151
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Jacobsen T, Dazzoni R, Renault MG, Bardiaux B, Nilges M, Shevchik V, Izadi-Pruneyre N. Secondary structure and 1H, 15 N & 13C resonance assignments of the periplasmic domain of OutG, major pseudopilin from Dickeya dadantii type II secretion system. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:231-236. [PMID: 35482172 PMCID: PMC9510105 DOI: 10.1007/s12104-022-10085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
The ability to interact and adapt to the surrounding environment is vital for bacteria that colonise various niches and organisms. One strategy developed by Gram-negative bacteria is to secrete exoprotein substrates via the type II secretion system (T2SS). The T2SS is a proteinaceous complex spanning the bacterial envelope that translocates folded proteins such as toxins and enzymes from the periplasm to the extracellular milieu. In the T2SS, a cytoplasmic ATPase elongates in the periplasm the pseudopilus, a non-covalent polymer composed of protein subunits named pseudopilins, and anchored in the inner membrane by a transmembrane helix. The pseudopilus polymerisation is coupled to the secretion of substrates. The T2SS of Dickeya dadantii secretes more than 15 substrates, essentially plant cell wall degrading enzymes. In D. dadantii, the major pseudopilin or the major subunit of the pseudopilus is called OutG. To better understand the mechanism of secretion of these numerous substrates via the pseudopilus, we have been studying the structure of OutG by NMR. Here, as the first part of this study, we report the 1H, 15N and 13C backbone and sidechain chemical shift assignment of the periplasmic domain of OutG and its NMR derived secondary structure.
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Affiliation(s)
- Theis Jacobsen
- CNRS UMR3528, Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- Sorbonne Université, Complexité du Vivant, 75005, Paris, France
| | - Régine Dazzoni
- CNRS UMR3528, Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Melvin G Renault
- Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, Microbiologie Adaptation et Pathogénie, 69622, Villeurbanne, France
| | - Benjamin Bardiaux
- CNRS UMR3528, Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Michael Nilges
- CNRS UMR3528, Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Vladimir Shevchik
- Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, Microbiologie Adaptation et Pathogénie, 69622, Villeurbanne, France
| | - Nadia Izadi-Pruneyre
- CNRS UMR3528, Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
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152
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Hussain A, Paukovich N, Henen MA, Vögeli B. Advances in the exact nuclear Overhauser effect 2018-2022. Methods 2022; 206:87-98. [PMID: 35985641 PMCID: PMC9596134 DOI: 10.1016/j.ymeth.2022.08.006] [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: 05/21/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
The introduction of the exact nuclear Overhauser enhancement (eNOE) methodology to solution-state nuclear magnetic resonance (NMR) spectroscopy results in tighter distance restraints from NOEs than in convention analysis. These improved restraints allow for higher resolution in structure calculation and even the disentanglement of different conformations of macromolecules. While initial work primarily focused on technical development of the eNOE, structural studies aimed at the elucidation of spatial sampling in proteins and nucleic acids were published in parallel prior to 2018. The period of 2018-2022 saw a continued series of technical innovation, but also major applications addressing biological questions. Here, we review both aspects, covering topics from the implementation of non-uniform sampling of NOESY buildups, novel pulse sequences, adaption of the eNOE to solid-state NMR, advances in eNOE data analysis, and innovations in structural ensemble calculation, to applications to protein, RNA, and DNA structure elucidation.
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Affiliation(s)
- Alya Hussain
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA
| | - Natasia Paukovich
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA
| | - Morkos A Henen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17(th) Avenue, Aurora, CO 80045, USA.
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153
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Walker K, Waters LC, Kelly G, Muskett FW, Carr MD. Sequence-specific 1H, 13C and 15N backbone NMR assignments for the N-terminal IgV-like domain (D1) and full extracellular region (D1D2) of PD-L1. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:281-288. [PMID: 35675028 PMCID: PMC9510113 DOI: 10.1007/s12104-022-10092-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 05/17/2023]
Abstract
The co-inhibitory immune checkpoint interaction between programmed cell death-protein 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) serves to regulate T-cell activation, promoting self-tolerance. Over-expression of PD-L1 is a mechanism through which tumour cells can evade detection by the immune system. Several therapeutic antibodies targeting PD-L1 or PD-1 have been approved for the treatment of a variety of cancers, however, the discovery and development of small-molecule inhibitors of PD-L1 remains a challenge. Here we report comprehensive sequence-specific backbone resonance assignments (1H, 13C, and 15N) obtained for the N-terminal IgV-like domain of PD-L1 (D1) and the full two domain extracellular region (D1D2). These NMR assignments will serve as a useful tool in the discovery of small-molecule therapeutics targeting PD-L1 and in the characterisation of functional interactions with other protein partners, such as CD80.
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Affiliation(s)
- Kayleigh Walker
- Leicester Institute of Structural and Chemical Biology, Leicester, UK.
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK.
| | - Lorna C Waters
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
| | - Geoff Kelly
- Medical Research Council (MRC) Biomedical NMR Centre, The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
| | - Frederick W Muskett
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
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154
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Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HD. Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell Rep 2022; 41:111537. [DOI: 10.1016/j.celrep.2022.111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
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155
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Petersen AB, Christensen IA, Rønne ME, Stender EGP, Teze D, Svensson B, Aachmann FL. 1H, 13C, 15N resonance assignment of the enzyme KdgF from Bacteroides eggerthii. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:343-347. [PMID: 36042150 PMCID: PMC9510102 DOI: 10.1007/s12104-022-10102-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
To fully utilize carbohydrates from seaweed biomass, the degradation of the family of polysaccharides known as alginates must be understood. A step in the degradation of alginate is the conversion of 4,5-unsaturated monouronates to 4-deoxy-L-erythro-5-hexoseulose catalysed by the enzyme KdgF. In this study BeKdgF from Bacteroides eggerthii from the human gut microbiota has been produced isotopically labelled in Escherichia coli. Here the 1H, 13C, and 15N NMR chemical shift assignment for BeKdgF is reported.
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Affiliation(s)
- Agnes Beenfeldt Petersen
- Department of Chemistry, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Idd Andrea Christensen
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Mette E Rønne
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Emil G P Stender
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - David Teze
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, DTU Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Finn Lillelund Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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156
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Davis JL, Hounslow AM, Baxter NJ, Mesnage S, Williamson MP. 1H, 13C, and 15N resonance assignments of a conserved putative cell wall binding domain from Enterococcus faecalis. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:247-251. [PMID: 35665899 PMCID: PMC9510096 DOI: 10.1007/s12104-022-10087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Enterococcus faecalis is a major causative agent of hospital acquired infections. The ability of E. faecalis to evade the host immune system is essential during pathogenesis, which has been shown to be dependent on the complete separation of daughter cells by peptidoglycan hydrolases. AtlE is a peptidoglycan hydrolase which is predicted to bind to the cell wall of E. faecalis, via six C-terminal repeat sequences. Here, we report the near complete assignment of one of these six repeats, as well as the predicted backbone structure and dynamics. This data will provide a platform for future NMR studies to explore the ligand recognition motif of AtlE and help to uncover its potential role in E. faecalis virulence.
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Affiliation(s)
- Jessica L Davis
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Andrea M Hounslow
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Nicola J Baxter
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Stéphane Mesnage
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK.
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157
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Kusunoki H, Hamaguchi I, Kobayashi N, Nagata T. Chemical shift assignments of a fusion protein comprising the C-terminal-deleted hepatitis B virus X protein BH3-like motif peptide and Bcl-x L. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:357-361. [PMID: 36044106 DOI: 10.1007/s12104-022-10104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Chronic hepatitis B virus (HBV) infection is a major risk factor for the development of liver diseases including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV has the multifunctional protein, HBV X protein (HBx, 154 residues), which plays key roles in HBV replication and liver disease development. Interaction of HBx through its BH3-like motif with the anti-apoptotic protein Bcl-xL leads to HBV replication and induction of apoptosis, resulting in HCC development. Our previous nuclear magnetic resonance (NMR) study revealed that the HBx BH3-like motif peptide (residues 101-136) binds to the common BH3-binding groove of Bcl-xL. Importantly, a C-terminal-truncated HBx, e.g., residues 1-120 of HBx, is strongly associated with the increased risk of HBV-related HCC development. However, the interaction mode between the C-terminal-truncated HBx and Bcl-xL remains unclear. To elucidate this interaction mode, the C-terminal-deleted HBx BH3-like motif peptide (residues 101-120) was used as a model peptide in this study. To facilitate the NMR analysis, we prepared a fusion protein of HBx (101-120) and Bcl-xL connected with five repeats of the glycine-serine dipeptide as a linker. Here, we report the 1H, 13C, and 15N resonance assignments of the fusion protein. This is the first step for the elucidation of the pathogenesis of liver diseases caused by the interaction between the C-terminal-truncated HBx and Bcl-xL.
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Affiliation(s)
- Hideki Kusunoki
- Research Center for Biological Products in the Next Generation, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan.
| | - Isao Hamaguchi
- Research Center for Biological Products in the Next Generation, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan
| | - Naohiro Kobayashi
- Laboratory for Advanced NMR Application and Development, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, 230-0045, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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158
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Pandit S. 1 H, 15 N and 13 C chemical shift assignments of the N-terminal domain of the two isoforms of the human apolipoprotein E. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:191-196. [PMID: 35451799 DOI: 10.1007/s12104-022-10078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Apolipoprotein E (ApoE) is one of the major lipid transporters in humans. It is also implicated in pathological conditions like Alzheimer's and cardiovascular diseases. The N-terminal domain of ApoE binds low-density lipoprotein receptors (LDLR) while the C-terminal domain binds to the lipid. I report the backbone and aliphatic side-chain NMR chemical shifts of the N-terminal domain of two isoforms of ApoE, namely ApoE3 NTD (BMRB No. 51,122) and ApoE4 NTD (BMRB No. 51,123) at pH 3.5 (20 °C).
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Affiliation(s)
- Subhendu Pandit
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, 500107, Hyderabad, India.
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159
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Lahfa M, Padilla A, de Guillen K, Pissarra J, Raji M, Cesari S, Kroj T, Gladieux P, Roumestand C, Barthe P. 1H, 13C, 15 N backbone and side-chain NMR assignments for three MAX effectors from Magnaporthe oryzae. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:305-309. [PMID: 35657473 DOI: 10.1007/s12104-022-10095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Effectors are small and very diverse proteins secreted by fungi and translocated in plant cells during infection. Among them, MAX effectors (for Magnaporthe Avrs and ToxB) were identified as a family of effectors that share an identical fold topology despite having highly divergent sequences. They are mostly secreted by ascomycetes from the Magnaporthe genus, a fungus that causes the rice blast, a plant disease leading to huge crop losses. As rice is the first source of calories in many countries, especially in Asia and Africa, this constitutes a threat for world food security. Hence, a better understanding of these effectors, including structural and functional characterization, constitutes a strategic milestone in the fight against phytopathogen fungi and may give clues for the development of resistant varieties of rice. We report here the near complete 1H, 15 N and 13C NMR resonance assignment of three new putative MAX effectors (MAX47, MAX60 and MAX67). Secondary structure determination using TALOS-N and CSI.3 demonstrates a high content of β-strands in all the three proteins, in agreement with the canonic ß-sandwich structure of MAX effectors. This preliminary study provides foundations for further structural characterization, that will help in turn to improve sequence predictions of other MAX effectors through data mining.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Joana Pissarra
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France.
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
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160
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Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site. Int J Mol Sci 2022; 23:ijms231911285. [PMID: 36232586 PMCID: PMC9569523 DOI: 10.3390/ijms231911285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphorylation plays a key role in plant biology, such as the accumulation of plant cells to form the observed proteome. Statistical analysis found that many phosphorylation sites are located in disordered regions. However, current force fields are mainly trained for structural proteins, which might not have the capacity to perfectly capture the dynamic conformation of the phosphorylated proteins. Therefore, we evaluated the performance of ff03CMAP, a balanced force field between structural and disordered proteins, for the sampling of the phosphorylated proteins. The test results of 11 different phosphorylated systems, including dipeptides, disordered proteins, folded proteins, and their complex, indicate that the ff03CMAP force field can better sample the conformations of phosphorylation sites for disordered proteins and disordered regions than ff03. For the solvent model, the results strongly suggest that the ff03CMAP force field with the TIP4PD water model is the best combination for the conformer sampling. Additional tests of CHARMM36m and FB18 force fields on two phosphorylated systems suggest that the overall performance of ff03CMAP is similar to that of FB18 and better than that of CHARMM36m. These results can help other researchers to choose suitable force field and solvent models to investigate the dynamic properties of phosphorylation proteins.
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161
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Ibáñez de Opakua A, Geraets JA, Frieg B, Dienemann C, Savastano A, Rankovic M, Cima-Omori MS, Schröder GF, Zweckstetter M. Molecular interactions of FG nucleoporin repeats at high resolution. Nat Chem 2022; 14:1278-1285. [PMID: 36138110 PMCID: PMC9630130 DOI: 10.1038/s41557-022-01035-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022]
Abstract
Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG–FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. ![]()
Proteins rich in phenylalanine-glycine (FG) repeats can phase separate through FG–FG interactions. The molecular interactions of an important FG-repeat protein, nucleoporin 98, have now been studied in liquid-like transient and amyloid-like cohesive states. These interactions underlie the behaviour of FG-repeat proteins and their function in physiological and pathological cell activities.
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Affiliation(s)
| | - James A Geraets
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Frieg
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | | | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany
| | | | - Gunnar F Schröder
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Göttingen, Germany. .,Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany.
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162
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Structural Insights into Mouse H-FABP. Life (Basel) 2022; 12:life12091445. [PMID: 36143481 PMCID: PMC9505153 DOI: 10.3390/life12091445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Intracellular fatty acid-binding proteins are evolutionarily highly conserved proteins. The major functions and responsibilities of this family are the regulation of FA uptake and intracellular transport. The structure of the H-FABP ortholog from mouse (Mus musculus) had not been revealed at the time this study was completed. Thus, further exploration of the structural properties of mouse H-FABP is expected to extend our knowledge of the model animal’s molecular mechanism of H-FABP function. Here, we report the high-resolution crystal structure and the NMR characterization of mouse H-FABP. Our work discloses the unique structural features of mouse H-FABP, offering a structural basis for the further development of small-molecule inhibitors for H-FABP.
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163
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Huang Q, Chu X, Zhang H, Yu S, Zhang L, Zhang X, Yu R, Guo C, Dai Q. Discovery and Structural and Functional Characterization of a Novel A-Superfamily Conotoxin Targeting α9α10 Nicotinic Acetylcholine Receptor. ACS Chem Biol 2022; 17:2483-2494. [PMID: 36048451 DOI: 10.1021/acschembio.2c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels widely distributed in the central peripheral nervous system and muscles which participate in rapid synaptic transmission. The α9α10 nAChR is an acetylcholine receptor subtype and is involved in chronic pain. In the present study, a new A-superfamily conotoxin Bt14.12 cloned from Conus betulinus was found to selectively inhibit α9α10 nAChRs with an IC50 of 62.3 nM. Unlike α-conotoxins and other A-superfamily conotoxins, Bt14.12 contains a four Cys (C-C-C-C) framework with a unique disulfide bond connection "C1-C4, C2-C3". The structure-activity studies of Bt14.12 demonstrate that all amino acid residues contribute to its potency. Interestingly, mutation experiments show that the deletion of Asp2 or the addition of three Arg residues at the N-terminus of Bt14.12 significantly enhances its inhibitory activity (IC50 is 21.9 nM or 12.7 nM, respectively) by 2- or 4-fold compared to the wild-type Bt14.12. The NMR structure of Bt14.12 shows that it contains α-helix- and β-turn-like elements, and further computational modelings of the interaction between Bt14.12 and the α9α10 nAChR demonstrate that Bt14.12 possesses a distinctive mode of action and displays a different structure-activity relationship from known α9α10 nAChR targeting α-conotoxins. Our findings provide a novel conotoxin that potently targets α9α10 nAChRs and a new motif for designing potent inhibitors against α9α10 nAChRs.
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Affiliation(s)
- Qiuyuan Huang
- Beijing Institute of Biotechnology, Beijing 100071, China.,Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Xin Chu
- Beijing Institute of Biotechnology, Beijing 100071, China.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Haoran Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shuo Yu
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Longxiao Zhang
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xuerong Zhang
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Chenyun Guo
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qiuyun Dai
- Beijing Institute of Biotechnology, Beijing 100071, China
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164
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Cobos C, Bansal PS, Wilson DT, Jones L, Zhao G, Field MA, Eichenberger RM, Pickering DA, Ryan RYM, Ratnatunga CN, Miles JJ, Ruscher R, Giacomin PR, Navarro S, Loukas A, Daly NL. Peptides derived from hookworm anti-inflammatory proteins suppress inducible colitis in mice and inflammatory cytokine production by human cells. Front Med (Lausanne) 2022; 9:934852. [PMID: 36186812 PMCID: PMC9524151 DOI: 10.3389/fmed.2022.934852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
A decline in the prevalence of parasites such as hookworms appears to be correlated with the rise in non-communicable inflammatory conditions in people from high- and middle-income countries. This correlation has led to studies that have identified proteins produced by hookworms that can suppress inflammatory bowel disease (IBD) and asthma in animal models. Hookworms secrete a family of abundant netrin-domain containing proteins referred to as AIPs (Anti-Inflammatory Proteins), but there is no information on the structure-function relationships. Here we have applied a downsizing approach to the hookworm AIPs to derive peptides of 20 residues or less, some of which display anti-inflammatory effects when co-cultured with human peripheral blood mononuclear cells and oral therapeutic activity in a chemically induced mouse model of acute colitis. Our results indicate that a conserved helical region is responsible, at least in part, for the anti-inflammatory effects. This helical region has potential in the design of improved leads for treating IBD and possibly other inflammatory conditions.
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Affiliation(s)
- Claudia Cobos
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paramjit S. Bansal
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - David T. Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Linda Jones
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Guangzu Zhao
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Matthew A. Field
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ramon M. Eichenberger
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren A. Pickering
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Rachael Y. M. Ryan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Champa N. Ratnatunga
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - John J. Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paul R. Giacomin
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Severine Navarro
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Health, Woolworths Centre for Childhood Nutrition Research, Queensland University of Technology, South Brisbane, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- *Correspondence: Alex Loukas,
| | - Norelle L. Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Norelle L. Daly,
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165
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Unusual Cytochrome c552 from Thioalkalivibrio paradoxus: Solution NMR Structure and Interaction with Thiocyanate Dehydrogenase. Int J Mol Sci 2022; 23:ijms23179969. [PMID: 36077365 PMCID: PMC9456337 DOI: 10.3390/ijms23179969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
The search of a putative physiological electron acceptor for thiocyanate dehydrogenase (TcDH) newly discovered in the thiocyanate-oxidizing bacteria Thioalkalivibrio paradoxus revealed an unusually large, single-heme cytochrome c (CytC552), which was co-purified with TcDH from the periplasm. Recombinant CytC552, produced in Escherichia coli as a mature protein without a signal peptide, has spectral properties similar to the endogenous protein and serves as an in vitro electron acceptor in the TcDH-catalyzed reaction. The CytC552 structure determined by NMR spectroscopy reveals significant differences compared to those of the typical class I bacterial cytochromes c: a high solvent accessible surface area for the heme group and so-called “intrinsically disordered” nature of the histidine-rich N- and C-terminal regions. Comparison of the signal splitting in the heteronuclear NMR spectra of oxidized, reduced, and TcDH-bound CytC552 reveals the heme axial methionine fluxionality. The TcDH binding site on the CytC552 surface was mapped using NMR chemical shift perturbations. Putative TcDH-CytC552 complexes were reconstructed by the information-driven docking approach and used for the analysis of effective electron transfer pathways. The best pathway includes the electron hopping through His528 and Tyr164 of TcDH, and His83 of CytC552 to the heme group in accordance with pH-dependence of TcDH activity with CytC552.
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166
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Observation of conformational changes that underlie the catalytic cycle of Xrn2. Nat Chem Biol 2022; 18:1152-1160. [PMID: 36008487 PMCID: PMC9512700 DOI: 10.1038/s41589-022-01111-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/07/2022] [Indexed: 12/19/2022]
Abstract
Nuclear magnetic resonance (NMR) methods that quantitatively probe motions on molecular and atomic levels have propelled the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we studied the structure and dynamics of the essential 100-kDa eukaryotic 5′→3′ exoribonuclease Xrn2. A combination of complementary fluorine and methyl-TROSY NMR spectroscopy reveals that the apo enzyme is highly dynamic around the catalytic center. These observed dynamics are in agreement with a transition of the enzyme from the ground state into a catalytically competent state. We show that the conformational equilibrium in Xrn2 shifts substantially toward the active state in the presence of substrate and magnesium. Finally, our data reveal that the dynamics in Xrn2 correlate with the RNA degradation rate, as a mutation that attenuates motions also affects catalytic activity. In that light, our results stress the importance of studies that go beyond static structural information. ![]()
Using methyl group and fluorine NMR spectroscopic methods, Overbeck et al revealed that the dynamics of the eukaryotic 5′→3′ exoribonuclease Xrn2 in the region around the active site are correlated with its catalytic activity.
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167
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Dang TT, Huang YH, Ott S, Harvey PJ, Gilding EK, Tombling BJ, Chan LY, Kaas Q, Claridge-Chang A, Craik DJ. The acyclotide ribe 31 from Rinorea bengalensis has selective cytotoxicity and potent insecticidal properties in Drosophila. J Biol Chem 2022; 298:102413. [PMID: 36007611 PMCID: PMC9513267 DOI: 10.1016/j.jbc.2022.102413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cyclotides and acyclic versions of cyclotides (acyclotides) are peptides involved in plant defense. These peptides contain a cystine knot motif formed by three interlocked disulfide bonds, with the main difference between the two classes being the presence or absence of a cyclic backbone, respectively. The insecticidal activity of cyclotides is well documented, but no study to date explores the insecticidal activity of acyclotides. Here, we present the first in vivo evaluation of the insecticidal activity of acyclotides from Rinorea bengalensis on the vinegar fly Drosophila melanogaster. Of a group of structurally comparable acyclotides, ribe 31 showed the most potent toxicity when fed to D. melanogaster. We screened a range of acyclotides and cyclotides and found their toxicity toward human red blood cells was substantially lower than toward insect cells, highlighting their selectivity and potential for use as bioinsecticides. Our confocal microscopy experiments indicated their cytotoxicity is likely mediated via membrane disruption. Furthermore, our surface plasmon resonance studies suggested ribe 31 preferentially binds to membranes containing phospholipids with phosphatidyl-ethanolamine headgroups. Despite having an acyclic backbone, we determined the three-dimensional NMR solution structure of ribe 31 is similar to that of cyclotides. In summary, our results suggest that, with further optimization, ribe 31 could have applications as an insecticide due to its potent in vivo activity against D. melanogaster. More broadly, this work advances the field by demonstrating that acyclotides are more common than previously thought, have potent insecticidal activity, and have the advantage of potentially being more easily manufactured than cyclotides.
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Affiliation(s)
- Tien T Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Stanislav Ott
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - 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, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Adam Claridge-Chang
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, 169857; Institute for Molecular and Cell Biology, A*STAR, Singapore, 138673; Department of Physiology, National University of Singapore, Singapore, 117593
| | - 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, 4072, Australia.
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168
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Momin AA, Mendes T, Barthe P, Faure C, Hong S, Yu P, Kadaré G, Jaremko M, Girault JA, Jaremko Ł, Arold ST. PYK2 senses calcium through a disordered dimerization and calmodulin-binding element. Commun Biol 2022; 5:800. [PMID: 35945264 PMCID: PMC9363500 DOI: 10.1038/s42003-022-03760-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity. Protein tyrosine kinase 2-beta is shown to function as a sensor and effector of cellular calcium influx through self-association.
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Affiliation(s)
- Afaque A Momin
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tiago Mendes
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Philippe Barthe
- Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France
| | - Camille Faure
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - SeungBeom Hong
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piao Yu
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gress Kadaré
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Mariusz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Łukasz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France.
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169
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Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature 2022; 608:390-396. [PMID: 35922513 PMCID: PMC9365693 DOI: 10.1038/s41586-022-05019-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/23/2022] [Indexed: 01/08/2023]
Abstract
Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance1–3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a β-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates. Using a combination of methods, the mechanism of the antibiotic teixobactin is revealed.
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170
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Paramonov AS, Shulepko MA, Makhonin AM, Bychkov ML, Kulbatskii DS, Chernikov AM, Myshkin MY, Shabelnikov SV, Shenkarev ZO, Kirpichnikov MP, Lyukmanova EN. New Three-Finger Protein from Starfish Asteria rubens Shares Structure and Pharmacology with Human Brain Neuromodulator Lynx2. Mar Drugs 2022; 20:md20080503. [PMID: 36005506 PMCID: PMC9410279 DOI: 10.3390/md20080503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Three-finger proteins (TFPs) are small proteins with characteristic three-finger β-structural fold stabilized by the system of conserved disulfide bonds. These proteins have been found in organisms from different taxonomic groups and perform various important regulatory functions or act as components of snake venoms. Recently, four TFPs (Lystars 1–4) with unknown function were identified in the coelomic fluid proteome of starfish A. rubens. Here we analyzed the genomes of A. rubens and A. planci starfishes and predicted additional five and six proteins containing three-finger domains, respectively. One of them, named Lystar5, is expressed in A. rubens coelomocytes and has sequence homology to the human brain neuromodulator Lynx2. The three-finger structure of Lystar5 close to the structure of Lynx2 was confirmed by NMR. Similar to Lynx2, Lystar5 negatively modulated α4β2 nicotinic acetylcholine receptors (nAChRs) expressed in X. laevis oocytes. Incubation with Lystar5 decreased the expression of acetylcholine esterase and α4 and α7 nAChR subunits in the hippocampal neurons. In summary, for the first time we reported modulator of the cholinergic system in starfish.
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Affiliation(s)
- Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Mikhail A. Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Alexey M. Makhonin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- AI Centre, National Research University Higher School of Economics, Myasnitskaya Str. 20, 101000 Moscow, Russia
| | - Maxim L. Bychkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Dmitrii S. Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Andrey M. Chernikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Mikhail Yu. Myshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
| | - Sergey V. Shabelnikov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Prospect 4, 194064 St. Petersburg, Russia;
| | - Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Moscow Institute of Physics and Technology, State University, Institutskiy Per. 9, 141701 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 119997 Moscow, Russia; (A.S.P.); (M.A.S.); (A.M.M.); (M.L.B.); (D.S.K.); (A.M.C.); (M.Y.M.); (Z.O.S.); (M.P.K.)
- Interdisciplinary Scientific and Educational School of Moscow University “Molecular Technologies of the Living Systems and Synthetic Biology”, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Institutskiy Per. 9, 141701 Moscow, Russia
- Correspondence:
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171
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Sayeesh PM, Ikeya T, Sugasawa H, Watanabe R, Mishima M, Inomata K, Ito Y. Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos. Biochem Biophys Res Commun 2022; 625:87-93. [DOI: 10.1016/j.bbrc.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
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172
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Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X. Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol 2022; 434:167760. [PMID: 35901867 DOI: 10.1016/j.jmb.2022.167760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA+ family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.
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Affiliation(s)
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marie Ley
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Yoann Abel
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, Biophysics and Structural Biology Core Facility, F-54000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Nelly Morellet
- Très Grandes Infrastructures de Recherche, Institut de Chimie des Substances Naturelles - CNRS, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | | | - Edouard Bertrand
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Célia Plisson-Chastang
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Céline Verheggen
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, Nancy F-54000, France
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173
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El Mammeri N, Dregni AJ, Duan P, Wang HK, Hong M. Microtubule-binding core of the tau protein. SCIENCE ADVANCES 2022; 8:eabo4459. [PMID: 35857846 PMCID: PMC9299549 DOI: 10.1126/sciadv.abo4459] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 05/15/2023]
Abstract
The protein tau associates with microtubules to maintain neuronal health. Posttranslational modifications of tau interfere with this binding, leading to tau aggregation in neurodegenerative disorders. Here, we use solid-state nuclear magnetic resonance (NMR) to investigate the structure of the microtubule-binding domain of tau. Wild-type tau that contains four microtubule-binding repeats and a pseudorepeat R' is studied. Complexed with taxol-stabilized microtubules, the immobilized residues exhibit well-resolved two-dimensional spectra that can be assigned to the amino-terminal region of R4 and the R' domain. When tau coassembles with tubulin to form unstable microtubules, the R' signals remain, whereas the R4 signals disappear, indicating that R' remains immobilized, whereas R4 becomes more mobile. Therefore, R' outcompetes the other four repeats to associate with microtubules. These NMR data, together with previous cryo-electron microscopy densities, indicate an extended conformation for microtubule-bound R'. R' contains the largest number of charged residues among all repeats, suggesting that charge-charge interaction drives tau-microtubule association.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Harrison K. Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
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174
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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175
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Poignavent V, Hoh F, Terral G, Yang Y, Gillet FX, Kim JH, Allemand F, Lacombe E, Brugidou C, Cianferani S, Déméné H, Vignols F. A flexible and original architecture of two unrelated zinc fingers underlies the role of the multitask P1 in RYMV spread. J Mol Biol 2022; 434:167715. [DOI: 10.1016/j.jmb.2022.167715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
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176
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Xie J, Robinson SD, Gilding EK, Jami S, Deuis JR, Rehm FBH, Yap K, Ragnarsson L, Chan LY, Hamilton BR, Harvey PJ, Craik DJ, Vetter I, Durek T. Neurotoxic and cytotoxic peptides underlie the painful stings of the tree nettle Urtica ferox. J Biol Chem 2022; 298:102218. [PMID: 35780839 PMCID: PMC9352542 DOI: 10.1016/j.jbc.2022.102218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
The stinging hairs of plants from the family Urticaceae inject compounds that inflict pain to deter herbivores. The sting of the New Zealand tree nettle (Urtica ferox) is among the most painful of these and can cause systemic symptoms that can even be life-threatening; however, the molecular species effecting this response have not been elucidated. Here we reveal that two classes of peptide toxin are responsible for the symptoms of U. ferox stings: Δ-Uf1a is a cytotoxic thionin that causes pain via disruption of cell membranes, while β/δ-Uf2a defines a new class of neurotoxin that causes pain and systemic symptoms via modulation of voltage-gated sodium (NaV) channels. We demonstrate using whole-cell patch-clamp electrophysiology experiments that β/δ-Uf2a is a potent modulator of human NaV1.5 (EC50: 55 nM), NaV1.6 (EC50: 0.86 nM), and NaV1.7 (EC50: 208 nM), where it shifts the activation threshold to more negative potentials and slows fast inactivation. We further found that both toxin classes are widespread among members of the Urticeae tribe within Urticaceae, suggesting that they are likely to be pain-causing agents underlying the stings of other Urtica species. Comparative analysis of nettles of Urtica, and the recently described pain-causing peptides from nettles of another genus, Dendrocnide, indicates that members of tribe Urticeae have developed a diverse arsenal of pain-causing peptides.
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Affiliation(s)
- Jing Xie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sina Jami
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lotten Ragnarsson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia.
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia.
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177
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Colcombet-Cazenave B, Cordier F, Zhu Y, Bouvier G, Litsardaki E, Laserre L, Prevost MS, Raynal B, Caillet-Saguy C, Wolff N. Deciphering the Molecular Interaction Between the Adhesion G Protein-Coupled Receptor ADGRV1 and its PDZ-Containing Regulator PDZD7. Front Mol Biosci 2022; 9:923740. [PMID: 35836927 PMCID: PMC9274004 DOI: 10.3389/fmolb.2022.923740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Hearing relies on the transduction of sound-evoked vibrations into electrical signals, occurring in the stereocilia bundle of inner ear hair cells. The G protein-coupled receptor (GPCR) ADGRV1 and the multi-PDZ protein PDZD7 play a critical role in the formation and function of stereocilia through their scaffolding and signaling properties. During hair cell development, the GPCR activity of ADGRV1 is specifically inhibited by PDZD7 through an unknown mechanism. Here, we describe the key interactions mediated by the two N-terminal PDZ domains of PDZD7 and the cytoplasmic domain of ADGRV1. Both PDZ domains can bind to the C-terminal PDZ binding motif (PBM) of ADGRV1 with the critical contribution of atypical C-terminal β extensions. The two PDZ domains form a supramodule in solution, stabilized upon PBM binding. Interestingly, we showed that the stability and binding properties of the PDZ tandem are affected by two deafness-causing mutations located in the binding grooves of PDZD7 PDZ domains.
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Affiliation(s)
- Baptiste Colcombet-Cazenave
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
- Complexité du Vivant, Sorbonne Université, Paris, France
| | - Florence Cordier
- Structural Bioinformatics Unit, UMR CNRS 3528, Institut Pasteur, Université de Paris, Paris, France
- Biological NMR and HDX-MS Technological Platform, UMR CNRS 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Yanlei Zhu
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Guillaume Bouvier
- Structural Bioinformatics Unit, UMR CNRS 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Eleni Litsardaki
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Louise Laserre
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Marie S. Prevost
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform-C2RT, UMR CNRS 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Célia Caillet-Saguy
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Nicolas Wolff
- Channel Receptors Unit, UMR CNRS 3571, Institut Pasteur, Université de Paris, Paris, France
- *Correspondence: Nicolas Wolff,
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178
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Almeida VS, Miller LL, Delia JPG, Magalhães AV, Caruso IP, Iqbal A, Almeida FCL. Deciphering the Path of S-nitrosation of Human Thioredoxin: Evidence of an Internal NO Transfer and Implication for the Cellular Responses to NO. Antioxidants (Basel) 2022; 11:antiox11071236. [PMID: 35883729 PMCID: PMC9311519 DOI: 10.3390/antiox11071236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 01/27/2023] Open
Abstract
Nitric oxide (NO) is a free radical with a signaling capacity. Its cellular functions are achieved mainly through S-nitrosation where thioredoxin (hTrx) is pivotal in the S-transnitrosation to specific cellular targets. In this study, we use NMR spectroscopy and mass spectrometry to follow the mechanism of S-(trans)nitrosation of hTrx. We describe a site-specific path for S-nitrosation by measuring the reactivity of each of the 5 cysteines of hTrx using cysteine mutants. We showed the interdependence of the three cysteines in the nitrosative site. C73 is the most reactive and is responsible for all S-transnitrosation to other cellular targets. We observed NO internal transfers leading to C62 S-nitrosation, which serves as a storage site for NO. C69-SNO only forms under nitrosative stress, leading to hTrx nuclear translocation.
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Affiliation(s)
- Vitor S. Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil
- Institute of Chemistry, Rural Federal University of Rio de Janeiro (UFRRJ), Seropédica 23897-000, Brazil
| | - Lara L. Miller
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - João P. G. Delia
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - Augusto V. Magalhães
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - Icaro P. Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Institute of Chemistry, Rural Federal University of Rio de Janeiro (UFRRJ), Seropédica 23897-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, Brazil
| | - Anwar Iqbal
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Department of Chemical Sciences, University of Lakki Marwat, Lakki Marwat 28420, Pakistan
| | - Fabio C. L. Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Correspondence:
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179
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Conformational Changes in Ff Phage Protein gVp upon Complexation with Its Viral Single-Stranded DNA Revealed Using Magic-Angle Spinning Solid-State NMR. Viruses 2022; 14:v14061264. [PMID: 35746735 PMCID: PMC9231167 DOI: 10.3390/v14061264] [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: 05/16/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Gene V protein (gVp) of the bacteriophages of the Ff family is a non-specific single-stranded DNA (ssDNA) binding protein. gVp binds to viral DNA during phage replication inside host Escherichia coli cells, thereby blocking further replication and signaling the assembly of new phage particles. gVp is a dimer in solution and in crystal form. A structural model of the complex between gVp and ssDNA was obtained via docking the free gVp to structures of short ssDNA segments and via the detection of residues involved in DNA binding in solution. Using solid-state NMR, we characterized structural features of the gVp in complex with full-length viral ssDNA. We show that gVp binds ssDNA with an average distance of 5.5 Å between the amino acid residues of the protein and the phosphate backbone of the DNA. Torsion angle predictions and chemical shift perturbations indicate that there were considerable structural changes throughout the protein upon complexation with ssDNA, with the most significant variations occurring at the ssDNA binding loop and the C-terminus. Our data suggests that the structure of gVp in complex with ssDNA differs significantly from the structure of gVp in the free form, presumably to allow for cooperative binding of dimers to form the filamentous phage particle.
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180
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Erdmann D, Contreras J, Le Meur RA, Vitorge B, Saverat V, Tafit A, Jallet C, Cadet-Daniel V, Bon C, Phansavath P, Ratovelomanana-Vidal V, Jeltsch A, Vichier-Guerre S, Guijarro JI, Arimondo PB. Identification of Chemical Probes Targeting MBD2. ACS Chem Biol 2022; 17:1415-1426. [PMID: 35649238 DOI: 10.1021/acschembio.1c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epigenetics has received much attention in the past decade. Many insights on epigenetic (dys)regulation in diseases have been obtained, and clinical therapies targeting them are in place. However, the readers of the epigenetic marks are lacking enlightenment behind this revolution, and it is poorly understood how DNA methylation is being read and translated to chromatin function and cellular responses. Chemical probes targeting the methyl-CpG readers, such as the methyl-CpG binding domain proteins (MBDs), could be used to study this mechanism. We have designed analogues of 5-methylcytosine to probe the MBD domain of human MBD2. By setting up a protein thermal shift assay and an AlphaScreen-based test, we were able to identify three fragments that bind MBD2 alone and disrupt the MBD2-methylated DNA interactions. Two-dimensional NMR experiments and virtual docking gave valuable insights into the interaction of the ligands with the protein showing that the compounds interact with residues that are important for DNA recognition. These constitute the starting point for the design of potent chemical probes for MBD proteins.
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Affiliation(s)
- Diane Erdmann
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Jean Contreras
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Rémy A. Le Meur
- Biological NMR and HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015 Paris, France
| | - Bruno Vitorge
- Biological NMR and HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015 Paris, France
| | - Vincent Saverat
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Ambre Tafit
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Corinne Jallet
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Véronique Cadet-Daniel
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Corentin Bon
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - Phannarath Phansavath
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, 75005 Paris, France
| | - Virginie Ratovelomanana-Vidal
- PSL University, Chimie ParisTech, Institute of Chemistry for Life & Health Sciences, CNRS UMR8060, 75005 Paris, France
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Sophie Vichier-Guerre
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
| | - J. Iñaki Guijarro
- Biological NMR and HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015 Paris, France
| | - Paola B. Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3523, 75015 Paris, France
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181
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Rahimi M, Lee Y, Nguyen H, Chiu A, Lee W. A toolset for the solid-state NMR-based 3D structure calculation of proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 339:107214. [PMID: 35490563 DOI: 10.1016/j.jmr.2022.107214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/11/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Proteins are the building blocks of life. The shape of the protein determines its functionality. This understanding of the 3D structure of proteins has applications in study of diseases, medicine, body functions, and other aspects of life. Nuclear magnetic resonance (NMR) has been a powerful tool for researchers to get insight into the metabolome of cells, tissues, biofluids, secretions, and overall etiology of the disease state. Solid-state NMR (ssNMR) spectroscopy is used for samples that have low solubility in common NMR solvents. The use of ssNMR for 3D structure determination of proteins has been on the rise in the recent years especially for such samples. Still, one of the challenges that researchers face in this area is a shortage of easy and user-friendly computational aids. To address this, we are introducing our comprehensive software solution by automating every step of the process and essentially transforming the task into a few clicks of the mouse. The workflow for 3D structure determination has been simplified down to only a few procedures. Starting with selection of an ssNMR spectrum, user can receive its 3D structure along with an abundance of statistical information and validation tools using our software. We have tested this toolset to test the usefulness and user-friendliness with different data sets available on biological magnetic resonance bank (BMRB).
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Affiliation(s)
- Mehdi Rahimi
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA
| | - Huong Nguyen
- Computer Science Department, University of Wisconsin-Madison, Madison, WI 53706, USA; URS Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Abigail Chiu
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
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182
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Dang TT, Harvey PJ, Chan LY, Huang Y, Kaas Q, Craik DJ. Mutagenesis of cyclotide Cter 27 exemplifies a robust folding strategy for bracelet cyclotides. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tien T. Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
- Institute of Applied Materials Science Vietnam Academy of Science and Technology Ho Chi Minh City Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - 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
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183
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Yang L, Lee KM, Yu CWH, Imai H, Choi AH, Banfield D, Ito K, Uchiumi T, Wong KB. The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation. Nucleic Acids Res 2022; 50:5335-5348. [PMID: 35544198 PMCID: PMC9122527 DOI: 10.1093/nar/gkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N-1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9-32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.
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Affiliation(s)
- Lei Yang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Conny Wing-Heng Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hirotatsu Imai
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Andrew Kwok-Ho Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - David K Banfield
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
- The Institute of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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184
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Khaje NA, Eletsky A, Biehn SE, Mobley CK, Rogals MJ, Kim Y, Mishra SK, Doerksen RJ, Lindert S, Prestegard JH, Sharp JS. Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol 2022; 5:452. [PMID: 35551273 PMCID: PMC9098640 DOI: 10.1038/s42003-022-03411-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure. A mass spectrometry-based method guides computational modeling for de novo protein structure prediction.
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Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Analytical Operations Department, Gilead Sciences, Foster City, CA, USA
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sarah E Biehn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Charles K Mobley
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Protein Discovery Department, Impossible Foods, Redwood City, CA, USA
| | - Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yoonkyoo Kim
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sushil K Mishra
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Robert J Doerksen
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA. .,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA. .,Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA.
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185
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ADP-Induced Conformational Transition of Human Adenylate Kinase 1 Is Triggered by Suppressing Internal Motion of α3α4 and α7α8 Fragments on the ps-ns Timescale. Biomolecules 2022; 12:biom12050671. [PMID: 35625598 PMCID: PMC9138365 DOI: 10.3390/biom12050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022] Open
Abstract
Human adenylate kinase 1 (hAK1) plays a vital role in the energetic and metabolic regulation of cell life, and impaired functions of hAK1 are closely associated with many diseases. In the presence of Mg2+ ions, hAK1 in vivo can catalyze two ADP molecules into one ATP and one AMP molecule, activating the downstream AMP signaling. The ADP-binding also initiates AK1 transition from an open conformation to a closed conformation. However, how substrate binding triggers the conformational transition of hAK1 is still unclear, and the underlying molecular mechanisms remain elusive. Herein, we determined the solution structure of apo-hAK1 and its key residues for catalyzing ADP, and characterized backbone dynamics characteristics of apo-hAK1 and hAK1-Mg2+-ADP complex (holo-hAK1) using NMR relaxation experiments. We found that ADP was primarily bound to a cavity surrounded by the LID, NMP, and CORE domains of hAK1, and identified several critical residues for hAK1 catalyzing ADP including G16, G18, G20, G22, T39, G40, R44, V67, D93, G94, D140, and D141. Furthermore, we found that apo-hAK1 adopts an open conformation with significant ps-ns internal mobility, and Mg2+-ADP binding triggered conformational transition of hAK1 by suppressing the ps-ns internal motions of α3α4 in the NMP domain and α7α8 in the LID domain. Both α3α4 and α7α8 fragments became more rigid so as to fix the substrate, while the catalyzing center of hAK1 experiences promoted µs-ms conformational exchange, potentially facilitating catalysis reaction and conformational transition. Our results provide the structural basis of hAK1 catalyzing ADP into ATP and AMP, and disclose the driving force that triggers the conformational transition of hAK1, which will deepen understanding of the molecular mechanisms of hAK1 functions.
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186
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Yang Y, Liu S, Egloff S, Eichhorn CD, Hadjian T, Zhen J, Kiss T, Zhou ZH, Feigon J. Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP. Mol Cell 2022; 82:1724-1736.e7. [PMID: 35320752 PMCID: PMC9081187 DOI: 10.1016/j.molcel.2022.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/27/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023]
Abstract
7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.
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Affiliation(s)
- Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvain Egloff
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tanya Hadjian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Zhen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamás Kiss
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France; Biological Research Centre, Szeged, Temesvári krt. 62, 6726, Hungary
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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187
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Herzig V, Chen YC, Chin YKY, Dekan Z, Chang YW, Yu HM, Alewood PF, Chen CC, King GF. The Tarantula Toxin ω-Avsp1a Specifically Inhibits Human CaV3.1 and CaV3.3 via the Extracellular S3-S4 Loop of the Domain 1 Voltage-Sensor. Biomedicines 2022; 10:biomedicines10051066. [PMID: 35625803 PMCID: PMC9138389 DOI: 10.3390/biomedicines10051066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/01/2022] Open
Abstract
Inhibition of T-type calcium channels (CaV3) prevents development of diseases related to cardiovascular and nerve systems. Further, knockout animal studies have revealed that some diseases are mediated by specific subtypes of CaV3. However, subtype-specific CaV3 inhibitors for therapeutic purposes or for studying the physiological roles of CaV3 subtypes are missing. To bridge this gap, we employed our spider venom library and uncovered that Avicularia spec. (“Amazonas Purple”, Peru) tarantula venom inhibited specific T-type CaV channel subtypes. By using chromatographic and mass-spectrometric techniques, we isolated and sequenced the active toxin ω-Avsp1a, a C-terminally amidated 36 residue peptide with a molecular weight of 4224.91 Da, which comprised the major peak in the venom. Both native (4.1 μM) and synthetic ω-Avsp1a (10 μM) inhibited 90% of CaV3.1 and CaV3.3, but only 25% of CaV3.2 currents. In order to investigate the toxin binding site, we generated a range of chimeric channels from the less sensitive CaV3.2 and more sensitive CaV3.3. Our results suggest that domain-1 of CaV3.3 is important for the inhibitory effect of ω-Avsp1a on T-type calcium channels. Further studies revealed that a leucine of T-type calcium channels is crucial for the inhibitory effect of ω-Avsp1a.
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Affiliation(s)
- Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.K.-Y.C.); (Z.D.); (P.F.A.)
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- Correspondence: (V.H.); (C.-C.C.); (G.F.K.); Tel.: +61-7-5456-5382 (V.H.); +886-2-2652-3522 (C.-C.C.); +61-7-3346-2025 (G.F.K.)
| | - Yong-Cyuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (Y.-C.C.); (Y.-W.C.)
| | - Yanni K.-Y. Chin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.K.-Y.C.); (Z.D.); (P.F.A.)
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zoltan Dekan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.K.-Y.C.); (Z.D.); (P.F.A.)
| | - Yu-Wang Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (Y.-C.C.); (Y.-W.C.)
| | - Hui-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan;
| | - Paul F. Alewood
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.K.-Y.C.); (Z.D.); (P.F.A.)
| | - Chien-Chang Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan; (Y.-C.C.); (Y.-W.C.)
- Correspondence: (V.H.); (C.-C.C.); (G.F.K.); Tel.: +61-7-5456-5382 (V.H.); +886-2-2652-3522 (C.-C.C.); +61-7-3346-2025 (G.F.K.)
| | - Glenn F. King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.K.-Y.C.); (Z.D.); (P.F.A.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: (V.H.); (C.-C.C.); (G.F.K.); Tel.: +61-7-5456-5382 (V.H.); +886-2-2652-3522 (C.-C.C.); +61-7-3346-2025 (G.F.K.)
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188
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Kraus J, Russell RW, Kudryashova E, Xu C, Katyal N, Perilla JR, Kudryashov DS, Polenova T. Magic angle spinning NMR structure of human cofilin-2 assembled on actin filaments reveals isoform-specific conformation and binding mode. Nat Commun 2022; 13:2114. [PMID: 35440100 PMCID: PMC9018683 DOI: 10.1038/s41467-022-29595-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022] Open
Abstract
Actin polymerization dynamics regulated by actin-binding proteins are essential for various cellular functions. The cofilin family of proteins are potent regulators of actin severing and filament disassembly. The structural basis for cofilin-isoform-specific severing activity is poorly understood as their high-resolution structures in complex with filamentous actin (F-actin) are lacking. Here, we present the atomic-resolution structure of the muscle-tissue-specific isoform, cofilin-2 (CFL2), assembled on ADP-F-actin, determined by magic-angle-spinning (MAS) NMR spectroscopy and data-guided molecular dynamics (MD) simulations. We observe an isoform-specific conformation for CFL2. This conformation is the result of a unique network of hydrogen bonding interactions within the α2 helix containing the non-conserved residue, Q26. Our results indicate F-site interactions that are specific between CFL2 and ADP-F-actin, revealing mechanistic insights into isoform-dependent F-actin disassembly.
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Affiliation(s)
- Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544-1014, United States
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, United States
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Nidhi Katyal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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189
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Vasconcelos AA, Succar BB, di Piero LB, Kurtenbach E, Zingali RB, Almeida FCL. 15N, 13C, and 1H resonance assignments of Jarastatin: a disintegrin of Bothrops jararaca. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:37-40. [PMID: 34826102 DOI: 10.1007/s12104-021-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Disintegrins are a group of cysteine-rich proteins found in a wide variety of snake venoms. These proteins selectively bind to integrins, which play a fundamental role in the regulation of many physiological and pathological processes. Here, we report the NMR chemical shift assignments for 1H, 15N, and 13C nuclei in the backbone and side chains of recombinant disintegrin Jarastatin (rJast), which was further validated by secondary structure prediction using the TALOS-N server. Taken together, these data are essential to perform NMR-based experiments, including structure determination, backbone dynamics, mapping ligand sites and enabling a deeper understanding of the effect of hydrophobic surface clusters, which are important elements to stabilize some 3D proteins structure/folding.
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Affiliation(s)
- Ariana Azevedo Vasconcelos
- Institute of Medical Biochemistry (IBqM) Leopoldo de Meis, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Barbara Barbosa Succar
- Laboratório de Hemostase e Venenos, Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Bartkevihi di Piero
- Institute of Medical Biochemistry (IBqM) Leopoldo de Meis, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eleonora Kurtenbach
- Laboratório de Biologia Molecular e Bioquímica de Proteínas (LBMBP), Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina Benedeta Zingali
- Laboratório de Hemostase e Venenos, Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fabio C L Almeida
- Institute of Medical Biochemistry (IBqM) Leopoldo de Meis, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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190
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Boll E, Cantrelle FX, Lamotte O, Aimé S, Wendehenne D, Trivelli X. 1H, 13C and 15N chemical shift backbone resonance NMR assignment of tobacco calmodulin 2. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:63-66. [PMID: 35020112 DOI: 10.1007/s12104-021-10060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Calcium is a ubiquitous second messenger regulating numbers of cellular processes in living organisms. It encodes and transmits information perceived by cells to downstream sensors, including calmodulin (CaM), that initiate cellular responses. In plants, CaM has been involved in the regulation of plant responses to biotic and abiotic environmental cues. Plant CaMs possess a cysteine residue in their first calcium-binding motif EF-hand, which is not conserved in other eucaryotic organisms. In this work, we report the near-complete backbone chemical shift assignment of tobacco CaM2 with calcium. These results will be useful to study the impact of this particular EF-hand domain regarding CaM interaction with partners involved in stress responses.
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Affiliation(s)
- Emmanuelle Boll
- ERL9002-Integrative Structural Biology, CNRS, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- ERL9002-Integrative Structural Biology, CNRS, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Olivier Lamotte
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - Sébastien Aimé
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - David Wendehenne
- AgroSup Dijon, CNRS, INRAE, Université de Bourgogne, Univ. Bourgogne Franche-Comté, Agroécologie, 17 Rue de Sully, BP 86510, F-21065, Dijon, France
| | - Xavier Trivelli
- Univ. Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR-2638-IMEC-Institut Michel-Eugène Chevreul, F-59000, Lille, France.
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191
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Sánta A, Czajlik A, Batta G, Péterfia B, Gáspári Z. Resonance assignment of the Shank1 PDZ domain. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:121-127. [PMID: 35083656 PMCID: PMC9068651 DOI: 10.1007/s12104-022-10069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Shank proteins are among the most abundant and well-studied postsynaptic scaffold proteins. Their PDZ domain has unique characteristics as one of its loop regions flanking the ligand-binding site is uniquely long and has also been implicated in the formation of PDZ dimers. Here we report the initial characterization of the Shank1 PDZ domain by solution NMR spectroscopy. The assigned chemical shifts are largely consistent with the common features of PDZ domains in general and the available Shank PDZ crystal structures in particular. Our analysis suggests that under the conditions investigated, the domain is monomeric and the unique loop harbors a short helical segment, observed in only one of the known X-ray structures so far. Our work stresses the importance of solution-state investigations to fully decipher the functional relevance of the structural and dynamical features unique to Shank PDZ domains.
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Affiliation(s)
- Anna Sánta
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - András Czajlik
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - Gyula Batta
- Faculty of Science and Technology, Institute of Chemistry, Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
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192
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Huang Q, Ng EY, Li Q, Kang C. 1 H, 15 N and 13 C resonance assignments of the Q61H mutant of human KRAS bound to GDP. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:51-56. [PMID: 34787842 DOI: 10.1007/s12104-021-10058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
KRAS proteins are small GTPases binding to the cell membrane and playing important roles in signal transduction. KRAS proteins form complexes with GTP and GDP to result in active and inactive conformations favouring interactions with different proteins. Mutations in KRAS have impact on the GTPase activity and some mutants are related to certain types of cancers. In addition to mutation at position 12, the Q61H mutant is also identified as an oncogenic mutant. Here, we describe resonance assignment for Q61H mutant of human KRAS-4B. A construct containing 1-169 residues of KRAS with a point mutation at position 61 (Q to H) was made for solution NMR studies. The backbone and some side chain resonance assignments were obtained using conventional multi-dimensional experiments. The secondary structures were analysed based on the assigned residues. As NMR is a powerful tool in probing target and ligand interactions, the assignment will be useful for later compound binding studies.
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Affiliation(s)
- Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore
| | - Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore.
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193
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Penna BR, de Oliveira DMP, Anobom CD, Valente AP. Backbone 1H, 15N, and 13C resonance assignments of the non-structural protein NS2B of Zika virus. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:31-35. [PMID: 34817802 DOI: 10.1007/s12104-021-10055-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Zika virus (ZIKV) emerged as a global public health concern due to its relationship with severe neurological disorders. Non-structural (NS) proteins of ZIKV are essential for viral replication, regulatory function, and subversion of host responses. NS2B is a membrane protein responsible for the regulation of viral protease activity. This protein has transmembrane domains critical for the localization of viral protease to the endoplasmic reticulum membrane and a hydrophilic domain essential for folding, recruitment, and protease activity. Therefore, NS2B is considered a cofactor of viral protease which processes viral polyprotein and is essential for virus replication, making it an attractive antiviral drug target. Here, we report the backbone 1H, 15N, 13C resonance assignments of the full-length NS2B by high-resolution NMR. The backbone assignment will be necessary for determining the three-dimensional structure and backbone dynamics of NS2B, interaction mapping and screening potential of antiviral drugs against ZIKV and related pathogenic flaviviruses.
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Affiliation(s)
- Beatriz Rosa Penna
- Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielle Maria P de Oliveira
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Dinis Anobom
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula Valente
- Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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194
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Kumar N, Ghosh M, Manikandan P, Basak S, Deepa A, Singh M. Resonance assignment and secondary structure of the tandem harmonin homology domains of human RTEL1. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:159-164. [PMID: 35320499 DOI: 10.1007/s12104-022-10074-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Regulator of telomere elongation helicase 1 (RTEL1) is an Fe-S cluster containing DNA helicase that plays important roles in telomere DNA maintenance, DNA repair, and genomic stability. It is a modular protein comprising an N-terminal helicase domain, two tandem harmonin homology domains 1 & 2 (HHD1 and HHD2), and a C-terminal C4C4 type RING domain. The N-terminal helicase domain disassembles the telomere t/D-loop and unwinds the G-quadruplex via its helicase activity. The C-terminal RING domain interacts with telomere DNA binding protein TRF2 and helps RTEL1 recruitment to the telomere. The tandem HHD1 and HHD2 are characterized as a putative protein-protein interaction domain and have recently been shown to interact with a DNA repair protein SLX4. Several mutations associated with Hoyeraal-Hreidarsson syndrome and pulmonary fibrosis have been found in HHD1 and HHD2 of RTEL1. However, these domains have not been characterized for their structures. We have expressed and purified HHD1 and HHD2 of human RTEL1 for their characterization using solution NMR spectroscopy. Here, we report near complete backbone and sidechain 1H, 13C and 15N chemical shift assignments and secondary structure of the HHD1 and HHD2 domains of human RTEL1.
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Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | | | - Sanmoyee Basak
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | - Akula Deepa
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
- Indian Institute of Technology, Hyderabad, 502285, India
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India.
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195
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Agback P, Lesovoy DM, Han X, Sun R, Sandalova T, Agback T, Achour A, Orekhov VY. 1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:135-145. [PMID: 35149939 PMCID: PMC9068680 DOI: 10.1007/s12104-022-10071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete 1H, 15N, and 13C backbone and 1H, 13C isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden.
| | - Dmitry M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, 117997, Moscow, Russia
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
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196
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Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
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Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
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197
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Sharma AK, Dyba M, Tonelli M, Smith B, Gillette WK, Esposito D, Nissley DV, McCormick F, Maciag AE. NMR 1H, 13C, 15N backbone resonance assignments of the T35S and oncogenic T35S/Q61L mutants of human KRAS4b in the active, GppNHp-bound conformation. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:1-8. [PMID: 34686998 PMCID: PMC9068649 DOI: 10.1007/s12104-021-10050-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
RAS proteins cycling between the active-form (GTP-bound) and inactive-form (GDP-bound) play a key role in cell signaling pathways that control cell survival, proliferation, and differentiation. Mutations at codon 12, 13, and 61 in RAS are known to attenuate its GTPase activity favoring the RAS active state and constitutively active downstream signaling. This hyperactivation accounts for various malignancies including pancreatic, lung, and colorectal cancers. Active KRAS is found to exist in equilibrium between two rapidly interconverting conformational states (State1-State2) in solution. Due to this dynamic feature of the protein, the 1H-15N correlation cross-peak signals of several amino acid (AA) residues of KRAS belonging to the flexible loop regions are absent from its 2D 1H-15N HSQC spectrum within and near physiological solution pH. A threonine to serine mutation at position 35 (T35S) shifts the interconverting equilibrium to State1 conformation and enables the emergence of such residues in the 2D 1H-15N HSQC spectrum due to gained conformational rigidity. We report here the 1HN, 15N, and 13C backbone resonance assignments for the 19.2 kDa (AA 1-169) protein constructs of KRAS-GppNHp harboring T35S mutation (KRAST35S/C118S-GppNHp) and of its oncogenic counterpart harboring the Q61L mutation (KRAST35S/Q61L/C118S-GppNHp) using heteronuclear, multidimensional NMR spectroscopy at 298 K. High resolution NMR data allowed the unambiguous assignments of 1H-15N correlation cross-peaks for all the residues except for Met1. Furthermore, 2D 1H-15N HSQC overlay of two proteins assisted in determination of Q61L mutation-induced chemical shift perturbations for select residues in the regions of P-loop, Switch-II, and helix α3.
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Affiliation(s)
- Alok K Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA.
- Leidos Biomedical Research, Inc., Post Office Box B, Frederick, MD, 21702, USA.
| | - Marcin Dyba
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian Smith
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - William K Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
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198
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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199
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Tossavainen H, Uğurlu H, Karjalainen M, Hellman M, Antenucci L, Fagerlund R, Saksela K, Permi P. Structure of SNX9 SH3 in complex with a viral ligand reveals the molecular basis of its unique specificity for alanine-containing class I SH3 motifs. Structure 2022; 30:828-839.e6. [PMID: 35390274 DOI: 10.1016/j.str.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/22/2021] [Accepted: 03/04/2022] [Indexed: 11/26/2022]
Abstract
Class I SH3 domain-binding motifs generally comply with the consensus sequence [R/K]xØPxxP, the hydrophobic residue Ø being proline or leucine. We have studied the unusual Ø = Ala-specificity of SNX9 SH3 by determining its complex structure with a peptide present in eastern equine encephalitis virus (EEEV) nsP3. The structure revealed the length and composition of the n-Src loop as important factors determining specificity. We also compared the affinities of EEEV nsP3 peptide, its mutants, and cellular ligands to SNX9 SH3. These data suggest that nsP3 has evolved to minimize reduction of conformational entropy upon binding, hence acquiring stronger affinity, enabling takeover of SNX9. The RxAPxxP motif was also found in human T cell leukemia virus-1 (HTLV-1) Gag polyprotein. We found that this motif was required for efficient HTLV-1 infection, and that the specificity of SNX9 SH3 for the RxAPxxP core binding motif was importantly involved in this process.
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Affiliation(s)
- Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Hasan Uğurlu
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Lina Antenucci
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland; Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland
| | - Riku Fagerlund
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki FI-00014 Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla FI-40014, Finland; Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla FI-40014, Finland.
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200
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Chagot ME, Boutilliat A, Kriznik A, Quinternet M. Structural Analysis of the Plasmodial Proteins ZNHIT3 and NUFIP1 Provides Insights into the Selectivity of a Conserved Interaction. Biochemistry 2022; 61:479-493. [PMID: 35315277 DOI: 10.1021/acs.biochem.1c00792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is a widespread and lethal disease caused by the Plasmodium parasites that can infect human beings through Anopheles mosquitoes. For that reason, the biology of Plasmodium needs to be studied to develop antimalarial treatments. By determining the three-dimensional structures of macromolecules, structural biology helps to understand the function of proteins and can reveal how interactions occur between biological partners. Here, we studied the ZNHIT3 and NUFIP1 proteins from Plasmodium falciparum, two proteins tightly linked to the ribosome biology. Due to their important functions in post-translational modifications of ribosomal RNAs and in ribophagy, these proteins participate in the survival of cells. In this study, we solved the three-dimensional structure of a thermally stable and species-dependent complex between fragments of these proteins. Our results were compared to the AlphaFold predictions, which motivated the study of the free ZNHIT3 fragment that binds NUFIP1. We showed that the latter fragment multimerized in vitro but also had the inner ability to change its conformation to escape the solvent exposition of key hydrophobic residues involved in the interaction with NUFIP1. Our data could open the gate to selective drug discovery processes involving these two proteins.
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Affiliation(s)
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.,Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
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