1
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Wang Y, Wang E, Anany M, Füllsack S, Huo YH, Dutta S, Ji B, Hoeppner LH, Kilari S, Misra S, Caulfield T, Vander Kooi CW, Wajant H, Mukhopadhyay D. The crosstalk between neuropilin-1 and tumor necrosis factor-α in endothelial cells. Front Cell Dev Biol 2024; 12:1210944. [PMID: 38994453 PMCID: PMC11236538 DOI: 10.3389/fcell.2024.1210944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
Tumor necrosis factor-α (TNFα) is a master cytokine which induces expression of chemokines and adhesion molecules, such as intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1), in endothelial cells to initiate the vascular inflammatory response. In this study, we identified neuropilin-1 (NRP1), a co-receptor of several structurally diverse ligands, as a modulator of TNFα-induced inflammatory response of endothelial cells. NRP1 shRNA expression suppressed TNFα-stimulated leukocyte adhesion and expression of ICAM-1 and VCAM-1 in human umbilical vein endothelial cells (HUVECs). Likewise, it reduced TNFα-induced phosphorylation of MAPK p38 but did not significantly affect other TNF-induced signaling pathways, such as the classical NFκB and the AKT pathway. Immunofluorescent staining demonstrated co-localization of NRP1 with the two receptors of TNF, TNFR1 and TNFR2. Co-immunoprecipitation further confirmed that NRP1 was in the same protein complex or membrane compartment as TNFR1 and TNFR2, respectively. Modulation of NRP1 expression, however, neither affected TNFR levels in the cell membrane nor the receptor binding affinities of TNFα. Although a direct interface between NRP1 and TNFα/TNFR1 appeared possible from a protein docking model, a direct interaction was not supported by binding assays in cell-free microplates and cultured cells. Furthermore, TNFα was shown to downregulate NRP1 in a time-dependent manner through TNFR1-NFκB pathway in HUVECs. Taken together, our study reveals a novel reciprocal crosstalk between NRP1 and TNFα in vascular endothelial cells.
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Affiliation(s)
- Ying Wang
- Department of Cardiovascular Medicine, Rochester, MN, United States
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Enfeng Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Mohamed Anany
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
- Department of Microbial Biotechnology, Institute of Biotechnology, National Research Centre, Giza, Egypt
| | - Simone Füllsack
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Yu Henry Huo
- Department of Cardiovascular Medicine, Rochester, MN, United States
| | - Shamit Dutta
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Baoan Ji
- Department of Cancer Biology, Jacksonville, FL, United States
| | - Luke H Hoeppner
- The Hormel Institute, University of Minnesota, Austin, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | | | - Sanjay Misra
- Department of Radiology, Mayo Clinic, Rochester, MN, United States
| | - Thomas Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States
| | - Harald Wajant
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, United States
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2
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Kiper AK, Wegner S, Kadala A, Rinné S, Schütte S, Winter Z, Bertoune MAR, Touska F, Matschke V, Wrobel E, Streit AK, Lang F, Schmidt C, Schulze-Bahr E, Schäfer MKH, Voelkl J, Seebohm G, Zimmermann K, Decher N. KCNQ1 is an essential mediator of the sex-dependent perception of moderate cold temperatures. Proc Natl Acad Sci U S A 2024; 121:e2322475121. [PMID: 38857404 PMCID: PMC11194602 DOI: 10.1073/pnas.2322475121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Low temperatures and cooling agents like menthol induce cold sensation by activating the peripheral cold receptors TRPM8 and TRPA1, cation channels belonging to the TRP channel family, while the reduction of potassium currents provides an additional and/or synergistic mechanism of cold sensation. Despite extensive studies over the past decades to identify the molecular receptors that mediate thermosensation, cold sensation is still not fully understood and many cold-sensitive peripheral neurons do not express the well-established cold sensor TRPM8. We found that the voltage-gated potassium channel KCNQ1 (Kv7.1), which is defective in cardiac LQT1 syndrome, is, in addition to its known function in the heart, a highly relevant and sex-specific sensor of moderately cold temperatures. We found that KCNQ1 is expressed in skin and dorsal root ganglion neurons, is sensitive to menthol and cooling agents, and is highly sensitive to moderately cold temperatures, in a temperature range at which TRPM8 is not thermosensitive. C-fiber recordings from KCNQ1-/- mice displayed altered action potential firing properties. Strikingly, only male KCNQ1-/- mice showed substantial deficits in cold avoidance at moderately cold temperatures, with a strength of the phenotype similar to that observed in TRPM8-/- animals. While sex-dependent differences in thermal sensitivity have been well documented in humans and mice, KCNQ1 is the first gene reported to play a role in sex-specific temperature sensation. Moreover, we propose that KCNQ1, together with TRPM8, is a key instrumentalist that orchestrates the range and intensity of cold sensation.
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Affiliation(s)
- Aytug K. Kiper
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Sven Wegner
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Aklesso Kadala
- Department of Anesthesiology, University of Erlangen-Nürnberg, 91054Erlangen, Germany
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Sven Schütte
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Zoltán Winter
- Department of Anesthesiology, University of Erlangen-Nürnberg, 91054Erlangen, Germany
| | - Mirjam A. R. Bertoune
- Institute for Anatomy and Cell Biology, Department of Medicinal Cellbiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Filip Touska
- Department of Anesthesiology, University of Erlangen-Nürnberg, 91054Erlangen, Germany
| | - Veronika Matschke
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801Bochum, Germany
| | - Eva Wrobel
- Faculty of Chemistry and Biochemistry, Department of Receptor Biochemistry, Ruhr-University Bochum, 44780Bochum, Germany
| | - Anne-Kathrin Streit
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Florian Lang
- Institute for Physiology I, Department of Physiology I, Eberhard Karls University Tübingen, 72074Tübingen, Germany
| | - Constanze Schmidt
- Department of Cardiology, University Hospital Heidelberg, 69120Heidelberg, Germany
| | - Eric Schulze-Bahr
- Department for Genetics of Heart Diseases (IfG), University Hospital Münster, 48149Münster, Germany
| | - Martin K.-H. Schäfer
- Institute for Anatomy and Cell Biology, Department of Medicinal Cellbiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
| | - Jakob Voelkl
- Institute for Physiology and Pathophysiology, Department of Physiology, Johannes Kepler University Linz, 4040Linz, Austria
| | - Guiscard Seebohm
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801Bochum, Germany
- Department for Genetics of Heart Diseases (IfG), University Hospital Münster, 48149Münster, Germany
| | - Katharina Zimmermann
- Department of Anesthesiology, University of Erlangen-Nürnberg, 91054Erlangen, Germany
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Department of Vegetative Physiology and Center for Mind, Brain and Behavior, Philipps-University Marburg, 35032Marburg, Germany
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3
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Deletti G, Green SD, Weber C, Patterson KN, Joshi SS, Khopade TM, Coban M, Veek-Wilson J, Caulfield TR, Viswanathan R, Lane AL. Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase. Nat Commun 2023; 14:2558. [PMID: 37137876 PMCID: PMC10156859 DOI: 10.1038/s41467-023-38168-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature's molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.
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Affiliation(s)
- Garrett Deletti
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Sajan D Green
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Caleb Weber
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Kristen N Patterson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Swapnil S Joshi
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Tushar M Khopade
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - James Veek-Wilson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rajesh Viswanathan
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India.
| | - Amy L Lane
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
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4
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Dunn T, Blaauw D, Das R, Narayanasamy S. nPoRe: n-polymer realigner for improved pileup-based variant calling. BMC Bioinformatics 2023; 24:98. [PMID: 36927439 PMCID: PMC10022090 DOI: 10.1186/s12859-023-05193-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/19/2023] [Indexed: 03/18/2023] Open
Abstract
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers ([Formula: see text]) and tandem repeats ([Formula: see text]). At the same precision, haplotype phasing improves INDEL recall from 63.76 to [Formula: see text] and nPoRe realignment improves it further to [Formula: see text].
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Affiliation(s)
- Tim Dunn
- University of Michigan, Ann Arbor, USA.
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5
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Fiesel FC, Fričová D, Hayes CS, Coban MA, Hudec R, Bredenberg JM, Broadway BJ, Markham BN, Yan T, Boneski PK, Fiorino G, Watzlawik JO, Hou X, McCarty AM, Lewis-Tuffin LJ, Zhong J, Madden BJ, Ordureau A, An H, Puschmann A, Wszolek ZK, Ross OA, Harper JW, Caulfield TR, Springer W. Substitution of PINK1 Gly411 modulates substrate receptivity and turnover. Autophagy 2022:1-22. [PMID: 36469690 DOI: 10.1080/15548627.2022.2151294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin (Ub) kinase-ligase pair PINK1-PRKN mediates the degradation of damaged mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and upon stress accumulates on the mitochondrial surface where it phosphorylates serine 65 of Ub to activate PRKN and to drive mitochondrial turnover. While loss of either PINK1 or PRKN is genetically linked to Parkinson disease (PD) and activating the pathway seems to have great therapeutic potential, there is no formal proof that stimulation of mitophagy is always beneficial. Here we used biochemical and cell biological methods to study single nucleotide variants in the activation loop of PINK1 to modulate the enzymatic function of this kinase. Structural modeling and in vitro kinase assays were used to investigate the molecular mechanism of the PINK1 variants. In contrast to the PD-linked PINK1G411S mutation that diminishes Ub kinase activity, we found that the PINK1G411A variant significantly boosted Ub phosphorylation beyond levels of PINK1 wild type. This resulted in augmented PRKN activation, mitophagy rates and increased viability after mitochondrial stress in midbrain-derived, gene-edited neurons. Mechanistically, the G411A variant stabilizes the kinase fold of PINK1 and transforms Ub to adopt the preferred, C-terminally retracted conformation for improved substrate turnover. In summary, we identify a critical role of residue 411 for substrate receptivity that may now be exploited for drug discovery to increase the enzymatic function of PINK1. The genetic substitution of Gly411 to Ala increases mitophagy and may be useful to confirm neuroprotection in vivo and might serve as a critical positive control during therapeutic development.Abbreviations: ATP: adenosine triphosphate; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; Ub-CR: ubiquitin with C-terminally retracted tail; CTD: C-terminal domain (of PINK1); ELISA: enzyme-linked immunosorbent assay; HCI: high-content imaging; IB: immunoblot; IF: immunofluorescence; NPC: neuronal precursor cells; MDS: molecular dynamics simulation; PD: Parkinson disease; p-S65-Ub: ubiquitin phosphorylated at Ser65; RMSF: root mean scare fluctuation; TOMM: translocase of outer mitochondrial membrane; TVLN: ubiquitin with T66V and L67N mutation, mimics Ub-CR; Ub: ubiquitin; WT: wild-type.
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Affiliation(s)
- Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Caleb S Hayes
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mathew A Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Tingxiang Yan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Paige K Boneski
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gabriella Fiorino
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Cytometry and Imaging Laboratory, Department of Research, Mayo Clinic, Jacksonville, FL, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin J Madden
- Proteomics Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Heeseon An
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andreas Puschmann
- Department of Neurology, Lund University, Skane University Hospital, Sweden
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Neuroscience PhD Program, Mayo Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
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6
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Körfer G, Besirlioglu V, Davari MD, Martinez R, Vojcic L, Schwaneberg U. Combinatorial InVitroFlow-assisted Mutagenesis (CombIMut) yields a 41-fold improved CelA2 cellulase. Biotechnol Bioeng 2022; 119:2076-2087. [PMID: 35451061 DOI: 10.1002/bit.28110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/21/2022] [Accepted: 04/03/2022] [Indexed: 11/11/2022]
Abstract
The combination of diversity generation methods and ultrahigh-throughput screening (uHTS) technologies is key to efficiently explore nature's sequence space and elucidate structure-function relationships of enzymes. Beneficial substitutions often cluster in a few regions and simultaneous amino acid substitutions at multiple positions (e.g., by OmniChange) will likely lead to further improved enzyme variants. An extensive screening effort is required to identify such variants, as the simultaneous randomization of four codons can easily yield over 105 potential enzyme variants. The combination of flow cytometer-based uHTS with cell-free compartmentalization technology using (w/o/w) double emulsions (InVitroFlow), provides analysis capabilities of up to 107 events per hour, thus enabling efficient screening. InVitroFlow is an elegant solution since diversity loss through a transformation of host cells is omitted and emulsion compartments provide a genotype-phenotype linkage through a fluorescence readout. In this work, a multi-site saturation mutagenesis (mSSM) and an OmniChange library with four simultaneously saturated positions in the active site of CelA2 cellulase were screened using InVitroFlow. Screening of over 36 million events, yielded a significantly improved cellulase variant CelA2-M3 (H288F/H524Q) with an 8-fold increase in specific activity compared to the parent CelA2-H288F (83.9 U/mg) and a 41-fold increased specific activity (674.5 U/mg) compared to wildtype CelA2 (16.6 U/mg) for the substrate 4-MUC (4-methylumbelliferyl-β D-cellobioside). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Georgette Körfer
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany
| | - Volkan Besirlioglu
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Ronny Martinez
- Universidad de La Serena, Departamento de Ingeniería en Alimentos, Av. Raúl Bitrán 1305, 1720010, La Serena, Chile
| | - Ljubica Vojcic
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany.,Current address: Codexis Inc., 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056, Aachen, Germany
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7
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Waespy M, Gbem TT, Dinesh Kumar N, Solaiyappan Mani S, Rosenau J, Dietz F, Kelm S. Cooperativity of catalytic and lectin-like domain of Trypanosoma congolense trans-sialidase modulates its catalytic activity. PLoS Negl Trop Dis 2022; 16:e0009585. [PMID: 35130274 PMCID: PMC8865650 DOI: 10.1371/journal.pntd.0009585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/23/2022] [Accepted: 01/23/2022] [Indexed: 12/15/2022] Open
Abstract
Trans-sialidases (TS) represent a multi-gene family of unusual enzymes, which catalyse the transfer of terminal sialic acids (Sia) from sialoglycoconjugates to terminal galactose or N-acetylgalactosamine residues of oligosaccharides without the requirement of CMP-Neu5Ac, the activated Sia used by typical sialyltransferases. Enzymes comprise a N-terminal catalytic domain (CD) followed by a lectin-like domain (LD). Most work on trypanosomal TS has been done on enzymatic activities focusing on the CD of TS from Trypanosoma cruzi (causing Chagas disease in Latin America), subspecies of Trypanosoma brucei, (causing human sleeping sickness in Africa) and Trypanosoma congolense (causing African Animal Trypanosomosis in livestock). Previously, we demonstrated that T. congolense TS (TconTS)-LD binds to several carbohydrates, such as 1,4-β-mannotriose. In this study we investigated the influence of TconTS3-LD on Sia transfer efficiency of TconTS1a-CD by swapping domains. in silico analysis on structure models of TconTS enzymes revealed the potential of domain swaps between TconTS1a and TconTS3 without structural disruptions of the enzymes overall topologies. Recombinant domain swapped TconTS1a/TS3 showed clear Sia transfer activity, when using fetuin and lactose as Sia donor and acceptor substrates, respectively. While Sia transfer activity remained unchanged from the level of TconTS1a, hydrolytic release of free Neu5Ac as a side product was suppressed resulting in increased transfer efficiency. Presence of 1,4-β-mannotriose during TS reactions modulates enzyme activities enhancing transfer efficiency possibly due to occupation of the binding site in TconTS1a-LD. Interestingly this effect was in the same range as that observed when swapping TconTS1a-CD and TconTS3-LD. In summary, this study demonstrate the proof-of-principle for swapping CDs and LDs of TconTS and that TconTS3-LD influences enzymatic activity of TconTS1a-CD providing evidence that LDs play pivotal roles in modulating activities and biological functions of TconTS and possibly other TS.
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Affiliation(s)
- Mario Waespy
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Thaddeus Termulun Gbem
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria, Africa
- Department of Biology, Ahmadu Bello University, Zaria, Nigeria, Africa
| | - Nilima Dinesh Kumar
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Shanmugam Solaiyappan Mani
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Jana Rosenau
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Frank Dietz
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Sørge Kelm
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria, Africa
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8
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Fricke PM, Lürkens M, Hünnefeld M, Sonntag CK, Bott M, Davari MD, Polen T. Highly tunable TetR-dependent target gene expression in the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2021; 105:6835-6852. [PMID: 34448898 PMCID: PMC8426231 DOI: 10.1007/s00253-021-11473-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/27/2022]
Abstract
Abstract For the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first tight system for regulatable target gene expression became available based on the heterologous repressor-activator protein AraC from Escherichia coli and the target promoter ParaBAD. In this study, we tested pure repressor-based TetR- and LacI-dependent target gene expression in G. oxydans by applying the same plasmid backbone and construction principles that we have used successfully for the araC-ParaBAD system. When using a pBBR1MCS-5-based plasmid, the non-induced basal expression of the Tn10-based TetR-dependent expression system was extremely low. This allowed calculated induction ratios of up to more than 3500-fold with the fluorescence reporter protein mNeonGreen (mNG). The induction was highly homogeneous and tunable by varying the anhydrotetracycline concentration from 10 to 200 ng/mL. The already strong reporter gene expression could be doubled by inserting the ribosome binding site AGGAGA into the 3’ region of the Ptet sequence upstream from mNG. Alternative plasmid constructs used as controls revealed a strong influence of transcription terminators and antibiotics resistance gene of the plasmid backbone on the resulting expression performance. In contrast to the TetR-Ptet-system, pBBR1MCS-5-based LacI-dependent expression from PlacUV5 always exhibited some non-induced basal reporter expression and was therefore tunable only up to 40-fold induction by IPTG. The leakiness of PlacUV5 when not induced was independent of potential read-through from the lacI promoter. Protein-DNA binding simulations for pH 7, 6, 5, and 4 by computational modeling of LacI, TetR, and AraC with DNA suggested a decreased DNA binding of LacI when pH is below 6, the latter possibly causing the leakiness of LacI-dependent systems hitherto tested in AAB. In summary, the expression performance of the pBBR1MCS-5-based TetR-Ptet system makes this system highly suitable for applications in G. oxydans and possibly in other AAB. Key Points • A pBBR1MCS-5-based TetR-Ptet system was tunable up to more than 3500-fold induction. • A pBBR1MCS-5-based LacI-PlacUV5 system was leaky and tunable only up to 40-fold. • Modeling of protein-DNA binding suggested decreased DNA binding of LacI at pH < 6. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11473-x.
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Affiliation(s)
- Philipp Moritz Fricke
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Martha Lürkens
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074 Aachen, Germany
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Christiane K. Sonntag
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Tino Polen
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
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9
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Cortés-Benítez F, Roy J, Perreault M, Maltais R, Poirier D. 16-Picolyl-androsterone derivative exhibits potent 17β-HSD3 inhibitory activity, improved metabolic stability and cytotoxic effect on various cancer cells: Synthesis, homology modeling and docking studies. J Steroid Biochem Mol Biol 2021; 210:105846. [PMID: 33609690 DOI: 10.1016/j.jsbmb.2021.105846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 11/18/2022]
Abstract
A new androsterone derivative bearing a 16β-picolyl group (compound 5; FCO-586-119) was synthetized in four steps from the lead compound 1 (RM-532-105). We measured its inhibitory activity on 17β-HSD3 using microsomal fraction of rat testes as well as transfected LNCaP[17β-HSD3] cells. We then assessed its metabolic stability as well as its cytotoxic effect against a panel of cancer cell lines. The addition of a picolyl moiety at C-16 of RM-532-105 steroid core improves the 17β-HSD3 inhibitory activity in the microsomal fraction of rat testes, but not in whole LNCaP[17β-HSD3] cells. Interestingly, this structural modification enhances 3-fold the metabolic stability in conjunction with a significant cytotoxic effect against pancreatic, ovarian, breast, lung, and prostate cancer cells. Because the inhibitory activity data against 17β-HSD3 suggested that both steroid derivatives are non-competitive inhibitors, we performed docking and molecular dynamics simulations using a homology model of this membrane-associated enzyme. The results of these simulations revealed that both RM-532-105 (1) and FCO-586-119 (5) can compete for the cofactor-binding site displaying better binding energy than NADP+.
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Affiliation(s)
- Francisco Cortés-Benítez
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU De Québec - Research Center, Québec City, Québec, G1V 4G2, Canada; Laboratory of Synthesis and Isolation of Bioactive Substances, Department of Biological Systems, Biological and Health Sciences Division, Metropolitan Autonomous University- Xochimilco (UAM-X), Mexico City 04960, Mexico
| | - Jenny Roy
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU De Québec - Research Center, Québec City, Québec, G1V 4G2, Canada
| | - Martin Perreault
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU De Québec - Research Center, Québec City, Québec, G1V 4G2, Canada
| | - René Maltais
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU De Québec - Research Center, Québec City, Québec, G1V 4G2, Canada
| | - Donald Poirier
- Laboratory of Medicinal Chemistry, Endocrinology and Nephrology Unit, CHU De Québec - Research Center, Québec City, Québec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, G1V 0A6, Canada.
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10
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Coban MA, Morrison J, Maharjan S, Hernandez Medina DH, Li W, Zhang YS, Freeman WD, Radisky ES, Le Roch KG, Weisend CM, Ebihara H, Caulfield TR. Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target Engagement. Biomolecules 2021; 11:biom11060787. [PMID: 34071060 PMCID: PMC8224684 DOI: 10.3390/biom11060787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is a devastating respiratory and inflammatory illness caused by a new coronavirus that is rapidly spreading throughout the human population. Over the past 12 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has already infected over 160 million (>20% located in United States) and killed more than 3.3 million people around the world (>20% deaths in USA). As we face one of the most challenging times in our recent history, there is an urgent need to identify drug candidates that can attack SARS-CoV-2 on multiple fronts. We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors-S/Ace2, Tmprss2, Cathepsins L and K, and Mpro-to prevent binding, membrane fusion and replication of the virus, respectively. All together, we generated an ensemble of structural conformations that increase high-quality docking outcomes to screen over >6 million compounds including all FDA-approved drugs, drugs under clinical trial (>3000) and an additional >30 million selected chemotypes from fragment libraries. Our results yielded an initial set of 350 high-value compounds from both new and FDA-approved compounds that can now be tested experimentally in appropriate biological model systems. We anticipate that our results will initiate screening campaigns and accelerate the discovery of COVID-19 treatments.
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Affiliation(s)
- Mathew A. Coban
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, 900 University, Riverside, CA 92521, USA;
| | - Sushila Maharjan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - David Hyram Hernandez Medina
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - Wanlu Li
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Landsdowne St, Cambridge, MA 02139, USA; (S.M.); (D.H.H.M.); (W.L.); (Y.S.Z.)
| | - William D. Freeman
- Department of Neurology, Mayo Clinic, 4500 San Pablo South, Jacksonville, FL 32224, USA;
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, 900 University, Riverside, CA 92521, USA;
| | - Carla M. Weisend
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA; (C.M.W.); (H.E.)
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA; (C.M.W.); (H.E.)
| | - Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA; (M.A.C.); (E.S.R.)
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Quantitative Health Science, Division of Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-904-953-6072
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11
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Norris GA, Tsai ACH, Schneider KW, Wu YH, Caulfield T, Green AL. A novel, germline, deactivating CBL variant p.L493F alters domain orientation and is associated with multiple childhood cancers. Cancer Genet 2021; 254-255:18-24. [PMID: 33550024 DOI: 10.1016/j.cancergen.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
CBL is a mammalian gene encoding the protein CBL, which is an E3 ubiquitin-protein ligase involved in cell signaling and protein ubiquitination. Pathogenic variants in this gene have been implicated in a number of human cancers, particularly acute myeloid leukemia (AML). Here, we present a 5-year-old male patient with a history of AML, diffuse midline glioma, and left brain lesion with histiocytic features. A variant of uncertain significance (VUS): p.L493F was detected in his CBL gene via clinical evaluation. Protein modeling predicts this variant to be pathogenic. Details of the clinical evaluation and modeling assay are discussed.
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Affiliation(s)
- Gregory A Norris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Kami Wolfe Schneider
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Yuan-Haw Wu
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA
| | - Thomas Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL USA
| | - Adam L Green
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO USA.
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12
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Richter JE, Hines S, Selvam P, Atwal H, Farres H, Caulfield TR, Atwal PS. Clinical description & molecular modeling of novel MAX pathogenic variant causing pheochromocytoma in family, supports paternal parent-of-origin effect. Cancer Genet 2021; 252-253:107-110. [PMID: 33493868 DOI: 10.1016/j.cancergen.2021.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/01/2020] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
The titular member of the MAX network of proteins, MYC-associated factor X (MAX), serves an important regulatory function in transcription of E-box genes associated with cell proliferation, differentiation, and apoptosis. Wild type MAX dimerizes with both MYC and MAD, both of which are members of the MAX network, and can promote or repress cell functions as needed. However, pathogenic variants in MAX are known to upset this balance, leading to uncontrolled oncogenic activity and disease phenotypes such as paragangliomas and pheochromocytomas. We report a 58-year-old male and his 32-year-old daughter, both of which have a history of pheochromocytoma and the unique nonsense MAX variant c.271C>T (p.Q91X). These individuals were diagnosed with pheochromocytomas in their early twenties that were later removed through corrective surgery. The father now presents with recurrent symptoms of hypertension, hyperhidrosis, and headaches, which accompany new pheochromocytomas of his remaining adrenal gland. Pathogenicity of this MAX variant is proven through molecular modeling. The case of this father-daughter pair supports both heritability of pheochromocytoma and the paternal parent-of-origin effect for MAX pathogenic variants.
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Affiliation(s)
- John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - S Hines
- Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Pavalan Selvam
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA
| | - Herjot Atwal
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA
| | - Houssam Farres
- Department of Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL, USA
| | - Paldeep S Atwal
- Atwal Clinic: Genomic & Personalized Medicine, Palm Beach, FL 33480, USA.
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13
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Ahuja AS, Selvam P, Vadlamudi C, Chopra H, Richter JE, Macklin SK, Samreen A, Helmi H, Mohammaad AN, Hines S, Davila MC, Atwal PS, Caulfield TR. Genomics combined with a protein informatics platform to assess a novel pathogenic variant c.1024 A>G (p.K342E) in OPA1 in a patient with autosomal dominant optic atrophy. Ophthalmic Genet 2020; 41:563-569. [PMID: 32940104 DOI: 10.1080/13816810.2020.1814344] [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]
Abstract
BACKGROUND Autosomal Dominant Optic Atrophy (ADOA) is caused by mutations in the Optic Atrophy 1 Gene which disrupts the OPA1 protein. This disruption affects the normal function of the protein; impairs fusion of the mitochondrial inner membrane; and prevents normal OPA1 protein degradation. These events cause damage in retinal ganglion cells that could affect the patients with symptoms ranging from none to legally blind. MATERIALS AND METHODS Our study identifies a missense variant mutation, c.1024 A > G (p.K342E), in OPA1 gene causing ADOA. Diagnosed clinically in three family members and the presence of this mutation was confirmed in two members by genetic testing. Pathogenic variants in OPA1 impact the secondary protein structure and function by causing non-conservative amino acid substitutions. We also modeled this mutation and compared it to the wild type using statistical mechanics. RESULTS AND CONCLUSIONS The proband's pathogenic variant, c.1024 A > G (p.K342E), is located in the GTPase domain of OPA1 and causes changes in the protein structure by affecting the oligomerization pattern thus resulting in ADOA. Identifying the pathogenic potential of the missense mutations in the OPA1 gene using neoteric protein modeling techniques would help in the early detection of ADOA in patients who have family history of blindness. This action would help in providing early follow up, possible treatment in the future, and genetic counseling. Abbreviations: ADOA: Autosomal Dominant Optic Atrophy; CYCS: Caspase Activator Cytochrome C; OPA1: Optic Atrophy Gene 1; RGC: Retinal Ganglion Cells; VUS: Variant of Uncertain Significance.
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Affiliation(s)
- Abhimanyu S Ahuja
- Charles E. Schmidt College of Medicine, Florida Atlantic University , Boca Raton, Florida, USA
| | - Pavalan Selvam
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Charitha Vadlamudi
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Hayley Chopra
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas, USA
| | | | | | - Ayesha Samreen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, Texas, USA
| | - Haytham Helmi
- Department of Endocrinology, Mayo Clinic , Jacksonville, Florida, USA
| | - Ahmed N Mohammaad
- Department of Endocrinology, Mayo Clinic , Jacksonville, Florida, USA
| | - Stephanie Hines
- Department of Medicine, Division of Diagnostic & Consultative Medicine, Mayo Clinic , Jacksonville, Florida, USA
| | | | - Paldeep S Atwal
- Department of Clinical Genomics, Atwal Clinic , Jacksonville, Florida, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic , Jacksonville, Florida, USA.,Department of Neurosurgery, Mayo Clinic , Jacksonville, Florida, USA.,Department of Cancer Biology, Mayo Clinic , Jacksonville, Florida, USA.,Department of Health Sciences Research, Mayo Clinic , Jacksonville, Florida, USA
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14
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Coban MA, Blackburn PR, Whitelaw ML, van Haelst MM, Atwal PS, Caulfield TR. Structural Models for the Dynamic Effects of Loss-of-Function Variants in the Human SIM1 Protein Transcriptional Activation Domain. Biomolecules 2020; 10:biom10091314. [PMID: 32932609 PMCID: PMC7563489 DOI: 10.3390/biom10091314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 02/02/2023] Open
Abstract
Single-minded homologue 1 (SIM1) is a transcription factor with numerous different physiological and developmental functions. SIM1 is a member of the class I basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factor family, that includes several other conserved proteins, including the hypoxia-inducible factors, aryl hydrocarbon receptor, neuronal PAS proteins, and the CLOCK circadian regulator. Recent studies of HIF-a-ARNT and CLOCK-BMAL1 protein complexes have revealed the organization of their bHLH, PASA, and PASB domains and provided insight into how these heterodimeric protein complexes form; however, experimental structures for SIM1 have been lacking. Here, we describe the first full-length atomic structural model for human SIM1 with its binding partner ARNT in a heterodimeric complex and analyze several pathogenic variants utilizing state-of-the-art simulations and algorithms. Using local and global positional deviation metrics, deductions to the structural basis for the individual mutants are addressed in terms of the deleterious structural reorganizations that could alter protein function. We propose new experiments to probe these hypotheses and examine an interesting SIM1 dynamic behavior. The conformational dynamics demonstrates conformational changes on local and global regions that represent a mechanism for dysfunction in variants presented. In addition, we used our ab initio hybrid model for further prediction of variant hotspots that can be engineered to test for counter variant (restoration of wild-type function) or basic research probe.
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Affiliation(s)
- Mathew A. Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Patrick R. Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Murray L. Whitelaw
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide SA 5000, Australia;
| | - Mieke M. van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Paldeep S. Atwal
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
- Atwal Clinic, Jacksonville, FL 32224, USA
| | - Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA, MN, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Correspondence: ; Tel.: +1-904-953-6072; Fax: +1-904-953-7370
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15
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Examination of Molecular Effects of MYLK Deletion in a Patient with Extensive Aortic, Carotid, and Abdominal Dissections That Underlie the Genetic Dysfunction. Case Rep Med 2020; 2020:5108052. [PMID: 32655646 PMCID: PMC7327611 DOI: 10.1155/2020/5108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 04/12/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022] Open
Abstract
We describe the phenotype of a patient with extensive aortic, carotid, and abdominal dissections. The proband was found to have a heterozygous deletion of exons 21-34 in MYLK, which is a rare finding, as deletions in this gene have been infrequently reported. We describe this finding following detection in a proband with an extensive history of aortic, carotid, and abdominal dissections. Neoteric molecular modeling techniques to help determine the impact of this deletion on protein function indicated loss of function due to lack of any kinase domain. We also provide the electrostatics calculations from the wild type and mutant variant. Through a combined multiomic approach of clinical, functional, and protein informatics, we arrive at a data fusion for determination of pathogenicity embedded within the genetic code for this particular genetic variant, which, as a platform, continues to broaden its scope across the field of variants of uncertain significance classification.
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16
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Characterization of a Pathogenic Variant in the ABCD1 Gene Through Protein Molecular Modeling. Case Rep Genet 2020; 2020:3256539. [PMID: 32047678 PMCID: PMC7003284 DOI: 10.1155/2020/3256539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/19/2019] [Indexed: 11/18/2022] Open
Abstract
Background The ATP-binding cassette, subfamily D, member 1 (ABCD1) protein is a peroxisomal half-transporter that allows for very long chain fatty acid (VLCFA) degradation. Pathogenic variants of ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Methods A newly characterized and suspected pathogenic variant in ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Results A case of adult onset adrenomyeloneuropathy (AMN) and a novel ABCD1 cause VLCFAs to build up in various tissues and bodily fluids, resulting in a disorder called X-linked adrenoleukodystrophy (X-ALD). This disorder is most commonly marked by adrenocortical insufficiency and high VLCFA concentration, and has varying levels of neurological involvement depending on phenotype. For example, the Addison-only form of X-ALD has no neurological impact, while the cerebral form of X-ALD often causes severe sensory loss, motor function impairment, cognitive decline, and death. Conclusions Data fusion from multiple sources was combined in a comprehensive approach yielding an enriched assessment of the patient's disease and prognosis. Molecular modeling was performed on the variant to better characterize its clinical significance and confirm pathogenicity.
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17
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Rocha-Garduño G, Hernández-Martínez NA, Colín-Lozano B, Estrada-Soto S, Hernández-Núñez E, Prieto-Martínez FD, Medina-Franco JL, Chale-Dzul JB, Moo-Puc R, Navarrete-Vázquez G. Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity, and Molecular Dynamics Studies. Molecules 2020; 25:molecules25040793. [PMID: 32059495 PMCID: PMC7071106 DOI: 10.3390/molecules25040793] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
We prepared a series of 10 carbamates derivatives based on two common antiprotozoal drugs: metronidazole (1–5) and secnidazole (6–10). The compounds were tested in vitro against a set of two amitochondriate protozoa: Giardia duodenalis and Trichomonas vaginalis. Compounds 1–10 showed strong antiprotozoal activities, with potency values in the low micromolar-to-nanomolar range, being more active than their parent drugs. Metronidazole carbamate (1) was the most active of the series, with nanomolar activities against G. duodenalis (IC50 = 460 nM) and T. vaginalis (IC50 = 60 nM). The potency of compound 1 was 10 times greater than that of metronidazole against both parasites. None of compounds showed in vitro cytotoxicity against VERO cells tested at 100 µM. Molecular dynamics of compounds 1–10, secnidazole, and metronidazole onto the ligand binding site of pyruvate–ferredoxin oxidoreductase of T. vaginalis and the modeled β-tubulin of G. duodenalis revealed putative molecular interactions with key residues in the binding site of both proteins implicated in the mode of action of the parent drugs.
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Affiliation(s)
- Genaro Rocha-Garduño
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (G.R.-G.); (N.A.H.-M.); (B.C.-L.); (S.E.-S.)
| | - Norma Angélica Hernández-Martínez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (G.R.-G.); (N.A.H.-M.); (B.C.-L.); (S.E.-S.)
| | - Blanca Colín-Lozano
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (G.R.-G.); (N.A.H.-M.); (B.C.-L.); (S.E.-S.)
| | - Samuel Estrada-Soto
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (G.R.-G.); (N.A.H.-M.); (B.C.-L.); (S.E.-S.)
| | - Emanuel Hernández-Núñez
- Cátedra CONACyT, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Mérida, Yucatán 97310, Mexico;
| | - Fernando Daniel Prieto-Martínez
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México City 04510, Mexico; (F.D.P.-M.); (J.L.M.-F.)
| | - José L. Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México City 04510, Mexico; (F.D.P.-M.); (J.L.M.-F.)
| | - Juan Bautista Chale-Dzul
- Laboratorio de Apoyo a la Vigilancia Epidemiológica, Hospital de Especialidades 1, Centro Médico Nacional Ignacio García Téllez, Instituto Mexicano del Seguro Social, Mérida 97150, Yucatán, Mexico;
| | - Rosa Moo-Puc
- Unidad de Investigación Médica Yucatán, Unidad Médica de Alta Especialidad, Centro Médico Nacional Ignacio García Téllez, Instituto Mexicano del Seguro Social, Mérida 97000, Yucatán, Mexico;
| | - Gabriel Navarrete-Vázquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (G.R.-G.); (N.A.H.-M.); (B.C.-L.); (S.E.-S.)
- Correspondence: ; Tel.: +52-777-329-7089
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18
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Hines SL, Mohammad AN, Jackson J, Macklin S, Caulfield TR. Integrative data fusion for comprehensive assessment of a novel CHEK2 variant using combined genomics, imaging, and functional-structural assessments via protein informatics. Mol Omics 2019; 15:59-66. [PMID: 30633282 DOI: 10.1039/c8mo00137e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CHEK2 gene and its encoded protein Chk2 have a well-known role in cancers, especially those related to breast cancer mediated through the BRCA1 gene. Additionally Chk2 has a crucial role in DNA repair, apoptosis and the cell cycle, which is why classification of variants of uncertain significance (VUS) is an area highly sought for a better elucidation of the "genomic effect" that results. Because it can often take years before enough clinical data is accumulated, and the costly and expensive functional analysis for individual variants presents a significant hurdle, it is important to identify other tools to help aid in clarifying the impact of specific variants on a protein's function and eventually the patient's health outcome. Here we describe a newly identified CHEK2 variant and analyze with an integrated approach combining genomics (whole exome analysis), clinical study, radiographic imaging, and protein informatics to identify and predict the functional impact of the VUS on the protein's behavior and predicted impact on the related pathways. The observed and analyzed defects in the protein were consistent with the expected clinical effect. Here, we support the use of personalized protein modeling and informatics and further our goal of developing a large-scale protein deposition archive for all protein-level VUS.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
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Genomic Observations of a Rare/Pathogenic SMAD3 Variant in Loeys⁻Dietz Syndrome 3 Confirmed by Protein Informatics and Structural Investigations. ACTA ACUST UNITED AC 2019; 55:medicina55050137. [PMID: 31096651 PMCID: PMC6571799 DOI: 10.3390/medicina55050137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/29/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
Background and objectives: Loeys–Dietz syndrome 3, also known as aneurysms-–osteoarthritis syndrome, is an autosomal dominant genetic connective tissue disease caused by pathogenic variants in SMAD3, a transcription factor involved in TGF-β signaling. This disorder is characterized by early-onset osteoarthritis and arterial aneurysms. Common features include scoliosis, uvula abnormalities, striae, and velvety skin. Materials and Methods: The pathogenicity of a variant of uncertain significance in the SMAD3 gene was evaluated (variant c.220C > T) through personalized protein informatics and molecular studies. Results: The case of a 44-year-old male, who was originally presumed to have Marfan syndrome, is presented. An expanded gene panel determined the probable cause to be a variant in SMAD3, c.220C > T (p.R74W). His case was complicated by a history of stroke, but his phenotype was otherwise characteristic for Loeys–Dietz syndrome 3. Conclusion: This case emphasizes the importance of comprehensive genetic testing to evaluate patients for connective tissue disorders, as well as the potential benefit of utilizing a protein informatics platform for the assessment of variant pathogenicity.
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Hines SL, Richter JE, Mohammad AN, Mahim J, Atwal PS, Caulfield TR. Protein informatics combined with multiple data sources enriches the clinical characterization of novel TRPV4 variant causing an intermediate skeletal dysplasia. Mol Genet Genomic Med 2019; 7:e566. [PMID: 30693671 PMCID: PMC6418443 DOI: 10.1002/mgg3.566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/02/2018] [Accepted: 12/02/2018] [Indexed: 01/19/2023] Open
Abstract
Background Transient receptor potential cation channel subfamily V member 4 (TRPV4) is an ion channel permeable to Ca2+ that is sensitive to physical, hormonal, and chemical stimuli. This protein is expressed in many cell types, including osteoclasts, chondrocytes, and sensory neurons. As such, pathogenic variants of this gene are associated with skeletal dysplasias and neuromuscular disorders. Pathogenesis of these phenotypes is not yet completely understood, but it is known that genotype–phenotype correlations for TRPV4 pathogenic variants often are not present. Methods Newly characterized, suspected pathogenic variant in TRPV4 was analyzed using protein informatics and personalized protein‐level molecular studies, genomic exome analysis, and clinical study. Results This statement is demonstrated in the family of our proband, a 47‐year‐old female having the novel c.2401A>G (p.K801E) variant of TRPV4. We discuss the common symptoms between the proband, her father, and her daughter, and compare her phenotype to known TRPV4‐associated skeletal dysplasias. Conclusions Protein informatics and molecular modeling are used to confirm the pathogenicity of the unique TRPV4 variant found in this family. Multiple data were combined in a comprehensive manner to give complete overall perspective on the patient disease and prognosis.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida.,Department of General Internal Medicine, Mayo Clinic, Jacksonville, Florida.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida
| | - John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Ahmed N Mohammad
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Jain Mahim
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Thomas R Caulfield
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida.,Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
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Hanna Al Shaikh R, Caulfield T, Strongosky AJ, Matthew M, Jansen-West KR, Prudencio M, Fryer JD, Petrucelli L, Uitti RJ, Wszolek ZK. TRIO gene segregation in a family with cerebellar ataxia. Neurol Neurochir Pol 2018; 52:743-749. [DOI: 10.1016/j.pjnns.2018.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
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22
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Körfer G, Novoa C, Kern J, Balla E, Grütering C, Davari MD, Martinez R, Vojcic L, Schwaneberg U. Directed evolution of an acid Yersinia mollaretii phytase for broadened activity at neutral pH. Appl Microbiol Biotechnol 2018; 102:9607-9620. [DOI: 10.1007/s00253-018-9308-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 01/25/2023]
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23
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Macklin S, Mohammed A, Jackson J, Hines SL, Atwal PS, Caulfield T. Personalized molecular modeling for pinpointing associations of protein dysfunction and variants associated with hereditary cancer syndromes. Mol Genet Genomic Med 2018; 6:805-810. [PMID: 30043523 PMCID: PMC6160717 DOI: 10.1002/mgg3.447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 11/07/2022] Open
Abstract
Background Although the process of reclassification of a variant of uncertain significance can be complex, they are commonly detected through molecular testing. It often takes years before enough clinical data are acquired, and it can be costly and time‐consuming to perform functional analysis of a single variant. It is important that other tools are developed to aid in clarifying how a specific genetic variant impacts a protein's function, and ultimately the health of the patient. Methods Two more newly characterized, suspected pathogenic variants in NBN and PTEN were analyzed through personalized protein modeling. Comparisons between the wild‐type and altered protein were studied using simulations, genomic exome analysis, and clinic study. Results Modeling of the new NBN and PTEN protein structures suggested loss of essential domains important for normal enzymatic function for these personalized genomic examples which matched the clinical findings. Conclusion The defects detected through modeling were consistent with the expected clinical effect. Personalized protein modeling is another tool for determination of correct variant classification, which can become further useful through construction of deposition archive.
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Affiliation(s)
- Sarah Macklin
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Ahmed Mohammed
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Jessica Jackson
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Stephanie L Hines
- Department of Medicine, Division of Diagnostic & Consultative Medicine, Mayo Clinic, Jacksonville, Florida
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida.,The Atwal Clinic, Jacksonville, Florida
| | - Thomas Caulfield
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida.,Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
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Caulfield TR, Richter JE, Brown EE, Mohammad AN, Judge DP, Atwal PS. Protein molecular modeling techniques investigating novel TAB2 variant R347X causing cardiomyopathy and congenital heart defects in multigenerational family. Mol Genet Genomic Med 2018; 6:666-672. [PMID: 29700987 PMCID: PMC6081229 DOI: 10.1002/mgg3.401] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Haploinsufficiency of TAB2 is known to cause congenital heart defects and cardiomyopathy due to its important roles in cardiovascular tissue, both during development and through adult life. We report a sibling pair displaying adult-onset cardiomyopathy, hypermobility, and mild myopia. Our proband, a 39-year-old male, presents only with the above symptoms, while his 36-year-old sister was also notable for a ventricular septal defect in her infancy. METHODS Whole-exome sequencing was utilized to identify the molecular basis of the phenotype found in two siblings. A molecular modeling technique that takes advantage of conformational sampling advances (Maxwell's demon molecular dynamics and Monte Carlo) were used to make a model of the mutant variant for comparative analytics to the wild-type. RESULTS Exome sequencing revealed a novel, heterogeneous pathogenic variant in TAB2, c.1039 C>T (p.R347X), that was present in both individuals. This pathogenic variant removes just over half the residues from the TAB2 protein and severely impacts its functional ability, which we describe in detail. CONCLUSIONS Analysis of the proband's family showed a history of cardiomyopathy, but no congenital heart defects or connective tissue disease. We highlight the heterogeneity in phenotype of TAB2 pathogenic variants and confirm the pathogenicity of this new variant through neoteric protein modeling techniques.
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Affiliation(s)
- Thomas R. Caulfield
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Mayo Graduate SchoolNeurobiology of DiseaseMayo ClinicJacksonvilleFLUSA
| | | | - Emily E. Brown
- Center for Inherited Heart DiseaseJohns Hopkins UniversityBaltimoreMDUSA
| | | | - Daniel P. Judge
- Center for Inherited Heart DiseaseJohns Hopkins UniversityBaltimoreMDUSA
- Division of CardiologyMedical University of South CarolinaCharlestonSCUSA
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25
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Richter JE, Robles HG, Mauricio E, Mohammad A, Atwal PS, Caulfield TR. Protein molecular modeling shows residue T599 is critical to wild-type function of POLG and description of a novel variant associated with the SANDO phenotype. Hum Genome Var 2018; 5:18016. [PMID: 29644085 PMCID: PMC5885040 DOI: 10.1038/hgv.2018.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/22/2017] [Accepted: 12/12/2017] [Indexed: 01/21/2023] Open
Abstract
Sensory ataxic neuropathy with dysarthria and ophthalmoparesis (SANDO) is a rare phenotype resulting from pathogenic variants of mitochondrial DNA polymerase gamma (POLG). We modeled a novel POLG variant, T599P, that causes the SANDO phenotype and another variant at the same residue, p.T599E, to observe their effect on protein function and confirm the pathogenicity of T599P. Through neoteric molecular modeling techniques, we show that changes at the T599 residue position introduce extra rigidity into the surrounding helix–loop–helix, which places steric pressure on nearby nucleotides. We also provide a clinical description of the T599P variant, which was found in a 42-year-old female proband. The proband presented a 1-year history of progressive gait instability, dysarthria and foot numbness. Her neurologic examination revealed ataxic dysarthria, restricted eye movements, head and palatal tremors, reduced lower limb reflexes, distal multimodal sensory loss and a wide, unsteady ataxic gait. Electromyography studies indicated a sensory neuropathy. Whole-exome sequencing was pursued after tests for infectious, inflammatory and paraneoplastic causes were negative.
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Affiliation(s)
- John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Ahmed Mohammad
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL, USA.,Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
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Whole Exome Sequencing and Molecular Modeling of a Missense Variant in TNFAIP3 That Segregates with Disease in a Family with Chronic Urticaria and Angioedema. Case Rep Genet 2018; 2018:6968395. [PMID: 29682366 PMCID: PMC5842716 DOI: 10.1155/2018/6968395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/18/2018] [Indexed: 11/17/2022] Open
Abstract
Chronic urticaria is a common condition characterized by recurrent hives lasting several weeks or months and is usually idiopathic. Approximately half of the individuals with chronic urticaria will present with episodes of angioedema that can be severe and debilitating. In this report, we describe a 47-year-old Hispanic male who presented initially for an evaluation of chronic hives following hospitalization due to hive-induced anaphylaxis. The individual had a history significant for urticaria and angioedema beginning in his early 30s. Interestingly, both the individual's 41-year-old sister and 12-year-old daughter were also affected with chronic urticaria and severe angioedema. Whole exome sequencing of the proband and several family members revealed a heterozygous variant of uncertain significance in exon 2 of TNFAIP3, denoted as c.65G>A (p.R22Q), in all affected members. Variants in TNFAIP3 have been associated with multiple autoimmune diseases, susceptibility to allergy and asthma, and periodic fever syndromes, suggesting that this variant could potentially play a role in disease.
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27
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Aronsson A, Güler F, Petoukhov MV, Crennell SJ, Svergun DI, Linares-Pastén JA, Nordberg Karlsson E. Structural insights of Rm Xyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:292-306. [DOI: 10.1016/j.bbapap.2017.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 10/05/2017] [Accepted: 11/12/2017] [Indexed: 02/02/2023]
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28
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Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nat Struct Mol Biol 2017; 25:61-72. [PMID: 29323272 PMCID: PMC5909405 DOI: 10.1038/s41594-017-0007-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/09/2017] [Indexed: 01/03/2023]
Abstract
Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. Unfortunately, the effects of SMARCA4 missense mutations have remained uncertain. Here we show that SMARCA4 cancer missense mutations target conserved ATPase surfaces and disrupt the mechanochemical cycle of remodeling. We find that heterozygous expression of mutants alters the open chromatin landscape at thousands of sites across the genome. Loss of DNA accessibility does not directly overlap with Polycomb accumulation, but is enriched in 'A compartments' at active enhancers, which lose H3K27ac but not H3K4me1. Affected positions include hundreds of sites identified as superenhancers in many tissues. Dominant-negative mutation induces pro-oncogenic expression changes, including increased expression of Myc and its target genes. Together, our data suggest that disruption of enhancer accessibility represents a key source of altered function in disorders with SMARCA4 mutations in a wide variety of tissues.
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29
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Ando M, Fiesel FC, Hudec R, Caulfield TR, Ogaki K, Górka-Skoczylas P, Koziorowski D, Friedman A, Chen L, Dawson VL, Dawson TM, Bu G, Ross OA, Wszolek ZK, Springer W. The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity. Mol Neurodegener 2017; 12:32. [PMID: 28438176 PMCID: PMC5404317 DOI: 10.1186/s13024-017-0174-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/14/2017] [Indexed: 01/24/2023] Open
Abstract
Background Mutations in PINK1 and PARKIN are the most common causes of recessive early-onset Parkinson’s disease (EOPD). Together, the mitochondrial ubiquitin (Ub) kinase PINK1 and the cytosolic E3 Ub ligase PARKIN direct a complex regulated, sequential mitochondrial quality control. Thereby, damaged mitochondria are identified and targeted to degradation in order to prevent their accumulation and eventually cell death. Homozygous or compound heterozygous loss of either gene function disrupts this protective pathway, though at different steps and by distinct mechanisms. While structure and function of PARKIN variants have been well studied, PINK1 mutations remain poorly characterized, in particular under endogenous conditions. A better understanding of the exact molecular pathogenic mechanisms underlying the pathogenicity is crucial for rational drug design in the future. Methods Here, we characterized the pathogenicity of the PINK1 p.I368N mutation on the clinical and genetic as well as on the structural and functional level in patients’ fibroblasts and in cell-based, biochemical assays. Results Under endogenous conditions, PINK1 p.I368N is expressed, imported, and N-terminally processed in healthy mitochondria similar to PINK1 wild type (WT). Upon mitochondrial damage, however, full-length PINK1 p.I368N is not sufficiently stabilized on the outer mitochondrial membrane (OMM) resulting in loss of mitochondrial quality control. We found that binding of PINK1 p.I368N to the co-chaperone complex HSP90/CDC37 is reduced and stress-induced interaction with TOM40 of the mitochondrial protein import machinery is abolished. Analysis of a structural PINK1 p.I368N model additionally suggested impairments of Ub kinase activity as the ATP-binding pocket was found deformed and the substrate Ub was slightly misaligned within the active site of the kinase. Functional assays confirmed the lack of Ub kinase activity. Conclusions Here we demonstrated that mutant PINK1 p.I368N can not be stabilized on the OMM upon mitochondrial stress and due to conformational changes in the active site does not exert kinase activity towards Ub. In patients’ fibroblasts, biochemical assays and by structural analyses, we unraveled two pathomechanisms that lead to loss of function upon mutation of p.I368N and highlight potential strategies for future drug development. Electronic supplementary material The online version of this article (doi:10.1186/s13024-017-0174-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maya Ando
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Paulina Górka-Skoczylas
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Warsaw, Poland
| | - Dariusz Koziorowski
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Friedman
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA. .,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA.
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A cobalt-containing eukaryotic nitrile hydratase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:107-112. [DOI: 10.1016/j.bbapap.2016.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022]
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Faraggi E, Kloczkowski A. Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X. Methods Mol Biol 2017; 1484:45-53. [PMID: 27787819 DOI: 10.1007/978-1-4939-6406-2_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict secondary structure as well as accessible surface area and dihedral angles ϕ and ψ. For secondary structure SPINE-X achieves an accuracy of between 81 and 84 % depending on the dataset and choice of tests. The Pearson correlation coefficient for accessible surface area prediction is 0.75 and the mean absolute error from the ϕ and ψ dihedral angles are 20∘ and 33∘, respectively. The source code and a Linux executables for SPINE-X are available from Research and Information Systems at http://mamiris.com .
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Affiliation(s)
- Eshel Faraggi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA
- Research and Information Systems, LLC, Indianapolis, IN, USA
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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32
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Puschmann A, Fiesel FC, Caulfield TR, Hudec R, Ando M, Truban D, Hou X, Ogaki K, Heckman MG, James ED, Swanberg M, Jimenez-Ferrer I, Hansson O, Opala G, Siuda J, Boczarska-Jedynak M, Friedman A, Koziorowski D, Rudzińska-Bar M, Aasly JO, Lynch T, Mellick GD, Mohan M, Silburn PA, Sanotsky Y, Vilariño-Güell C, Farrer MJ, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Springer W. Heterozygous PINK1 p.G411S increases risk of Parkinson's disease via a dominant-negative mechanism. Brain 2016; 140:98-117. [PMID: 27807026 PMCID: PMC5379862 DOI: 10.1093/brain/aww261] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 01/31/2023] Open
Abstract
See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. Heterozygous mutations in recessive Parkinson’s disease genes have been postulated to increase disease risk. Puschmann et al. report a genetic association between heterozygous PINK1 p.G411S and Parkinson’s disease. They provide structural and functional explanations for a partial dominant-negative effect of the mutant protein, which impairs wild-type PINK1 activity through hetero-dimerization. See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. It has been postulated that heterozygous mutations in recessive Parkinson’s genes may increase the risk of developing the disease. In particular, the PTEN-induced putative kinase 1 (PINK1) p.G411S (c.1231G>A, rs45478900) mutation has been reported in families with dominant inheritance patterns of Parkinson’s disease, suggesting that it might confer a sizeable disease risk when present on only one allele. We examined families with PINK1 p.G411S and conducted a genetic association study with 2560 patients with Parkinson’s disease and 2145 control subjects. Heterozygous PINK1 p.G411S mutations markedly increased Parkinson’s disease risk (odds ratio = 2.92, P = 0.032); significance remained when supplementing with results from previous studies on 4437 additional subjects (odds ratio = 2.89, P = 0.027). We analysed primary human skin fibroblasts and induced neurons from heterozygous PINK1 p.G411S carriers compared to PINK1 p.Q456X heterozygotes and PINK1 wild-type controls under endogenous conditions. While cells from PINK1 p.Q456X heterozygotes showed reduced levels of PINK1 protein and decreased initial kinase activity upon mitochondrial damage, stress-response was largely unaffected over time, as expected for a recessive loss-of-function mutation. By contrast, PINK1 p.G411S heterozygotes showed no decrease of PINK1 protein levels but a sustained, significant reduction in kinase activity. Molecular modelling and dynamics simulations as well as multiple functional assays revealed that the p.G411S mutation interferes with ubiquitin phosphorylation by wild-type PINK1 in a heterodimeric complex. This impairs the protective functions of the PINK1/parkin-mediated mitochondrial quality control. Based on genetic and clinical evaluation as well as functional and structural characterization, we established p.G411S as a rare genetic risk factor with a relatively large effect size conferred by a partial dominant-negative function phenotype.
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Affiliation(s)
- Andreas Puschmann
- 1 Lund University, Department of Clinical Sciences Lund, Neurology, Sweden .,2 Department of Neurology, Skåne University Hospital, Sweden.,3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Fabienne C Fiesel
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Roman Hudec
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maya Ando
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dominika Truban
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Xu Hou
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Kotaro Ogaki
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G Heckman
- 4 Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Elle D James
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maria Swanberg
- 5 Lund University, Department of Experimental Medical Science, Lund, Sweden
| | | | - Oskar Hansson
- 6 Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Sweden.,7 Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Grzegorz Opala
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Siuda
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | | | | | | | | | - Jan O Aasly
- 10 Department of Neurology, St. Olav's Hospital, and Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Timothy Lynch
- 11 Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - George D Mellick
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Megha Mohan
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Peter A Silburn
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.,13 University of Queensland, Asia-Pacific Centre for Neuromodulation, Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Carles Vilariño-Güell
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Matthew J Farrer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Li Chen
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Valina L Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,20 Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,21 Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Owen A Ross
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,23 School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA .,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
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Young BH, Caldwell TA, McKenzie AM, Kokhan O, Berndsen CE. Characterization of the structure and catalytic activity of Legionella pneumophila VipF. Proteins 2016; 84:1422-30. [PMID: 27315603 DOI: 10.1002/prot.25087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 11/05/2022]
Abstract
The pathogenic bacteria Legionella pneumophila is known to cause Legionnaires' Disease, a severe pneumonia that can be fatal to immunocompromised individuals and the elderly. Shohdy et al. identified the L. pneumophila vacuole sorting inhibitory protein VipF as a putative N-acetyltransferase based on sequence homology. We have characterized the basic structural and functional properties of VipF to confirm this original functional assignment. Sequence conservation analysis indicates two putative CoA-binding regions within VipF. Homology modeling and small angle X-ray scattering suggest a monomeric, dual-domain structure joined by a flexible linker. Each domain contains the characteristic beta-splay motif found in many acetyltransferases, suggesting that VipF may contain two active sites. Docking experiments suggest reasonable acetyl-CoA binding locations within each beta-splay motif. Broad substrate screening indicated that VipF is capable of acetylating chloramphenicol and both domains are catalytically active. Given that chloramphenicol is not known to be N-acetylated, this is a surprising finding suggesting that VipF is capable of O-acetyltransferase activity. Proteins 2016; 84:1422-1430. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Byron H Young
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Tracy A Caldwell
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Aidan M McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807.
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Waespy M, Gbem TT, Elenschneider L, Jeck AP, Day CJ, Hartley-Tassell L, Bovin N, Tiralongo J, Haselhorst T, Kelm S. Carbohydrate Recognition Specificity of Trans-sialidase Lectin Domain from Trypanosoma congolense. PLoS Negl Trop Dis 2015; 9:e0004120. [PMID: 26474304 PMCID: PMC4608562 DOI: 10.1371/journal.pntd.0004120] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/05/2015] [Indexed: 12/18/2022] Open
Abstract
Fourteen different active Trypanosoma congolense trans-sialidases (TconTS), 11 variants of TconTS1 besides TconTS2, TconTS3 and TconTS4, have been described. Notably, the specific transfer and sialidase activities of these TconTS differ by orders of magnitude. Surprisingly, phylogenetic analysis of the catalytic domains (CD) grouped each of the highly active TconTS together with the less active enzymes. In contrast, when aligning lectin-like domains (LD), the highly active TconTS grouped together, leading to the hypothesis that the LD of TconTS modulates its enzymatic activity. So far, little is known about the function and ligand specificity of these LDs. To explore their carbohydrate-binding potential, glycan array analysis was performed on the LD of TconTS1, TconTS2, TconTS3 and TconTS4. In addition, Saturation Transfer Difference (STD) NMR experiments were done on TconTS2-LD for a more detailed analysis of its lectin activity. Several mannose-containing oligosaccharides, such as mannobiose, mannotriose and higher mannosylated glycans, as well as Gal, GalNAc and LacNAc containing oligosaccharides were confirmed as binding partners of TconTS1-LD and TconTS2-LD. Interestingly, terminal mannose residues are not acceptor substrates for TconTS activity. This indicates a different, yet unknown biological function for TconTS-LD, including specific interactions with oligomannose-containing glycans on glycoproteins and GPI anchors found on the surface of the parasite, including the TconTS itself. Experimental evidence for such a scenario is presented.
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Affiliation(s)
- Mario Waespy
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Thaddeus T. Gbem
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
| | - Leroy Elenschneider
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - André-Philippe Jeck
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
| | - Christopher J. Day
- Institute for Glycomics, Griffith University Gold Coast Campus, Queensland, Australia
| | | | - Nicolai Bovin
- Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Joe Tiralongo
- Institute for Glycomics, Griffith University Gold Coast Campus, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University Gold Coast Campus, Queensland, Australia
| | - Sørge Kelm
- Centre for Biomolecular Interactions Bremen, Faculty for Biology and Chemistry, University Bremen, Bremen, Germany
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Institute for Glycomics, Griffith University Gold Coast Campus, Queensland, Australia
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Tong J, Pei J, Otwinowski Z, Grishin NV. Refinement by shifting secondary structure elements improves sequence alignments. Proteins 2015; 83:411-27. [PMID: 25546158 DOI: 10.1002/prot.24746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/25/2014] [Accepted: 12/10/2014] [Indexed: 01/09/2023]
Abstract
Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa.
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Affiliation(s)
- Jing Tong
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390; Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390
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Caulfield TR, Fiesel FC, Moussaud-Lamodière EL, Dourado DFAR, Flores SC, Springer W. Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol 2014; 10:e1003935. [PMID: 25375667 PMCID: PMC4222639 DOI: 10.1371/journal.pcbi.1003935] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/25/2014] [Indexed: 11/19/2022] Open
Abstract
Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease. Both gene products, the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin, functionally cooperate in a mitochondrial quality control pathway. Upon stress, PINK1 activates Parkin and enables its translocation to and ubiquitination of damaged mitochondria to facilitate their clearance from the cell. Though PINK1-dependent phosphorylation of Ser65 is an important initial step, the molecular mechanisms underlying the activation of Parkin's enzymatic functions remain unclear. Using molecular modeling, we generated a complete structural model of human Parkin at all atom resolution. At steady state, the Ub ligase is maintained inactive in a closed, auto-inhibited conformation that results from intra-molecular interactions. Evidently, Parkin has to undergo major structural rearrangements in order to unleash its catalytic activity. As a spark, we have modeled PINK1-dependent Ser65 phosphorylation in silico and provide the first molecular dynamics simulation of Parkin conformations along a sequential unfolding pathway that could release its intertwined domains and enable its catalytic activity. We combined free (unbiased) molecular dynamics simulation, Monte Carlo algorithms, and minimal-biasing methods with cell-based high content imaging and biochemical assays. Phosphorylation of Ser65 results in widening of a newly defined cleft and dissociation of the regulatory N-terminal UBL domain. This motion propagates through further opening conformations that allow binding of an Ub-loaded E2 co-enzyme. Subsequent spatial reorientation of the catalytic centers of both enzymes might facilitate the transfer of the Ub moiety to charge Parkin. Our structure-function study provides the basis to elucidate regulatory mechanisms and activity of the neuroprotective Parkin. This may open up new avenues for the development of small molecule Parkin activators through targeted drug design. Parkinson's disease (PD) is a devastating neurological condition caused by the selective and progressive degeneration of dopaminergic neurons in the brain. Loss-of-function mutations in the PINK1 or PARKIN genes are the most common causes of recessively inherited PD. Together the encoded proteins coordinate a protective cellular quality control pathway that allows elimination of impaired mitochondria in order to prevent further cellular damage and ultimately death. Although it is known that the kinase PINK1 operates upstream and activates the E3 Ubiquitin ligase Parkin, the molecular mechanisms remain elusive. Here, we combined state-of-the art computational and functional biological methods to demonstrate that Parkin is sequentially activated through PINK1-dependent phosphorylation and subsequent structural rearrangement. The induced motions result in release of Parkin's closed, auto-inhibited conformation to liberate its enzymatic functions. We provide for the first time a complete protein structure of Parkin at an all atom resolution and a comprehensive molecular dynamics simulation of its activation and opening conformations. The generated models will allow uncovering the exact mechanisms of regulation and enzymatic activity of Parkin and potentially the development of novel therapeutics through a structure-function-based drug design.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
| | | | - Daniel F. A. R. Dourado
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Samuel C. Flores
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
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Hauptmann J, Kater L, Löffler P, Merkl R, Meister G. Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage. RNA (NEW YORK, N.Y.) 2014; 20:1532-1538. [PMID: 25114291 PMCID: PMC4174435 DOI: 10.1261/rna.045203.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/18/2014] [Indexed: 06/03/2023]
Abstract
Argonaute proteins bind small RNAs and mediate cleavage of complementary target RNAs. The human Argonaute protein Ago4 is catalytically inactive, although it is highly similar to catalytic Ago2. Here, we have generated Ago2-Ago4 chimeras and analyzed their cleavage activity in vitro. We identify several specific features that inactivate Ago4: the catalytic center, short sequence elements in the N-terminal domain, and an Ago4-specific insertion in the catalytic domain. In addition, we show that Ago2-mediated cleavage of the noncanonical miR-451 precursor can be carried out by any catalytic human Ago protein. Finally, phylogenetic analyses establish evolutionary distances between the Ago proteins. Interestingly, these distances do not fully correlate with the structural changes inactivating them, suggesting functional adaptations of individual human Ago proteins.
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Affiliation(s)
- Judith Hauptmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Lukas Kater
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Patrick Löffler
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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Raasch K, Bocola M, Labahn J, Leitner A, Eggeling L, Bott M. Interaction of 2-oxoglutarate dehydrogenase OdhA with its inhibitor OdhI in Corynebacterium glutamicum: Mutants and a model. J Biotechnol 2014; 191:99-105. [PMID: 24905147 DOI: 10.1016/j.jbiotec.2014.05.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 01/25/2023]
Abstract
Pyruvate dehydrogenase and oxoglutarate dehydrogenase catalyze key reactions in central metabolism. In Corynebacterium glutamicum and related bacteria like Mycobacterium tuberculosis both activities reside in a novel protein supercomplex with the fusion protein OdhA catalyzing the conversion of oxoglutarate to succinyl-coenzyme A. This activity is inhibited by the forkhead-associated (FHA) domain of the small autoinhibitory protein OdhI. Here we used a biological screen which enabled us to isolate suppressor mutants that are influenced in OdhA-OdhI interaction. Five mutants carrying an OdhI mutation were isolated and one with an OdhA mutation. The OdhA mutein OdhA-C704E and three additional C704 variants were constructed. They exhibited unaltered or even slightly enhanced OdhA activity but showed reduced inhibition and interaction with OdhI. The FHA domain of OdhI was crystallized and its structure found in full agreement with previously determined NMR structures. Based on further structural studies, OdhA-OdhI crosslinking experiments, and modeling we discuss the experimental data generated on OdhA-OdhI interaction, with the latter protein representing a rare example of an FHA domain also recognizing a non-phosphorylated interaction partner.
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Affiliation(s)
- Katharina Raasch
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Marco Bocola
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jörg Labahn
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Center for Structural Systems Biology, c/o DESY, Hamburg, Germany
| | - Alexander Leitner
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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39
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Structural basis of PI(4,5)P2-dependent regulation of GluA1 by phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP5K2A). Pflugers Arch 2014; 466:1885-97. [PMID: 24389605 PMCID: PMC4159565 DOI: 10.1007/s00424-013-1424-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/21/2013] [Accepted: 12/08/2013] [Indexed: 12/19/2022]
Abstract
Ionotropic glutamate receptors are the most important excitatory receptors in the central nervous system, and their impairment can lead to multiple neuronal diseases. Here, we show that glutamate-induced currents in oocytes expressing GluA1 are increased by coexpression of the schizophrenia-associated phosphoinositide kinase PIP5K2A. This effect was due to enhanced membrane abundance and was blunted by a point mutation (N251S) in PIP5K2A. An increase in GluA1 currents was also observed upon acute injection of PI(4,5)P2, the main product of PIP5K2A. By expression of wild-type and mutant PIP5K2A in human embryonic kidney cells, we were able to provide evidence of impaired kinase activity of the mutant PIP5K2A. We defined the region K813–K823 of GluA1 as critical for the PI(4,5)P2 effect by performing an alanine scan that suggested PI(4,5)P2 binding to this area. A PIP strip assay revealed PI(4,5)P2 binding to the C-terminal GluA1 peptide. The present observations disclose a novel mechanism in the regulation of GluA1.
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40
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Zhu L, Cheng F, Piatkowski V, Schwaneberg U. Protein Engineering of the Antitumor Enzyme PpADI for Improved Thermal Resistance. Chembiochem 2013; 15:276-83. [DOI: 10.1002/cbic.201300433] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 11/10/2022]
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41
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Abstract
Motivation: Alignment errors are still the main bottleneck for current template-based protein modeling (TM) methods, including protein threading and homology modeling, especially when the sequence identity between two proteins under consideration is low (<30%). Results: We present a novel protein threading method, CNFpred, which achieves much more accurate sequence–template alignment by employing a probabilistic graphical model called a Conditional Neural Field (CNF), which aligns one protein sequence to its remote template using a non-linear scoring function. This scoring function accounts for correlation among a variety of protein sequence and structure features, makes use of information in the neighborhood of two residues to be aligned, and is thus much more sensitive than the widely used linear or profile-based scoring function. To train this CNF threading model, we employ a novel quality-sensitive method, instead of the standard maximum-likelihood method, to maximize directly the expected quality of the training set. Experimental results show that CNFpred generates significantly better alignments than the best profile-based and threading methods on several public (but small) benchmarks as well as our own large dataset. CNFpred outperforms others regardless of the lengths or classes of proteins, and works particularly well for proteins with sparse sequence profiles due to the effective utilization of structure information. Our methodology can also be adapted to protein sequence alignment. Contact:j3xu@ttic.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jianzhu Ma
- Toyota Technological Institute at Chicago, IL 60637, USA
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42
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A conserved threonine in the S1-S2 loop of KV7.2 and K V7.3 channels regulates voltage-dependent activation. Pflugers Arch 2012; 465:797-804. [PMID: 23271449 DOI: 10.1007/s00424-012-1184-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 11/02/2012] [Accepted: 11/09/2012] [Indexed: 12/12/2022]
Abstract
The voltage-gated potassium channels KV7.2 and KV7.3 (KCNQ2/3 genes) play an important role in regulating neuronal excitability. More than 50 KCNQ2/3 mutations have been identified to cause an inherited form of epilepsy in newborns. For two of those (E119G and S122L) found in the S1-S2 region of KV7.2, we previously showed a decreased channel availability mainly at action potential subthreshold voltages caused by a slight depolarizing shift of the activation curve. Interestingly, recent studies revealed that a threonine residue within the S1-S2 loop, highly conserved among different classes of KV channels, is crucial for both their function and surface expression. To investigate the functional role of the homologous threonine residues in KV7.2 (T114) and KV7.3 (T144) channels, we replaced them with alanine and examined the electrophysiological properties using heterologous expression in CHO cells and whole cell patch clamping. Channels comprising mutant subunits yielded decreased potassium currents with slowed activation and accelerated deactivation kinetics. However, the most striking effect was a depolarizing shift in the voltage dependence of activation reaching +30 mV upon co-expression of both mutant subunits. Potential interactions of T114 within the channel were analyzed by creating a 3D homology model of KV7.2 in an open state suggesting that this residue plays a central role in the formation of a stable interface between the S1-S2 and the S5 segment helices. This could be the explanation why substitution of the conserved threonine in KV7.2 and KV7.3 channels destabilizes the open and favors the closed state of these channels.
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43
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Adenosiland: Walking through adenosine receptors landscape. Eur J Med Chem 2012; 58:248-57. [DOI: 10.1016/j.ejmech.2012.10.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 11/22/2022]
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44
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Jakoblinnert A, Bocola M, Bhattacharjee M, Steinsiek S, Bönitz-Dulat M, Schwaneberg U, Ansorge-Schumacher MB. Who's Who? Allocation of Carbonyl Reductase Isoenzymes from Candida parapsilosis by Combining Bio- and Computational Chemistry. Chembiochem 2012; 13:803-9. [DOI: 10.1002/cbic.201200023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Indexed: 11/10/2022]
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45
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Peng J, Xu J. RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins 2011; 79 Suppl 10:161-71. [PMID: 21987485 DOI: 10.1002/prot.23175] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 07/25/2011] [Accepted: 08/19/2011] [Indexed: 12/13/2022]
Abstract
This work presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single-template threading, alignment quality prediction, and multiple-template threading. This work summarizes the methods used by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template-based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single-template and multiple-template protein threading especially when closely-related templates are unavailable, and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu.
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Affiliation(s)
- Jian Peng
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL 60637, USA
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46
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Wang C, Yan RX, Wang XF, Si JN, Zhang Z. Comparison of linear gap penalties and profile-based variable gap penalties in profile–profile alignments. Comput Biol Chem 2011; 35:308-18. [DOI: 10.1016/j.compbiolchem.2011.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 05/06/2011] [Accepted: 07/11/2011] [Indexed: 10/18/2022]
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47
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Koliwer-Brandl H, Gbem TT, Waespy M, Reichert O, Mandel P, Drebitz E, Dietz F, Kelm S. Biochemical characterization of trans-sialidase TS1 variants from Trypanosoma congolense. BMC BIOCHEMISTRY 2011; 12:39. [PMID: 21801439 PMCID: PMC3173295 DOI: 10.1186/1471-2091-12-39] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/30/2011] [Indexed: 02/01/2023]
Abstract
Background Animal African trypanosomiasis, sleeping sickness in humans and Nagana in cattle, is a resurgent disease in Africa caused by Trypanosoma parasites. Trans-sialidases expressed by trypanosomes play an important role in the infection cycle of insects and mammals. Whereas trans-sialidases of other trypanosomes like the American T. cruzi are well investigated, relatively little research has been done on these enzymes of T. congolense. Results Based on a partial sequence and an open reading frame in the WTSI database, DNA sequences encoding for eleven T. congolense trans-sialidase 1 variants with 96.3% overall amino acid identity were amplified. Trans-sialidase 1 variants were expressed as recombinant proteins, isolated and assayed for trans-sialylation activity. The purified proteins produced α2,3-sialyllactose from lactose by desialylating fetuin, clearly demonstrating their trans-sialidase activity. Using an HPLC-based assay, substrate specificities and kinetic parameters of two variants were characterized in detail indicating differences in substrate specificities for lactose, fetuin and synthetic substrates. Both enzymes were able to sialylate asialofetuin to an extent, which was sufficient to reconstitute binding sites for Siglec-4. A mass spectrometric analysis of the sialylation pattern of glycopeptides from fetuin revealed clear but generally similar changes in the sialylation pattern of the N-glycans on fetuin catalyzed by the trans-sialidases investigated. Conclusions The identification and characterization of a trans-sialidase gene family of the African parasite T. congolense has opened new perspectives for investigating the biological role of these enzymes in Nagana and sleeping sickness. Based on this study it will be interesting to address the expression pattern of these genes and their activities in the different stages of the parasite in its infection cycle. Furthermore, these trans-sialidases have the biotechnological potential to be used for enzymatic modification of sialylated glycoconjugates.
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Affiliation(s)
- Hendrik Koliwer-Brandl
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, Germany
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Hijikata A, Yura K, Noguti T, Go M. Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins 2011; 79:1868-77. [PMID: 21465562 PMCID: PMC3110861 DOI: 10.1002/prot.23011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 01/23/2011] [Accepted: 01/28/2011] [Indexed: 12/27/2022]
Abstract
In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three-dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, introducing multiple sequences, replacing dynamic programming with hidden Markov models, and incorporating 3D structure information. Improvements in the gap penalty have not been a major focus, however, following the development of the affine gap penalty and of the secondary structure dependent gap penalty. We revisited the correlation between protein 3D structure and gap location in a large protein 3D structure data set, and found that the frequency of gap locations approximated to an exponential function of the solvent accessibility of the inserted residues. The nonlinearity of the gap frequency as a function of accessibility corresponded well to the relationship between residue mutation pattern and residue accessibility. By introducing this relationship into the gap penalty calculation for pairwise alignment between template and target amino acid sequences, we were able to obtain a sequence alignment much closer to the structural alignment. The quality of the alignments was substantially improved on a pair of sequences with identity in the “twilight zone” between 20 and 40%. The relocation of gaps by our new method made a significant improvement in comparative modeling, exemplified here by the Bacillus subtilis yitF protein. The method was implemented in a computer program, ALAdeGAP (ALignment with Accessibility dependent GAp Penalty), which is available at http://cib.cf.ocha.ac.jp/target_protein/. Proteins 2011; © 2011 Wiley-Liss, Inc.
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Affiliation(s)
- Atsushi Hijikata
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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Abstract
Motivation: The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases. Results: We present a profile-entropy dependent scoring function for low-homology protein threading. This method will model correlation among various protein features and determine their relative importance according to the amount of homologous information available. When proteins under consideration are low-homology, our method will rely more on structure information; otherwise, homologous information. Experimental results indicate that our threading method greatly outperforms the best profile-based method HHpred and all the top CASP8 servers on low-homology proteins. Tested on the CASP8 hard targets, our threading method is also better than all the top CASP8 servers but slightly worse than Zhang-Server. This is significant considering that Zhang-Server and other top CASP8 servers use a combination of multiple structure-prediction techniques including consensus method, multiple-template modeling, template-free modeling and model refinement while our method is a classical single-template-based threading method without any post-threading refinement. Contact:jinboxu@gmail.com
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Affiliation(s)
- Jian Peng
- Toyota Technological Institute at Chicago, IL 60637, USA
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Cavara NA, Orth A, Hicking G, Seebohm G, Hollmann M. Residues at the tip of the pore loop of NR3B-containing NMDA receptors determine Ca2+ permeability and Mg2+ block. BMC Neurosci 2010; 11:133. [PMID: 20958962 PMCID: PMC2974739 DOI: 10.1186/1471-2202-11-133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 10/19/2010] [Indexed: 11/26/2022] Open
Abstract
Background Members of the complex N-methyl-D-aspartate receptor (NMDAR) subfamily of ionotropic glutamate receptors (iGluRs) conventionally assemble from NR1 and NR2 subunits, the composition of which determines receptor properties. Hallmark features of conventional NMDARs include the requirement for a coagonist, voltage-dependent block by Mg2+, and high permeability for Ca2+. Both Mg2+ sensitivity and Ca2+ permeability are critically dependent on the amino acids at the N and N+1 positions of NR1 and NR2. The recently discovered NR3 subunits feature an unprecedented glycine-arginine combination at those critical sites within the pore. Diheteromers assembled from NR1 and NR3 are not blocked by Mg2+ and are not permeable for Ca2+. Results Employing site-directed mutagenesis of receptor subunits, electrophysiological characterization of mutants in a heterologous expression system, and molecular modeling of the NMDAR pore region, we have investigated the contribution of the unusual NR3 N and N+1 site residues to the unique functional characteristics of receptors containing these subunits. Contrary to previous studies, we provide evidence that both the NR3 N and N+1 site amino acids are critically involved in mediating the unique pore properties. Ca2+ permeability could be rescued by mutating the NR3 N site glycine to the NR1-like asparagine. Voltage-dependent Mg2+ block could be established by providing an Mg2+ coordination site at either the NR3 N or N+1 positions. Conversely, "conventional" receptors assembled from NR1 and NR2 could be made Mg2+ insensitive and Ca2+ impermeable by equipping either subunit with the NR3-like glycine at their N positions, with a stronger contribution of the NR1 subunit. Conclusions This study sheds light on the structure-function relationship of the least characterized member of the NMDAR subfamily. Contrary to previous reports, we provide evidence for a critical functional involvement of the NR3 N and N+1 site amino acids, and propose them to be the essential determinants for the unique pore properties mediated by this subunit.
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Affiliation(s)
- Nora A Cavara
- Department of Biochemistry I - Receptor Biochemistry, Ruhr University Bochum, Universitaetsstrasse 150, D-44780 Bochum, Germany
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