1
|
Barylko B, Taylor CA, Wang J, Hedde PN, Chen Y, Hur KH, Binns DD, Brautigam CA, DeMartino GN, Mueller JD, Jameson DM, Albanesi JP. Analysis of Arc/Arg3.1 Oligomerization In Vitro and in Living Cells. Int J Mol Sci 2024; 25:6454. [PMID: 38928159 PMCID: PMC11203824 DOI: 10.3390/ijms25126454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Arc (also known as Arg3.1) is an activity-dependent immediate early gene product enriched in neuronal dendrites. Arc plays essential roles in long-term potentiation, long-term depression, and synaptic scaling. Although its mechanisms of action in these forms of synaptic plasticity are not completely well established, the activities of Arc include the remodeling of the actin cytoskeleton, the facilitation of AMPA receptor (AMPAR) endocytosis, and the regulation of the transcription of AMPAR subunits. In addition, Arc has sequence and structural similarity to retroviral Gag proteins and self-associates into virus-like particles that encapsulate mRNA and perhaps other cargo for intercellular transport. Each of these activities is likely to be influenced by Arc's reversible self-association into multiple oligomeric species. Here, we used mass photometry to show that Arc exists predominantly as monomers, dimers, and trimers at approximately 20 nM concentration in vitro. Fluorescence fluctuation spectroscopy revealed that Arc is almost exclusively present as low-order (monomer to tetramer) oligomers in the cytoplasm of living cells, over a 200 nM to 5 μM concentration range. We also confirmed that an α-helical segment in the N-terminal domain contains essential determinants of Arc's self-association.
Collapse
Affiliation(s)
- Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Clinton A. Taylor
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Jason Wang
- Department of Physiology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB 222, Honolulu, HI 96813, USA;
- Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - Kwang-Ho Hur
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - Derk D. Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Chad A. Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA;
| | - George N. DeMartino
- Department of Physiology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB 222, Honolulu, HI 96813, USA;
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| |
Collapse
|
2
|
Lautenbach V, Onishchukov G, Wawra SE, Frank U, Hartmann L, Peukert W, Walter J. Development of an advanced multiwavelength emission detector for the analytical ultracentrifuge. NANOSCALE ADVANCES 2024; 6:2611-2622. [PMID: 38752146 PMCID: PMC11093262 DOI: 10.1039/d3na00980g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/18/2024] [Indexed: 05/18/2024]
Abstract
An advanced design of the analytical ultracentrifuge with multiwavelength emission detection (MWE-AUC) is presented which offers outstanding performance concerning the spectral resolution and range flexibility as well as the quality of the data acquired. The excitation by a 520 nm laser is complemented with a 405 nm laser. An external spectrograph with three switchable tunable gratings permits optimisation of the spectral resolution in an order of magnitude range while keeping the spectral region broad. The new system design leads also to a significant reduction of systematic signal noise and allows the assessment and control of inner filter effects. Details regarding the very large signal dynamic range are presented, an important aspect when studying samples in a broad concentration range of up to five orders of magnitude. Our system is validated by complementary studies on two biological systems, fluorescent BSA and GFP, using the commercial Optima AUC with absorbance detection for comparison. Finally, we demonstrate the capabilities of our second generation MWE-AUC with respect to multiwavelength characterisation of gold nanoclusters, which exhibit specific fluorescence depending on their structure. Overall, this work depicts an important stepping stone for the concept of multiwavelength emission detection in AUC. The MWE-AUC developed, being to our knowledge the first and sole one of its kind, has reached the development level suitable for the future in-depth studies of size-, shape- and composition-dependent emission properties of colloids.
Collapse
Affiliation(s)
- Vanessa Lautenbach
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
| | - Georgy Onishchukov
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
- Max Planck Institute for the Science of Light Staudtstraße 2 91058 Erlangen Germany
| | - Simon E Wawra
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Uwe Frank
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Lukas Hartmann
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Johannes Walter
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstraße 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| |
Collapse
|
3
|
Li M, Cao L, Liu D, Su T, Cheng W, Li G, Ma T. Efficient bio-remediation of multiple aromatic hydrocarbons using different types of thermotolerant, ring-cleaving dioxygenases derived from Aeribacillus pallidus HB-1. BIORESOURCE TECHNOLOGY 2024; 398:130472. [PMID: 38387841 DOI: 10.1016/j.biortech.2024.130472] [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: 11/06/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
As toxic contaminants, aromatic compounds are widespread in most environmental matrices, and bioenzymatic catalysis plays a critical role in the degradation of xenobiotics. Here, a thermophillic aromatic hydrocarbon degrader Aeribacillus pallidus HB-1 was found. Bioinformatic analysis of the HB-1 genome revealed two ring-cleaving extradiol dioxygenases (EDOs), among which, EDO-0418 was assigned to a new subfamily of type I.1 EDOs and exhibited a broad substrate specificity, particularly towards biarylic substrate. Both EDOs exhibited optimal activities at elevated temperatures (55 and 65 °C, respectively) and showed remarkable thermostability, pH stability, metal ion resistance and tolerance to chemical reagents. Most importantly, simulated wastewater bioreactor experiments demonstrated efficient and uniform degradation performance of mixed aromatic substrates under harsh environments by the two enzymes combined for potential industrial applications. The unveiling of two thermostable dioxygenases with broad substrate specificities and stress tolerance provides a novel approach for highly efficient environmental bioremediation using composite enzyme systems.
Collapse
Affiliation(s)
- Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lu Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dakun Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wei Cheng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
| |
Collapse
|
4
|
Xu G, Ma J, Fang Q, Peng Q, Jiao X, Hu W, Zhao Q, Kong Y, Liu F, Shi X, Tang DJ, Tang JL, Ming Z. Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway. Commun Biol 2024; 7:255. [PMID: 38429435 PMCID: PMC10907753 DOI: 10.1038/s42003-024-05921-3] [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: 01/09/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) plays an important role in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) via the nicotinamide (NAM) salvage pathway. While the structural biochemistry of eukaryote NAMPT has been well studied, the catalysis mechanism of prokaryote NAMPT at the molecular level remains largely unclear. Here, we demonstrated the NAMPT-mediated salvage pathway is functional in the Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) for the synthesis of NAD+, and the enzyme activity of NAMPT in this bacterium is significantly higher than that of human NAMPT in vitro. Our structural analyses of Xcc NAMPT, both in isolation and in complex with either the substrate NAM or the product nicotinamide mononucleotide (NMN), uncovered significant details of substrate recognition. Specifically, we revealed the presence of a NAM binding tunnel that connects the active site, and this tunnel is essential for both catalysis and inhibitor binding. We further demonstrated that NAM binding in the tunnel has a positive cooperative effect with NAM binding in the catalytic site. Additionally, we discovered that phosphorylation of the His residue at position 229 enhances the substrate binding affinity of Xcc NAMPT and is important for its catalytic activity. This work reveals the importance of NAMPT in bacterial NAD+ synthesis and provides insights into the substrate recognition and the catalytic mechanism of bacterial type II phosphoribosyltransferases.
Collapse
Affiliation(s)
- Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Jinxue Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiong Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Wei Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiaoqiao Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Yanqiong Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Fenmei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xueqi Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
| |
Collapse
|
5
|
Tran THN, Takada R, Krayukhina E, Maruno T, Mii Y, Uchiyama S, Takada S. Soluble Frizzled-related proteins promote exosome-mediated Wnt re-secretion. Commun Biol 2024; 7:254. [PMID: 38429359 PMCID: PMC10907715 DOI: 10.1038/s42003-024-05881-8] [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: 08/14/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
Wnt proteins are thought to be transported in several ways in the extracellular space. For instance, they are known to be carried by exosomes and by Wnt-carrier proteins, such as sFRP proteins. However, little is known about whether and/or how these two transport systems are related. Here, we show that adding sFRP1 or sFRP2, but not sFRP3 or sFRP4, to culture medium containing Wnt3a or Wnt5a increases re-secretion of exosome-loaded Wnt proteins from cells. This effect of sFRP2 is counteracted by heparinase, which removes sugar chains on heparan sulfate proteoglycans (HSPGs), but is independent of LRP5/6, Wnt co-receptors essential for Wnt signaling. Wnt3a and Wnt5a specifically dimerize with sFRP2 in culture supernatant. Furthermore, a Wnt3a mutant defective in heterodimerization with sFRP2 impairs the ability to increase exosome-mediated Wnt3a re-secretion. Based on these results, we propose that Wnt heterodimerization with its carrier protein, sFRP2, enhances Wnt accumulation at sugar chains on HSPGs on the cell surface, leading to increased endocytosis and exosome-mediated Wnt re-secretion. Our results suggest that the range of action of Wnt ligands is controlled by coordination of different transport systems.
Collapse
Affiliation(s)
- Thi Hong Nguyen Tran
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan
| | - Ritsuko Takada
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Elena Krayukhina
- U-Medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Analytical Development Department, Chugai Pharmaceutical Co., Ltd., 5-5-1 Ukima, Kita-ku, Tokyo, 115-8543, Japan
| | - Takahiro Maruno
- U-Medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusuke Mii
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan
- PREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan
| | - Susumu Uchiyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- U-Medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinji Takada
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan.
| |
Collapse
|
6
|
Kamba K, Wan L, Unzai S, Morishita R, Takaori-Kondo A, Nagata T, Katahira M. Direct inhibition of human APOBEC3 deaminases by HIV-1 Vif independent of the proteolysis pathway. Biophys J 2024; 123:294-306. [PMID: 38115583 PMCID: PMC10870137 DOI: 10.1016/j.bpj.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
HIV-1 Vif is known to counteract the antiviral activity of human apolipoprotein B mRNA-editing catalytic polypeptide-like (A3), a cytidine deaminase, in various ways. However, the precise mechanism behind this interaction has remained elusive. Within infected cells, Vif forms a complex called VβBCC, comprising CBFβ and the components of E3 ubiquitin ligase, Elongin B, Elongin C, and Cullin5. Together with the ubiquitin-conjugating enzyme, VβBCC induces ubiquitination-mediated proteasomal degradation of A3. However, Vif exhibits additional counteractive effects. In this study, we elucidate that VβBCC inhibits deamination by A3G, A3F, and A3B independently of proteasomal degradation. Surprisingly, we discovered that this inhibition for A3G is directly attributed to the interaction between VβBCC and the C-terminal domain of A3G. Previously, it was believed that Vif did not interact with the C-terminal domain. Our findings suggest that inhibiting the interaction between VβBCC and the C-terminal domain, as well as the N-terminal domain known to be targeted for ubiquitination, of A3G may be needed to prevent counteraction by Vif.
Collapse
Affiliation(s)
- Keisuke Kamba
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Li Wan
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Ryo Morishita
- CellFree Sciences Co., Ltd., Matsuyama, Ehime, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.
| |
Collapse
|
7
|
Barylko B, Taylor CA, Wang J, Earnest S, Stippec S, Binns DD, Brautigam CA, Jameson DM, DeMartino GN, Cobb MH, Albanesi JP. Mimicking Protein Kinase C Phosphorylation Inhibits Arc/Arg3.1 Palmitoylation and Its Interaction with Nucleic Acids. Int J Mol Sci 2024; 25:780. [PMID: 38255853 PMCID: PMC10815921 DOI: 10.3390/ijms25020780] [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: 12/11/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) plays essential roles in diverse forms of synaptic plasticity, including long-term potentiation (LTP), long-term depression (LTD), and homeostatic plasticity. In addition, it assembles into virus-like particles that may deliver mRNAs and/or other cargo between neurons and neighboring cells. Considering this broad range of activities, it is not surprising that Arc is subject to regulation by multiple types of post-translational modification, including phosphorylation, palmitoylation, SUMOylation, ubiquitylation, and acetylation. Here we explore the potential regulatory role of Arc phosphorylation by protein kinase C (PKC), which occurs on serines 84 and 90 within an α-helical segment in the N-terminal domain. To mimic the effect of PKC phosphorylation, we mutated the two serines to negatively charged glutamic acid. A consequence of introducing these phosphomimetic mutations is the almost complete inhibition of Arc palmitoylation, which occurs on nearby cysteines and contributes to synaptic weakening. The mutations also inhibit the binding of nucleic acids and destabilize high-order Arc oligomers. Thus, PKC phosphorylation of Arc may limit the full expression of LTD and may suppress the interneuronal transport of mRNAs.
Collapse
Affiliation(s)
- Barbara Barylko
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Clinton A. Taylor
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Jason Wang
- Department of Physiology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Svetlana Earnest
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Steve Stippec
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Derk D. Binns
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Chad A. Brautigam
- Department of Biophysics, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA;
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96844, USA;
| | - George N. DeMartino
- Department of Physiology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Melanie H. Cobb
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| | - Joseph P. Albanesi
- Department of Pharmacology, U.T. Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.); (M.H.C.)
| |
Collapse
|
8
|
Alfonso C, Sobrinos-Sanguino M, Luque-Ortega JR, Zorrilla S, Monterroso B, Nuero OM, Rivas G. Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:89-107. [PMID: 38507202 DOI: 10.1007/978-3-031-52193-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.
Collapse
Affiliation(s)
- Carlos Alfonso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Marta Sobrinos-Sanguino
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Silvia Zorrilla
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Monterroso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Germán Rivas
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| |
Collapse
|
9
|
Ishida H, Matsumoto A, Tanaka H, Okuda A, Morishima K, Wade PA, Kurumizaka H, Sugiyama M, Kono H. Structural and Dynamic Changes of Nucleosome upon GATA3 Binding. J Mol Biol 2023; 435:168308. [PMID: 37805066 PMCID: PMC10843466 DOI: 10.1016/j.jmb.2023.168308] [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: 08/03/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Pioneer factors, which can directly bind to nucleosomes, have been considered to change chromatin conformations. However, the binding impact on the nucleosome is little known. Here, we show how the pioneer factor GATA3 binds to nucleosomal DNA and affects the conformation and dynamics of nucleosomes by using a combination of SAXS, molecular modeling, and molecular dynamics simulations. Our structural models, consistent with the SAXS data, indicate that only one of the two DNA binding domains, N- and C-fingers, of GATA3 binds to an end of the DNA in solution. Our MD simulations further showed that the other unbound end of the DNA increases the fluctuation and enhances the DNA dissociation from the histone core when the N-finger binds to a DNA end, a site near the entry or exit of the nucleosome. However, this was not true for the binding of the C-finger that binds to a location about 15 base pairs distant from the DNA end. In this case, DNA dissociation occurred on the bound end. Taken together, we suggest that the N-finger and C-finger bindings of GATA3 commonly enhance DNA dissociation at one of the two DNA ends (the bound end for the C-finger binding and the unbound end for the N-finger binding), leading to triggering a conformational change in the chromatin.
Collapse
Affiliation(s)
- Hisashi Ishida
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Present address: Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan; Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.
| |
Collapse
|
10
|
Katina N, Marchenkov V, Ryabova N, Ilyina N, Marchenko N, Balobanov V, Finkelstein A. Influence of Amino Acid Substitutions in ApoMb on Different Stages of Unfolding of Amyloids. Molecules 2023; 28:7736. [PMID: 38067466 PMCID: PMC10707739 DOI: 10.3390/molecules28237736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
To date, most research on amyloid aggregation has focused on describing the structure of amyloids and the kinetics of their formation, while the conformational stability of fibrils remains insufficiently explored. The aim of this work was to investigate the effect of amino acid substitutions on the stability of apomyoglobin (ApoMb) amyloids. A study of the amyloid unfolding of ApoMb and its six mutant variants by urea has been carried out. Changes in the structural features of aggregates during unfolding were recorded by far-UV CD and native electrophoresis. It was shown that during the initial stage of denaturation, amyloids' secondary structure partially unfolds. Then, the fibrils undergo dissociation and form intermediate aggregates weighing approximately 1 MDa, which at the last stage of unfolding decompose into 18 kDa monomeric unfolded molecules. The results of unfolding transitions suggest that the stability of the studied amyloids relative to the intermediate aggregates and of the latter relative to unfolded monomers is higher for ApoMb variants with substitutions that increase the hydrophobicity of the residues. The results presented provide a new insight into the mechanism of stabilization of protein aggregates and can serve as a base for further investigations of the amyloids' stability.
Collapse
Affiliation(s)
- Natalya Katina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 142290 Pushchino, Russia
| | - Victor Marchenkov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalya Ryabova
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Nelly Ilyina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalia Marchenko
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Vitalii Balobanov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Alexey Finkelstein
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| |
Collapse
|
11
|
Salmen W, Hu L, Bok M, Chaimongkol N, Ettayebi K, Sosnovtsev SV, Soni K, Ayyar BV, Shanker S, Neill FH, Sankaran B, Atmar RL, Estes MK, Green KY, Parreño V, Prasad BVV. A single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity. Nat Commun 2023; 14:6516. [PMID: 37845211 PMCID: PMC10579229 DOI: 10.1038/s41467-023-42146-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
Acute gastroenteritis caused by human noroviruses (HuNoVs) is a significant global health and economic burden and is without licensed vaccines or antiviral drugs. The GII.4 HuNoV causes most epidemics worldwide. This virus undergoes epochal evolution with periodic emergence of variants with new antigenic profiles and altered specificity for histo-blood group antigens (HBGA), the determinants of cell attachment and susceptibility, hampering the development of immunotherapeutics. Here, we show that a llama-derived nanobody M4 neutralizes multiple GII.4 variants with high potency in human intestinal enteroids. The crystal structure of M4 complexed with the protruding domain of the GII.4 capsid protein VP1 revealed a conserved epitope, away from the HBGA binding site, fully accessible only when VP1 transitions to a "raised" conformation in the capsid. Together with dynamic light scattering and electron microscopy of the GII.4 VLPs, our studies suggest a mechanism in which M4 accesses the epitope by altering the conformational dynamics of the capsid and triggering its disassembly to neutralize GII.4 infection.
Collapse
Affiliation(s)
- Wilhelm Salmen
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Marina Bok
- Virology Institute and Technology Innovation, IVIT, CONICET-INTA, Hurlingham, Buenos Aires, Argentina
| | - Natthawan Chaimongkol
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stanislav V Sosnovtsev
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaundal Soni
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - B Vijayalakshmi Ayyar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sreejesh Shanker
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Kim Y Green
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Viviana Parreño
- Virology Institute and Technology Innovation, IVIT, CONICET-INTA, Hurlingham, Buenos Aires, Argentina
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
12
|
Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
Collapse
Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| |
Collapse
|
13
|
Humphreys JM, Teixeira LR, Akella R, He H, Kannangara AR, Sekulski K, Pleinis J, Liwocha J, Jiou J, Servage KA, Orth K, Joachimiak L, Rizo J, Cobb MH, Brautigam CA, Rodan AR, Goldsmith EJ. Hydrostatic Pressure Sensing by WNK kinases. Mol Biol Cell 2023; 34:ar109. [PMID: 37585288 PMCID: PMC10559305 DOI: 10.1091/mbc.e23-03-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Previous study has demonstrated that the WNK kinases 1 and 3 are direct osmosensors consistent with their established role in cell-volume control. WNK kinases may also be regulated by hydrostatic pressure. Hydrostatic pressure applied to cells in culture with N2 gas or to Drosophila Malpighian tubules by centrifugation induces phosphorylation of downstream effectors of endogenous WNKs. In vitro, the autophosphorylation and activity of the unphosphorylated kinase domain of WNK3 (uWNK3) is enhanced to a lesser extent than in cells by 190 kPa applied with N2 gas. Hydrostatic pressure measurably alters the structure of uWNK3. Data from size exclusion chromatography in line with multi-angle light scattering (SEC-MALS), SEC alone at different back pressures, analytical ultracentrifugation (AUC), NMR, and chemical crosslinking indicate a change in oligomeric structure in the presence of hydrostatic pressure from a WNK3 dimer to a monomer. The effects on the structure are related to those seen with osmolytes. Potential mechanisms of hydrostatic pressure activation of uWNK3 and the relationships of pressure activation to WNK osmosensing are discussed.
Collapse
Affiliation(s)
- John M. Humphreys
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Liliana R. Teixeira
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Radha Akella
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Haixia He
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ashari R. Kannangara
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kamil Sekulski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - John Pleinis
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Joanna Liwocha
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jenny Jiou
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lukasz Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Josep Rizo
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Melanie H. Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aylin R. Rodan
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Elizabeth J. Goldsmith
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| |
Collapse
|
14
|
Yuan L, Ma X, Yang Y, Qu Y, Li X, Zhu X, Ma W, Duan J, Xue J, Yang H, Huang JW, Yi S, Zhang M, Cai N, Zhang L, Ding Q, Lai K, Liu C, Zhang L, Liu X, Yao Y, Zhou S, Li X, Shen P, Chang Q, Malwal SR, He Y, Li W, Chen C, Chen CC, Oldfield E, Guo RT, Zhang Y. Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate Vγ9Vδ2 T cells. Nature 2023; 621:840-848. [PMID: 37674084 PMCID: PMC10533412 DOI: 10.1038/s41586-023-06525-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023]
Abstract
In both cancer and infections, diseased cells are presented to human Vγ9Vδ2 T cells through an 'inside out' signalling process whereby structurally diverse phosphoantigen (pAg) molecules are sensed by the intracellular domain of butyrophilin BTN3A11-4. Here we show how-in both humans and alpaca-multiple pAgs function as 'molecular glues' to promote heteromeric association between the intracellular domains of BTN3A1 and the structurally similar butyrophilin BTN2A1. X-ray crystallography studies visualized that engagement of BTN3A1 with pAgs forms a composite interface for direct binding to BTN2A1, with various pAg molecules each positioned at the centre of the interface and gluing the butyrophilins with distinct affinities. Our structural insights guided mutagenesis experiments that led to disruption of the intracellular BTN3A1-BTN2A1 association, abolishing pAg-mediated Vγ9Vδ2 T cell activation. Analyses using structure-based molecular-dynamics simulations, 19F-NMR investigations, chimeric receptor engineering and direct measurement of intercellular binding force revealed how pAg-mediated BTN2A1 association drives BTN3A1 intracellular fluctuations outwards in a thermodynamically favourable manner, thereby enabling BTN3A1 to push off from the BTN2A1 ectodomain to initiate T cell receptor-mediated γδ T cell activation. Practically, we harnessed the molecular-glue model for immunotherapeutics design, demonstrating chemical principles for developing both small-molecule activators and inhibitors of human γδ T cell function.
Collapse
MESH Headings
- Animals
- Humans
- Antigens, CD/immunology
- Antigens, CD/metabolism
- Butyrophilins/immunology
- Butyrophilins/metabolism
- Camelids, New World/immunology
- Lymphocyte Activation
- Molecular Dynamics Simulation
- Phosphoproteins/immunology
- Phosphoproteins/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Crystallography, X-Ray
- Nuclear Magnetic Resonance, Biomolecular
- Thermodynamics
Collapse
Affiliation(s)
- Linjie Yuan
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xianqiang Ma
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yunyun Yang
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yingying Qu
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xin Li
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xiaoyu Zhu
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Weiwei Ma
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | | | - Jing Xue
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Haoyu Yang
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Simin Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Mengting Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ningning Cai
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Lin Zhang
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qingyang Ding
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Kecheng Lai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Chang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xinyi Liu
- School of Medicine, Tsinghua University, Beijing, China
| | - Yirong Yao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuqi Zhou
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xian Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Panpan Shen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qing Chang
- School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Technology Center for Protein Sciences, Tsinghua University, Beijing, China
| | - Satish R Malwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuan He
- Research Beyond Borders, Boehringer Ingelheim (China), Shanghai, China
| | - Wenqi Li
- School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Technology Center for Protein Sciences, Tsinghua University, Beijing, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China.
| | - Yonghui Zhang
- Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
15
|
Richter K, Wurm C, Strasser K, Bauer J, Bakou M, VerHeul R, Sternisha S, Hawe A, Salomon M, Menzen T, Bhattacharya A. Purity and DNA content of AAV capsids assessed by analytical ultracentrifugation and orthogonal biophysical techniques. Eur J Pharm Biopharm 2023; 189:68-83. [PMID: 37196871 DOI: 10.1016/j.ejpb.2023.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Development and manufacturing adeno-associated virus (AAV)-based vectors for gene therapy requires suitable analytical methods to assess the quality of the formulations during development, as well as the quality of different batches and the consistency of the processes. Here, we compare biophysical methods to characterize purity and DNA content of viral capsids from five different serotypes (AAV2, AAV5, AAV6, AAV8, and AAV9). For this purpose, we apply multiwavelength sedimentation velocity analytical ultracentrifugation (SV-AUC) to obtain the species' contents and to derive the wavelength-specific correction factors for the respective insert-size. In an orthogonal manner we perform anion exchange chromatography (AEX) and UV-spectroscopy and the three methods yield comparable results on empty/filled capsid contents with these correction factors. Whereas AEX and UV-spectroscopy can quantify empty and filled AAVs, only SV-AUC could identify the low amounts of partially filled capsids present in the samples used in this study. Finally, we employ negative-staining transmission electron microscopy and mass photometry to support the empty/filled ratios with methods that classify individual capsids. The obtained ratios are consistent throughout the orthogonal approaches as long as no other impurities and aggregates are present. Our results show that the combination of selected orthogonal methods can deliver consistent empty/filled contents on non-standard genome sizes, as well as information on other relevant critical quality attributes, such as AAV capsid concentration, genome concentration, insert size length and sample purity to characterize and compare AAV preparations.
Collapse
Affiliation(s)
- Klaus Richter
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany.
| | - Christine Wurm
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Kim Strasser
- Sirion Biotech GmbH, am Haag 6, 82166 Gräfelfing, Germany
| | - Jana Bauer
- Sirion Biotech GmbH, am Haag 6, 82166 Gräfelfing, Germany
| | - Maria Bakou
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Ross VerHeul
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA
| | - Shawn Sternisha
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA
| | - Andrea Hawe
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | | | - Tim Menzen
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Akash Bhattacharya
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA.
| |
Collapse
|
16
|
Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. J Biol Chem 2023; 299:105017. [PMID: 37414145 PMCID: PMC10406627 DOI: 10.1016/j.jbc.2023.105017] [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: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication.
Collapse
Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuwen Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fabian Mendoza
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tao Wu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| |
Collapse
|
17
|
Ma Y, Li X, Wang F, Zhang L, Zhou S, Che X, Yu D, Liu X, Li Z, Sun H, Yu G, Zhang H. Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax. PLoS Biol 2023; 21:e3002189. [PMID: 37459330 PMCID: PMC10374108 DOI: 10.1371/journal.pbio.3002189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/27/2023] [Accepted: 06/08/2023] [Indexed: 07/29/2023] Open
Abstract
Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin degradation (iad) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax iad operon products and identified 2 proteins, IadK2 and IadD, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that IadK2 is a highly IAA-specific ATP-binding cassette (ABC) transporter solute-binding protein (SBP), likely involved in IAA uptake. IadD interacts with IadE to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene iadC to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of iadC/D/E genes could enable IAA transformation by Escherichia coli, suggesting a promising strategy for repurposing the iad operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture.
Collapse
Affiliation(s)
- Yongjian Ma
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xuzichao Li
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Lingling Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shengmin Zhou
- YDS Pharmatech, Albany, New York, United States of America
| | - Xing Che
- YDS Pharmatech, Albany, New York, United States of America
| | - Dehao Yu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University; Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Huabing Sun
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University; Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Guimei Yu
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Heng Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| |
Collapse
|
18
|
Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
Collapse
Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
| |
Collapse
|
19
|
Sołtys K, Ożyhar A. Phase separation propensity of the intrinsically disordered AB region of human RXRβ. Cell Commun Signal 2023; 21:92. [PMID: 37143076 PMCID: PMC10157963 DOI: 10.1186/s12964-023-01113-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/25/2023] [Indexed: 05/06/2023] Open
Abstract
RXRβ is one of three subtypes of human retinoid X receptor (RXR), a transcription factor that belongs to the nuclear receptor superfamily. Its expression can be detected in almost all tissues. In contrast to other subtypes - RXRα and RXRγ - RXRβ has the longest and unique N-terminal sequence called the AB region, which harbors a ligand-independent activation function. In contrast to the functional properties of this sequence, the molecular properties of the AB region of human RXRβ (AB_hRXRB) have not yet been characterized. Here, we present a systematic biochemical and biophysical analysis of recombinant AB_hRXRB, along with in silico examinations, which demonstrate that AB_hRXRB exhibits properties of a coil-like intrinsically disordered region. AB_hRXRB possesses a flexible structure that is able to adopt a more ordered conformation under the influence of different environmental factors. Interestingly, AB_hRXRB promotes the formation of liquid-liquid phase separation (LLPS), a phenomenon previously observed for the AB region of another human subtype of RXR - RXRγ (AB_hRXRG). Although both AB regions seem to be similar in terms of their ability to induce phase separation, they clearly differ in the sensitivity to factors driving and regulating LLPS. This distinct LLPS response to environmental factors driven by the unique amino acid compositions of AB_hRXRB and AB_hRXRG can be significant for the specific modulation of the transcriptional activation of target genes by different subtypes of RXR. Video Abstract.
Collapse
Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| |
Collapse
|
20
|
Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
Collapse
Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
| |
Collapse
|
21
|
Javorsky A, Maddumage JC, Mackie ERR, Soares da Costa TP, Humbert PO, Kvansakul M. Structural insight into the Scribble PDZ domains interaction with the oncogenic Human T-cell lymphotrophic virus-1 (HTLV-1) Tax1 PBM. FEBS J 2023; 290:974-987. [PMID: 36029163 PMCID: PMC10952772 DOI: 10.1111/febs.16607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022]
Abstract
Scribble (Scrib) is a highly conserved cell polarity regulator that harbours potent tumour suppressor activity and plays an important role in cell migration. Dysregulation of polarity is associated with poor prognosis during viral infections. Human T-cell lymphotrophic virus-1 (HTLV-1) encodes for the oncogenic Tax1 protein, a modulator of the transcription of viral and human proteins that can cause cell cycle dysregulation as well as a loss of genomic integrity. Previous studies established that Scribble interacts with Tax1 via its C-terminal PDZ-binding motif (PBM), leading to aggregation of polarity regulators and subsequent perturbation of host cell adhesion, proliferation, and signalling. Using isothermal titration calorimetry, we now show that all four PDZ domains of Scribble bind to Tax1 PBM. We then determined crystal structures of Scribble PDZ1, PDZ2 and PDZ3 domains bound to Tax1 PBM. Our findings establish a structural basis for Tax1-mediated subversion of Scribble-mediated cell polarity signalling and provide the platform for mechanistic studies to examine Tax1 induced mislocalization of Scribble and the associated changes in cellular architecture and subsequent tumorigenesis.
Collapse
Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Janesha C. Maddumage
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Emily R. R. Mackie
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Patrick O. Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
- Research Centre for Molecular Cancer PreventionLa Trobe UniversityMelbourneVic.Australia
- Department of Biochemistry & PharmacologyUniversity of MelbourneMelbourneVic.Australia
- Department of Clinical PathologyUniversity of MelbourneMelbourneVic.Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
- Research Centre for Molecular Cancer PreventionLa Trobe UniversityMelbourneVic.Australia
| |
Collapse
|
22
|
Oligomer-to-monomer transition underlies the chaperone function of AAGAB in AP1/AP2 assembly. Proc Natl Acad Sci U S A 2023; 120:e2205199120. [PMID: 36598941 PMCID: PMC9926252 DOI: 10.1073/pnas.2205199120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Assembly of protein complexes is facilitated by assembly chaperones. Alpha and gamma adaptin-binding protein (AAGAB) is a chaperone governing the assembly of the heterotetrameric adaptor complexes 1 and 2 (AP1 and AP2) involved in clathrin-mediated membrane trafficking. Here, we found that before AP1/2 binding, AAGAB exists as a homodimer. AAGAB dimerization is mediated by its C-terminal domain (CTD), which is critical for AAGAB stability and is missing in mutant proteins found in patients with the skin disease punctate palmoplantar keratoderma type 1 (PPKP1). We solved the crystal structure of the dimerization-mediating CTD, revealing an antiparallel dimer of bent helices. Interestingly, AAGAB uses the same CTD to recognize and stabilize the γ subunit in the AP1 complex and the α subunit in the AP2 complex, forming binary complexes containing only one copy of AAGAB. These findings demonstrate a dual role of CTD in stabilizing resting AAGAB and binding to substrates, providing a molecular explanation for disease-causing AAGAB mutations. The oligomerization state transition mechanism may also underlie the functions of other assembly chaperones.
Collapse
|
23
|
Kappes EC, Kattamuri C, Czepnik M, Yarawsky AE, Brûlé E, Wang Y, Ongaro L, Herr AB, Walton KL, Bernard DJ, Thompson TB. Follistatin Forms a Stable Complex With Inhibin A That Does Not Interfere With Activin A Antagonism. Endocrinology 2023; 164:7010688. [PMID: 36718082 DOI: 10.1210/endocr/bqad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/01/2023]
Abstract
Inhibins are transforming growth factor-β family heterodimers that suppress follicle-stimulating hormone (FSH) secretion by antagonizing activin class ligands. Inhibins share a common β chain with activin ligands. Follistatin is another activin antagonist, known to bind the common β chain of both activins and inhibins. In this study, we characterized the antagonist-antagonist complex of inhibin A and follistatin to determine if their interaction impacted activin A antagonism. We isolated the inhibin A:follistatin 288 complex, showing that it forms in a 1:1 stoichiometric ratio, different from previously reported homodimeric ligand:follistatin complexes, which bind in a 1:2 ratio. Small angle X-ray scattering coupled with modeling provided a low-resolution structure of inhibin A in complex with follistatin 288. Inhibin binds follistatin via the shared activin β chain, leaving the α chain free and flexible. The inhibin A:follistatin 288 complex was also shown to bind heparin with lower affinity than follistatin 288 alone or in complex with activin A. Characterizing the inhibin A:follistatin 288 complex in an activin-responsive luciferase assay and by surface plasmon resonance indicated that the inhibitor complex readily dissociated upon binding type II receptor activin receptor type IIb, allowing both antagonists to inhibit activin signaling. Additionally, injection of the complex in ovariectomized female mice did not alter inhibin A suppression of FSH. Taken together, this study shows that while follistatin binds to inhibin A with a substochiometric ratio relative to the activin homodimer, the complex can dissociate readily, allowing both proteins to effectively antagonize activin signaling.
Collapse
Affiliation(s)
- Emily C Kappes
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| | - Chandramohan Kattamuri
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| | - Magdalena Czepnik
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| | | | - Emilie Brûlé
- Departments of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Ying Wang
- Departments of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Luisina Ongaro
- Departments of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Andrew B Herr
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kelly L Walton
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Daniel J Bernard
- Departments of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Departments of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Thomas B Thompson
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| |
Collapse
|
24
|
Surya W, Queralt-Martin M, Mu Y, Aguilella VM, Torres J. SARS-CoV-2 accessory protein 7b forms homotetramers in detergent. Virol J 2022; 19:193. [PMID: 36414943 PMCID: PMC9680129 DOI: 10.1186/s12985-022-01920-0] [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: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
A global pandemic is underway caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome, like its predecessor SARS-CoV, contains open reading frames that encode accessory proteins involved in virus-host interactions active during infection and which likely contribute to pathogenesis. One of these accessory proteins is 7b, with only 44 (SARS-CoV) and 43 (SARS-CoV-2) residues. It has one predicted transmembrane domain fully conserved, which suggests a functional role, whereas most variability is contained in the predicted cytoplasmic C-terminus. In SARS-CoV, 7b protein is expressed in infected cells, and the transmembrane domain was necessary and sufficient for Golgi localization. Also, anti-p7b antibodies have been found in the sera of SARS-CoV convalescent patients. In the present study, we have investigated the hypothesis that SARS-2 7b protein forms oligomers with ion channel activity. We show that in both SARS viruses 7b is almost completely α-helical and has a single transmembrane domain. In SDS, 7b forms various oligomers, from monomers to tetramers, but only monomers when exposed to reductants. Combination of SDS gel electrophoresis and analytical ultracentrifugation (AUC) in both equilibrium and velocity modes suggests a dimer-tetramer equilibrium, but a monomer-dimer-tetramer equilibrium in the presence of reductant. This data suggests that although disulfide-linked dimers may be present, they are not essential to form tetramers. Inclusion of pentamers or higher oligomers in the SARS-2 7b model were detrimental to fit quality. Preliminary models of this association was generated with AlphaFold2, and two alternative models were exposed to a molecular dynamics simulation in presence of a model lipid membrane. However, neither of the two models provided any evident pathway for ions. To confirm this, SARS-2 p7b was studied using Planar Bilayer Electrophysiology. Addition of p7b to model membranes produced occasional membrane permeabilization, but this was not consistent with bona fide ion channels made of a tetrameric assembly of α-helices.
Collapse
Affiliation(s)
- Wahyu Surya
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Maria Queralt-Martin
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Yuguang Mu
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Vicente M. Aguilella
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Jaume Torres
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| |
Collapse
|
25
|
Whitten AE, Jeffries CM. Data analysis and modeling of small-angle neutron scattering data with contrast variation from bio-macromolecular complexes. Methods Enzymol 2022; 678:55-96. [PMID: 36641217 DOI: 10.1016/bs.mie.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Small-angle neutron scattering (SANS) with contrast variation (CV) is a valuable technique in the structural biology toolchest. Accurate structural parameters-e.g., radii of gyration, volumes, dimensions, and distance distribution(s)-can be derived from the SANS-CV data to yield the shape and disposition of the individual components within stable complexes. Contrast variation is achieved through the substitution of hydrogen isotopes (1H for 2H) in molecules and solvents to alter the neutron scattering properties of each component of a complex. While SANS-CV can be used a stand-alone technique for interrogating the overall structure of biomacromolecules in solution, it also complements other methods such as small-angle X-ray scattering, crystallography, nuclear magnetic resonance, and cryo-electron microscopy. Undertaking a SANS-CV experiment is challenging, due in part to the preparation of significant quantities of monodisperse samples that may require deuterium (2H) labeling. Nevertheless, SANS-CV can be used to study a diverse range biomacromolecular complexes including protein-protein and protein-nucleic acid systems, membrane proteins, and flexible systems resistant to crystallization. This chapter describes how to approach the data analysis and modeling of SANS data, including: (1) Analysis of the forward scattering (I(0)) and calculation of theoretical estimates of contrast; (2) Analysis of the contrast dependence of the radius of gyration using the Stuhrmann plot and parallel axis theorem; (3) Calculation of composite scattering functions to evaluate the size, shape, and dispositions of individual components within a complex, and; (4) Development of real-space models to fit the SANS-CV data using volume-element bead modeling or atomistic rigid body modeling.
Collapse
Affiliation(s)
- Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron, Hamburg, Germany.
| |
Collapse
|
26
|
Surya W, Torres J. Oligomerization-Dependent Beta-Structure Formation in SARS-CoV-2 Envelope Protein. Int J Mol Sci 2022; 23:13285. [PMID: 36362071 PMCID: PMC9658050 DOI: 10.3390/ijms232113285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 08/13/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. In SARS-CoV-2, the channel-forming envelope (E) protein is almost identical to the E protein in SARS-CoV, and both share an identical α-helical channel-forming domain. Structures for the latter are available in both detergent and lipid membranes. However, models of the extramembrane domains have only been obtained from solution NMR in detergents, and show no β-strands, in contrast to secondary-structure predictions. Herein, we have studied the conformation of purified SARS-CoV-2 E protein in lipid bilayers that mimic the composition of ER-Golgi intermediate compartment (ERGIC) membranes. The full-length E protein at high protein-to-lipid ratios produced a clear shoulder at 1635 cm-1, consistent with the β-structure, but this was absent when the E protein was diluted, which instead showed a band at around 1688 cm-1, usually assigned to β-turns. The results were similar with a mixture of POPC:POPG (2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine/3-glycerol) and also when using an E-truncated form (residues 8-65). However, the latter only showed β-structure formation at the highest concentration tested, while having a weaker oligomerization tendency in detergents than in full-length E protein. Therefore, we conclude that E monomer-monomer interaction triggers formation of the β-structure from an undefined structure (possibly β-turns) in at least about 15 residues located at the C-terminal extramembrane domain. Due to its proximity to the channel, this β-structure domain could modulate channel activity or modify membrane structure at the time of virion formation inside the cell.
Collapse
Affiliation(s)
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| |
Collapse
|
27
|
Pauly T, Bolakhrif N, Kaiser J, Nagel-Steger L, Gremer L, Gohlke H, Willbold D. Met/Val129 polymorphism of the full-length human prion protein dictates distinct pathways of amyloid formation. J Biol Chem 2022; 298:102430. [PMID: 36037966 PMCID: PMC9513279 DOI: 10.1016/j.jbc.2022.102430] [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: 05/17/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Methionine/valine polymorphism at position 129 of the human prion protein, huPrP, is tightly associated with the pathogenic phenotype, disease progress, and age of onset of neurodegenerative diseases such as Creutzfeldt–Jakob disease or Fatal Familial Insomnia. This raises the question of whether and how the amino acid type at position 129 influences the structural properties of huPrP, affecting its folding, stability, and amyloid formation behavior. Here, our detailed biophysical characterization of the 129M and 129V variants of recombinant full-length huPrP(23–230) by amyloid formation kinetics, CD spectroscopy, molecular dynamics simulations, and sedimentation velocity analysis reveals differences in their aggregation propensity and oligomer content, leading to deviating pathways for the conversion into amyloid at acidic pH. We determined that the 129M variant exhibits less secondary structure content before amyloid formation and higher resistance to thermal denaturation compared to the 129V variant, whereas the amyloid conformation of both variants shows similar thermal stability. Additionally, our molecular dynamics simulations and rigidity analyses at the atomistic level identify intramolecular interactions responsible for the enhanced monomer stability of the 129M variant, involving more frequent minimum distances between E196 and R156, forming a salt bridge. Removal of the N-terminal half of the 129M full-length variant diminishes its differences compared to the 129V full-length variant and highlights the relevance of the flexible N terminus in huPrP. Taken together, our findings provide insight into structural properties of huPrP and the effects of the amino acid identity at position 129 on amyloid formation behavior.
Collapse
Affiliation(s)
- Thomas Pauly
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Najoua Bolakhrif
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; John von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
28
|
Teakel S, Marama M, Aragão D, Tsimbalyuk S, Mackie ERR, Soares da‐Costa TP, Forwood JK, Cahill MA. Structural characterization of a
MAPR
‐related archaeal cytochrome
b
5M
protein. FEBS Lett 2022; 596:2409-2417. [DOI: 10.1002/1873-3468.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah Teakel
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Michealla Marama
- School of Animal and Veterinary Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - David Aragão
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation 800 Blackburn Road Clayton VIC 3168 Australia
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Sofiya Tsimbalyuk
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Emily R. R. Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Bundoora VIC 3086 Australia
- School of Agriculture, Food & Wine and Waite Research Institute, University of Adelaide Waite Campus Glen Osmond SA 5064 Australia
| | - Tatiana P. Soares da‐Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Bundoora VIC 3086 Australia
- School of Agriculture, Food & Wine and Waite Research Institute, University of Adelaide Waite Campus Glen Osmond SA 5064 Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Michael A. Cahill
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
- The John Curtin School of Medical Research The Australian National University ACT 2601 Australia
| |
Collapse
|
29
|
Hauptstein N, Pouyan P, Wittwer K, Cinar G, Scherf-Clavel O, Raschig M, Licha K, Lühmann T, Nischang I, Schubert US, Pfaller CK, Haag R, Meinel L. Polymer selection impacts the pharmaceutical profile of site-specifically conjugated Interferon-α2a. J Control Release 2022; 348:881-892. [PMID: 35764249 DOI: 10.1016/j.jconrel.2022.05.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 05/15/2022] [Indexed: 12/15/2022]
Abstract
Conjugation of poly(ethylene glycol) (PEG) to biologics is a successful strategy to favorably impact the pharmacokinetics and efficacy of the resulting bioconjugate. We compare bioconjugates synthesized by strain-promoted azide-alkyne cycloaddition (SPAAC) using PEG and linear polyglycerol (LPG) of about 20 kDa or 40 kDa, respectively, with an azido functionalized human Interferon-α2a (IFN-α2a) mutant. Site-specific PEGylation and LPGylation resulted in IFN-α2a bioconjugates with improved in vitro potency compared to commercial Pegasys. LPGylated bioconjugates had faster disposition kinetics despite comparable hydrodynamic radii to their PEGylated analogues. Overall exposure of the PEGylated IFN-α2a with a 40 kDa polymer exceeded Pegasys, which, in return, was similar to the 40 kDa LPGylated conjugates. The study points to an expanded polymer design space through which the selected polymer class may result in a different distribution of the studied bioconjugates.
Collapse
Affiliation(s)
- Niklas Hauptstein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Paria Pouyan
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Kevin Wittwer
- Paul-Ehrlich-Institute, Division of Veterinary Medicine, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Gizem Cinar
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Oliver Scherf-Clavel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martina Raschig
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kai Licha
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Tessa Lühmann
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivo Nischang
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Christian K Pfaller
- Paul-Ehrlich-Institute, Division of Veterinary Medicine, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research (HIRI), 97080 Würzburg, Germany.
| |
Collapse
|
30
|
Nanoparticle sizing in the field of nanomedicine: Power of an analytical ultracentrifuge. Anal Chim Acta 2022; 1205:339741. [DOI: 10.1016/j.aca.2022.339741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/23/2022]
|
31
|
Hawkins WD, Leary KA, Andhare D, Popelka H, Klionsky DJ, Ragusa MJ. Dimerization-dependent membrane tethering by Atg23 is essential for yeast autophagy. Cell Rep 2022; 39:110702. [PMID: 35443167 PMCID: PMC9097366 DOI: 10.1016/j.celrep.2022.110702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 12/24/2022] Open
Abstract
Eukaryotes maintain cellular health through the engulfment and subsequent degradation of intracellular cargo using macroautophagy. The function of Atg23, despite being critical to the efficiency of this process, is unclear due to a lack of biochemical investigations and an absence of any structural information. In this study, we use a combination of in vitro and in vivo methods to show that Atg23 exists primarily as a homodimer, a conformation facilitated by a putative amphipathic helix. We utilize small-angle X-ray scattering to monitor the overall shape of Atg23, revealing that it contains an extended rod-like structure spanning approximately 320 Å. We also demonstrate that Atg23 interacts with membranes directly, primarily through electrostatic interactions, and that these interactions lead to vesicle tethering. Finally, mutation of the hydrophobic face of the putative amphipathic helix completely precludes dimer formation, leading to severely impaired subcellular localization, vesicle tethering, Atg9 binding, and autophagic efficiency.
Collapse
Affiliation(s)
- Wayne D Hawkins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kelsie A Leary
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Devika Andhare
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Michael J Ragusa
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA.
| |
Collapse
|
32
|
Bleuler-Martinez S, Varrot A, Olieric V, Schubert M, Vogt E, Fetz C, Wohlschlager T, Plaza DF, Wälti M, Duport Y, Capitani G, Aebi M, Künzler M. Structure-function relationship of a novel fucoside-binding fruiting body lectin from Coprinopsis cinerea exhibiting nematotoxic activity. Glycobiology 2022; 32:600-615. [PMID: 35323921 PMCID: PMC9191617 DOI: 10.1093/glycob/cwac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 11/14/2022] Open
Abstract
Lectins are non-immunoglobulin-type proteins that bind to specific carbohydrate epitopes and play important roles in intra- and inter-organismic interactions. Here, we describe a novel fucose-specific lectin, termed CML1, which we identified from fruiting body extracts of Coprinopsis cinerea. For further characterization, the coding sequence for CML1 was cloned and heterologously expressed in Escherichia coli. Feeding of CML1-producing bacteria inhibited larval development of the bacterivorous nematode Caenorhabditis tropicalis, but not of C. elegans. The crystal structure of the recombinant protein in its apo-form and in complex with H type I or Lewis A blood group antigens was determined by X-ray crystallography. The protein folds as a sandwich of 2 antiparallel β-sheets and forms hexamers resulting from a trimer of dimers. The hexameric arrangement was confirmed by small-angle X-ray scattering (SAXS). One carbohydrate-binding site per protomer was found at the dimer interface with both protomers contributing to ligand binding, resulting in a hexavalent lectin. In terms of lectin activity of recombinant CML1, substitution of the carbohydrate-interacting residues His54, Asn55, Trp94, and Arg114 by Ala abolished carbohydrate-binding and nematotoxicity. Although no similarities to any characterized lectin were found, sequence alignments identified many non-characterized agaricomycete proteins. These results suggest that CML1 is the founding member of a novel family of fucoside-binding lectins involved in the defense of agaricomycete fruiting bodies against predation by fungivorous nematodes.
Collapse
Affiliation(s)
- Silvia Bleuler-Martinez
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Annabelle Varrot
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Vincent Olieric
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
| | - Eva Vogt
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Fetz
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Therese Wohlschlager
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - David Fernando Plaza
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.,Division of Infectious Diseases, Karolinska University Hospital, 171 64, Solna, Sweden
| | - Martin Wälti
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Yannick Duport
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Guido Capitani
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| |
Collapse
|
33
|
Detecting Micro- and Nanoplastics Released from Food Packaging: Challenges and Analytical Strategies. Polymers (Basel) 2022; 14:polym14061238. [PMID: 35335568 PMCID: PMC8954753 DOI: 10.3390/polym14061238] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Micro- and nanoplastic (pMP and pNP, respectively) release is an emerging issue since these particles constitute a ubiquitous and growing pollutant, which not only threatens the environment but may have potential consequences for human health. In particular, there is concern about the release of secondary pMP and pNP from the degradation of plastic consumer products. The phenomenon is well-documented in relation to plastic waste in the environment but, more recently, reports of pMP generated even during the normal use of plastic food contact materials, such as water bottles, tea bags, and containers, have been published. So far, a validated and harmonized strategy to tackle the issue is not available. In this study, we demonstrate that plastic breakdown to pMP and pNP can occur during the normal use of polyethylene (PE) rice cooking bags and ice-cube bags as well as of nylon teabags. A multi-instrumental approach based on Raman microscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and particular attention on the importance of sample preparation were applied to evaluate the chemical nature of the released material and their morphology. In addition, a simple method based on Fourier transform infrared (FT-IR) spectroscopy is proposed for pNP mass quantification, resulting in the release of 1.13 ± 0.07 mg of nylon 6 from each teabag. However, temperature was shown to have a strong impact on the morphology and aggregation status of the released materials, posing to scientists and legislators a challenging question: are they micro- or nanoplastics or something else altogether?
Collapse
|
34
|
Xiong X, Blakely A, Kim JH, Menting JG, Schäfer IB, Schubert HL, Agrawal R, Gutmann T, Delaine C, Zhang YW, Artik GO, Merriman A, Eckert D, Lawrence MC, Coskun Ü, Fisher SJ, Forbes BE, Safavi-Hemami H, Hill CP, Chou DHC. Symmetric and asymmetric receptor conformation continuum induced by a new insulin. Nat Chem Biol 2022; 18:511-519. [PMID: 35289328 PMCID: PMC9248236 DOI: 10.1038/s41589-022-00981-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Cone snail venoms contain a wide variety of bioactive peptides, including insulin-like molecules with distinct structural features, binding modes and biochemical properties. Here, we report an active humanized cone snail venom insulin with an elongated A chain and a truncated B chain, and use cryo-electron microscopy (cryo-EM) and protein engineering to elucidate its interactions with the human insulin receptor (IR) ectodomain. We reveal how an extended A chain can compensate for deletion of B-chain residues, which are essential for activity of human insulin but also compromise therapeutic utility by delaying dissolution from the site of subcutaneous injection. This finding suggests approaches to developing improved therapeutic insulins. Curiously, the receptor displays a continuum of conformations from the symmetric state to a highly asymmetric low-abundance structure that displays coordination of a single humanized venom insulin using elements from both of the previously characterized site 1 and site 2 interactions.
Collapse
Affiliation(s)
- Xiaochun Xiong
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University, Stanford, CA, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Alan Blakely
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jin Hwan Kim
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - John G Menting
- WEHI, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ingmar B Schäfer
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Rahul Agrawal
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Theresia Gutmann
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carlie Delaine
- Discipline of Medical Biochemistry and Cell Biology, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Yi Wolf Zhang
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University, Stanford, CA, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Gizem Olay Artik
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Membrane Biochemistry and Lipid Research, University Clinic Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Allanah Merriman
- Discipline of Medical Biochemistry and Cell Biology, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Debbie Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael C Lawrence
- WEHI, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ünal Coskun
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Membrane Biochemistry and Lipid Research, University Clinic Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Simon J Fisher
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA.,Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Briony E Forbes
- Discipline of Medical Biochemistry and Cell Biology, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Helena Safavi-Hemami
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA. .,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University, Stanford, CA, USA. .,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
35
|
Chen Y, Yang WH, Chen HF, Huang LM, Gao JY, Lin CW, Wang YC, Yang CS, Liu YL, Hou MH, Tsai CL, Chou YZ, Huang BY, Hung CF, Hung YL, Wang WJ, Su WC, Kumar V, Wu YC, Chao SW, Chang CS, Chen JS, Chiang YP, Cho DY, Jeng LB, Tsai CH, Hung MC. Tafenoquine and its derivatives as inhibitors for the severe acute respiratory syndrome coronavirus 2. J Biol Chem 2022; 298:101658. [PMID: 35101449 PMCID: PMC8800562 DOI: 10.1016/j.jbc.2022.101658] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/15/2022] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely affected human lives around the world as well as the global economy. Therefore, effective treatments against COVID-19 are urgently needed. Here, we screened a library containing Food and Drug Administration (FDA)-approved compounds to identify drugs that could target the SARS-CoV-2 main protease (Mpro), which is indispensable for viral protein maturation and regard as an important therapeutic target. We identified antimalarial drug tafenoquine (TFQ), which is approved for radical cure of Plasmodium vivax and malaria prophylaxis, as a top candidate to inhibit Mpro protease activity. The crystal structure of SARS-CoV-2 Mpro in complex with TFQ revealed that TFQ noncovalently bound to and reshaped the substrate-binding pocket of Mpro by altering the loop region (residues 139–144) near the catalytic Cys145, which could block the catalysis of its peptide substrates. We also found that TFQ inhibited human transmembrane protease serine 2 (TMPRSS2). Furthermore, one TFQ derivative, compound 7, showed a better therapeutic index than TFQ on TMPRSS2 and may therefore inhibit the infectibility of SARS-CoV-2, including that of several mutant variants. These results suggest new potential strategies to block infection of SARS-CoV-2 and rising variants.
Collapse
Affiliation(s)
- Yeh Chen
- Institute of New Drug Development, China Medical University, Taichung, Taiwan; Drug Development Center, China Medical University, Taichung, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
| | - Wen-Hao Yang
- Drug Development Center, China Medical University, Taichung, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jing-Yan Gao
- Drug Development Center, China Medical University, Taichung, Taiwan; School of Pharmacy, College of Pharmacy, China Medical University, Taichung, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Yu-Chuan Wang
- Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | - Chia-Shin Yang
- Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Hui Hou
- Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | - Chia-Ling Tsai
- Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | - Yi-Zhen Chou
- Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | - Bao-Yue Huang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chian-Fang Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yu-Lin Hung
- Program of Digital Health Innovation, China Medical University, Taichung, Taiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan; Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Vathan Kumar
- Drug Development Center, China Medical University, Taichung, Taiwan
| | - Yu-Chieh Wu
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung, Taiwan
| | - Shih-Wei Chao
- Drug Development Center, China Medical University, Taichung, Taiwan
| | - Chih-Shiang Chang
- Drug Development Center, China Medical University, Taichung, Taiwan; School of Pharmacy, College of Pharmacy, China Medical University, Taichung, Taiwan
| | - Jin-Shing Chen
- Department of Surgery, College of Medicine, National Taiwan University Hospital and National Taiwan University, Taipei, Taiwan
| | - Yu-Ping Chiang
- Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Der-Yang Cho
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Department of Neurosurgery, China Medical University Hospital, Taichung, Taiwan
| | - Long-Bin Jeng
- School of Medicine, China Medical University, Taichung, Taiwan; Department of Surgery, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chang-Hai Tsai
- School of Medicine, China Medical University, Taichung, Taiwan; China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Mien-Chie Hung
- Drug Development Center, China Medical University, Taichung, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Center for Molecular Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan.
| |
Collapse
|
36
|
Bou-Assaf GM, Budyak IL, Brenowitz M, Day ES, Hayes D, Hill J, Majumdar R, Ringhieri P, Schuck P, Lin JC. Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci 2022; 111:2121-2133. [PMID: 34986360 DOI: 10.1016/j.xphs.2021.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.
Collapse
Affiliation(s)
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Eric S Day
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080
| | - David Hayes
- IntlSoSci, 23 Washington St., Gorham, NH 03581
| | - John Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98105
| | - Ranajoy Majumdar
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paola Ringhieri
- Analytical Development Biotech Department, Merck Serono S.p.a, Guidonia, RM, Italy; an affiliate of Merck KGaA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Jasper C Lin
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080.
| |
Collapse
|
37
|
Pohl C, Polimeni M, Indrakumar S, Streicher W, Peters GHJ, Nørgaard A, Lund M, Harris P. Electrostatics Drive Oligomerization and Aggregation of Human Interferon Alpha-2a. J Phys Chem B 2021; 125:13657-13669. [PMID: 34898211 PMCID: PMC8713289 DOI: 10.1021/acs.jpcb.1c07090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Aggregation is a
common phenomenon in the field of protein therapeutics
and can lead to function loss or immunogenic patient responses. Two
strategies are currently used to reduce aggregation: (1) finding a
suitable formulation, which is labor-intensive and requires large
protein quantities, or (2) engineering the protein, which requires
extensive knowledge about the protein aggregation pathway. We present
a biophysical characterization of the oligomerization and aggregation
processes by Interferon alpha-2a (IFNα-2a), a protein drug with
antiviral and immunomodulatory properties. This study combines experimental
high throughput screening with detailed investigations by small-angle
X-ray scattering and analytical ultracentrifugation. Metropolis Monte
Carlo simulations are used to gain insight into the underlying intermolecular
interactions. IFNα-2a forms soluble oligomers that are controlled
by a fast pH and concentration-dependent equilibrium. Close to the
isoelectric point of 6, IFNα-2a forms insoluble aggregates which
can be prevented by adding salt. We show that monomer attraction is driven mainly by molecular anisotropic dipole–dipole interactions
that increase with increasing pH. Repulsion is due
to monopole–monopole interactions and depends on the charge
of IFNα-2a. The study highlights how combining multiple methods
helps to systematically dissect the molecular mechanisms driving oligomer
formation and to design ultimately efficient strategies for preventing
detrimental protein aggregation.
Collapse
Affiliation(s)
- Christin Pohl
- Novozymes A/S, Bagsvaerd, 2880, Denmark.,Department of Chemistry, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Marco Polimeni
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00, Lund, Sweden
| | - Sowmya Indrakumar
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | | | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | | | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, 221 00, Lund, Sweden
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| |
Collapse
|
38
|
The Structure and Function of Modular Escherichia coli O157:H7 Bacteriophage FTBEc1 endolysin, LysT84: Defining a New Endolysin Catalytic Subfamily. Biochem J 2021; 479:207-223. [PMID: 34935873 DOI: 10.1042/bcj20210701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/12/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
Bacteriophage endolysins degrade peptidoglycan and have been identified as antibacterial candidates to combat antimicrobial resistance. Considering the catalytic and structural diversity of endolysins, there is a paucity of structural data to inform how these enzymes work at the molecular level-key data that is needed to realize the potential of endolysin-based antibacterial agents. Here, we determine the atomic structure and define the enzymatic function of Escherichia coli O157:H7 phage FTEBc1 endolysin, LysT84. Bioinformatic analysis reveals that LysT84 is a modular endolysin, which is unusual for Gram-negative endolysins, comprising a peptidoglycan binding domain and an enzymatic domain. The crystal structure of LysT84 (2.99 Å) revealed a mostly α-helical protein with two domains connected by a linker region but packed together. LysT84 was determined to be a monomer in solution using analytical ultracentrifugation. Small-angle X-ray scattering data revealed that LysT84 is a flexible protein but does not have the expected bimodal P(r) function of a multidomain protein, suggesting that the domains of LysT84 pack closely creating a globular protein as seen in the crystal structure. Structural analysis reveals two key glutamate residues positioned on either side of the active site cavity; mutagenesis demonstrating these residues are critical for peptidoglycan degradation. Molecular dynamic simulations suggest that the enzymatically active domain is dynamic, allowing the appropriate positioning of these catalytic residues for hydrolysis of the β(1-4) bond. Overall, our study defines the structural basis for peptidoglycan degradation by LysT84 which supports rational engineering of related endolysins into effective antibacterial agents.
Collapse
|
39
|
Liao S, Wei L, Abriata LA, Stellacci F. Control and Characterization of the Compactness of Single-Chain Nanoparticles. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c02071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suiyang Liao
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Lixia Wei
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| | - Luciano A. Abriata
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
- Interfaculty Bioengineering Institute, École Polytechnique Fédérale de Lausanne, Station 12, 1015 Lausanne, Switzerland
| |
Collapse
|
40
|
Zhang H, Cheng N, Li Z, Bai L, Fang C, Li Y, Zhang W, Dong X, Jiang M, Liang Y, Zhang S, Mi J, Zhu J, Zhang Y, Chen SJ, Zhao Y, Weng XQ, Hu W, Chen Z, Huang J, Meng G. DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia. Cancer Commun (Lond) 2021; 41:1116-1136. [PMID: 34699692 PMCID: PMC8626599 DOI: 10.1002/cac2.12234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 10/12/2021] [Indexed: 02/05/2023] Open
Abstract
Background Abnormal alternative splicing is frequently associated with carcinogenesis. In B‐cell acute lymphoblastic leukemia (B‐ALL), double homeobox 4 fused with immunoglobulin heavy chain (DUX4/IGH) can lead to the aberrant production of E‐26 transformation‐specific family related gene abnormal transcript (ERGalt) and other splicing variants. However, the molecular mechanism underpinning this process remains elusive. Here, we aimed to know how DUX4/IGH triggers abnormal splicing in leukemia. Methods The differential intron retention analysis was conducted to identify novel DUX4/IGH‐driven splicing in B‐ALL patients. X‐ray crystallography, small angle X‐ray scattering (SAXS), and analytical ultracentrifugation were used to investigate how DUX4/IGH recognize double DUX4 responsive element (DRE)‐DRE sites. The ERGalt biogenesis and B‐cell differentiation assays were performed to characterize the DUX4/IGH crosslinking activity. To check whether recombination‐activating gene 1/2 (RAG1/2) was required for DUX4/IGH‐driven splicing, the proximity ligation assay, co‐immunoprecipitation, mammalian two hybrid characterizations, in vitro RAG1/2 cleavage, and shRNA knock‐down assays were performed. Results We reported previously unrecognized intron retention events in C‐type lectin domain family 12, member A abnormal transcript (CLEC12Aalt) and chromosome 6 open reading frame 89 abnormal transcript (C6orf89alt), where also harbored repetitive DRE‐DRE sites. Supportively, X‐ray crystallography and SAXS characterization revealed that DUX4 homeobox domain (HD)1‐HD2 might dimerize into a dumbbell‐shape trans configuration to crosslink two adjacent DRE sites. Impaired DUX4/IGH‐mediated crosslinking abolishes ERGalt, CLEC12Aalt, and C6orf89alt biogenesis, resulting in marked alleviation of its inhibitory effect on B‐cell differentiation. Furthermore, we also observed a rare RAG1/2‐mediated recombination signal sequence‐like DNA edition in DUX4/IGH target genes. Supportively, shRNA knock‐down of RAG1/2 in leukemic Reh cells consistently impaired the biogenesis of ERGalt, CLEC12Aalt, and C6orf89alt. Conclusions All these results suggest that DUX4/IGH‐driven DNA crosslinking is required for RAG1/2 recruitment onto the double tandem DRE‐DRE sites, catalyzing V(D)J‐like recombination and oncogenic splicing in acute lymphoblastic leukemia.
Collapse
Affiliation(s)
- Hao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Nuo Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Zhihui Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Ling Bai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China.,Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, P. R. China
| | - Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yuwen Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Weina Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Xue Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Minghao Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Yang Liang
- Department of Hematologic Oncology, State key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Sujiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Jianqing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Jiang Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Yajie Zhao
- Department of Geriatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China.,Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Xiang-Qin Weng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Weiguo Hu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China.,Department of Geriatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China.,Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| | - Jinyan Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China.,Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310000, P. R. China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310000, P. R. China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China
| |
Collapse
|
41
|
Lassé M, Stampfli AR, Orban T, Bothara RK, Gerrard JA, Fairbanks AJ, Pattinson NR, Dobson RCJ. Reaction dynamics and residue identification of haemoglobin modification by acrolein, a lipid-peroxidation by-product. Biochim Biophys Acta Gen Subj 2021; 1865:130013. [PMID: 34534644 DOI: 10.1016/j.bbagen.2021.130013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Lipid hydroperoxides decompose to reactive aldehydes, such as acrolein. Measurement of oxidative stress markers in the clinic could improve risk stratification for patients. METHODS To aid the development of diagnostic oxidative stress markers, we defined the acrolein modifications of haemoglobin using mass spectrometry. RESULTS Acrolein modifications have little effect on the secondary structure of haemoglobin. They do not disrupt the quaternary structure, but instead promote crosslinked octamers. For acrolein modified haemoglobin the response to O2 binding is altered such that cooperativity is lost. Mass spectrometry experiments at a 1:1 acrolein:haemoglobin molar ratio demonstrate that the α-chain quickly forms an aza-Michael adduct (+56 Da), which then forms a more stable adduct, Nε-(3-methylpyridinium)lysine (MP-lysine, +76 Da) over 7 days. The β-chain remains relatively unchanged over the duration of the 7 days and the aza-Michael adduct is dominant. At 2:1 and 5:1 molar ratios the α-chain was consistently modified at K7, H20, H50, and the β-chain at C93 and H97 with the aza-Michael adduct. Beyond 5 h, an MP-adduct (+76 Da) was located predominantly at K7 of the α-chain, while an FDP-adduct (+94 Da) was observed at K95 of the β-chain. CONCLUSIONS We have generated qualitative evidence identifying the acrolein target sites on haemoglobin, a potential oxidative stress marker that is easily measured in circulation. GENERAL SIGNIFICANCE We provide data for the community to develop targeted mass spectrometric or immunometric assays for acrolein modified haemoglobin to further validate the potential of haemoglobin as an oxidative stress marker in patients .
Collapse
Affiliation(s)
- Moritz Lassé
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Anja R Stampfli
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Thomas Orban
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Juliet A Gerrard
- Faculty of Science, Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Antony J Fairbanks
- Biomolecular Interaction Centre, and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Neil R Pattinson
- Canterbury Scientific Ltd, 71 Whiteleigh Ave, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
42
|
Nonis SG, Haywood J, Schmidberger JW, Mackie ERR, Soares da Costa TP, Bond CS, Mylne JS. Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase. THE PLANT CELL 2021; 33:2794-2811. [PMID: 34235541 PMCID: PMC8408470 DOI: 10.1093/plcell/koab130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Over 30 years ago, an intriguing posttranslational modification was found responsible for creating concanavalin A (conA), a carbohydrate-binding protein from jack bean (Canavalia ensiformis) seeds and a common carbohydrate chromatography reagent. ConA biosynthesis involves what was then an unprecedented rearrangement in amino-acid sequence, whereby the N-terminal half of the gene-encoded conA precursor (pro-conA) is swapped to become the C-terminal half of conA. Asparaginyl endopeptidase (AEP) was shown to be involved, but its mechanism was not fully elucidated. To understand the structural basis and consequences of circular permutation, we generated recombinant jack bean pro-conA plus jack bean AEP (CeAEP1) and solved crystal structures for each to 2.1 and 2.7 Å, respectively. By reconstituting conA biosynthesis in vitro, we prove CeAEP1 alone can perform both cleavage and cleavage-coupled transpeptidation to form conA. CeAEP1 structural analysis reveals how it is capable of carrying out both reactions. Biophysical assays illustrated that pro-conA is less stable than conA. This observation was explained by fewer intermolecular interactions between subunits in the pro-conA crystal structure and consistent with a difference in the prevalence for tetramerization in solution. These findings elucidate the consequences of circular permutation in the only posttranslation example known to occur in nature.
Collapse
Affiliation(s)
- Samuel G. Nonis
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Jason W. Schmidberger
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Emily R. R. Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Charles S. Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| |
Collapse
|
43
|
Nagaoka S, Sugiyama N, Yatsunami R, Nakamura S. Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica. Biosci Biotechnol Biochem 2021; 85:1986-1994. [PMID: 34215877 DOI: 10.1093/bbb/zbab122] [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: 04/11/2021] [Accepted: 06/21/2021] [Indexed: 11/12/2022]
Abstract
3-Isopropylmalate dehydrogenase (IPMDH) catalyzes oxidative decarboxylation of (2R, 3S)-3-isopropylmalate to 2-oxoisocaproate in leucine biosynthesis. In this study, recombinant IPMDH (HjIPMDH) from an extremely halophilic archaeon, Haloarcula japonica TR-1, was characterized. Activity of HjIPMDH increased as KCl concentration increased, and the maximum activity was observed at 3.0 m KCl. Analytical ultracentrifugation revealed that HjIPMDH formed a homotetramer at high KCl concentrations, and it dissociated to a monomer at low KCl concentrations. Additionally, HjIPMDH was thermally stabilized by higher KCl concentrations. This is the first report on haloarchaeal IPMDH.
Collapse
Affiliation(s)
- Shintaro Nagaoka
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Noriko Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,National Institute of Technology (KOSEN), Numazu College, Numazu, Shizuoka, Japan
| |
Collapse
|
44
|
Nguyen B, Shinn MK, Weiland E, Lohman TM. Regulation of E. coli Rep helicase activity by PriC. J Mol Biol 2021; 433:167072. [PMID: 34081984 DOI: 10.1016/j.jmb.2021.167072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/28/2022]
Abstract
Stalled DNA replication forks can result in incompletely replicated genomes and cell death. DNA replication restart pathways have evolved to deal with repair of stalled forks and E. coli Rep helicase functions in this capacity. Rep and an accessory protein, PriC, assemble at a stalled replication fork to facilitate loading of other replication proteins. A Rep monomer is a rapid and processive single stranded (ss) DNA translocase but needs to be activated to function as a helicase. Activation of Rep in vitro requires self-assembly to form a dimer, removal of its auto-inhibitory 2B sub-domain, or interactions with an accessory protein. Rep helicase activity has been shown to be stimulated by PriC, although the mechanism of activation is not clear. Using stopped flow kinetics, analytical sedimentation and single molecule fluorescence methods, we show that a PriC dimer activates the Rep monomer helicase and can also stimulate the Rep dimer helicase. We show that PriC can self-assemble to form dimers and tetramers and that Rep and PriC interact in the absence of DNA. We further show that PriC serves as a Rep processivity factor, presumably co-translocating with Rep during DNA unwinding. Activation is specific for Rep since PriC does not activate the UvrD helicase. Interaction of PriC with the C-terminal acidic tip of the ssDNA binding protein, SSB, eliminates Rep activation by stabilizing the PriC monomer. This suggests a likely mechanism for Rep activation by PriC at a stalled replication fork.
Collapse
Affiliation(s)
- Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Min Kyung Shinn
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
| |
Collapse
|
45
|
González-Rubio G, Hilbert H, Rosenberg R, Ni B, Fuhrer L, Cölfen H. Simple Determination of Gold Nanocrystal Dimensions by Analytical Ultracentrifugation via Surface Ligand-Solvent Density Matching. NANOMATERIALS 2021; 11:nano11061427. [PMID: 34071534 PMCID: PMC8228700 DOI: 10.3390/nano11061427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
Abstract
Analytical ultracentrifugation (AUC) is a powerful technique to observe colloidal nanocrystals (NCs) directly in solution and obtain critical information about their physical-chemical properties. Nevertheless, a more comprehensive implementation of AUC for the characterisation of such a class of crystalline colloids has been traditionally impaired by the requirement of having a priori knowledge of the complex, multilayered structure formed by NC in solution. This includes the nature (density and mass) of the surface ligands (SLs) that provide NC colloidal stability and the shell of solvent molecules formed on it. Herein, we propose a methodology to determine the NCs size by using SLs with a density equal to that of the solvent. Thereby, the buoyancy force of the SL shell is neutral, and the density of the NCs is sufficient a priori knowledge to calculate their related mass and size distributions. The simplicity and reliability of the method are evaluated with cetyltrimethylammonium bromide (CTAB) stabilized spherical gold NCs (AuNCs) of dimensions ranging from 1 to 17 nm. The proposed method has great potential to be transferred to any non-crystalline and crystalline colloids of different nature and composition, which have a density that is equal to the bulk and can be stabilized by SLs having a density that matches that of the solvent.
Collapse
|
46
|
Madru C, Tekpinar AD, Rosario S, Czernecki D, Brûlé S, Sauguet L, Delarue M. Fast and efficient purification of SARS-CoV-2 RNA dependent RNA polymerase complex expressed in Escherichia coli. PLoS One 2021; 16:e0250610. [PMID: 33914787 PMCID: PMC8084133 DOI: 10.1371/journal.pone.0250610] [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: 08/05/2020] [Accepted: 04/09/2021] [Indexed: 01/18/2023] Open
Abstract
To stop the COVID-19 pandemic due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which caused more than 2.5 million deaths to date, new antiviral molecules are urgently needed. The replication of SARS-CoV-2 requires the RNA-dependent RNA polymerase (RdRp), making RdRp an excellent target for antiviral agents. RdRp is a multi-subunit complex composed of 3 viral proteins named nsp7, nsp8 and nsp12 that ensure the ~30 kb RNA genome’s transcription and replication. The main strategies employed so far for the overproduction of RdRp consist of expressing and purifying the three subunits separately before assembling the complex in vitro. However, nsp12 shows limited solubility in bacterial expression systems and is often produced in insect cells. Here, we describe an alternative strategy to co-express the full SARS-CoV-2 RdRp in E. coli, using a single plasmid. Characterization of the purified recombinant SARS-CoV-2 RdRp shows that it forms a complex with the expected (nsp7)(nsp8)2(nsp12) stoichiometry. RNA polymerization activity was measured using primer-extension assays showing that the purified enzyme is functional. The purification protocol can be achieved in one single day, surpassing in speed all other published protocols. Our construct is ideally suited for screening RdRp and its variants against very large chemical compounds libraries and has been made available to the scientific community through the Addgene plasmid depository (Addgene ID: 165451).
Collapse
Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Ayten Dizkirici Tekpinar
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van, Turkey
| | - Sandrine Rosario
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Dariusz Czernecki
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- École Doctorale Complexité du Vivant, Sorbonne Université, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR, Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
| |
Collapse
|
47
|
Park SH, Lee CW, Bae DW, Do H, Jeong CS, Hwang J, Cha SS, Lee JH. Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554. Int J Biol Macromol 2021; 183:213-221. [PMID: 33910038 DOI: 10.1016/j.ijbiomac.2021.04.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/01/2022]
Abstract
Citrate synthase (CS) catalyzes the formation of citrate and coenzyme A from acetyl-CoA and oxaloacetate. CS exists in two forms: type I and type II. We determined the citrate-bound crystal structure of type II CS from the Hymenobacter sp. PAMC 26554 bacterium (HyCS; isolated from Antarctic lichen). Citrate molecules bound to a cleft between the large and small domains of HyCS. Structural comparison of HyCS with other type II CSs revealed that type II CSs have a highly conserved flexible hinge region (residues G264-P265 in HyCS), enabling correct positioning of active site residues. Notably, the catalytic His266 residue of HyCS interacted with Trp262 in the inactive (unliganded open) state of other type II CSs, whereas the His266 residue moved to the active site via a small-domain swing motion, interacting with the bound citrate in the closed conformation of HyCS. However, type I CSs lack this tryptophan residue and face-to-edge interactions. Thus, type II CSs might have a unique domain-motion control mechanism enabling a tight allosteric regulation. An activity assay using a W262A mutant showed a Hill coefficient of 2.4; thus, the interaction between Trp262 and His266 was closely related to the positive cooperative ligand binding of type II CS.
Collapse
Affiliation(s)
- Sun-Ha Park
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Da-Woon Bae
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang-Sook Jeong
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
| |
Collapse
|
48
|
Bednarczyk D, Tor-Cohen C, Das PK, Noy D. Direct Assembly in Aqueous Solutions of Stable Chlorophyllide Complexes with Type II Water-soluble Chlorophyll Proteins. Photochem Photobiol 2021; 97:732-738. [PMID: 33570189 DOI: 10.1111/php.13398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/08/2021] [Indexed: 01/28/2023]
Abstract
Water-soluble chlorophyll-binding proteins (WSCPs) from Brassicaceae constitute a small family of non-photosynthetic proteins that may provide a useful benchmark and model system for studying molecular aspects of chlorophyll-protein interactions such as the tuning of absorption and emission spectra, and binding selectivity. WSCP apo-proteins are readily expressed by recombinant DNA techniques and can be assembled in vitro with natural and synthetic chlorophyll derivatives. The complexes with native chlorophylls are exceptionally stable toward thermal dissociation and protein denaturation due to hydrophobic interactions with the chlorophyll's phytyl chains that stabilize the core of the WSCP tetrameric complexes. However, assembly requires the use of detergents or water-in-oil emulsions to introduce the hydrophobic pigments into the water-soluble apo-proteins. Here, we explore the direct assembly of recombinant WSCPs with the water-soluble phytyl-free chlorophyll analogue chlorophyllide a in aqueous solutions. We show that the complexes formed by mixing chlorophyllide and WSCP apo-proteins are exclusively tetrameric, and while they lack the extreme thermostability of the respective chlorophyll complexes, they are still thermostable up to around 60°C. Their absorption and CD spectra are very similar to the chlorophyll complexes albeit slight peak shifts and broadening of the bands indicate variations in pigment and protein conformations, and less rigid structures. Simplifying the assembly process of WSCPs opens new possibilities for their use in modelling natural chlorophyll-protein complexes, and as templates for designing novel artificial protein-pigment complexes.
Collapse
Affiliation(s)
- Dominika Bednarczyk
- Migal-Galilee Research Institute, Kiryat Shmona, Israel.,Agricultural Research Organization, Volcani Center, Rishon Lezyion, Israel
| | | | | | - Dror Noy
- Migal-Galilee Research Institute, Kiryat Shmona, Israel.,Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| |
Collapse
|
49
|
Hall CJ, Lee M, Boarder MP, Mangion AM, Gendall AR, Panjikar S, Perugini MA, Soares da Costa TP. Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. FEBS J 2021; 288:4973-4986. [PMID: 33586321 DOI: 10.1111/febs.15766] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/16/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022]
Abstract
Lysine biosynthesis in plants occurs via the diaminopimelate pathway. The first committed and rate-limiting step of this pathway is catalysed by dihydrodipicolinate synthase (DHDPS), which is allosterically regulated by the end product, l-lysine (lysine). Given that lysine is a common nutritionally limiting amino acid in cereal crops, there has been much interest in probing the regulation of DHDPS. Interestingly, knockouts in Arabidopsis thaliana of each isoform (AtDHDPS1 and AtDHDPS2) result in different phenotypes, despite the enzymes sharing > 85% protein sequence identity. Accordingly, in this study, we compared the catalytic activity, lysine-mediated inhibition and structures of both A. thaliana DHDPS isoforms. We found that although the recombinantly produced enzymes have similar kinetic properties, AtDHDPS1 is 10-fold more sensitive to lysine. We subsequently used X-ray crystallography to probe for structural differences between the apo- and lysine-bound isoforms that could account for the differential allosteric inhibition. Despite no significant changes in the overall structures of the active or allosteric sites, we noted differences in the rotamer conformation of a key allosteric site residue (Trp116) and proposed that this could result in differences in lysine dissociation. Microscale thermophoresis studies supported our hypothesis, with AtDHDPS1 having a ~ 6-fold tighter lysine dissociation constant compared to AtDHDPS2, which agrees with the lower half minimal inhibitory concentration for lysine observed. Thus, we highlight that subtle differences in protein structures, which could not have been predicted from the primary sequences, can have profound effects on the allostery of a key enzyme involved in lysine biosynthesis in plants. DATABASES: Structures described are available in the Protein Data Bank under the accession numbers 6VVH and 6VVI.
Collapse
Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Matthew P Boarder
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Alexandra M Mangion
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| |
Collapse
|
50
|
Characterization of the different oligomeric states of the DAN family antagonists SOSTDC1 and SOST. Biochem J 2021; 477:3167-3182. [PMID: 32779697 PMCID: PMC7473711 DOI: 10.1042/bcj20200552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022]
Abstract
The DAN (differential screening-selected gene aberrative in neuroblastoma) family are a group of secreted extracellular proteins which typically bind to and antagonize BMP (bone morphogenetic protein) ligands. Previous studies have revealed discrepancies between the oligomerization state of certain DAN family members, with SOST (a poor antagonist of BMP signaling) forming a monomer while Grem1, Grem2, and NBL1 (more potent BMP antagonists) form non-disulfide linked dimers. The protein SOSTDC1 (Sclerostin domain containing protein 1) is sequentially similar to SOST, but has been shown to be a better BMP inhibitor. In order to determine the oligomerization state of SOSTDC1 and determine what effect dimerization might have on the mechanism of DAN family antagonism of BMP signaling, we isolated the SOSTDC1 protein and, using a battery of biophysical, biochemical, and structural techniques, showed that SOSTDC1 forms a highly stable non-covalent dimer. Additionally, this SOSTDC1 dimer was shown, using an in vitro cell based assay system, to be an inhibitor of multiple BMP signaling growth factors, including GDF5, while monomeric SOST was a very poor antagonist. These results demonstrate that SOSTDC1 is distinct from paralogue SOST in terms of both oligomerization and strength of BMP inhibition.
Collapse
|