1
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Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM. Cross polarization stability in multidimensional NMR spectroscopy of biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107724. [PMID: 38991266 DOI: 10.1016/j.jmr.2024.107724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 07/13/2024]
Abstract
Magic-angle spinning (MAS) solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a powerful and versatile technique for probing structure and dynamics in large, insoluble biological systems at atomic resolution. With many recent advances in instrumentation and polarization methods, technology development in SSNMR remains an active area of research and presents opportunities to further improve data collection, processing, and analysis of samples with low sensitivity and complex tertiary and quaternary structures. SSNMR spectra are often collected as multidimensional data, requiring stable experimental conditions to minimize signal fluctuations (t1 noise). In this work, we examine the factors adversely affecting signal stability as well as strategies used to mitigate them, considering laboratory environmental requirements, configuration of amplifiers, and pulse sequence parameter selection. We show that Thermopad® temperature variable attenuators (TVAs) can partially compensate for the changes in amplifier output power as a function of temperature and thereby ameliorate one significant source of instability for some spectrometers and pulse sequences. We also consider the selection of tangent ramped cross polarization (CP) waveform shapes, to balance the requirements of sensitivity and instrumental stability. These findings collectively enable improved stability and overall performance for CP-based multidimensional spectra of microcrystalline, membrane, and fibrous proteins performed at multiple magnetic field strengths.
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Affiliation(s)
- Benjamin D Harding
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dennis W Piehl
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ashley Hiett
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Owen A Warmuth
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ruixian Han
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA; Morgridge Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706 USA.
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2
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Emmanouilidis L, Bartalucci E, Kan Y, Ijavi M, Pérez ME, Afanasyev P, Boehringer D, Zehnder J, Parekh SH, Bonn M, Michaels TCT, Wiegand T, Allain FHT. A solid beta-sheet structure is formed at the surface of FUS droplets during aging. Nat Chem Biol 2024; 20:1044-1052. [PMID: 38467846 PMCID: PMC11288893 DOI: 10.1038/s41589-024-01573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Phase transitions are important to understand cell dynamics, and the maturation of liquid droplets is relevant to neurodegenerative disorders. We combined NMR and Raman spectroscopies with microscopy to follow, over a period of days to months, droplet maturation of the protein fused in sarcoma (FUS). Our study reveals that the surface of the droplets plays a critical role in this process, while RNA binding prevents it. The maturation kinetics are faster in an agarose-stabilized biphasic sample compared with a monophasic condensed sample, owing to the larger surface-to-volume ratio. In addition, Raman spectroscopy reports structural differences upon maturation between the inside and the surface of droplets, which is comprised of β-sheet content, as revealed by solid-state NMR. In agreement with these observations, a solid crust-like shell is observed at the surface using microaspiration. Ultimately, matured droplets were converted into fibrils involving the prion-like domain as well as the first RGG motif.
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Affiliation(s)
- Leonidas Emmanouilidis
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
| | - Ettore Bartalucci
- Max Planck Institute for Chemical Energy Conversion, Mülheim/Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Yelena Kan
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mahdiye Ijavi
- Department of Materials, ETH Zurich, Zurich, Switzerland
| | - Maria Escura Pérez
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | | | - Johannes Zehnder
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sapun H Parekh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Mülheim/Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany.
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland.
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
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3
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Fonda BD, Kato M, Li Y, Murray DT. Cryo-EM and Solid State NMR Together Provide a More Comprehensive Structural Investigation of Protein Fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596698. [PMID: 38853912 PMCID: PMC11160737 DOI: 10.1101/2024.05.30.596698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.
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Affiliation(s)
- Blake D. Fonda
- Department of Chemistry, University of California, Davis, California, 95616, United States of America
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - Dylan T. Murray
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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4
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Cotten ML, Starich MR, He Y, Yin J, Yuan Q, Tjandra N. NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10178-2. [PMID: 38822991 DOI: 10.1007/s12104-024-10178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
The odorant binding protein, OBP44a is one of the most abundant proteins expressed in the brain of the developing fruit fly Drosophila melanogaster. Its cellular function has not yet been determined. The OBP family of proteins is well established to recognize hydrophobic molecules. In this study, NMR is employed to structurally characterize OBP44a. NMR chemical shift perturbation measurements confirm that OBP44a binds to fatty acids. Complete assignments of the backbone chemical shifts and secondary chemical shift analysis demonstrate that the apo state of OBP44a is comprised of six α-helices. Upon binding 8(Z)-eicosenoic acid (8(Z)-C20:1), the OBP44a C-terminal region undergoes a conformational change, from unstructured to α-helical. In addition to C-terminal restructuring upon ligand binding, some hydrophobic residues show dramatic chemical shift changes. Surprisingly, several charged residues are also strongly affected by lipid binding. Some of these residues could represent key structural features that OBP44a relies on to perform its cellular function. The NMR chemical shift assignment is the first step towards characterizing the structure of OBP44a and how specific residues might play a role in lipid binding and release. This information will be important in deciphering the biological function of OBP44a during fly brain development.
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Affiliation(s)
- Myriam L Cotten
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Mary R Starich
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi He
- Fermentation Facility, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jun Yin
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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5
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Ludzia P, Hayashi H, Robinson T, Akiyoshi B, Redfield C. NMR study of the structure and dynamics of the BRCT domain from the kinetochore protein KKT4. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:15-25. [PMID: 38453826 PMCID: PMC11081923 DOI: 10.1007/s12104-024-10163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/18/2024] [Indexed: 03/09/2024]
Abstract
KKT4 is a multi-domain kinetochore protein specific to kinetoplastids, such as Trypanosoma brucei. It lacks significant sequence similarity to known kinetochore proteins in other eukaryotes. Our recent X-ray structure of the C-terminal region of KKT4 shows that it has a tandem BRCT (BRCA1 C Terminus) domain fold with a sulfate ion bound in a typical binding site for a phosphorylated serine or threonine. Here we present the 1H, 13C and 15N resonance assignments for the BRCT domain of KKT4 (KKT4463-645) from T. brucei. We show that the BRCT domain can bind phosphate ions in solution using residues involved in sulfate ion binding in the X-ray structure. We have used these assignments to characterise the secondary structure and backbone dynamics of the BRCT domain in solution. Mutating the residues involved in phosphate ion binding in T. brucei KKT4 BRCT results in growth defects confirming the importance of the BRCT phosphopeptide-binding activity in vivo. These results may facilitate rational drug design efforts in the future to combat diseases caused by kinetoplastid parasites.
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Affiliation(s)
- Patryk Ludzia
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hanako Hayashi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Timothy Robinson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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6
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Asakura T, Shimokawatoko H, Nakazawa Y. Characterization and promotion of endothelialization of Bombyx mori silk fibroin functionalized with REDV peptide. Int J Biol Macromol 2024; 261:129746. [PMID: 38302025 DOI: 10.1016/j.ijbiomac.2024.129746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
In the development of small-diameter vascular grafts, it is crucial to achieve early-stage endothelialization to prevent thrombus formation and intimal hyperplasia. Silk fibroin (SF) from Bombyx mori is commonly used for such grafts. However, there is a need to expedite endothelialization post-implantation. In this study, we functionalized SF with Arg-Glu-Asp-Val (REDV) (SF + REDV) using cyanuric chloride to enhance endothelialization. The immobilization of REDV onto SF was confirmed and the amount of immobilized REDV could be calculated by 1H NMR. Furthermore, the conformational changes in Tyr, Ser, and Ala residues in [3-13C]Tyr- and [3-13C]Ser-SF due to REDV immobilization were monitored using 13C solid-state NMR. The REDV immobilized onto the SF film was found to be exposed on the film's surface, as confirmed by biotin-avidin system. Cell culture experiments, including adhesiveness, proliferation, and extensibility, were conducted using normal human umbilical vein endothelial cells (HUVEC) and normal human aortic smooth muscle cells (HAoSMC) on both SF and SF + REDV films to evaluate the impact of REDV on endothelialization. The results indicated a trend towards promoting HUVEC proliferation while inhibiting HAoSMC proliferation. Therefore, these findings suggest that SF + REDV may be more suitable than SF alone for coating small-diameter SF knitted tubes made of SF threads.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan.
| | - Haruka Shimokawatoko
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yasumoto Nakazawa
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
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7
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Wilson CB, Yau WM, Tycko R. Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein. PHYSICAL REVIEW LETTERS 2024; 132:048402. [PMID: 38335342 DOI: 10.1103/physrevlett.132.048402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/27/2023] [Indexed: 02/12/2024]
Abstract
Prior work has shown that small proteins can fold (i.e., convert from unstructured to structured states) within 10 μs. Here we use time-resolved solid state nuclear magnetic resonance (ssNMR) methods to show that full folding of the 35-residue villin headpiece subdomain (HP35) requires a slow annealing process that has not been previously detected. ^{13}C ssNMR spectra of frozen HP35 solutions, acquired with a variable time τ_{e} at 30 °C after rapid cooling from 95 °C and before rapid freezing, show changes on the 3-10 ms timescale, attributable to slow rearrangements of protein sidechains during τ_{e}.
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Affiliation(s)
- C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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8
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Medeiros-Silva J, Dregni AJ, Hong M. Distinguishing Different Hydrogen-Bonded Helices in Proteins by Efficient 1H-Detected Three-Dimensional Solid-State NMR. Biochemistry 2024; 63:181-190. [PMID: 38127783 PMCID: PMC10880114 DOI: 10.1021/acs.biochem.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Helical structures in proteins include not only α-helices but also 310 and π helices. These secondary structures differ in the registry of the C═O···H-N hydrogen bonds, which are i to i + 4 for α-helices, i to i + 3 for 310 helices, and i to i + 5 for π-helices. The standard NMR observable of protein secondary structures are chemical shifts, which are, however, insensitive to the precise type of helices. Here, we introduce a three-dimensional (3D) 1H-detected experiment that measures and assigns CO-HN cross-peaks to distinguish the different types of hydrogen-bonded helices. This hCOhNH experiment combines efficient cross-polarization from CO to HN with 13C, 15N, and 1H chemical shift correlation to detect the relative proximities of the COi-Hi+jN spin pairs. We demonstrate this experiment on the membrane-bound transmembrane domain of the SARS-CoV-2 envelope (E) protein (ETM). We show that the C-terminal five residues of ETM form a 310-helix, whereas the rest of the transmembrane domain have COi-Hi+4N hydrogen bonds that are characteristic of α-helices. This result confirms the recent high-resolution solid-state NMR structure of the open state of ETM, which was solved in the absence of explicit hydrogen-bonding restraints. This C-terminal 310 helix may facilitate proton and calcium conduction across the hydrophobic gate of the channel. This hCOhNH experiment is generally applicable and can be used to distinguish not only different types of helices but also different types of β-strands and other hydrogen-bonded conformations in proteins.
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Affiliation(s)
- Joao Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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9
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Alderson TR, Pritišanac I, Kolarić Đ, Moses AM, Forman-Kay JD. Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2. Proc Natl Acad Sci U S A 2023; 120:e2304302120. [PMID: 37878721 PMCID: PMC10622901 DOI: 10.1073/pnas.2304302120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023] Open
Abstract
The AlphaFold Protein Structure Database contains predicted structures for millions of proteins. For the majority of human proteins that contain intrinsically disordered regions (IDRs), which do not adopt a stable structure, it is generally assumed that these regions have low AlphaFold2 confidence scores that reflect low-confidence structural predictions. Here, we show that AlphaFold2 assigns confident structures to nearly 15% of human IDRs. By comparison to experimental NMR data for a subset of IDRs that are known to conditionally fold (i.e., upon binding or under other specific conditions), we find that AlphaFold2 often predicts the structure of the conditionally folded state. Based on databases of IDRs that are known to conditionally fold, we estimate that AlphaFold2 can identify conditionally folding IDRs at a precision as high as 88% at a 10% false positive rate, which is remarkable considering that conditionally folded IDR structures were minimally represented in its training data. We find that human disease mutations are nearly fivefold enriched in conditionally folded IDRs over IDRs in general and that up to 80% of IDRs in prokaryotes are predicted to conditionally fold, compared to less than 20% of eukaryotic IDRs. These results indicate that a large majority of IDRs in the proteomes of human and other eukaryotes function in the absence of conditional folding, but the regions that do acquire folds are more sensitive to mutations. We emphasize that the AlphaFold2 predictions do not reveal functionally relevant structural plasticity within IDRs and cannot offer realistic ensemble representations of conditionally folded IDRs.
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Affiliation(s)
- T. Reid Alderson
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Đesika Kolarić
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Alan M. Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
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10
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Liu Y, Yang J, Ruan M, Zhang H, Wang J, Li Y. NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes. Int J Mol Sci 2023; 24:14657. [PMID: 37834108 PMCID: PMC10572626 DOI: 10.3390/ijms241914657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In mitochondria, the major subunits of oxidative phosphorylation complexes are translated by the mitochondrial ribosome (mito-ribosome). The correct insertion and assembly of these subunits into the inner mitochondrial membrane (IMM) are facilitated by mitochondrial oxidase assembly protein 1 (Oxa1) during the translation process. This co-translational insertion process involves an association between the mito-ribosome and the C-terminus of Oxa1 (Oxa1-CTD) Nuclear magnetic resonance (NMR) methods were mainly used to investigate the structural characterization of yeast Oxa1-CTD and its mode of interaction with the E. coli 70S ribosome. Oxa1-CTD forms a transient α-helical structure within the residues P342-Q385, which were reported to form an α-helix when combining with the ribosome. Two conserved contact sites that could interact with the ribosome were further identified. The first site was located on the very end of the N-terminus (V321-I327), and the second one encompassed a stretch of amino acid residues I348-Q370. Based on our discoveries and previous reports, a model has been proposed in which Oxa1-CTD interacts with ribosomes, accompanied by transient-to-stable transitions at the second contact site. These observations may enhance our understanding of the potential role of Oxa1-CTD in facilitating the assembly of oxidative phosphorylation complexes and provide insight into the structural characteristics of Oxa1-CTD.
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Affiliation(s)
- Yong Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Jing Yang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
| | - Maosen Ruan
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
| | - Huiqin Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yunyan Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
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11
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Pandey AK, Ganguly HK, Sinha SK, Daniels KE, Yap GPA, Patel S, Zondlo NJ. An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation. ACS Chem Biol 2023; 18:1938-1958. [PMID: 37595155 DOI: 10.1021/acschembio.3c00068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted ϕ (ϕ ∼ -60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n → π* interaction between consecutive carbonyls, and an n → σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C-Hβ that restricts the χ2 side-chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are ϕ,ψ = polyproline II helix > α-helix (ϕ ∼ -60°); χ1 = g-; χ2 ∼ +115° (eclipsed C-H/O-P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.
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Affiliation(s)
- Anil K Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sudipta Kumar Sinha
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar 140001, India
| | - Kelly E Daniels
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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12
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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13
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Smith AA, Pacull EM, Stecher S, Hildebrand PW, Vogel A, Huster D. Analysis of the Dynamics of the Human Growth Hormone Secretagogue Receptor Reveals Insights into the Energy Landscape of the Molecule. Angew Chem Int Ed Engl 2023; 62:e202302003. [PMID: 37205715 DOI: 10.1002/anie.202302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors initiate signal transduction in response to ligand binding. Growth hormone secretagogue receptor (GHSR), the focus of this study, binds the 28 residue peptide ghrelin. While structures of GHSR in different states of activation are available, dynamics within each state have not been investigated in depth. We analyze long molecular dynamics simulation trajectories using "detectors" to compare dynamics of the apo and ghrelin-bound states yielding timescale-specific amplitudes of motion. We identify differences in dynamics between apo and ghrelin-bound GHSR in the extracellular loop 2 and transmembrane helices 5-7. NMR of the GHSR histidine residues reveals chemical shift differences in these regions. We evaluate timescale specific correlation of motions between residues of ghrelin and GHSR, where binding yields a high degree of correlation for the first 8 ghrelin residues, but less correlation for the helical end. Finally, we investigate the traverse of GHSR over a rugged energy landscape via principal component analysis.
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Affiliation(s)
- Albert A Smith
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Emelyne M Pacull
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Sabrina Stecher
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
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14
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Asakura T, Williamson MP. A review on the structure of Bombyx mori silk fibroin fiber studied using solid-state NMR: An antipolar lamella with an 8-residue repeat. Int J Biol Macromol 2023:125537. [PMID: 37379946 DOI: 10.1016/j.ijbiomac.2023.125537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Silk fibroin (SF) fiber from the silkworm Bombyx mori in the Silk II form has been used as an excellent textile fiber for over 5000 years. Recently it has been developed for a range of biomedical applications. Further expansion of these uses builds on the excellent mechanical strength of SF fiber, which derives from its structure. This relationship between strength and SF structure has been studied for over 50 years, but it is still not well understood. In this review, we report the use of solid-state NMR to study stable-isotope labeled SF fiber and stable-isotope labeled peptides including (Ala-Gly)15 and (Ala-Gly-Ser-Gly-Ala-Gly)5 as models of the crystalline fraction. We show that the crystalline fraction is a lamellar structure with a repetitive folding using β-turns every eighth amino acid, and that the sidechains adopt an antipolar arrangement rather than the more well-known polar structure described by Marsh, Corey and Pauling (that is, the Ala methyls in each layer point in opposite directions in alternate strands). The amino acids Ser, Tyr and Val are the next most common in B. mori SF after Gly and Ala, and occur in the crystalline and semi-crystalline regions, probably defining the edges of the crystalline region. Thus, we now have an understanding of the main features of Silk II but there is still a long way to go.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan.
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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15
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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16
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Li T, Hendrix E, He Y. Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server. J Phys Chem B 2023; 127:2177-2186. [PMID: 36827446 DOI: 10.1021/acs.jpcb.2c08945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded proteins, resulting in a lack of hydrophobic core(s) and a tendency to adopt rapidly interconverting structures rather than well-defined structures. The structural heterogeneity of IDPs, encoded by the amino acid sequence, is closely related to their unique roles in biological pathways, which require them to interact with different binding partners. Recently, Robustelli and co-workers have demonstrated that a balanced all-atom force field can be used to sample heterogeneous structures of disordered proteins ( Proc. Natl. Acad. Sci. U.S.A. 2018, 115, E4758-E4766). However, such a solution requires extensive computational resources, such as Anton supercomputers. Here, we propose a simple and effective solution to sample the conformational space of IDPs using a publicly available web server, namely, the UNited-RESidue (UNRES) web server. Our proposed solution requires no investment in computational resources and no prior knowledge of UNRES. UNRES Replica Exchange Molecular Dynamics (REMD) simulations were carried out on a set of eight disordered proteins at temperatures spanning from 270 to 430 K. Utilizing the latest UNRES force field designed for structured proteins, with proper selections of temperatures, we were able to produce comparable results to all-atom force fields as reported in work done by Robustelli and co-workers. In addition, NMR observables and the radius of gyration calculated from UNRES ensembles were directly compared with the experimental data to further evaluate the accuracy of the UNRES model at all temperatures. Our results suggest that carrying out the UNRES simulations at optimal temperatures using the UNRES web server can be a good alternative to sample heterogeneous structures of IDPs.
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Affiliation(s)
- Tongtong Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, United States
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17
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Metamorphism in TDP-43 prion-like domain determines chaperone recognition. Nat Commun 2023; 14:466. [PMID: 36709343 PMCID: PMC9884275 DOI: 10.1038/s41467-023-36023-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
The RNA binding protein TDP-43 forms cytoplasmic inclusions via its C-terminal prion-like domain in several neurodegenerative diseases. Aberrant TDP-43 aggregation arises upon phase de-mixing and transitions from liquid to solid states, following still unknown structural conversions which are primed by oxidative stress and chaperone inhibition. Despite the well-established protective roles for molecular chaperones against protein aggregation pathologies, knowledge on the determinants of chaperone recognition in disease-related prions is scarce. Here we show that chaperones and co-chaperones primarily recognize the structured elements in TDP-43´s prion-like domain. Significantly, while HSP70 and HSP90 chaperones promote TDP-43 phase separation, co-chaperones from the three classes of the large human HSP40 family (namely DNAJA2, DNAJB1, DNAJB4 and DNAJC7) show strikingly different effects on TDP-43 de-mixing. Dismantling of the second helical element in TDP-43 prion-like domain by methionine sulfoxidation impacts phase separation and amyloid formation, abrogates chaperone recognition and alters phosphorylation by casein kinase-1δ. Our results show that metamorphism in the post-translationally modified TDP-43 prion-like domain encodes determinants that command mechanisms with major relevance in disease.
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18
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Becker N, Frieg B, Gremer L, Kupreichyk T, Gardon L, Freiburg P, Neudecker P, Willbold D, Gohlke H, Heise H. Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1-42) Amyloid Fibrils. J Am Chem Soc 2023; 145:2161-2169. [PMID: 36653015 PMCID: PMC9896559 DOI: 10.1021/jacs.2c09231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder associated with the deposition of misfolded aggregates of the amyloid-β protein (Aβ). Aβ(1-42) is one of the most aggregation-prone components in senile plaques of AD patients. We demonstrated that relatively homogeneous Aβ(1-42) fibrils with one predominant fold visible in solid-state NMR spectra can be obtained at acidic pH. The structure of these fibrils differs remarkably from some other polymorphs obtained at neutral pH. In particular, the entire N-terminal region is part of the rigid fibril core. Here, we investigate the effects of a pH shift on the stability and the fold of these fibrils at higher pH values. Fibril bundling at neutral pH values renders cryo-EM studies impractical, but solid-state NMR spectroscopy, molecular dynamics simulations, and biophysical methods provide residue-specific structural information under these conditions. The LS-fold of the Aβ(1-42) fibrils does not change over the complete pH range from pH 2 to pH 7; in particular, the N-terminus remains part of the fibril core. We observe changes in the protonation state of charged residues starting from pH 5 on a residue-specific level. The deprotonation of the C-terminal carboxyl group of A42 in the intermolecular salt bridge with D1 and K28 is slow on the NMR time scale, with a local pKa of 5.4, and local conformations of the involved residues are affected by deprotonation of A42. Thus, we demonstrate that this fibril form is stable at physiological pH values.
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Affiliation(s)
- Nina Becker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Benedikt Frieg
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Lothar Gremer
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Luis Gardon
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Patrick Freiburg
- Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Philipp Neudecker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany,Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany,
| | - Henrike Heise
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany,
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19
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Li S, Yang H, Hofstetter H, Tonelli M, Cavagnero S. Magnetic-Field Dependence of LC-Photo-CIDNP in the Presence of Target Molecules Carrying a Quasi-Isolated Spin Pair. APPLIED MAGNETIC RESONANCE 2023; 54:59-75. [PMID: 37483563 PMCID: PMC10358788 DOI: 10.1007/s00723-022-01506-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/04/2022] [Accepted: 09/30/2022] [Indexed: 07/25/2023]
Abstract
NMR spectroscopy is well known for its superb resolution, especially at high applied magnetic field. However, the sensitivity of this technique is very low. Liquid-state low-concentration photo-chemically-induced dynamic nuclear polarization (LC-photo-CIDNP) is a promising emerging methodology capable of enhancing NMR sensitivity in solution. LC-photo-CIDNP works well on solvent-exposed Trp and Tyr residues, either in isolation or within proteins. This study explores the magnetic-field dependence of the LC-photo-CIDNP experienced by two tryptophan isotopologs in solution upon in situ LED-mediated optical irradiation. Out of the two uniformly 13C,15N-labeled Trp (Trp-U-13C,15N) and Trp-α-13C-β,β,2,4,5,6,7-d7 species employed here, only the latter bears a quasi-isolated 1Hα-13Cα spin pair. Computer simulations of the predicted polarization due to geminate recombination of both species display a roughly bell-shaped field dependence. However, while Trp-U-13C,15N is predicted to show a maximum at ca. 500 MHz (11.7 T) and a fairly weak field dependence, Trp-α-13C-β,β,2,4,5,6,7-d7 is expected to display a much sharper field dependence accompanied by a dramatic polarization increase at lower field (ca. 200 MHz, 4.7 T). Experimental LC-photo-CIDNP studies on both Trp isotopologs at 1μM concentration, performed at selected fields, are consistent with the theoretical predictions. In summary, this study highlights the prominent field-dependence of LC-photo-CIDNP enhancements (ε ) experienced by Trp isotopologs bearing a quasi-isolated spin pair.
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Affiliation(s)
- Siyu Li
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave., Madison, Wisconsin, 53706, USA
| | - Hanming Yang
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave., Madison, Wisconsin, 53706, USA
| | - Heike Hofstetter
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave., Madison, Wisconsin, 53706, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave., Madison, Wisconsin, 53706, USA
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20
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Asakura T, Nishimura A, Naito A. Stretching-Induced Conformational Transition of [3- 13C]Ser- and [3- 13C]Tyr- Antheraea yamamai Silk Fibroin before Spinning Investigated with 13C Solid-State NMR Spectroscopy. Biomacromolecules 2022; 23:5095-5105. [PMID: 36449573 DOI: 10.1021/acs.biomac.2c00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The conformational transition of [3-13C]Ser- and [3-13C]Tyr-Antheraea yamamai silk fibroin before spinning induced by stretching was investigated with 13C CP/MAS NMR spectroscopy. The α-helix content of the silk fibroin before stretching was found to be 31.6% based on the Ala and Ser peaks. With increasing stretching ratio, the α-helix and the random coil Ala Cβ peaks decreased gradually, while the β-sheet peak was observed at a stretching ratio of ×5 and increased rapidly upon further stretching. For Ser residue, the α-helix peak decreased monotonically with increasing stretching ratio, but the random coil peak increased slightly till the stretching ratio of ×5 and then decreased. A small β-sheet peak was observed before stretching and then increased rapidly starting from the stretching ratio of ×7. In contrast, a gradual decrease of random coil peak and an increase of β-sheet peak were observed for the Tyr residue. The results of this investigation may be helpful for further studies of fiber formation mechanism in A. yamamai and in the future design of artificial silk materials.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akio Nishimura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
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21
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Al-Hilaly YK, Hurt C, Rickard JE, Harrington CR, Storey JMD, Wischik CM, Serpell LC, Siemer AB. Solid-state NMR of paired helical filaments formed by the core tau fragment tau(297-391). Front Neurosci 2022; 16:988074. [PMID: 36570831 PMCID: PMC9774000 DOI: 10.3389/fnins.2022.988074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Aggregation of the tau protein into fibrillar cross-β aggregates is a hallmark of Alzheimer's diseases (AD) and many other neurodegenerative tauopathies. Recently, several core structures of patient-derived tau paired helical filaments (PHFs) have been solved revealing a structural variability that often correlates with a specific tauopathy. To further characterize the dynamics of these fibril cores, to screen for strain-specific small molecules as potential biomarkers and therapeutics, and to develop strain-specific antibodies, recombinant in-vitro models of tau filaments are needed. We recently showed that a 95-residue fragment of tau (from residue 297 to 391), termed dGAE, forms filaments in vitro in the absence of polyanionic co-factors often used for in vitro aggregation of full-length tau. Tau(297-391) was identified as the proteolytic resistant core of tau PHFs and overlaps with the structures characterized by cryo-electron microscopy in ex vivo PHFs, making it a promising model for the study of AD tau filaments in vitro. In the present study, we used solid-state NMR to characterize tau(297-391) filaments and show that such filaments assembled under non-reducing conditions are more dynamic and less ordered than those made in the presence of the reducing agent DTT. We further report the resonance assignment of tau(297-391)+DTT filaments and compare it to existing core structures of tau.
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Affiliation(s)
- Youssra K. Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom,Chemistry Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Connor Hurt
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Janet E. Rickard
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Charles R. Harrington
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - John M. D. Storey
- TauRx Therapeutics Ltd., Aberdeen, United Kingdom,Department of Chemistry, University of Aberdeen, Aberdeen, United Kingdom
| | - Claude M. Wischik
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Ansgar B. Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,*Correspondence: Ansgar B. Siemer,
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22
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Fischer ES, Yu CWH, Hevler JF, McLaughlin SH, Maslen SL, Heck AJR, Freund SMV, Barford D. Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly. Nat Commun 2022; 13:6381. [PMID: 36289199 PMCID: PMC9605988 DOI: 10.1038/s41467-022-34058-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
In response to improper kinetochore-microtubule attachments in mitosis, the spindle assembly checkpoint (SAC) assembles the mitotic checkpoint complex (MCC) to inhibit the anaphase-promoting complex/cyclosome, thereby delaying entry into anaphase. The MCC comprises Mad2:Cdc20:BubR1:Bub3. Its assembly is catalysed by unattached kinetochores on a Mad1:Mad2 platform. Mad1-bound closed-Mad2 (C-Mad2) recruits open-Mad2 (O-Mad2) through self-dimerization. This interaction, combined with Mps1 kinase-mediated phosphorylation of Bub1 and Mad1, accelerates MCC assembly, in a process that requires O-Mad2 to C-Mad2 conversion and concomitant binding of Cdc20. How Mad1 phosphorylation catalyses MCC assembly is poorly understood. Here, we characterized Mps1 phosphorylation of Mad1 and obtained structural insights into a phosphorylation-specific Mad1:Cdc20 interaction. This interaction, together with the Mps1-phosphorylation dependent association of Bub1 and Mad1, generates a tripartite assembly of Bub1 and Cdc20 onto the C-terminal domain of Mad1 (Mad1CTD). We additionally identify flexibility of Mad1:Mad2 that suggests how the Cdc20:Mad1CTD interaction brings the Mad2-interacting motif (MIM) of Cdc20 near O-Mad2. Thus, Mps1-dependent formation of the MCC-assembly scaffold functions to position and orient Cdc20 MIM near O-Mad2, thereby catalysing formation of C-Mad2:Cdc20.
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Affiliation(s)
- Elyse S Fischer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, University of Utrecht, 3584 CH, Utrecht, The Netherlands
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, University of Utrecht, 3584 CH, Utrecht, The Netherlands
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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23
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Yang Y, Delcourte L, Fogeron ML, Böckmann A, Lecoq L. 1H, 15N and 13C backbone and side chain solution NMR assignments of the truncated small hepatitis delta antigen Δ60-S-HDAg. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:311-316. [PMID: 35749039 DOI: 10.1007/s12104-022-10096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Hepatitis D virus (HDV) is a defective virus that relies on hepatitis B virus envelope proteins to complete its replication cycle. The HDV genome contains two isoforms of hepatitis delta antigen: the small and the large hepatitis delta antigens (S- and L-HDAg). Here we report the 1H, 13C and 15 N backbone and side chain resonance assignments of an N-terminally truncated form of S-HDAg (SΔ60), which lacks the 1-60 oligomerization domain. We derived secondary structures based on NMR chemical shifts, which will be used in further structural and functional studies. We show that SΔ60 is partially disordered, and that the central structured part contains two well-defined α-helices of 22 and 17 residues, respectively. A temperature titration allowed to identify the residues involved in hydrogen bonds.
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Affiliation(s)
- Yang Yang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086, CNRS, Université de Lyon, Labex Ecofect, 7 passage du Vercors, 69367, Lyon, France
| | - Loïc Delcourte
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086, CNRS, Université de Lyon, Labex Ecofect, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086, CNRS, Université de Lyon, Labex Ecofect, 7 passage du Vercors, 69367, Lyon, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086, CNRS, Université de Lyon, Labex Ecofect, 7 passage du Vercors, 69367, Lyon, France.
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086, CNRS, Université de Lyon, Labex Ecofect, 7 passage du Vercors, 69367, Lyon, France.
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24
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Kim DI, Han SH, Park H, Choi S, Kaur M, Hwang E, Han SJ, Ryu JY, Cheong HK, Barnwal RP, Lim YB. Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets. J Am Chem Soc 2022; 144:15519-15528. [PMID: 35972994 DOI: 10.1021/jacs.2c03858] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.
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Affiliation(s)
- Dong-In Kim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - So-Hee Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sehwan Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Euimin Hwang
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seong-Jae Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-Yeon Ryu
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | | | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
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25
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Yang H, Li S, Mickles CA, Guzman-Luna V, Sugisaki K, Thompson CM, Dang HH, Cavagnero S. Selective Isotope Labeling and LC-Photo-CIDNP Enable NMR Spectroscopy at Low-Nanomolar Concentration. J Am Chem Soc 2022; 144:11608-11619. [PMID: 35700317 DOI: 10.1021/jacs.2c01809] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
NMR spectroscopy is a powerful tool to investigate molecular structure and dynamics. The poor sensitivity of this technique, however, limits its ability to tackle questions requiring dilute samples. Low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP) is an optically enhanced NMR technology capable of addressing the above challenge by increasing the detection limit of aromatic amino acids in solution up to 1000-fold, either in isolation or within proteins. Here, we show that the absence of NMR-active nuclei close to a magnetically active site of interest (e.g., the structurally diagnostic 1Hα-13Cα pair of amino acids) is expected to significantly increase LC-photo-CIDNP hyperpolarization. Then, we exploit the spin-diluted tryptophan isotopolog Trp-α-13C-β,β,2,4,5,6,7-d7 and take advantage of the above prediction to experimentally achieve a ca 4-fold enhancement in NMR sensitivity over regular LC-photo-CIDNP. This advance enables the rapid (within seconds) detection of 20 nM concentrations or the molecule of interest, corresponding to a remarkable 3 ng detection limit. Finally, the above Trp isotopolog is amenable to incorporation within proteins and is readily detectable at a 1 μM concentration in complex cell-like media, including Escherichia coli cell-free extracts.
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Affiliation(s)
- Hanming Yang
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Siyu Li
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Clayton A Mickles
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kenji Sugisaki
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.,JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Clayton M Thompson
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Hung H Dang
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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26
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Ramírez de Mingo D, Pantoja-Uceda D, Hervás R, Carrión-Vázquez M, Laurents DV. Conformational dynamics in the disordered region of human CPEB3 linked to memory consolidation. BMC Biol 2022; 20:129. [PMID: 35658951 PMCID: PMC9166367 DOI: 10.1186/s12915-022-01310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Current understanding of the molecular basis of memory consolidation points to an important function of amyloid formation by neuronal-specific isoforms of the cytoplasmic polyadenylation element binding (CPEB) protein family. In particular, CPEB is thought to promote memory persistence through formation of self-sustaining prion-like amyloid assemblies at synapses, mediated by its intrinsically disordered region (IDR) and leading to permanent physical alterations at the basis of memory persistence. Although the molecular mechanisms by which amyloid formation takes place in CPEB have been described in invertebrates, the way amyloid formation occurs in the human homolog CPEB3 (hCPEB3) remains unclear. Here, we characterize by NMR spectroscopy the atomic level conformation and ps-ms dynamics of the 426-residue IDR of hCPEB3, which has been associated with episodic memory in humans. Results We show that the 426-residue N-terminal region of hCPEB3 is a dynamic, intrinsically disordered region (IDR) which lacks stable folded structures. The first 29 residues, M1QDDLLMDKSKTQPQPQQQQRQQQQPQP29, adopt a helical + disordered motif, and residues 86–93: P83QQPPPP93, and 166–175: P166PPPAPAPQP175 form polyproline II (PPII) helices. The (VG)5 repeat motif is completely disordered, and residues 200–250 adopt three partially populated α-helices. Residues 345–355, which comprise the nuclear localization signal (NLS), form a modestly populated α-helix which may mediate STAT5B binding. These findings allow us to suggest a model for nascent hCPEB3 structural transitions at single residue resolution, advancing that amyloid breaker residues, like proline, are a key difference between functional versus pathological amyloids. Conclusion Our NMR spectroscopic analysis of hCPEB3 provides insights into the first structural transitions involved in protein–protein and protein-mRNA interactions. The atomic level understanding of these structural transitions involved in hCPEB3 aggregation is a key first step toward understanding memory persistence in humans, as well as sequence features that differentiate beneficial amyloids from pathological ones. Areas Biophysics, Structural Biology, Biochemistry & Neurosciences. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01310-6.
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27
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Lu Y, Sharma B, Soon WL, Shi X, Zhao T, Lim YT, Sobota RM, Hoon S, Pilloni G, Usadi A, Pervushin K, Miserez A. Complete Sequences of the Velvet Worm Slime Proteins Reveal that Slime Formation is Enabled by Disulfide Bonds and Intrinsically Disordered Regions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201444. [PMID: 35585665 PMCID: PMC9218773 DOI: 10.1002/advs.202201444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/24/2022] [Indexed: 06/02/2023]
Abstract
The slime of velvet worms (Onychophora) is a strong and fully biodegradable protein material, which upon ejection undergoes a fast liquid-to-solid transition to ensnare prey. However, the molecular mechanisms of slime self-assembly are still not well understood, notably because the primary structures of slime proteins are yet unknown. Combining transcriptomic and proteomic studies, the authors have obtained the complete primary sequences of slime proteins and identified key features for slime self-assembly. The high molecular weight slime proteins contain cysteine residues at the N- and C-termini that mediate the formation of multi-protein complexes via disulfide bonding. Low complexity domains in the N-termini are also identified and their propensity for liquid-liquid phase separation is established, which may play a central role in slime biofabrication. Using solid-state nuclear magnetic resonance, rigid and flexible domains of the slime proteins are mapped to specific peptide domains. The complete sequencing of major slime proteins is an important step toward sustainable fabrication of polymers inspired by the velvet worm slime.
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Affiliation(s)
- Yang Lu
- Centre for Sustainable Materials (SusMat)School of Materials Science and EngineeringNanyang Technological University (NTU)Singapore639798Singapore
| | - Bhargy Sharma
- Centre for Sustainable Materials (SusMat)School of Materials Science and EngineeringNanyang Technological University (NTU)Singapore639798Singapore
| | - Wei Long Soon
- Centre for Sustainable Materials (SusMat)School of Materials Science and EngineeringNanyang Technological University (NTU)Singapore639798Singapore
| | - Xiangyan Shi
- Department of BiologyShenzhen MSU‐BIT UniversityNo. 1 International University Park Road, Longgang DistrictShenzhenGuangdong Province518172P. R. China
| | - Tianyun Zhao
- Functional Proteomics LaboratoryInstitute for Molecular and Cell Biology (IMCB)Agency for Science, Technology, and Research (A*Star)ProteosSingapore138673Singapore
| | - Yan Ting Lim
- Functional Proteomics LaboratoryInstitute for Molecular and Cell Biology (IMCB)Agency for Science, Technology, and Research (A*Star)ProteosSingapore138673Singapore
| | - Radoslaw M. Sobota
- Functional Proteomics LaboratoryInstitute for Molecular and Cell Biology (IMCB)Agency for Science, Technology, and Research (A*Star)ProteosSingapore138673Singapore
| | - Shawn Hoon
- Molecular Engineering LabIMCBA*StarProteosSingapore138673Singapore
| | | | - Adam Usadi
- ExxonMobil Asia Pacific Pte LtdSingapore098633Singapore
| | - Konstantin Pervushin
- School of Biological ScienceNanyang Technological UniversitySingapore637551Singapore
| | - Ali Miserez
- Centre for Sustainable Materials (SusMat)School of Materials Science and EngineeringNanyang Technological University (NTU)Singapore639798Singapore
- School of Biological ScienceNanyang Technological UniversitySingapore637551Singapore
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28
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29
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Characterization of polyurethane and a silk fibroin-polyurethane composite fiber studied with NMR spectroscopies. Polym J 2022. [DOI: 10.1038/s41428-022-00629-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Abstract
![]()
Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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31
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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32
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Probing the Influence of Single-Site Mutations in the Central Cross-β Region of Amyloid β (1-40) Peptides. Biomolecules 2021; 11:biom11121848. [PMID: 34944492 PMCID: PMC8699037 DOI: 10.3390/biom11121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Amyloid β (Aβ) is a peptide known to form amyloid fibrils in the brain of patients suffering from Alzheimer’s disease. A complete mechanistic understanding how Aβ peptides form neurotoxic assemblies and how they kill neurons has not yet been achieved. Previous analysis of various Aβ40 mutants could reveal the significant importance of the hydrophobic contact between the residues Phe19 and Leu34 for cell toxicity. For some mutations at Phe19, toxicity was completely abolished. In the current study, we assessed if perturbations introduced by mutations in the direct proximity of the Phe19/Leu34 contact would have similar relevance for the fibrillation kinetics, structure, dynamics and toxicity of the Aβ assemblies. To this end, we rationally modified positions Phe20 or Gly33. A small library of Aβ40 peptides with Phe20 mutated to Lys, Tyr or the non-proteinogenic cyclohexylalanine (Cha) or Gly33 mutated to Ala was synthesized. We used electron microscopy, circular dichroism, X-ray diffraction, solid-state NMR spectroscopy, ThT fluorescence and MTT cell toxicity assays to comprehensively investigate the physicochemical properties of the Aβ fibrils formed by the modified peptides as well as toxicity to a neuronal cell line. Single mutations of either Phe20 or Gly33 led to relatively drastic alterations in the Aβ fibrillation kinetics but left the global, as well as the local structure, of the fibrils largely unchanged. Furthermore, the introduced perturbations caused a severe decrease or loss of cell toxicity compared to wildtype Aβ40. We suggest that perturbations at position Phe20 and Gly33 affect the fibrillation pathway of Aβ40 and, thereby, influence the especially toxic oligomeric species manifesting so that the region around the Phe19/Leu34 hydrophobic contact provides a promising site for the design of small molecules interfering with the Aβ fibrillation pathway.
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33
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Mompeán M, Treviño MÁ, Laurents DV. Partial structure, dampened mobility, and modest impact of a His tag in the SARS-CoV-2 Nsp2 C-terminal region. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:1129-1137. [PMID: 34633480 PMCID: PMC8503394 DOI: 10.1007/s00249-021-01575-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/10/2021] [Accepted: 10/03/2021] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many viruses use their own IDPs to "hack" these processes to deactivate host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational preferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2, whose C-terminal region (CtR) is predicted to be disordered, interacts with human proteins that regulate translation initiation and endosome vesicle sorting. Molecules that block these interactions could be valuable leads for drug development. The 13Cβ and backbone 13CO, 1HN, 13Cα, and 15N nuclei of Nsp2's 45-residue CtR were assigned and used to characterize its structure and dynamics in three contexts; namely: (1) retaining an N-terminal His tag, (2) without the His tag and with an adventitious internal cleavage, and (3) lacking both the His tag and the internal cleavage. Two five-residue segments adopting a minor extended population were identified. Overall, the dynamic behavior is midway between a completely rigid and a fully flexible chain. Whereas the presence of an N-terminal His tag and internal cleavage stiffen and loosen, respectively, neighboring residues, they do not affect the tendency of two regions to populate extended conformations.
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Affiliation(s)
- Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Á Treviño
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain.
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34
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Asakura T, Ibe Y, Jono T, Matsuda H, Kuwabara N, Naito A. Structural investigations of polyurethane and
silk‐polyurethane
composite fiber studied by
13
C
solid‐state
NMR
spectroscopy. J Appl Polym Sci 2021. [DOI: 10.1002/app.51178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology Tokyo University of Agriculture and Technology Koganei Tokyo Japan
| | - Yusuke Ibe
- Polyurethane Research Laboratory Tosoh Corporation Yokkaichi Mie Japan
| | - Takaki Jono
- Polyurethane Research Laboratory Tosoh Corporation Yokkaichi Mie Japan
| | - Hironori Matsuda
- Department of Biotechnology Tokyo University of Agriculture and Technology Koganei Tokyo Japan
| | - Nobuo Kuwabara
- Gunma Sericultural Technology Center Maebashi Gunma Japan
| | - Akira Naito
- Department of Biotechnology Tokyo University of Agriculture and Technology Koganei Tokyo Japan
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35
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Das M, Chen N, LiWang A, Wang LP. Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers 2021; 112:e23473. [PMID: 34528703 DOI: 10.1002/bip.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
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Affiliation(s)
- Madhurima Das
- School of Natural Sciences, University of California, Merced, California, USA
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, California, USA.,Department of Chemistry and Biochemistry, University of California, Merced, California, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA.,Health Sciences Research Institute, University of California, Merced, California, USA.,Center for Circadian Biology, University of California, San Diego, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California, USA
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36
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Asakura T, Ibe Y, Jono T, Naito A. Structure and dynamics of biodegradable polyurethane-silk fibroin composite materials in the dry and hydrated states studied using 13C solid-state NMR spectroscopy. Polym Degrad Stab 2021. [DOI: 10.1016/j.polymdegradstab.2021.109645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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37
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Butrón D, Zamora-Carreras H, Devesa I, Treviño MA, Abian O, Velázquez-Campoy A, Bonache MÁ, Lagartera L, Martín-Martínez M, González-Rodríguez S, Baamonde A, Fernández-Carvajal A, Ferrer-Montiel A, Jiménez MÁ, González-Muñiz R. DD04107-Derived neuronal exocytosis inhibitor peptides: Evidences for synaptotagmin-1 as a putative target. Bioorg Chem 2021; 115:105231. [PMID: 34388485 DOI: 10.1016/j.bioorg.2021.105231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
The analgesic peptide DD04107 (Pal-EEMQRR-NH2) and its acetylated analogue inhibit α-calcitonin gene-related peptide (α-CGRP) exocytotic release from primary sensory neurons. Examining the crystal structure of the SNARE-Synaptotagmin-1(Syt1) complex, we hypothesized that these peptides could inhibit neuronal exocytosis by binding to Syt1, hampering at least partially its interaction with the SNARE complex. To address this hypothesis, we first interrogate the role of individual side-chains on the inhibition of α-CGRP release, finding that E1, M3, Q4 and R6 residues were crucial for activity. CD and NMR conformational analysis showed that linear peptides have tendency to adopt α-helical conformations, but the results with cyclic analogues indicated that this secondary structure is not needed for activity. Isothermal titration calorimetry (ITC) measurements demonstrate a direct interaction of some of these peptides with Syt1-C2B domain, but not with Syt7-C2B region, indicating selectivity. As expected for a compound able to inhibit α-CGRP release, cyclic peptide derivative Pal-E-cyclo[EMQK]R-NH2 showed potent in vivo analgesic activity, in a model of inflammatory pain. Molecular dynamics simulations provided a model consistent with KD values for the interaction of peptides with Syt1-C2B domain, and with their biological activity. Altogether, these results identify Syt1 as a potential new analgesic target.
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Affiliation(s)
- Daniel Butrón
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Isabel Devesa
- IDiBE, Universidad Miguel Hernández, Avda. de la Universidad s/n, 03202 Elche, Spain
| | - Miguel A Treviño
- Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain; Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain; Aragon Health Sciences Institute (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain; Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain; ARAID Foundation, Government of Aragon, 50018 Zaragoza, Spain
| | - M Ángeles Bonache
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Laura Lagartera
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | | | - Ana Baamonde
- Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Julián Clavería 6, 33006 Oviedo, Asturias, Spain
| | | | | | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain.
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38
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Somberg NH, Gelenter MD, Hong M. Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:151-166. [PMID: 33844106 PMCID: PMC8828358 DOI: 10.1007/s10858-021-00364-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/24/2021] [Indexed: 05/19/2023]
Abstract
Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. The 13C chemical shifts are shown in 2D 13C-13C correlation maps, and the amino acid residues are categorized by two criteria: (1) whether they occur in β-strand segments or in loops and turns; (2) whether they are water-exposed or dry, facing other residues or lipids. We also examine the abundance of each amino acid in amyloid proteins and β-barrels and compare the sidechain rotameric populations. The 13C chemical shifts indicate that hydrophobic methyl-rich residues and aromatic residues exhibit larger static sidechain conformational disorder in amyloid fibrils than in β-barrels. In comparison, hydroxyl- and amide-containing polar residues have more ordered sidechains and more ordered backbones in amyloid fibrils than in β-barrels. These trends can be explained by steric zipper interactions between β-sheet planes in cross-β fibrils, and by the interactions of β-barrel residues with lipid and water in the membrane. These conformational trends should be useful for structural analysis of amyloid fibrils and β-barrels based principally on NMR chemical shifts.
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Affiliation(s)
- Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
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39
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Ludzia P, Lowe ED, Marcianò G, Mohammed S, Redfield C, Akiyoshi B. Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein. Structure 2021; 29:1014-1028.e8. [PMID: 33915106 PMCID: PMC8443799 DOI: 10.1016/j.str.2021.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/17/2021] [Accepted: 04/08/2021] [Indexed: 01/01/2023]
Abstract
The kinetochore is the macromolecular machinery that drives chromosome segregation by interacting with spindle microtubules. Kinetoplastids (such as Trypanosoma brucei), a group of evolutionarily divergent eukaryotes, have a unique set of kinetochore proteins that lack any significant homology to canonical kinetochore components. To date, KKT4 is the only kinetoplastid kinetochore protein that is known to bind microtubules. Here we use X-ray crystallography, NMR spectroscopy, and crosslinking mass spectrometry to characterize the structure and dynamics of KKT4. We show that its microtubule-binding domain consists of a coiled-coil structure followed by a positively charged disordered tail. The structure of the C-terminal BRCT domain of KKT4 reveals that it is likely a phosphorylation-dependent protein-protein interaction domain. The BRCT domain interacts with the N-terminal region of the KKT4 microtubule-binding domain and with a phosphopeptide derived from KKT8. Taken together, these results provide structural insights into the unconventional kinetoplastid kinetochore protein KKT4. Structures of microtubule-binding and BRCT domains in KKT4 are reported The microtubule-binding domain consists of a coiled coil and a disordered tail KKT4 interacts with microtubules via a basic surface at the coiled-coil N terminus KKT4 has a phosphopeptide-binding BRCT domain
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Affiliation(s)
- Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriele Marcianò
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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40
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Gaussmann S, Gopalswamy M, Eberhardt M, Reuter M, Zou P, Schliebs W, Erdmann R, Sattler M. Membrane Interactions of the Peroxisomal Proteins PEX5 and PEX14. Front Cell Dev Biol 2021; 9:651449. [PMID: 33937250 PMCID: PMC8086558 DOI: 10.3389/fcell.2021.651449] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/11/2021] [Indexed: 11/17/2022] Open
Abstract
Human PEX5 and PEX14 are essential components of the peroxisomal translocon, which mediates import of cargo enzymes into peroxisomes. PEX5 is a soluble receptor for cargo enzymes comprised of an N-terminal intrinsically disordered domain (NTD) and a C-terminal tetratricopeptide (TPR) domain, which recognizes peroxisomal targeting signal 1 (PTS1) peptide motif in cargo proteins. The PEX5 NTD harbors multiple WF peptide motifs (WxxxF/Y or related motifs) that are recognized by a small globular domain in the NTD of the membrane-associated protein PEX14. How the PEX5 or PEX14 NTDs bind to the peroxisomal membrane and how the interaction between the two proteins is modulated at the membrane is unknown. Here, we characterize the membrane interactions of the PEX5 NTD and PEX14 NTD in vitro by membrane mimicking bicelles and nanodiscs using NMR spectroscopy and isothermal titration calorimetry. The PEX14 NTD weakly interacts with membrane mimicking bicelles with a surface that partially overlaps with the WxxxF/Y binding site. The PEX5 NTD harbors multiple interaction sites with the membrane that involve a number of amphipathic α-helical regions, which include some of the WxxxF/Y-motifs. The partially formed α-helical conformation of these regions is stabilized in the presence of bicelles. Notably, ITC data show that the interaction between the PEX5 and PEX14 NTDs is largely unaffected by the presence of the membrane. The PEX5/PEX14 interaction exhibits similar free binding enthalpies, where reduced binding enthalpy in the presence of bicelles is compensated by a reduced entropy loss. This demonstrates that docking of PEX5 to PEX14 at the membrane does not reduce the overall binding affinity between the two proteins, providing insights into the initial phase of PEX5-PEX14 docking in the assembly of the peroxisome translocon.
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Affiliation(s)
- Stefan Gaussmann
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mohanraj Gopalswamy
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maike Eberhardt
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maren Reuter
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Peijian Zou
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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41
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sevastyan O. Rabdano
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Sergei A. Izmailov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Rudra N. Purusottam
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | | | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
- Department of Chemistry Purdue University West Lafayette IN 47906 USA
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42
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021; 60:6480-6487. [PMID: 33522067 DOI: 10.1002/anie.202012046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/15/2020] [Indexed: 12/21/2022]
Abstract
The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).
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Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | - Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Rudra N Purusottam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation.,Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
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43
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Scherpelz KP, Wang S, Pytel P, Madhurapantula RS, Srivastava AK, Sachleben JR, Orgel J, Ishii Y, Meredith SC. Atomic-level differences between brain parenchymal- and cerebrovascular-seeded Aβ fibrils. Sci Rep 2021; 11:247. [PMID: 33420184 PMCID: PMC7794565 DOI: 10.1038/s41598-020-80042-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/02/2020] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease is characterized by neuritic plaques, the main protein components of which are β-amyloid (Aβ) peptides deposited as β-sheet-rich amyloid fibrils. Cerebral Amyloid Angiopathy (CAA) consists of cerebrovascular deposits of Aβ peptides; it usually accompanies Alzheimer's disease, though it sometimes occurs in the absence of neuritic plaques, as AD also occurs without accompanying CAA. Although neuritic plaques and vascular deposits have similar protein compositions, one of the characteristic features of amyloids is polymorphism, i.e., the ability of a single pure peptide to adopt multiple conformations in fibrils, depending on fibrillization conditions. For this reason, we asked whether the Aβ fibrils in neuritic plaques differed structurally from those in cerebral blood vessels. To address this question, we used seeding techniques, starting with amyloid-enriched material from either brain parenchyma or cerebral blood vessels (using meninges as the source). These amyloid-enriched preparations were then added to fresh, disaggregated solutions of Aβ to make replicate fibrils, as described elsewhere. Such fibrils were then studied by solid-state NMR, fiber X-ray diffraction, and other biophysical techniques. We observed chemical shift differences between parenchymal vs. vascular-seeded replicate fibrils in select sites (in particular, Ala2, Phe4, Val12, and Gln15 side chains) in two-dimensional 13C-13C correlation solid-state NMR spectra, strongly indicating structural differences at these sites. X-ray diffraction studies also indicated that vascular-seeded fibrils displayed greater order than parenchyma-seeded fibrils in the "side-chain dimension" (~ 10 Å reflection), though the "hydrogen-bond dimensions" (~ 5 Å reflection) were alike. These results indicate that the different nucleation conditions at two sites in the brain, parenchyma and blood vessels, affect the fibril products that get formed at each site, possibly leading to distinct pathophysiological outcomes.
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Affiliation(s)
| | - Songlin Wang
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, 60607, USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Rama S Madhurapantula
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Atul K Srivastava
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph R Sachleben
- Biomolecular NMR Facility, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph Orgel
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Stephen C Meredith
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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44
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Pradhan T, Annamalai K, Sarkar R, Huhn S, Hegenbart U, Schönland S, Fändrich M, Reif B. Seeded fibrils of the germline variant of human λ-III immunoglobulin light chain FOR005 have a similar core as patient fibrils with reduced stability. J Biol Chem 2020; 295:18474-18484. [PMID: 33093170 PMCID: PMC7939468 DOI: 10.1074/jbc.ra120.016006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/21/2020] [Indexed: 11/26/2022] Open
Abstract
Systemic antibody light chains (AL) amyloidosis is characterized by deposition of amyloid fibrils derived from a particular antibody light chain. Cardiac involvement is a major risk factor for mortality. Using MAS solid-state NMR, we studied the fibril structure of a recombinant light chain fragment corresponding to the fibril protein from patient FOR005, together with fibrils formed by protein sequence variants that are derived from the closest germline (GL) sequence. Both analyzed fibril structures were seeded with ex-vivo amyloid fibrils purified from the explanted heart of this patient. We find that residues 11-42 and 69-102 adopt β-sheet conformation in patient protein fibrils. We identify arginine-49 as a key residue that forms a salt bridge to aspartate-25 in the patient protein fibril structure. In the germline sequence, this residue is replaced by a glycine. Fibrils from the GL protein and from the patient protein harboring the single point mutation R49G can be both heterologously seeded using patient ex-vivo fibrils. Seeded R49G fibrils show an increased heterogeneity in the C-terminal residues 80-102, which is reflected by the disappearance of all resonances of these residues. By contrast, residues 11-42 and 69-77, which are visible in the MAS solid-state NMR spectra, show 13Cα chemical shifts that are highly like patient fibrils. The mutation R49G thus induces a conformational heterogeneity at the C terminus in the fibril state, whereas the overall fibril topology is retained. These findings imply that patient mutations in FOR005 can stabilize the fibril structure.
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Affiliation(s)
- Tejaswini Pradhan
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural Biology (STB), Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at the Dept. of Chemistry, Technische Universität München (TUM), Garching, Germany
| | | | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural Biology (STB), Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at the Dept. of Chemistry, Technische Universität München (TUM), Garching, Germany
| | - Stefanie Huhn
- Medical Department V, Multiple Myeloma Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Schönland
- Medical Department V, Amyloidosis Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und UmweltInstitute of Structural Biology (STB), Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at the Dept. of Chemistry, Technische Universität München (TUM), Garching, Germany.
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45
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Oroz J, Félix SS, Cabrita EJ, Laurents DV. Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation. J Biol Chem 2020; 295:18122-18133. [PMID: 33093173 PMCID: PMC7939463 DOI: 10.1074/jbc.ra120.015211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
The recent structural elucidation of ex vivo Drosophila Orb2 fibrils revealed a novel amyloid formed by interdigitated Gln and His residue side chains belonging to the prion-like domain. However, atomic-level details on the conformational transitions associated with memory consolidation remain unknown. Here, we have characterized the nascent conformation and dynamics of the prion-like domain (PLD) of Orb2A using a nonconventional liquid-state NMR spectroscopy strategy based on 13C detection to afford an essentially complete set of 13Cα, 13Cβ, 1Hα, and backbone 13CO and 15N assignments. At pH 4, where His residues are protonated, the PLD is disordered and flexible, except for a partially populated α-helix spanning residues 55-60, and binds RNA oligos, but not divalent cations. At pH 7, in contrast, His residues are predominantly neutral, and the Q/H segments adopt minor populations of helical structure, show decreased mobility and start to self-associate. At pH 7, the His residues do not bind RNA or Ca2+, but do bind Zn2+, which promotes further association. These findings represent a remarkable case of structural plasticity, based on which an updated model for Orb2A functional amyloidogenesis is suggested.
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Affiliation(s)
- Javier Oroz
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | - Sara S Félix
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- Departamento de Química Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal
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46
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Araujo NA, Bruix M, Laurents DV. Disorder and partial folding in the regulatory subunit hinge region of Trypanosoma brucei protein kinase A: The C-linker portion inhibits the parasite's protein kinase A. Arch Biochem Biophys 2020; 698:108731. [PMID: 33359563 DOI: 10.1016/j.abb.2020.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022]
Abstract
Microbial pathogens, such as Trypanosoma brucei, have an enormous impact on global health and economic systems. Protein kinase A of T. brucei is an attractive drug target as it is an essential enzyme which differs significantly from its human homolog. The hinge region of this protein's regulatory domain is vital for enzymatic function, but its conformation is unknown. Here, the secondary structure of this region has been characterized using NMR and CD spectroscopies. More specifically, three overlapping peptides corresponding to residues T187-I211, G198-Y223 and V220-S245 called peptide 1, peptide 2 and peptide 3, respectively, were studied. The peptide 1 and peptide 2 are chiefly unfolded; only low populations (<10%) of α-helix were detected under the conditions studied. In contrast, the peptide 3 contains a long α-helix whose population is significantly higher; namely, 36% under the conditions studied. Utilizing the dihedral φ and ψ angles calculated on the basis of the NMR data, the conformation of the peptide 3 was calculated and revealed an α-helix spanning residues E230-N241. This α-helix showed amphiphilicity and reversible unfolding and refolding upon heating and cooling. Most fascinating, however, is its capacity to inhibit the activity of the catalytic domain of Trypanosoma equiperdum protein kinase A even though it is quite distinct from the canonical inhibitor motif. Based on this property, we advance that peptoids based on the peptide 3 α-helix could be novel leads for developing anti-trypanosomal therapeutics.
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Affiliation(s)
- Nelson A Araujo
- Departamento de Biología Celular, Universidad Simón Bolívar, Apartado 89.000, Valle de Sartenejas, Baruta, Caracas, 1081-A, Venezuela.
| | - Marta Bruix
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Douglas V Laurents
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain.
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Spitz C, Schlosser C, Guschtschin-Schmidt N, Stelzer W, Menig S, Götz A, Haug-Kröper M, Scharnagl C, Langosch D, Muhle-Goll C, Fluhrer R. Non-canonical Shedding of TNFα by SPPL2a Is Determined by the Conformational Flexibility of Its Transmembrane Helix. iScience 2020; 23:101775. [PMID: 33294784 PMCID: PMC7689174 DOI: 10.1016/j.isci.2020.101775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
Ectodomain (EC) shedding defines the proteolytic removal of a membrane protein EC and acts as an important molecular switch in signaling and other cellular processes. Using tumor necrosis factor (TNF)α as a model substrate, we identify a non-canonical shedding activity of SPPL2a, an intramembrane cleaving aspartyl protease of the GxGD type. Proline insertions in the TNFα transmembrane (TM) helix strongly increased SPPL2a non-canonical shedding, while leucine mutations decreased this cleavage. Using biophysical and structural analysis, as well as molecular dynamic simulations, we identified a flexible region in the center of the TNFα wildtype TM domain, which plays an important role in the processing of TNFα by SPPL2a. This study combines molecular biology, biochemistry, and biophysics to provide insights into the dynamic architecture of a substrate's TM helix and its impact on non-canonical shedding. Thus, these data will provide the basis to identify further physiological substrates of non-canonical shedding in the future.
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Affiliation(s)
- Charlotte Spitz
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christine Schlosser
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Nadja Guschtschin-Schmidt
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Alexander Götz
- Present Address: Leibniz Supercomputing Centre, Boltzmannstr. 1, 85748 Garching, Germany
| | - Martina Haug-Kröper
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Claudia Muhle-Goll
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
- DZNE – German Center for Neurodegenerative Diseases, Feodor-Lynen-Str 17, 81377 Munich, Germany
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48
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Hendus-Altenburger R, Vogensen J, Pedersen ES, Luchini A, Araya-Secchi R, Bendsoe AH, Prasad NS, Prestel A, Cardenas M, Pedraz-Cuesta E, Arleth L, Pedersen SF, Kragelund BB. The intracellular lipid-binding domain of human Na +/H + exchanger 1 forms a lipid-protein co-structure essential for activity. Commun Biol 2020; 3:731. [PMID: 33273619 PMCID: PMC7713384 DOI: 10.1038/s42003-020-01455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pHi) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical αα-hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pHi and the rate of pHi recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Jens Vogensen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Emilie Skotte Pedersen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Raul Araya-Secchi
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Anne H Bendsoe
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Nanditha Shyam Prasad
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Marité Cardenas
- Biofilms Research Center for Biointerfaces, Malmö University, Per Albin Hanssons Väg 35, 214 32, Malmö, Sweden
| | - Elena Pedraz-Cuesta
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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49
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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50
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Maris C, Jayne S, Damberger FF, Beusch I, Dorn G, Ravindranathan S, Allain FHT. A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure. Nucleic Acids Res 2020; 48:4521-4537. [PMID: 32170319 PMCID: PMC7192611 DOI: 10.1093/nar/gkaa155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alternative splicing, mRNA localization, stabilization, polyadenylation and translation initiation from internal ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5′-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA recognition motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.
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Affiliation(s)
| | - Sandrine Jayne
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | | | - Irene Beusch
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
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