1
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Brookner DE, Hekstra DR. MatchMaps: non-isomorphous difference maps for X-ray crystallography. J Appl Crystallogr 2024; 57:885-895. [PMID: 38846758 PMCID: PMC11151677 DOI: 10.1107/s1600576724003510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands and time. A popular method for detecting structural differences between crystallographic data sets is the isomorphous difference map. These maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even modest changes in unit-cell properties can render isomorphous difference maps useless. This is unnecessary. Described here is a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. This procedure is implemented in an open-source Python package, MatchMaps, that can be run in any software environment supporting PHENIX [Liebschner et al. (2019). Acta Cryst. D75, 861-877] and CCP4 [Agirre et al. (2023). Acta Cryst. D79, 449-461]. Worked examples show that MatchMaps 'rescues' observed difference electron-density maps for poorly isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit or across altogether different crystal forms.
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Affiliation(s)
- Dennis E. Brookner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Doeke R. Hekstra
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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2
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Brookner DE, Hekstra DR. MatchMaps: Non-isomorphous difference maps for X-ray crystallography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.01.555333. [PMID: 37732267 PMCID: PMC10508726 DOI: 10.1101/2023.09.01.555333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands, and time. The isomorphous difference map remains the gold standard for detecting structural differences between datasets. Isomorphous difference maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even minute changes in unit cell properties can render isomorphous difference maps useless. This is unnecessary. Here we describe a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. We have implemented this procedure in an open-source python package, MatchMaps, that can be run in any software environment supporting PHENIX and CCP4. Through examples, we show that MatchMaps "rescues" observed difference electron density maps for poorly-isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit, or across altogether different crystal forms.
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Affiliation(s)
- Dennis E Brookner
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Doeke R Hekstra
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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3
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Wu X, Xu M, Geng M, Chen S, Little PJ, Xu S, Weng J. Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies. Signal Transduct Target Ther 2023; 8:220. [PMID: 37244925 DOI: 10.1038/s41392-023-01439-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 05/29/2023] Open
Abstract
The ever-increasing prevalence of noncommunicable diseases (NCDs) represents a major public health burden worldwide. The most common form of NCD is metabolic diseases, which affect people of all ages and usually manifest their pathobiology through life-threatening cardiovascular complications. A comprehensive understanding of the pathobiology of metabolic diseases will generate novel targets for improved therapies across the common metabolic spectrum. Protein posttranslational modification (PTM) is an important term that refers to biochemical modification of specific amino acid residues in target proteins, which immensely increases the functional diversity of the proteome. The range of PTMs includes phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, neddylation, glycosylation, palmitoylation, myristoylation, prenylation, cholesterylation, glutathionylation, S-nitrosylation, sulfhydration, citrullination, ADP ribosylation, and several novel PTMs. Here, we offer a comprehensive review of PTMs and their roles in common metabolic diseases and pathological consequences, including diabetes, obesity, fatty liver diseases, hyperlipidemia, and atherosclerosis. Building upon this framework, we afford a through description of proteins and pathways involved in metabolic diseases by focusing on PTM-based protein modifications, showcase the pharmaceutical intervention of PTMs in preclinical studies and clinical trials, and offer future perspectives. Fundamental research defining the mechanisms whereby PTMs of proteins regulate metabolic diseases will open new avenues for therapeutic intervention.
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Affiliation(s)
- Xiumei Wu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China
| | - Mengyun Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mengya Geng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Shuo Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Peter J Little
- School of Pharmacy, University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, 4102, Australia
- Sunshine Coast Health Institute and School of Health and Behavioural Sciences, University of the Sunshine Coast, Birtinya, QLD, 4575, Australia
| | - Suowen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jianping Weng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China.
- Bengbu Medical College, Bengbu, 233000, China.
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4
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Martin GJ, Lower SE, Suvorov A, Bybee SM. Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae). INSECTS 2021; 12:insects12060561. [PMID: 34207188 PMCID: PMC8235688 DOI: 10.3390/insects12060561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022]
Abstract
Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication; as well as a diversity of ecologies. Here; using transcriptomics; we examine the phototransduction pathway in this non-model organism; and provide some of the first evidence for positive selection in the phototransduction pathway beyond opsins in beetles. Evidence for gene duplications within Lampyridae are found in inactivation no afterpotential C and inactivation no afterpotential D. We also find strong support for positive selection in arrestin-2; inactivation no afterpotential D; and transient receptor potential-like; with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. Taken with other recent work in flies; butterflies; and moths; this represents an exciting new avenue of study as we seek to further understand diversification and constraint on the phototransduction pathway in light of organism ecology.
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Affiliation(s)
- Gavin J. Martin
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
- Correspondence:
| | - Sarah E. Lower
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA;
| | - Anton Suvorov
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Seth M. Bybee
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
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5
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Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Sci Rep 2021; 11:1484. [PMID: 33452274 PMCID: PMC7810883 DOI: 10.1038/s41598-020-79398-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
The PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.
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Affiliation(s)
- Miroslav Jurásek
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jitender Kumar
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Petra Paclíková
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Alka Kumari
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic
| | - Konstantinos Tripsianes
- grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Vítězslav Bryja
- grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500 Czech Republic ,grid.418095.10000 0001 1015 3316Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65 Czech Republic
| | - Robert Vácha
- grid.10267.320000 0001 2194 0956National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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6
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Shieh BH, Nuzum L, Kristaponyte I. Exploring Excitotoxicity and Regulation of a Constitutively Active TRP Ca 2+ Channel in Drosophila. Fly (Austin) 2020; 15:8-27. [PMID: 33200658 DOI: 10.1080/19336934.2020.1851586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Unregulated Ca2+ influx affects intracellular Ca2+ homoeostasis, which may lead to neuronal death. In Drosophila, following the activation of rhodopsin the TRP Ca2+ channel is open to mediate the light-dependent depolarization. A constitutively active TRP channel triggers the degeneration of TrpP365 /+ photoreceptors. To explore retinal degeneration, we employed a multidisciplinary approach including live imaging using GFP tagged actin and arrestin 2. Importantly, we demonstrate that the major rhodopsin (Rh1) was greatly reduced before the onset of rhabdomere degeneration; a great reduction of Rh1 affects the maintenance of rhabdomere leading to degeneration of photoreceptors. TrpP365 /+ also led to the up-regulation of CaMKII, which is beneficial as suppression of CaMKII accelerated retinal degeneration. We explored the regulation of TRP by investigating the genetic interaction between TrpP365 /+ and mutants affecting the turnover of diacylglycerol (DAG). We show a loss of phospholipase C in norpAP24 exhibited a great reduction of the DAG content delayed degeneration of TrpP365 /+ photoreceptors. In contrast, knockdown or mutations in DAG lipase (InaE) that is accompanied by slightly reduced levels of most DAG but an increased level of DAG 34:1, exacerbated retinal degeneration of TrpP365 /+. Together, our findings support the notion that DAG plays a role in regulating TRP. Interestingly, DAG lipase is likely required during photoreceptor development as TrpP365 /+; inaEN125 double mutants contained severely degenerated rhabdomeres.
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Affiliation(s)
- Bih-Hwa Shieh
- Department of Pharmacology, Center for Molecular Neuroscience and Vanderbilt Vision Research Center, Vanderbilt University , Nashville, TN, USA
| | - Lucinda Nuzum
- Department of Pharmacology, Center for Molecular Neuroscience and Vanderbilt Vision Research Center, Vanderbilt University , Nashville, TN, USA
| | - Inga Kristaponyte
- Department of Pharmacology, Center for Molecular Neuroscience and Vanderbilt Vision Research Center, Vanderbilt University , Nashville, TN, USA
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7
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Adem GD, Chen G, Shabala L, Chen ZH, Shabala S. GORK Channel: A Master Switch of Plant Metabolism? TRENDS IN PLANT SCIENCE 2020; 25:434-445. [PMID: 31964604 DOI: 10.1016/j.tplants.2019.12.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 05/18/2023]
Abstract
Potassium regulates a plethora of metabolic and developmental response in plants, and upon exposure to biotic and abiotic stresses a substantial K+ loss occurs from plant cells. The outward-rectifying potassium efflux GORK channels are central to this stress-induced K+ loss from the cytosol. In the mammalian systems, signaling molecules such as gamma-aminobutyric acid, G-proteins, ATP, inositol, and protein phosphatases were shown to operate as ligands controlling many K+ efflux channels. Here we present the evidence that the same molecules may also regulate GORK channels in plants. This mechanism enables operation of the GORK channels as a master switch of the cell metabolism, thus adjusting intracellular K+ homeostasis to altered environmental conditions, to maximize plant adaptive potential.
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Affiliation(s)
- Getnet D Adem
- Tasmanian Institute for Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Guang Chen
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lana Shabala
- Tasmanian Institute for Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia.
| | - Sergey Shabala
- Tasmanian Institute for Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China.
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8
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Ca2+ Signaling in Drosophila Photoreceptor Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:857-879. [DOI: 10.1007/978-3-030-12457-1_34] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Liu X, Fuentes EJ. Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 343:129-218. [PMID: 30712672 PMCID: PMC7185565 DOI: 10.1016/bs.ircmb.2018.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Post-synaptic density-95, disks-large and zonula occludens-1 (PDZ) domains are small globular protein-protein interaction domains widely conserved from yeast to humans. They are composed of ∼90 amino acids and form a classical two α-helical/six β-strand structure. The prototypical ligand is the C-terminus of partner proteins; however, they also bind internal peptide sequences. Recent findings indicate that PDZ domains also bind phosphatidylinositides and cholesterol. Through their ligand interactions, PDZ domain proteins are critical for cellular trafficking and the surface retention of various ion channels. In addition, PDZ proteins are essential for neuronal signaling, memory, and learning. PDZ proteins also contribute to cytoskeletal dynamics by mediating interactions critical for maintaining cell-cell junctions, cell polarity, and cell migration. Given their important biological roles, it is not surprising that their dysfunction can lead to multiple disease states. As such, PDZ domain-containing proteins have emerged as potential targets for the development of small molecular inhibitors as therapeutic agents. Recent data suggest that the critical binding function of PDZ domains in cell signaling is more than just glue, and their binding function can be regulated by phosphorylation or allosterically by other binding partners. These studies also provide a wealth of structural and biophysical data that are beginning to reveal the physical features that endow this small modular domain with a central role in cell signaling.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Ernesto J. Fuentes
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
- Corresponding author: E-mail:
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10
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Ye F, Huang Y, Li J, Ma Y, Xie C, Liu Z, Deng X, Wan J, Xue T, Liu W, Zhang M. An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors. eLife 2018; 7:41848. [PMID: 30526850 PMCID: PMC6300352 DOI: 10.7554/elife.41848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/08/2018] [Indexed: 01/08/2023] Open
Abstract
INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. However, the molecular mechanism that governs the interaction between INAD and NORPA (phospholipase Cβ, PLCβ), a key step for the fast kinetics of the light signaling, is not known. Here, we show that the NORPA C-terminal coiled-coil domain and PDZ-binding motif (CC-PBM) synergistically bind to INAD PDZ45 tandem with an unexpected mode and unprecedented high affinity. Guided by the structure of the INAD-NORPA complex, we discover that INADL is probably a mammalian counterpart of INAD. The INADL PDZ89 tandem specifically binds to PLCβ4 with a mode that is strikingly similar to that of the INAD-NORPA complex, as revealed by the structure of the INADL PDZ89-PLCβ4 CC-PBM complex. Therefore, our study suggests that the highly specific PDZ tandem - PLCβ interactions are an evolutionarily conserved mechanism in PLCβ signaling in the animal kingdom.
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Affiliation(s)
- Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuxin Huang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuqian Ma
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chensu Xie
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zexu Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoying Deng
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Tian Xue
- Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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11
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Katz B, Minke B. The Drosophila light-activated TRP and TRPL channels - Targets of the phosphoinositide signaling cascade. Prog Retin Eye Res 2018; 66:200-219. [DOI: 10.1016/j.preteyeres.2018.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/29/2018] [Accepted: 05/02/2018] [Indexed: 01/28/2023]
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12
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Salinas VH, Ranganathan R. Coevolution-based inference of amino acid interactions underlying protein function. eLife 2018; 7:34300. [PMID: 30024376 PMCID: PMC6117156 DOI: 10.7554/elife.34300] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/18/2018] [Indexed: 02/02/2023] Open
Abstract
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in several homologs of a protein family - a deep coupling scan (DCS). The data show that cooperative interactions between residues are loaded in a sparse, evolutionarily conserved, spatially contiguous network of amino acids. The pattern of amino acid coupling is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work exposes the collective nature of physical constraints on protein function and clarifies its link with sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.
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Affiliation(s)
- Victor H Salinas
- Green Center for Systems BiologyUT Southwestern Medical CenterDallasUnited States
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Biochemistry and Molecular BiologyThe University of ChicagoChicagoUnited States,Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
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13
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Zhu J, Shang Y, Zhang M. Mechanistic basis of MAGUK-organized complexes in synaptic development and signalling. Nat Rev Neurosci 2016; 17:209-23. [DOI: 10.1038/nrn.2016.18] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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An Exquisitely Specific PDZ/Target Recognition Revealed by the Structure of INAD PDZ3 in Complex with TRP Channel Tail. Structure 2016; 24:383-91. [DOI: 10.1016/j.str.2015.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 12/09/2015] [Accepted: 12/22/2015] [Indexed: 11/22/2022]
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15
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Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P. A two-step binding mechanism for the self-binding peptide recognition of target domains. MOLECULAR BIOSYSTEMS 2016; 12:1201-13. [DOI: 10.1039/c5mb00800j] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By using state-of-the-art molecular dynamics to reconstruct the complete structural dynamics picture of self-binding peptides, a two-step binding mechanism was proposed, including a fast, nonspecific diffusive phase and a slow, specific organizational phase.
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Affiliation(s)
- Chao Yang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shilei Zhang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Zhengya Bai
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shasha Hou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Di Wu
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Jian Huang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Peng Zhou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
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16
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Abstract
The function of scaffolding proteins is to bring together two or more proteins in a relatively stable configuration, hence their name. Numerous scaffolding proteins are found in nature, many having multiple protein–protein interaction modules. Over the past decade, examples of scaffolding complexes long thought to be stable have instead been found to be surprisingly dynamic. These studies are scattered among different biological systems, and so the concept that scaffolding complexes might not always represent stable entities and that their dynamics can be regulated has not garnered general attention. We became aware of this issue in our studies of a scaffolding protein in microvilli, which forced us to reevaluate its contribution to their structure. The purpose of this Perspective is to draw attention to this phenomenon and discuss why complexes might show regulated dynamics. We also wish to encourage more studies on the dynamics of “stable” complexes and to provide a word of caution about how functionally important dynamic associations may be missed in biochemical and proteomic studies.
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Affiliation(s)
- Damien Garbett
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Anthony Bretscher
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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17
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Hardie RC, Juusola M. Phototransduction in Drosophila. Curr Opin Neurobiol 2015; 34:37-45. [DOI: 10.1016/j.conb.2015.01.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/10/2015] [Indexed: 10/24/2022]
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18
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A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat Commun 2015; 5:3287. [PMID: 24518821 DOI: 10.1038/ncomms4287] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/20/2014] [Indexed: 12/30/2022] Open
Abstract
Allosteric modifiers have the potential to fine-tune enzyme activity. Therefore, targeting allosteric sites is gaining increasing recognition as a strategy in drug design. Here we report the use of computational methods for the discovery of the first small-molecule allosteric inhibitor of the collagenolytic cysteine peptidase cathepsin K, a major target for the treatment of osteoporosis. The molecule NSC13345 is identified by high-throughput docking of compound libraries to surface sites on the peptidase that are connected to the active site by an evolutionarily conserved network of residues (protein sector). The crystal structure of the complex shows that NSC13345 binds to a novel allosteric site on cathepsin K. The compound acts as a hyperbolic mixed modifier in the presence of a synthetic substrate, it completely inhibits collagen degradation and has good selectivity for cathepsin K over related enzymes. Altogether, these properties qualify our methodology and NSC13345 as promising candidates for allosteric drug design.
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19
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Zernii EY, Nazipova AA, Gancharova OS, Kazakov AS, Serebryakova MV, Zinchenko DV, Tikhomirova NK, Senin II, Philippov PP, Permyakov EA, Permyakov SE. Light-induced disulfide dimerization of recoverin under ex vivo and in vivo conditions. Free Radic Biol Med 2015; 83:283-95. [PMID: 25772009 DOI: 10.1016/j.freeradbiomed.2015.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/10/2015] [Accepted: 03/02/2015] [Indexed: 12/13/2022]
Abstract
Despite vast knowledge of the molecular mechanisms underlying photochemical damage of photoreceptors, linked to progression of age-related macular degeneration, information on specific protein targets of the light-induced oxidative stress is scarce. Here, we demonstrate that prolonged intense illumination (halogen bulb, 1500 lx, 1-5 h) of mammalian eyes under ex vivo (cow) or in vivo (rabbit) conditions induces disulfide dimerization of recoverin, a Ca(2+)-dependent inhibitor of rhodopsin kinase. Western blotting and mass spectrometry analysis of retinal extracts reveals illumination time-dependent accumulation of disulfide homodimers of recoverin and its higher order disulfide cross-linked species, including a minor fraction of mixed disulfides with intracellular proteins (tubulins, etc.). Meanwhile, monomeric bovine recoverin remains mostly reduced. These effects are accompanied by accumulation of disulfide homodimers of visual arrestin. Histological studies demonstrate that the light-induced oxidation of recoverin and arrestin occurs in intact retina (illumination for 2 h), while illumination for 5 h is associated with damage of the photoreceptor layer. A comparison of ex vivo levels of disulfide homodimers of bovine recoverin with redox dependence of its in vitro thiol-disulfide equilibrium (glutathione redox pair) gives the lowest estimate of redox potential in rod outer segments under illumination from -160 to -155 mV. Chemical crosslinking and dynamic light scattering data demonstrate an increased propensity of disulfide dimer of bovine recoverin to multimerization/aggregation. Overall, the oxidative stress caused by the prolonged intense illumination of retina might affect rhodopsin desensitization via concerted disulfide dimerization of recoverin and arrestin. The developed herein models of eye illumination are useful for studies of the light-induced thiol oxidation of visual proteins.
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Affiliation(s)
- Evgeni Yu Zernii
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia.
| | - Aliya A Nazipova
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Olga S Gancharova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Alexey S Kazakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Marina V Serebryakova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Dmitry V Zinchenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Natalya K Tikhomirova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Ivan I Senin
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Pavel P Philippov
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Eugene A Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290 Russia
| | - Sergei E Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290 Russia
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20
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Jansen F, Kalbe B, Scholz P, Fränzel B, Osterloh M, Wolters D, Hatt H, Neuhaus EM, Osterloh S. Biochemical Large-Scale Interaction Analysis of Murine Olfactory Receptors and Associated Signaling Proteins with Post-Synaptic Density 95, Drosophila Discs Large, Zona-Occludens 1 (PDZ) Domains. Mol Cell Proteomics 2015; 14:2072-84. [PMID: 25979994 DOI: 10.1074/mcp.m114.045997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family among mammalian membrane proteins and are capable of initiating numerous essential signaling cascades. Various GPCR-mediated pathways are organized into protein microdomains that can be orchestrated and regulated through scaffolding proteins, such as PSD-95/discs-large/ZO1 (PDZ) domain proteins. However, detailed binding characteristics of PDZ-GPCR interactions remain elusive because these interactions seem to be more complex than previously thought. To address this issue, we analyzed binding modalities using our established model system. This system includes the 13 individual PDZ domains of the multiple PDZ domain protein 1 (MUPP1; the largest PDZ protein), a broad range of murine olfactory receptors (a multifaceted gene cluster within the family of GPCRs), and associated olfactory signaling proteins. These proteins were analyzed in a large-scale peptide microarray approach and continuative interaction studies. As a result, we demonstrate that canonical binding motifs were not overrepresented among the interaction partners of MUPP1. Furthermore, C-terminal phosphorylation and distinct amino acid replacements abolished PDZ binding promiscuity. In addition to the described in vitro experiments, we identified new interaction partners within the murine olfactory epithelium using pull-down-based interactomics and could verify the partners through co-immunoprecipitation. In summary, the present study provides important insight into the complexity of the binding characteristics of PDZ-GPCR interactions based on olfactory signaling proteins, which could identify novel clinical targets for GPCR-associated diseases in the future.
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Affiliation(s)
- Fabian Jansen
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology
| | - Benjamin Kalbe
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology
| | - Paul Scholz
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology
| | - Benjamin Fränzel
- §Department of Analytical Chemistry, Faculty for Chemistry and Biochemistry, Ruhr-University Bochum, Germany
| | - Markus Osterloh
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology
| | - Dirk Wolters
- §Department of Analytical Chemistry, Faculty for Chemistry and Biochemistry, Ruhr-University Bochum, Germany
| | - Hanns Hatt
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology
| | | | - Sabrina Osterloh
- From the ‡Department of Cell Physiology, Faculty for Biology and Biotechnology,
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21
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Voolstra O, Spät P, Oberegelsbacher C, Claussen B, Pfannstiel J, Huber A. Light-dependent phosphorylation of the Drosophila inactivation no afterpotential D (INAD) scaffolding protein at Thr170 and Ser174 by eye-specific protein kinase C. PLoS One 2015; 10:e0122039. [PMID: 25799587 PMCID: PMC4370639 DOI: 10.1371/journal.pone.0122039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Drosophila inactivation no afterpotential D (INAD) is a PDZ domain-containing scaffolding protein that tethers components of the phototransduction cascade to form a supramolecular signaling complex. Here, we report the identification of eight INAD phosphorylation sites using a mass spectrometry approach. PDZ1, PDZ2, and PDZ4 each harbor one phosphorylation site, three phosphorylation sites are located in the linker region between PDZ1 and 2, one site is located between PDZ2 and PDZ3, and one site is located in the N-terminal region. Using a phosphospecific antibody, we found that INAD phosphorylated at Thr170/Ser174 was located within the rhabdomeres of the photoreceptor cells, suggesting that INAD becomes phosphorylated in this cellular compartment. INAD phosphorylation at Thr170/Ser174 depends on light, the phototransduction cascade, and on eye-Protein kinase C that is attached to INAD via one of its PDZ domains.
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Affiliation(s)
- Olaf Voolstra
- Department of Biosensorics, Institute of Physiology, Universität Hohenheim, Stuttgart, Germany
- * E-mail:
| | - Philipp Spät
- Department of Biosensorics, Institute of Physiology, Universität Hohenheim, Stuttgart, Germany
| | - Claudia Oberegelsbacher
- Department of Biosensorics, Institute of Physiology, Universität Hohenheim, Stuttgart, Germany
| | - Björn Claussen
- Department of Biosensorics, Institute of Physiology, Universität Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Mass Spectrometry Core Facility, Universität Hohenheim, Stuttgart, Germany
| | - Armin Huber
- Department of Biosensorics, Institute of Physiology, Universität Hohenheim, Stuttgart, Germany
- Mass Spectrometry Core Facility, Universität Hohenheim, Stuttgart, Germany
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22
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Consonni SV, Brouwer PM, van Slobbe ES, Bos JL. The PDZ domain of the guanine nucleotide exchange factor PDZGEF directs binding to phosphatidic acid during brush border formation. PLoS One 2014; 9:e98253. [PMID: 24858808 PMCID: PMC4032295 DOI: 10.1371/journal.pone.0098253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/30/2014] [Indexed: 12/30/2022] Open
Abstract
PDZGEF is a guanine nucleotide exchange factor for the small G protein Rap. It was recently found that PDZGEF contributes to establishment of intestinal epithelial polarity downstream of the kinase Lkb1. By binding to phosphatidic acid enriched at the apical membrane, PDZGEF locally activates Rap2a resulting in induction of brush border formation via a pathway that includes the polarity players TNIK, Mst4 and Ezrin. Here we show that the PDZ domain of PDZGEF is essential and sufficient for targeting PDZGEF to the apical membrane of polarized intestinal epithelial cells. Inhibition of PLD and consequently production of phosphatidic acid inhibitis targeting of PDZGEF to the plasma membrane. Furthermore, localization requires specific positively charged residues within the PDZ domain. We conclude that local accumulation of PDZGEF at the apical membrane during establishment of epithelial polarity is mediated by electrostatic interactions between positively charged side chains in the PDZ domain and negatively charged phosphatidic acid.
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Affiliation(s)
- Sarah V. Consonni
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Patricia M. Brouwer
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleonora S. van Slobbe
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes L. Bos
- Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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23
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Shieh BH, Kristaponyte I, Hong Y. Distinct roles of arrestin 1 protein in photoreceptors during Drosophila development. J Biol Chem 2014; 289:18526-34. [PMID: 24838243 DOI: 10.1074/jbc.m114.571224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arrestin regulates many facets of G-protein coupled receptor signaling. In Drosophila, Arrestin 1 (Arr1) is expressed at a lower level than Arrestin 2 (Arr2), and the role of Arr1 in visual physiology is less understood. Here we generated transgenic flies expressing enhanced green fluorescent protein tagged Arr1 (Arr1-eGFP) and explored its trafficking in live photoreceptors. We show that Arr1-eGFP is localized in the cytoplasm and displays light-dependent translocation to the rhabdomere possibly by interacting with photoactivated rhodopsin 1 (Rh1*). In the adult, translocation of Arr1-eGFP occurs with slower kinetics when compared with that of Arr2-eGFP. This slower kinetic activity may be attributable to a reduced level of phosphorylated Rh1*. Indeed, a reduced level of phosphorylated Rh1* recruits a lower level of Arr1-eGFP to rhabdomeres. To investigate whether Arr1 is required for the deactivation of phosphorylated Rh1*, we show that in flies with reduced Arr1 prolonged depolarizing afterpotential can be triggered with fewer light pulses, indicating that inactivation of phosphorylated Rh1* is compromised when the Arr1 level is reduced. Consistently, Arr1 is no longer required for deactivation of Rh1 in flies expressing phosphorylation-deficient Rh1. Previously it was reported that Arr1 displays light-dependent internalization. Unexpectedly, in adult photoreceptors we failed to observe endocytosis of Arr1-eGFP. In contrast, we show that in pupal photoreceptors Arr1-eGFP becomes internalized and sequestered in vesicles within the cytoplasm. Taken together, we propose that Arr1 plays distinct roles during development and adulthood. Arr1 orchestrates the recycling of phosphorylated Rh1* in pupae whereas it regulates the deactivation in adult.
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Affiliation(s)
- Bih-Hwa Shieh
- From the Department of Pharmacology and the Center for Molecular Neuroscience and the Vision Research Center, Vanderbilt University, Nashville, Tennessee 37232
| | - Inga Kristaponyte
- From the Department of Pharmacology and the Center for Molecular Neuroscience and the Vision Research Center, Vanderbilt University, Nashville, Tennessee 37232
| | - Yuan Hong
- From the Department of Pharmacology and the Center for Molecular Neuroscience and the Vision Research Center, Vanderbilt University, Nashville, Tennessee 37232
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24
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Abstract
Nuclear magnetic resonance (NMR) is a powerful technique capable of monitoring a wide range of motions in proteins on a per residue basis. A variety of (2)H relaxation experiments have been developed for monitoring side-chain methyl group motions on the picosecond-nanosecond timescale. These experiments enable determination of the order parameter, S (2) axis, which reports on the rigidity of the C-CH3 bond for side-chain methyl groups. The application of a commonly used subset of these experiments is described in this chapter. It is intended to serve as a practical guide to investigators interested in monitoring side-chain motions.
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Affiliation(s)
- Chad M Petit
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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25
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Abstract
The Drosophila "transient receptor potential" channel is the prototypical TRP channel, belonging to and defining the TRPC subfamily. Together with a second TRPC channel, trp-like (TRPL), TRP mediates the transducer current in the fly's photoreceptors. TRP and TRPL are also implicated in olfaction and Malpighian tubule function. In photoreceptors, TRP and TRPL are localised in the ~30,000 packed microvilli that form the photosensitive "rhabdomere"-a light-guiding rod, housing rhodopsin and the rest of the phototransduction machinery. TRP (but not TRPL) is assembled into multimolecular signalling complexes by a PDZ-domain scaffolding protein (INAD). TRPL (but not TRP) undergoes light-regulated translocation between cell body and rhabdomere. TRP and TRPL are also found in photoreceptor synapses where they may play a role in synaptic transmission. Like other TRPC channels, TRP and TRPL are activated by a G protein-coupled phospholipase C (PLCβ4) cascade. Although still debated, recent evidence indicates the channels can be activated by a combination of PIP2 depletion and protons released by the PLC reaction. PIP2 depletion may act mechanically as membrane area is reduced by cleavage of PIP2's bulky inositol headgroup. TRP, which dominates the light-sensitive current, is Ca(2+) selective (P Ca:P Cs >50:1), whilst TRPL has a modest Ca(2+) permeability (P Ca:P Cs ~5:1). Ca(2+) influx via the channels has profound positive and negative feedback roles, required for the rapid response kinetics, with Ca(2+) rapidly facilitating TRP (but not TRPL) and also inhibiting both channels. In trp mutants, stimulation by light results in rapid depletion of microvillar PIP2 due to lack of Ca(2+) influx required to inhibit PLC. This accounts for the "transient receptor potential" phenotype that gives the family its name and, over a period of days, leads to light-dependent retinal degeneration. Gain-of-function trp mutants with uncontrolled Ca(2+) influx also undergo retinal degeneration due to Ca(2+) cytotoxicity. In vertebrate retina, mice knockout studies suggest that TRPC6 and TRPC7 mediate a PLCβ4-activated transducer current in intrinsically photosensitive retinal ganglion cells, expressing melanopsin. TRPA1 has been implicated as a "photo-sensing" TRP channel in human melanocytes and light-sensitive neurons in the body wall of Drosophila.
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26
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Liu J, Duan X, Sun J, Yin Y, Li G, Wang L, Liu B. Bi-factor analysis based on noise-reduction (BIFANR): a new algorithm for detecting coevolving amino acid sites in proteins. PLoS One 2013; 8:e79764. [PMID: 24278175 PMCID: PMC3835919 DOI: 10.1371/journal.pone.0079764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/29/2013] [Indexed: 11/23/2022] Open
Abstract
Previous statistical analyses have shown that amino acid sites in a protein evolve in a correlated way instead of independently. Even though located distantly in the linear sequence, the coevolved amino acids could be spatially adjacent in the tertiary structure, and constitute specific protein sectors. Moreover, these protein sectors are independent of one another in structure, function, and even evolution. Thus, systematic studies on protein sectors inside a protein will contribute to the clarification of protein function. In this paper, we propose a new algorithm BIFANR (Bi-factor Analysis Based on Noise-reduction) for detecting protein sectors in amino acid sequences. After applying BIFANR on S1A family and PDZ family, we carried out internal correlation test, statistical independence test, evolutionary rate analysis, evolutionary independence analysis, and function analysis to assess the prediction. The results showed that the amino acids in certain predicted protein sector are closely correlated in structure, function, and evolution, while protein sectors are nearly statistically independent. The results also indicated that the protein sectors have distinct evolutionary directions. In addition, compared with other algorithms, BIFANR has higher accuracy and robustness under the influence of noise sites.
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Affiliation(s)
- Juntao Liu
- School of Mathematics, Shandong University, Jinan, China
| | - Xiaoyun Duan
- School of Life Science, Shandong University, Jinan, China
| | - Jianyang Sun
- School of Mathematics, Shandong University, Jinan, China
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, China
| | - Lushan Wang
- School of Life Science, Shandong University, Jinan, China
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, China
- * E-mail: Bingqiang Liu:
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27
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Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures. Biochem J 2013; 455:1-14. [DOI: 10.1042/bj20130783] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PDZ domains are highly abundant protein–protein interaction modules and are often found in multidomain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and clustering receptors and ion channels at defined membrane regions, organizing and targeting signalling complexes at specific cellular compartments, interfacing cytoskeletal structures with membranes, and maintaining various cellular structures. PDZ domains, each with ~90-amino-acid residues folding into a highly similar structure, are best known to bind to short C-terminal tail peptides of their target proteins. A series of recent studies have revealed that, in addition to the canonical target-binding mode, many PDZ–target interactions involve amino acid residues beyond the regular PDZ domain fold, which we refer to as extensions. Such extension sequences often form an integral structural and functional unit with the attached PDZ domain, which is defined as a PDZ supramodule. Correspondingly, PDZ-domain-binding sequences from target proteins are frequently found to require extension sequences beyond canonical short C-terminal tail peptides. Formation of PDZ supramodules not only affords necessary binding specificities and affinities demanded by physiological functions of PDZ domain targets, but also provides regulatory switches to be built in the PDZ–target interactions. At the 20th anniversary of the discovery of PDZ domain proteins, we try to summarize structural features and target-binding properties of such PDZ supramodules emerging from studies in recent years.
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28
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Dell'Orco D. A physiological role for the supramolecular organization of rhodopsin and transducin in rod photoreceptors. FEBS Lett 2013; 587:2060-6. [PMID: 23684654 DOI: 10.1016/j.febslet.2013.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Vertebrate vision in rod photoreceptors begins when a photon hits the visual pigment rhodopsin (Rh) and triggers the phototransduction cascade. Although the fine biochemical and biophysical details of this paradigmatic signalling pathway have been studied for decades, phototransduction still presents unclear mechanistic aspects. Increasing lines of evidence suggest that the visual pigment rhodopsin (Rh) is natively organized in dimers on the surface of disc membranes, and may form higher order "paracrystalline" assemblies, which are not easy to reconcile with the classical collision-coupling mechanistic scenario evoked to explain the extremely fast molecular processes required in phototransduction. The questioned and criticized existence of paracrystalline Rh rafts can be fully accepted only if it can be explained in functional terms by a solid mechanistic picture. Here we discuss how recent data suggest a physiological role for supramolecular assemblies of Rh and its cognate G protein transducin (Gt), which by forming transient complexes in the dark may ensure rapid activation of the cascade even in a crowded environment that, according to the classical picture, would otherwise stop the cascade.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Life Sciences and Reproduction, Section of Biological Chemistry, and Centre for Biomedical Computing, University of Verona, Strada le Grazie 8, 37134 Verona, Italy.
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29
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Urano D, Chen JG, Botella JR, Jones AM. Heterotrimeric G protein signalling in the plant kingdom. Open Biol 2013. [PMID: 23536550 DOI: 10.1098/rsob.12.0186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
In animals, heterotrimeric G proteins, comprising α-, β-and γ-subunits, perceive extracellular stimuli through cell surface receptors, and transmit signals to ion channels, enzymes and other effector proteins to affect numerous cellular behaviours. In plants, G proteins have structural similarities to the corresponding molecules in animals but transmit signals by atypical mechanisms and effector proteins to control growth, cell proliferation, defence, stomate movements, channel regulation, sugar sensing and some hormonal responses. In this review, we summarize the current knowledge on the molecular regulation of plant G proteins, their effectors and the physiological functions studied mainly in two model organisms: Arabidopsis thaliana and rice (Oryza sativa). We also look at recent progress on structural analyses, systems biology and evolutionary studies.
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Affiliation(s)
- Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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30
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Urano D, Chen JG, Botella JR, Jones AM. Heterotrimeric G protein signalling in the plant kingdom. Open Biol 2013; 3:120186. [PMID: 23536550 PMCID: PMC3718340 DOI: 10.1098/rsob.120186] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/05/2013] [Indexed: 12/18/2022] Open
Abstract
In animals, heterotrimeric G proteins, comprising α-, β-and γ-subunits, perceive extracellular stimuli through cell surface receptors, and transmit signals to ion channels, enzymes and other effector proteins to affect numerous cellular behaviours. In plants, G proteins have structural similarities to the corresponding molecules in animals but transmit signals by atypical mechanisms and effector proteins to control growth, cell proliferation, defence, stomate movements, channel regulation, sugar sensing and some hormonal responses. In this review, we summarize the current knowledge on the molecular regulation of plant G proteins, their effectors and the physiological functions studied mainly in two model organisms: Arabidopsis thaliana and rice (Oryza sativa). We also look at recent progress on structural analyses, systems biology and evolutionary studies.
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Affiliation(s)
- Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alan M. Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
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31
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Abstract
Modular protein interaction domains (PIDs) that recognize linear peptide motifs are found in hundreds of proteins within the human genome. Some PIDs such as SH2, 14-3-3, Chromo, and Bromo domains serve to recognize posttranslational modification (PTM) of amino acids (such as phosphorylation, acetylation, methylation, etc.) and translate these into discrete cellular responses. Other modules such as SH3 and PSD-95/Discs-large/ZO-1 (PDZ) domains recognize linear peptide epitopes and serve to organize protein complexes based on localization and regions of elevated concentration. In both cases, the ability to nucleate-specific signaling complexes is in large part dependent on the selectivity of a given protein module for its cognate peptide ligand. High-throughput (HTP) analysis of peptide-binding domains by peptide or protein arrays, phage display, mass spectrometry, or other HTP techniques provides new insight into the potential protein-protein interactions prescribed by individual or even whole families of modules. Systems level analyses have also promoted a deeper understanding of the underlying principles that govern selective protein-protein interactions and how selectivity evolves. Lastly, there is a growing appreciation for the limitations and potential pitfalls associated with HTP analysis of protein-peptide interactomes. This review will examine some of the common approaches utilized for large-scale studies of PIDs and suggest a set of standards for the analysis and validation of datasets from large-scale studies of peptide-binding modules. We will also highlight how data from large-scale studies of modular interaction domain families can provide insight into systems level properties such as the linguistics of selective interactions.
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Affiliation(s)
- Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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Abstract
Arrestins belong to a family of multifunctional adaptor proteins that regulate internalization of diverse receptors including G-protein-coupled receptors (GPCRs). Defects associated with endocytosis of GPCRs have been linked to human diseases. We used enhanced green fluorescent protein-tagged arrestin 2 (Arr2) to monitor the turnover of the major rhodopsin (Rh1) in live Drosophila. We demonstrate that during degeneration of norpA(P24) photoreceptors the loss of Rh1 is parallel to the disappearance of rhabdomeres, the specialized visual organelle that houses Rh1. The cause of degeneration in norpA(P24) is the failure to activate CaMKII (Ca(2+)/calmodulin-dependent protein kinase II) and retinal degeneration C (RDGC) because of a loss of light-dependent Ca(2+) entry. A lack of activation in CaMKII, which phosphorylates Arr2, leads to hypophosphorylated Arr2, while a lack of activation of RDGC, which dephosphorylates Rh1, results in hyperphosphorylated Rh1. We investigated how reversible phosphorylation of Rh1 and Arr2 contributes to photoreceptor degeneration. To uncover the consequence underlying a lack of CaMKII activation, we characterized ala(1) flies in which CaMKII was suppressed by an inhibitory peptide, and showed that morphology of rhabdomeres was not affected. In contrast, we found that expression of phosphorylation-deficient Rh1s, which either lack the C terminus or contain Ala substitution in the phosphorylation sites, was able to prevent degeneration of norpA(P24) photoreceptors. This suppression is not due to a loss of Arr2 interaction. Importantly, co-expression of these modified Rh1s offered protective effects, which greatly delayed photoreceptor degeneration. Together, we conclude that phosphorylation of Rh1 is the major determinant that orchestrates its internalization leading to retinal degeneration.
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Bradley JM, Marritt SJ, Kihlken MA, Haynes K, Hemmings AM, Berks BC, Cheesman MR, Butt JN. Redox and chemical activities of the hemes in the sulfur oxidation pathway enzyme SoxAX. J Biol Chem 2012; 287:40350-9. [PMID: 23060437 DOI: 10.1074/jbc.m112.396192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND SoxAX enzymes initiate microbial oxidation of reduced inorganic sulfur compounds. Their catalytic mechanism is unknown. RESULTS Cyanide displaces the CysS(-) ligand to the active site heme following reduction by S(2)O(4)(2-) but not Eu(II). CONCLUSION An active site heme ligand becomes labile on exposure to substrate analogs. SIGNIFICANCE Elucidation of SoxAX mechanism is necessary to understand a widespread pathway for sulfur compound oxidation. SoxAX enzymes couple disulfide bond formation to the reduction of cytochrome c in the first step of the phylogenetically widespread Sox microbial sulfur oxidation pathway. Rhodovulum sulfidophilum SoxAX contains three hemes. An electrochemical cell compatible with magnetic circular dichroism at near infrared wavelengths has been developed to resolve redox and chemical properties of the SoxAX hemes. In combination with potentiometric titrations monitored by electronic absorbance and EPR, this method defines midpoint potentials (E(m)) at pH 7.0 of approximately +210, -340, and -400 mV for the His/Met, His/Cys(-), and active site His/CysS(-)-ligated heme, respectively. Exposing SoxAX to S(2)O(4)(2-), a substrate analog with E(m) ~-450 mV, but not Eu(II) complexed with diethylene triamine pentaacetic acid (E(m) ~-1140 mV), allows cyanide to displace the cysteine persulfide (CysS(-)) ligand to the active site heme. This provides the first evidence for the dissociation of CysS(-) that has been proposed as a key event in SoxAX catalysis.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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Pan CQ, Sudol M, Sheetz M, Low BC. Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling. Cell Signal 2012; 24:2143-65. [PMID: 22743133 DOI: 10.1016/j.cellsig.2012.06.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 05/22/2012] [Accepted: 06/16/2012] [Indexed: 01/14/2023]
Abstract
Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.
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Affiliation(s)
- Catherine Qiurong Pan
- Cell Signaling and Developmental Biology Laboratory, Department of Biological Sciences, National University of Singapore, Republic of Singapore.
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Torchio GM, Ermácora MR, Sica MP. Equilibrium unfolding of the PDZ domain of β2-syntrophin. Biophys J 2012; 102:2835-44. [PMID: 22735534 DOI: 10.1016/j.bpj.2012.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 04/23/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022] Open
Abstract
β2-syntrophin, a dystrophin-associated protein, plays a pivotal role in insulin secretion by pancreatic β-cells. It contains a PDZ domain (β2S-PDZ) that, in complex with protein-tyrosine phosphatase ICA512, anchors the dense insulin granules to actin filaments. The phosphorylation state of β2-syntrophin allosterically regulates the affinity of β2S-PDZ for ICA512, and the disruption of the complex triggers the mobilization of the insulin granule stores. Here, we investigate the thermal unfolding of β2S-PDZ at different pH and urea concentrations. Our results indicate that, unlike other PDZ domains, β2S-PDZ is marginally stable. Thermal denaturation experiments show broad transitions and cold denaturation, and a two-state model fit reveals a significant unfolded fraction under physiological conditions. Furthermore, T(m) and T(max) denaturant-dependent shifts and noncoincidence of melting curves monitored at different wavelengths suggest that two-state and three-state models fail to explain the equilibrium data properly and are in better agreement with a downhill scenario. Its higher stability at pH >9 and the results of molecular dynamics simulations indicate that this behavior of β2S-PDZ might be related to its charge distribution. All together, our results suggest a link between the conformational plasticity of the native ensemble of this PDZ domain and the regulation of insulin secretion.
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Affiliation(s)
- Gabriela María Torchio
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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Stochastic, adaptive sampling of information by microvilli in fly photoreceptors. Curr Biol 2012; 22:1371-80. [PMID: 22704990 PMCID: PMC3420010 DOI: 10.1016/j.cub.2012.05.047] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/14/2012] [Accepted: 05/25/2012] [Indexed: 01/02/2023]
Abstract
Background In fly photoreceptors, light is focused onto a photosensitive waveguide, the rhabdomere, consisting of tens of thousands of microvilli. Each microvillus is capable of generating elementary responses, quantum bumps, in response to single photons using a stochastically operating phototransduction cascade. Whereas much is known about the cascade reactions, less is known about how the concerted action of the microvilli population encodes light changes into neural information and how the ultrastructure and biochemical machinery of photoreceptors of flies and other insects evolved in relation to the information sampling and processing they perform. Results We generated biophysically realistic fly photoreceptor models, which accurately simulate the encoding of visual information. By comparing stochastic simulations with single cell recordings from Drosophila photoreceptors, we show how adaptive sampling by 30,000 microvilli captures the temporal structure of natural contrast changes. Following each bump, individual microvilli are rendered briefly (∼100–200 ms) refractory, thereby reducing quantum efficiency with increasing intensity. The refractory period opposes saturation, dynamically and stochastically adjusting availability of microvilli (bump production rate: sample rate), whereas intracellular calcium and voltage adapt bump amplitude and waveform (sample size). These adapting sampling principles result in robust encoding of natural light changes, which both approximates perceptual contrast constancy and enhances novel events under different light conditions, and predict information processing across a range of species with different visual ecologies. Conclusions These results clarify why fly photoreceptors are structured the way they are and function as they do, linking sensory information to sensory evolution and revealing benefits of stochasticity for neural information processing.
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Abstract
The oxidation of cysteine sulphydryl in proteins produces sulphenic acid that can form a reversible disulphide bond with another cysteine. The disulphide bond formation often triggers switches in protein structure and activity, especially when the distance between the two cysteine sulphur atoms is longer than the resulting disulphide bond distance. As an early example for the reversible disulphide bond-mediated functional switches, the reduced and oxidized forms of the bacterial transcription factor OxyR were characterized by X-ray crystallography. Recently, the Drosophila vision signalling protein, the association of inactivation-no-afterpotential D (INAD) was analysed by structural and functional methods. The two conserved cysteines of INAD were found to cycle between reduced and oxidized states during the light signal processing in Drosophila eyes, which was achieved by conformation dependent modulation of the disulphide bond redox potential. The production of the hypertension control peptide angiotensins was also shown to be controlled by the reversible disulphide bond in the precursor protein angiotensinogen. The crystal structure of the complex of angiotensiongen with its processing enzyme renin elucidated the role of the disulphide bond in stabilizing the precursor-enzyme complex facilitating the production of angiotensins. The increasing importance of the disulphide bond-mediated redox switches in normal and diseased states has implications in the development of novel antioxidant-based therapeutic approaches.
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Affiliation(s)
- Seong Eon Ryu
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, Korea.
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38
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Ivarsson Y. Plasticity of PDZ domains in ligand recognition and signaling. FEBS Lett 2012; 586:2638-47. [PMID: 22576124 PMCID: PMC7094393 DOI: 10.1016/j.febslet.2012.04.015] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022]
Abstract
The PDZ domain is a protein-protein interacting module that plays an important role in the organization of signaling complexes. The recognition of short intrinsically disordered C-terminal peptide motifs is the archetypical PDZ function, but the functional repertoire of this versatile module also includes recognition of internal peptide sequences, dimerization and phospholipid binding. The PDZ function can be tuned by various means such as allosteric effects, changes of physiological buffer conditions and phosphorylation of PDZ domains and/or ligands, which poses PDZ domains as dynamic regulators of cell signaling. This review is focused on the plasticity of the PDZ interactions.
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Affiliation(s)
- Ylva Ivarsson
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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39
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Montell C. Drosophila visual transduction. Trends Neurosci 2012; 35:356-63. [PMID: 22498302 DOI: 10.1016/j.tins.2012.03.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 03/06/2012] [Accepted: 03/11/2012] [Indexed: 11/26/2022]
Abstract
Visual transduction in the Drosophila compound eye functions through a pathway that couples rhodopsin to phospholipase C (PLC) and the opening of transient receptor potential (TRP) channels. This cascade differs from phototransduction in mammalian rods and cones, but is remarkably similar to signaling in mammalian intrinsically photosensitive retinal ganglion cells (ipRGCs). In this review, I focus on recent advances in the fly visual system, including the discovery of a visual cycle and insights into the machinery and mechanisms involved in generating a light response in photoreceptor cells.
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Affiliation(s)
- Craig Montell
- Departments of Biological Chemistry and Neuroscience, Center for Sensory Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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40
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Luck K, Charbonnier S, Travé G. The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains. FEBS Lett 2012; 586:2648-61. [PMID: 22709956 DOI: 10.1016/j.febslet.2012.03.056] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/26/2012] [Accepted: 03/27/2012] [Indexed: 12/18/2022]
Abstract
The canonical binding mode of PDZ domains to target motifs involves a small interface, unlikely to fully account for PDZ-target interaction specificities. Here, we review recent work on sequence context, defined as the regions surrounding not only the PDZ domains but also their target motifs. We also address the theoretical problem of defining the core of PDZ domains and the practical issue of designing PDZ constructs. Sequence context is found to introduce structural diversity, to impact the stability and solubility of constructs, and to deeply influence binding affinity and specificity, thereby increasing the difficulty of predicting PDZ-motif interactions. We expect that sequence context will have similar importance for other protein interactions mediated by globular domains binding to short linear motifs.
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Affiliation(s)
- Katja Luck
- UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Bd Sébastien Brant, BP 10413, 67412 Illkirch, Cedex, France.
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41
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Phototransduction in Drosophila. SCIENCE CHINA-LIFE SCIENCES 2012; 55:27-34. [PMID: 22314488 DOI: 10.1007/s11427-012-4272-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/12/2011] [Indexed: 10/14/2022]
Abstract
The Drosophila visual transduction is the fastest known G protein-coupled signaling cascade and has been served as a model for understanding the molecular mechanisms of other G protein-coupled signaling cascades. Numbers of components in visual transduction machinery have been identified. Based on the functional characterization of these genes, a model for Drosophila phototransduction has been outlined, including rhodopsin activation, phosphoinoside signaling, and the opening of TRP and TRPL channels. Recently, the characterization of mutants, showing slow termination, revealed the physiological significance and the mechanism of rapid termination of light response.
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42
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Pak WL, Shino S, Leung HT. PDA (prolonged depolarizing afterpotential)-defective mutants: the story of nina's and ina's--pinta and santa maria, too. J Neurogenet 2012; 26:216-37. [PMID: 22283778 PMCID: PMC3433705 DOI: 10.3109/01677063.2011.642430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Our objective is to present a comprehensive view of the PDA (prolonged depolarizing afterpotential)-defective Drosophila mutants, nina's and ina's, from the discussion of the PDA and the PDA-based mutant screening strategy to summaries of the knowledge gained through the studies of mutants generated using the strategy. The PDA is a component of the light-evoked photoreceptor potential that is generated when a substantial fraction of rhodopsin is photoconverted to its active form, metarhodopsin. The PDA-based mutant screening strategy was adopted to enhance the efficiency and efficacy of ERG (electroretinogram)-based screening for identifying phototransduction-defective mutants. Using this strategy, two classes of PDA-defective mutants were identified and isolated, nina and ina, each comprising multiple complementation groups. The nina mutants are characterized by allele-dependent reduction in the major rhodopsin, Rh1, whereas the ina mutants display defects in some aspects of functions related to the transduction channel, TRP (transient receptor potential). The signaling proteins that have been identified and elucidated through the studies of nina mutants include the Drosophila opsin protein (NINAE), the chaperone protein for nascent opsin (NINAA), and the multifunctional protein, NINAC, required in multiple steps of the Drosophila phototransduction cascade. Also identified by the nina mutants are some of the key enzymes involved in the biogenesis of the rhodopsin chromophore. As for the ina mutants, they led to the discovery of the scaffold protein, INAD, responsible for the nucleation of the supramolecular signaling complex. Also identified by the ina mutants is one of the key members of the signaling complex, INAC (ePKC), and two other proteins that are likely to be important, though their roles in the signaling cascade have not yet been fully elucidated. In most of these cases, the protein identified is the first member of its class to be so recognized.
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Affiliation(s)
- William L Pak
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
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43
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A dynamic scaffolding mechanism for rhodopsin and transducin interaction in vertebrate vision. Biochem J 2012; 440:263-71. [PMID: 21843151 DOI: 10.1042/bj20110871] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The early steps in vertebrate vision require fast interactions between Rh (rhodopsin) and Gt (transducin), which are classically described by a collisional coupling mechanism driven by the free diffusion of monomeric proteins on the disc membranes of rod and cone cells. Recent findings, however, point to a very low mobility for Rh and support a substantially different supramolecular organization. Moreover, Rh-G(t) interactions seem to possibly occur even prior to light stimuli, which is also difficult to reconcile with the classical scenario. We investigated the kinetics of interaction between native Rh and G(t) in different conditions by surface plasmon resonance and analysed the results in the general physiological context by employing a holistic systems modelling approach. The results from the present study point to a mechanism that is intermediate between pure collisional coupling and physical scaffolding. Such a 'dynamic scaffolding', in which prevalently dimeric Rh and G(t) interact in the dark by forming transient complexes (~25% of G(t) is precoupled to Rh), does not slow down the phototransduction cascade, but is compatible with the observed photoresponses on a broad scale of light stimuli. We conclude that Rh molecules and Rh-G(t) complexes can both absorb photons and trigger the visual cascade.
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Du QS, Meng JZ, Wang CH, Long SY, Huang RB. Structural position correlation analysis (SPCA) for protein family. PLoS One 2011; 6:e28206. [PMID: 22163002 PMCID: PMC3230615 DOI: 10.1371/journal.pone.0028206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/03/2011] [Indexed: 11/18/2022] Open
Abstract
Background The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by two or three catalytic residues with the collaboration of several functional residues at key positions. Communication signals are conducted in a position network, adjusting the biological functions in the protein family. Methodology A computational approach, namely structural position correlation analysis (SPCA), is developed to analyze the correlation relationship between structural segments (or positions). The basic hypothesis of SPCA is that in a protein family the structural conservation is more important than the sequence conservation, and the local structural changes may contain information of biology functional evolution. A standard protein P(0) is defined in a protein family, which consists of the most-frequent amino acids and takes the average structure of the protein family. The foundational variables of SPCA is the structural position displacements between the standard protein P(0) and individual proteins Pi of the family. The structural positions are organized as segments, which are the stable units in structural displacements of the protein family. The biological function differences of protein members are determined by the position structural displacements of individual protein Pi to the standard protein P(0). Correlation analysis is used to analyze the communication network among segments. Conclusions The structural position correlation analysis (SPCA) is able to find the correlation relationship among the structural segments (or positions) in a protein family, which cannot be detected by the amino acid sequence and frequency-based methods. The functional communication network among the structural segments (or positions) in protein family, revealed by SPCA approach, well illustrate the distantly allosteric interactions, and contains valuable information for protein engineering study.
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Affiliation(s)
- Qi-Shi Du
- State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China.
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Hardie RC. Phototransduction mechanisms in Drosophila microvillar photoreceptors. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/wmts.20] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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46
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Zhang J, Petit CM, King DS, Lee AL. Phosphorylation of a PDZ domain extension modulates binding affinity and interdomain interactions in postsynaptic density-95 (PSD-95) protein, a membrane-associated guanylate kinase (MAGUK). J Biol Chem 2011; 286:41776-41785. [PMID: 21965656 DOI: 10.1074/jbc.m111.272583] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Postsynaptic density-95 is a multidomain scaffolding protein that recruits glutamate receptors to postsynaptic sites and facilitates signal processing and connection to the cytoskeleton. It is the leading member of the membrane-associated guanylate kinase family of proteins, which are defined by the PSD-95/Discs large/ZO-1 (PDZ)-Src homology 3 (SH3)-guanylate kinase domain sequence. We used NMR to show that phosphorylation of conserved tyrosine 397, which occurs in vivo and is located in an atypical helical extension (α3), initiates a rapid equilibrium of docked and undocked conformations. Undocking reduced ligand binding affinity allosterically and weakened the interaction of PDZ3 with SH3 even though these domains are separated by a ~25-residue linker. Additional phosphorylation at two linker sites further disrupted the interaction, implicating α3 and the linker in tuning interdomain communication. These experiments revealed a novel mode of regulation by a detachable PDZ element and offer a first glimpse at the dynamic interaction of PDZ and SH3-guanylate kinase domains in membrane-associated guanylate kinases.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Chad M Petit
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David S King
- Howard Hughes Medical Institute Mass Spectrometry Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599.
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McCann JJ, Zheng L, Chiantia S, Bowen ME. Domain orientation in the N-Terminal PDZ tandem from PSD-95 is maintained in the full-length protein. Structure 2011; 19:810-20. [PMID: 21645852 DOI: 10.1016/j.str.2011.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/24/2011] [Accepted: 02/21/2011] [Indexed: 12/19/2022]
Abstract
Tandem PDZ domains have been suggested to form structurally independent supramodules. However, dissimilarity between crystallography and NMR models emphasize their malleable conformation. Studies in full-length scaffold proteins are needed to examine the effect of tertiary interactions within their native context. Using single-molecule fluorescence to characterize the N-terminal PDZ tandem in PSD-95, we provide the first direct evidence that PDZ tandems can be structurally independent within a full-length scaffold protein. Molecular refinement using our data converged on a single structure with an antiparallel alignment of the ligand-binding sites. Devoid of interaction partners, single-molecule conditions captured PSD-95 in its unbound, ground state. Interactions between PDZ domains could not be detected while fluctuation correlation spectroscopy showed that other conformations are dynamically sampled. We conclude that ultra-weak interactions stabilize the conformation providing a "low-relief" energy landscape that allows the domain orientation to be flipped by environmental interactions.
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Affiliation(s)
- James J McCann
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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48
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Affiliation(s)
- Kian L. Tan
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
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49
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Liu W, Wen W, Wei Z, Yu J, Ye F, Liu CH, Hardie R, Zhang M. The INAD Scaffold Is a Dynamic, Redox-Regulated Modulator of Signaling in the Drosophila Eye. Cell 2011; 145:1088-101. [DOI: 10.1016/j.cell.2011.05.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 03/08/2011] [Accepted: 05/04/2011] [Indexed: 01/08/2023]
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50
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Abstract
A highly regioselective hydroformylation of allylic alcohols is reported toward the synthesis of β-hydroxy-acid and aldehyde products. The selectivity is achieved through the use of a ligand that reversibly binds to alcohols in situ, allowing for a directed hydroformylation to occur. The application to trisubstituted olefins was also demonstrated, which yields a single diastereomer product consistent with a stereospecific addition of CO and hydrogen.
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Affiliation(s)
| | - Omar A. De Paolis
- Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467-3860
| | - Ka H. Cheng
- Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467-3860
| | - Kian L. Tan
- Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467-3860
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