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Klukowski P, Damberger FF, Allain FHT, Iwai H, Kadavath H, Ramelot TA, Montelione GT, Riek R, Güntert P. The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis. Sci Data 2024; 11:30. [PMID: 38177162 PMCID: PMC10767026 DOI: 10.1038/s41597-023-02879-5] [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: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
Multidimensional NMR spectra are the basis for studying proteins by NMR spectroscopy and crucial for the development and evaluation of methods for biomolecular NMR data analysis. Nevertheless, in contrast to derived data such as chemical shift assignments in the BMRB and protein structures in the PDB databases, this primary data is in general not publicly archived. To change this unsatisfactory situation, we present a standardized set of solution NMR data comprising 1329 2-4-dimensional NMR spectra and associated reference (chemical shift assignments, structures) and derived (peak lists, restraints for structure calculation, etc.) annotations. With the 100-protein NMR spectra dataset that was originally compiled for the development of the ARTINA deep learning-based spectra analysis method, 100 protein structures can be reproduced from their original experimental data. The 100-protein NMR spectra dataset is expected to help the development of computational methods for NMR spectroscopy, in particular machine learning approaches, and enable consistent and objective comparisons of these methods.
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Affiliation(s)
- Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Fred F Damberger
- Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Hideo Iwai
- Institute of Biotechnology, University of Helsinki, 00100, Helsinki, Finland
| | | | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
- Institute of Biophysical Chemistry, Goethe University, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, 192-0397, Tokyo, Japan.
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2
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Mason K, LaMontagne-Mueller E, Sauer M, Heese A. Arabidopsis clathrin adaptor EPSIN1 but not MODIFIED TRANSPORT TO THE VACOULE1 contributes to effective plant immunity against pathogenic Pseudomonas bacteria. PLANT SIGNALING & BEHAVIOR 2023; 18:2163337. [PMID: 36603596 PMCID: PMC9828777 DOI: 10.1080/15592324.2022.2163337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
In eukaryotes, EPSINs are Epsin N-terminal Homology (ENTH) domain-containing proteins that serve as monomeric clathrin adaptors at the plasma membrane (PM) or the trans-Golgi Network (TGN)/early endosomes (EE). The model plant Arabidopsis thaliana encodes for seven ENTH proteins, of which so far, only AtEPSIN1 (AtEPS1) and MODIFIED TRANSPORT TO THE VACUOLE1 (AtMTV1) localize to the TGN/EE and contribute to cargo trafficking to both the cell surface and the vacuole. However, relatively little is known about role(s) of any plant EPSIN in governing physiological responses. We have recently shown that AtEPS1 is a positive modulator of plant immune signaling and pattern-triggered immunity against flagellated Pseudomonas syringae pv. tomato (Pto) DC3000 bacteria. In eps1 mutants, impaired immune responses correlate with reduced accumulation of the receptor FLAGELLIN SENSING2 (AtFLS2) and the convergent immune co-receptor BRASSINOSTEROID INSENTIVE1-ASSOCIATED RECEPTOR KINASE1 (AtBAK1) in the PM. Here, we report that in contrast to AtEPS1, the TGN/EE-localized AtMTV1 did not contribute significantly to immunity against pathogenic Pto DC3000 bacteria. We also compared the amino acid sequences, peptide motif structures and in silico tertiary structures of the ENTH domains of AtEPS1 and AtMTV1 in more detail. We conclude that despite sharing the classical tertiary alpha helical ENTH-domain structure and clathrin-binding motifs, the overall low amino acid identity and differences in peptide motifs may explain their role(s) in trafficking of some of the same as well as distinct cargo components to their site of function, with the latter potentially contributing to differences in physiological responses.
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Affiliation(s)
- Kelly Mason
- University of Missouri-Columbia, Division of Biochemistry, Interdisciplinary Plant Group (IPG), Columbia, MO, USA
| | - Erica LaMontagne-Mueller
- University of Missouri-Columbia, Division of Biochemistry, Interdisciplinary Plant Group (IPG), Columbia, MO, USA
| | - Michael Sauer
- Department of Plant Physiology, University of Potsdam, Potsdam, Germany
| | - Antje Heese
- University of Missouri-Columbia, Division of Biochemistry, Interdisciplinary Plant Group (IPG), Columbia, MO, USA
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3
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Fowler NJ, Albalwi MF, Lee S, Hounslow AM, Williamson MP. Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1. Structure 2023; 31:975-986.e3. [PMID: 37311460 DOI: 10.1016/j.str.2023.05.012] [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: 03/10/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
Protein structures calculated using NMR data are less accurate and less well-defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
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Affiliation(s)
- Nicholas J Fowler
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
| | - Marym F Albalwi
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Subin Lee
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Andrea M Hounslow
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
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4
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Titaux-Delgado G, Lopez-Giraldo AE, Carrillo E, Cofas-Vargas LF, Carranza LE, López-Vera E, García-Hernández E, Del Rio-Portilla F. Beta-KTx14.3, a scorpion toxin, blocks the human potassium channel KCNQ1. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140906. [PMID: 36918120 DOI: 10.1016/j.bbapap.2023.140906] [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: 09/29/2022] [Revised: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
Abstract
Potassium channels play a key role in regulating many physiological processes, thus, alterations in their proper functioning can lead to the development of several diseases. Hence, the search for compounds capable of regulating the activity of these channels constitutes an intense field of investigation. Potassium scorpion toxins are grouped into six subfamilies (α, β, γ, κ, δ, and λ). However, experimental structures and functional analyses of the long chain β-KTx subfamily are lacking. In this study, we recombinantly produced the toxins TcoKIK and beta-KTx14.3 present in the venom of Tityus costatus and Lychas mucronatus scorpions, respectively. The 3D structures of these β-KTx toxins were determined by nuclear magnetic resonance. In both toxins, the N-terminal region is unstructured, while the C-terminal possesses the classic CSα/β motif. TcoKIK did not show any clear activity against frog Shaker and human KCNQ1 potassium channels; however, beta-KTx14.3 was able to block the KCNQ1 channel. The toxin-channel interaction mode was investigated using molecular dynamics simulations. The results showed that this toxin could form a stable network of polar-to-polar and hydrophobic interactions with KCNQ1, involving key conserved residues in both molecular partners. The discovery and characterization of a toxin capable of inhibiting KCNQ1 pave the way for the future development of novel drugs for the treatment of human diseases caused by the malfunction of this potassium channel. STATEMENT OF SIGNIFICANCE: Scorpion toxins have been shown to rarely block human KCNQ1 channels, which participate in the regulation of cardiac processes. In this study, we obtained recombinant beta-KTx14.3 and TcoKIK toxins and determined their 3D structures by nuclear magnetic resonance. Electrophysiological studies and molecular dynamics models were employed to examine the interactions between these two toxins and the human KCNQ1, which is the major driver channel of cardiac repolarization; beta-KTx14.3 was found to block effectively this channel. Our findings provide insights for the development of novel toxin-based drugs for the treatment of cardiac channelopathies involving KCNQ1-like channels.
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Affiliation(s)
- Gustavo Titaux-Delgado
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico
| | - Andrea Estefanía Lopez-Giraldo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico
| | - Elisa Carrillo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Luis Fernando Cofas-Vargas
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico
| | - Luis Enrique Carranza
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico
| | - Estuardo López-Vera
- Laboratorio de Toxinología Marina, Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Enrique García-Hernández
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico.
| | - Federico Del Rio-Portilla
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México 04510, Mexico.
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5
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Hoch JC, Baskaran K, Burr H, Chin J, Eghbalnia H, Fujiwara T, Gryk M, Iwata T, Kojima C, Kurisu G, Maziuk D, Miyanoiri Y, Wedell J, Wilburn C, Yao H, Yokochi M. Biological Magnetic Resonance Data Bank. Nucleic Acids Res 2023; 51:D368-D376. [PMID: 36478084 PMCID: PMC9825541 DOI: 10.1093/nar/gkac1050] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 12/12/2022] Open
Abstract
The Biological Magnetic Resonance Data Bank (BMRB, https://bmrb.io) is the international open data repository for biomolecular nuclear magnetic resonance (NMR) data. Comprised of both empirical and derived data, BMRB has applications in the study of biomacromolecular structure and dynamics, biomolecular interactions, drug discovery, intrinsically disordered proteins, natural products, biomarkers, and metabolomics. Advances including GHz-class NMR instruments, national and trans-national NMR cyberinfrastructure, hybrid structural biology methods and machine learning are driving increases in the amount, type, and applications of NMR data in the biosciences. BMRB is a Core Archive and member of the World-wide Protein Data Bank (wwPDB).
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Affiliation(s)
- Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Kumaran Baskaran
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Harrison Burr
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - John Chin
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Hamid R Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Toshimichi Fujiwara
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
| | - Michael R Gryk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Takeshi Iwata
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
| | - Chojiro Kojima
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Genji Kurisu
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
| | - Dmitri Maziuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Yohei Miyanoiri
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
| | - Jonathan R Wedell
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Colin Wilburn
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Hongyang Yao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
| | - Masashi Yokochi
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871. Japan
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6
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Gu J, Isozumi N, Gao B, Ohki S, Zhu S. Mutation-driven evolution of antibacterial function in an ancestral antifungal scaffold: Significance for peptide engineering. Front Microbiol 2022; 13:1053078. [PMID: 36532476 PMCID: PMC9751787 DOI: 10.3389/fmicb.2022.1053078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/15/2022] [Indexed: 07/02/2024] Open
Abstract
Mutation-driven evolution of novel function on an old gene has been documented in many development- and adaptive immunity-related genes but is poorly understood in immune effector molecules. Drosomycin-type antifungal peptides (DTAFPs) are a family of defensin-type effectors found in plants and ecdysozoans. Their primitive function was to control fungal infection and then co-opted for fighting against bacterial infection in plants, insects, and nematodes. This provides a model to study the structural and evolutionary mechanisms behind such functional diversification. In the present study, we determined the solution structure of mehamycin, a DTAFP from the Northern root-knot nematode Meloidogyne hapla with antibacterial activity and an 18-mer insert, and studied the mutational effect through using a mutant with the insert deleted. Mehamycin adopts an expected cysteine-stabilized α-helix and β-sheet fold in its core scaffold and the inserted region, called single Disulfide Bridge-linked Domain (abbreviated as sDBD), forms an extended loop protruding from the scaffold. The latter folds into an amphipathic architecture stabilized by one disulfide bridge, which likely confers mehamycin a bacterial membrane permeability. Deletion of the sDBD remarkably decreased the ability but accompanying an increase in thermostability, indicative of a structure-function trade-off in the mehamycin evolution. Allosteric analysis revealed an interior interaction between the two domains, which might promote point mutations at some key sites of the core domain and ultimately give rise to the emergence of antibacterial function. Our work may be valuable in guiding protein engineering of mehamycin to improve its activity and stability.
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Affiliation(s)
- Jing Gu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Noriyoshi Isozumi
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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7
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Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA. Nat Commun 2022; 13:6151. [PMID: 36257955 PMCID: PMC9579175 DOI: 10.1038/s41467-022-33879-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a major technique in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size proteins in solution, living cells, and solids, but has been limited by the tedious data analysis process. It typically requires weeks or months of manual work of a trained expert to turn NMR measurements into a protein structure. Automation of this process is an open problem, formulated in the field over 30 years ago. We present a solution to this challenge that enables the completely automated analysis of protein NMR data within hours after completing the measurements. Using only NMR spectra and the protein sequence as input, our machine learning-based method, ARTINA, delivers signal positions, resonance assignments, and structures strictly without human intervention. Tested on a 100-protein benchmark comprising 1329 multidimensional NMR spectra, ARTINA demonstrated its ability to solve structures with 1.44 Å median RMSD to the PDB reference and to identify 91.36% correct NMR resonance assignments. ARTINA can be used by non-experts, reducing the effort for a protein assignment or structure determination by NMR essentially to the preparation of the sample and the spectra measurements.
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8
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Furuita K, Inomata K, Sugiki T, Kobayashi N, Fujiwara T, Kojima C. 1H, 13C, and 15N resonance assignments of human glutathione peroxidase 4. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:267-271. [PMID: 35616778 DOI: 10.1007/s12104-022-10090-7] [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: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Glutathione peroxidase 4 (GPx4) behaves as an antioxidant enzyme capable of directly reducing peroxidized phospholipids within cell membranes. Recently, GPx4 has attracted attention as a target molecule for cancer therapy because it induces the immortalization of cancer cells suppressing ferroptosis. In this study, to analyze the function and structure of GPx4 by solution NMR, we performed resonance assignments of GPx4 and assigned almost all backbone 1H, 13C, and 15N resonances and most of the side chain 1H and 13C resonances. Using these assignments, the secondary structure of GPx4 was analyzed by the TALOS + program. GPx4 has six helices and seven strands. Then, the backbone dynamics were examined by the {1H}-15N heteronuclear NOE experiment. GPx4 was found to be rigid except for a short loop region. These results will provide basis for functional analysis and the first solution structure determination of GPx4.
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Affiliation(s)
- Kyoko Furuita
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Kouki Inomata
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | | | | | | | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Suita, Japan.
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan.
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9
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Sayeesh PM, Ikeya T, Sugasawa H, Watanabe R, Mishima M, Inomata K, Ito Y. Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos. Biochem Biophys Res Commun 2022; 625:87-93. [DOI: 10.1016/j.bbrc.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
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10
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Structural and functional studies of LaIT2, an antimicrobial and insecticidal peptide from Liocheles australasiae. Toxicon 2022; 214:8-17. [DOI: 10.1016/j.toxicon.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022]
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11
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Zhu S, Gao B, Umetsu Y, Peigneur S, Li P, Ohki S, Tytgat J. Adaptively evolved human oral actinomyces-sourced defensins show therapeutic potential. EMBO Mol Med 2021; 14:e14499. [PMID: 34927385 PMCID: PMC8819291 DOI: 10.15252/emmm.202114499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
The development of eukaryote‐derived antimicrobial peptides as systemically administered drugs has proven a challenging task. Here, we report the first human oral actinomyces‐sourced defensin—actinomycesin—that shows promise for systemic therapy. Actinomycesin and its homologs are only present in actinobacteria and myxobacteria, and share similarity with a group of ancient invertebrate‐type defensins reported in fungi and invertebrates. Signatures of natural selection were detected in defensins from the actinomyces colonized in human oral cavity and ruminant rumen and dental plaque, highlighting their role in adaptation to complex multispecies bacterial communities. Consistently, actinomycesin exhibited potent antibacterial activity against oral bacteria and clinical isolates of Staphylococcus and synergized with two classes of human salivary antibacterial factors. Actinomycesin specifically inhibited bacterial peptidoglycan synthesis and displayed weak immunomodulatory activity and low toxicity on human and mammalian cells and ion channels in the heart and central nervous system. Actinomycesin was highly efficient in mice infected with Streptococcus pneumoniae and mice with MRSA‐induced experimental peritoneal infection. This work identifies human oral bacteria as a new source of systemic anti‐infective drugs.
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Affiliation(s)
- Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yoshitaka Umetsu
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
| | - Ping Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), National Center for Nanoscience and Technology, Beijing, China
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
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12
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Zhang R, Isozumi N, Mori M, Okuta R, Singkaravanit-Ogawa S, Imamura T, Kurita JI, Gan P, Shirasu K, Ohki S, Takano Y. Fungal effector SIB1 of Colletotrichum orbiculare has unique structural features and can suppress plant immunity in Nicotiana benthamiana. J Biol Chem 2021; 297:101370. [PMID: 34756891 PMCID: PMC8633582 DOI: 10.1016/j.jbc.2021.101370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fungal plant pathogens secrete virulence-related proteins, called effectors, to establish host infection; however, the details are not fully understood yet. Functional screening of effector candidates using Agrobacterium-mediated transient expression assay in Nicotiana benthamiana identified two virulence-related effectors, named SIB1 and SIB2 (Suppression of Immunity in N. benthamiana), of an anthracnose fungus Colletotrichum orbiculare, which infects both cucurbits and N. benthamiana. The Agrobacterium-mediated transient expression of SIB1 or SIB2 increased the susceptibility of N. benthamiana to C. orbiculare, which suggested these effectors can suppress immune responses in N. benthamiana. The presence of SIB1 and SIB2 homologs was found to be limited to the genus Colletotrichum. SIB1 suppressed both (i) the generation of reactive oxygen species triggered by two different pathogen-associated molecular patterns, chitin and flg22, and (ii) the cell death response triggered by the Phytophthora infestans INF1 elicitin in N. benthamiana. We determined the NMR-based structure of SIB1 to obtain its structural insights. The three-dimensional structure of SIB1 comprises five β-strands, each containing three disulfide bonds. The overall conformation was found to be a cylindrical shape, such as the well-known antiparallel β-barrel structure. However, the β-strands were found to display a unique topology, one pair of these β-strands formed a parallel β-sheet. These results suggest that the effector SIB1 present in Colletotrichum fungi has unique structural features and can suppress pathogen-associated molecular pattern-triggered immunity in N. benthamiana.
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Affiliation(s)
- Ru Zhang
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Noriyoshi Isozumi
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan.
| | - Ryuta Okuta
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Tomohiro Imamura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Pamela Gan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan.
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13
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Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment. Molecules 2021; 26:molecules26123699. [PMID: 34204416 PMCID: PMC8235258 DOI: 10.3390/molecules26123699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65% success rate and could assign some of the atoms that could not be assigned by other methods.
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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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15
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The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity. Nat Commun 2021; 12:1859. [PMID: 33767140 PMCID: PMC7994586 DOI: 10.1038/s41467-021-22077-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/26/2021] [Indexed: 12/25/2022] Open
Abstract
Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic interactions between the Rsa1p-encoding gene and genes involved in chromatin organization including RTT106 that codes for the H3-H4 histone chaperone Rtt106p controlling H3K56ac deposition. We show that Bcd1p binds Rtt106p and controls its transcription-dependent recruitment by reducing its association with RNA polymerase II, modulating H3K56ac levels at gene body. We reveal the 3D structures of the free and Rtt106p-bound forms of Bcd1p using nuclear magnetic resonance and X-ray crystallography. The interaction is also studied by a combination of biophysical and proteomic techniques. Bcd1p interacts with a region that is distinct from the interaction interface between the histone chaperone and histone H3. Our results are evidence for a protein interaction interface for Rtt106p that controls its transcription-associated activity. Biogenesis of small nucleolar RNAs ribonucleoproteins (snoRNPs) requires dedicated assembly machinery. Here, the authors show that a subset of snoRNP assembly factors interacts, genetically or directly, with factors modulating chromatin architecture, suggesting a link between ribosome formation and chromatin functions.
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17
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Cárdenas-Hernández H, Titaux-Delgado GA, Castañeda-Ortiz EJ, Torres-Larios A, Brieba LG, Del Río-Portilla F, Azuara-Liceaga E. Genome-wide and structural analysis of the Myb-SHAQKYF family in Entamoeba histolytica. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140601. [PMID: 33422669 DOI: 10.1016/j.bbapap.2021.140601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/19/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Amoebiasis is the third leading cause of death among protozoon parasitic diseases in the lower-middle income countries. Understanding the molecular events that control gene expression such as transcription factors, their DNA binding mode and target sequences can help to develop new antiamoebic drugs against Entamoeba histolytica. In this paper we performed a genome and structural analysis of a specific transcription factor. The genome of E. histolytica codifies for 9 EhMybSHAQKYF proteins, which are a family within a large group of 34 Myb-DNA-binding domain (Myb-DBD) containing proteins. Here we compared Entamoeba Myb-SHAQKYF proteins with Myb-like proteins from the Reveille (RVE) family, important regulators of plant circadian networks. This comparison could lead to stablish their role in E. histolytica life cycle. We show that the ehmybshaqkyf genes are differentially expressed in trophozoites under basal cell culture conditions. An in-silico analysis predicts that members of this group harbor a highly conserved and structured Myb-DBD and a large portion of intrinsically disordered residues. As the Myb-DBD of these proteins harbors a distinctive Q[VI]R[ST]HAQK[YF]F sequence in its putative third α-helix, we consider relevant to determine the three-dimensional (3D) structure of one of them. An NMR structure of the Myb-DBD of EhMybS3 shows that this protein is composed of three α-helices stabilized by a hydrophobic core, similar to Myb proteins of different kingdoms. It is remarkable that despite not sharing similarities in their amino acid sequences, the structure of the Myb-DBD of the EhMybS3 is well conserved in this early branching eukaryote.
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Affiliation(s)
- Helios Cárdenas-Hernández
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | | | | | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis G Brieba
- Grupo de Bioquímica Estructural, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México
| | | | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México.
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18
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Trindade IB, Invernici M, Cantini F, Louro RO, Piccioli M. PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems. FEBS J 2020; 288:3010-3023. [PMID: 33124176 DOI: 10.1111/febs.15615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023]
Abstract
Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).
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Affiliation(s)
- Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Michele Invernici
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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Rehic E, Hoenig D, Kamba BE, Goehring A, Hofmann E, Gasper R, Matena A, Bayer P. Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei. Biomolecules 2019; 9:biom9030093. [PMID: 30866577 PMCID: PMC6468809 DOI: 10.3390/biom9030093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
Trypanosoma brucei is a unicellular eukaryotic parasite, which causes the African sleeping sickness in humans. The recently discovered trypanosomal protein Parvulin 42 (TbPar42) plays a key role in parasite cell proliferation. Homologues of this two-domain protein are exclusively found in protozoa species. TbPar42 exhibits an N-terminal forkhead associated (FHA)-domain and a peptidyl-prolyl-cis/trans-isomerase (PPIase) domain, both connected by a linker. Using NMR and X-ray analysis as well as activity assays, we report on the structures of the single domains of TbPar42, discuss their intra-molecular interplay, and give some initial hints as to potential cellular functions of the protein.
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Affiliation(s)
- Edisa Rehic
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Dana Hoenig
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Bianca E Kamba
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Anna Goehring
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Raphael Gasper
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany.
| | - Anja Matena
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Peter Bayer
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
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20
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Shapiguzov A, Vainonen JP, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, Van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjärvi J. Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 2019; 8:43284. [PMID: 30767893 PMCID: PMC6414205 DOI: 10.7554/elife.43284] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/14/2019] [Indexed: 01/17/2023] Open
Abstract
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles. Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments. At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS. To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work. On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments. Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.
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Affiliation(s)
- Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Kerri Hunter
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Arjun Tiwari
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Sari Järvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Fayezeh Aarabi
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Brecht Wybouw
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lauri Nikkanen
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Krasensky-Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Eevi Rintamäki
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Eva-Mari Aro
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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22
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Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex. Structure 2018; 26:1196-1209.e8. [DOI: 10.1016/j.str.2018.06.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/04/2018] [Accepted: 06/08/2018] [Indexed: 12/22/2022]
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Niesteruk A, Jonker HRA, Richter C, Linhard V, Sreeramulu S, Schwalbe H. The domain architecture of PtkA, the first tyrosine kinase from Mycobacterium tuberculosis, differs from the conventional kinase architecture. J Biol Chem 2018; 293:11823-11836. [PMID: 29884774 PMCID: PMC6066317 DOI: 10.1074/jbc.ra117.000120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 05/27/2018] [Indexed: 12/19/2022] Open
Abstract
The discovery that MptpA (low-molecular-weight protein tyrosine phosphatase A) from Mycobacterium tuberculosis (Mtb) has an essential role for Mtb virulence has motivated research of tyrosine-specific phosphorylation in Mtb and other pathogenic bacteria. The phosphatase activity of MptpA is regulated via phosphorylation on Tyr128 and Tyr129 Thus far, only a single tyrosine-specific kinase, protein-tyrosine kinase A (PtkA), encoded by the Rv2232 gene has been identified within the Mtb genome. MptpA undergoes phosphorylation by PtkA. PtkA is an atypical bacterial tyrosine kinase, as its sequence differs from the sequence consensus within this family. The lack of structural information on PtkA hampers the detailed characterization of the MptpA-PtkA interaction. Here, using NMR spectroscopy, we provide a detailed structural characterization of the PtkA architecture and describe its intra- and intermolecular interactions with MptpA. We found that PtkA's domain architecture differs from the conventional kinase architecture and is composed of two domains, the N-terminal highly flexible intrinsically disordered domain (IDDPtkA) and the C-terminal rigid kinase core domain (KCDPtkA). The interaction between the two domains, together with the structural model of the complex proposed in this study, reveal that the IDDPtkA is unstructured and highly dynamic, allowing for a "fly-casting-like" mechanism of transient interactions with the rigid KCDPtkA This interaction modulates the accessibility of the KCDPtkA active site. In general, the structural and functional knowledge of PtkA gained in this study is crucial for understanding the MptpA-PtkA interactions, the catalytic mechanism, and the role of the kinase-phosphatase regulatory system in Mtb virulence.
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Affiliation(s)
- Anna Niesteruk
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Hendrik R A Jonker
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Christian Richter
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Verena Linhard
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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24
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Tossavainen H, Raulinaitis V, Kauppinen L, Pentikäinen U, Maaheimo H, Permi P. Structural and Functional Insights Into Lysostaphin-Substrate Interaction. Front Mol Biosci 2018; 5:60. [PMID: 30018958 PMCID: PMC6038053 DOI: 10.3389/fmolb.2018.00060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity toward pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications. To this end, we have used NMR, SAXS and molecular dynamics simulations to characterize lysostaphin structure and dynamics, to address the inter-domain interaction, the enzyme-substrate interaction as well as the catalytic properties of pentaglycine cleavage in solution. Our NMR structure confirms the recent crystal structure, yet, together with the molecular dynamics simulations, emphasizes the dynamic nature of the loops embracing the catalytic site. We found no evidence for inter-domain interaction, but, interestingly, the SAXS data delineate two preferred conformation subpopulations. Catalytic H329 and H360 were observed to bind a second zinc ion, which reduces lysostaphin pentaglycine cleaving activity. Binding of pentaglycine or its lysine derivatives to the targeting domain was found to be of very low affinity. The pentaglycine interaction site was located to the N-terminal groove of the domain. Notably, the targeting domain binds the peptidoglycan stem peptide Ala-d-γ-Glu-Lys-d-Ala-d-Ala with a much higher, micromolar affinity. Binding site mapping reveals two interaction sites of different affinities on the surface of the domain for this peptide.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Linda Kauppinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku Centre for Biotechnology, Turku, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
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25
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Sugiki T, Furuita K, Fujiwara T, Kojima C. Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance. Biochemistry 2018; 57:3576-3589. [PMID: 29924600 DOI: 10.1021/acs.biochem.8b00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13C atoms experience less isotope scrambling than the main-chain 15N atoms do. However, little is known about the side-chain 13C atoms. Here, the 13C scrambling profiles of the Cα and side-chain carbons were investigated for 15N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13Cα and 13C side-chain labeling than in 15N labeling. We utilized this reduced scrambling-prone character of 13C as a simple and efficient method for amino acid selective 13C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1H-15N heteronuclear single-quantum coherence signals of the 15N scrambling-prone amino acid were also easily filtered using 15N-{13Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Kyoko Furuita
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Chojiro Kojima
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Graduate School of Engineering Science , Yokohama National University , 79-5 Tokiwadai , Hodogaya-ku, Yokohama 240-8501 , Japan
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26
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Nerli S, McShan AC, Sgourakis NG. Chemical shift-based methods in NMR structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:1-25. [PMID: 31047599 PMCID: PMC6788782 DOI: 10.1016/j.pnmrs.2018.03.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
Abstract
Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools.
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Affiliation(s)
- Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States.
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27
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Maurizy C, Quinternet M, Abel Y, Verheggen C, Santo PE, Bourguet M, C F Paiva A, Bragantini B, Chagot ME, Robert MC, Abeza C, Fabre P, Fort P, Vandermoere F, M F Sousa P, Rain JC, Charpentier B, Cianférani S, Bandeiras TM, Pradet-Balade B, Manival X, Bertrand E. The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones. Nat Commun 2018; 9:2093. [PMID: 29844425 PMCID: PMC5974087 DOI: 10.1038/s41467-018-04431-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 04/19/2018] [Indexed: 12/22/2022] Open
Abstract
R2TP is an HSP90 co-chaperone that assembles important macro-molecular machineries. It is composed of an RPAP3-PIH1D1 heterodimer, which binds the two essential AAA+ATPases RUVBL1/RUVBL2. Here, we resolve the structure of the conserved C-terminal domain of RPAP3, and we show that it directly binds RUVBL1/RUVBL2 hexamers. The human genome encodes two other proteins bearing RPAP3-C-terminal-like domains and three containing PIH-like domains. Systematic interaction analyses show that one RPAP3-like protein, SPAG1, binds PIH1D2 and RUVBL1/2 to form an R2TP-like complex termed R2SP. This co-chaperone is enriched in testis and among 68 of the potential clients identified, some are expressed in testis and others are ubiquitous. One substrate is liprin-α2, which organizes large signaling complexes. Remarkably, R2SP is required for liprin-α2 expression and for the assembly of liprin-α2 complexes, indicating that R2SP functions in quaternary protein folding. Effects are stronger at 32 °C, suggesting that R2SP could help compensating the lower temperate of testis. R2TP is an HSP90 co-chaperone composed of an RPAP3-PIH1D1 heterodimer, which binds two essential AAA+ ATPases RUVBL1/RUVBL2. Here authors use a structural approach to study RPAP3 and find an RPAP3-like protein (SPAG1) which also forms a co-chaperone complex with PIH1D2 and RUVBL1/2 enriched in testis.
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Affiliation(s)
- Chloé Maurizy
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Marc Quinternet
- CNRS, INSERM, IBSLOR, Université de Lorraine, Nancy, F-54000, France
| | - Yoann Abel
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Céline Verheggen
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | | | - Marie-Cécile Robert
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Claire Abeza
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France
| | - Philippe Fabre
- CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France
| | - Philippe Fort
- CRBM, University of Montpellier, CNRS, 1919 Route de Mende, Montpellier, 34090, France
| | | | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | | | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France
| | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | | | - Xavier Manival
- CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France.
| | - Edouard Bertrand
- IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France. .,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France.
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28
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Titaux-Delgado G, Carrillo E, Mendoza A, Mayorga-Flores M, Escobedo-González FC, Cano-Sánchez P, López-Vera E, Corzo G, Del Rio-Portilla F. Successful refolding and NMR structure of rMagi3: A disulfide-rich insecticidal spider toxin. Protein Sci 2018; 27:692-701. [PMID: 29247580 DOI: 10.1002/pro.3363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 11/07/2022]
Abstract
The need for molecules with high specificity against noxious insects leads the search towards spider venoms that have evolved highly selective toxins for insect preys. In this respect, spiders as a highly diversified group of almost exclusive insect predators appear to possess infinite potential for the discovery of novel insect-selective toxins. In 2003, a group of toxins was isolated from the spider Macrothele gigas and the amino acid sequence was reported. We obtained, by molecular biology techniques in a heterologous system, one of these toxins. Purification process was optimized by chromatographic methods to determine the three-dimensional structure by nuclear magnetic resonance in solution, and, finally, their biological activity was tested. rMagi3 resulted to be a specific insect toxin with no effect on mice.
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Affiliation(s)
- Gustavo Titaux-Delgado
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México, 04510, México
| | - Elisa Carrillo
- Laboratorio de Toxinología Marina, Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Angeles Mendoza
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Col. Lomas del Campestre León, Gto, 37150, México
| | - Marlen Mayorga-Flores
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México, 04510, México
| | - Fátima C Escobedo-González
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México, 04510, México
| | - Patricia Cano-Sánchez
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México, 04510, México
| | - Estuardo López-Vera
- Laboratorio de Toxinología Marina, Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, México
| | - Federico Del Rio-Portilla
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, CU, Ciudad de México, 04510, México
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29
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Sasmal S, Lincoff J, Head-Gordon T. Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β. Biophys J 2017; 113:1002-1011. [PMID: 28877484 DOI: 10.1016/j.bpj.2017.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/16/2017] [Accepted: 06/30/2017] [Indexed: 10/18/2022] Open
Abstract
Paramagnetic relaxation enhancement is an NMR technique that has yielded important insight into the structure of folded proteins, although the perturbation introduced by the large spin probe might be thought to diminish its usefulness when applied to characterizing the structural ensembles of intrinsically disordered proteins (IDPs). We compare the computationally generated structural ensembles of the IDP amyloid-β42 (Aβ42) to an alternative sequence in which a nitroxide spin label attached to cysteine has been introduced at its N-terminus. Based on this internally consistent computational comparison, we find that the spin label does not perturb the signature population of the β-hairpin formed by residues 16-21 and 29-36 that is dominant in the Aβ42 reference ensemble. However, the presence of the tag induces a strong population shift in a subset of the original Aβ42 structural sub-populations, including a sevenfold enhancement of the β-hairpin formed by residues 27-31 and 33-38. Through back-calculation of NMR observables from the computational structural ensembles, we show that the structural differences between the labeled and unlabeled peptide would be evident in local residual dipolar couplings, and possibly differences in homonuclear 1H-1H nuclear Overhauser effects (NOEs) and heteronuclear 1H-15N NOEs if the paramagnetic contribution to the longitudinal relaxation does not suppress the NOE intensities in the real experiment. This work shows that molecular simulation provides a complementary approach to resolving the potential structural perturbations introduced by reporter tags that can aid in the interpretation of paramagnetic relaxation enhancement, double electron-electron resonance, and fluorescence resonance energy transfer experiments applied to IDPs.
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Affiliation(s)
- Sukanya Sasmal
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - James Lincoff
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California; Department of Chemistry, University of California, Berkeley, Berkeley, California; Department of Bioengineering, University of California, Berkeley, Berkeley, California; Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California.
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30
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Raulinaitis V, Tossavainen H, Aitio O, Juuti JT, Hiramatsu K, Kontinen V, Permi P. Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family. Sci Rep 2017; 7:6020. [PMID: 28729697 PMCID: PMC5519744 DOI: 10.1038/s41598-017-06135-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
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Affiliation(s)
- Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Olli Aitio
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Jarmo T Juuti
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland
| | - Keiichi Hiramatsu
- Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Vesa Kontinen
- Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, P.O. Box 30, FI-00271, Helsinki, Finland.,Research Centre for Infection Control Science, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland. .,Department of Biological and Environmental Science, and Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyvaskyla, Finland.
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31
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Mobli M, Undheim EAB, Rash LD. Modulation of Ion Channels by Cysteine-Rich Peptides: From Sequence to Structure. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2017; 79:199-223. [PMID: 28528669 DOI: 10.1016/bs.apha.2017.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Venom peptides are natural ligands of ion channels and have been used extensively in pharmacological characterization of various ion channels and receptors. In this chapter, we survey all known venom peptide ion-channel modulators. Our survey reveals that the majority of venom peptides characterized to date target voltage-gated sodium or potassium channels. We further find that the majority of these peptides are found in scorpion and spider venoms. We discuss the influence of the pharmacological tools available in biasing discovery and the classical "toxin-to-sequence" approach to venom peptide biodiscovery. The impact of high-throughput sequencing on the existing discovery framework is likely to be significant and we propose here an alternative "sequence-to-toxin" approach to peptide screening, relying more on recently developed high-throughput methods. Methods for production and characterization of disulfide rich toxins in a high-throughput setting are then described, focusing on bacterial protein expression and solution state structural characterization by NMR spectroscopy. Finally, the role of X-ray crystallography and cryo-EM are highlighted by discussing the currently known channel-peptide complexes.
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Affiliation(s)
- Mehdi Mobli
- Centre for Advanced Imaging, St Lucia, QLD, Australia.
| | | | - Lachlan D Rash
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
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32
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NMR-based automated protein structure determination. Arch Biochem Biophys 2017; 628:24-32. [PMID: 28263718 DOI: 10.1016/j.abb.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/18/2017] [Accepted: 02/28/2017] [Indexed: 11/21/2022]
Abstract
NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures.
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33
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Lane AN, Fan TWM. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry. Arch Biochem Biophys 2017; 628:123-131. [PMID: 28263717 DOI: 10.1016/j.abb.2017.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 01/23/2023]
Abstract
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA.
| | - Teresa W-M Fan
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA
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34
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Smith AA. INFOS: spectrum fitting software for NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2017; 67:77-94. [PMID: 28160196 DOI: 10.1007/s10858-016-0085-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit. Estimation of error on fitting parameters is performed using a Monte-Carlo approach. Many fitting options allow the software to be flexible enough for a wide array of applications, while still being straightforward to set up with minimal user input.
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Affiliation(s)
- Albert A Smith
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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35
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Würz JM, Güntert P. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK. JOURNAL OF BIOMOLECULAR NMR 2017; 67:63-76. [PMID: 28160195 DOI: 10.1007/s10858-016-0084-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.
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Affiliation(s)
- Julia M Würz
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
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36
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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37
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Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, Vuister GW. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2016; 66:111-124. [PMID: 27663422 PMCID: PMC5095159 DOI: 10.1007/s10858-016-0060-y] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/10/2016] [Indexed: 05/06/2023]
Abstract
NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.
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Affiliation(s)
- Simon P Skinner
- Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK
| | - Rasmus H Fogh
- Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Ragan
- Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK
| | - Luca G Mureddu
- Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK.
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38
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Quinternet M, Chagot ME, Rothé B, Tiotiu D, Charpentier B, Manival X. Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species. Structure 2016; 24:1693-1706. [PMID: 27594683 DOI: 10.1016/j.str.2016.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/15/2022]
Abstract
Box C/D small nucleolar ribonucleoparticles (snoRNPs) support 2'-O-methylation of several target RNAs. They share a common set of four core proteins (SNU13, NOP58, NOP56, and FBL) that are assembled on different guide small nucleolar RNAs. Assembly of these entities involves additional protein factors that are absent in the mature active particle. In this context, the platform protein NUFIP1/Rsa1 establishes direct and simultaneous contacts with core proteins and with the components of the assembly machinery. Here, we solve the nuclear magnetic resonance (NMR) structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Using yeast two-hybrid and complementation assays, protein co-expression, isothermal titration calorimetry, and NMR, we demonstrate that yeast and human complexes involving NUFIP1/Rsa1p, ZNHIT3/Hit1p, and SNU13/Snu13p share strong structural similarities, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species.
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Affiliation(s)
- Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie-Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France; Ecole polytechnique fédérale de Lausanne (EPFL) SV ISREC, Station 19, 1015 Lausanne, Switzerland
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Biopôle, Campus Biologie Santé, 9 Avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France.
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39
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Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc 2016; 138:9730-42. [PMID: 27387657 PMCID: PMC5051545 DOI: 10.1021/jacs.6b06543] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.
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Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - David H. Brookes
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037
| | - Julie D. Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Daniel Gunter
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | | | - Gregory L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter E. Wright
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
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40
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Hoppstock L, Trusch F, Lederer C, van West P, Koenneke M, Bayer P. NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase. BMC Biol 2016; 14:53. [PMID: 27349962 PMCID: PMC4922055 DOI: 10.1186/s12915-016-0274-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022] Open
Abstract
Background Peptidyl-prolyl isomerases (PPIases) are present in all forms of life and play a crucial role in protein folding and regulation. They catalyze the cis-trans isomerization of the peptide bond that precedes proline residues in numerous proteins. The parvulins, which is one family of PPIases, have been extensively investigated in several eukaryotes. However, nothing is known about their expression, function and localization in archaea. Results Here, we describe the endogenous expression, molecular structure, function and cellular localization of NmPin, a single-domain parvulin-type PPIase from Nitrosopumilus maritimus. This marine chemolithoautotrophic archaeon belongs to the globally abundant phylum Thaumarchaeota. Using high resolution NMR spectroscopy we demonstrate that the 3D structure of NmPin adopts a parvulin fold and confirmed its peptidyl-prolyl isomerase activity by protease-coupled assays and mutagenesis studies. A detailed topological analysis revealed a positively charged lysine-rich patch on the protein surface, which is conserved in all known parvulin sequences of thaumarchaeotes and targets NmPin to lipids in vitro. Immunofluorescence microscopy confirms that the protein is attached to the outer archaeal cell membrane in vivo. Transmission electron microscopy uncovered that NmPin has a uniform distribution at the membrane surface, which is correlated with a native cell shape of the prokaryote. Conclusion We present a novel solution structure of a catalytically active thaumarchaeal parvulin. Our results reveal that a lysine-rich patch in NmPin mediates membrane localization. These findings provide a model whereby NmPin is located between the archaeal membrane and the surface layer and hence suggest proteins of the S-layer as the key target substrates of this parvulin. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0274-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lukas Hoppstock
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 1-4, 45141, Essen, Germany
| | - Franziska Trusch
- Aberdeen Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, AB25 2ZD, Aberdeen, UK
| | - Christoph Lederer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 1-4, 45141, Essen, Germany
| | - Pieter van West
- Aberdeen Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, AB25 2ZD, Aberdeen, UK
| | - Martin Koenneke
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Str. MARUM, 28359, Bremen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 1-4, 45141, Essen, Germany.
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41
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Tossavainen H, Aitio O, Hellman M, Saksela K, Permi P. Structural Basis of the High Affinity Interaction between the Alphavirus Nonstructural Protein-3 (nsP3) and the SH3 Domain of Amphiphysin-2. J Biol Chem 2016; 291:16307-17. [PMID: 27268056 DOI: 10.1074/jbc.m116.732412] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/25/2022] Open
Abstract
We show that a peptide from Chikungunya virus nsP3 protein spanning residues 1728-1744 binds the amphiphysin-2 (BIN1) Src homology-3 (SH3) domain with an unusually high affinity (Kd 24 nm). Our NMR solution complex structure together with isothermal titration calorimetry data on several related viral and cellular peptide ligands reveal that this exceptional affinity originates from interactions between multiple basic residues in the target peptide and the extensive negatively charged binding surface of amphiphysin-2 SH3. Remarkably, these arginines show no fixed conformation in the complex structure, indicating that a transient or fluctuating polyelectrostatic interaction accounts for this affinity. Thus, via optimization of such dynamic electrostatic forces, viral peptides have evolved a superior binding affinity for amphiphysin-2 SH3 compared with typical cellular ligands, such as dynamin, thereby enabling hijacking of amphiphysin-2 SH3-regulated host cell processes by these viruses. Moreover, our data show that the previously described consensus sequence PXRPXR for amphiphysin SH3 ligands is inaccurate and instead define it as an extended Class II binding motif PXXPXRpXR, where additional positive charges between the two constant arginine residues can give rise to extraordinary high SH3 binding affinity.
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Affiliation(s)
- Helena Tossavainen
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Olli Aitio
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Maarit Hellman
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Kalle Saksela
- the Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland and
| | - Perttu Permi
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and the Departments of Biological and Environmental Science and Chemistry, Nanoscience Center, University of Jyvaskyla, FI-40014 Jyvaskyla, Finland
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42
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Brookes DH, Head-Gordon T. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins. J Am Chem Soc 2016; 138:4530-8. [PMID: 26967199 DOI: 10.1021/jacs.6b00351] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We develop a Bayesian approach to determine the most probable structural ensemble model from candidate structures for intrinsically disordered proteins (IDPs) that takes full advantage of NMR chemical shifts and J-coupling data, their known errors and variances, and the quality of the theoretical back-calculation from structure to experimental observables. Our approach differs from previous formulations in the optimization of experimental and back-calculation nuisance parameters that are treated as random variables with known distributions, as opposed to structural or ensemble weight optimization or use of a reference ensemble. The resulting experimental inferential structure determination (EISD) method is size extensive with O(N) scaling, with N = number of structures, that allows for the rapid ranking of large ensemble data comprising tens of thousands of conformations. We apply the EISD approach on singular folded proteins and a corresponding set of ∼25 000 misfolded states to illustrate the problems that can arise using Boltzmann weighted priors. We then apply the EISD method to rank IDP ensembles most consistent with the NMR data and show that the primary error for ranking or creating good IDP ensembles resides in the poor back-calculation from structure to simulated experimental observable. We show that a reduction by a factor of 3 in the uncertainty of the back-calculation error can improve the discrimination among qualitatively different IDP ensembles for the amyloid-beta peptide.
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Affiliation(s)
- David H Brookes
- Department of Chemistry, ‡Department of Bioengineering, §Department of Chemical and Biomolecular Engineering, ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California , Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Department of Chemistry, ‡Department of Bioengineering, §Department of Chemical and Biomolecular Engineering, ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California , Berkeley, California 94720, United States
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43
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Baek MH, Kamiya M, Kushibiki T, Nakazumi T, Tomisawa S, Abe C, Kumaki Y, Kikukawa T, Demura M, Kawano K, Aizawa T. Lipopolysaccharide-bound structure of the antimicrobial peptide cecropin P1 determined by nuclear magnetic resonance spectroscopy. J Pept Sci 2016; 22:214-21. [PMID: 26939541 DOI: 10.1002/psc.2865] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/03/2016] [Accepted: 01/28/2016] [Indexed: 11/10/2022]
Abstract
Antimicrobial peptides (AMPs) are components of the innate immune system and may be potential alternatives to conventional antibiotics because they exhibit broad-spectrum antimicrobial activity. The AMP cecropin P1 (CP1), isolated from nematodes found in the stomachs of pigs, is known to exhibit antimicrobial activity against Gram-negative bacteria. In this study, we investigated the interaction between CP1 and lipopolysaccharide (LPS), which is the main component of the outer membrane of Gram-negative bacteria, using circular dichroism (CD) and nuclear magnetic resonance (NMR). CD results showed that CP1 formed an α-helical structure in a solution containing LPS. For NMR experiments, we expressed (15) N-labeled and (13) C-labeled CP1 in bacterial cells and successfully assigned almost all backbone and side-chain proton resonance peaks of CP1 in water for transferred nuclear Overhauser effect (Tr-NOE) experiments in LPS. We performed (15) N-edited and (13) C-edited Tr-NOE spectroscopy for CP1 bound to LPS. Tr-NOE peaks were observed at the only C-terminal region of CP1 in LPS. The results of structure calculation indicated that the C-terminal region (Lys15-Gly29) formed the well-defined α-helical structure in LPS. Finally, the docking study revealed that Lys15/Lys16 interacted with phosphate at glucosamine I via an electrostatic interaction and that Ile22/Ile26 was in close proximity with the acyl chain of lipid A.
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Affiliation(s)
- Mi-Hwa Baek
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Masakatsu Kamiya
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Takahiro Kushibiki
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Taichi Nakazumi
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Satoshi Tomisawa
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Chiharu Abe
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Yasuhiro Kumaki
- Graduate School of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Takashi Kikukawa
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Makoto Demura
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Keiichi Kawano
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Chitose Institute of Science and Technology, 758-65 Bibi, Chitose, Hokkaido, 066-8655, Japan
| | - Tomoyasu Aizawa
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
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44
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Li DW, Brüschweiler R. Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations. J Chem Theory Comput 2015; 10:1781-7. [PMID: 26580385 DOI: 10.1021/ct4010646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center and Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center and Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
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45
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Laitaoja M, Tossavainen H, Pihlajamaa T, Valjakka J, Viiri K, Lohi O, Permi P, Jänis J. Redox-dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function. Protein Sci 2015; 25:572-86. [PMID: 26609676 DOI: 10.1002/pro.2849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/14/2015] [Indexed: 11/08/2022]
Abstract
Sin3A-associated protein 30-like (SAP30L) is one of the key proteins in a multi-subunit protein complex involved in transcriptional regulation via histone deacetylation. SAP30L, together with a highly homologous SAP30 as well as other SAP proteins (i.e., SAP25, SAP45, SAP130, and SAP180), is an essential component of the Sin3A corepressor complex, although its actual role has remained elusive. SAP30L is thought to function as an important stabilizing and bridging molecule in the complex and to mediate its interactions with other corepressors. SAP30L has been previously shown to contain an N-terminal Cys3 His type zinc finger (ZnF) motif, which is responsible for the key protein-protein, protein-DNA, and protein-lipid interactions. By using high-resolution mass spectrometry, we studied a redox-dependent disulfide bond formation in SAP30L ZnF as a regulatory mechanism for its structure and function. We showed that upon oxidative stress SAP30L undergoes the formation of two specific disulfide bonds, a vicinal Cys29-Cys30 and Cys38-Cys74, with a concomitant release of the coordinated zinc ion. The oxidized protein was shown to remain folded in solution and to bind signaling phospholipids. We also determined a solution NMR structure for SAP30L ZnF that showed an overall fold similar to that of SAP30, determined earlier. The NMR titration experiments with lipids and DNA showed that the binding is mediated by the C-terminal tail as well as both α-helices of SAP30L ZnF. The implications of these results for the structure and function of SAP30L are discussed.
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Affiliation(s)
- Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | | | - Tero Pihlajamaa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Keijo Viiri
- Center for Child Health Research and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Olli Lohi
- Center for Child Health Research and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Perttu Permi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
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46
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Yilmaz EM, Güntert P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. JOURNAL OF BIOMOLECULAR NMR 2015; 63:21-37. [PMID: 26123317 DOI: 10.1007/s10858-015-9959-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/22/2015] [Indexed: 05/15/2023]
Abstract
An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.
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Affiliation(s)
- Emel Maden Yilmaz
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Peter Güntert
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, Switzerland.
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
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47
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Abstract
Three-dimensional structures of proteins in solution can be calculated on the basis of conformational restraints derived from NMR measurements. This chapter gives an overview of the computational methods for NMR protein structure analysis highlighting recent automated methods for the assignment of NMR spectra, the collection of conformational restraints, and the structure calculation.
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48
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Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. JOURNAL OF BIOMOLECULAR NMR 2015; 62:481-95. [PMID: 25900069 PMCID: PMC4569665 DOI: 10.1007/s10858-015-9933-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/15/2015] [Indexed: 05/21/2023]
Abstract
The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
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Affiliation(s)
- Hesam Dashti
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Claudia C Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Fariba M Assadi-Porter
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Hamid R Eghbalnia
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
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49
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Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, Lee HW, Prestegard JH, Yee A, Wu B, Lemak A, Houliston S, Arrowsmith CH, Kennedy M, Acton TB, Xiao R, Liu G, Montelione GT, Vuister GW. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. JOURNAL OF BIOMOLECULAR NMR 2015; 62:413-24. [PMID: 26071966 PMCID: PMC4569658 DOI: 10.1007/s10858-015-9953-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 05/28/2015] [Indexed: 05/21/2023]
Abstract
The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.
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Affiliation(s)
- Antonio Rosato
- Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- (IB)2 Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
| | - Rasmus H Fogh
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Timothy J Ragan
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Roberto Tejero
- Departamento de Química Física, Universidad de Valencia, Avda. Dr. Moliner 50, 46100, Burjassot (Valencia), Spain
| | - Kari Pederson
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Adelinda Yee
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Bin Wu
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alexander Lemak
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Scott Houliston
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Michael Kennedy
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Thomas B Acton
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK.
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50
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Güntert P, Buchner L. Combined automated NOE assignment and structure calculation with CYANA. JOURNAL OF BIOMOLECULAR NMR 2015; 62:453-71. [PMID: 25801209 DOI: 10.1007/s10858-015-9924-9] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 05/12/2023]
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.
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Affiliation(s)
- Peter Güntert
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Laboratory of Physical Chemistry, ETH Zürich, Zurich, Switzerland.
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
| | - Lena Buchner
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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