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Voigt B, Bhatia T, Hesselbarth J, Baumann M, Schmidt C, Ott M, Balbach J. The Prenucleation Equilibrium of the Parathyroid Hormone Determines the Critical Aggregation Concentration and Amyloid Fibril Nucleation. Chemphyschem 2023; 24:e202300439. [PMID: 37477386 DOI: 10.1002/cphc.202300439] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Nucleation and growth of amyloid fibrils were found to only occur in supersaturated solutions above a critical concentration (ccrit ). The biophysical meaning of ccrit remained mostly obscure, since typical low values of ccrit in the sub-μM range hamper investigations of potential oligomeric states and their structure. Here, we investigate the parathyroid hormone PTH84 as an example of a functional amyloid fibril forming peptide with a comparably high ccrit of 67±21 μM. We describe a complex concentration dependent prenucleation ensemble of oligomers of different sizes and secondary structure compositions and highlight the occurrence of a trimer and tetramer at ccrit as possible precursors for primary fibril nucleation. Furthermore, the soluble state found in equilibrium with fibrils adopts to the prenucleation state present at ccrit . Our study sheds light onto early events of amyloid formation directly related to the critical concentration and underlines oligomer formation as a key feature of fibril nucleation. Our results contribute to a deeper understanding of the determinants of supersaturated peptide solutions. In the current study we present a biophysical approach to investigate ccrit of amyloid fibril formation of PTH84 in terms of secondary structure, cluster size and residue resolved intermolecular interactions during oligomer formation. Throughout the investigated range of concentrations (1 μM to 500 μM) we found different states of oligomerization with varying ability to contribute to primary fibril nucleation and with a concentration dependent equilibrium. In this context, we identified the previously described ccrit of PTH84 to mark a minimum concentration for the formation of homo-trimers/tetramers. These investigations allowed us to characterize molecular interactions of various oligomeric states that are further converted into elongation competent fibril nuclei during the lag phase of a functional amyloid forming peptide.
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Affiliation(s)
- Bruno Voigt
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
| | - Twinkle Bhatia
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Julia Hesselbarth
- present address: Johannes Gutenberg University Mainz, Institute of Chemistry - Biochemistry, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Martin Luther University Halle-Wittenberg, Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3a, 06120, Halle, Germany
| | - Monika Baumann
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
| | - Carla Schmidt
- present address: Johannes Gutenberg University Mainz, Institute of Chemistry - Biochemistry, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Martin Luther University Halle-Wittenberg, Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3a, 06120, Halle, Germany
| | - Maria Ott
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Jochen Balbach
- Martin Luther University Halle-Wittenberg, Institute of Physics, Betty-Heimann-Straße 7, 06120, Halle, Germany
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2
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Ceccon A, Kubatova N, Louis JM, Clore GM, Tugarinov V. Global Dynamics of a Protein on the Surface of Anisotropic Lipid Nanoparticles Derived from Relaxation-Based NMR Spectroscopy. J Phys Chem B 2022; 126:5646-5654. [PMID: 35877206 DOI: 10.1021/acs.jpcb.2c03519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG):1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles are described. The shapes of POPG:DHPC bicelles prepared with high molar ratios q of POPG to DHPC can be approximated by prolate ellipsoids, with the ratio of ellipsoid dimensions and dimensions themselves increasing with higher values of q. Adaptation of the nuclear magnetic resonance (NMR) relaxation-based approach that we previously developed for interactions of ubiquitin with spherical POPG liposomes (Ceccon, A. J. Am. Chem. Soc. 2016, 138, 5789-5792) allowed us to quantitatively analyze the variation in lifetime line broadening of NMR signals (ΔR2) measured for ubiquitin in the presence of q = 2 POPG:DHPC bicelles and the associated transverse spin relaxation rates (R2,B) of bicelle-bound ubiquitin. Ubiquitin, transiently bound to POPG:DHPC bicelles, undergoes internal rotation about an axis orthogonal to the surface of the bicelle and perpendicular to the principal axis of its rotational diffusion tensor on the low microsecond time scale (∼3 μs), while the rotation axis itself wobbles in a cone on a submicrosecond time scale (≤ 500 ns).
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Nina Kubatova
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, 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
| | - Vitali Tugarinov
- 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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3
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An Y, Sedinkin SL, Venditti V. Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria. NANOSCALE ADVANCES 2022; 4:2583-2607. [PMID: 35769933 PMCID: PMC9195484 DOI: 10.1039/d2na00099g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/07/2022] [Indexed: 05/09/2023]
Abstract
Characterization of dynamic processes occurring at the nanoparticle (NP) surface is crucial for developing new and more efficient NP catalysts and materials. Thus, a vast amount of research has been dedicated to developing techniques to characterize sorption equilibria. Over recent years, solution NMR spectroscopy has emerged as a preferred tool for investigating ligand-NP interactions. Indeed, due to its ability to probe exchange dynamics over a wide range of timescales with atomic resolution, solution NMR can provide structural, kinetic, and thermodynamic information on sorption equilibria involving multiple adsorbed species and intermediate states. In this contribution, we review solution NMR methods for characterizing ligand-NP interactions, and provide examples of practical applications using these methods as standalone techniques. In addition, we illustrate how the integrated analysis of several NMR datasets was employed to elucidate the role played by support-substrate interactions in mediating the phenol hydrogenation reaction catalyzed by ceria-supported Pd nanoparticles.
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Affiliation(s)
- Yeongseo An
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Sergey L Sedinkin
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University Ames Iowa 50011 USA
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4
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Tugarinov V, Ceccon A, Clore GM. NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:1-24. [PMID: 35282867 PMCID: PMC8921508 DOI: 10.1016/j.pnmrs.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR2) NMR methodology. Some limitations of the DEST/ΔR2 methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR2 methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | - Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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5
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Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon 2021; 201:127-140. [PMID: 34454969 DOI: 10.1016/j.toxicon.2021.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
Peptide toxins are potent and often exquisitely selective probes of the structure and function of ion channels and receptors, and are therefore of significant interest to the pharmaceutical and biotech industries as both pharmacological tools and therapeutic leads. The three-dimensional structures of peptide toxins are essential as a basis for understanding their structure-activity relationships and their binding to target receptors, as well as in guiding the design of analogues with modified potency and/or selectivity for key targets. NMR spectroscopy has played a key role in elucidating the structures of peptide toxins and probing their structure-function relationships. In this article, we highlight the additional important contribution of NMR to characterising the dynamics of peptide toxins. We also compare the information available from NMR measurements with that afforded by molecular dynamics simulations. We describe several examples of the importance of dynamics measurements over a range of timescales for understanding the structure-function relationships of peptide toxins and their receptor engagement. Peptide toxins that inhibit the voltage-gated potassium channel KV1.3 with pM affinities display different degrees of conformational flexibility, even though they contain multiple disulfide bonds, and this flexibility can affect the relative orientation of residues that have been shown to be critical for channel binding. Information on the dynamic properties of peptide toxins is important in the design of analogues or mimetics where receptor-bound structures are not available.
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Affiliation(s)
- Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia.
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6
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Leite JP, Gimeno A, Taboada P, Jiménez-Barbero JJ, Gales L. Dissection of the key steps of amyloid-β peptide 1-40 fibrillogenesis. Int J Biol Macromol 2020; 164:2240-2246. [PMID: 32771514 DOI: 10.1016/j.ijbiomac.2020.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 11/27/2022]
Abstract
The aggregation kinetics of Aβ1-40 peptide was characterized using a synergistic approach by a combination of nuclear magnetic resonance, thioflavin-T fluorescence, transmission electron microscopy and dynamic light scattering. A major finding is the experimental detection of high molecular weight oligomers (HMWO) that converts into fibrils nuclei. Our observations are consistent with a mechanism of Aβ1-40 fibrillogenesis that includes the following key steps: i) slow formation of HMWO (Rh ~ 20 nm); ii) conversion of the HMWO into more compact Rh ~ 10 nm fibrils nuclei; iii) fast formation of additional fibrils nuclei through fibril surface catalysed processes; and iv) growth of fibrils by addition of soluble Aβ species. Moreover, NMR diffusion experiments show that at 37 °C soluble Aβ1-40 remains intrinsically disordered and mostly in monomeric form despite evidences of the presence of dimers and/or other small oligomers. A mathematical model is proposed to simulate the aggregation kinetics of Aβ1-40.
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Affiliation(s)
- José P Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Rua Alfredo Allen, 208, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Pablo Taboada
- Colloids and Polymers Physics Group, Particle Physics Department, 15782 Campus Vida, Universidade de Santiago de Compostela, Spain
| | - Jesús J Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain; Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain; Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Luís Gales
- i3S - Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Rua Alfredo Allen, 208, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira 228, Porto, Portugal.
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7
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Xue M, Sampath J, Gebhart RN, Haugen HJ, Lyngstadaas SP, Pfaendtner J, Drobny G. Studies of Dynamic Binding of Amino Acids to TiO 2 Nanoparticle Surfaces by Solution NMR and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10341-10350. [PMID: 32693593 PMCID: PMC8098425 DOI: 10.1021/acs.langmuir.0c01256] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Adsorption of biomolecules onto material surfaces involves a potentially complex mechanism where molecular species interact to varying degrees with a heterogeneous material surface. Surface adsorption studies by atomic force microscopy, sum frequency generation spectroscopy, and solid-state NMR detect the structures and interactions of biomolecular species that are bound to material surfaces, which, in the absence of a solid-liquid interface, do not exchange rapidly between surface-bound forms and free molecular species in bulk solution. Solution NMR has the potential to complement these techniques by detecting and studying transiently bound biomolecules at the liquid-solid interface. Herein, we show that dark-state exchange saturation transfer (DEST) NMR experiments on gel-stabilized TiO2 nanoparticle (NP) samples detect several forms of biomolecular adsorption onto titanium(IV) oxide surfaces. Specifically, we use the DEST approach to study the interaction of amino acids arginine (Arg), lysine (Lys), leucine (Leu), alanine (Ala), and aspartic acid (Asp) with TiO2 rutile NP surfaces. Whereas Leu, Ala, and Asp display only a single weakly interacting form in the presence of TiO2 NPs, Arg and Lys displayed at least two distinct bound forms: a species that is surface bound and retains a degree of reorientational motion and a second more tightly bound form characterized by broadened DEST profiles upon the addition of TiO2 NPs. Molecular dynamics simulations indicate different surface bound states for both Lys and Arg depending on the degree of TiO2 surface hydroxylation but only a single bound state for Asp regardless of the degree of surface hydroxylation, in agreement with results obtained from the analysis of DEST profiles.
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Affiliation(s)
- Mengjun Xue
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Janani Sampath
- Department of Chemical Engineering, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Rachel N Gebhart
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Havard J Haugen
- Department for Biomaterials, Faculty for Odontology, University of Oslo, P.O. Box 1109, Blindern, Oslo NO-0317, Norway
| | - S Petter Lyngstadaas
- Department for Biomaterials, Faculty for Odontology, University of Oslo, P.O. Box 1109, Blindern, Oslo NO-0317, Norway
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
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8
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Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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9
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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10
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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11
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Sarkar D, Chakraborty I, Condorelli M, Ghosh B, Mass T, Weingarth M, Mandal AK, La Rosa C, Subramanian V, Bhunia A. Self‐Assembly and Neurotoxicity of β‐Amyloid (21–40) Peptide Fragment: The Regulatory Role of GxxxG Motifs. ChemMedChem 2019; 15:293-301. [DOI: 10.1002/cmdc.201900620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Ipsita Chakraborty
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | | | - Baijayanti Ghosh
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Thorben Mass
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Markus Weingarth
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Atin K Mandal
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Carmelo La Rosa
- Department of Chemical Sciences University of Catania 95125 Catania Italy
| | | | - Anirban Bhunia
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
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12
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Vugmeyster L, Au DF, Ostrovsky D, Kierl B, Fu R, Hu ZW, Qiang W. Effect of Post-Translational Modifications and Mutations on Amyloid-β Fibrils Dynamics at N Terminus. Biophys J 2019; 117:1524-1535. [PMID: 31570231 PMCID: PMC6817547 DOI: 10.1016/j.bpj.2019.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 02/04/2023] Open
Abstract
We investigate the variability in the dynamics of the disordered N-terminal domain of amyloid-β fibrils (Aβ), comprising residues 1-16 of Aβ1-40, due to post-translational modifications and mutations in the β-bend regions known to modulate aggregation properties. Using 2H static solid-state NMR approaches, we compare the dynamics in the wild-type Aβ fibrils in the threefold symmetric polymorph with the fibrils from three post-translational modification sequences: isoaspartate-D7, the phosphorylation of S8, and an N-terminal truncation ΔE3. Additional comparisons are made with the mutants in the β-bend region (residues 21-23) corresponding to the familial Osaka E22Δ deletion and D23N Iowa mutation. We also include the aggregates induced by Zn2+ ions. The dynamics are probed at the F4 and G9 positions. The main motional model involves two free states undergoing diffusion and conformational exchanges with the bound state in which the diffusion is quenched because of transient interactions involving fibril core and other intrastrand contacts. The fraction of the bound state increases in a sigmoidal fashion with a decrease in temperature. There is clear variability in the dynamics: the phosphorylation of S8 variant is the most rigid at the G9 site in line with structural studies, the ΔE3 fibrils are more flexible at the G9 site in line with the morphological fragmentation pattern, the Zn-induced aggregates are the most mobile, and the two β-bend mutants have the strongest changes at the F4 site toward higher rigidity. Overall, the changes underlie the potential role of conformational ensembles in setting the stage for aggregation-prone states.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, Colorado.
| | - Dan F Au
- Department of Chemistry, University of Colorado Denver, Denver, Colorado
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, Colorado
| | - Brian Kierl
- Department of Chemistry, University of Colorado Denver, Denver, Colorado
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, Florida
| | - Zhi-Wen Hu
- Department of Chemistry, Binghamton University, Binghamton, New York
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York
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13
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Tugarinov V, Clore GM. Exchange saturation transfer and associated NMR techniques for studies of protein interactions involving high-molecular-weight systems. JOURNAL OF BIOMOLECULAR NMR 2019; 73:461-469. [PMID: 31407202 PMCID: PMC6819251 DOI: 10.1007/s10858-019-00244-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/27/2019] [Indexed: 05/15/2023]
Abstract
A brief overview of theoretical and experimental aspects of the Dark state Exchange Saturation Transfer (DEST) and lifetime line broadening ([Formula: see text]) NMR methodologies is presented from a physico-chemical perspective. We describe how the field-dependence of [Formula: see text] can be used for determining the exchange regime on the transverse spin relaxation time-scale. Some limitations of DEST/[Formula: see text] methodology in applications to molecular systems with intermediate molecular weights are discussed, and the means of overcoming these limitations via the use of closely related exchange NMR techniques is presented. Finally, several applications of DEST/[Formula: see text] methodology are described from a methodological viewpoint, with an emphasis on providing examples of how kinetic and relaxation parameters of exchange can be reliably extracted from the experimental data in each particular case.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - 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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14
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Vugmeyster L, Au DF, Ostrovsky D, Fu R. Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils. Chemphyschem 2019; 20:1680-1689. [PMID: 31087613 PMCID: PMC6663588 DOI: 10.1002/cphc.201900363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/12/2019] [Indexed: 12/26/2022]
Abstract
We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs-ms timescale motions in the flexible N-terminal subdomain of Aβ1-40 amyloid fibrils, which spans residues 1-16. In particular, we utilized a rotating frame (R1ρ ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile "free" states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7-1 ⋅ 108 and 0.3-3 ⋅ 106 ad2 s-1 . The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2-3 ⋅ 105 s-1 and 2-3 ⋅ 104 s-1 for the fast and slow diffusion free states, respectively.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO, USA, 80204
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, 32310
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15
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Bhattacharyya D, Mohite GM, Krishnamoorthy J, Gayen N, Mehra S, Navalkar A, Kotler SA, Ratha BN, Ghosh A, Kumar R, Garai K, Mandal AK, Maji SK, Bhunia A. Lipopolysaccharide from Gut Microbiota Modulates α-Synuclein Aggregation and Alters Its Biological Function. ACS Chem Neurosci 2019; 10:2229-2236. [PMID: 30855940 DOI: 10.1021/acschemneuro.8b00733] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Altered intestinal permeability has been correlated with Parkinson's pathophysiology in the enteric nervous system, before manifestations in the central nervous system (CNS). The inflammatory endotoxin or lipopolysaccharide (LPS) released by gut bacteria is known to modulate α-synuclein amyloidogenesis through the formation of intermediate nucleating species. Here, biophysical techniques in conjunction with microscopic images revealed the molecular interaction between lipopolysaccharide and α-synuclein that induce rapid nucleation events. This heteromolecular interaction stabilizes the α-helical intermediates in the α-synuclein aggregation pathway. Multitude NMR studies probed the residues involved in the LPS-binding structural motif that modulates the nucleating forms, affecting the cellular internalization and associated cytotoxicity. Collectively, our data characterizes this heteromolecular interaction associated with an alternative pathway in Parkinson's disease progression.
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Affiliation(s)
| | - Ganesh M. Mohite
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | | | - Nilanjan Gayen
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Samuel A. Kotler
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bhisma N. Ratha
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Anirban Ghosh
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Kanchan Garai
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Hyderabad 500075, India
| | - Atin K. Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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16
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Brender JR, Ghosh A, Kotler SA, Krishnamoorthy J, Bera S, Morris V, Sil TB, Garai K, Reif B, Bhunia A, Ramamoorthy A. Probing transient non-native states in amyloid beta fiber elongation by NMR. Chem Commun (Camb) 2019; 55:4483-4486. [PMID: 30917192 DOI: 10.1039/c9cc01067j] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using NMR to probe transient binding of Aβ1-40 monomers to fibers, we find partially bound conformations with the highest degree of interaction near F19-K28 and a lesser degree of interaction near the C-terminus (L34-G37). This represents a shift away from the KLVFFA recognition sequence (residues 16-21) currently used for inhibitor design.
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17
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Edwards JM, Bramham JE, Podmore A, Bishop SM, van der Walle CF, Golovanov AP. 19F Dark-State Exchange Saturation Transfer NMR Reveals Reversible Formation of Protein-Specific Large Clusters in High-Concentration Protein Mixtures. Anal Chem 2019; 91:4702-4708. [PMID: 30801173 PMCID: PMC6492951 DOI: 10.1021/acs.analchem.9b00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/25/2019] [Indexed: 11/28/2022]
Abstract
Proteins frequently exist as high-concentration mixtures, both in biological environments and increasingly in biopharmaceutical co-formulations. Such crowded conditions promote protein-protein interactions, potentially leading to formation of protein clusters, aggregation, and phase separation. Characterizing these interactions and processes in situ in high-concentration mixtures is challenging due to the complexity and heterogeneity of such systems. Here we demonstrate the application of the dark-state exchange saturation transfer (DEST) NMR technique to a mixture of two differentially 19F-labeled 145 kDa monoclonal antibodies (mAbs) to assess reversible temperature-dependent formation of small and large protein-specific clusters at concentrations up to 400 mg/mL. 19F DEST allowed quantitative protein-specific characterization of the cluster populations and sizes for both mAbs in the mixture under a range of conditions. Additives such as arginine glutamate and NaCl also had protein-specific effects on the dark-state populations and cluster characteristics. Notably, both mAbs appear to largely exist as separate self-associated clusters, which mechanistically respond differently to changes in solution conditions. We show that for mixtures of differentially 19F-labeled proteins DEST NMR can characterize clustering in a protein-specific manner, offering unique tracking of clustering pathways and a means to understand and control them.
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Affiliation(s)
- John M. Edwards
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jack E. Bramham
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Adrian Podmore
- Dosage
Form Design & Development, AstraZeneca
plc, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Steven M. Bishop
- Biopharmaceutical
Development, AstraZeneca plc, Gaithersburg, Maryland 20878, United States
| | | | - Alexander P. Golovanov
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, Manchester M1 7DN, United Kingdom
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18
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Au DF, Ostrovsky D, Fu R, Vugmeyster L. Solid-state NMR reveals a comprehensive view of the dynamics of the flexible, disordered N-terminal domain of amyloid-β fibrils. J Biol Chem 2019; 294:5840-5853. [PMID: 30737281 DOI: 10.1074/jbc.ra118.006559] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/08/2019] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits observed in Alzheimer's disease comprise amyloid-β (Aβ) protein possessing a structured hydrophobic core and a disordered N-terminal domain (residues 1-16). The internal flexibility of the disordered domain is likely essential for Aβ aggregation. Here, we used 2H static solid-state NMR methods to probe the dynamics of selected side chains of the N-terminal domain of Aβ1-40 fibrils. Line shape and relaxation data suggested a two-state model in which the domain's free state undergoes a diffusive motion that is quenched in the bound state, likely because of transient interactions with the structured C-terminal domain. At 37 °C, we observed freezing of the dynamics progressively along the Aβ sequence, with the fraction of the bound state increasing and the rate of diffusion decreasing. We also found that without solvation, the diffusive motion is quenched. The solvent acted as a plasticizer reminiscent of its role in the onset of global dynamics in globular proteins. As the temperature was lowered, the fraction of the bound state exhibited sigmoidal behavior. The midpoint of the freezing curve coincided with the bulk solvent freezing for the N-terminal residues and increased further along the sequence. Using 2H R 1ρ measurements, we determined the conformational exchange rate constant between the free and bound states under physiological conditions. Zinc-induced aggregation leads to the enhancement of the dynamics, manifested by the faster conformational exchange, faster diffusion, and lower freezing-curve midpoints.
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Affiliation(s)
- Dan Fai Au
- From the Department of Chemistry, University of Colorado, Denver, Colorado 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado, Denver, Colorado 80204
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, Florida 32310
| | - Liliya Vugmeyster
- From the Department of Chemistry, University of Colorado, Denver, Colorado 80204.
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19
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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20
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Milles S, Salvi N, Blackledge M, Jensen MR. Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:79-100. [PMID: 30527137 DOI: 10.1016/j.pnmrs.2018.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 05/08/2023]
Abstract
Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments. We describe the complementarity of different NMR parameters for quantifying the conformational propensities of IDPs in their isolated and phosphorylated states, and we discuss the challenges associated with obtaining structural models of dynamic protein-protein complexes involving IDPs. In addition, we review recent progress in understanding the conformational behavior of IDPs in cell-like environments such as in the presence of crowding agents, in membrane-less organelles and in the complex environment of the human cell.
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Affiliation(s)
- Sigrid Milles
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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21
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Boswell ZK, Latham MP. Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes. Biochemistry 2018; 58:144-155. [PMID: 30336000 DOI: 10.1021/acs.biochem.8b00953] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
NMR spectroscopy is particularly adept at site-specifically monitoring dynamic processes in proteins, such as protein folding, domain movements, ligand binding, and side-chain rotations. By coupling the favorable spectroscopic properties of highly dynamic side-chain methyl groups with transverse-relaxation-optimized spectroscopy (TROSY), it is now possible to routinely study such dynamic processes in high-molecular-weight proteins and complexes approaching 1 MDa. In this Perspective, we describe many elegant methyl-based NMR experiments that probe slow (second) to fast (picosecond) dynamics in large systems. To demonstrate the power of these methods, we also provide interesting examples of studies that utilized each methyl-based NMR technique to uncover functionally important dynamics. In many cases, the NMR experiments are paired with site-directed mutagenesis and/or other biochemical assays to put the dynamics and function into context. Our vision of the future of structural biology involves pairing methyl-based NMR spectroscopy with biochemical studies to advance our knowledge of the motions large proteins and macromolecular complexes use to choreograph complex functions. Such studies will be essential in elucidating the critical structural dynamics that underlie function and characterizing alterations in these processes that can lead to human disease.
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Affiliation(s)
- Zachary K Boswell
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79423 , United States
| | - Michael P Latham
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79423 , United States
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22
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Ceccon A, Clore GM, Tugarinov V. Decorrelating Kinetic and Relaxation Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal Huntingtin Peptides Binding to Unilamellar Lipid Vesicles. J Phys Chem B 2018; 122:11271-11278. [PMID: 30156416 DOI: 10.1021/acs.jpcb.8b07112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dark state exchange saturation transfer (DEST) and lifetime line-broadening (Δ R2, the difference in the measured transverse relaxation rates for the observable species in the presence and absence of exchange with a species characterized by very large intrinsic transverse relaxation rates) have proven to be powerful NMR tools for studying exchange phenomena between a NMR visible species and a high-molecular weight, "dark", NMR invisible state. However, in the exchange regime, where the transverse spin relaxation rates in the bound state ( R2bound) are smaller than the strength of the DEST saturation radio frequency field, typically corresponding to systems below ∼6 MDa, the combination of DEST and Δ R2 data, while sufficient to define the apparent association rate constant, cannot unambiguously determine the population of the bound state pB and R2bound values independently. We show that the latter exchange and relaxation parameters can be decorrelated by the measurement of the maximal value of the contribution of the fast-relaxing magnetization component to the total NMR signal, Cfastmax, an observable that is directly proportional to pB. When integrated into the analysis of DEST/Δ R2 data, Cfastmax provides an indispensable source of information for quantitative studies of exchange involving high-molecular-weight dark states. We demonstrate the utility of this approach by investigating the binding kinetics of two huntingtin exon-1-derived peptides to small unilamellar lipid vesicles (SUV), ∼ 31 nm in diameter and 4.3 MDa in molecular weight. The interaction of the N-terminal amphiphilic domain of huntingtin exon-1 with membrane surfaces promotes polyglutamine-mediated aggregation and, as such, is thought to play a role in the etiology of Huntington's disease, an autosomal dominant fatal neurodegenerative condition. The first peptide comprises the 16-residue N-terminal amphiphilic domain (httNT) alone, while the second contains an additional seven residue polyglutamine tract at the C-terminus (httNTQ7). At a peptide-to-lipid molar ratio of 1:4, the population of peptide bound to the SUV surface is substantial, ∼ 7-8%, while exchange between the free and SUV-bound peptide is slow on the relaxation time-scale ( kex ∼ 200 s-1). The last two C-terminal residues of httNT and the last 9 of httNTQ7 remain flexible in the SUV-bound form due to transient detachment from the lipid surface that occurs on a time-scale several-fold faster than binding.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , 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
| | - Vitali Tugarinov
- 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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23
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Gorman SD, Sahu D, O'Rourke KF, Boehr DD. Assigning methyl resonances for protein solution-state NMR studies. Methods 2018; 148:88-99. [PMID: 29958930 DOI: 10.1016/j.ymeth.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022] Open
Abstract
Solution-state NMR is an important tool for studying protein structure and function. The ability to probe methyl groups has substantially expanded the scope of proteins accessible by NMR spectroscopy, including facilitating study of proteins and complexes greater than 100 kDa in size. While the toolset for studying protein structure and dynamics by NMR continues to grow, a major rate-limiting step in these studies is the initial resonance assignments, especially for larger (>50 kDa) proteins. In this practical review, we present strategies to efficiently isotopically label proteins, delineate NMR pulse sequences that can be used to determine methyl resonance assignments in the presence and absence of backbone assignments, and outline computational methods for NMR data analysis. We use our experiences from assigning methyl resonances for the aromatic biosynthetic enzymes tryptophan synthase and chorismate mutase to provide advice for all stages of experimental set-up and data analysis.
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Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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24
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Yuwen T, Brady JP, Kay LE. Probing Conformational Exchange in Weakly Interacting, Slowly Exchanging Protein Systems via Off-Resonance R1ρ Experiments: Application to Studies of Protein Phase Separation. J Am Chem Soc 2018; 140:2115-2126. [DOI: 10.1021/jacs.7b09576] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tairan Yuwen
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Jacob P. Brady
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Lewis E. Kay
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Hospital for Sick Children, Program in Molecular Medicine, Toronto, Ontario, Canada M5G 1X8
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25
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Abstract
The GroEL/ES chaperonin is known to prevent protein aggregation during folding by passive containment within the central cavity. The possible role of more active intervention is controversial. The HX MS method documents an organized hydrophobically stabilized folding preintermediate in the collapsed ensemble of maltose binding protein. A mutational defect destabilizes the preintermediate and greatly slows folding of the subsequent on-pathway H-bonded intermediate. GroEL encapsulation alone, without ATP and substrate protein cycling, restabilizes the preintermediate and restores fast folding. The mechanism appears to depend on forceful compression during confinement. More generally, these results suggest that GroEL can repair different folding defects in different ways. We used hydrogen exchange–mass spectrometry (HX MS) and fluorescence to compare the folding of maltose binding protein (MBP) in free solution and in the GroEL/ES cavity. Upon refolding, MBP initially collapses into a dynamic molten globule-like ensemble, then forms an obligatory on-pathway native-like folding intermediate (1.2 seconds) that brings together sequentially remote segments and then folds globally after a long delay (30 seconds). A single valine to glycine mutation imposes a definable folding defect, slows early intermediate formation by 20-fold, and therefore subsequent global folding by approximately twofold. Simple encapsulation within GroEL repairs the folding defect and reestablishes fast folding, with or without ATP-driven cycling. Further examination exposes the structural mechanism. The early folding intermediate is stabilized by an organized cluster of 24 hydrophobic side chains. The cluster preexists in the collapsed ensemble before the H-bond formation seen by HX MS. The V9G mutation slows folding by disrupting the preintermediate cluster. GroEL restores wild-type folding rates by restabilizing the preintermediate, perhaps by a nonspecific equilibrium compression effect within its tightly confining central cavity. These results reveal an active GroEL function other than previously proposed mechanisms, suggesting that GroEL possesses different functionalities that are able to relieve different folding problems. The discovery of the preintermediate, its mutational destabilization, and its restoration by GroEL encapsulation was made possible by the measurement of a previously unexpected type of low-level HX protection, apparently not dependent on H-bonding, that may be characteristic of proteins in confined spaces.
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26
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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27
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Ban D, Smith CA, de Groot BL, Griesinger C, Lee D. Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Arch Biochem Biophys 2017; 628:81-91. [PMID: 28576576 DOI: 10.1016/j.abb.2017.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 12/25/2022]
Abstract
Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this "hidden-time" window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions.
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Affiliation(s)
- David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Colin A Smith
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany; Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Bert L de Groot
- Department for Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077 Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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28
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Vallurupalli P, Sekhar A, Yuwen T, Kay LE. Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer. JOURNAL OF BIOMOLECULAR NMR 2017; 67:243-271. [PMID: 28317074 DOI: 10.1007/s10858-017-0099-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/20/2017] [Indexed: 05/25/2023]
Abstract
Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.
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Affiliation(s)
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada.
- Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, ON, Canada.
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29
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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30
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Chakrabarti KS, Ban D, Pratihar S, Reddy JG, Becker S, Griesinger C, Lee D. High-power (1)H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:65-69. [PMID: 27240144 DOI: 10.1016/j.jmr.2016.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/16/2016] [Accepted: 05/20/2016] [Indexed: 05/25/2023]
Abstract
Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of (15)N chemical shift offsets where the applied (15)N irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of (15)N chemical shift offsets where the applied (15)N irradiation field-strength is on the order of tens of Hertz during the EST period. The (1)H decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates. Currently two different (1)H decoupling schemes have been employed, intermittently applied 180° pulses and composite-pulse-decoupling (CPD), for situations where a wide range, or narrow range of (15)N chemical shift offsets are scanned, respectively. We show that high-power CPD provides artifact free EST experiments, which can be universally implemented regardless of the offset range or irradiation field-strengths.
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Affiliation(s)
- Kalyan S Chakrabarti
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Ban
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Supriya Pratihar
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jithender G Reddy
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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31
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Vugmeyster L, Clark MA, Falconer IB, Ostrovsky D, Gantz D, Qiang W, Hoatson GL. Flexibility and Solvation of Amyloid-β Hydrophobic Core. J Biol Chem 2016; 291:18484-95. [PMID: 27402826 DOI: 10.1074/jbc.m116.740530] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-β (Aβ) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the μs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aβ1-40 protein. Using solid-state (2)H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aβ as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aβ, with methyl axis motions persisting down to 230-200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-β subunits but has a clear effect on the motions at the hydrophobic interface between the cross-β subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.
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Affiliation(s)
| | | | | | | | - Donald Gantz
- Boston University School of Medicine, Boston, Massachusetts 02118
| | - Wei Qiang
- Binghamton University, Binghamton, New York 13902, and
| | - Gina L Hoatson
- College of William and Mary, Williamsburg, Virginia 23187
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32
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
| | - Yu Peng
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
- Campus Chemical Instrument Center The Ohio State University 460 W. 12th Avenue Columbus OH 43210 USA
- Department of Biological Chemistry and Pharmacology The Ohio State University 1645 Neil Avenue Columbus OH 43210 USA
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33
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Gu Y, Hansen AL, Peng Y, Brüschweiler R. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl 2016; 55:3117-9. [PMID: 26821600 DOI: 10.1002/anie.201511711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 01/03/2023]
Abstract
Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.
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Affiliation(s)
- Yina Gu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Yu Peng
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA. .,Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, 1645 Neil Avenue, Columbus, OH, 43210, USA.
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34
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Roche J, Shen Y, Lee JH, Ying J, Bax A. Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil. Biochemistry 2016; 55:762-75. [PMID: 26780756 PMCID: PMC4750080 DOI: 10.1021/acs.biochem.5b01259] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
pathogenesis of Alzheimer’s disease is characterized
by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid
plaques. Despite strong potential therapeutic interest, the structural
pathways associated with the conversion of monomeric Aβ peptides
into oligomeric species remain largely unknown. In particular, the
higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity
of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic
resonance (NMR) parameters, including chemical shifts, nuclear Overhauser
effects (NOEs), and J couplings. Systematic comparisons
show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like
conformations. Nuclear Overhauser effect spectra collected at very
high resolution remove assignment ambiguities and show no long-range
NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded
for Aβ1–40 were used as input for the recently
developed MERA Ramachandran map analysis, yielding residue-specific
backbone ϕ/ψ torsion angle distributions that closely
resemble random coil distributions, the absence of a significantly
elevated propensity for β-conformations in the C-terminal region
of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of
Aβ peptides into toxic oligomers is not driven by elevated propensities
of the monomeric species to adopt β-strand-like conformations.
Instead, the accelerated disappearance of Aβ NMR signals in
D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between
the hydrophobic regions of the peptide dominate the aggregation process.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jung Ho Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
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35
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Wiesner S, Sprangers R. Methyl groups as NMR probes for biomolecular interactions. Curr Opin Struct Biol 2015; 35:60-7. [DOI: 10.1016/j.sbi.2015.08.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 11/26/2022]
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36
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Karamanos TK, Kalverda AP, Thompson GS, Radford SE. Mechanisms of amyloid formation revealed by solution NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:86-104. [PMID: 26282197 PMCID: PMC4568309 DOI: 10.1016/j.pnmrs.2015.05.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 05/29/2023]
Abstract
Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein-protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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37
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Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR. Proc Natl Acad Sci U S A 2015; 112:8817-23. [PMID: 26124125 DOI: 10.1073/pnas.1510083112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The prototypical chaperonin GroEL assists protein folding through an ATP-dependent encapsulation mechanism. The details of how GroEL folds proteins remain elusive, particularly because encapsulation is not an absolute requirement for successful re/folding. Here we make use of a metastable model protein substrate, comprising a triple mutant of Fyn SH3, to directly demonstrate, by simultaneous analysis of three complementary NMR-based relaxation experiments (lifetime line broadening, dark state exchange saturation transfer, and Carr-Purcell-Meinboom-Gill relaxation dispersion), that apo GroEL accelerates the overall interconversion rate between the native state and a well-defined folding intermediate by about 20-fold, under conditions where the "invisible" GroEL-bound states have occupancies below 1%. This is largely achieved through a 500-fold acceleration in the folded-to-intermediate transition of the protein substrate. Catalysis is modulated by a kinetic deuterium isotope effect that reduces the overall interconversion rate between the GroEL-bound species by about 3-fold, indicative of a significant hydrophobic contribution. The location of the GroEL binding site on the folding intermediate, mapped from (15)N, (1)HN, and (13)Cmethyl relaxation dispersion experiments, is composed of a prominent, surface-exposed hydrophobic patch.
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38
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The study of transient protein-nanoparticle interactions by solution NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:102-14. [PMID: 25936778 DOI: 10.1016/j.bbapap.2015.04.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nanobio interfaces. Nanoparticles exhibit unique structures and properties, often different from the corresponding bulk materials, and the nature of their interactions with biological systems remains poorly characterized. Solution NMR spectroscopy is a mature technique for the investigation of biomolecular structure, dynamics, and intermolecular associations, however its use in protein-nanoparticle interaction studies remains scarce and highly challenging, particularly due to unfavorable hydrodynamic properties of most nanoscale assemblies. Nonetheless, recent efforts demonstrated that a number of NMR observables, such as chemical shifts, signal intensities, amide exchange rates and relaxation parameters, together with newly designed saturation transfer experiments, could be successfully employed to characterize the orientation, structure and dynamics of proteins adsorbed onto nanoparticle surfaces. This review provides the first survey and critical assessment of the contributions from solution NMR spectroscopy to the study of transient interactions between proteins and both inorganic (gold, silver, and silica) and organic (polymer, carbon and lipid based) nanoparticles. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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39
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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