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Konermann L, Scrosati PM. Hydrogen/Deuterium Exchange Mass Spectrometry: Fundamentals, Limitations, and Opportunities. Mol Cell Proteomics 2024:100853. [PMID: 39383946 DOI: 10.1016/j.mcpro.2024.100853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/11/2024] [Accepted: 10/02/2024] [Indexed: 10/11/2024] Open
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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2
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Schwalbe H, Audergon P, Haley N, Amaro CA, Agirre J, Baldus M, Banci L, Baumeister W, Blackledge M, Carazo JM, Carugo KD, Celie P, Felli I, Hart DJ, Hauß T, Lehtiö L, Lindorff-Larsen K, Márquez J, Matagne A, Pierattelli R, Rosato A, Sobott F, Sreeramulu S, Steyaert J, Sussman JL, Trantirek L, Weiss MS, Wilmanns M. The future of integrated structural biology. Structure 2024; 32:1563-1580. [PMID: 39293444 DOI: 10.1016/j.str.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/22/2024] [Indexed: 09/20/2024]
Abstract
Instruct-ERIC, "the European Research Infrastructure Consortium for Structural biology research," is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. Here, we describe the current state-of-the-art of integrated structural biology and discuss potential future scientific developments as an impulse for the scientific community, many of which are located in Europe and are associated with Instruct. We reflect on where to focus scientific and technological initiatives within the distributed Instruct research infrastructure. This review does not intend to make recommendations on funding requirements or initiatives directly, neither at the national nor the European level. However, it addresses future challenges and opportunities for the field, and foresees the need for a stronger coordination within the European and international research field of integrated structural biology to be able to respond timely to thematic topics that are often prioritized by calls for funding addressing societal needs.
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Affiliation(s)
- Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/M., Germany; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK.
| | - Pauline Audergon
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Natalie Haley
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Claudia Alen Amaro
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, UK
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucia Banci
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS UMR5075, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jose Maria Carazo
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | | | - Patrick Celie
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Isabella Felli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Darren J Hart
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS UMR5075, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Thomas Hauß
- Macromolecular Crystallography, Helmholtz-Zentrum, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - José Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000 Liège (Sart-Tilman), Belgium
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/M., Germany
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, Brussels, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lukas Trantirek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL) Hamburg, Hamburg, Germany
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Schiffrin B, Crossley JA, Walko M, Machin JM, Nasir Khan G, Manfield IW, Wilson AJ, Brockwell DJ, Fessl T, Calabrese AN, Radford SE, Zhuravleva A. Dual client binding sites in the ATP-independent chaperone SurA. Nat Commun 2024; 15:8071. [PMID: 39277579 PMCID: PMC11401910 DOI: 10.1038/s41467-024-52021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
The ATP-independent chaperone SurA protects unfolded outer membrane proteins (OMPs) from aggregation in the periplasm of Gram-negative bacteria, and delivers them to the β-barrel assembly machinery (BAM) for folding into the outer membrane (OM). Precisely how SurA recognises and binds its different OMP clients remains unclear. Escherichia coli SurA comprises three domains: a core and two PPIase domains (P1 and P2). Here, by combining methyl-TROSY NMR, single-molecule Förster resonance energy transfer (smFRET), and bioinformatics analyses we show that SurA client binding is mediated by two binding hotspots in the core and P1 domains. These interactions are driven by aromatic-rich motifs in the client proteins, leading to SurA core/P1 domain rearrangements and expansion of clients from collapsed, non-native states. We demonstrate that the core domain is key to OMP expansion by SurA, and uncover a role for SurA PPIase domains in limiting the extent of expansion. The results reveal insights into SurA-OMP recognition and the mechanism of activation for an ATP-independent chaperone, and suggest a route to targeting the functions of a chaperone key to bacterial virulence and OM integrity.
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Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, UK
| | - Jonathan M Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, UK
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc 2024; 146:8394-8406. [PMID: 38477601 DOI: 10.1021/jacs.3c14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.
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Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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Shukla VK, Siemons L, Hansen DF. Intrinsic structural dynamics dictate enzymatic activity and inhibition. Proc Natl Acad Sci U S A 2023; 120:e2310910120. [PMID: 37782780 PMCID: PMC10576142 DOI: 10.1073/pnas.2310910120] [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: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
Enzymes are known to sample various conformations, many of which are critical for their biological function. However, structural characterizations of enzymes predominantly focus on the most populated conformation. As a result, single-point mutations often produce structures that are similar or essentially identical to those of the wild-type enzyme despite large changes in enzymatic activity. Here, we show for mutants of a histone deacetylase enzyme (HDAC8) that reduced enzymatic activities, reduced inhibitor affinities, and reduced residence times are all captured by the rate constants between intrinsically sampled conformations that, in turn, can be obtained independently by solution NMR spectroscopy. Thus, for the HDAC8 enzyme, the dynamic sampling of conformations dictates both enzymatic activity and inhibitor potency. Our analysis also dissects the functional role of the conformations sampled, where specific conformations distinct from those in available structures are responsible for substrate and inhibitor binding, catalysis, and product dissociation. Precise structures alone often do not adequately explain the effect of missense mutations on enzymatic activity and drug potency. Our findings not only assign functional roles to several conformational states of HDAC8 but they also underscore the paramount role of dynamics, which will have general implications for characterizing missense mutations and designing inhibitors.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Lucas Siemons
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - D. Flemming Hansen
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
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Ghosh S, Tugarinov V, Clore GM. Quantitative NMR analysis of the mechanism and kinetics of chaperone Hsp104 action on amyloid-β42 aggregation and fibril formation. Proc Natl Acad Sci U S A 2023; 120:e2305823120. [PMID: 37186848 PMCID: PMC10214214 DOI: 10.1073/pnas.2305823120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
The chaperone Hsp104, a member of the Hsp100/Clp family of translocases, prevents fibril formation of a variety of amyloidogenic peptides in a paradoxically substoichiometric manner. To understand the mechanism whereby Hsp104 inhibits fibril formation, we probed the interaction of Hsp104 with the Alzheimer's amyloid-β42 (Aβ42) peptide using a variety of biophysical techniques. Hsp104 is highly effective at suppressing the formation of Thioflavin T (ThT) reactive mature fibrils that are readily observed by atomic force (AFM) and electron (EM) microscopies. Quantitative kinetic analysis and global fitting was performed on serially recorded 1H-15N correlation spectra to monitor the disappearance of Aβ42 monomers during the course of aggregation over a wide range of Hsp104 concentrations. Under the conditions employed (50 μM Aβ42 at 20 °C), Aβ42 aggregation occurs by a branching mechanism: an irreversible on-pathway leading to mature fibrils that entails primary and secondary nucleation and saturating elongation; and a reversible off-pathway to form nonfibrillar oligomers, unreactive to ThT and too large to be observed directly by NMR, but too small to be visualized by AFM or EM. Hsp104 binds reversibly with nanomolar affinity to sparsely populated Aβ42 nuclei present in nanomolar concentrations, generated by primary and secondary nucleation, thereby completely inhibiting on-pathway fibril formation at substoichiometric ratios of Hsp104 to Aβ42 monomers. Tight binding to sparsely populated nuclei likely constitutes a general mechanism for substoichiometric inhibition of fibrillization by a variety of chaperones. Hsp104 also impacts off-pathway oligomerization but to a much smaller degree initially reducing and then increasing the rate of off-pathway oligomerization.
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Affiliation(s)
- Shreya Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
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Karamanos TK. Chasing long-range evolutionary couplings in the AlphaFold era. Biopolymers 2023; 114:e23530. [PMID: 36752285 PMCID: PMC10909459 DOI: 10.1002/bip.23530] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
Abstract
Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA and searches for couplings that are not satisfied in any of the AF models of members of the identified protein family. Application of this method on 2012 protein families suggests that ~12% of the total identified coevolving residue pairs are spatially distant and more likely to be disordered than their contacting counterparts. We expect that this analysis will help improve the quality of coevolutionary distance restraints used for structure determination and will be useful in identifying potentially functional/allosteric cross-talk between distant residues.
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Clore GM. NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease. J Cell Sci 2022; 135:jcs258695. [PMID: 35703323 PMCID: PMC9270955 DOI: 10.1242/jcs.258695] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for analyzing three-dimensional structure and dynamics of macromolecules at atomic resolution. Recent advances have exploited the unique properties of NMR in exchanging systems to detect, characterize and visualize excited sparsely populated states of biological macromolecules and their complexes, which are only transient. These states are invisible to conventional biophysical techniques, and play a key role in many processes, including molecular recognition, protein folding, enzyme catalysis, assembly and fibril formation. All the NMR techniques make use of exchange between sparsely populated NMR-invisible and highly populated NMR-visible states to transfer a magnetization property from the invisible state to the visible one where it can be easily detected and quantified. There are three classes of NMR experiments that rely on differences in distance, chemical shift or transverse relaxation (molecular mass) between the NMR-visible and -invisible species. Here, I illustrate the application of these methods to unravel the complex mechanism of sub-millisecond pre-nucleation oligomerization of the N-terminal region of huntingtin, encoded by exon-1 of the huntingtin gene, where CAG expansion leads to Huntington's disease, a fatal autosomal-dominant neurodegenerative condition. I also discuss how inhibition of tetramerization blocks the much slower (by many orders of magnitude) process of fibril formation.
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Affiliation(s)
- G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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