1
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Ru G, Liu X, Ge Y, Wang L, Jiang L, Pielak G, Liu M, Li C. Trimethylamine N-oxide (TMAO) doubly locks the hydrophobic core and surfaces of protein against desiccation stress. Protein Sci 2024; 33:e5107. [PMID: 38989549 PMCID: PMC11237552 DOI: 10.1002/pro.5107] [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: 04/03/2024] [Revised: 06/14/2024] [Accepted: 06/23/2024] [Indexed: 07/12/2024]
Abstract
Interactions between proteins and osmolytes are ubiquitous within cells, assisting in response to environmental stresses. However, our understanding of protein-osmolyte interactions underlying desiccation tolerance is limited. Here, we employ solid-state NMR (ssNMR) to derive information about protein conformation and site-specific interactions between the model protein, SH3, and the osmolyte trimethylamine N-oxide (TMAO). The data show that SH3-TMAO interactions maintain key structured regions during desiccation and facilitate reversion to the protein's native state once desiccation stress is even slightly relieved. We identify 10 types of residues at 28 sites involved in the SH3-TMAO interactions. These sites comprise hydrophobic, positively charged, and aromatic amino acids located in SH3's hydrophobic core and surface clusters. TMAO locks both the hydrophobic core and surface clusters through its zwitterionic and trimethyl ends. This double locking is responsible for desiccation tolerance and differs from ideas based on exclusion, vitrification, and water replacement. ssNMR is a powerful tool for deepening our understanding of extremely weak protein-osmolyte interactions and providing insight into the evolutionary mechanism of environmental tolerance.
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Affiliation(s)
- Geying Ru
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Yuwei Ge
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Liying Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Gary Pielak
- Department of Chemistry, Department of Biochemistry & Biophysics, Lineberger Cancer Center, Integrative Program for Biological and Genome Sciences of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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2
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Sayeesh PM, Iguchi M, Inomata K, Ikeya T, Ito Y. Structure and Dynamics of Drk-SH2 Domain and Its Site-Specific Interaction with Sev Receptor Tyrosine Kinase. Int J Mol Sci 2024; 25:6386. [PMID: 38928093 PMCID: PMC11203457 DOI: 10.3390/ijms25126386] [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: 04/30/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the receptor tyrosine kinases (RTKs). Here, we present the solution NMR structure of the SH2 domain of Drk (Drk-SH2), which was determined in the presence of a phosphotyrosine (pY)-containing peptide derived from a receptor tyrosine kinase, Sevenless (Sev). The solution structure of Drk-SH2 possess a common SH2 domain architecture, consisting of three β strands imposed between two α helices. Additionally, we interpret the site-specific interactions of the Drk-SH2 domain with the pY-containing peptide through NMR titration experiments. The dynamics of Drk-SH2 were also analysed through NMR-relaxation experiments as well as the molecular dynamic simulation. The docking simulations of the pY-containing peptide onto the protein surface of Drk-SH2 provided the orientation of the peptide, which showed a good agreement with the analysis of the SH2 domain of GRB2.
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Affiliation(s)
| | | | | | - Teppei Ikeya
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; (P.M.S.); (M.I.); (K.I.)
| | - Yutaka Ito
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; (P.M.S.); (M.I.); (K.I.)
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3
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Sayeesh PM, Iguchi M, Suemoto Y, Inoue J, Inomata K, Ikeya T, Ito Y. Interactions of the N- and C-Terminal SH3 Domains of Drosophila Drk with the Proline-Rich Peptides from Sos and Dos. Int J Mol Sci 2023; 24:14135. [PMID: 37762438 PMCID: PMC10532153 DOI: 10.3390/ijms241814135] [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: 08/22/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Drk, a homologue of human GRB2 in Drosophila, receives signals from outside the cells through the interaction of its SH2 domain with the phospho-tyrosine residues in the intracellular regions of receptor tyrosine kinases (RTKs) such as Sevenless, and transduces the signals downstream through the association of its N- and C-terminal SH3 domains (Drk-NSH3 and Drk-CSH3, respectively) with proline-rich motifs (PRMs) in Son of Sevenless (Sos) or Daughter of Sevenless (Dos). Isolated Drk-NSH3 exhibits a conformational equilibrium between the folded and unfolded states, while Drk-CSH3 adopts only a folded confirmation. Drk interacts with PRMs of the PxxPxR motif in Sos and the PxxxRxxKP motif in Dos. Our previous study has shown that Drk-CSH3 can bind to Sos, but the interaction between Drk-NSH3 and Dos has not been investigated. To assess the affinities of both SH3 domains towards Sos and Dos, we conducted NMR titration experiments using peptides derived from Sos and Dos. Sos-S1 binds to Drk-NSH3 with the highest affinity, strongly suggesting that the Drk-Sos multivalent interaction is initiated by the binding of Sos-S1 and NSH3. Our results also revealed that the two Sos-derived PRMs clearly favour NSH3 for binding, whereas the two Dos-derived PRMs show almost similar affinity for NSH3 and CSH3. We have also performed docking simulations based on the chemical shift perturbations caused by the addition of Sos- and Dos-derived peptides. Finally, we discussed the various modes in the interactions of Drk with Sos/Dos.
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Grants
- JPMJCR13M3, JPMJCR21E5 Japan Science and Technology Agency
- JP15K06979, JP19H05645, JP15H01645, JP16H00847, JP17H05887, JP19H05773, JP26102538, JP25120003, JP16H00779, JP21K06114 Japan Society for the Promotion of Science
- Shimadzu foundation Shimadzu foundation
- the Precise Measurement Technology Promotion Foundation the Precise Measurement Technology Promotion Foundation
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Affiliation(s)
| | | | | | | | | | - Teppei Ikeya
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0373, Japan; (P.M.S.); (M.I.); (J.I.); (K.I.)
| | - Yutaka Ito
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0373, Japan; (P.M.S.); (M.I.); (J.I.); (K.I.)
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4
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. J Phys Chem B 2023; 127:4746-4760. [PMID: 37200094 PMCID: PMC10875986 DOI: 10.1021/acs.jpcb.3c01619] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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5
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.531990. [PMID: 36993592 PMCID: PMC10054940 DOI: 10.1101/2023.03.12.531990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory Random Coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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6
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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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7
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Okuno Y, Schwieters CD, Yang Z, Clore GM. Theory and Applications of Nitroxide-based Paramagnetic Cosolutes for Probing Intermolecular and Electrostatic Interactions on Protein Surfaces. J Am Chem Soc 2022; 144:21371-21388. [DOI: 10.1021/jacs.2c10035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Charles D. Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Zhilin Yang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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8
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Sayeesh PM, Ikeya T, Sugasawa H, Watanabe R, Mishima M, Inomata K, Ito Y. Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos. Biochem Biophys Res Commun 2022; 625:87-93. [DOI: 10.1016/j.bbrc.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
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9
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Jain S, Sekhar A. Elucidating the mechanisms underlying protein conformational switching using NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100034. [PMID: 35586549 PMCID: PMC7612731 DOI: 10.1016/j.jmro.2022.100034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
How proteins switch between various ligand-free and ligand-bound structures has been a key biophysical question ever since the postulation of the Monod-Wyman-Changeux and Koshland-Nemethy-Filmer models over six decades ago. The ability of NMR spectroscopy to provide structural and kinetic information on biomolecular conformational exchange places it in a unique position as an analytical tool to interrogate the mechanisms of biological processes such as protein folding and biomolecular complex formation. In addition, recent methodological developments in the areas of saturation transfer and relaxation dispersion have expanded the scope of NMR for probing the mechanics of transitions in systems where one or more states constituting the exchange process are sparsely populated and 'invisible' in NMR spectra. In this review, we highlight some of the strategies available from NMR spectroscopy for examining the nature of multi-site conformational exchange, using five case studies that have employed NMR, either in isolation, or in conjunction with other biophysical tools.
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10
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Structural basis of protein substrate processing by human mitochondrial high-temperature requirement A2 protease. Proc Natl Acad Sci U S A 2022; 119:e2203172119. [PMID: 35452308 PMCID: PMC9170070 DOI: 10.1073/pnas.2203172119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein aggregates are often toxic, leading to impaired cellular activities and disease. The human HtrA2 trimeric enzyme cleaves such aggregates, and mutations in HtrA2 are causative for various neurodegenerative disorders, such as Parkinson’s disease and essential tremor. The mechanism by which cleavage occurs has been studied using small peptides, but little information is available as to how HtrA2 protects cells from the pathologic effects of aggregation involving protein molecules that can form well-folded structures. Using solution NMR spectroscopy, we investigated the structural dynamics of the interaction between HtrA2 and a model protein substrate, demonstrating that HtrA2 preferentially binds to an unfolded substrate ensemble and providing insights into how HtrA2 function is regulated. The human high-temperature requirement A2 (HtrA2) protein is a trimeric protease that cleaves misfolded proteins to protect cells from stresses caused by toxic, proteinaceous aggregates, and the aberrant function of HtrA2 is closely related to the onset of neurodegenerative disorders. Our methyl-transverse relaxation optimized spectroscopy (TROSY)–based NMR studies using small-peptide ligands have previously revealed a stepwise activation mechanism involving multiple distinct conformational states. However, very little is known about how HtrA2 binds to protein substrates and if the distinct conformational states observed in previous peptide studies might be involved in the processing of protein clients. Herein, we use solution-based NMR spectroscopy to investigate the interaction between the N-terminal Src homology 3 domain from downstream of receptor kinase (drk) with an added C-terminal HtrA2-binding motif (drkN SH3-PDZbm) that exhibits marginal folding stability and serves as a mimic of a physiological protein substrate. We show that drkN SH3-PDZbm binds to HtrA2 via a two-pronged interaction, involving both its C-terminal PDZ-domain binding motif and a central hydrophobic region, with binding occurring preferentially via an unfolded ensemble of substrate molecules. Multivalent interactions between several clients and a single HtrA2 trimer significantly stimulate the catalytic activity of HtrA2, suggesting that binding avidity plays an important role in regulating substrate processing. Our results provide a thermodynamic, kinetic, and structural description of the interaction of HtrA2 with protein substrates and highlight the importance of a trimeric architecture for function as a stress-protective protease that mitigates aggregation.
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11
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Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement. Proc Natl Acad Sci U S A 2021; 118:2112021118. [PMID: 34404723 DOI: 10.1073/pnas.2112021118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cosolvent effect arises from the interaction of cosolute molecules with a protein and alters the equilibrium between native and unfolded states. Denaturants shift the equilibrium toward the latter, while osmolytes stabilize the former. The molecular mechanism whereby cosolutes perturb protein stability is still the subject of considerable debate. Probing the molecular details of the cosolvent effect is experimentally challenging as the interactions are very weak and transient, rendering them invisible to most conventional biophysical techniques. Here, we probe cosolute-protein interactions by means of NMR solvent paramagnetic relaxation enhancement together with a formalism we recently developed to quantitatively describe, at atomic resolution, the energetics and dynamics of cosolute-protein interactions in terms of a concentration normalized equilibrium average of the interspin distance, [Formula: see text], and an effective correlation time, τc The system studied is the metastable drkN SH3 domain, which exists in dynamic equilibrium between native and unfolded states, thereby permitting us to probe the interactions of cosolutes with both states simultaneously under the same conditions. Two paramagnetic cosolute denaturants were investigated, one neutral and the other negatively charged, differing in the presence of a carboxyamide group versus a carboxylate. Our results demonstrate that attractive cosolute-protein backbone interactions occur largely in the unfolded state and some loop regions in the native state, electrostatic interactions reduce the [Formula: see text] values, and temperature predominantly impacts interactions with the unfolded state. Thus, destabilization of the native state in this instance arises predominantly as a consequence of interactions of the cosolutes with the unfolded state.
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12
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Thole JF, Fadero TC, Bonin JP, Stadmiller SS, Giudice JA, Pielak GJ. Danio rerio Oocytes for Eukaryotic In-Cell NMR. Biochemistry 2021; 60:451-459. [PMID: 33534998 DOI: 10.1021/acs.biochem.0c00922] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Understanding how the crowded and complex cellular milieu affects protein stability and dynamics has only recently become possible by using techniques such as in-cell nuclear magnetic resonance. However, the combination of stabilizing and destabilizing interactions makes simple predictions difficult. Here we show the potential of Danio rerio oocytes as an in-cell nuclear magnetic resonance model that can be widely used to measure protein stability and dynamics. We demonstrate that in eukaryotic oocytes, which are 3-6-fold less crowded than other cell types, attractive chemical interactions still dominate effects on protein stability and slow tumbling times, compared to the effects of dilute buffer.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tanner C Fadero
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey P Bonin
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha S Stadmiller
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan A Giudice
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gary J Pielak
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Stadmiller SS, Aguilar JS, Parnham S, Pielak GJ. Protein–Peptide Binding Energetics under Crowded Conditions. J Phys Chem B 2020; 124:9297-9309. [DOI: 10.1021/acs.jpcb.0c05578] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jhoan S. Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stuart Parnham
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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14
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Ferrie JJ, Petersson EJ. A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins. J Phys Chem B 2020; 124:5538-5548. [PMID: 32525675 DOI: 10.1021/acs.jpcb.0c02924] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As recognition of the abundance and relevance of intrinsically disordered proteins (IDPs) continues to grow, demand increases for methods that can rapidly predict the conformational ensembles populated by these proteins. To date, IDP simulations have largely been dominated by molecular dynamics (MD) simulations, which require significant compute times and/or complex hardware. Recent developments in MD have afforded methods capable of simulating both ordered and disordered proteins, yet to date, accurate fold prediction from a sequence has been dominated by Monte Carlo (MC)-based methods such as Rosetta. To overcome the limitations of current approaches in IDP simulation using Rosetta while maintaining its utility for modeling folded domains, we developed PyRosetta-based algorithms that allow for the accurate de novo prediction of proteins across all degrees of foldedness along with structural ensembles of disordered proteins. Our simulations have accuracy comparable to state-of-the-art MD with vastly reduced computational demands.
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Affiliation(s)
- John J Ferrie
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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15
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Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States. Commun Chem 2020; 3:74. [PMID: 32775701 PMCID: PMC7409953 DOI: 10.1038/s42004-020-0323-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, that calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.
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16
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 PMCID: PMC7231920 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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17
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Szekely O, Olsen GL, Novakovic M, Rosenzweig R, Frydman L. Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR. J Am Chem Soc 2020; 142:9267-9284. [PMID: 32338002 PMCID: PMC7304870 DOI: 10.1021/jacs.0c00807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Hyperpolarized water
can be a valuable aid in protein NMR, leading
to amide group 1H polarizations that are orders of magnitude
larger than their thermal counterparts. Suitable procedures can exploit
this to deliver 2D 1H–15N correlations
with good resolution and enhanced sensitivity. These enhancements
depend on the exchange rates between the amides and the water, thereby
yielding diagnostic information about solvent accessibility. This
study applied this “HyperW” method to four proteins
exhibiting a gamut of exchange behaviors: PhoA(350–471), an unfolded 122-residue fragment; barstar, a fully folded ribonuclease
inhibitor; R17, a 13.3 kDa system possessing folded and unfolded forms
under slow interconversion; and drkN SH3, a protein domain whose folded
and unfolded forms interchange rapidly and with temperature-dependent
population ratios. For PhoA4(350–471) HyperW sensitivity
enhancements were ≥300×, as expected for an unfolded protein
sequence. Though fully folded, barstar also exhibited substantial
enhancements; these, however, were not uniform and, according to CLEANEX
experiments, reflected the solvent-exposed residues. R17 showed the
expected superposition of ≥100-fold enhancements for its unfolded
form, coexisting with more modest enhancements for their folded counterparts.
Unexpected, however, was the behavior of drkN SH3, for which HyperW
enhanced the unfolded but, surprisingly, enhanced even more certain folded protein sites. These preferential enhancements were
repeatedly and reproducibly observed. A number of explanations—including
three-site exchange magnetization transfers between water and the
unfolded and folded states; cross-correlated relaxation processes
from hyperpolarized “structural” waters and labile side-chain
protons; and the possibility that faster solvent exchange rates characterize
certain folded sites over their unfolded counterparts—are considered
to account for them.
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18
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Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder. Biophys J 2019; 115:328-340. [PMID: 30021108 DOI: 10.1016/j.bpj.2018.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/15/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sequence patterns of charge, hydrophobicity, hydrogen bonding, and other amino acid physicochemical properties contribute to mechanisms of protein folding, but how sequence composition and patterns influence the conformational dynamics of the denatured state ensemble is not fully understood. To investigate structure-sequence relationships in the denatured state, we reversed the sequence of staphylococcal nuclease and characterized its structure, thermodynamic character, and hydrodynamic radius using circular dichroism spectroscopy, dynamic light scattering, analytical ultracentrifugation, and size-exclusion chromatography as a function of temperature. The macromolecular size of "Retro-nuclease" is highly expanded in solution with characteristics similar to biological intrinsically disordered proteins. In contradistinction to a disordered state, Retro-nuclease exhibits a broad sigmoid transition of its hydrodynamic dimensions as temperature is increased, indicating a thermodynamically controlled compaction. Counterintuitively, the magnitude of these temperature-induced hydrodynamic changes exceed that observed from thermal denaturation of folded unaltered staphylococcal nuclease. Undetectable by calorimetry and intrinsic tryptophan fluorescence, the lack of heat capacity or fluorescence changes throughout the thermal transition indicate canonical hydrophobic collapse did not drive the Retro-nuclease structural transitions. Temperature-dependent circular dichroism spectroscopy performed on Retro-nuclease and computer simulations correlate to temperature sensitivity in the intrinsic sampling of backbone conformations for polyproline II and α-helix. The experimental results indicate a role for sequence direction in mediating the collapse of the polypeptide chain, whereas the simulation trends illustrate the generality of the observed heat effects on disordered protein structure.
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19
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Sekhar A, Velyvis A, Zoltsman G, Rosenzweig R, Bouvignies G, Kay LE. Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions. eLife 2018; 7:32764. [PMID: 29460778 PMCID: PMC5819949 DOI: 10.7554/elife.32764] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/27/2017] [Indexed: 12/17/2022] Open
Abstract
Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. Proteins are the workhorses of a cell and are involved in almost all biological processes. Newly made proteins need to ‘fold’ into precise three-dimensional shapes in order to carry out their roles. However, proteins sometimes fold incorrectly or unfold. These protein forms are not able to work effectively and in some cases may even cause diseases. Chaperone proteins help other proteins to fold correctly and are found in living organisms ranging in complexity from bacteria to humans. There are many different types of chaperones that play different roles inside cells. One, called Hsp70, binds to proteins that are incorrectly folded to help them to mature into their correct structures. However, it was not clear whether Hsp70 can also associate with the mature, correctly folded form of the proteins. A technique called Nuclear Magnetic Resonance (NMR) spectroscopy can distinguish between mature, unfolded and chaperone-bound forms of the same protein. Sekhar et al. therefore used NMR to investigate which forms of a protein Hsp70 binds to. This revealed that both the bacterial and human versions of the Hsp70 chaperone interact only with unfolded proteins. The results presented by Sekhar et al. also explain why Hsp70 does not disrupt the routine workings of the cell: because it does not bind to mature forms of proteins. These observations extend our understanding of how chaperones assist in folding proteins, and fit into a broader research theme exploring how proteins recognize one another. It will now be interesting to see whether the same mechanism holds for more complex forms of proteins, such as aggregates, or larger protein structures with regions of both folded and unfolded elements.
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Affiliation(s)
- Ashok Sekhar
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Algirdas Velyvis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Guy Zoltsman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rina Rosenzweig
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, Paris, France.,Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Hospital for Sick Children, Program in Molecular Medicine, University Avenue, Toronto, Canada
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20
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Dudola D, Kovács B, Gáspári Z. CoNSEnsX+ Webserver for the Analysis of Protein Structural Ensembles Reflecting Experimentally Determined Internal Dynamics. J Chem Inf Model 2017; 57:1728-1734. [DOI: 10.1021/acs.jcim.7b00066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Dániel Dudola
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1083 Budapest, Práter u. 50/A, Hungary
| | - Bertalan Kovács
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1083 Budapest, Práter u. 50/A, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1083 Budapest, Práter u. 50/A, Hungary
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21
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Gorensek-Benitez AH, Smith AE, Stadmiller SS, Perez Goncalves GM, Pielak GJ. Cosolutes, Crowding, and Protein Folding Kinetics. J Phys Chem B 2017; 121:6527-6537. [PMID: 28605189 PMCID: PMC5982521 DOI: 10.1021/acs.jpcb.7b03786] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long accepted as the most important interaction, recent work shows that steric repulsions alone cannot explain the effects of macromolecular cosolutes on the equilibrium thermodynamics of protein stability. Instead, chemical interactions have been shown to modulate, and even dominate, crowding-induced steric repulsions. Here, we use 19F NMR to examine the effects of small and large cosolutes on the kinetics of protein folding and unfolding using the metastable 7 kDa N-terminal SH3 domain of the Drosophila signaling protein drk (SH3), which folds by a two-state mechanism. The small cosolutes consist of trimethylamine N-oxide and sucrose, which increase equilibrium protein stability, and urea, which destabilizes proteins. The macromolecules comprise the stabilizing sucrose polymer, Ficoll, and the destabilizing globular protein, lysozyme. We assessed the effects of these cosolutes on the differences in free energy between the folded state and the transition state and between the unfolded ensemble and the transition state. We then examined the temperature dependence to assess changes in activation enthalpy and entropy. The enthalpically mediated effects are more complicated than suggested by equilibrium measurements. We also observed enthalpic effects with the supposedly inert sucrose polymer, Ficoll, that arise from its macromolecular nature. Assessment of activation entropies shows important contributions from solvent and cosolute, in addition to the configurational entropy of the protein that, again, cannot be gleaned from equilibrium data. Comparing the effects of Ficoll to those of the more physiologically relevant cosolute lysozyme reveals that synthetic polymers are not appropriate models for understanding the kinetics of protein folding in cells.
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Affiliation(s)
| | - Austin E. Smith
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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22
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Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model. Biophys J 2016; 110:1510-1522. [PMID: 27074677 DOI: 10.1016/j.bpj.2016.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
Conformational states of the metastable drkN SH3 domain were characterized using single-molecule fluorescence techniques. Under nondenaturing conditions, two Förster resonance energy transfer (FRET) populations were observed that corresponded to a folded and an unfolded state. FRET-estimated radii of gyration and hydrodynamic radii estimated by fluorescence correlation spectroscopy of the two coexisting conformations are in agreement with previous ensemble x-ray scattering and NMR measurements. Surprisingly, when exposed to high concentrations of urea and GdmCl denaturants, the protein still exhibits two distinct FRET populations. The dominant conformation is expanded, showing a low FRET efficiency, consistent with the expected behavior of a random chain with excluded volume. However, approximately one-third of the drkN SH3 conformations showed high, nearly 100%, FRET efficiency, which is shown to correspond to denaturation-induced looped conformations that remain stable on a timescale of at least 100 μs. These loops may contain interconverting conformations that are more globally collapsed, hairpin-like, or circular, giving rise to the observed heterogeneous broadening of this population. Although the underlying mechanism of chain looping remains elusive, FRET experiments in formamide and dimethyl sulfoxide suggest that interactions between hydrophobic groups in the distal regions may play a significant role in the formation of the looped state.
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23
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Woods KE, Perera YR, Davidson MB, Wilks CA, Yadav DK, Fitzkee NC. Understanding Protein Structure Deformation on the Surface of Gold Nanoparticles of Varying Size. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:27944-27953. [PMID: 28348716 PMCID: PMC5365237 DOI: 10.1021/acs.jpcc.6b08089] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Gold nanoparticles (AuNPs) have been of recent interest due to their unique optical properties and their biocompatibility. Biomolecules spontaneously adsorb to their surface, a trait that could potentially be exploited for drug targeting. Currently, it is unclear whether protein-AuNP interactions at the nanoparticle surface are dependent on nanoparticle size. In this work, we investigate whether varying surface curvature can induce protein unfolding and multilayer binding in citrate-coated AuNPs of various sizes. A recently developed NMR-based approach was utilized to determine the adsorption capacity, and protein NMR spectra were compared to determine whether nanoparticle size influences protein interactions at the surface. In addition, transmission electron microscopy (TEM) and dynamic light scattering (DLS) were employed to corroborate the NMR studies. Over a broad range of AuNP sizes (14-86 nm), we show that adsorption capacity can be predicted by assuming that proteins are compact and globular on the nanoparticle surface. Additionally, roughly one layer of proteins is adsorbed regardless of AuNP size. Our results hold for two proteins of significantly different sizes, GB3 (6 kDa) and bovine carbonic anhydrase (BCA, 29 kDa). However, the unstable drkN SH3 domain (ΔḠ0 ≈ 0, 7 kDa) does not appear to follow the same trend seen for stable, globular proteins. This observation suggests that unstable proteins can deform significantly when bound to AuNP surfaces. Taken together, the results of this work can be used to improve our knowledge of the mechanism of protein-AuNP interactions to optimize their use in the biomedical field.
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Affiliation(s)
- Karen E. Woods
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Y. Randika Perera
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Mackenzie B. Davidson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Chloe A. Wilks
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Dinesh K. Yadav
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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24
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Senske M, Smith AE, Pielak GJ. Protein Stability in Reverse Micelles. Angew Chem Int Ed Engl 2016; 55:3586-9. [DOI: 10.1002/anie.201508981] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/14/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Austin E. Smith
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill NC 27599-3290 USA
| | - Gary J. Pielak
- Department of Chemistry; University of North Carolina at Chapel Hill; Chapel Hill NC 27599-3290 USA
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25
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Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II Ruhr-Universität Bochum 44780 Bochum Germany
| | - Austin E. Smith
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599-3290 USA
| | - Gary J. Pielak
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599-3290 USA
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26
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Panigrahi P, Sule M, Ghanate A, Ramasamy S, Suresh CG. Engineering Proteins for Thermostability with iRDP Web Server. PLoS One 2015; 10:e0139486. [PMID: 26436543 PMCID: PMC4593602 DOI: 10.1371/journal.pone.0139486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 09/13/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.
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Affiliation(s)
- Priyabrata Panigrahi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Manas Sule
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Avinash Ghanate
- Division of Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - C. G. Suresh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
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27
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Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone. Proc Natl Acad Sci U S A 2015. [PMID: 26195753 DOI: 10.1073/pnas.1505173112] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The molecular chaperone heat shock protein 70 (Hsp70) plays a vital role in cellular processes, including protein folding and assembly, and helps prevent aggregation under physiological and stress-related conditions. Although the structural changes undergone by full-length client proteins upon interaction with DnaK (i.e., Escherichia coli Hsp70) are fundamental to understand chaperone-mediated protein folding, these changes are still largely unexplored. Here, we show that multiple conformations of the SRC homology 3 domain (SH3) client protein interact with the ADP-bound form of the DnaK chaperone. Chaperone-bound SH3 is largely unstructured yet distinct from the unfolded state in the absence of DnaK. The bound client protein shares a highly flexible N terminus and multiple slowly interconverting conformations in different parts of the sequence. In all, there is significant structural and dynamical heterogeneity in the DnaK-bound client protein, revealing that proteins may undergo some conformational sampling while chaperone-bound. This result is important because it shows that the surface of the Hsp70 chaperone provides an aggregation-free environment able to support part of the search for the native state.
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28
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Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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29
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Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R. Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:53-59. [PMID: 24656080 DOI: 10.1016/j.jmr.2013.11.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Celestine Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Martina Minges
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Hachioji, 192-0397 Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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Mazouchi A, Bahram A, Gradinaru CC. Sub-diffusion decays in fluorescence correlation spectroscopy: dye photophysics or protein dynamics? J Phys Chem B 2013; 117:11100-11. [PMID: 23675915 DOI: 10.1021/jp4010746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transitions between bright and dark fluorescent states of several rhodamine dyes were investigated by fluorescence correlation spectroscopy. We resolved two sub-diffusion exponential decays for free rhodamines in aqueous solutions, of which the slower component scales linearly with the viscosity of the solution. Correlation data for proteins and DNA labeled with tetramethylrhodamine were fitted with three to four exponential decays describing flickering dynamics on a time scale between 0.5 and 100 μs. We investigated the nature of these processes by performing experiments under different experimental conditions and for different samples. On the basis of how their population and lifetime change with viscosity, the oxygen content of the solution, the laser irradiance, and the detection geometry, we assigned these states, in the order of increasing lifetimes, to a triplet state, a hybrid between twisted-intramolecular-charge-transfer state and a ground state lactonic state, a lactonic state, and a photoionized state, respectively. Our data suggests that none of the observed sub-diffusion correlation decays can be directly assigned to the intramolecular dynamics of the labeled biomolecules. However, we found evidence that the intrinsic conformational dynamics of the biomolecule appears in the correlation curves as a modulation of the photophysics of the dye label. This shows the importance of accurate control measurements and appropriate modeling of the dye photophysics in fluorescence correlation studies, and it cautions against direct assignments of dark-state relaxation times to folding kinetics in proteins and nucleic acids.
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Affiliation(s)
- Amir Mazouchi
- Department of Physics, University of Toronto , and Department of Chemical and Physical Sciences, University of Toronto Mississauga , Mississauga, Ontario L5L 1C6, Canada
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Marsh JA, Forman-Kay JD. Ensemble modeling of protein disordered states: experimental restraint contributions and validation. Proteins 2011; 80:556-72. [PMID: 22095648 DOI: 10.1002/prot.23220] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/11/2011] [Indexed: 12/13/2022]
Abstract
Disordered states of proteins include the biologically functional intrinsically disordered proteins and the unfolded states of normally folded proteins. In recent years, ensemble-modeling strategies using various experimental measurements as restraints have emerged as powerful means for structurally characterizing disordered states. However, these methods are still in their infancy compared with the structural determination of folded proteins. Here, we have addressed several issues important to ensemble modeling using our ENSEMBLE methodology. First, we assessed how calculating ensembles containing different numbers of conformers affects their structural properties. We find that larger ensembles have very similar properties to smaller ensembles fit to the same experimental restraints, thus allowing a considerable speed improvement in our calculations. In addition, we analyzed the contributions of different experimental restraints to the structural properties of calculated ensembles, enabling us to make recommendations about the experimental measurements that should be made for optimal ensemble modeling. The effects of different restraints, most significantly from chemical shifts, paramagnetic relaxation enhancements and small-angle X-ray scattering, but also from other data, underscore the importance of utilizing multiple sources of experimental data. Finally, we validate our ENSEMBLE methodology using both cross-validation and synthetic experimental restraints calculated from simulated ensembles. Our results suggest that secondary structure and molecular size distribution can generally be modeled very accurately, whereas the accuracy of calculated tertiary structure is dependent on the number of distance restraints used.
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Affiliation(s)
- Joseph A Marsh
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; MRC Laboratory of Molecular Biology, Cambridge CB2 02H, United Kingdom
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Chevelkov V, Xue Y, Rao DK, Forman-Kay JD, Skrynnikov NR. 15N H/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: application to denatured drkN SH3. JOURNAL OF BIOMOLECULAR NMR 2010; 46:227-244. [PMID: 20195703 DOI: 10.1007/s10858-010-9398-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 02/03/2010] [Indexed: 05/28/2023]
Abstract
Amide solvent exchange rates are regarded as a valuable source of information on structure/dynamics of unfolded (disordered) proteins. Proton-based saturation transfer experiments, normally used to measure solvent exchange, are known to meet some serious difficulties. The problems mainly arise from the need to (1) manipulate water magnetization and (2) discriminate between multiple magnetization transfer pathways that occur within the proton pool. Some of these issues are specific to unfolded proteins. For example, the compensation scheme used to cancel the Overhauser effect in the popular CLEANEX experiment is not designed for use with unfolded proteins. In this report we describe an alternative experimental strategy, where amide (15)N is used as a probe of solvent exchange. The experiment is performed in 50% H(2)O-50% D(2)O solvent and is based on the (HACACO)NH pulse sequence. The resulting spectral map is fully equivalent to the conventional HSQC. To fulfill its purpose, the experiment monitors the conversion of deuterated species, (15)N(D), into protonated species, (15)N(H), as effected by the solvent exchange. Conceptually, this experiment is similar to EXSY which prompted the name of (15)N(H/D)-SOLEXSY (SOLvent EXchange SpectroscopY). Of note, our experimental scheme, which relies on nitrogen rather than proton to monitor solvent exchange, is free of the complications described above. The developed pulse sequence was used to measure solvent exchange rates in the chemically denatured state of the drkN SH3 domain. The results were found to correlate well with the CLEANEX-PM data, r = 0.97, thus providing a measure of validation for both techniques. When the experimentally measured exchange rates are converted into protection factors, most of the values fall in the range 0.5-2, consistent with random-coil behavior. However, elevated values, ca. 5, are obtained for residues R38 and A39, as well as the side-chain indole of W36. This is surprising, given that high protection factors imply hydrogen bonding or hydrophobic burial not expected to occur in a chemically denatured state of a protein. We, therefore, hypothesized that elevated protection factors are an artefact arising from the calculation of the reference (random-coil) exchange rates. To confirm this hypothesis, we prepared samples of several short peptides derived from the sequence of the drkN SH3 domain; these samples were used to directly measure the reference exchange rates. The revised protection factors obtained in this manner proved to be close to 1.0. These results also have implications for the more compact unfolded state of drkN SH3, which appears to be fully permeable to water as well, with no manifestations of hydrophobic burial.
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Affiliation(s)
- Veniamin Chevelkov
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
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Marsh JA, Forman-Kay JD. Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints. J Mol Biol 2009; 391:359-74. [PMID: 19501099 DOI: 10.1016/j.jmb.2009.06.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/27/2009] [Accepted: 06/01/2009] [Indexed: 12/01/2022]
Abstract
Obtaining detailed structural models of disordered states of proteins under nondenaturing conditions is important for a better understanding of both functional intrinsically disordered proteins and unfolded states of folded proteins. Extensive experimental characterization of the drk N-terminal SH3 domain unfolded state has shown that, although it appears to be highly disordered, it possesses significant nonrandom secondary and tertiary structure. In our previous attempts to generate structural models of the unfolded state using the program ENSEMBLE, we were limited by insufficient experimental restraints and conformational sampling. In this study, we have vastly expanded our experimental restraint set to include (1)H-(15)N residual dipolar couplings, small-angle X-ray scattering measurements, nitroxide paramagnetic relaxation enhancements, O(2)-induced (13)C paramagnetic shifts, hydrogen-exchange protection factors, and (15)N R(2) data, in addition to the previously used nuclear Overhauser effects, amino terminal Cu(2+)-Ni(2+) binding paramagnetic relaxation enhancements, J-couplings, chemical shifts, hydrodynamic radius, and solvent accessibility restraints. We have also implemented a new ensemble calculation methodology that uses iterative conformational sampling and seeks to calculate the simplest possible ensemble models. As a result, we can now generate ensembles that are consistent with much larger experimental data sets than was previously possible. Although highly heterogeneous and having broad molecular size distributions, the calculated drk N-terminal SH3 domain unfolded-state ensembles have very different properties than expected for random or statistical coils and possess significant nonnative alpha-helical structure and both native-like and nonnative tertiary structure.
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Affiliation(s)
- Joseph A Marsh
- Molecular Structure and Function, Hospital for Sick Children, Ontario, Canada
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Marsh JA, Neale C, Jack FE, Choy WY, Lee AY, Crowhurst KA, Forman-Kay JD. Improved Structural Characterizations of the drkN SH3 Domain Unfolded State Suggest a Compact Ensemble with Native-like and Non-native Structure. J Mol Biol 2007; 367:1494-510. [PMID: 17320108 DOI: 10.1016/j.jmb.2007.01.038] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 01/15/2007] [Accepted: 01/16/2007] [Indexed: 11/24/2022]
Abstract
Due to their dynamic ensemble nature and a deficiency of experimental restraints, disordered states of proteins are difficult to characterize structurally. Here, we have expanded upon our previous work on the unfolded state of the Drosophila drk N-terminal (drkN) SH3 domain with our program ENSEMBLE, which assigns population weights to pregenerated conformers in order to calculate ensembles of structures whose properties are collectively consistent with experimental measurements. The experimental restraint set has been enlarged with newly measured paramagnetic relaxation enhancements from Cu(2+) bound to an amino terminal Cu(2+)-Ni(2+) binding (ATCUN) motif as well as nuclear Overhauser effect (NOE) and hydrogen exchange data from recent studies. In addition, two new pseudo-energy minimization algorithms have been implemented that have dramatically improved the speed of ENSEMBLE population weight assignment. Finally, we have greatly improved our conformational sampling by utilizing a variety of techniques to generate both random structures and structures that are biased to contain elements of native-like or non-native structure. Although it is not possible to uniquely define a representative structural ensemble, we have been able to assess various properties of the drkN SH3 domain unfolded state by performing ENSEMBLE minimizations of different conformer pools. Specifically, we have found that the experimental restraint set enforces a compact structural distribution that is not consistent with an overall native-like topology but shows preference for local non-native structure in the regions corresponding to the diverging turn and the beta5 strand of the folded state and for local native-like structure in the region corresponding to the beta6 and beta7 strands. We suggest that this approach could be generally useful for the structural characterization of disordered states.
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Affiliation(s)
- Joseph A Marsh
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
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Bezsonova I, Evanics F, Marsh JA, Forman-Kay JD, Prosser RS. Oxygen as a Paramagnetic Probe of Clustering and Solvent Exposure in Folded and Unfolded States of an SH3 Domain. J Am Chem Soc 2007; 129:1826-35. [PMID: 17253684 DOI: 10.1021/ja065173o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (Fexch) and highly populated unfolded (Uexch) state under nondenaturing buffer conditions, enabling both Fexch and Uexch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via 13C NMR paramagnetic shifts in 1H,13C HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the Fexch and Uexch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the Fexch and Uexch states could also be assessed through 13C paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the Fexch state, the 13C nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The Uexch state displayed less varied 13C paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.
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Affiliation(s)
- Irina Bezsonova
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 1A8
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Wales TE, Engen JR. Partial unfolding of diverse SH3 domains on a wide timescale. J Mol Biol 2006; 357:1592-604. [PMID: 16487539 DOI: 10.1016/j.jmb.2006.01.075] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 01/13/2006] [Accepted: 01/19/2006] [Indexed: 11/28/2022]
Abstract
SH3 domains are small, modular domains that are found in many proteins, especially signal transduction proteins such as tyrosine kinases. While much is known about the sequences and tertiary structures of SH3 domains, far less is known about their solution dynamics. A slow, partial unfolding event that occurs under physiological conditions was previously identified in the Hck SH3 domain using hydrogen exchange (HX) mass spectrometry (MS). To determine if this unfolding was unique to Hck SH3, HX MS was used to analyze 11 other SH3 domains: seven SH3 domains from Src-family kinases and five SH3 domains from various proteins. A wide variety of unfolding rates were found, with unfolding half-lives ranging from 1s to 1h. The Lyn and alpha-spectrin SH3 domains exhibited slow, partial unfolding in beta strands D and E and part of the RT-loop. Hck SH3 also underwent partial unfolding in the same region, implying that a unique feature in this area of the domains is responsible for the partial unfolding. Partial unfolding was, however, not a function of sequence conservation. Although the Fyn and Yes SH3 domains are very similar to Hck SH3 in sequence, they exhibited no evidence of partial unfolding. Overall, the results suggest that while the tertiary structure of SH3 domains is highly conserved, the dynamics of SH3 domains are variable.
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Affiliation(s)
- Thomas E Wales
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131, USA
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