1
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Oshiro KGN, Freitas CDP, Rezende SB, Orozco RMQ, Chan LY, Lawrence N, Lião LM, Macedo MLR, Craik DJ, Cardoso MH, Franco OL. Deciphering the structure and mechanism of action of computer-designed mastoparan peptides. FEBS J 2024; 291:865-883. [PMID: 37997610 DOI: 10.1111/febs.17010] [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: 05/24/2023] [Revised: 10/05/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Mastoparans are cationic peptides with multifunctional pharmacological properties. Mastoparan-R1 and mastoparan-R4 were computationally designed based on native mastoparan-L from wasps and have improved therapeutic potential for the control of bacterial infections. Here, we evaluated whether these peptides maintain their activity against Escherichia coli strains under a range of salt concentrations. We found that mastoparan-R1 and mastoparan-R4 preserved their activity under the conditions tested, including having antibacterial activities at physiological salt concentrations. The overall structure of the peptides was investigated using circular dichroism spectroscopy in a range of solvents. No significant changes in secondary structure were observed (random coil in aqueous solutions and α-helix in hydrophobic and anionic environments). The three-dimensional structures of mastoparan-R1 and mastoparan-R4 were elucidated through nuclear magnetic resonance spectroscopy, revealing amphipathic α-helical segments for Leu3-Ile13 (mastoparan-R1) and Leu3-Ile14 (mastoparan-R4). Possible membrane-association mechanisms for mastoparan-R1 and mastoparan-R4 were investigated through surface plasmon resonance and leakage studies with synthetic POPC and POPC/POPG (4:1) lipid bilayers. Mastoparan-L had the highest affinity for both membrane systems, whereas the two analogs had weaker association, but improved selectivity for lysing anionic membranes. This finding was also supported by molecular dynamics simulations, in which mastoparan-R1 and mastoparan-R4 were found to have greater interactions with bacteria-like membranes compared with model mammalian membranes. Despite having a few differences in their functional and structural profiles, the mastoparan-R1 analog stood out with the highest activity, greater bacteriostatic potential, and selectivity for lysing anionic membranes. This study reinforces the potential of mastoparan-R1 as a drug candidate.
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Affiliation(s)
- Karen G N Oshiro
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Carlos D P Freitas
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Samilla B Rezende
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Raquel M Q Orozco
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Luciano M Lião
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Maria L R Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
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2
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Sorokina M, Belapure J, Tüting C, Paschke R, Papasotiriou I, Rodrigues JP, Kastritis PL. An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation. J Mol Biol 2022; 434:167637. [PMID: 35595165 PMCID: PMC9112565 DOI: 10.1016/j.jmb.2022.167637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022]
Abstract
After two years since the outbreak, the COVID-19 pandemic remains a global public health emergency. SARS-CoV-2 variants with substitutions on the spike (S) protein emerge increasing the risk of immune evasion and cross-species transmission. Here, we analyzed the evolution of the S protein as recorded in 276,712 samples collected before the start of vaccination efforts. Our analysis shows that most variants destabilize the S protein trimer, increase its conformational heterogeneity and improve the odds of the recognition by the host cell receptor. Most frequent substitutions promote overall hydrophobicity by replacing charged amino acids, reducing stabilizing local interactions in the unbound S protein trimer. Moreover, our results identify "forbidden" regions that rarely show any sequence variation, and which are related to conformational changes occurring upon fusion. These results are significant for understanding the structure and function of SARS-CoV-2 related proteins which is a critical step in vaccine development and epidemiological surveillance.
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Affiliation(s)
- Marija Sorokina
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany,RGCC International GmbH, Baarerstrasse 95, Zug 6300, Switzerland,BioSolutions GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Jaydeep Belapure
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany
| | - Reinhard Paschke
- BioSolutions GmbH, Weinbergweg 22, 06120 Halle/Saale, Germany,Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale, Germany
| | | | | | - Panagiotis L. Kastritis
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany,Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle/Saale, Germany,Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale, Germany,Corresponding author at: Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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3
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Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
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Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
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4
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Xie Q, Yoshioka CK, Chapman MS. Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Å Resolution. Viruses 2020; 12:E1194. [PMID: 33092282 PMCID: PMC7589773 DOI: 10.3390/v12101194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/12/2023] Open
Abstract
Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 Å or higher resolution, and AAV-DJ nearly matches the highest resolutions ever attained through X-ray diffraction of virus crystals. However, cryo-EM has the advantage that most of the hydrogens are clear, improving the accuracy of atomic refinement, and removing ambiguity in hydrogen bond identification. Outside of secondary structures where hydrogen bonding was predictable a priori, the networks of hydrogen bonds coming from direct observation of hydrogens and acceptor atoms are quite different from those inferred even at 2.8 Å resolution. The implications for understanding viral assembly mean that cryo-EM will likely become the favored approach for high resolution structural virology.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Craig K. Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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5
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Krichel C, Möckel C, Schillinger O, Huesgen PF, Sticht H, Strodel B, Weiergräber OH, Willbold D, Neudecker P. Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site. Sci Rep 2019; 9:14167. [PMID: 31578424 PMCID: PMC6775092 DOI: 10.1038/s41598-019-48155-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/26/2019] [Indexed: 11/09/2022] Open
Abstract
(Macro-)autophagy is a compartmental degradation pathway conserved from yeast to mammals. The yeast protein Atg8 mediates membrane tethering/hemifusion and cargo recruitment and is essential for autophagy. The human MAP1LC3/GABARAP family proteins show high sequence identity with Atg8, but MAP1LC3C is distinguished by a conspicuous amino-terminal extension with unknown functional significance. We have determined the high-resolution three-dimensional structure and measured the backbone dynamics of MAP1LC3C by NMR spectroscopy. From Ser18 to Ala120, MAP1LC3C forms an α-helix followed by the ubiquitin-like tertiary fold with two hydrophobic binding pockets used by MAP1LC3/GABARAP proteins to recognize targets presenting LC3-interacting regions (LIRs). Unlike other MAP1LC3/GABARAP proteins, the amino-terminal region of MAP1LC3C does not form a stable helix α1 but a "sticky arm" consisting of a polyproline II motif on a flexible linker. Ser18 at the interface between this linker and the structural core can be phosphorylated in vitro by protein kinase A, which causes additional conformational heterogeneity as monitored by NMR spectroscopy and molecular dynamics simulations, including changes in the LIR-binding interface. Based on these results we propose that the amino-terminal polyproline II motif mediates specific interactions with the microtubule cytoskeleton and that Ser18 phosphorylation modulates the interplay of MAP1LC3C with its various target proteins.
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Affiliation(s)
- Carsten Krichel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Christina Möckel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Oliver Schillinger
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Pitter F Huesgen
- ZEA-3 (Analytik), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Heinrich Sticht
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Birgit Strodel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Oliver H Weiergräber
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
| | - Philipp Neudecker
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
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6
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El Hamdaoui Y, Wu X, Clark RJ, Giribaldi J, Anangi R, Craik DJ, King GF, Dutertre S, Kaas Q, Herzig V, Nicke A. Periplasmic Expression of 4/7 α-Conotoxin TxIA Analogs in E. coli Favors Ribbon Isomer Formation - Suggestion of a Binding Mode at the α7 nAChR. Front Pharmacol 2019; 10:577. [PMID: 31214027 PMCID: PMC6554660 DOI: 10.3389/fphar.2019.00577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/06/2019] [Indexed: 01/02/2023] Open
Abstract
Peptides derived from animal venoms provide important research tools for biochemical and pharmacological characterization of receptors, ion channels, and transporters. Some venom peptides have been developed into drugs (such as the synthetic ω-conotoxin MVIIA, ziconotide) and several are currently undergoing clinical trials for various clinical indications. Challenges in the development of peptides include their usually limited supply from natural sources, cost-intensive chemical synthesis, and potentially complicated stereoselective disulfide-bond formation in the case of disulfide-rich peptides. In particular, if extended structure–function analysis is performed or incorporation of stable isotopes for NMR studies is required, the comparatively low yields and high costs of synthesized peptides might constitute a limiting factor. Here we investigated the expression of the 4/7 α-conotoxin TxIA, a potent blocker at α3β2 and α7 nicotinic acetylcholine receptors (nAChRs), and three analogs in the form of maltose binding protein fusion proteins in Escherichia coli. Upon purification via nickel affinity chromatography and release of the toxins by protease cleavage, HPLC analysis revealed one major peak with the correct mass for all peptides. The final yield was 1–2 mg of recombinant peptide per liter of bacterial culture. Two-electrode voltage clamp analysis on oocyte-expressed nAChR subtypes demonstrated the functionality of these peptides but also revealed a 30 to 100-fold potency decrease of expressed TxIA compared to chemically synthesized TxIA. NMR spectroscopy analysis of TxIA and two of its analogs confirmed that the decreased activity was due to an alternative disulfide linkage rather than the missing C-terminal amidation, a post-translational modification that is common in α-conotoxins. All peptides preferentially formed in the ribbon conformation rather than the native globular conformation. Interestingly, in the case of the α7 nAChR, but not the α3β2 subtype, the loss of potency could be rescued by an R5D substitution. In conclusion, we demonstrate efficient expression of functional but alternatively folded ribbon TxIA variants in E. coli and provide the first structure–function analysis for a ribbon 4/7-α-conotoxin at α7 and α3β2 nAChRs. Computational analysis based on these data provide evidence for a ribbon α-conotoxin binding mode that might be exploited to design ligands with optimized selectivity.
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Affiliation(s)
- Yamina El Hamdaoui
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Xiaosa Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Julien Giribaldi
- CNRS, Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, Montpellier, France
| | - Raveendra Anangi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Sebastien Dutertre
- CNRS, Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, Montpellier, France
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
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7
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8
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Harrer N, Schindler CEM, Bruetzel LK, Forné I, Ludwigsen J, Imhof A, Zacharias M, Lipfert J, Mueller-Planitz F. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling. Structure 2018; 26:282-294.e6. [PMID: 29395785 DOI: 10.1016/j.str.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/25/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022]
Abstract
Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module.
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Affiliation(s)
- Nadine Harrer
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Christina E M Schindler
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
| | - Ignasi Forné
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Johanna Ludwigsen
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Axel Imhof
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Martin Zacharias
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany.
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany.
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9
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Bratkowski M, Unarta IC, Zhu L, Shubbar M, Huang X, Liu X. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk. J Biol Chem 2017; 293:1651-1665. [PMID: 29158257 DOI: 10.1074/jbc.m117.811521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/10/2017] [Indexed: 11/06/2022] Open
Abstract
Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that the TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. We propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk.
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Affiliation(s)
- Matthew Bratkowski
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Ilona Christy Unarta
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Lizhe Zhu
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Murtada Shubbar
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Xuhui Huang
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xin Liu
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and .,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
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10
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Catazaro J, Periago J, Shortridge MD, Worley B, Kirchner A, Powers R, Griep MA. Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain. Biochemistry 2017; 56:932-943. [PMID: 28125218 PMCID: PMC6476306 DOI: 10.1021/acs.biochem.6b01273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interface between the DnaG primase C-terminal domain (CTD) and the N-terminal domain of DnaB helicase is essential for bacterial DNA replication because it allows coordinated priming of DNA synthesis at the replication fork while the DNA is being unwound. Because these two proteins are conserved in all bacteria and distinct from those in eukaryotes, their interface is an attractive antibiotic target. To learn more about this interface, we determined the solution structure and dynamics of the DnaG primase CTD from Staphylococcus aureus, a medically important bacterial species. Comparison with the known primase CTD structures shows there are two biologically relevant conformations, an open conformation that likely binds to DnaB helicase and a closed conformation that does not. The S. aureus primase CTD is in the closed conformation, but nuclear magnetic resonance (NMR) dynamic studies indicate there is considerable movement in the linker between the two subdomains and that N564 is the most dynamic residue within the linker. A high-throughput NMR ligand affinity screen identified potential binding compounds, among which were acycloguanosine and myricetin. Although the affinity for these compounds and adenosine was in the millimolar range, all three bind to a common pocket that is present only on the closed conformation of the CTD. This binding pocket is at the opposite end of helices 6 and 7 from N564, the key hinge residue. The identification of this binding pocket should allow the development of stronger-binding ligands that can prevent formation of the CTD open conformation that binds to DnaB helicase.
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Affiliation(s)
| | | | | | - Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Andrew Kirchner
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Mark A. Griep
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
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11
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Tian Y, Schwieters CD, Opella SJ, Marassi FM. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH. JOURNAL OF BIOMOLECULAR NMR 2017; 67:35-49. [PMID: 28035651 PMCID: PMC5487259 DOI: 10.1007/s10858-016-0082-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision, and conformation, and that structure refinement can be obtained by short relaxation with EEFx to obtain improvements in these key metrics. These developments broaden the range of biomolecular structures that can be calculated with high fidelity from NMR restraints.
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Affiliation(s)
- Ye Tian
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Charles D Schwieters
- Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD, 20892-5624, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0307, USA
| | - Francesca M Marassi
- Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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12
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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches. Methods Mol Biol 2016. [PMID: 27924488 DOI: 10.1007/978-1-4939-6563-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.
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13
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Schindler CEM, Chauvot de Beauchêne I, de Vries SJ, Zacharias M. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins 2016; 85:391-398. [PMID: 27785830 DOI: 10.1002/prot.25196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/13/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022]
Abstract
The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed. Proteins 2017; 85:391-398. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Christina E M Schindler
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
| | | | - Sjoerd J de Vries
- Physics Department T38, Technische Universität München, Garching, 85748, Germany
| | - Martin Zacharias
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
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14
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Sala D, Giachetti A, Luchinat C, Rosato A. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. JOURNAL OF BIOMOLECULAR NMR 2016; 66:175-185. [PMID: 27771862 DOI: 10.1007/s10858-016-0065-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.
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Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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15
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Deuis JR, Dekan Z, Inserra MC, Lee TH, Aguilar MI, Craik DJ, Lewis RJ, Alewood PF, Mobli M, Schroeder CI, Henriques ST, Vetter I. Development of a μO-Conotoxin Analogue with Improved Lipid Membrane Interactions and Potency for the Analgesic Sodium Channel NaV1.8. J Biol Chem 2016; 291:11829-42. [PMID: 27026701 DOI: 10.1074/jbc.m116.721662] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Indexed: 12/19/2022] Open
Abstract
The μO-conotoxins MrVIA, MrVIB, and MfVIA inhibit the voltage-gated sodium channel NaV1.8, a well described target for the treatment of pain; however, little is known about the residues or structural elements that define this activity. In this study, we determined the three-dimensional structure of MfVIA, examined its membrane binding properties, performed alanine-scanning mutagenesis, and identified residues important for its activity at human NaV1.8. A second round of mutations resulted in (E5K,E8K)MfVIA, a double mutant with greater positive surface charge and greater affinity for lipid membranes compared with MfVIA. This analogue had increased potency at NaV1.8 and was analgesic in the mouse formalin assay.
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Affiliation(s)
- Jennifer R Deuis
- From the Institute for Molecular Bioscience and School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4102, Australia, and
| | | | - Marco C Inserra
- From the Institute for Molecular Bioscience and School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4102, Australia, and
| | - Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | | | | | | | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | | | | | - Irina Vetter
- From the Institute for Molecular Bioscience and School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4102, Australia, and
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16
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Structure determination of helical filaments by solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2016; 113:E272-81. [PMID: 26733681 DOI: 10.1073/pnas.1513119113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVS(CARD) filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers.
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17
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Heering J, Jonker HRA, Löhr F, Schwalbe H, Dötsch V. Structural investigations of the p53/p73 homologs from the tunicate species Ciona intestinalis reveal the sequence requirements for the formation of a tetramerization domain. Protein Sci 2015; 25:410-22. [PMID: 26473758 DOI: 10.1002/pro.2830] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 11/09/2022]
Abstract
Most members of the p53 family of transcription factors form tetramers. Responsible for determining the oligomeric state is a short oligomerization domain consisting of one β-strand and one α-helix. With the exception of human p53 all other family members investigated so far contain a second α-helix as part of their tetramerization domain. Here we have used nuclear magnetic resonance spectroscopy to characterize the oligomerization domains of the two p53-like proteins from the tunicate Ciona intestinalis, representing the closest living relative of vertebrates. Structure determination reveals for one of the two proteins a new type of packing of this second α-helix on the core domain that was not predicted based on the sequence, while the other protein does not form a second helix despite the presence of crucial residues that are conserved in all other family members that form a second helix. By mutational analysis, we identify a proline as well as large hydrophobic residues in the hinge region between both helices as the crucial determinant for the formation of a second helix.
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Affiliation(s)
- Jan Heering
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt/Main, Germany
| | - Hendrik R A Jonker
- Institute of Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt/Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt/Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt/Main, Germany
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18
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Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. Biochem J 2015; 472:121-33. [PMID: 26371375 PMCID: PMC4692082 DOI: 10.1042/bj20150059] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 09/11/2015] [Indexed: 01/05/2023]
Abstract
Structural plasticity plays a major role in determining differential binding of CXCL8 monomer and dimer to glycosaminoglycans (GAGs) and that dimer is the high-affinity GAG ligand. We propose that these properties play important roles in orchestrating in vivo chemokine-mediated neutrophil function. Chemokine CXCL8/interleukin-8 (IL-8) plays a crucial role in directing neutrophils and oligodendrocytes to combat infection/injury and tumour cells in metastasis development. CXCL8 exists as monomers and dimers and interaction of both forms with glycosaminoglycans (GAGs) mediate these diverse cellular processes. However, very little is known regarding the structural basis underlying CXCL8–GAG interactions. There are conflicting reports on the affinities, geometry and whether the monomer or dimer is the high-affinity GAG ligand. To resolve these issues, we characterized the binding of a series of heparin-derived oligosaccharides [heparin disaccharide (dp2), heparin tetrasaccharide (dp4), heparin octasaccharide (dp8) and heparin 14-mer (dp14)] to the wild-type (WT) dimer and a designed monomer using solution NMR spectroscopy. The pattern and extent of binding-induced chemical shift perturbation (CSP) varied between dimer and monomer and between longer and shorter oligosaccharides. NMR-based structural models show that different interaction modes coexist and that the nature of interactions varied between monomer and dimer and oligosaccharide length. MD simulations indicate that the binding interface is structurally plastic and provided residue-specific details of the dynamic nature of the binding interface. Binding studies carried out under conditions at which WT CXCL8 exists as monomers and dimers provide unambiguous evidence that the dimer is the high-affinity GAG ligand. Together, our data indicate that a set of core residues function as the major recognition/binding site, a set of peripheral residues define the various binding geometries and that the structural plasticity of the binding interface allows multiplicity of binding interactions. We conclude that structural plasticity most probably regulates in vivo CXCL8 monomer/dimer–GAG interactions and function.
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19
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Tian Y, Schwieters CD, Opella SJ, Marassi FM. A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins. Biophys J 2015; 109:574-85. [PMID: 26244739 PMCID: PMC4572468 DOI: 10.1016/j.bpj.2015.06.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 01/22/2023] Open
Abstract
The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.
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Affiliation(s)
- Ye Tian
- Sanford-Burnham Medical Research Institute, La Jolla, California; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
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20
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Mareuil F, Malliavin TE, Nilges M, Bardiaux B. Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA. JOURNAL OF BIOMOLECULAR NMR 2015; 62:425-438. [PMID: 25861734 PMCID: PMC4569677 DOI: 10.1007/s10858-015-9928-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/03/2015] [Indexed: 05/30/2023]
Abstract
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD-NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD-NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.
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Affiliation(s)
- Fabien Mareuil
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 25-28 rue du Dr Roux, 75724, Paris Cedex 15, France
- Cellule d'Informatique pour la Biologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 25-28 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Michael Nilges
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 25-28 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Benjamin Bardiaux
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 25-28 rue du Dr Roux, 75724, Paris Cedex 15, France.
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21
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Jiang H, Sheong FK, Zhu L, Gao X, Bernauer J, Huang X. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement. PLoS Comput Biol 2015; 11:e1004404. [PMID: 26181723 PMCID: PMC4504477 DOI: 10.1371/journal.pcbi.1004404] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 01/17/2023] Open
Abstract
Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems. In RNA interference, Argonaute proteins and microRNAs together form the functional core that regulates the gene expression with high sequence specificity. Elucidating the detailed mechanism of molecular recognition between Argonaute proteins and microRNAs is thus important not only for the fundamental understanding of RNA interference, but also for the further development of microRNA-based therapeutic application. In this work, we propose a two-step model to understand the mechanism of microRNA loading into human Argonaute-2: selective binding followed by structural re-arrangement. Our model is based on the results from a combined approach of molecular dynamics simulations, Markov State Models and protein-RNA docking. In particular, we identify a metastable open state of apo hAgo2 in rapid equilibrium with other states. Some of conformations in this open state have largely exposed RNA binding groove that can accommodate microRNA. We further show that the initial Argonaute-microRNA binding complex undergoes structural re-arrangement to reach stable binary crystal structure. These results provide novel insights into the underlying mechanism of Argonaute-microRNA recognition. In addition, our method is readily applicable to the investigation of other complex molecular recognition events such as protein-protein interactions and protein-ligand binding.
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Affiliation(s)
- Hanlun Jiang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lizhe Zhu
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julie Bernauer
- Inria Saclay-Île de France, Bâtiment Alan Turing, Campus de l’École Polytechnique, Palaiseau, France
- Laboratoire d’Informatique de l’École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France
- * E-mail: (JB); (XH)
| | - Xuhui Huang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail: (JB); (XH)
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22
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Cho CC, Hung KW, Gorja DR, Yu C. The solution structure of human calcium-bound S100A4 mutated at four cysteine loci. JOURNAL OF BIOMOLECULAR NMR 2015; 62:233-238. [PMID: 25855140 DOI: 10.1007/s10858-015-9927-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Ching Chang Cho
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
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23
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Buchko GW, Yee A, Semesi A, Myler PJ, Arrowsmith CH, Hui R. Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) from Plasmodium falciparum. Acta Crystallogr F Struct Biol Commun 2015; 71:514-21. [PMID: 25945703 PMCID: PMC4427159 DOI: 10.1107/s2053230x1402799x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/23/2014] [Indexed: 12/22/2022] Open
Abstract
Protozoa of the genus Plasmodium are responsible for malaria, which is perhaps the most important parasitic disease to infect mankind. The emergence of Plasmodium strains resistant to current therapeutics and prophylactics makes the development of new treatment strategies urgent. Among the potential targets for new antimalarial drugs is the BolA-like protein PFE0790c from Plasmodium falciparum (Pf-BolA). While the function of BolA is unknown, it has been linked to cell morphology by regulating transcription in response to stress. Using an NMR-based method, an ensemble of 20 structures of Pf-BolA was determined and deposited in the PDB (PDB entry 2kdn). The overall topology of the Pf-BolA structure, α1-β1-β2-η1-α2/η2-β3-α3, with the β-strands forming a mixed β-sheet, is similar to the fold observed in other BolA structures. A helix-turn-helix motif similar to the class II KH fold associated with nucleic acid-binding proteins is present, but contains an FXGXXXL signature sequence that differs from the GXXG signature sequence present in class II KH folds, suggesting that the BolA family of proteins may use a novel protein-nucleic acid interface. A well conserved arginine residue, Arg50, hypothesized to play a role in governing the formation of the C-terminal α-helix in the BolA family of proteins, is too distant to form polar contacts with any side chains in this α-helix in Pf-BolA, suggesting that this conserved arginine may only serve a role in guiding the orientation of this C-terminal helix in some BolA proteins. A survey of BolA structures suggests that the C-terminal helix may not have a functional role and that the third helix (α2/η2) has a `kink' that appears to be conserved among the BolA protein structures. Circular dichroism spectroscopy shows that Pf-BolA is fairly robust, partially unfolding when heated to 353 K and refolding upon cooling to 298 K.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Adelinda Yee
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anthony Semesi
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle BioMed, Seattle, Washington, USA
- Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Cheryl H. Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Structural Genomics Consortium, England
| | - Raymond Hui
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Structural Genomics Consortium, England
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Schindler CEM, de Vries SJ, Zacharias M. iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement. Proteins 2014; 83:248-58. [PMID: 25402278 DOI: 10.1002/prot.24728] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/30/2014] [Accepted: 11/12/2014] [Indexed: 11/12/2022]
Abstract
Protein-protein interactions are abundant in the cell but to date structural data for a large number of complexes is lacking. Computational docking methods can complement experiments by providing structural models of complexes based on structures of the individual partners. A major caveat for docking success is accounting for protein flexibility. Especially, interface residues undergo significant conformational changes upon binding. This limits the performance of docking methods that keep partner structures rigid or allow limited flexibility. A new docking refinement approach, iATTRACT, has been developed which combines simultaneous full interface flexibility and rigid body optimizations during docking energy minimization. It employs an atomistic molecular mechanics force field for intermolecular interface interactions and a structure-based force field for intramolecular contributions. The approach was systematically evaluated on a large protein-protein docking benchmark, starting from an enriched decoy set of rigidly docked protein-protein complexes deviating by up to 15 Å from the native structure at the interface. Large improvements in sampling and slight but significant improvements in scoring/discrimination of near native docking solutions were observed. Complexes with initial deviations at the interface of up to 5.5 Å were refined to significantly better agreement with the native structure. Improvements in the fraction of native contacts were especially favorable, yielding increases of up to 70%.
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25
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Mechelke M, Habeck M. Bayesian weighting of statistical potentials in NMR structure calculation. PLoS One 2014; 9:e100197. [PMID: 24956116 PMCID: PMC4067304 DOI: 10.1371/journal.pone.0100197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/23/2014] [Indexed: 11/24/2022] Open
Abstract
The use of statistical potentials in NMR structure calculation improves the accuracy of the final structure but also raises issues of double counting and possible bias. Because statistical potentials are averaged over a large set of structures, they may not reflect the preferences of a particular structure or data set. We propose a Bayesian method to incorporate a knowledge-based backbone dihedral angle potential into an NMR structure calculation. To avoid bias exerted through the backbone potential, we adjust its weight by inferring it from the experimental data. We demonstrate that an optimally weighted potential leads to an improvement in the accuracy and quality of the final structure, especially with sparse and noisy data. Our findings suggest that no universally optimal weight exists, and that the weight should be determined based on the experimental data. Other knowledge-based potentials can be incorporated using the same approach.
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Affiliation(s)
- Martin Mechelke
- Institute for Mathematical Stochastics, Georg August University Göttingen, Göttingen, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Habeck
- Institute for Mathematical Stochastics, Georg August University Göttingen, Göttingen, Germany
- * E-mail:
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26
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Tian Y, Schwieters CD, Opella SJ, Marassi FM. A practical implicit solvent potential for NMR structure calculation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 243:54-64. [PMID: 24747742 PMCID: PMC4037354 DOI: 10.1016/j.jmr.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 05/30/2023]
Abstract
The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide templates. Here we describe a new implicit solvation potential, EEFx (Effective Energy Function for XPLOR-NIH), for NMR-restrained structure calculations of proteins in XPLOR-NIH. The key components of EEFx are an energy term for solvation energy that works together with other nonbonded energy functions, and a dedicated force field for conformational and nonbonded protein interaction parameters. The initial results obtained with EEFx show that significant improvements in structural quality can be obtained. EEFx is computationally efficient and can be used both to fold and refine structures. Overall, EEFx improves the quality of protein conformation and nonbonded atomic interactions. Moreover, such benefits are accompanied by enhanced structural precision and enhanced structural accuracy, reflected in improved agreement with the cross-validated dipolar coupling data. Finally, implementation of EEFx calculations is straightforward and computationally efficient. Overall, EEFx provides a useful method for the practical calculation of experimental protein structures in a physically realistic environment.
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Affiliation(s)
- Ye Tian
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | - Francesca M Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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27
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Jia X, Kwon S, Wang CIA, Huang YH, Chan LY, Tan CC, Rosengren KJ, Mulvenna JP, Schroeder CI, Craik DJ. Semienzymatic cyclization of disulfide-rich peptides using Sortase A. J Biol Chem 2014; 289:6627-6638. [PMID: 24425873 DOI: 10.1074/jbc.m113.539262] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Disulfide-rich cyclic peptides have generated great interest in the development of peptide-based therapeutics due to their exceptional stability toward chemical, enzymatic, or thermal attack. In particular, they have been used as scaffolds onto which bioactive epitopes can be grafted to take advantage of the favorable biophysical properties of disulfide-rich cyclic peptides. To date, the most commonly used method for the head-to-tail cyclization of peptides has been native chemical ligation. In recent years, however, enzyme-mediated cyclization has become a promising new technology due to its efficiency, safety, and cost-effectiveness. Sortase A (SrtA) is a bacterial enzyme with transpeptidase activity. It recognizes a C-terminal penta-amino acid motif, LPXTG, and cleaves the amide bond between Thr and Gly to form a thioacyl-linked intermediate. This intermediate undergoes nucleophilic attack by an N-terminal poly-Gly sequence to form an amide bond between the Thr and N-terminal Gly. Here, we demonstrate that sortase A can successfully be used to cyclize a variety of small disulfide-rich peptides, including the cyclotide kalata B1, α-conotoxin Vc1.1, and sunflower trypsin inhibitor 1. These peptides range in size from 14 to 29 amino acids and contain three, two, or one disulfide bond, respectively, within their head-to-tail cyclic backbones. Our findings provide proof of concept for the potential broad applicability of enzymatic cyclization of disulfide-rich peptides with therapeutic potential.
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Affiliation(s)
- Xinying Jia
- From QIMR Berghofer Medical Research, Brisbane 4000, Queensland, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Soohyun Kwon
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ching-I Anderson Wang
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Chia Chia Tan
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Jason P Mulvenna
- From QIMR Berghofer Medical Research, Brisbane 4000, Queensland, Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia.
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Curd RD, Birdsall B, Kadekoppala M, Ogun SA, Kelly G, Holder AA. The structure of Plasmodium yoelii merozoite surface protein 119, antibody specificity and implications for malaria vaccine design. Open Biol 2014; 4:130091. [PMID: 24403012 PMCID: PMC3909271 DOI: 10.1098/rsob.130091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/06/2013] [Indexed: 11/12/2022] Open
Abstract
Merozoite surface protein 1 (MSP1) has been identified as a target antigen for protective immune responses against asexual blood stage malaria, but effective vaccines based on MSP1 have not been developed so far. We have modified the sequence of Plasmodium yoelii MSP119 (the C-terminal region of the molecule) and examined the ability of the variant proteins to bind protective monoclonal antibodies and to induce protection by immunization. In parallel, we examined the structure of the protein and the consequences of the amino acid changes. Naturally occurring sequence polymorphisms reduced the binding of individual protective antibodies, indicating that they contribute to immune evasion, but immunization with these variant proteins still provided protective immunity. One variant that resulted in the localized distortion of a loop close to the N-terminus of MSP119 almost completely ablated protection by immunization, indicating the importance of this region of MSP119 as a target for protective immunity and in vaccine development.
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Affiliation(s)
- Rachel D. Curd
- Divisions of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Berry Birdsall
- Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Madhusudan Kadekoppala
- Divisions of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Solabomi A. Ogun
- Divisions of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoffrey Kelly
- NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Anthony A. Holder
- Divisions of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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29
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Luo S, Zhangsun D, Schroeder CI, Zhu X, Hu Y, Wu Y, Weltzin MM, Eberhard S, Kaas Q, Craik DJ, McIntosh JM, Whiteaker P. A novel α4/7-conotoxin LvIA from Conus lividus that selectively blocks α3β2 vs. α6/α3β2β3 nicotinic acetylcholine receptors. FASEB J 2014; 28:1842-53. [PMID: 24398291 DOI: 10.1096/fj.13-244103] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This study was performed to discover and characterize the first potent α3β2-subtype-selective nicotinic acetylcholine receptor (nAChR) ligand. A novel α4/7-conotoxin, α-CTxLvIA, was cloned from Conus lividus. Its pharmacological profile at Xenopus laevis oocyte-expressed rat nAChR subtypes was determined by 2-electrode voltage-clamp electrophysiology, and its 3-dimensional (3D) structure was determined by NMR spectroscopy. α-CTx LvIA is a 16-aa C-terminally-amidated peptide with 2-disulfide bridges. Using rat subunits expressed in Xenopus oocytes, we found the highest affinity of α-CTxLvIA was for α3β2 nAChRs (IC50 8.7 nM), where blockade was reversible within 2 min. IC50 values were >100 nM at α6/α3β2β3, α6/α3β4, and α3β4 nAChRs, and ≥3 μM at all other subtypes tested. α3β2 vs. α6β2 subtype selectivity was confirmed for human-subunit nAChRs with much greater preference (300-fold) for α3β2 over α6β2 nAChRs. This is the first α-CTx reported to show high selectivity for human α3β2 vs. α6β2 nAChRs. α-CTxLvIA adopts two similarly populated conformations water: one (assumed to be bioactive) is highly structured, whereas the other is mostly random coil in nature. Selectivity differences with the similarly potent, but less selective, α3β2 nAChR antagonist α-CTx PeIA probably reside within the three residues, which differ in loop 2, given their otherwise similar 3D structures. α4/7-CTx LvIA is a new, potent, selective α3β2 nAChR antagonist, which will enable detailed studies of α3β2 nAChR structure, function, and physiological roles.
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Affiliation(s)
- Sulan Luo
- 1Key Laboratory of Tropical Biological Resources, Ministry of Education, Hainan University; Haikou, Hainan, 570228 China.
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30
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Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: identification of an RGFRRR motif governing fungal cell entry. PLoS One 2013; 8:e82485. [PMID: 24324798 PMCID: PMC3853197 DOI: 10.1371/journal.pone.0082485] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/25/2013] [Indexed: 01/27/2023] Open
Abstract
MtDef4 is a 47-amino acid cysteine-rich evolutionary conserved defensin from a model legume Medicago truncatula. It is an apoplast-localized plant defense protein that inhibits the growth of the ascomycetous fungal pathogen Fusarium graminearum in vitro at micromolar concentrations. Little is known about the mechanisms by which MtDef4 mediates its antifungal activity. In this study, we show that MtDef4 rapidly permeabilizes fungal plasma membrane and is internalized by the fungal cells where it accumulates in the cytoplasm. Furthermore, analysis of the structure of MtDef4 reveals the presence of a positively charged γ-core motif composed of β2 and β3 strands connected by a positively charged RGFRRR loop. Replacement of the RGFRRR sequence with AAAARR or RGFRAA abolishes the ability of MtDef4 to enter fungal cells, suggesting that the RGFRRR loop is a translocation signal required for the internalization of the protein. MtDef4 binds to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Amino acid substitutions in the RGFRRR sequence which abolish the ability of MtDef4 to enter fungal cells also impair its ability to bind PA. These findings suggest that MtDef4 is a novel antifungal plant defensin capable of entering into fungal cells and affecting intracellular targets and that these processes are mediated by the highly conserved cationic RGFRRR loop via its interaction with PA.
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31
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Liao S, Zhang W, Fan K, Ye K, Zhang X, Zhang J, Xu C, Tu X. Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP2) from Haloferax volcanii. Sci Rep 2013; 3:2136. [PMID: 23823798 PMCID: PMC3701171 DOI: 10.1038/srep02136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/13/2013] [Indexed: 11/23/2022] Open
Abstract
Ubiquitin-like proteins play important roles in diverse biological processes. In this study, we present an unexpected finding that a ubiquitin-like small archaeal modifier protein (SAMP2) from Haloferax volcanii adopts two distinct states under low ionic condition. One of these is similar to the β-grasp structure conserved in ubiquitin-like proteins from eukaryotes; the other is disordered, like prokaryotic ubiquitin-like protein, Pup. Furthermore, our study reveals that the conformation of SAMP2 is dependent on ionic strength. With the increase of ion concentration, SAMP2 undergoes a conformational conversion from disorder to order, indicating that the ordered conformation is the functional form of SAMP2 under the physiological condition of H. volcanii.
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Affiliation(s)
- Shanhui Liao
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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32
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Fadden AJ, Schalbetter S, Bowles M, Harris R, Lally J, Carr AM, McDonald NQ. A winged helix domain in human MUS81 binds DNA and modulates the endonuclease activity of MUS81 complexes. Nucleic Acids Res 2013; 41:9741-52. [PMID: 23982516 PMCID: PMC3834828 DOI: 10.1093/nar/gkt760] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MUS81-EME1 endonuclease maintains metazoan genomic integrity by cleaving branched DNA structures that arise during the resolution of recombination intermediates. In humans, MUS81 also forms a poorly characterized complex with EME2. Here, we identify and determine the structure of a winged helix (WH) domain from human MUS81, which binds DNA. WH domain mutations greatly reduce binding of the isolated domain to DNA and impact on incision activity of MUS81-EME1/EME2 complexes. Deletion of the WH domain reduces the endonuclease activity of both MUS81-EME1 and MUS81-EME2 complexes, and incisions made by MUS81-EME2 are made closer to the junction on substrates containing a downstream duplex, such as fork structures and nicked Holliday junctions. WH domain mutation or deletion in Schizosaccharomyces pombe phenocopies the DNA-damage sensitivity of strains deleted for mus81. Our results indicate an important role for the WH domain in both yeast and human MUS81 complexes.
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Affiliation(s)
- Andrew J Fadden
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK, Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK and Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
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33
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van Lierop BJ, Robinson SD, Kompella SN, Belgi A, McArthur JR, Hung A, MacRaild CA, Adams DJ, Norton RS, Robinson AJ. Dicarba α-conotoxin Vc1.1 analogues with differential selectivity for nicotinic acetylcholine and GABAB receptors. ACS Chem Biol 2013; 8:1815-21. [PMID: 23768016 DOI: 10.1021/cb4002393] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Conotoxins have emerged as useful leads for the development of novel therapeutic analgesics. These peptides, isolated from marine molluscs of the genus Conus, have evolved exquisite selectivity for receptors and ion channels of excitable tissue. One such peptide, α-conotoxin Vc1.1, is a 16-mer possessing an interlocked disulfide framework. Despite its emergence as a potent analgesic lead, the molecular target and mechanism of action of Vc1.1 have not been elucidated to date. In this paper we describe the regioselective synthesis of dicarba analogues of Vc1.1 using olefin metathesis. The ability of these peptides to inhibit acetylcholine-evoked current at rat α9α10 and α3β4 nicotinic acetylcholine receptors (nAChR) expressed in Xenopus oocytes has been assessed in addition to their ability to inhibit high voltage-activated (HVA) calcium channel current in isolated rat DRG neurons. Their solution structures were determined by NMR spectroscopy. Significantly, we have found that regioselective replacement of the native cystine framework with a dicarba bridge can be used to selectively tune the cyclic peptide's innate biological activity for one receptor over another. The 2,8-dicarba Vc1.1 isomer retains activity at γ-aminobutyric acid (GABAB) G protein-coupled receptors, whereas the isomeric 3,16-dicarba Vc1.1 peptide retains activity at the α9α10 nAChR subtype. These singularly acting analogues will enable the elucidation of the biological target responsible for the peptide's potent analgesic activity.
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Affiliation(s)
| | - Samuel D. Robinson
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Shiva N. Kompella
- Health Innovations Research Institute, RMIT University, Bundoora 3083, Victoria, Australia
| | - Alessia Belgi
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
| | - Jeffrey R. McArthur
- Health Innovations Research Institute, RMIT University, Bundoora 3083, Victoria, Australia
| | - Andrew Hung
- Health Innovations Research Institute, RMIT University, Bundoora 3083, Victoria, Australia
| | - Christopher A. MacRaild
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - David J. Adams
- Health Innovations Research Institute, RMIT University, Bundoora 3083, Victoria, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Andrea J. Robinson
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
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Ye K, Liao S, Zhang W, Fan K, Zhang X, Zhang J, Xu C, Tu X. Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP1) from Haloferax volcanii. Protein Sci 2013; 22:1174-82. [PMID: 23818097 DOI: 10.1002/pro.2302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 06/18/2013] [Accepted: 06/20/2013] [Indexed: 11/11/2022]
Abstract
Eukaryotic ubiquitin and ubiquitin-like systems play crucial roles in various cellular biological processes. In this work, we determined the solution structure of SAMP1 from Haloferax volcanii by NMR spectroscopy. Under low ionic conditions, SAMP1 presented two distinct conformations, one folded β-grasp and the other disordered. Interestingly, SAMP1 underwent a conformational conversion from disorder to order with ion concentration increasing, indicating that the ordered conformation is the functional form of SAMP1 under the physiological condition of H. volcanii. Furthermore, SAMP1 could interact with proteasome-activating nucleotidase B, supposing a potential role of SAMP1 in the protein degradation pathway mediated by proteasome.
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Affiliation(s)
- Kaiqin Ye
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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Rani R, Jentzsch K, Lecher J, Hartmann R, Willbold D, Jaeger KE, Krauss U. Conservation of dark recovery kinetic parameters and structural features in the pseudomonadaceae "short" light, oxygen, voltage (LOV) protein family: implications for the design of LOV-based optogenetic tools. Biochemistry 2013; 52:4460-73. [PMID: 23746326 DOI: 10.1021/bi400311r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In bacteria and fungi, various light, oxygen, voltage (LOV) sensory systems that lack a fused effector domain but instead contain only short N- and C-terminal extensions flanking the LOV core exist. In the prokaryotic kingdom, this so-called "short" LOV protein family represents the third largest LOV photoreceptor family. This observation prompted us to study their distribution and phylogeny as well as their photochemical and structural properties in more detail. We recently described the slow and fast reverting "short" LOV proteins PpSB1-LOV and PpSB2-LOV from Pseudomonas putida KT2440 whose adduct state lifetimes varied by 3 orders of magnitude [Jentzsch, K., Wirtz, A., Circolone, F., Drepper, T., Losi, A., Gärtner, W., Jaeger, K. E., and Krauss, U. (2009) Biochemistry 48, 10321-10333]. We now present evidence of the conservation of similar fast and slow-reverting "short" LOV proteins in different Pseudomonas species. Truncation studies conducted with PpSB1-LOV and PpSB2-LOV suggested that the short N- and C-terminal extensions outside of the LOV core domain are essential for the structural integrity and folding of the two proteins. While circular dichroism and solution nuclear magnetic resonance experiments verify that the two short C-terminal extensions of PpSB1-LOV and PpSB2-LOV form independently folding helical structures in solution, bioinformatic analyses imply the formation of coiled coils of the respective structural elements in the context of the dimeric full-length proteins. Given their prototypic architecture, conserved in most more complex LOV photoreceptor systems, "short" LOV proteins could represent ideally suited building blocks for the design of genetically encoded photoswitches (i.e., LOV-based optogenetic tools).
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Affiliation(s)
- Raj Rani
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, D-52426 Jülich, Germany
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36
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Vance SJ, McDonald RE, Cooper A, Smith BO, Kennedy MW. The structure of latherin, a surfactant allergen protein from horse sweat and saliva. J R Soc Interface 2013; 10:20130453. [PMID: 23782536 PMCID: PMC4043175 DOI: 10.1098/rsif.2013.0453] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Latherin is a highly surface-active allergen protein found in the sweat and saliva of horses and other equids. Its surfactant activity is intrinsic to the protein in its native form, and is manifest without associated lipids or glycosylation. Latherin probably functions as a wetting agent in evaporative cooling in horses, but it may also assist in mastication of fibrous food as well as inhibition of microbial biofilms. It is a member of the PLUNC family of proteins abundant in the oral cavity and saliva of mammals, one of which has also been shown to be a surfactant and capable of disrupting microbial biofilms. How these proteins work as surfactants while remaining soluble and cell membrane-compatible is not known. Nor have their structures previously been reported. We have used protein nuclear magnetic resonance spectroscopy to determine the conformation and dynamics of latherin in aqueous solution. The protein is a monomer in solution with a slightly curved cylindrical structure exhibiting a ‘super-roll’ motif comprising a four-stranded anti-parallel β-sheet and two opposing α-helices which twist along the long axis of the cylinder. One end of the molecule has prominent, flexible loops that contain a number of apolar amino acid side chains. This, together with previous biophysical observations, leads us to a plausible mechanism for surfactant activity in which the molecule is first localized to the non-polar interface via these loops, and then unfolds and flattens to expose its hydrophobic interior to the air or non-polar surface. Intrinsically surface-active proteins are relatively rare in nature, and this is the first structure of such a protein from mammals to be reported. Both its conformation and proposed method of action are different from other, non-mammalian surfactant proteins investigated so far.
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Affiliation(s)
- Steven J Vance
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
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37
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Favretto F, Assfalg M, Gallo M, Cicero DO, D'Onofrio M, Molinari H. Ligand Binding Promiscuity of Human Liver Fatty Acid Binding Protein: Structural and Dynamic Insights from an Interaction Study with Glycocholate and Oleate. Chembiochem 2013; 14:1807-19. [DOI: 10.1002/cbic.201300156] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 11/09/2022]
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38
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Bobby R, Medini K, Neudecker P, Lee TV, Brimble MA, McDonald FJ, Lott JS, Dingley AJ. Structure and dynamics of human Nedd4-1 WW3 in complex with the αENaC PY motif. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1632-41. [PMID: 23665454 DOI: 10.1016/j.bbapap.2013.04.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) is an E3 ubiquitin ligase that interacts with and negatively regulates the epithelial Na(+) channel (ENaC). The WW domains of Nedd4-1 bind to the ENaC subunits via recognition of PY motifs. Human Nedd4-1 (hNedd4-1) contains four WW domains with the third domain (WW3*) showing the strongest affinity to the PY motif. To understand the mechanism underlying this binding affinity, we have carried out NMR structural and dynamics analyses of the hNedd4-1 WW3* domain in complex with a peptide comprising the C-terminal tail of the human ENaC α-subunit. The structure reveals that the peptide interacts in a similar manner to other WW domain-ENaC peptide structures. Crucial interactions that likely provide binding affinity are the broad XP groove facilitating additional contacts between the WW3* domain and the peptide, compared to similar complexes, and the large surface area buried (83Å(2)) between R430 (WW3*) and L647' (αENaC). This corroborates the model-free analysis of the (15)N backbone relaxation data, which showed that R430 is the most rigid residue in the domain (S(2)=0.90±0.01). Carr-Purcell-Meiboom-Gill relaxation dispersion analysis identified two different conformational exchange processes on the μs-ms time-scale. One of these processes involves residues located at the peptide binding interface, suggesting conformational exchange may play a role in peptide recognition. Thus, both structural and dynamic features of the complex appear to define the high binding affinity. The results should aid interpretation of biochemical data and modeling interfaces between Nedd4-1 and other interacting proteins.
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Affiliation(s)
- Romel Bobby
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
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39
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Kateb F, Perrin H, Tripsianes K, Zou P, Spadaccini R, Bottomley M, Franzmann TM, Buchner J, Ansieau S, Sattler M. Structural and functional analysis of the DEAF-1 and BS69 MYND domains. PLoS One 2013; 8:e54715. [PMID: 23372760 PMCID: PMC3555993 DOI: 10.1371/journal.pone.0054715] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
DEAF-1 is an important transcriptional regulator that is required for embryonic development and is linked to clinical depression and suicidal behavior in humans. It comprises various structural domains, including a SAND domain that mediates DNA binding and a MYND domain, a cysteine-rich module organized in a Cys(4)-Cys(2)-His-Cys (C4-C2HC) tandem zinc binding motif. DEAF-1 transcription regulation activity is mediated through interactions with cofactors such as NCoR and SMRT. Despite the important biological role of the DEAF-1 protein, little is known regarding the structure and binding properties of its MYND domain.Here, we report the solution structure, dynamics and ligand binding of the human DEAF-1 MYND domain encompassing residues 501-544 determined by NMR spectroscopy. The structure adopts a ββα fold that exhibits tandem zinc-binding sites with a cross-brace topology, similar to the MYND domains in AML1/ETO and other proteins. We show that the DEAF-1 MYND domain binds to peptides derived from SMRT and NCoR corepressors. The binding surface mapped by NMR titrations is similar to the one previously reported for AML1/ETO. The ligand binding and molecular functions of the related BS69 MYND domain were studied based on a homology model and mutational analysis. Interestingly, the interaction between BS69 and its binding partners (viral and cellular proteins) seems to require distinct charged residues flanking the predicted MYND domain fold, suggesting a different binding mode. Our findings demonstrate that the MYND domain is a conserved zinc binding fold that plays important roles in transcriptional regulation by mediating distinct molecular interactions with viral and cellular proteins.
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Affiliation(s)
- Fatiha Kateb
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Helene Perrin
- Institut National de la Santé Et de la Recherche Médicale U590, Centre Léon Bérard, Université Claude Bernard Lyon I, Lyon, France
| | - Konstantinos Tripsianes
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Peijian Zou
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Roberta Spadaccini
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | | | - Titus M. Franzmann
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Stephane Ansieau
- Institut National de la Santé Et de la Recherche Médicale U590, Centre Léon Bérard, Université Claude Bernard Lyon I, Lyon, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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40
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Mechelke M, Habeck M. Calibration of Boltzmann distribution priors in Bayesian data analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:066705. [PMID: 23368076 DOI: 10.1103/physreve.86.066705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/24/2012] [Indexed: 06/01/2023]
Abstract
The Boltzmann distribution is commonly used as a prior probability in Bayesian data analysis. Examples include the Ising model in statistical image analysis and the canonical ensemble based on molecular dynamics force fields in protein structure calculation. These models involve a temperature or weighting factor that needs to be inferred from the data. Bayesian inference stipulates to determine the temperature based on the model evidence. This is challenging because the model evidence, a ratio of two high-dimensional normalization integrals, cannot be calculated analytically. We outline a replica-exchange Monte Carlo scheme that allows us to estimate the model evidence by use of multiple histogram reweighting. The method is illustrated for an Ising model and examples in protein structure determination.
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Affiliation(s)
- Martin Mechelke
- Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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41
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Conibear AC, Rosengren KJ, Harvey PJ, Craik DJ. Structural characterization of the cyclic cystine ladder motif of θ-defensins. Biochemistry 2012; 51:9718-26. [PMID: 23148585 DOI: 10.1021/bi301363a] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The θ-defensins are, to date, the only known ribosomally synthesized cyclic peptides in mammals, and they have promising antimicrobial bioactivities. The characteristic structural motif of the θ-defensins is the cyclic cystine ladder, comprising a cyclic peptide backbone and three parallel disulfide bonds. In contrast to the cyclic cystine knot, which characterizes the plant cyclotides, the cyclic cystine ladder has not been as well described as a structural motif. Here we report the solution structures and nuclear magnetic resonance relaxation properties in aqueous solution of three representative θ-defensins from different species. Our data suggest that the θ-defensins are more rigid and structurally defined than previously thought. In addition, all three θ-defensins were found to self-associate in aqueous solution in a concentration-dependent and reversible manner, a property that might have a role in their mechanism of action. The structural definition of the θ-defensins and the cyclic cystine ladder will help to guide exploitation of these molecules as structural frameworks for the design of peptide drugs.
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Affiliation(s)
- Anne C Conibear
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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42
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Ballaré C, Lange M, Lapinaite A, Martin GM, Morey L, Pascual G, Liefke R, Simon B, Shi Y, Gozani O, Carlomagno T, Benitah SA, Di Croce L. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012; 19:1257-65. [PMID: 23104054 DOI: 10.1038/nsmb.2434] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 10/03/2012] [Indexed: 12/12/2022]
Abstract
Polycomb-group proteins are transcriptional repressors with essential roles in embryonic development. Polycomb repressive complex 2 (PRC2) contains the methyltransferase activity for Lys27. However, the role of other histone modifications in regulating PRC2 activity is just beginning to be understood. Here we show that direct recognition of methylated histone H3 Lys36 (H3K36me), a mark associated with activation, by the PRC2 subunit Phf19 is required for the full enzymatic activity of the PRC2 complex. Using NMR spectroscopy, we provide structural evidence for this interaction. Furthermore, we show that Phf19 binds to a subset of PRC2 targets in mouse embryonic stem cells and that this is required for their repression and for H3K27me3 deposition. These findings show that the interaction of Phf19 with H3K36me2 and H3K36me3 is essential for PRC2 complex activity and for proper regulation of gene repression in embryonic stem cells.
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Affiliation(s)
- Cecilia Ballaré
- Department of Gene Regulation and Stem Cells, Centre for Genomic Regulation (CRG), Barcelona, Spain
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43
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Foloppe N, Vlamis-Gardikas A, Nilsson L. The -Cys-X1-X2-Cys- motif of reduced glutaredoxins adopts a consensus structure that explains the low pK(a) of its catalytic cysteine. Biochemistry 2012; 51:8189-207. [PMID: 22966829 DOI: 10.1021/bi3006576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The -Cys-X1-X2-Cys- active site motif is central to the function of enzymes of the thioredoxin superfamily, including glutaredoxins. Their chemistry depends on the lowered pK(a) of the N-terminal thiolate cysteine of the -Cys-X1-X2-Cys- sequence; therefore its structure, dynamics, and electrostatics matter. Much information about the glutaredoxin structures was obtained by nuclear magnetic resonance (NMR), yet these various NMR structures produced heterogeneous and discordant views of the -Cys-X1-X2-Cys- motifs. This study addresses these inconsistencies by a computational and experimental investigation of three diverse reduced -Cys-X1-X2-Cys- motifs, from human glutaredoxin 1 (hGrx1), Escherichia coli glutaredoxin 2 (EcGrx2), and T4 virus glutaredoxin (T4Grx). The NMR models do not account for the low pK(a) of the N-terminal cysteine. However, extensive investigations of the NMR conformers by simulations yielded consensus structures for the -Cys-X1-X2-Cys- motif, with well-defined orientations for the cysteines. pK(a) calculations indicated that the consensus structure stabilizes the thiolate by local hydrogen bonds. The consensus structures of EcGrx2 and T4Grx formed the basis for predicting low pK(a) values for their N-terminal cysteines. Subsequent experimental titrations showed that these pK(a) values are <5, supporting the validity of the consensus structure. The simulations also revisited the conformational dynamics of side chains around the -Cys-X1-X2-Cys- motif, which allowed reconciliation of calculated and measured pK(a) values for important hGrx1 mutants. The conformational spread of these side chains, which differs between NMR and molecular dynamics models, is likely to be relevant to substrate recognition. The new structural models determined in this work should prove to be valuable in future molecular studies of the glutaredoxins.
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44
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Jaudzems K, Jia X, Yagi H, Zhulenkovs D, Graham B, Otting G, Liepinsh E. Structural basis for 5'-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2. J Mol Biol 2012; 424:42-53. [PMID: 22999958 DOI: 10.1016/j.jmb.2012.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/07/2012] [Accepted: 09/12/2012] [Indexed: 10/27/2022]
Abstract
The R3H domain is a conserved sequence motif in nucleic acid binding proteins. Previously, we reported the solution structure of the R3H domain and identified a putative nucleic acid binding site composed of three conserved basic residues [Liepinsh, E., Leonchiks, A., Sharipo, A., Guignard, L. & Otting, G. (2003). Solution structure of the R3H domain from human Sμbp-2. J. Mol. Biol.326, 217-223]. Here, we determine the binding affinities of mononucleotides and dinucleotides for the R3H domain from human Sμbp-2 (Sμbp2-R3H) and map their binding sites on the protein's surface. Although the binding affinities show up to 260-fold selectivity between different nucleotides, their binding sites and conformations seem very similar. Further, we report the NMR structure of the Sμbp2-R3H in complex with deoxyguanosine 5'-monophosphate (dGMP) mimicking the 5'-end of single-stranded DNA. Pseudocontact shifts from a paramagnetic lanthanide tag attached to residue 731 in the mutant A731C confirmed that binding of dGMP brings a loop of the protein into closer proximity. The structure provides the first structural insight into single-stranded nucleic acid recognition by the R3H domain and shows that the R3H domain specifically binds the phosphorylated 5'-end through electrostatic interactions with the two conserved arginines and stacking interactions with the highly conserved histidine.
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Affiliation(s)
- Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Latvia.
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45
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pH‐Dependent Dimerization of Spider Silk N-Terminal Domain Requires Relocation of a Wedged Tryptophan Side Chain. J Mol Biol 2012; 422:477-87. [DOI: 10.1016/j.jmb.2012.06.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 11/23/2022]
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46
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Henriksen NM, Davis DR, Cheatham TE. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure. JOURNAL OF BIOMOLECULAR NMR 2012; 53:321-39. [PMID: 22714631 PMCID: PMC3405240 DOI: 10.1007/s10858-012-9642-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to "update" older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.
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Affiliation(s)
- Niel M Henriksen
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, UT 84112, USA.
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47
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D'Onofrio M, Gianolio E, Ceccon A, Arena F, Zanzoni S, Fushman D, Aime S, Molinari H, Assfalg M. High Relaxivity Supramolecular Adducts Between Human-Liver Fatty-Acid-Binding Protein and Amphiphilic GdIII Complexes: Structural Basis for the Design of Intracellular Targeting MRI Probes. Chemistry 2012; 18:9919-28. [DOI: 10.1002/chem.201103778] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 05/08/2012] [Indexed: 01/14/2023]
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48
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Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS. Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures. JOURNAL OF BIOMOLECULAR NMR 2012; 53:167-180. [PMID: 22678091 DOI: 10.1007/s10858-012-9637-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/15/2012] [Indexed: 06/01/2023]
Abstract
In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating "equivalent resolution" from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 Å) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure "Resolution-by-Proxy" or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect. The ResProx web server is available at http://www.resprox.ca.
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Affiliation(s)
- Mark Berjanskii
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
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49
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Mainz A, Bardiaux B, Kuppler F, Multhaup G, Felli IC, Pierattelli R, Reif B. Structural and mechanistic implications of metal binding in the small heat-shock protein αB-crystallin. J Biol Chem 2012; 287:1128-38. [PMID: 22090033 PMCID: PMC3256888 DOI: 10.1074/jbc.m111.309047] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/08/2011] [Indexed: 12/20/2022] Open
Abstract
The human small heat-shock protein αB-crystallin (αB) rescues misfolded proteins from irreversible aggregation during cellular stress. Binding of Cu(II) was shown to modulate the oligomeric architecture and the chaperone activity of αB. However, the mechanistic basis of this stimulation is so far not understood. We provide here first structural insights into this Cu(II)-mediated modulation of chaperone function using NMR spectroscopy and other biophysical approaches. We show that the α-crystallin domain is the elementary Cu(II)-binding unit specifically coordinating one Cu(II) ion with picomolar binding affinity. Putative Cu(II) ligands are His(83), His(104), His(111), and Asp(109) at the dimer interface. These loop residues are conserved among different metazoans, but also for human αA-crystallin, HSP20, and HSP27. The involvement of Asp(109) has direct implications for dimer stability, because this residue forms a salt bridge with the disease-related Arg(120) of the neighboring monomer. Furthermore, we observe structural reorganization of strands β2-β3 triggered by Cu(II) binding. This N-terminal region is known to mediate both the intermolecular arrangement in αB oligomers and the binding of client proteins. In the presence of Cu(II), the size and the heterogeneity of αB multimers are increased. At the same time, Cu(II) increases the chaperone activity of αB toward the lens-specific protein β(L)-crystallin. We therefore suggest that Cu(II) binding unblocks potential client binding sites and alters quaternary dynamics of both the dimeric building block as well as the higher order assemblies of αB.
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Affiliation(s)
- Andi Mainz
- From the Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin-Buch 13125, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Benjamin Bardiaux
- From the Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin-Buch 13125, Germany
| | - Frank Kuppler
- the Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Gerd Multhaup
- the Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Isabella C. Felli
- the Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy, and
| | - Roberta Pierattelli
- the Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy, and
| | - Bernd Reif
- From the Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin-Buch 13125, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
- the Center for Integrated Protein Science Munich, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching 85747, Germany
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50
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Bagaria A, Jaravine V, Huang YJ, Montelione GT, Güntert P. Protein structure validation by generalized linear model root-mean-square deviation prediction. Protein Sci 2012; 21:229-38. [PMID: 22113924 DOI: 10.1002/pro.2007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/17/2011] [Accepted: 11/19/2011] [Indexed: 01/03/2023]
Abstract
Large-scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD-NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root-mean-square deviation (RMSD) value between the present structure and the (unavailable) "true" structure (GLM-RMSD). For two sets of structural models from the CASD-NMR and CASP projects, this GLM-RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. "true") heavy-atom RMSDs were 0.69 and 0.76, for the two datasets from CASD-NMR and CASP, respectively, which is considerably higher than those for the individual scores (-0.24 to 0.68). The GLM-RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate-based quality scores.
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Affiliation(s)
- Anurag Bagaria
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt, Frankfurt am Main, Germany
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