local minima of the free energy landscape. Little is known about the structural properties of such lowly-occupied states since they are difficult to trap and hence inaccessible to conventional structural and biophysical techniques. Yet these states play a crucial role in a variety of dynamical processes including molecular recognition and binding, allostery, induced-fit and self-assembly. Here we highlight recent progress in paramagnetic nuclear magnetic resonance to detect, visualize and characterize lowly-populated transient species at equilibrium. The underlying principle involves the application of paramagnetic relaxation enhancement (PRE) in the fast exchange regime. Under these conditions the footprint of the minor species can be observed in the PRE profiles measured for the major species, providing distances between the paramagnetic label and protons of interest are shorter in the minor species than the major one. Ensemble simulated annealing refinement directly against the PRE data permits one to obtain structural data on the minor species. We have used the PRE (a) to detect and characterize the stochastic target search process whereby a sequence-specific transcription factor (the Hox-D9 homeodomain) binds to non-cognate DNA sites as a means of enhancing the rate of specific association via intramolecular sliding and intermolecular translocation; (b) to directly visualize the distribution of non-specific transient encounter complexes involved in the formation of stereospecific protein-protein complexes; (c) to detect and visualize ultra-weak self-association of a protein, a process that is relevant to early nucleation events involved in the formation of higher order structures; and (d) to determine the structure of a minor species for a multidomain protein (maltose binding protein) where large interdomain motions are associated with ligand binding, thereby shedding direct light on the fundamental question of allostery versus induced fit in this system. The PRE offers unique opportunities to directly probe and explore in structural terms lowly-populated regions of the free energy landscape and promises to yield fundamental new insights into biophysical processes.
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Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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Ding F, Layten M, Simmerling C. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments. J Am Chem Soc 2008; 130:7184-5. [PMID: 18479129 PMCID: PMC3390170 DOI: 10.1021/ja800893d] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The introduction of multidrug treatment regimens has dramatically prolonged the progression and survival of AIDS patients. However, the success of the long-term treatment has been hindered by strains of HIV that are increasingly resistant to inhibitors of targets such as HIV protease (HIV PR). Therefore, the need for a thorough understanding of the structure and dynamics of HIV PR and how these are altered in resistant mutants is crucial for the design of more effective treatments. Crystal structures of unbound HIV PR show significant heterogeneity and often have extensive crystal packing interactions. Recent site-directed spin labeling (SDSL) and double electron-electron resonance (DEER) spectroscopy studies characterized flap conformations in HIV-1 protease in an inhibited and uninhibited form and distinguished the extent of flap opening in an unbound form. However, the correlation between EPR-measured interspin distances and structural/dynamic features of the flaps has not been established. In this report, we link EPR-based data and 900 ns of MD simulation in explicit water to gain insight into the ensemble of conformations sampled by HIV PR flaps in solution, both in the presence and in the absence of an FDA-approved HIV PR inhibitor.
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Affiliation(s)
- Fangyu Ding
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Melinda Layten
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794
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Sicoli G, Mathis G, Delalande O, Boulard Y, Gasparutto D, Gambarelli S. Double Electron–Electron Resonance (DEER): A Convenient Method To Probe DNA Conformational Changes. Angew Chem Int Ed Engl 2008; 47:735-7. [DOI: 10.1002/anie.200704133] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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47
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Sicoli G, Mathis G, Delalande O, Boulard Y, Gasparutto D, Gambarelli S. Double Electron–Electron Resonance (DEER): A Convenient Method To Probe DNA Conformational Changes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Stone KM, Townsend JE, Sarver J, Sapienza PJ, Saxena S, Jen-Jacobson L. Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes. Angew Chem Int Ed Engl 2008; 47:10192-4. [PMID: 19021169 PMCID: PMC2792891 DOI: 10.1002/anie.200803588] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katherine M. Stone
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Jacqueline E. Townsend
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
| | - Jessica Sarver
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Paul J. Sapienza
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
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