1
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Streit JO, Bukvin IV, Chan SHS, Bashir S, Woodburn LF, Włodarski T, Figueiredo AM, Jurkeviciute G, Sidhu HK, Hornby CR, Waudby CA, Cabrita LD, Cassaignau AME, Christodoulou J. The ribosome lowers the entropic penalty of protein folding. Nature 2024:10.1038/s41586-024-07784-4. [PMID: 39112704 DOI: 10.1038/s41586-024-07784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
Abstract
Most proteins fold during biosynthesis on the ribosome1, and co-translational folding energetics, pathways and outcomes of many proteins have been found to differ considerably from those in refolding studies2-10. The origin of this folding modulation by the ribosome has remained unknown. Here we have determined atomistic structures of the unfolded state of a model protein on and off the ribosome, which reveal that the ribosome structurally expands the unfolded nascent chain and increases its solvation, resulting in its entropic destabilization relative to the peptide chain in isolation. Quantitative 19F NMR experiments confirm that this destabilization reduces the entropic penalty of folding by up to 30 kcal mol-1 and promotes formation of partially folded intermediates on the ribosome, an observation that extends to other protein domains and is obligate for some proteins to acquire their active conformation. The thermodynamic effects also contribute to the ribosome protecting the nascent chain from mutation-induced unfolding, which suggests a crucial role of the ribosome in supporting protein evolution. By correlating nascent chain structure and dynamics to their folding energetics and post-translational outcomes, our findings establish the physical basis of the distinct thermodynamics of co-translational protein folding.
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Affiliation(s)
- Julian O Streit
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Ivana V Bukvin
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
| | - Shahzad Bashir
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Lauren F Woodburn
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Tomasz Włodarski
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Angelo Miguel Figueiredo
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Gabija Jurkeviciute
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Haneesh K Sidhu
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Charity R Hornby
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology, University College London, London, UK.
- Department of Biological Sciences, Birkbeck College, London, UK.
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2
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Zhang O, Haghighatlari M, Li J, Liu ZH, Namini A, Teixeira JMC, Forman-Kay JD, Head-Gordon T. Learning to evolve structural ensembles of unfolded and disordered proteins using experimental solution data. J Chem Phys 2023; 158:174113. [PMID: 37144719 PMCID: PMC10163956 DOI: 10.1063/5.0141474] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/06/2023] Open
Abstract
The structural characterization of proteins with a disorder requires a computational approach backed by experiments to model their diverse and dynamic structural ensembles. The selection of conformational ensembles consistent with solution experiments of disordered proteins highly depends on the initial pool of conformers, with currently available tools limited by conformational sampling. We have developed a Generative Recurrent Neural Network (GRNN) that uses supervised learning to bias the probability distributions of torsions to take advantage of experimental data types such as nuclear magnetic resonance J-couplings, nuclear Overhauser effects, and paramagnetic resonance enhancements. We show that updating the generative model parameters according to the reward feedback on the basis of the agreement between experimental data and probabilistic selection of torsions from learned distributions provides an alternative to existing approaches that simply reweight conformers of a static structural pool for disordered proteins. Instead, the biased GRNN, DynamICE, learns to physically change the conformations of the underlying pool of the disordered protein to those that better agree with experiments.
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Affiliation(s)
- Oufan Zhang
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Mojtaba Haghighatlari
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jie Li
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Ashley Namini
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
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3
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Yagi-Utsumi M, Kato K. Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154787. [PMID: 35897966 PMCID: PMC9369837 DOI: 10.3390/molecules27154787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022]
Abstract
Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and polymorphisms of amyloidogenic proteins. This review provides an overview of the conformational diversity of amyloid-β (Aβ) characterized from experimental and theoretical approaches. Aβ exhibits a high degree of conformational variability upon transiently interacting with various binding molecules in an unstructured conformation in a solution, forming an α-helical intermediate conformation on the membrane and undergoing a structural transition to the β-conformation of amyloid fibrils. This review also outlines the structural polymorphism of Aβ amyloid fibrils depending on environmental factors. A comprehensive understanding of the energy landscape of amyloid formation considering various environmental factors will promote drug discovery and therapeutic strategies by controlling the fibril formation pathway and targeting the consequent morphology of aggregated structures.
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Affiliation(s)
- Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
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4
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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5
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Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. J Phys Chem B 2021; 125:12401-12412. [PMID: 34748336 PMCID: PMC9096987 DOI: 10.1021/acs.jpcb.1c05820] [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] [Indexed: 11/28/2022]
Abstract
Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.
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Affiliation(s)
- Adam K Nijhawan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Arnold M Chan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Darren J Hsu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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6
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Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States. Commun Chem 2020; 3:74. [PMID: 32775701 PMCID: PMC7409953 DOI: 10.1038/s42004-020-0323-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, that calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.
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7
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Niu Z, Prade E, Malideli E, Hille K, Jussupow A, Mideksa YG, Yan L, Qian C, Fleisch M, Messias AC, Sarkar R, Sattler M, Lamb DC, Feige MJ, Camilloni C, Kapurniotu A, Reif B. Structural Insight into IAPP-Derived Amyloid Inhibitors and Their Mechanism of Action. Angew Chem Int Ed Engl 2020; 59:5771-5781. [PMID: 31863711 PMCID: PMC7154662 DOI: 10.1002/anie.201914559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Indexed: 11/12/2022]
Abstract
Designed peptides derived from the islet amyloid polypeptide (IAPP) cross-amyloid interaction surface with Aβ (termed interaction surface mimics or ISMs) have been shown to be highly potent inhibitors of Aβ amyloid self-assembly. However, the molecular mechanism of their function is not well understood. Using solution-state and solid-state NMR spectroscopy in combination with ensemble-averaged dynamics simulations and other biophysical methods including TEM, fluorescence spectroscopy and microscopy, and DLS, we characterize ISM structural preferences and interactions. We find that the ISM peptide R3-GI is highly dynamic, can adopt a β-like structure, and oligomerizes into colloid-like assemblies in a process that is reminiscent of liquid-liquid phase separation (LLPS). Our results suggest that such assemblies yield multivalent surfaces for interactions with Aβ40. Sequestration of substrates into these colloid-like structures provides a mechanistic basis for ISM function and the design of novel potent anti-amyloid molecules.
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Affiliation(s)
- Zheng Niu
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
| | - Elke Prade
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
| | - Eleni Malideli
- Technische Universität München (TUM)TUM School of Life SciencesDivision of Peptide BiochemistryEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Kathleen Hille
- Technische Universität München (TUM)TUM School of Life SciencesDivision of Peptide BiochemistryEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Alexander Jussupow
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
- Technische Universität München (TUM)Institute for Advanced StudyLichtenbergstr. 2a85748GarchingGermany
| | - Yonatan G. Mideksa
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
- Technische Universität München (TUM)Institute for Advanced StudyLichtenbergstr. 2a85748GarchingGermany
| | - Li‐Mei Yan
- Technische Universität München (TUM)TUM School of Life SciencesDivision of Peptide BiochemistryEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Chen Qian
- Ludwig-Maximilians-Universität, MunichDepartment of ChemistryCenter for Integrated Protein Science Munich (CIPSM)Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS)Butenandtstr. 581377MünchenGermany
| | - Markus Fleisch
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
| | - Ana C. Messias
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
| | - Michael Sattler
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
| | - Don C. Lamb
- Ludwig-Maximilians-Universität, MunichDepartment of ChemistryCenter for Integrated Protein Science Munich (CIPSM)Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS)Butenandtstr. 581377MünchenGermany
| | - Matthias J. Feige
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
- Technische Universität München (TUM)Institute for Advanced StudyLichtenbergstr. 2a85748GarchingGermany
| | - Carlo Camilloni
- Technische Universität München (TUM)Institute for Advanced StudyLichtenbergstr. 2a85748GarchingGermany
- Università degli Studi di MilanoDipartimento di BioscienzeVia Giovanni Celoria 2620133MilanoItaly
| | - Aphrodite Kapurniotu
- Technische Universität München (TUM)TUM School of Life SciencesDivision of Peptide BiochemistryEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural BiologyIngolstädter Landstr. 185764NeuherbergGermany
- Technische Universität München (TUM)Munich Center for Integrated Protein Science (CIPS-M) at the Department of ChemistryLichtenbergstr. 485747GarchingGermany
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8
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Niu Z, Prade E, Malideli E, Hille K, Jussupow A, Mideksa YG, Yan L, Qian C, Fleisch M, Messias AC, Sarkar R, Sattler M, Lamb DC, Feige MJ, Camilloni C, Kapurniotu A, Reif B. Structural Insight into IAPP‐Derived Amyloid Inhibitors and Their Mechanism of Action. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zheng Niu
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
| | - Elke Prade
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
| | - Eleni Malideli
- Technische Universität München (TUM) TUM School of Life Sciences Division of Peptide Biochemistry Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Kathleen Hille
- Technische Universität München (TUM) TUM School of Life Sciences Division of Peptide Biochemistry Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Alexander Jussupow
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
- Technische Universität München (TUM) Institute for Advanced Study Lichtenbergstr. 2a 85748 Garching Germany
| | - Yonatan G. Mideksa
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
- Technische Universität München (TUM) Institute for Advanced Study Lichtenbergstr. 2a 85748 Garching Germany
| | - Li‐Mei Yan
- Technische Universität München (TUM) TUM School of Life Sciences Division of Peptide Biochemistry Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Chen Qian
- Ludwig-Maximilians-Universität, Munich Department of Chemistry Center for Integrated Protein Science Munich (CIPSM) Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS) Butenandtstr. 5 81377 München Germany
| | - Markus Fleisch
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
| | - Ana C. Messias
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
| | - Michael Sattler
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
| | - Don C. Lamb
- Ludwig-Maximilians-Universität, Munich Department of Chemistry Center for Integrated Protein Science Munich (CIPSM) Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS) Butenandtstr. 5 81377 München Germany
| | - Matthias J. Feige
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
- Technische Universität München (TUM) Institute for Advanced Study Lichtenbergstr. 2a 85748 Garching Germany
| | - Carlo Camilloni
- Technische Universität München (TUM) Institute for Advanced Study Lichtenbergstr. 2a 85748 Garching Germany
- Università degli Studi di Milano Dipartimento di Bioscienze Via Giovanni Celoria 26 20133 Milano Italy
| | - Aphrodite Kapurniotu
- Technische Universität München (TUM) TUM School of Life Sciences Division of Peptide Biochemistry Emil-Erlenmeyer-Forum 5 85354 Freising Germany
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU) Deutsches Forschungszentrum für Gesundheit und Umwelt Institute of Structural Biology Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Technische Universität München (TUM) Munich Center for Integrated Protein Science (CIPS-M) at the Department of Chemistry Lichtenbergstr. 4 85747 Garching Germany
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9
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Yagi-Utsumi M. NMR Characterization of Conformational Dynamics and Molecular Assemblies of Proteins. Biol Pharm Bull 2019; 42:867-872. [PMID: 31155585 DOI: 10.1248/bpb.b19-00115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dynamic conformational transitions and molecular assemblies are essential properties of proteins, and relevant to their biological and pathological functions. Neurodegenerative diseases are known to be caused by abnormal, toxic assemblies of related proteins, e.g., amyloid β (Aβ) in Alzheimer's disease. Growing evidence indicates that the aggregation of various amyloidogenic proteins, including Aβ, can be highly enhanced at glycolipid membranes, suggesting that dynamic glycolipid-dependent conformational changes of proteins constitute crucial steps for their subsequent pathogenic amyloid fibril formation. It has also been proposed that several proteins, including molecular chaperones, can capture amyloidogenic proteins and thereby suppress their fibrillization. NMR spectroscopy provides a powerful tool for characterizing the conformational dynamics and intermolecular interactions of proteins, as well as for exploring transiently formed weak interactions among proteins in solution with various biomolecules, such as glycolipids. Our research group therefore attempted to elucidate the structural basis of protein-glycolipid and protein-protein interactions that either promote or suppress molecular assemblies of amyloidogenic proteins, using both solution and solid-state NMR methods in conjunction with other biophysical techniques. Our findings provide structural views of molecular processes involving amyloidogenic proteins of clinical and pathological interest and offer clues for the development of drugs to prevent and treat neurodegenerative diseases.
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Affiliation(s)
- Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of National Sciences.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences.,Graduate School of Pharmaceutical Sciences, Nagoya City University
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10
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Kooshapur H, Schwieters CD, Tjandra N. Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute; National Institutes of Health; Bethesda MD 20892 USA
| | - Charles D. Schwieters
- Office of Intramural Research; Center for Information Technology; National Institutes of Health; Bethesda MD 20892 USA
| | - Nico Tjandra
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute; National Institutes of Health; Bethesda MD 20892 USA
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11
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Kooshapur H, Schwieters CD, Tjandra N. Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE). Angew Chem Int Ed Engl 2018; 57:13519-13522. [PMID: 30125451 DOI: 10.1002/anie.201807365] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/27/2018] [Indexed: 01/05/2023]
Abstract
Characterization of the conformational ensemble of disordered proteins is highly important for understanding protein folding and aggregation mechanisms, but remains a computational and experimental challenge owing to the dynamic nature of these proteins. New observables that can provide unique insights into transient residual structures in disordered proteins are needed. Here using denatured ubiquitin as a model system, NMR solvent paramagnetic relaxation enhancement (sPRE) measurements provide an accurate and highly sensitive probe for detecting low populations of residual structure in a disordered protein. Furthermore, a new ensemble calculation approach based on sPRE restraints in conjunction with residual dipolar couplings (RDCs) and small-angle X-ray scattering (SAXS) is used to define the conformational ensemble of disordered proteins at atomic resolution. The approach presented should be applicable to a wide range of dynamic macromolecules.
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Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nico Tjandra
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules 2018; 23:E1937. [PMID: 30081441 PMCID: PMC6205158 DOI: 10.3390/molecules23081937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (¹H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N⁻13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.
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Affiliation(s)
- Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Madison, WI 53706, USA.
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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Fusco G, Sanz-Hernandez M, Ruggeri FS, Vendruscolo M, Dobson CM, De Simone A. Molecular determinants of the interaction of EGCG with ordered and disordered proteins. Biopolymers 2018; 109:e23117. [DOI: 10.1002/bip.23117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Giuliana Fusco
- Department of Life Sciences; Imperial College London; London SW7 2AZ United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | | | - Francesco S. Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences; Imperial College London; London SW7 2AZ United Kingdom
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Olivieri C, Subrahmanian MV, Xia Y, Kim J, Porcelli F, Veglia G. Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2018; 70:133-140. [PMID: 29396770 PMCID: PMC6029865 DOI: 10.1007/s10858-018-0165-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner is labeled with stable isotopes (15N or 13C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein-protein complexes, making this approach time consuming and expensive. Here, we show a new strategy that combines a modified pulse sequence (1HN-Γ2-CCLS) with an asymmetric labeling scheme to enable the detection of both intra- and inter-molecular PREs simultaneously using only one sample preparation. We applied this strategy to the non-covalent dimer of ubiquitin. Our method confirmed the previously identified binding interface for the transient di-ubiquitin complex, and at the same time, unveiled the internal structural dynamics rearrangements of ubiquitin upon interaction. In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein-protein complexes.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Manu Veliparambil Subrahmanian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonggul Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
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15
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Gibbs EB, Cook EC, Showalter SA. Application of NMR to studies of intrinsically disordered proteins. Arch Biochem Biophys 2017; 628:57-70. [PMID: 28502465 DOI: 10.1016/j.abb.2017.05.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022]
Abstract
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels. Across the range of functional assembly states accessed by disordered regions, post-translational modifications and regulatory macromolecular interactions, which can also be investigated by NMR spectroscopy, feature prominently. Here we will explore the many ways in which NMR has advanced our understanding of the physical-chemical phase space occupied by disordered protein regions and provide prospectus for the future role of NMR in this emerging and exciting field.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik C Cook
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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