1
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Crabtree MD, Holland J, Pillai AS, Kompella PS, Babl L, Turner NN, Eaton JT, Hochberg GKA, Aarts DGAL, Redfield C, Baldwin AJ, Nott TJ. Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions. Cell Rep 2023; 42:113375. [PMID: 37980572 PMCID: PMC10935546 DOI: 10.1016/j.celrep.2023.113375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/14/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
Abstract
Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.
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Affiliation(s)
- Michael D Crabtree
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jack Holland
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Arvind S Pillai
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Purnima S Kompella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Leon Babl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Noah N Turner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James T Eaton
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK
| | - Georg K A Hochberg
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Straße 14, 35032 Marburg, Germany
| | - Dirk G A L Aarts
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK.
| | - Timothy J Nott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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2
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Rowbotham JS, Nicholson JH, Ramirez MA, Urata K, Todd PMT, Karunanithy G, Lauterbach L, Reeve HA, Baldwin AJ, Vincent KA. Biocatalytic reductive amination as a route to isotopically labelled amino acids suitable for analysis of large proteins by NMR. Chem Sci 2023; 14:12160-12165. [PMID: 37969586 PMCID: PMC10631221 DOI: 10.1039/d3sc01718d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 11/17/2023] Open
Abstract
We demonstrate an atom-efficient and easy to use H2-driven biocatalytic platform for the enantioselective incorporation of 2H-atoms into amino acids. By combining the biocatalytic deuteration catalyst with amino acid dehydrogenase enzymes capable of reductive amination, we synthesised a library of multiply isotopically labelled amino acids from low-cost isotopic precursors, such as 2H2O and 15NH4+. The chosen approach avoids the use of pre-labeled 2H-reducing agents, and therefore vastly simplifies product cleanup. Notably, this strategy enables 2H, 15N, and an asymmetric centre to be introduced at a molecular site in a single step, with full selectivity, under benign conditions, and with near 100% atom economy. The method facilitates the preparation of amino acid isotopologues on a half-gram scale. These amino acids have wide applicability in the analytical life sciences, and in particular for NMR spectroscopic analysis of proteins. To demonstrate the benefits of the approach for enabling the workflow of protein NMR chemists, we prepared l-[α-2H,15N, β-13C]-alanine and integrated it into a large (>400 kDa) heat-shock protein oligomer, which was subsequently analysable by methyl-TROSY techniques, revealing new structural information.
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Affiliation(s)
- Jack S Rowbotham
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Jake H Nicholson
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Miguel A Ramirez
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Kouji Urata
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Peter M T Todd
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Gogulan Karunanithy
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory Oxford UK
| | - Lars Lauterbach
- Technische Universität Berlin, Institute for Chemistry Straße des 17. Juni 135 10437 Berlin Germany
| | - Holly A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory Oxford UK
- Kavli Institute for Nanoscience Discovery, University of Oxford Oxford OX1 3QU UK
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
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3
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El-Baba TJ, Lutomski CA, Burnap SA, Bolla JR, Baker LA, Baldwin AJ, Struwe WB, Robinson CV. Uncovering the Role of N-Glycan Occupancy on the Cooperative Assembly of Spike and Angiotensin Converting Enzyme 2 Complexes: Insights from Glycoengineering and Native Mass Spectrometry. J Am Chem Soc 2023; 145:8021-8032. [PMID: 37000485 PMCID: PMC10103161 DOI: 10.1021/jacs.3c00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address these unanswered questions by combining a glycoengineering strategy with high-resolution native mass spectrometry (MS) to investigate the impact of N-glycan occupancy on the assembly of multiple Spike-ACE2 complexes. We confirmed that intact Spike trimers have all 66 N-linked sites occupied. For monomeric ACE2, all seven N-linked glycan sites are occupied to various degrees; six sites have >90% occupancy, while the seventh site (Asn690) is only partially occupied (∼30%). By resolving the glycoforms on ACE2, we deciphered the influence of each N-glycan on ACE2 dimerization. Unexpectedly, we found that Asn432 plays a role in mediating dimerization, a result confirmed by site-directed mutagenesis. We also found that glycosylated dimeric ACE2 and Spike trimers form complexes with multiple stoichiometries (Spike-ACE2 and Spike2-ACE2) with dissociation constants (Kds) of ∼500 and <100 nM, respectively. Comparing these values indicates that positive cooperativity may drive ACE2 dimers to complex with multiple Spike trimers. Overall, our results show that occupancy has a key regulatory role in mediating interactions between ACE2 dimers and Spike trimers. More generally, since soluble ACE2 (sACE2) retains an intact SARS-CoV-2 interaction site, the importance of glycosylation in ACE2 dimerization and the propensity for Spike and ACE2 to assemble into higher oligomers are molecular details important for developing strategies for neutralizing the virus.
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Affiliation(s)
- Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Corinne A Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Sean A Burnap
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Lindsay A Baker
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3TA, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
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4
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Isenegger PG, Josephson B, Gaunt B, Davy MJ, Gouverneur V, Baldwin AJ, Davis BG. Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via 19F-nuclear magnetic resonance. Nat Protoc 2023; 18:1543-1562. [PMID: 36806799 DOI: 10.1038/s41596-022-00800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/23/2022] [Indexed: 02/22/2023]
Abstract
The fluorination of amino acid residues represents a near-isosteric alteration with the potential to report on biological pathways, yet the site-directed editing of carbon-hydrogen (C-H) bonds in complex biomolecules to carbon-fluorine (C-F) bonds is challenging, resulting in its limited exploitation. Here, we describe a protocol for the posttranslational and site-directed alteration of native γCH2 to γCF2 in protein sidechains. This alteration allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both native and modified states. This chemical editing is robust, mild, fast and highly efficient, exploiting photochemical- and radical-mediated C-C bonds grafted onto easy-to-access cysteine-derived dehydroalanine-containing proteins as starting materials. The heteroaryl-sulfonyl reagent required for generating the key carbon-centered C• radicals that install the sidechain can be synthesized in two to six steps from commercially available precursors. This workflow allows the nonexpert to create fluorinated proteins within 24 h, starting from a corresponding purified cysteine-containing protein precursor, without the need for bespoke biological systems. As an example, we readily introduce three γCF2-containing methionines in all three progressive oxidation states (sulfide, sulfoxide and sulfone) as D-/L- forms into histone eH3.1 at site 4 (a relevant lysine to methionine oncomutation site), and each can be detected by 19F-nuclear magnetic resonance of the γCF2 group, as well as the two diastereomers of the sulfoxide, even when found in a complex protein mixture of all three. The site-directed editing of C-H→C-F enables the use of γCF2 as a highly sensitive, 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenomena, protein structures and/or protein-ligand interactions by 19F-based detection methods.
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Affiliation(s)
| | | | - Ben Gaunt
- The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthew J Davy
- The Rosalind Franklin Institute, Oxfordshire, UK.,Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Department of Pharmacology, University of Oxford, Oxford, UK.
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5
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Buchanan CJ, Gaunt B, Harrison PJ, Yang Y, Liu J, Khan A, Giltrap AM, Le Bas A, Ward PN, Gupta K, Dumoux M, Tan TK, Schimaski L, Daga S, Picchiotti N, Baldassarri M, Benetti E, Fallerini C, Fava F, Giliberti A, Koukos PI, Davy MJ, Lakshminarayanan A, Xue X, Papadakis G, Deimel LP, Casablancas-Antràs V, Claridge TDW, Bonvin AMJJ, Sattentau QJ, Furini S, Gori M, Huo J, Owens RJ, Schaffitzel C, Berger I, Renieri A, Naismith JH, Baldwin AJ, Davis BG. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 2022; 377:eabm3125. [PMID: 35737812 DOI: 10.1126/science.abm3125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.
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Affiliation(s)
- Charles J Buchanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Ben Gaunt
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Peter J Harrison
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Yun Yang
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Jiwei Liu
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Aziz Khan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew M Giltrap
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Audrey Le Bas
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Philip N Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lisa Schimaski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthew J Davy
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Abirami Lakshminarayanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Xiaochao Xue
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Sir William Dunn School of Pathology, Oxford, UK
| | | | | | - Virgínia Casablancas-Antràs
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | | | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | | | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Gori
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Maasai, I3S CNRS, Université Côte d'Azur, Nice, France
| | - Jiandong Huo
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J Owens
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Christiane Schaffitzel
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Imre Berger
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Andrew J Baldwin
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Benjamin G Davis
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
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6
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Mollner TA, Giltrap AM, Zeng Y, Demyanenko Y, Buchanan C, Oehlrich D, Baldwin AJ, Anthony DC, Mohammed S, Davis BG. Reductive site-selective atypical C, Z-type/N2-C2 cleavage allows C-terminal protein amidation. Sci Adv 2022; 8:eabl8675. [PMID: 35394836 PMCID: PMC8993120 DOI: 10.1126/sciadv.abl8675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biomolecule environments can enhance chemistries with the potential to mediate and modulate self-modification (e.g., self-cleavage). While these enhanced modes are found in certain biomolecules (e.g., RNA ribozymes), it is more rare in proteins. Targeted proteolytic cleavage is vital to physiology, biotechnology, and even emerging therapy. Yet, purely chemically induced methods for the site-selective cleavage of proteins remain scarce. Here, as a proof of principle, we designed and tested a system intended to combine protein-enhanced chemistry with tag modification to enable synthetic reductive protein chemistries promoted by diboron. This reductively driven, single-electron chemistry now enables an operationally simple, site-selective cleavage protocol for proteins directed to readily accessible dehydroalanine (Dha) residues as tags under aqueous conditions and in cell lysates. In this way, a mild, efficient, enzyme-free method now allows not only precise chemical proteolysis but also simultaneous use in the removal of affinity tags and/or protein-terminus editing to create altered N- and C-termini such as protein amidation (─CONH2).
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Affiliation(s)
- Tim A. Mollner
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | | | - Yibo Zeng
- The Rosalind Franklin Institute, Oxfordshire, UK
| | | | - Charles Buchanan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Daniel Oehlrich
- Global Medicinal Chemistry, Janssen Research & Development, Beerse, Belgium
| | - Andrew J. Baldwin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Oxfordshire, UK
| | | | - Shabaz Mohammed
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Oxfordshire, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Benjamin G. Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Oxfordshire, UK
- Department of Pharmacology, University of Oxford, Oxford, UK
- Corresponding author.
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7
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Casablancas-Antras V, Demanze S, Sharman G, Kerridge C, Bose S, Baldwin AJ. Mechanism of tau R3 aggregation and inhibition revealed by NMR-based chemical kinetics. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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8
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Mollner TA, Isenegger PG, Josephson B, Buchanan C, Lercher L, Oehlrich D, Hansen DF, Mohammed S, Baldwin AJ, Gouverneur V, Davis BG. Publisher Correction: Post-translational insertion of boron in proteins to probe and modulate function. Nat Chem Biol 2021; 18:116. [PMID: 34903852 PMCID: PMC8709785 DOI: 10.1038/s41589-021-00957-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Tim A Mollner
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Patrick G Isenegger
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Brian Josephson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Charles Buchanan
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Lukas Lercher
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Daniel Oehlrich
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Beerse, Belgium
| | | | - Shabaz Mohammed
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.,Department of Biochemistry, University of Oxford, Oxford, UK.,The Rosalind Franklin Institute, Oxfordshire, Oxford, UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Rosalind Franklin Institute, Oxfordshire, Oxford, UK
| | - Véronique Gouverneur
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, Oxford, UK.
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9
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Yao K, Karunanithy G, Howarth A, Holdship P, Thompson AL, Christensen KE, Baldwin AJ, Faulkner S, Farrer NJ. Cell-permeable lanthanide-platinum(IV) anti-cancer prodrugs. Dalton Trans 2021; 50:8761-8767. [PMID: 34080595 PMCID: PMC8237448 DOI: 10.1039/d1dt01688a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022]
Abstract
Platinum compounds are a vital part of our anti-cancer arsenal, and determining the location and speciation of platinum compounds is crucial. We have synthesised a lanthanide complex bearing a salicylic group (Ln = Gd, Eu) which demonstrates excellent cellular accumulation and minimal cytotoxicity. Derivatisation enabled access to bimetallic lanthanide-platinum(ii) and lanthanide-platinum(iv) complexes. Luminescence from the europium-platinum(iv) system was quenched, and reduction to platinum(ii) with ascorbic acid resulted in a "switch-on" luminescence enhancement. We used diffusion-based 1H NMR spectroscopic methods to quantify cellular accumulation. The gadolinium-platinum(ii) and gadolinium-platinum(iv) complexes demonstrated appreciable cytotoxicity. A longer delay following incubation before cytotoxicity was observed for the gadolinium-platinum(iv) compared to the gadolinium-platinum(ii) complex. Functionalisation with octanoate ligands resulted in enhanced cellular accumulation and an even greater latency in cytotoxicity.
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Affiliation(s)
- Kezi Yao
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | - Gogulan Karunanithy
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | - Alison Howarth
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | - Philip Holdship
- Department of Earth Sciences, University of Oxford, OX1 3AN, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | | | - Andrew J Baldwin
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | - Stephen Faulkner
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
| | - Nicola J Farrer
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 3TA, UK.
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10
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Alderson TR, Adriaenssens E, Asselbergh B, Pritišanac I, Van Lent J, Gastall HY, Wälti MA, Louis JM, Timmerman V, Baldwin AJ, Lp Benesch J. A weakened interface in the P182L variant of HSP27 associated with severe Charcot-Marie-Tooth neuropathy causes aberrant binding to interacting proteins. EMBO J 2021; 40:e103811. [PMID: 33644875 PMCID: PMC8047445 DOI: 10.15252/embj.2019103811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
HSP27 is a human molecular chaperone that forms large, dynamic oligomers and functions in many aspects of cellular homeostasis. Mutations in HSP27 cause Charcot‐Marie‐Tooth (CMT) disease, the most common inherited disorder of the peripheral nervous system. A particularly severe form of CMT disease is triggered by the P182L mutation in the highly conserved IxI/V motif of the disordered C‐terminal region, which interacts weakly with the structured core domain of HSP27. Here, we observed that the P182L mutation disrupts the chaperone activity and significantly increases the size of HSP27 oligomers formed in vivo, including in motor neurons differentiated from CMT patient‐derived stem cells. Using NMR spectroscopy, we determined that the P182L mutation decreases the affinity of the HSP27 IxI/V motif for its own core domain, leaving this binding site more accessible for other IxI/V‐containing proteins. We identified multiple IxI/V‐bearing proteins that bind with higher affinity to the P182L variant due to the increased availability of the IxI/V‐binding site. Our results provide a mechanistic basis for the impact of the P182L mutation on HSP27 and suggest that the IxI/V motif plays an important, regulatory role in modulating protein–protein interactions.
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Affiliation(s)
- T Reid Alderson
- Chemistry Research Laboratory, University of Oxford, Oxford, UK.,Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD, USA
| | - Elias Adriaenssens
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Bob Asselbergh
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerpen, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Iva Pritišanac
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Heidi Y Gastall
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Marielle A Wälti
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, MD, USA
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
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11
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Josephson B, Fehl C, Isenegger PG, Nadal S, Wright TH, Poh AWJ, Bower BJ, Giltrap AM, Chen L, Batchelor-McAuley C, Roper G, Arisa O, Sap JBI, Kawamura A, Baldwin AJ, Mohammed S, Compton RG, Gouverneur V, Davis BG. Light-driven post-translational installation of reactive protein side chains. Nature 2020; 585:530-537. [PMID: 32968259 DOI: 10.1038/s41586-020-2733-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) greatly expand the structures and functions of proteins in nature1,2. Although synthetic protein functionalization strategies allow mimicry of PTMs3,4, as well as formation of unnatural protein variants with diverse potential functions, including drug carrying5, tracking, imaging6 and partner crosslinking7, the range of functional groups that can be introduced remains limited. Here we describe the visible-light-driven installation of side chains at dehydroalanine residues in proteins through the formation of carbon-centred radicals that allow C-C bond formation in water. Control of the reaction redox allows site-selective modification with good conversions and reduced protein damage. In situ generation of boronic acid catechol ester derivatives generates RH2C• radicals that form the native (β-CH2-γ-CH2) linkage of natural residues and PTMs, whereas in situ potentiation of pyridylsulfonyl derivatives by Fe(II) generates RF2C• radicals that form equivalent β-CH2-γ-CF2 linkages bearing difluoromethylene labels. These reactions are chemically tolerant and incorporate a wide range of functionalities (more than 50 unique residues/side chains) into diverse protein scaffolds and sites. Initiation can be applied chemoselectively in the presence of sensitive groups in the radical precursors, enabling installation of previously incompatible side chains. The resulting protein function and reactivity are used to install radical precursors for homolytic on-protein radical generation; to study enzyme function with natural, unnatural and CF2-labelled post-translationally modified protein substrates via simultaneous sensing of both chemo- and stereoselectivity; and to create generalized 'alkylator proteins' with a spectrum of heterolytic covalent-bond-forming activity (that is, reacting diversely with small molecules at one extreme or selectively with protein targets through good mimicry at the other). Post-translational access to such reactions and chemical groups on proteins could be useful in both revealing and creating protein function.
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Affiliation(s)
- Brian Josephson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlie Fehl
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Simon Nadal
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tom H Wright
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Adeline W J Poh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ben J Bower
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew M Giltrap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
| | - Lifu Chen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Grace Roper
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Oluwatobi Arisa
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeroen B I Sap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew J Baldwin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Richard G Compton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronique Gouverneur
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- The Rosalind Franklin Institute, Harwell, UK.
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12
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Stelzl LS, Mavridou DAI, Saridakis E, Gonzalez D, Baldwin AJ, Ferguson SJ, Sansom MSP, Redfield C. Local frustration determines loop opening during the catalytic cycle of an oxidoreductase. eLife 2020; 9:e54661. [PMID: 32568066 PMCID: PMC7347389 DOI: 10.7554/elife.54661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/21/2020] [Indexed: 11/13/2022] Open
Abstract
Local structural frustration, the existence of mutually exclusive competing interactions, may explain why some proteins are dynamic while others are rigid. Frustration is thought to underpin biomolecular recognition and the flexibility of protein-binding sites. Here, we show how a small chemical modification, the oxidation of two cysteine thiols to a disulfide bond, during the catalytic cycle of the N-terminal domain of the key bacterial oxidoreductase DsbD (nDsbD), introduces frustration ultimately influencing protein function. In oxidized nDsbD, local frustration disrupts the packing of the protective cap-loop region against the active site allowing loop opening. By contrast, in reduced nDsbD the cap loop is rigid, always protecting the active-site thiols from the oxidizing environment of the periplasm. Our results point toward an intricate coupling between the dynamics of the active-site cysteines and of the cap loop which modulates the association reactions of nDsbD with its partners resulting in optimized protein function.
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Affiliation(s)
- Lukas S Stelzl
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Despoina AI Mavridou
- Department of Molecular Biosciences, University of Texas at AustinAustinUnited States
| | - Emmanuel Saridakis
- Institute of Nanoscience and Nanotechnology, NCSR DemokritosAthensGreece
| | - Diego Gonzalez
- Laboratoire de Microbiologie, Institut de Biologie, Université de NeuchâtelNeuchâtelSwitzerland
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of OxfordOxfordUnited Kingdom
| | - Stuart J Ferguson
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Mark SP Sansom
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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13
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Broderick D, Kyzas P, Baldwin AJ, Graham RM, Duncan T, Chaintoutis C, Boultoukas E, Vassiliou L. Surgical tracheostomies in COVID-19 patients: A multidisciplinary approach and lessons learned. Oral Oncol 2020; 106:104767. [PMID: 32389538 PMCID: PMC7196417 DOI: 10.1016/j.oraloncology.2020.104767] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023]
Abstract
Surgical tracheostomies have a role in the management of COVID-19 patients. MDT guided and protocol-driven tracheostomy procedures are safe and effective. “CORONA-steps” and “5Ts” tracheostomy protocols have shown safety and efficacy in COVID-19 patients. COVID-19 transmission risk is minimised with the use of appropriate PPE and adherence to the protocol. Case selection helps in ensuring good patients’ outcomes.
Surgical tracheostomies have a role in the weaning process of COVID-19 patients treated in intensive care units. A multidisciplinary team approach (MDT) is required for decision making. This process is augmented by specific standard operating practices implemented by senior clinicians. Here, we report on our early experience and outcomes with open tracheostomies in a cohort of COVID-19 patients. We outline the criteria that guide decision making and explore the challenges faced by our intensive care colleagues in the management of these patients. The cohort was 100% male with 90% of them having a raised Body Mass Index (BMI) and other comorbidities (hypertension and diabetes). 60% have been decannulated and have been stepped down the intensive care unit. We recorded no surgical complications or adverse events. The service to date has been shown to be effective, safe, largely reproducible and reflective.
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Affiliation(s)
- Damian Broderick
- Department of Oral and Maxillofacial Surgery, North Manchester General Hospital, United Kingdom
| | - Panayiotis Kyzas
- Department of Oral and Maxillofacial Surgery, North Manchester General Hospital, United Kingdom.
| | - Andrew J Baldwin
- Department of Oral and Maxillofacial Surgery, North Manchester General Hospital, United Kingdom
| | - Richard M Graham
- Department of Oral and Maxillofacial Surgery, North Manchester General Hospital, United Kingdom
| | - Tracy Duncan
- Intensive Care Unit, North Manchester General Hospital, United Kingdom
| | | | | | - Leandros Vassiliou
- Department of Oral and Maxillofacial Surgery, North Manchester General Hospital, United Kingdom
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14
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Alderson TR, Ying J, Bax A, Benesch JLP, Baldwin AJ. Conditional Disorder in Small Heat-shock Proteins. J Mol Biol 2020; 432:3033-3049. [PMID: 32081587 PMCID: PMC7245567 DOI: 10.1016/j.jmb.2020.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/27/2020] [Accepted: 02/09/2020] [Indexed: 12/31/2022]
Abstract
Small heat-shock proteins (sHSPs) are molecular chaperones that respond to cellular stresses to combat protein aggregation. HSP27 is a critical human sHSP that forms large, dynamic oligomers whose quaternary structures and chaperone activities depend on environmental factors. Upon exposure to cellular stresses, such as heat shock or acidosis, HSP27 oligomers can dissociate into dimers and monomers, which leads to significantly enhanced chaperone activity. The structured core of the protein, the α-crystallin domain (ACD), forms dimers and can prevent the aggregation of substrate proteins to a similar degree as the full-length protein. When the ACD dimer dissociates into monomers, it partially unfolds and exhibits enhanced activity. Here, we used solution-state NMR spectroscopy to characterize the structure and dynamics of the HSP27 ACD monomer. Web show that the monomer is stabilized at low pH and that its backbone chemical shifts, 15N relaxation rates, and 1H-15N residual dipolar couplings suggest structural changes and rapid motions in the region responsible for dimerization. By analyzing the solvent accessible and buried surface areas of sHSP structures in the context of a database of dimers that are known to dissociate into disordered monomers, we predict that ACD dimers from sHSPs across all kingdoms of life may partially unfold upon dissociation. We propose a general model in which conditional disorder-the partial unfolding of ACDs upon monomerization-is a common mechanism for sHSP activity.
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Affiliation(s)
- T Reid Alderson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Justin L P Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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15
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Juárez-Jiménez J, Gupta AA, Karunanithy G, Mey ASJS, Georgiou C, Ioannidis H, De Simone A, Barlow PN, Hulme AN, Walkinshaw MD, Baldwin AJ, Michel J. Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A. Chem Sci 2020; 11:2670-2680. [PMID: 34084326 PMCID: PMC8157532 DOI: 10.1039/c9sc04696h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins need to interconvert between many conformations in order to function, many of which are formed transiently, and sparsely populated. Particularly when the lifetimes of these states approach the millisecond timescale, identifying the relevant structures and the mechanism by which they interconvert remains a tremendous challenge. Here we introduce a novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore these 'excited' conformational states. Applying this to the highly dynamic protein CypA, a protein involved in immune response and associated with HIV infection, we identify five principally populated conformational states and the atomistic mechanism by which they interconvert. A rational design strategy predicted that the mutant D66A should stabilise the minor conformations and substantially alter the dynamics, whereas the similar mutant H70A should leave the landscape broadly unchanged. These predictions are confirmed using CPMG and R1ρ solution state NMR measurements. By efficiently exploring functionally relevant, but sparsely populated conformations with millisecond lifetimes in silico, our aMD/MSM method has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery.
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Affiliation(s)
- Jordi Juárez-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Arun A Gupta
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Gogulan Karunanithy
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Charis Georgiou
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Harris Ioannidis
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alessio De Simone
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Paul N Barlow
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alison N Hulme
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Malcolm D Walkinshaw
- School of Biological Sciences Michael Swann Building, Max Born Crescent Edinburgh EH9 3BF UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
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16
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Hutchison IL, Ridout F, Cheung SMY, Shah N, Hardee P, Surwald C, Thiruchelvam J, Cheng L, Mellor TK, Brennan PA, Baldwin AJ, Shaw RJ, Halfpenny W, Danford M, Whitley S, Smith G, Bailey MW, Woodwards B, Patel M, McManners J, Chan CH, Burns A, Praveen P, Camilleri AC, Avery C, Putnam G, Jones K, Webster K, Smith WP, Edge C, McVicar I, Grew N, Hislop S, Kalavrezos N, Martin IC, Hackshaw A. Nationwide randomised trial evaluating elective neck dissection for early stage oral cancer (SEND study) with meta-analysis and concurrent real-world cohort. Br J Cancer 2019; 121:827-836. [PMID: 31611612 PMCID: PMC6888839 DOI: 10.1038/s41416-019-0587-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Guidelines remain unclear over whether patients with early stage oral cancer without overt neck disease benefit from upfront elective neck dissection (END), particularly those with the smallest tumours. METHODS We conducted a randomised trial of patients with stage T1/T2 N0 disease, who had their mouth tumour resected either with or without END. Data were also collected from a concurrent cohort of patients who had their preferred surgery. Endpoints included overall survival (OS) and disease-free survival (DFS). We conducted a meta-analysis of all six randomised trials. RESULTS Two hundred fifty randomised and 346 observational cohort patients were studied (27 hospitals). Occult neck disease was found in 19.1% (T1) and 34.7% (T2) patients respectively. Five-year intention-to-treat hazard ratios (HR) were: OS HR = 0.71 (p = 0.18), and DFS HR = 0.66 (p = 0.04). Corresponding per-protocol results were: OS HR = 0.59 (p = 0.054), and DFS HR = 0.56 (p = 0.007). END was effective for small tumours. END patients experienced more facial/neck nerve damage; QoL was largely unaffected. The observational cohort supported the randomised findings. The meta-analysis produced HR OS 0.64 and DFS 0.54 (p < 0.001). CONCLUSION SEND and the cumulative evidence show that within a generalisable setting oral cancer patients who have an upfront END have a lower risk of death/recurrence, even with small tumours. CLINICAL TRIAL REGISTRATION NIHR UK Clinical Research Network database ID number: UKCRN 2069 (registered on 17/02/2006), ISCRTN number: 65018995, ClinicalTrials.gov Identifier: NCT00571883.
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Affiliation(s)
- Iain L Hutchison
- Barts Health NHS Trust, London, UK.
- Saving Faces-The Facial Surgery Research Foundation, London, UK.
| | - Fran Ridout
- Saving Faces-The Facial Surgery Research Foundation, London, UK
| | | | - Neil Shah
- Barking, Havering and Redbridge University Hospitals NHS Trust, Romford, UK
| | | | | | | | | | | | | | | | - Richard J Shaw
- Aintree University Hospital NHS Foundation Trust, Liverpool, UK
| | | | - Martin Danford
- Royal Surrey County Hospital NHS Foundation Trust, Guildford, UK
| | | | - Graham Smith
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Malcolm W Bailey
- Royal Surrey County Hospital NHS Foundation Trust, Guildford, UK
| | | | - Manu Patel
- University Hospital of South Manchester NHS Foundation Trust, Manchester, UK
| | | | - Chi-Hwa Chan
- Luton and Dunstable Hospital NHS Foundation Trust, Luton, UK
| | - Andrew Burns
- City Hospitals Sunderland NHS Foundation Trust, Sunderland, UK
| | - Prav Praveen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Chris Avery
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Graham Putnam
- North Cumbria University Hospitals NHS Trust, Carlisle, UK
| | - Keith Jones
- Derby Teaching Hospitals NHS Foundation Trust, Derby, UK
| | - Keith Webster
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Colin Edge
- South Tees Hospitals NHS Foundation Trust, Middlesbrough, UK
| | - Iain McVicar
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Nick Grew
- The Royal Wolverhampton NHS Trust, Wolverhampton, UK
| | | | | | - Ian C Martin
- City Hospitals Sunderland NHS Foundation Trust, Sunderland, UK
| | - Allan Hackshaw
- University College London, Cancer Research UK & UCL Cancer Trials Centre, London, UK
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17
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Collier MP, Alderson TR, de Villiers CP, Nicholls D, Gastall HY, Allison TM, Degiacomi MT, Jiang H, Mlynek G, Fürst DO, van der Ven PFM, Djinovic-Carugo K, Baldwin AJ, Watkins H, Gehmlich K, Benesch JLP. HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C. Sci Adv 2019; 5:eaav8421. [PMID: 31131323 PMCID: PMC6530996 DOI: 10.1126/sciadv.aav8421] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/16/2019] [Indexed: 05/13/2023]
Abstract
Mechanical force-induced conformational changes in proteins underpin a variety of physiological functions, typified in muscle contractile machinery. Mutations in the actin-binding protein filamin C (FLNC) are linked to musculoskeletal pathologies characterized by altered biomechanical properties and sometimes aggregates. HspB1, an abundant molecular chaperone, is prevalent in striated muscle where it is phosphorylated in response to cues including mechanical stress. We report the interaction and up-regulation of both proteins in three mouse models of biomechanical stress, with HspB1 being phosphorylated and FLNC being localized to load-bearing sites. We show how phosphorylation leads to increased exposure of the residues surrounding the HspB1 phosphosite, facilitating their binding to a compact multidomain region of FLNC proposed to have mechanosensing functions. Steered unfolding of FLNC reveals that its extension trajectory is modulated by the phosphorylated region of HspB1. This may represent a posttranslationally regulated chaperone-client protection mechanism targeting over-extension during mechanical stress.
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Affiliation(s)
- Miranda P. Collier
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - T. Reid Alderson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Carin P. de Villiers
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Headington, Oxford OX3 9DU, UK
| | - Daisy Nicholls
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Heidi Y. Gastall
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Timothy M. Allison
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matteo T. Degiacomi
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - He Jiang
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Headington, Oxford OX3 9DU, UK
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Dieter O. Fürst
- Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, D53121 Bonn, Germany
| | - Peter F. M. van der Ven
- Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, D53121 Bonn, Germany
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Andrew J. Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Headington, Oxford OX3 9DU, UK
| | - Katja Gehmlich
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence Oxford, University of Oxford, Headington, Oxford OX3 9DU, UK
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Corresponding author. (J.L.P.B.); (K.G.)
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- Corresponding author. (J.L.P.B.); (K.G.)
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18
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Karunanithy G, Wheeler RJ, Tear LR, Farrer NJ, Faulkner S, Baldwin AJ. INDIANA: An in-cell diffusion method to characterize the size, abundance and permeability of cells. J Magn Reson 2019; 302:1-13. [PMID: 30904779 PMCID: PMC7611012 DOI: 10.1016/j.jmr.2018.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 05/13/2023]
Abstract
NMR and MRI diffusion experiments contain information describing the shape, size, abundance, and membrane permeability of cells although extracting this information can be challenging. Here we present the INDIANA (IN-cell DIffusion ANAlysis) method to simultaneously and non-invasively measure cell abundance, effective radius, permeability and intrinsic relaxation rates and diffusion coefficients within the inter- and intra-cellular populations. The method couples an experimental dataset comprising stimulated-echo diffusion measurements, varying both the gradient strength and the diffusion delay, together with software to fit a model based on the Kärger equations to robustly extract the relevant parameters. A detailed error analysis is presented by comparing the results from fitting simulated data from Monte Carlo simulations, establishing its effectiveness. We note that for parameters typical of mammalian cells the approach is particularly effective, and the shape of the underlying cells does not unduly affect the results. Finally, we demonstrate the performance of the experiment on systems of suspended yeast and mammalian cells. The extracted parameters describing cell abundance, size, permeability and relaxation are independently validated.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Richard J Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Louise R Tear
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Nicola J Farrer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Stephen Faulkner
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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19
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Yuwen T, Sekhar A, Baldwin AJ, Vallurupalli P, Kay LE. Measuring Diffusion Constants of Invisible Protein Conformers by Triple‐Quantum
1
H CPMG Relaxation Dispersion. Angew Chem Int Ed Engl 2018; 57:16777-16780. [DOI: 10.1002/anie.201810868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and ChemistryUniversity of Toronto Toronto Ontario M5S 1A8 Canada
| | - Ashok Sekhar
- Molecular Biophysics UnitIndian Institute of Science Bangalore Karnataka 560012 India
| | - Andrew J. Baldwin
- Physical and Theoretical Chemistry LaboratoryUniversity of Oxford Oxford OX1 3QZ UK
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad Telangana 500107 India
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and ChemistryUniversity of Toronto Toronto Ontario M5S 1A8 Canada
- Program in Molecular MedicineHospital for Sick Children 555 University Avenue Toronto Ontario M5G 1X8 Canada
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20
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Yuwen T, Sekhar A, Baldwin AJ, Vallurupalli P, Kay LE. Measuring Diffusion Constants of Invisible Protein Conformers by Triple‐Quantum
1
H CPMG Relaxation Dispersion. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and ChemistryUniversity of Toronto Toronto Ontario M5S 1A8 Canada
| | - Ashok Sekhar
- Molecular Biophysics UnitIndian Institute of Science Bangalore Karnataka 560012 India
| | - Andrew J. Baldwin
- Physical and Theoretical Chemistry LaboratoryUniversity of Oxford Oxford OX1 3QZ UK
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad Telangana 500107 India
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and ChemistryUniversity of Toronto Toronto Ontario M5S 1A8 Canada
- Program in Molecular MedicineHospital for Sick Children 555 University Avenue Toronto Ontario M5G 1X8 Canada
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21
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Kim SY, Morgan LA, Baldwin AJ, Suh DW. Comparison of the characteristics of retinal hemorrhages in abusive head trauma versus normal vaginal delivery. J AAPOS 2018; 22:139-144. [PMID: 29548839 DOI: 10.1016/j.jaapos.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 12/06/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Retinal hemorrhage (RH) is one of the hallmarks of abusive head trauma (AHT); however, RH is also encountered with normal vaginal deliveries (NVD) and thus presents the clinician with a diagnostic dilemma. The purpose of this study was to compare RHs in AHT with those of NVD. METHODS Records of with AHT and NVD infants with RH evaluated from 2013 to 2015 were reviewed retrospectively. Pattern, size, extent, and severity were compared using RetCam images. Severities were calculated using the RH grading scale. RESULTS A total of 20 patients with AHT and 200 NVD infants were included. RH size was significantly larger in AHT patients compared to the NVD group (3.1 ± 0.512 vs 0.96 ± 0.046 disk diameters, resp.). The AHT group also demonstrated a higher RH incidence involving all three retinal layers compared to the NVD group (60% vs 0.6%, resp. [P < 0.001]). Vitreous hemorrhages were more common in the AHT group compared to the NVD group (54.3% vs 1.5% [P < 0.001]). Also, the grading scale demonstrated higher scores in the AHT group than the NVD group (7.15 ± 0.948 vs 3.59 ± 0.274, resp.). CONCLUSIONS AHT and NVD share similar retinal findings, but they also have unique differentiators. In our subjects, AHT presented with more severe retinal findings than NVD, including larger RH size, a higher percentage involving all three retinal layers, a higher percentage of vitreous hemorrhages, and higher RH grading scale scores. Also, NVD retinal hemorrhages resolved quickly, within 4 weeks of birth in 95% of the patients.
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Affiliation(s)
- So Young Kim
- Children's Hospital and Medical Center, Omaha, Nebraska
| | - Linda A Morgan
- Children's Hospital and Medical Center, Omaha, Nebraska.
| | | | - Donny W Suh
- Children's Hospital and Medical Center, Omaha, Nebraska; University of Nebraska Medical Center, Omaha, Nebraska
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22
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Hochberg GKA, Shepherd DA, Marklund EG, Santhanagoplan I, Degiacomi MT, Laganowsky A, Allison TM, Basha E, Marty MT, Galpin MR, Struwe WB, Baldwin AJ, Vierling E, Benesch JLP. Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science 2018; 359:930-935. [PMID: 29472485 PMCID: PMC6587588 DOI: 10.1126/science.aam7229] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 09/25/2017] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
Oligomeric proteins assemble with exceptional selectivity, even in the presence of closely related proteins, to perform their cellular roles. We show that most proteins related by gene duplication of an oligomeric ancestor have evolved to avoid hetero-oligomerization and that this correlates with their acquisition of distinct functions. We report how coassembly is avoided by two oligomeric small heat-shock protein paralogs. A hierarchy of assembly, involving intermediates that are populated only fleetingly at equilibrium, ensures selective oligomerization. Conformational flexibility at noninterfacial regions in the monomers prevents coassembly, allowing interfaces to remain largely conserved. Homomeric oligomers must overcome the entropic benefit of coassembly and, accordingly, homomeric paralogs comprise fewer subunits than homomers that have no paralogs.
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Affiliation(s)
- Georg K A Hochberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dale A Shepherd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Erik G Marklund
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Indu Santhanagoplan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Matteo T Degiacomi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Arthur Laganowsky
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Timothy M Allison
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Eman Basha
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Marty
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Martin R Galpin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
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23
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Imiołek M, Karunanithy G, Ng WL, Baldwin AJ, Gouverneur V, Davis BG. Selective Radical Trifluoromethylation of Native Residues in Proteins. J Am Chem Soc 2018; 140:1568-1571. [PMID: 29301396 PMCID: PMC5806083 DOI: 10.1021/jacs.7b10230] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/20/2022]
Abstract
The incorporation of fluorine can not only significantly facilitate the study of proteins but also potentially modulate their function. Though some biosynthetic methods allow global residue-replacement, post-translational fluorine incorporation would constitute a fast and efficient alternative. Here, we reveal a mild method for direct protein radical trifluoromethylation at native residues as a strategy for symmetric-multifluorine incorporation on mg scales with high recoveries. High selectivity toward tryptophan residues enhanced the utility of this direct trifluoromethylation technique allowing ready study of fluorinated protein constructs using 19F-NMR.
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Affiliation(s)
- Mateusz Imiołek
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Gogulan Karunanithy
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Wai-Lung Ng
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Andrew J. Baldwin
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Véronique Gouverneur
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Benjamin G. Davis
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
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24
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Brady JP, Farber PJ, Sekhar A, Lin YH, Huang R, Bah A, Nott TJ, Chan HS, Baldwin AJ, Forman-Kay JD, Kay LE. Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation. Proc Natl Acad Sci U S A 2017; 114:E8194-E8203. [PMID: 28894006 PMCID: PMC5625912 DOI: 10.1073/pnas.1706197114] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Membrane encapsulation is frequently used by the cell to sequester biomolecules and compartmentalize their function. Cells also concentrate molecules into phase-separated protein or protein/nucleic acid "membraneless organelles" that regulate a host of biochemical processes. Here, we use solution NMR spectroscopy to study phase-separated droplets formed from the intrinsically disordered N-terminal 236 residues of the germ-granule protein Ddx4. We show that the protein within the concentrated phase of phase-separated Ddx4, [Formula: see text], diffuses as a particle of 600-nm hydrodynamic radius dissolved in water. However, NMR spectra reveal sharp resonances with chemical shifts showing [Formula: see text] to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of [Formula: see text] have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions. The diffusion of a series of small probes and the compact but disordered 4E binding protein 2 (4E-BP2) protein in [Formula: see text] are explained by an excluded volume effect, similar to that found for globular protein solvents. No changes in structural propensities of 4E-BP2 dissolved in [Formula: see text] are observed, while changes to DNA and RNA molecules have been reported, highlighting the diverse roles that proteinaceous solvents play in dictating the properties of dissolved solutes.
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Affiliation(s)
- Jacob P Brady
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Patrick J Farber
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Ashok Sekhar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Rui Huang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Alaji Bah
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Timothy J Nott
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Hue Sun Chan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Julie D Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8;
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8;
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
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25
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Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, AB E, Siegal G, Baldwin AJ. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. J Am Chem Soc 2017; 139:9523-9533. [DOI: 10.1021/jacs.6b11358] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iva Pritišanac
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Matteo T. Degiacomi
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - T. Reid Alderson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Marta G. Carneiro
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Eiso AB
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Gregg Siegal
- ZoBio BV, BioPartner 2 building,
J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Andrew J. Baldwin
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
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26
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Alderson TR, Benesch JLP, Baldwin AJ. Proline isomerization in the C-terminal region of HSP27. Cell Stress Chaperones 2017; 22:639-651. [PMID: 28547731 PMCID: PMC5465039 DOI: 10.1007/s12192-017-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022] Open
Abstract
In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond. The cis-P194 state is populated to near 15% at physiological temperatures, and, although both cis- and trans-P194 forms of the CTR are flexible and dynamic, both states show a residual but differing tendency to adopt β-strand conformations. In NMR spectra of an isolated CTR peptide, we observed similar evidence for isomerization involving proline 182, found within the IPI/V motif. Collectively, these data indicate a potential role for cis-trans proline isomerization in regulating the oligomerization of sHSPs.
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Affiliation(s)
- T Reid Alderson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin L P Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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27
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Leung RC, Robinson MDM, Ajabali AAA, Karunanithy G, Lyons B, Raj R, Raoufmoghaddam S, Mohammed S, Claridge TDW, Baldwin AJ, Davis BG. Monitoring the Disassembly of Virus-like Particles by 19F-NMR. J Am Chem Soc 2017; 139:5277-5280. [PMID: 28350443 PMCID: PMC5425944 DOI: 10.1021/jacs.6b11040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 12/12/2022]
Abstract
Virus-like particles (VLPs) are stable protein cages derived from virus coats. They have been used extensively as biomolecular platforms, e.g., nanocarriers or vaccines, but a convenient in situ technique is lacking for tracking functional status. Here, we present a simple way to monitor disassembly of 19F-labeled VLPs derived from bacteriophage Qβ by 19F NMR. Analysis of resonances, under a range of conditions, allowed determination not only of the particle as fully assembled but also as disassembled, as well as detection of a degraded state upon digestion by cells. This in turn allowed mutational redesign of disassembly and testing in both bacterial and mammalian systems as a strategy for the creation of putative, targeted-VLP delivery systems.
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Affiliation(s)
| | | | - Alaa A. A. Ajabali
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Gogulan Karunanithy
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Brian Lyons
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Ritu Raj
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Saeed Raoufmoghaddam
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Shabaz Mohammed
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Andrew J. Baldwin
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Benjamin G. Davis
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
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28
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Ray KJ, Larkin JR, Tee YK, Khrapitchev AA, Karunanithy G, Barber M, Baldwin AJ, Chappell MA, Sibson NR. Determination of an optimally sensitive and specific chemical exchange saturation transfer MRI quantification metric in relevant biological phantoms. NMR Biomed 2016; 29:1624-1633. [PMID: 27686882 PMCID: PMC5095597 DOI: 10.1002/nbm.3614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 05/08/2023]
Abstract
The purpose of this study was to develop realistic phantom models of the intracellular environment of metastatic breast tumour and naïve brain, and using these models determine an analysis metric for quantification of CEST MRI data that is sensitive to only labile proton exchange rate and concentration. The ability of the optimal metric to quantify pH differences in the phantoms was also evaluated. Novel phantom models were produced, by adding perchloric acid extracts of either metastatic mouse breast carcinoma cells or healthy mouse brain to bovine serum albumin. The phantom model was validated using 1 H NMR spectroscopy, then utilized to determine the sensitivity of CEST MRI to changes in pH, labile proton concentration, T1 time and T2 time; six different CEST MRI analysis metrics (MTRasym , APT*, MTRRex , AREX and CESTR* with and without T1 /T2 compensation) were compared. The new phantom models were highly representative of the in vivo intracellular environment of both tumour and brain tissue. Of the analysis methods compared, CESTR* with T1 and T2 time compensation was optimally specific to changes in the CEST effect (i.e. minimal contamination from T1 or T2 variation). In phantoms with identical protein concentrations, pH differences between phantoms could be quantified with a mean accuracy of 0.6 pH units. We propose that CESTR* with T1 and T2 time compensation is the optimal analysis method for these phantoms. Analysis of CEST MRI data with T1 /T2 time compensated CESTR* is reproducible between phantoms, and its application in vivo may resolve the intracellular alkalosis associated with breast cancer brain metastases without the need for exogenous contrast agents.
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Affiliation(s)
- Kevin J Ray
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7LE, UK
| | - James R Larkin
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7LE, UK
| | - Yee K Tee
- Department of Mechatronics and Biomedical Engineering, Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Malaysia
| | - Alexandre A Khrapitchev
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7LE, UK
| | - Gogulan Karunanithy
- Physical and Theoretical Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
| | - Michael Barber
- Physical and Theoretical Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
| | - Michael A Chappell
- Institute for Biomedical Engineering, University of Oxford, Oxford, OX3 7LE, UK
| | - Nicola R Sibson
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7LE, UK.
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29
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Wright TH, Bower BJ, Chalker JM, Bernardes GJL, Wiewiora R, Ng WL, Raj R, Faulkner S, Vallée MRJ, Phanumartwiwath A, Coleman OD, Thézénas ML, Khan M, Galan SRG, Lercher L, Schombs MW, Gerstberger S, Palm-Espling ME, Baldwin AJ, Kessler BM, Claridge TDW, Mohammed S, Davis BG. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity. Science 2016; 354:science.aag1465. [PMID: 27708059 DOI: 10.1126/science.aag1465] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/12/2016] [Indexed: 12/26/2022]
Abstract
Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically plausible (including unnatural but functionally relevant) side chains is not readily accessible. We describe C (sp3)-C (sp3) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free-radical chemistry, and use them to form Cβ-Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide diversity of natural, unnatural, posttranslationally modified (methylated, glycosylated, phosphorylated, hydroxylated), and labeled (fluorinated, isotopically labeled) side chains to be added to a common, readily accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for access to diverse proteins.
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Affiliation(s)
- Tom H Wright
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ben J Bower
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Justin M Chalker
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Rafal Wiewiora
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Wai-Lung Ng
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ritu Raj
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Sarah Faulkner
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | - Oliver D Coleman
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Marie-Laëtitia Thézénas
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | - Maola Khan
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Lukas Lercher
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | | | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
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Nott TJ, Craggs TD, Baldwin AJ. Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters. Nat Chem 2016; 8:569-75. [PMID: 27219701 DOI: 10.1038/nchem.2519] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/21/2016] [Indexed: 12/26/2022]
Abstract
Membraneless organelles are cellular compartments made from drops of liquid protein inside a cell. These compartments assemble via the phase separation of disordered regions of proteins in response to changes in the cellular environment and the cell cycle. Here we demonstrate that the solvent environment within the interior of these cellular bodies behaves more like an organic solvent than like water. One of the most-stable biological structures known, the DNA double helix, can be melted once inside the liquid droplet, and simultaneously structures formed from regulatory single-stranded nucleic acids are stabilized. Moreover, proteins are shown to have a wide range of absorption or exclusion from these bodies, and can act as importers for otherwise-excluded nucleic acids, which suggests the existence of a protein-mediated trafficking system. A common strategy in organic chemistry is to utilize different solvents to influence the behaviour of molecules and reactions. These results reveal that cells have also evolved this capability by exploiting the interiors of membraneless organelles.
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Affiliation(s)
- Timothy J Nott
- Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Timothy D Craggs
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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Sarwar S, Clearfield E, Soliman MK, Sadiq MA, Baldwin AJ, Hanout M, Agarwal A, Sepah YJ, Do DV, Nguyen QD. Aflibercept for neovascular age-related macular degeneration. Cochrane Database Syst Rev 2016; 2:CD011346. [PMID: 26857947 PMCID: PMC5030844 DOI: 10.1002/14651858.cd011346.pub2] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Central vision loss caused by age-related macular degeneration (AMD) is the leading cause of blindness among the elderly in developed countries. Neovascular AMD is characterized by choroidal neovascularization (CNV). Growth of new blood vessels in patients with neovascular AMD is driven by a complex process that involves a signal protein called vascular endothelial growth factor A (VEGF-A). Anti-VEGF drugs that block this protein include ranibizumab, bevacizumab, and aflibercept. OBJECTIVES To assess and compare the effectiveness and safety of intravitreal injections of aflibercept versus ranibizumab, bevacizumab, or sham for treatment of patients with neovascular AMD. SEARCH METHODS We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (which contains the Cochrane Eyes and Vision Trials Register) (Issue 11, 2015), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE (January 1946 to November 2015), EMBASE (January 1980 to November 2015), PubMed (1948 to November 2015), Latin American and Caribbean Health Sciences Literature Database (LILACS) (1982 to November 2015), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com) (last searched December 4, 2014), ClinicalTrials.gov (www.clinicaltrials.gov), and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic search for trials. We last searched the electronic databases on November 30, 2015. SELECTION CRITERIA We included randomized controlled trials (RCTs) in which aflibercept monotherapy was compared with ranibizumab, bevacizumab, or sham for participants with neovascular AMD who were treatment-naive. DATA COLLECTION AND ANALYSIS We used standard methodological procedures of The Cochrane Collaboration for screening, data abstraction, and study assessment. Two review authors independently screened records, abstracted data, and assessed risk of bias of included studies; we resolved discrepancies by discussion or with the help of a third review author when needed. MAIN RESULTS We included two RCTs (total of 2457 participants, 2457 eyes). Trial participants had neovascular AMD with active subfoveal choroidal neovascular lesions. Both trials followed the same protocol and compared aflibercept at various doses versus ranibizumab, but they were carried out in different countries. One trial enrolled participants from the United States and Canada, and the second trial was conducted at 172 sites in Europe, Asia Pacific, Latin America, and the Middle East. The overall quality of the evidence was high, and included trials were at low risk for most bias domains assessed; however, both trials were funded by the manufacturers of aflibercept. For the purposes of analysis, we combined aflibercept groups regardless of dosing and analyzed them as a single group.Visual acuity outcomes were similar between aflibercept and ranibizumab groups; at one year, participants in the aflibercept groups showed mean change in best-corrected visual acuity (BCVA) from baseline similar to that of participants in the ranibizumab groups (mean difference (MD) -0.15 Early Treatment Diabetic Retinopathy Study (ETDRS) letters, 95% confidence interval (95% CI) -1.47 to 1.17; high-quality evidence). At two years, the mean change in BCVA from baseline was 7.2 ETDRS letters for aflibercept groups versus 7.9 for ranibizumab groups. Sufficient data were not available for calculation of confidence intervals.The proportion of participants who gained 15 or more letters of BCVA by one year of follow-up was approximately 32% for both aflibercept and ranibizumab (RR 0.97, 95% CI 0.85 to 1.11; high-quality evidence), and by two years of follow-up was approximately 31% (RR 0.98, 95% CI 0.85 to 1.12; high-quality evidence). Similar small proportions of participants in the aflibercept and ranibizumab groups lost 15 or more letters of BCVA at one year (RR 0.89, 95% CI 0.61 to 1.30; high-quality evidence); this outcome was not reported for two-year follow-up. Data were not reported on the proportion of participants with BCVA worse than 20/200 at one- or two-year follow-up.Participants treated with aflibercept or ranibizumab showed similar improvement in morphological outcomes, as assessed from images (central retinal thickness and CNV size). At one year, the proportion of eyes that achieved dry retina was similar between aflibercept and ranibizumab groups (absence of cystic intraretinal fluid and subretinal fluid on optical coherence tomography (OCT); RR 1.06, 95% CI 0.98 to 1.14; high-quality evidence). In addition, investigators reported no difference in reduction of CNV area between aflibercept- and ranibizumab-treated eyes at one year (MD -0.24 mm(2), 95% CI -0.78 to 0.29; high-quality evidence). Data were not reported for the proportion of eyes with absence of leakage on fluorescein angiography at one- or two-year follow-up.Overall, occurrence of serious systemic adverse events was similar and comparable in aflibercept- and ranibizumab-treated groups at one year (RR 0.99, 95% CI 0.79 to 1.25). Risk of any serious ocular adverse event was lower in the aflibercept group than in the ranibizumab group, but the risk estimate is imprecise (RR 0.62, 95% CI 0.36 to 1.07). As the result of imprecision, we graded the quality of evidence for all adverse events as moderate. AUTHORS' CONCLUSIONS Results of this review document the comparative effectiveness of aflibercept versus ranibizumab for visual acuity and morphological outcomes in eyes with neovascular AMD. Current available information on adverse effects of each medication suggests that the safety profile of aflibercept is comparable with that of ranibizumab; however, the number of participants who experienced adverse events was small, leading to imprecise estimates of absolute and relative effect sizes. The eight-week dosing regimen of aflibercept represents reduced treatment requirements in comparison with monthly dosing regimens and thus has the potential to reduce treatment burden and risks associated with frequent injections.
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Affiliation(s)
- Salman Sarwar
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Elizabeth Clearfield
- Johns Hopkins Bloomberg School of Public HealthDepartment of Epidemiology615 N. Wolfe StreetRoom 6014BaltimoreMarylandUSA21205
| | - Mohamed Kamel Soliman
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Mohammad Ali Sadiq
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Andrew J Baldwin
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Mostafa Hanout
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Aniruddha Agarwal
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Yasir J Sepah
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Diana V Do
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
| | - Quan Dong Nguyen
- University of Nebraska Medical CenterStanley M. Truhlsen Eye Institute3902 Leavenworth StreetOmahaNebraskaUSA68105
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Karunanithy G, Cnossen A, Müller H, Peeks MD, Rees NH, Claridge TDW, Anderson HL, Baldwin AJ. Harnessing NMR relaxation interference effects to characterise supramolecular assemblies. Chem Commun (Camb) 2016; 52:7450-3. [DOI: 10.1039/c6cc02544g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Supramolecular assemblies can show unusual splitting patterns in their NMR spectra, with the magnitude of the effect increasing with molecular size. A simple NMR relaxation experiment reveals the origin of the effect and provides information on tumbling rates and local electronic structure.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Chemistry
- University of Oxford
- Physical and Theoretical Chemistry Laboratory
- Oxford
- UK
| | - Arjen Cnossen
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Henrik Müller
- Department of Chemistry
- University of Oxford
- Physical and Theoretical Chemistry Laboratory
- Oxford
- UK
| | - Martin D. Peeks
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Nicholas H. Rees
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | | | - Harry L. Anderson
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Andrew J. Baldwin
- Department of Chemistry
- University of Oxford
- Physical and Theoretical Chemistry Laboratory
- Oxford
- UK
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33
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Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 2015; 57:936-947. [PMID: 25747659 PMCID: PMC4352761 DOI: 10.1016/j.molcel.2015.01.013] [Citation(s) in RCA: 1129] [Impact Index Per Article: 125.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/12/2014] [Accepted: 12/29/2014] [Indexed: 11/15/2022]
Abstract
Cells chemically isolate molecules in compartments to both facilitate and regulate their interactions. In addition to membrane-encapsulated compartments, cells can form proteinaceous and membraneless organelles, including nucleoli, Cajal and PML bodies, and stress granules. The principles that determine when and why these structures form have remained elusive. Here, we demonstrate that the disordered tails of Ddx4, a primary constituent of nuage or germ granules, form phase-separated organelles both in live cells and in vitro. These bodies are stabilized by patterned electrostatic interactions that are highly sensitive to temperature, ionic strength, arginine methylation, and splicing. Sequence determinants are used to identify proteins found in both membraneless organelles and cell adhesion. Moreover, the bodies provide an alternative solvent environment that can concentrate single-stranded DNA but largely exclude double-stranded DNA. We propose that phase separation of disordered proteins containing weakly interacting blocks is a general mechanism for forming regulated, membraneless organelles. Intrinsically disordered N terminus of Ddx4 forms organelles in cells and in vitro Phase transition to form organelles is driven by electrostatic interactions Methylation, ionic strength, and temperature changes can dissolve the organelles Sequence determinants of formation are common in membraneless organelle proteins
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Affiliation(s)
- Timothy J Nott
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Evangelia Petsalaki
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Patrick Farber
- Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Dylan Jervis
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, ON M5S 1A7, Canada
| | - Eden Fussner
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | | | - David P Bazett-Jones
- Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Julie D Forman-Kay
- Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
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34
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Baldwin AJ, Egan DL, Warren F, Barker PD, Dobson CM, Butterworth PJ, Ellis PR. Investigating the mechanisms of amylolysis of starch granules by solution-state NMR. Biomacromolecules 2015; 16:1614-21. [PMID: 25815624 PMCID: PMC4429494 DOI: 10.1021/acs.biomac.5b00190] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/26/2015] [Indexed: 11/30/2022]
Abstract
Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch.
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Affiliation(s)
- Andrew J. Baldwin
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Danielle L. Egan
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Fredrick
J. Warren
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Paul D. Barker
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Christopher M. Dobson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Peter J. Butterworth
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
| | - Peter R. Ellis
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United
Kingdom
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Marty MT, Baldwin AJ, Marklund EG, Hochberg GKA, Benesch JLP, Robinson CV. Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal Chem 2015; 87:4370-6. [PMID: 25799115 PMCID: PMC4594776 DOI: 10.1021/acs.analchem.5b00140] [Citation(s) in RCA: 546] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.
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Affiliation(s)
- Michael T. Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Andrew J. Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Erik G. Marklund
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Georg K. A. Hochberg
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
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Stelzl LS, Mavridou DA, Ferguson SJ, Baldwin AJ, Sansom MS, Redfield C. Studying the Conformational Equilibrium of the N-Terminal Domain of Dsbd by NMR and Computer Simulation. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.1017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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Baldwin AJ. An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange. J Magn Reson 2014; 244:114-24. [PMID: 24852115 PMCID: PMC4067747 DOI: 10.1016/j.jmr.2014.02.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 05/03/2023]
Abstract
The Carr-Purcell-Meiboom-Gill (CPMG) experiment is widely used to quantitatively analyse the effects of chemical exchange on NMR spectra. In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically measured as a function of the pulse frequency, νCPMG. Here, an exact expression for how R2,eff varies with νCPMG is derived for the commonly encountered scenario of two-site chemical exchange of in-phase magnetisation. This result, summarised in Appendix A, generalises a frequently used equation derived by Carver and Richards, published in 1972. The expression enables more rapid analysis of CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor of ca. 130, and yields exact derivatives for use in data analysis. Moreover, the derivation provides insight into the physical principles behind the experiment.
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Affiliation(s)
- Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
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Laganowsky A, Reading E, Allison TM, Ulmschneider MB, Degiacomi MT, Baldwin AJ, Robinson CV. Membrane proteins bind lipids selectively to modulate their structure and function. Nature 2014; 510:172-175. [PMID: 24899312 PMCID: PMC4087533 DOI: 10.1038/nature13419] [Citation(s) in RCA: 565] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/28/2014] [Indexed: 01/04/2023]
Abstract
Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding.
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Affiliation(s)
- Arthur Laganowsky
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Eamonn Reading
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Matteo T. Degiacomi
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Andrew J. Baldwin
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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Nott TJ, Farber P, Petsalakis E, Jervis D, Baldwin AJ, Forman-Kay JD. Phase Separation of Disordered Protein in the Formation of Membrane-Less Organelles. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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40
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Hilton GR, Hochberg GKA, Laganowsky A, McGinnigle SI, Baldwin AJ, Benesch JLP. C-terminal interactions mediate the quaternary dynamics of αB-crystallin. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110405. [PMID: 23530258 PMCID: PMC3638394 DOI: 10.1098/rstb.2011.0405] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
αB-crystallin is a highly dynamic, polydisperse small heat-shock protein that can form oligomers ranging in mass from 200 to 800 kDa. Here we use a multifaceted mass spectrometry approach to assess the role of the C-terminal tail in the self-assembly of αB-crystallin. Titration experiments allow us to monitor the binding of peptides representing the C-terminus to the αB-crystallin core domain, and observe individual affinities to both monomeric and dimeric forms. Notably, we find that binding the second peptide equivalent to the core domain dimer is considerably more difficult than the first, suggesting a role of the C-terminus in regulating assembly. This finding motivates us to examine the effect of point mutations in the C-terminus in the full-length protein, by quantifying the changes in oligomeric distribution and corresponding subunit exchange rates. Our results combine to demonstrate that alterations in the C-terminal tail have a significant impact on the thermodynamics and kinetics of αB-crystallin. Remarkably, we find that there is energy compensation between the inter- and intra-dimer interfaces: when one interaction is weakened, the other is strengthened. This allosteric communication between binding sites on αB-crystallin is likely important for its role in binding target proteins.
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Affiliation(s)
- Gillian R Hilton
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Baldwin AJ, Kay LE. An R(1ρ) expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates. J Biomol NMR 2013; 55:211-8. [PMID: 23340732 DOI: 10.1007/s10858-012-9694-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 12/06/2012] [Indexed: 05/22/2023]
Abstract
An analytical expression is derived for the rotating frame relaxation rate, R(1ρ), of a spin exchanging between two sites with different transverse relaxation times. A number of limiting cases are examined, with the equation reducing to formulae derived previously under the assumption of equivalent relaxation rates at each site. The measurement of a pair off-resonance R(1ρ) values, with the carrier displaced equally on either side of the observed correlation, forms the basis of one of the approaches for obtaining signs of chemical shift differences, Δω, of exchanging nuclei. The results presented here establish that this method is relatively insensitive to differential transverse relaxation rates between the exchaning states, greatly simplifying the calculation of optimal parameters in R(1ρ) based experiments that are used for measurement of signs of Δω.
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Affiliation(s)
- Andrew J Baldwin
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Abstract
The small heat-shock proteins (sHSPs) comprise a family of molecular chaperones which are widespread but poorly understood. Despite considerable effort, comparatively few high-resolution structures have been determined for the sHSPs, a likely consequence of their tendency to populate ensembles of inter-converting conformational and oligomeric states at equilibrium. This dynamic structure appears to underpin the sHSPs' ability to bind and sequester target proteins rapidly, and renders them the first line of defence against protein aggregation during disease and cellular stress. Here we describe recent studies on the sHSPs, with a particular focus on those which have provided insight into the structure and dynamics of these proteins. The combined literature reveals a picture of a remarkable family of molecular chaperones whose thermodynamic and kinetic properties are exquisitely balanced to allow functional regulation by subtle changes in cellular conditions.
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Baldwin AJ, Walsh P, Hansen DF, Hilton GR, Benesch JLP, Sharpe S, Kay LE. Probing Dynamic Conformations of the High-Molecular-Weight αB-Crystallin Heat Shock Protein Ensemble by NMR Spectroscopy. J Am Chem Soc 2012; 134:15343-50. [DOI: 10.1021/ja307874r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Baldwin
- Departments
of Molecular Genetics
and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8,
Canada
| | - Patrick Walsh
- Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8,
Canada
- Program in Molecular
Structure, Hospital for Sick Children,
555 University Avenue,
Toronto, Ontario M5G 1X8, Canada
| | - D. Flemming Hansen
- Departments
of Molecular Genetics
and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gillian R. Hilton
- Physical and Theoretical Chemistry
Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Justin L. P. Benesch
- Physical and Theoretical Chemistry
Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K
| | - Simon Sharpe
- Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8,
Canada
- Program in Molecular
Structure, Hospital for Sick Children,
555 University Avenue,
Toronto, Ontario M5G 1X8, Canada
| | - Lewis E. Kay
- Departments
of Molecular Genetics
and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, Ontario M5S 1A8,
Canada
- Program in Molecular
Structure, Hospital for Sick Children,
555 University Avenue,
Toronto, Ontario M5G 1X8, Canada
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Stengel F, Baldwin AJ, Bush MF, Hilton GR, Lioe H, Basha E, Jaya N, Vierling E, Benesch JL. Dissecting heterogeneous molecular chaperone complexes using a mass spectrum deconvolution approach. Chem Biol 2012; 19:599-607. [PMID: 22633411 PMCID: PMC3458707 DOI: 10.1016/j.chembiol.2012.04.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/02/2012] [Accepted: 04/06/2012] [Indexed: 11/30/2022]
Abstract
Small heat-shock proteins (sHSPs) are molecular chaperones that prevent irreversible aggregation through binding nonnative target proteins. Due to their heterogeneity, these sHSP:target complexes remain poorly understood. We present a nanoelectrospray mass spectrometry analysis algorithm for estimating the distribution of stoichiometries comprising a polydisperse ensemble of oligomers. We thus elucidate the organization of complexes formed between sHSPs and different target proteins. We find that binding is mass dependent, with the resultant complexes reflecting the native quaternary architecture of the target, indicating that protection happens early in the denaturation. Our data therefore explain the apparent paradox of how variable complex morphologies result from the generic mechanism of protection afforded by sHSPs. Our approach is applicable to a range of polydisperse proteins and provides a means for the automated and accurate interpretation of mass spectra derived from heterogeneous protein assemblies.
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Affiliation(s)
- Florian Stengel
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew J. Baldwin
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Matthew F. Bush
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Gillian R. Hilton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Hadi Lioe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Eman Basha
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, AZ, USA
| | - Nomalie Jaya
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, AZ, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Justin L.P. Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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Baldwin AJ, Kay LE. Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R(1ρ): an application to αB-crystallin. J Biomol NMR 2012; 53:1-12. [PMID: 22476760 DOI: 10.1007/s10858-012-9617-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/10/2012] [Indexed: 05/31/2023]
Abstract
Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible 'excited' conformational states. Recently it has also become possible to determine atomic resolution structural models of excited states using a wide array of CPMG RD approaches. Analysis of CPMG RD datasets provides the magnitudes of the chemical shift differences between the ground and excited states, Δϖ, but not the sign. In order to obtain detailed structural insights from, for example, excited state chemical shifts and residual dipolar coupling measurements, these signs are required. Here we present an NMR experiment for obtaining signs of (13)C chemical shift differences of (13)CH(3) methyl groups using weak field off-resonance R(1ρ) relaxation measurements. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering sample conditions so that the signs of Δϖ values obtained from the spin-lock approach can be validated against those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring signs of chemical shift differences and the relative strengths of each method are discussed. In the case of the 650 kDa human αB-crystallin complex where there are large transverse relaxation differences between ground and excited state spins the R(1ρ) method is shown to be superior to more 'traditional' experiments for sign determination.
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Affiliation(s)
- Andrew J Baldwin
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
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Baldwin AJ, Lioe H, Hilton GR, Baker LA, Rubinstein JL, Kay LE, Benesch JLP. The polydispersity of αB-crystallin is rationalized by an interconverting polyhedral architecture. Structure 2012; 19:1855-63. [PMID: 22153508 DOI: 10.1016/j.str.2011.09.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/15/2011] [Accepted: 09/17/2011] [Indexed: 01/30/2023]
Abstract
We report structural models for the most abundant oligomers populated by the polydisperse molecular chaperone αB-crystallin. Subunit connectivity is determined by using restraints obtained from nuclear magnetic resonance spectroscopy and mass spectrometry measurements, enabling the construction of various oligomeric models. These candidate structures are filtered according to their correspondence with ion-mobility spectrometry data and cross-validated by using electron microscopy. The ensuing best-fit structures reveal the polyhedral architecture of αB-crystallin oligomers, and provide a rationale for their polydispersity and facile interconversion.
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Affiliation(s)
- Andrew J Baldwin
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, ON M5S 1A8, Canada.
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Forman CJ, Nickson AA, Anthony-Cahill SJ, Baldwin AJ, Kaggwa G, Feber U, Sheikh K, Jarvis SP, Barker PD. The morphology of decorated amyloid fibers is controlled by the conformation and position of the displayed protein. ACS Nano 2012; 6:1332-1346. [PMID: 22276813 DOI: 10.1021/nn204140a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Self-assembled structures capable of mediating electron transfer are an attractive scientific and technological goal. Therefore, systematic variants of SH3-Cytochrome b(562) fusion proteins were designed to make amyloid fibers displaying heme-b(562) electron transfer complexes. TEM and AFM data show that fiber morphology responds systematically to placement of b(562) within the fusion proteins. UV-vis spectroscopy shows that, for the fusion proteins under test, only half the fiber-borne b(562) binds heme with high affinity. Cofactor binding also improves the AFM imaging properties and changes the fiber morphology through changes in cytochrome conformation. Systematic observations and measurements of fiber geometry suggest that longitudinal registry of subfilaments within the fiber, mediated by the interaction and conformation of the displayed proteins and their interaction with surfaces, gives rise to the observed morphologies, including defects and kinks. Of most interest is the role of small molecule modulation of fiber structure and mechanical stability. A minimum complexity model is proposed to capture and explain the fiber morphology in the light of these results. Understanding the complex interplay between these factors will enable a fiber design that supports longitudinal electron transfer.
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Affiliation(s)
- Christopher J Forman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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48
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Abstract
The small heat-shock proteins (sHSPs) comprise a family of molecular chaperones which are widespread but poorly understood. Despite considerable effort, comparatively few high-resolution structures have been determined for the sHSPs, a likely consequence of their tendency to populate ensembles of inter-converting conformational and oligomeric states at equilibrium. This dynamic structure appears to underpin the sHSPs' ability to bind and sequester target proteins rapidly, and renders them the first line of defence against protein aggregation during disease and cellular stress. Here we describe recent studies on the sHSPs, with a particular focus on those which have provided insight into the structure and dynamics of these proteins. The combined literature reveals a picture of a remarkable family of molecular chaperones whose thermodynamic and kinetic properties are exquisitely balanced to allow functional regulation by subtle changes in cellular conditions.
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49
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Baldwin AJ, Hilton GR, Lioe H, Bagnéris C, Benesch JL, Kay LE. Quaternary Dynamics of αB-Crystallin as a Direct Consequence of Localised Tertiary Fluctuations in the C-Terminus. J Mol Biol 2011; 413:310-20. [DOI: 10.1016/j.jmb.2011.07.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 07/08/2011] [Accepted: 07/11/2011] [Indexed: 11/16/2022]
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50
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Baldwin AJ, Lioe H, Robinson CV, Kay LE, Benesch JL. αB-Crystallin Polydispersity Is a Consequence of Unbiased Quaternary Dynamics. J Mol Biol 2011; 413:297-309. [DOI: 10.1016/j.jmb.2011.07.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 07/08/2011] [Accepted: 07/11/2011] [Indexed: 12/20/2022]
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