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Sanjeevi M, Mohan A, Ramachandran D, Jeyaraman J, Sekar K. CSSP-2.0: A refined consensus method for accurate protein secondary structure prediction. Comput Biol Chem 2024; 112:108158. [PMID: 39053174 DOI: 10.1016/j.compbiolchem.2024.108158] [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: 12/23/2023] [Revised: 06/19/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Studying the relationship between sequences and their corresponding three-dimensional structure assists structural biologists in solving the protein-folding problem. Despite several experimental and in-silico approaches, still understanding or decoding the three-dimensional structures from the sequence remains a mystery. In such cases, the accuracy of the structure prediction plays an indispensable role. To address this issue, an updated web server (CSSP-2.0) has been created to improve the accuracy of our previous version of CSSP by deploying the existing algorithms. It uses input as probabilities and predicts the consensus for the secondary structure as a highly accurate three-state Q3 (helix, strand, and coil). This prediction is achieved using six recent top-performing methods: MUFOLD-SS, RaptorX, PSSpred v4, PSIPRED, JPred v4, and Porter 5.0. CSSP-2.0 validation includes datasets involving various protein classes from the PDB, CullPDB, and AlphaFold databases. Our results indicate a significant improvement in the accuracy of the consensus Q3 prediction. Using CSSP-2.0, crystallographers can sort out the stable regular secondary structures from the entire complex structure, which would aid in inferring the functional annotation of hypothetical proteins. The web server is freely available at https://bioserver3.physics.iisc.ac.in/cgi-bin/cssp-2/.
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Affiliation(s)
- Madhumathi Sanjeevi
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India; Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630004, India
| | - Ajitha Mohan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India
| | | | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630004, India.
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
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2
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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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3
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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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Dutta S, Chhabra R, Muthusamy V, Gain N, Subramani R, Sarika K, Devi EL, Madhavan J, Zunjare RU, Hossain F. Allelic variation and haplotype diversity of Matrilineal ( MTL) gene governing in vivo maternal haploid induction in maize. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:823-838. [PMID: 38846462 PMCID: PMC11150217 DOI: 10.1007/s12298-024-01456-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Diverse haploid inducer lines with > 6% of haploid induction rate are now routinely used to develop doubled haploid lines. Though MTL gene regulates haploid induction, its molecular characterization and haplotype analysis in maize and its related species have not been undertaken so far. In the present study, the entire 1812 bp long MTL gene was sequenced among two mutant and eight wild-type inbreds. A 4 bp insertion differentiated the mutant from the wild-type allele. Sequence analysis further revealed 103 polymorphic sites including 38 InDels and 65 SNPs. A total of 15 conserved regions were detected, of which exon-4 was the most conserved. Ten gene-based markers specific to MTL revealed the presence of 40 haplotypes among diverse 48 inbreds of exotic and indigenous origin. It generated 20 alleles with an average of two alleles per locus. The mean polymorphic information content was 0.3247 with mean gene diversity of 0.4135. A total of 15 paralogous sequences of MTL were detected in maize genome with 3-7 exons. Maize MTL proteins of both wild-type and mutant were non-polar in nature, and they possessed four domains. R1-nj-based haploid inducer (HI) lines viz., Pusa-HI-101 and Pusa-HI-102 had an average haploid induction rate of 8.45 ± 0.96% and 10.46 ± 1.15%, respectively. Lines wild-type MTL gene did not generate any haploid. In comparison with 27 orthologues of 21 grass species, maize MTL gene had the closest ancestry with Saccharum spontaneum and Sorghum. The information generated here assumes great significance in understanding the diversity of MTL gene and presence of paralogues and orthologues. This is the first report on haplotype analysis and molecular characterization of MTL gene in maize and related grass species. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01456-3.
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Affiliation(s)
- Suman Dutta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rashmi Chhabra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nisrita Gain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Konsam Sarika
- ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, India
| | - Elangbam L. Devi
- ICAR Research Complex for NEH Region, Sikkim Centre, Gangtok, India
| | - Jayanthi Madhavan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajkumar U. Zunjare
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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5
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Mani H, Chang CC, Hsu HJ, Yang CH, Yen JH, Liou JW. Comparison, Analysis, and Molecular Dynamics Simulations of Structures of a Viral Protein Modeled Using Various Computational Tools. Bioengineering (Basel) 2023; 10:1004. [PMID: 37760106 PMCID: PMC10525864 DOI: 10.3390/bioengineering10091004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The structural analysis of proteins is a major domain of biomedical research. Such analysis requires resolved three-dimensional structures of proteins. Advancements in computer technology have led to progress in biomedical research. In silico prediction and modeling approaches have facilitated the construction of protein structures, with or without structural templates. In this study, we used three neural network-based de novo modeling approaches-AlphaFold2 (AF2), Robetta-RoseTTAFold (Robetta), and transform-restrained Rosetta (trRosetta)-and two template-based tools-the Molecular Operating Environment (MOE) and iterative threading assembly refinement (I-TASSER)-to construct the structure of a viral capsid protein, hepatitis C virus core protein (HCVcp), whose structure have not been fully resolved by laboratory techniques. Templates with sufficient sequence identity for the homology modeling of complete HCVcp are currently unavailable. Therefore, we performed domain-based homology modeling for MOE simulations. The templates for each domain were obtained through sequence-based searches on NCBI and the Protein Data Bank. Then, the modeled domains were assembled to construct the complete structure of HCVcp. The full-length structure and two truncated forms modeled using various computational tools were compared. Molecular dynamics (MD) simulations were performed to refine the structures. The root mean square deviation of backbone atoms, root mean square fluctuation of Cα atoms, and radius of gyration were calculated to monitor structural changes and convergence in the simulations. The model quality was evaluated through ERRAT and phi-psi plot analysis. In terms of the initial prediction for protein modeling, Robetta and trRosetta outperformed AF2. Regarding template-based tools, MOE outperformed I-TASSER. MD simulations resulted in compactly folded protein structures, which were of good quality and theoretically accurate. Thus, the predicted structures of certain proteins must be refined to obtain reliable structural models. MD simulation is a promising tool for this purpose.
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Affiliation(s)
- Hemalatha Mani
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Chun-Chun Chang
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 97004, Taiwan
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
| | - Hao-Jen Hsu
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien 97004, Taiwan
| | - Chin-Hao Yang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Jui-Hung Yen
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan
| | - Je-Wen Liou
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
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6
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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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7
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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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8
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Figueiredo MRAD, Strader LC. Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics. Trends Biochem Sci 2022; 47:865-874. [PMID: 35817652 PMCID: PMC9464691 DOI: 10.1016/j.tibs.2022.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 01/03/2023]
Abstract
The plant hormone auxin acts through regulated degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins to regulate transcriptional events. In this review, we examine the composition and function of each Aux/IAA structural motif. We then focus on recent characterization of Aux/IAA N-terminal disordered regions, formation of secondary structure within these disordered regions, and post-translational modifications (PTMs) that affect Aux/IAA function and stability. We propose how structural variations between Aux/IAA family members may be tuned for differential transcriptional repression and degradation dynamics.
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9
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Nacar C. Propensities of Some Amino Acid Pairings in α-Helices Vary with Length. Protein J 2022; 41:551-562. [PMID: 36169766 DOI: 10.1007/s10930-022-10076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/29/2022]
Abstract
The results of secondary structure prediction methods are widely used in applications in biotechnology and bioinformatics. However, the accuracy limit of these methods could be improved up to 92%. One approach to achieve this goal is to harvest information from the primary structure of the peptide. This study aims to contribute to this goal by investigating the variations in propensity of amino acid pairings to α-helices in globular proteins depending on helix length. (n):(n + 4) residue pairings were determined using a comprehensive peptide data set according to backbone hydrogen bond criterion which states that backbone hydrogen bond is the dominant driving force of protein folding. Helix length is limited to 13 to 26 residues. Findings of this study show that propensities of ALA:GLY and GLY:GLU pairings to α-helix in globular protein increase with increasing helix length but of ALA:ALA and ALA:VAL decrease. While the frequencies of ILE:ALA, LEU:ALA, LEU:GLN, LEU:GLU, LEU:LEU, MET:ILE and VAL:LEU pairings remain roughly constant with length, the 25 residue pairings have varying propensities in narrow helix lengths. The remaining pairings have no prominent propensity to α-helices.
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Affiliation(s)
- Cevdet Nacar
- Department of Biophysics, School of Medicine, Marmara University, Istanbul, Turkey.
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10
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
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11
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Talà A, Guerra F, Calcagnile M, Romano R, Resta SC, Paiano A, Chiariello M, Pizzolante G, Bucci C, Alifano P. HrpA anchors meningococci to the dynein motor and affects the balance between apoptosis and pyroptosis. J Biomed Sci 2022; 29:45. [PMID: 35765029 PMCID: PMC9241232 DOI: 10.1186/s12929-022-00829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Neisseria meningitidis the HrpA/HrpB two-partner secretion system (TPS) was implicated in diverse functions including meningococcal competition, biofilm formation, adherence to epithelial cells, intracellular survival and vacuolar escape. These diverse functions could be attributed to distinct domains of secreted HrpA. METHODS A yeast two-hybrid screening, in vitro pull-down assay and immunofluorescence microscopy experiments were used to investigate the interaction between HrpA and the dynein light-chain, Tctex-type 1 (DYNLT1). In silico modeling was used to analyze HrpA structure. Western blot analysis was used to investigate apoptotic and pyroptotic markers. RESULTS The HrpA carboxy-terminal region acts as a manganese-dependent cell lysin, while the results of a yeast two-hybrid screening demonstrated that the HrpA middle region has the ability to bind the dynein light-chain, Tctex-type 1 (DYNLT1). This interaction was confirmed by in vitro pull-down assay and immunofluorescence microscopy experiments showing co-localization of N. meningitidis with DYNLT1 in infected epithelial cells. In silico modeling revealed that the HrpA-M interface interacting with the DYNLT1 has similarity with capsid proteins of neurotropic viruses that interact with the DYNLT1. Indeed, we found that HrpA plays a key role in infection of and meningococcal trafficking within neuronal cells, and is implicated in the modulation of the balance between apoptosis and pyroptosis. CONCLUSIONS Our findings revealed that N. meningitidis is able to effectively infect and survive in neuronal cells, and that this ability is dependent on HrpA, which establishes a direct protein-protein interaction with DYNLTI in these cells, suggesting that the HrpA interaction with dynein could be fundamental for N. meningitidis spreading inside the neurons. Moreover, we found that the balance between apoptotic and pyroptotic pathways is heavily affected by HrpA.
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Affiliation(s)
- Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Silvia Caterina Resta
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Aurora Paiano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Mario Chiariello
- Core Research Laboratory-Siena, Institute for Cancer Research and Prevention (ISPRO), 53100, Siena, Italy.,Institute of Clinical Physiology (IFC), National Research Council (CNR), 53100, Siena, Italy
| | - Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
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12
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Performance of Novel Antimicrobial Protein Bg_9562 and In Silico Predictions on Its Properties with Reference to Its Antimicrobial Efficiency against Rhizoctonia solani. Antibiotics (Basel) 2022; 11:antibiotics11030363. [PMID: 35326826 PMCID: PMC8944631 DOI: 10.3390/antibiotics11030363] [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: 01/25/2022] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice. In the present study, in vitro antifungal assays showed that Bg_9562 was efficient at 35 °C and 45 °C and ineffective either at high acidic pH (3.0) or alkaline pH (9.5) conditions. Compatibility studies between the native bioagents Trichoderma asperellum TAIK1 and Bacillus subtilis BIK3 indicated that Bg_9562 was compatible with the bioagents. A field study using foliar spray of the Bg_9562 protein indicated the need of formulating the protein before its application. In silico analysis predicted that Bg_9562 possess 111 amino acid residues (46 hydrophobic residues, 12 positive and 8 negative residues) with the high aliphatic index of 89.92, attributing to its thermostability with a half-life of 30 h. Bg_9562 (C491H813N137O166S5) possessed a protein binding potential of 1.27 kcal/mol with a better possibility of interacting and perturbing the membrane, the main target for antimicrobial proteins. The secondary structure revealed the predominance of random coils in its structure, and the best 3D model of Bg_9562 was predicted using an ab initio method with Robetta and AlphaFold 2. The predicted binding ligands were nucleic acids and zinc with confidence scores of 0.07 and 0.05, respectively. The N-terminal region (1–14 residues) and C-terminal region (101 to 111) of Bg_9562 residues were predicted to be disordered regions. Stability and binding properties of the protein from the above studies would help to encapsulate Bg_9562 using a suitable carrier to maintain efficiency and improve delivery against Rhizoctonia solani in the most challenging rice ecosphere.
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13
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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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14
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Denisov SS. CXCL17: The Black Sheep in the Chemokine Flock. Front Immunol 2021; 12:712897. [PMID: 34335630 PMCID: PMC8320810 DOI: 10.3389/fimmu.2021.712897] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/28/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Stepan S Denisov
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), University of Maastricht, Maastricht, Netherlands
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15
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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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16
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Shailaja A, Srinath M, Bindu BVB, Giri CC. Isolation of 4-hydroxy 3-methyl 2-butenyl 4-diphosphate reductase ( ApHDR) gene of methyl erythritol diphosphate (MEP) pathway, in silico analysis and differential tissue specific ApHDR expression in Andrographis paniculata (Burm. f) Nees. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:223-235. [PMID: 33707865 PMCID: PMC7907293 DOI: 10.1007/s12298-021-00952-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/23/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED The full length Andrographis paniculate 4-hydroxy 3-methyl 2-butenyl 4-diphosphate reductase (ApHDR) gene of MEP pathway was isolated for the first time. The ApHDR ORF with 1404 bp flanked by 100 bp 5'UTR and 235 bp 3'UTR encoding 467 amino acids (NCBI accession number: MK503970) and cloned in pET 102, transformed and expressed in E. coli BL21. The ApHDR protein physico-chemical properties, secondary and tertiary structure were analyzed. The Ramachandran plot showed 93.8% amino acids in the allowed regions, suggesting high reliability. The cluster of 16 ligands for binding site in ApHDR involved six amino acid residues having 5-8 ligands. The Fe-S cluster binding site was formed with three conserved residues of cysteine at positions C123, C214, C251 of ApHDR. The substrate HMBPP and inhibitors clomazone, paraquat, benzyl viologen's interactions with ApHDR were also assessed using docking. The affinity of Fe-S cluster binding to the cleft was found similar to HMBPP. The HPLC analysis of different type of tissue (plant parts) revealed highest andrographolide content in young leaves followed by mature leaves, stems and roots. The differential expression profile of ApHDR suggested a significant variation in the expression pattern among different tissues such as mature leaves, young leaves, stem and roots. A 16-fold higher expression of ApHDR was observed in the mature leaves of A. paniculata as compared to roots. The young leaves and stem showed 5.5 fold and fourfold higher expression than roots of A. paniculata. Our result generated new genomic information on ApHDR which may open up prospects of manipulation for enhanced diterpene lactone andrographolide production in A. paniculata. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00952-0.
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Affiliation(s)
- Aayeti Shailaja
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana 500007 India
| | - Mote Srinath
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana 500007 India
| | | | - Charu Chandra Giri
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, Telangana 500007 India
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17
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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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18
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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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Mangabeira-Silva IS, Soares PET, Lanza DCF. Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei. J Invertebr Pathol 2020; 177:107498. [PMID: 33137318 DOI: 10.1016/j.jip.2020.107498] [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: 03/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
Despite the considerable number of genetic markers published for Penaeus vannamei, the classification of these markers and their standardization in specific databases is still insufficient. As a consequence, access to these markers is difficult, hampering their application in genetic association studies. In this study, all previously described single nucleotide polymorphisms (SNPs) related to resistance for P. vannamei were revised, and 512 SNPs were identified and classified in detail. We observed that most of the SNPs occurred in the proteins including Toll like receptors 1 and 3, hemocyanin large and small subunits, and anti-lipopolysaccharide factors 1 and 2, allowing to propose to use them as targets in association studies involving resistance in P. vannamei. Additionally, the potential effects of the most frequent non-synonymous coding SNPs in the secondary structure of the main target proteins were evaluated using an in silico approach. These data can serve as the starting point for the development of new genetic and computational tools as well as for the design of new association studies that involve resistance in P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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20
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Study of the Interaction of a Novel Semi-Synthetic Peptide with Model Lipid Membranes. MEMBRANES 2020; 10:membranes10100294. [PMID: 33086635 PMCID: PMC7603383 DOI: 10.3390/membranes10100294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022]
Abstract
Most linear peptides directly interact with membranes, but the mechanisms of interaction are far from being completely understood. Here, we present an investigation of the membrane interactions of a designed peptide containing a non-natural, synthetic amino acid. We selected a nonapeptide that is reported to interact with phospholipid membranes, ALYLAIRKR, abbreviated as ALY. We designed a modified peptide (azoALY) by substituting the tyrosine residue of ALY with an antimicrobial azobenzene-bearing amino acid. Both of the peptides were examined for their ability to interact with model membranes, assessing the penetration of phospholipid monolayers, and leakage across the bilayer of large unilamellar vesicles (LUVs) and giant unilamellar vesicles (GUVs). The latter was performed in a microfluidic device in order to study the kinetics of leakage of entrapped calcein from the vesicles at the single vesicle level. Both types of vesicles were prepared from a 9:1 (mol/mol) mixture of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1′-rac-glycerol). Calcein leakage from the vesicles was more pronounced at a low concentration in the case of azoALY than for ALY. Increased vesicle membrane disturbance in the presence of azoALY was also evident from an enzymatic assay with LUVs and entrapped horseradish peroxidase. Molecular dynamics simulations of ALY and azoALY in an anionic POPC/POPG model bilayer showed that ALY peptide only interacts with the lipid head groups. In contrast, azoALY penetrates the hydrophobic core of the bilayers causing a stronger membrane perturbation as compared to ALY, in qualitative agreement with the experimental results from the leakage assays.
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21
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Jha RK, Khan RJ, Amera GM, Singh E, Pathak A, Jain M, Muthukumaran J, Singh AK. Identification of promising molecules against MurD ligase from Acinetobacter baumannii: insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis. J Mol Model 2020; 26:304. [DOI: 10.1007/s00894-020-04557-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
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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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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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Kashani-Amin E, Tabatabaei-Malazy O, Sakhteman A, Larijani B, Ebrahim-Habibi A. A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools. Curr Drug Discov Technol 2020; 16:159-172. [PMID: 29493456 DOI: 10.2174/1570163815666180227162157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 02/15/2018] [Accepted: 02/22/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. OBJECTIVE A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. METHODS Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. RESULTS Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. CONCLUSION This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.
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Affiliation(s)
- Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ozra Tabatabaei-Malazy
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Medicinal Chemistry and Natural Products Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus. Molecules 2020; 25:molecules25173861. [PMID: 32854275 PMCID: PMC7503981 DOI: 10.3390/molecules25173861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 11/17/2022] Open
Abstract
Fungi contain many plant-nitrilase (NLase) homologues according to database searches. In this study, enzymes NitTv1 from Trametes versicolor and NitAb from Agaricus bisporus were purified and characterized as the representatives of this type of fungal NLase. Both enzymes were slightly more similar to NIT4 type than to NIT1/NIT2/NIT3 type of plant NLases in terms of their amino acid sequences. Expression of the synthetic genes in Escherichia coli Origami B (DE3) was induced with 0.02 mM isopropyl β-D-1-thiogalactopyranoside at 20 °C. Purification of NitTv1 and NitAb by cobalt affinity chromatography gave ca. 6.6 mg and 9.6 mg of protein per 100 mL of culture medium, respectively. Their activities were determined with 25 mM of nitriles in 50 mM Tris/HCl buffer, pH 8.0, at 30 °C. NitTv1 and NitAb transformed β-cyano-L-alanine (β-CA) with the highest specific activities (ca. 132 and 40 U mg−1, respectively) similar to plant NLase NIT4. β-CA was transformed into Asn and Asp as in NIT4 but at lower Asn:Asp ratios. The fungal NLases also exhibited significant activities for (aryl)aliphatic nitriles such as 3-phenylpropionitrile, cinnamonitrile and fumaronitrile (substrates of NLase NIT1). NitTv1 was more stable than NitAb (at pH 5–9 vs. pH 5–7). These NLases may participate in plant–fungus interactions by detoxifying plant nitriles and/or producing plant hormones. Their homology models elucidated the molecular interactions with various nitriles in their active sites.
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Biochemical Characterization of Human Retroviral-Like Aspartic Protease 1 (ASPRV1). Biomolecules 2020; 10:biom10071004. [PMID: 32640672 PMCID: PMC7408472 DOI: 10.3390/biom10071004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022] Open
Abstract
The human retroviral-like aspartic protease 1 (ASPRV1) is a mammalian retroviral-like enzyme that catalyzes a critical proteolytic step during epidermal differentiation; therefore, it is also referred to as skin-specific aspartic protease (SASPase). Neutrophil granulocytes were also found recently to express ASPRV1 that is involved in the progression of acute chronic inflammation of the central nervous system, especially in autoimmune encephalomyelitis. Thus, investigation of ASPRV1 is important due to its therapeutic or diagnostic potential. We investigated the structural characteristics of ASPRV1 by homology modeling; analysis of the proposed structure was used for interpretation of in vitro specificity studies. For in-vitro characterization, activities of SASP28 and SASP14 enzyme forms were measured using synthetic oligopeptide substrates. We demonstrated that self-processing of SASP28 precursor causes autoactivation of the protease. The highest activity was measured for GST-SASP14 at neutral pH and at high ionic strength, and we proved that pepstatin A and acetyl-pepstatin can also inhibit the protease. In agreement with the structural characteristics, the relatively lower urea dissociation constant implied lower dimer stability of SASP14 compared to that of HIV-1 protease. The obtained structural and biochemical characteristics support better understanding of ASPRV1 function in the skin and central nervous system.
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Jain M, Muthukumaran J, Singh AK. Comparative structural and functional analysis of STL and SLL, chitin-binding lectins from Solanum spp. J Biomol Struct Dyn 2020; 39:4907-4922. [DOI: 10.1080/07391102.2020.1781693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
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28
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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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Matsuo K, Gekko K. Circular-Dichroism and Synchrotron-Radiation Circular-Dichroism Spectroscopy as Tools to Monitor Protein Structure in a Lipid Environment. Methods Mol Biol 2020; 2003:253-279. [PMID: 31218622 DOI: 10.1007/978-1-4939-9512-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Circular-dichroism (CD) spectroscopy is a powerful tool for the secondary-structure analysis of proteins. The structural information obtained by CD does not have atomic-level resolution (unlike X-ray crystallography and NMR spectroscopy), but it has the great advantage of being applicable to both nonnative and native proteins in a wide range of solution conditions containing lipids and detergents. The development of synchrotron-radiation CD (SRCD) instruments has greatly expanded the utility of this method by extending the spectra to the vacuum-ultraviolet region below 190 nm and producing information that is unobtainable by conventional CD instruments. Combining SRCD data with bioinformatics provides new insight into the conformational changes of proteins in a membrane environment.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan.
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30
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Jain M, Muthukumaran J, Singh AK. Structural and functional characterization of chitin binding lectin from Datura stramonium: insights from phylogenetic analysis, protein structure prediction, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1698-1716. [DOI: 10.1080/07391102.2020.1737234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
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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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Abstract
A class of secondary structure prediction algorithms use the information from the statistics of the residue pairs found in secondary structural elements. Because the protein folding process is dominated by backbone hydrogen bonding, an approach based on backbone hydrogen-bonded residue pairings would improve the predicting capabilities of these class algorithms. The reliability of the prediction algorithms depends on the quality of the statistics, therefore, of the data set. In this study, it was aimed to determine the propensities of the backbone hydrogen-bonded residue pairings for secondary structural elements of α-helix and β-sheet in globular proteins using a new and comprehensive data set created from the peptides deposited in Worldwide Protein Data Bank. A master data set including 4882 globular peptide chains with resolution better than 2.5 Å, sequence identity smaller than 25% and length of no shorter than 100 residues were created. Separate data sub sets also were created for helix and sheet structures from master set and each sub set includes 4594 and 4483 chains, respectively. Backbone hydrogen-bonded residue pairings in helices and sheets were detected and the propensities of them were represented as odds ratios (observed/[random or expected]) in matrices. Propensities assigned by this study to the residue pairings in secondary structural elements (as helix, overall strands, parallel strands and antiparallel strands) differ from the previous studies by 19 to 34%. These dissimilarities are important and they would cause further improvements in secondary structure prediction algorithms.
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Affiliation(s)
- Cevdet Nacar
- Department of Biophysics, School of Medicine, Marmara University, Istanbul, Turkey.
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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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Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
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Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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36
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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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37
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Ibrahim MAA, Hassan AMA. Comparative Modeling and Evaluation of Leukotriene B4 Receptors for Selective Drug Discovery Towards the Treatment of Inflammatory Diseases. Protein J 2019; 37:518-530. [PMID: 30267300 DOI: 10.1007/s10930-018-9797-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Leukotriene B4 (LTB4) exerts its biological effects through stimulation of specific G protein-coupled receptors (GPCRs)-namely BLT1 and BLT2. Due to the absence of human BLT1 and BLT2 crystal structures, the current study was set to predict the 3D structures of these two receptors for structure-based anti-inflammatory drug discovery. Homology modeling of the BLT1 receptor was first constructed, based on various X-ray and NMR GPCR templates, followed by molecular dynamics (MD) refinement. Using a single-template approach, nine well-established alignment methods and ten secondary structure prediction methods during the backbone generation were implemented and assessed. The binding sites of the BLT1 receptor were then mapped using fifteen chemical probes with the help of FTMAP and AutoDock Vina 4.2 software. Model validation was performed through the docking of eight specific antagonists that have experimental inhibition constants (ki) towards BLT1. The antagonists-BLT1 docked structures were then subjected to AMBER-based molecular mechanical minimization and the corresponding binding energies were calculated using molecular mechanics-generalized Born surface area (MM/GBSA) approach. According to the results, the most energetically stable models were constructed using SAlign method for the alignment process and PSIPRED for secondary structure prediction. In comparison, the refined BLT1 model built on 2KS9 as an NMR template has the lowest DOPE energy compared to those built on 4EA3 and 4XT1 as X-ray templates. According to the mapping results, two main binding sites were identified: one was among TMs II, III and VII and the other was among TMs III, IV and V. For the antagonists, correlation between binding energies and experimental data was in a good agreement, with a correlation coefficient (R2 value) of 0.91. Due to the great amino acid sequence similarity between BLT1 and BLT2 receptors (calculated as 45.2%), BLT2 model was constructed based on the predicted BLT1 model.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt.
| | - Alaa M A Hassan
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
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38
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Kenri T, Kawakita Y, Kudo H, Matsumoto U, Mori S, Furukawa Y, Tahara YO, Shibayama K, Hayashi Y, Arai M, Miyata M. Production and characterization of recombinant P1 adhesin essential for adhesion, gliding, and antigenic variation in the human pathogenic bacterium, Mycoplasma pneumoniae. Biochem Biophys Res Commun 2018; 508:1050-1055. [PMID: 30551878 DOI: 10.1016/j.bbrc.2018.11.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/05/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
Abstract
Mycoplasma pneumoniae forms an attachment organelle at one cell pole, binds to the host cell surface, and glides via a unique mechanism. A 170-kDa protein, P1 adhesin, present on the organelle surface plays a critical role in the binding and gliding process. In this study, we obtained a recombinant P1 adhesin comprising 1476 amino acid residues, excluding the C-terminal domain of 109 amino acids that carried the transmembrane segment, that were fused to additional 17 amino acid residues carrying a hexa-histidine (6 × His) tag using an Escherichia coli expression system. The recombinant protein showed solubility, and chirality in circular dichroism (CD). The results of analytical gel filtration, ultracentrifugation, negative-staining electron microscopy, and small-angle X-ray scattering (SAXS) showed that the recombinant protein exists in a monomeric form with a uniformly folded structure. SAXS analysis suggested the presence of a compact and ellipsoidal structure rather than random or molten globule-like conformation. Structure model based on SAXS results fitted well with the corresponding structure obtained with cryo-electron tomography from a closely related species, M. genitalium. This recombinant protein may be useful for structural and functional studies as well as for the preparation of antibodies for medical applications.
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Affiliation(s)
- Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Yoshito Kawakita
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - U Matsumoto
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan; Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan; The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.
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39
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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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40
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Tanaka K, Teramura N, Hayashida O, Iijima K, Okitsu T, Hattori S. The C-terminal segment of collagenase in Grimontia hollisae binds collagen to enhance collagenolysis. FEBS Open Bio 2018; 8:1691-1702. [PMID: 30338219 PMCID: PMC6168687 DOI: 10.1002/2211-5463.12510] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
The collagenase secreted by Grimontia hollisae strain 1706B is a 74 kDa protein that consists of two parts: the catalytic module and a C‐terminal segment that includes the bacterial pre‐peptidase C‐terminal domain. Here, we produced a recombinant C‐terminal segment protein and examined its ability to bind collagen and other characteristics as compared with collagen‐binding domains (CBDs) derived from Hathewaya histolytica (Clostridium histolyticum) collagenases; these CBDs are the only ones thus far identified in bacterial collagenases. We found that the C‐terminal segment binds to collagen only when the collagen is in its triple‐helical conformation. Moreover, the C‐terminal segment and the CBDs from H. histolytica have comparable characteristics, including binding affinity to type I collagen, substrate spectrum, and binding conditions with respect to salt concentration and pH. However, the C‐terminal segment has a completely different primary structure from those of the CBDs from H. histolytica. As regards secondary structure, in silico prediction indicates that the C‐terminal segment may be homologous to those in CBDs from H. histolytica. Furthermore, we performed collagenase assays using fluorescein isothiocyanate‐labeled type I collagen to show that the C‐terminal segment positively contributes to the collagenolytic activity of the 74 kDa collagenase from G. hollisae.
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Affiliation(s)
| | | | | | | | - Teru Okitsu
- Institute of Industrial Science The University of Tokyo Japan
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41
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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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42
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Rotem E, Faingold O, Charni M, Klug YA, Harari D, Shmuel-Galia L, Nudelman A, Rotter V, Shai Y. The HTLV-1 gp21 fusion peptide inhibits antigen specific T-cell activation in-vitro and in mice. PLoS Pathog 2018; 14:e1007044. [PMID: 29727445 PMCID: PMC5955599 DOI: 10.1371/journal.ppat.1007044] [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: 03/06/2018] [Revised: 05/16/2018] [Accepted: 04/18/2018] [Indexed: 11/17/2022] Open
Abstract
The ability of the Lentivirus HIV-1 to inhibit T-cell activation by its gp41 fusion protein is well documented, yet limited data exists regarding other viral fusion proteins. HIV-1 utilizes membrane binding region of gp41 to inhibit T-cell receptor (TCR) complex activation. Here we examined whether this T-cell suppression strategy is unique to the HIV-1 gp41. We focused on T-cell modulation by the gp21 fusion peptide (FP) of the Human T-lymphotropic Virus 1 (HTLV-1), a Deltaretrovirus that like HIV infects CD4+ T-cells. Using mouse and human in-vitro T-cell models together with in-vivo T-cell hyper activation mouse model, we reveal that HTLV-1's FP inhibits T-cell activation and unlike the HIV FP, bypasses the TCR complex. HTLV FP inhibition induces a decrease in Th1 and an elevation in Th2 responses observed in mRNA, cytokine and transcription factor profiles. Administration of the HTLV FP in a T-cell hyper activation mouse model of multiple sclerosis alleviated symptoms and delayed disease onset. We further pinpointed the modulatory region within HTLV-1's FP to the same region previously identified as the HIV-1 FP active region, suggesting that through convergent evolution both viruses have obtained the ability to modulate T-cells using the same region of their fusion protein. Overall, our findings suggest that fusion protein based T-cell modulation may be a common viral trait.
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Affiliation(s)
- Etai Rotem
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Omri Faingold
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Meital Charni
- Department of molecular cell biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoel A Klug
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Harari
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Liraz Shmuel-Galia
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Alon Nudelman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of molecular cell biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yechiel Shai
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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43
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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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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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Structural and Functional Characterization of the Interaction of Snapin with the Dopamine Transporter: Differential Modulation of Psychostimulant Actions. Neuropsychopharmacology 2018; 43:1041-1051. [PMID: 28905875 PMCID: PMC5854797 DOI: 10.1038/npp.2017.217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 12/12/2022]
Abstract
The importance of dopamine (DA) neurotransmission is emphasized by its direct implication in several neurological and psychiatric disorders. The DA transporter (DAT), target of psychostimulant drugs, is the key protein that regulates spatial and temporal activity of DA in the synaptic cleft via the rapid reuptake of DA into the presynaptic terminal. There is strong evidence suggesting that DAT-interacting proteins may have a role in its function and regulation. Performing a two-hybrid screening, we identified snapin, a SNARE-associated protein implicated in synaptic transmission, as a new binding partner of the carboxyl terminal of DAT. Our data show that snapin is a direct partner and regulator of DAT. First, we determined the domains required for this interaction in both proteins and characterized the DAT-snapin interface by generating a 3D model. Using different approaches, we demonstrated that (i) snapin is expressed in vivo in dopaminergic neurons along with DAT; (ii) both proteins colocalize in cultured cells and brain and, (iii) DAT and snapin are present in the same protein complex. Moreover, by functional studies we showed that snapin produces a significant decrease in DAT uptake activity. Finally, snapin downregulation in mice produces an increase in DAT levels and transport activity, hence increasing DA concentration and locomotor response to amphetamine. In conclusion, snapin/DAT interaction represents a direct link between exocytotic and reuptake mechanisms and is a potential target for DA transmission modulation.
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46
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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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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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Groeneweg S, Lima de Souza EC, Meima ME, Peeters RP, Visser WE, Visser TJ. Outward-Open Model of Thyroid Hormone Transporter Monocarboxylate Transporter 8 Provides Novel Structural and Functional Insights. Endocrinology 2017; 158:3292-3306. [PMID: 28977587 DOI: 10.1210/en.2017-00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/06/2017] [Indexed: 12/28/2022]
Abstract
Monocarboxylate transporter 8 (MCT8) facilitates cellular uptake and efflux of thyroid hormone (TH). Mutations in MCT8 result in severe intellectual and motor disability known as the Allan-Herndon-Dudley syndrome (AHDS). Previous studies have provided valuable insights into the putative mechanism of substrate binding in the inward-open conformation, required for TH efflux. The current study aims to delineate the mechanism of substrate binding in the outward-open conformation, required for TH uptake. Extensive chemical modification and site-directed mutagenesis studies were used to guide protein homology modeling of MCT8 in the outward-open conformation. Arg271 and Arg445 were modified by phenylglyoxal, which was partially prevented in the presence of substrate. Substrate docking in our outward-open model suggested an important role for His192 and Arg445 in substrate binding. Interestingly, mutations affecting these residues have been identified in patients who have AHDS. In addition, our outward-open model predicted the location of Phe189, Met227, Phe279, Gly282, Phe287, and Phe501 at the substrate-binding center, and their Ala substitution differentially affected the apparent Vmax and Km of T3 transport, with F189A, F279A, and F287A showing the highest impact. Thus, here we present an MCT8 homology model in the outward-open conformation, which supports the important role of His192 and Arg445 in substrate docking and identifies critical residues at the putative substrate-binding center. Our findings provide insights into MCT8 structure and function, which add to our understanding of the pathogenic mechanism of mutations found in patients who have AHDS and can be used to screen for novel substrates and inhibitors.
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Affiliation(s)
- Stefan Groeneweg
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Elaine C Lima de Souza
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Marcel E Meima
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Robin P Peeters
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - W Edward Visser
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Theo J Visser
- The Rotterdam Thyroid Center & Department of Internal Medicine, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands
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Regulation of the Human Phosphatase PTPN4 by the inter-domain linker connecting the PDZ and the phosphatase domains. Sci Rep 2017; 7:7875. [PMID: 28801650 PMCID: PMC5554198 DOI: 10.1038/s41598-017-08193-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/05/2017] [Indexed: 11/21/2022] Open
Abstract
Human protein tyrosine phosphatase non-receptor type 4 (PTPN4) has been shown to prevent cell death. The active form of human PTPN4 consists of two globular domains, a PDZ (PSD-95/Dlg/ZO-1) domain and a phosphatase domain, tethered by a flexible linker. Targeting its PDZ domain abrogates this protection and triggers apoptosis. We previously demonstrated that the PDZ domain inhibits the phosphatase activity of PTPN4 and that the mere binding of a PDZ ligand is sufficient to release the catalytic inhibition. We demonstrate here that the linker connecting the PDZ domain and the phosphatase domain is involved in the regulation of the phosphatase activity in both PDZ-related inhibition and PDZ ligand-related activation events. We combined bioinformatics and kinetic studies to decipher the role of the linker in the PTPN4 activity. By comparing orthologous sequences, we identified a conserved patch of hydrophobic residues in the linker. We showed that mutations in this patch affect the regulation of the PTPN4 bidomain indicating that the PDZ-PDZ ligand regulation of PTPN4 is a linker-mediated mechanism. However, the mutations do not alter the binding of the PDZ ligand. This study strengthens the notion that inter-domain linker can be of functional importance in enzyme regulation of large multi-domain proteins.
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Welner DH, Shin D, Tomaleri GP, DeGiovanni AM, Tsai AYL, Tran HM, Hansen SF, Green DT, Scheller HV, Adams PD. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. PLoS One 2017; 12:e0177591. [PMID: 28598995 PMCID: PMC5466300 DOI: 10.1371/journal.pone.0177591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/28/2017] [Indexed: 11/28/2022] Open
Abstract
Molecular characterization of plant cell wall glycosyltransferases is a critical step towards understanding the biosynthesis of the complex plant cell wall, and ultimately for efficient engineering of biofuel and agricultural crops. The majority of these enzymes have proven very difficult to obtain in the needed amount and purity for such molecular studies, and recombinant cell wall glycosyltransferase production efforts have largely failed. A daunting number of strategies can be employed to overcome this challenge, including optimization of DNA and protein sequences, choice of expression organism, expression conditions, co-expression partners, purification methods, and optimization of protein solubility and stability. Hence researchers are presented with thousands of potential conditions to test. Ultimately, the subset of conditions that will be sampled depends on practical considerations and prior knowledge of the enzyme(s) being studied. We have developed a rational approach to this process. We devise a pipeline comprising in silico selection of targets and construct design, and high-throughput expression screening, target enrichment, and hit identification. We have applied this pipeline to a test set of Arabidopsis thaliana cell wall glycosyltransferases known to be challenging to obtain in soluble form, as well as to a library of cell wall glycosyltransferases from other plants including agricultural and biofuel crops. The screening results suggest that recombinant cell wall glycosyltransferases in general have a very low soluble:insoluble ratio in lysates from heterologous expression cultures, and that co-expression of chaperones as well as lysis buffer optimization can increase this ratio. We have applied the identified preferred conditions to Reversibly Glycosylated Polypeptide 1 from Arabidopsis thaliana, and processed this enzyme to near-purity in unprecedented milligram amounts. The obtained preparation of Reversibly Glycosylated Polypeptide 1 has the expected arabinopyranose mutase and autoglycosylation activities.
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Affiliation(s)
- Ditte Hededam Welner
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
| | - David Shin
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Giovani P. Tomaleri
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Andy M. DeGiovanni
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Alex Yi-Lin Tsai
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Huu M. Tran
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California, United States of America
| | - Sara Fasmer Hansen
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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