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Neubergerová M, Pleskot R. Plant protein-lipid interfaces studied by molecular dynamics simulations. J Exp Bot 2024:erae228. [PMID: 38761107 DOI: 10.1093/jxb/erae228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Indexed: 05/20/2024]
Abstract
The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions is challenging by experimental techniques. Molecular dynamics (MD) simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to the MD simulations. We describe different steps of performing the MD simulations and provide a broad survey of the MD studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining the MD simulations with artificial intelligence-based protein structure determination opens unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.
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Affiliation(s)
- Michaela Neubergerová
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Roman Pleskot
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
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2
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Esapa CT, McIlhinney RAJ, Waite AJ, Benson MA, Mirzayan J, Piko H, Herczegfalvi Á, Horvath R, Karcagi V, Walter MC, Lochmüller H, Rizkallah PJ, Lu QL, Blake DJ. Misfolding of fukutin-related protein (FKRP) variants in congenital and limb girdle muscular dystrophies. Front Mol Biosci 2023; 10:1279700. [PMID: 38161385 PMCID: PMC10755465 DOI: 10.3389/fmolb.2023.1279700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Fukutin-related protein (FKRP, MIM ID 606596) variants cause a range of muscular dystrophies associated with hypo-glycosylation of the matrix receptor, α-dystroglycan. These disorders are almost exclusively caused by homozygous or compound heterozygous missense variants in the FKRP gene that encodes a ribitol phosphotransferase. To understand how seemingly diverse FKRP missense mutations may contribute to disease, we examined the synthesis, intracellular dynamics, and structural consequences of a panel of missense mutations that encompass the disease spectrum. Under non-reducing electrophoresis conditions, wild type FKRP appears to be monomeric whereas disease-causing FKRP mutants migrate as high molecular weight, disulfide-bonded aggregates. These results were recapitulated using cysteine-scanning mutagenesis suggesting that abnormal disulfide bonding may perturb FKRP folding. Using fluorescence recovery after photobleaching, we found that the intracellular mobility of most FKRP mutants in ATP-depleted cells is dramatically reduced but can, in most cases, be rescued with reducing agents. Mass spectrometry showed that wild type and mutant FKRP differentially associate with several endoplasmic reticulum (ER)-resident chaperones. Finally, structural modelling revealed that disease-associated FKRP missense variants affected the local environment of the protein in small but significant ways. These data demonstrate that protein misfolding contributes to the molecular pathophysiology of FKRP-deficient muscular dystrophies and suggest that molecules that rescue this folding defect could be used to treat these disorders.
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Affiliation(s)
| | | | - Adrian J. Waite
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | - Jasmin Mirzayan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Henriett Piko
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Ágnes Herczegfalvi
- Semmelweis University Pediatric Center Tűzoltó Street Unit, Budapest, Hungary
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Veronika Karcagi
- National Institute of Environmental Health, Department of Molecular Genetics and Diagnostics, Istenhegyi Genetic Diagnostic Centre, Budapest, Hungary
| | - Maggie C. Walter
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, Munich, Germany
| | - Hanns Lochmüller
- Children’s Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Pierre J. Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Qi L. Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Carolinas Medical Center, Charlotte, United States
| | - Derek J. Blake
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Curd A, Cleasby A, Baird M, Peckham M. Modelling 3D supramolecular structure from sparse single-molecule localisation microscopy data. J Microsc 2023. [PMID: 37877157 DOI: 10.1111/jmi.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/19/2023] [Accepted: 10/07/2023] [Indexed: 10/26/2023]
Abstract
Single-molecule localisation microscopy (SMLM) has the potential to reveal the underlying organisation of specific molecules within supramolecular complexes and their conformations, which is not possible with conventional microscope resolution. However, the detection efficiency for fluorescent molecules in cells can be limited in SMLM, even to below 1% in thick and dense samples. Segmentation of individual complexes can also be challenging. To overcome these problems, we have developed a software package termed PERPL: Pattern Extraction from Relative Positions of Localisations. This software assesses the relative likelihoods of models for underlying patterns behind incomplete SMLM data, based on the relative positions of pairs of localisations. We review its principles and demonstrate its use on the 3D lattice of Z-disk proteins in mammalian cardiomyocytes. We find known and novel features at ~20 nm with localisations of less than 1% of the target proteins, using mEos fluorescent protein constructs.
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Affiliation(s)
- Alistair Curd
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Alexa Cleasby
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Michelle Baird
- Cell and Developmental Biology Centre, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michelle Peckham
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | | | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
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Satyaveanthan MV, Ng CL, Awang A, Lam KW, Hassan M. Isolation, purification and biochemical characterization of Conopomorpha cramerella farnesol dehydrogenase. Insect Mol Biol 2023; 32:143-159. [PMID: 36454188 DOI: 10.1111/imb.12820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
In Southeast Asia, Conopomorpha cramerella (Snellen) which is commonly known as the cocoa pod borer (CPB) moth has been identified as the most detrimental pest of Theobroma cacao L. Apart from the various side effects on human health and non-target organisms, heavily relying on synthetic pyrethroid insecticides to control CPB infestations also increases the environmental contamination risks. Thus, developing biorational insecticides that minimally affect the non-target organism and environment by targeting the insect growth regulation process is needed to manage the pest population. In insects, juvenile hormones (JH) regulate critical biological events, especially metamorphosis, development and reproduction. Since the physiological roles of JH III vary among different organisms, the biochemical properties, especially substrate specificity and analogue inhibition, may also be different. Therefore, studies on the JH III biosynthetic pathway enzymes in both plants and insects are beneficial to discover more effective analogues. Bioinformatic analysis and biochemical characterization of a NADP+ -dependent farnesol dehydrogenase, an intermediate enzyme of the JH III pathway, from C. cramerella (CcFolDH), were described in this study. In addition, the farnesol analogues that may act as a potent analogue inhibitor for CcFolDH ware determined using in vitro enzymatic study. The phylogenetic analysis indicated that CcFolDH shared a close phylogenetic relationship to the honeybee's short-chain dehydrogenase/reductase. The 27 kDa CcFolDH has an NADP(H) binding domain with a typical Rossmann fold and is likely a homotetrameric protein in the solution. The enzyme had a greater preference for substrate trans, trans-farnesol and coenzyme NADP+ . In terms of analogue inhibitor inhibition, hexahydroxyfarnesyl acetone showed the highest inhibition (the lowest Ki ) compared to other farnesol analogues. Thus, hexahydroxyfarnesyl acetone would serve as the most potent active ingredient for future biorational pesticide management for C. cramerella infestation. Based on the bioinformatic analyses and biochemical characterizations conducted in this research, we proposed that rCcFolDH differs slightly from other reported farnesol dehydrogenases in terms of molecular weight, substrate preference, coenzymes utilization and analogue inhibitors selection.
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Affiliation(s)
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Alias Awang
- Cocoa Research & Development Centre (Bagan Datuk), Malaysian Cocoa Board, Sg. Sumun, Malaysia
| | - Kok Wai Lam
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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Kumar S, Choudhary N, Faruq M, Kumar A, Saran RK, Indercanti PK, Singh V, Sait H, Jaitley S, Valis M, Kuca K, Polipalli SK, Kumar M, Singh T, Suravajhala P, Sharma R, Kapoor S. Anastrozole-mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: an initial perspective. J Biomol Struct Dyn 2023; 41:14063-14079. [PMID: 36815262 DOI: 10.1080/07391102.2023.2176927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
The mitochondrial permeability transition pore (mtPTP) plays a vital role in altering the structure and function of mitochondria. Cyclophilin D (CypD) is a mitochondrial protein that regulates mtPTP function and a known drug target for therapeutic studies involving mitochondria. While the effect of aromatase inhibition on the mtPTP has been studied previously, the effect of anastrozole on the mtPTP has not been completely elucidated. The role of anastrozole in modulating the mtPTP was evaluated by docking, molecular dynamics and network-guided studies using human CypD data. The peripheral blood mononuclear cells (PBMCs) of patients with mitochondrial disorders and healthy controls were treated with anastrozole and evaluated for mitochondrial permeability transition pore (mtPTP) function and apoptosis using a flow cytometer. Spectrophotometry was employed for estimating total ATP levels. The anastrozole-CypD complex is more stable than cyclosporin A (CsA)-CypD. Anastrozole performed better than cyclosporine in inhibiting mtPTP. Additional effects included inducing mitochondrial membrane depolarization and a reduction in mitochondrial swelling and superoxide generation, intrinsic caspase-3 activity and cellular apoptosis, along with an increase in ATP levels. Anastrozole may serve as a potential therapeutic agent for mitochondrial disorders and ameliorate the clinical phenotype by regulating the activity of mtPTP. However, further studies are required to substantiate our preliminary findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Somesh Kumar
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Neha Choudhary
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamsala, India
| | - Mohammed Faruq
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Arun Kumar
- Department of Emergency Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
| | - Ravindra K Saran
- Department of Pathology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research, Delhi, India
| | | | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamsala, India
| | - Haseena Sait
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Sunita Jaitley
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Králové, Hradec Králové, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Sunil K Polipalli
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
| | - Manoj Kumar
- Department of Emergency Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Department of Microbiology, World College of Medical Science and Research, Jhajjar, Haryana, India
| | - Tejveer Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | | | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Seema Kapoor
- Pediatrics Genetics & Research Laboratory, Department of Pediatrics, Maulana Azad Medical College & Associated LN Hospital, Delhi, India
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Baribeau DA, Vigod S, Brittain H, Vaillancourt T, Szatmari P, Pullenayegum E. Application of Transactional (Cross-lagged panel) Models in Mental Health Research: An Introduction and Review of Methodological Considerations. J Can Acad Child Adolesc Psychiatry 2022; 31:124-134. [PMID: 35919904 PMCID: PMC9275371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Transactional models employing cross-lagged panels have been used for over 40 years to examine the longitudinal relations and directional associations between variables of interest to child and adolescent mental health. Through a narrative synthesis of the literature, we provide an accessible overview of cross-lagged panels with attention to developing a research question, study design and assumptions, dynamic effects (including the random-intercept cross-lagged panel model), and reporting and interpretation of results. Implications and critical appraisal guidelines for readers are discussed throughout. Overall, several key points are highlighted, with particular emphasis on the intended level of inference, model and measure selection, and timing of assessments. Despite limitations in establishing causation, cross-lagged panel models are fundamental to non-experimental epidemiologic research in child mental health and development.
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Affiliation(s)
- Danielle A Baribeau
- Department of Psychiatry, University of Toronto, Toronto, Ontario
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario
| | - Simone Vigod
- Department of Psychiatry, University of Toronto, Toronto, Ontario
- Department of Psychiatry, Women's College Hospital and Women's College Research Institute, Toronto, Ontario
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario
| | - Heather Brittain
- Counselling Psychology, Faculty of Education, University of Ottawa, Ottawa, Ontario
| | - Tracy Vaillancourt
- Counselling Psychology, Faculty of Education, University of Ottawa, Ottawa, Ontario
| | - Peter Szatmari
- Department of Psychiatry, University of Toronto, Toronto, Ontario
- Centre for Addiction and Mental Health and The Hospital for Sick Children, Toronto, Ontario
| | - Eleanor Pullenayegum
- Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario
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Ayipo YO, Alananzeh WA, Ahmad I, Patel H, Mordi MN. Structural modelling and in silico pharmacology of β-carboline alkaloids as potent 5-HT1A receptor antagonists and reuptake inhibitors. J Biomol Struct Dyn 2022:1-17. [PMID: 35881145 DOI: 10.1080/07391102.2022.2104376] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Serotonin (5-HT) antagonists and reuptake inhibitors (SARIs) are atypical antidepressants for managing major depressive disorder. They are oftentimes applied as adjuvants for ameliorating aftereffects of SSRI antidepressants including insomnia and sexual dysfunction. The few available candidates of this class including lorpiprazole and trazodone also display some daunting side effects, making a continuous search for improved alternatives essential. Natural β-carboline alkaloids (NβCs) are interestingly renowned with broad pharmacological spectrum against several neuropsychiatric disorders including depression. However, their potentials as SARIs remain underexplored. In this study, 982 NβCs retrieved from the Ambinter-Greenpharma (Amb) database were virtually screened for potent SARI alternatives using computational and biocheminformatics approaches: homology modelling of 5-HT1A receptor, Glide HTVS, SP and XP molecular docking, molecular dynamics (MD) simulation, ADMET and mutagenicity predictions. The homology receptor was validated as a good representative of human 5HT1A receptor using the RCSB structure validation and quality protocols. From the virtual screening against the 5-HT1A receptor, Amb ligands, Amb18709727 and Amb37857532 showed higher binding affinities by XP scores of -8.725 and -7.976 kcal/mol, and MMGBSA of -87.972 and -107.585 kcal/mol respectively compared to lorpiprazole, a reference SARI with XP score and MMGBSA of -6.512 and -62.788 kcal/mol respectively. They maintained ideal contacts with pharmacologically essential amino acid residues implicated in SARI mechanisms and expressed higher stability and compactness than lorpiprazole throughout the trajectories of 100 ns MD simulation. They also displayed interesting ADME, druggability, low toxicity and mutagenicity profiles, ideal for CNS drug prospects, thus, recommended as putative SARI candidates for further study.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia.,Department of Chemistry and Industrial Chemistry, Kwara State University, Malete, Ilorin, Nigeria
| | - Waleed A Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
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Thomas NW. Phase transitions and (p-T-X) behaviour of centrosymmetric perovskites: modelling with transformed crystallographic data. Acta Crystallogr B Struct Sci Cryst Eng Mater 2022; 78:40-60. [PMID: 35129119 PMCID: PMC8819707 DOI: 10.1107/s2052520621012713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
A reversible transformation of the unit-cell parameters and atomic coordinates of centrosymmetric perovskites ABX3 into a Cartesian space is defined. Analytical expressions for the three vectors for the pseudocubic cell and three vectors for a BX6 octahedron are derived for space groups Pbmn, Cmcm, Ibmm, P4/mbm, P4/nmc, I4/mcm and R3c. The following structural parameters may be derived from these vectors: up to six pseudocubic parameters defining octahedral geometry; length- and angle-based octahedral distortion parameters λ and σ; inclination angles of tilted octahedra, θ1, θ2 and θ3; angles of tilt of octahedra; AX12:BX6 polyhedral volume ratio, VA/VB; parameters ηA and ηB defining the relative contraction of inner AX8 polyhedra and expansion of BX6 octahedra due to octahedral tilting. The application of these parameters is demonstrated by reference to published crystal structures. The variation of ηA and ηB with temperature in the compositional series SrxBa1-xSnO3 and SrxBa1-xHfO3, as well as the temperature series of BaPbO3 and CaTiO3, is related to the sequence of phases Pbmn → Ibmm→ Pm3m. Stabilization of the Cmcm phase is likewise interpreted in terms of these two parameters for NaTaO3 and NaNbO3. The pressure evolution of the structures of MgSiO3, YAlO3, (La1-xNdx)GaO3 (0 ≤ x ≤ 1) and YAl0.25Cr0.75O3 is modelled with the appropriate structural parameters, thereby also addressing the characteristics of the Pbmn → R3c transition. Simulation of MgSiO3 up to 125 GPa and of YAlO3 up to 52 GPa in space group Pbnm is carried out by using the Birch-Murnaghan equation of state. In both cases, full sets of oxygen coordinates assuming regular octahedra are generated. Octahedral distortion is also modelled in the latter system and predicted to have a key influence on structural evolution and the sequence of phase transitions. The core modelling procedures are made available as a Microsoft Excel file.
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Affiliation(s)
- Noel W. Thomas
- Werkstofftechnik Glas and Keramik, Hochschule Koblenz, Rheinstrasse 56, 56203 Hoehr-Grenzhausen, Germany
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Scarsbrook HL, Urban R, Streather BR, Moores A, Mulligan C. Topological analysis of a bacterial DedA protein associated with alkaline tolerance and antimicrobial resistance. Microbiology (Reading) 2021; 167. [PMID: 34914576 DOI: 10.1099/mic.0.001125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Maintaining membrane integrity is of paramount importance to the survival of bacteria as the membrane is the site of multiple crucial cellular processes including energy generation, nutrient uptake and antimicrobial efflux. The DedA family of integral membrane proteins are widespread in bacteria and are associated with maintaining the integrity of the membrane. In addition, DedA proteins have been linked to resistance to multiple classes of antimicrobials in various microorganisms. Therefore, the DedA family are attractive targets for the development of new antibiotics. Despite DedA family members playing a key physiological role in many bacteria, their structure, function and physiological role remain unclear. To help illuminate the structure of the bacterial DedA proteins, we performed substituted cysteine accessibility method (SCAM) analysis on the most comprehensively characterized bacterial DedA protein, YqjA from Escherichia coli. By probing the accessibility of 15 cysteine residues across the length of YqjA using thiol reactive reagents, we mapped the topology of the protein. Using these data, we experimentally validated a structural model of YqjA generated using evolutionary covariance, which consists of an α-helical bundle with two re-entrant hairpin loops reminiscent of several secondary active transporters. In addition, our cysteine accessibility data suggest that YqjA forms an oligomer wherein the protomers are arranged in a parallel fashion. This experimentally verified model of YqjA lays the foundation for future work in understanding the function and mechanism of this interesting and important family.
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Affiliation(s)
- Hollie L Scarsbrook
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Roman Urban
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Bree R Streather
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Alexandra Moores
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
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Fischhoff IR, Castellanos AA, Rodrigues JPGLM, Varsani A, Han BA. Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2. Proc Biol Sci 2021; 288:20211651. [PMID: 34784766 PMCID: PMC8596006 DOI: 10.1098/rspb.2021.1651] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Back and forth transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between humans and animals will establish wild reservoirs of virus that endanger long-term efforts to control COVID-19 in people and to protect vulnerable animal populations. Better targeting surveillance and laboratory experiments to validate zoonotic potential requires predicting high-risk host species. A major bottleneck to this effort is the few species with available sequences for angiotensin-converting enzyme 2 receptor, a key receptor required for viral cell entry. We overcome this bottleneck by combining species' ecological and biological traits with three-dimensional modelling of host-virus protein-protein interactions using machine learning. This approach enables predictions about the zoonotic capacity of SARS-CoV-2 for greater than 5000 mammals-an order of magnitude more species than previously possible. Our predictions are strongly corroborated by in vivo studies. The predicted zoonotic capacity and proximity to humans suggest enhanced transmission risk from several common mammals, and priority areas of geographic overlap between these species and global COVID-19 hotspots. With molecular data available for only a small fraction of potential animal hosts, linking data across biological scales offers a conceptual advance that may expand our predictive modelling capacity for zoonotic viruses with similarly unknown host ranges.
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Affiliation(s)
- Ilya R. Fischhoff
- Cary Institute of Ecosystem Studies, Box AB Millbrook, NY 12545, USA
| | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7700 Cape Town, Rondebosch, South Africa
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Box AB Millbrook, NY 12545, USA
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12
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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13
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Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HDT, Gruzinov A, Borges C, Jeffries CM, Svergun DI, Franke D. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 2021; 54:343-355. [PMID: 33833657 PMCID: PMC7941305 DOI: 10.1107/s1600576720013412] [Citation(s) in RCA: 363] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022] Open
Abstract
The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- Karen Manalastas-Cantos
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Maxim V. Petoukhov
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Clemente Borges
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
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14
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Korneev AA, Krichevets AN, Sugonyaev KV, Ushakov DV, Vinogradov AG, Fomichev AA. Sources of Artifacts in SLODR Detection. Psychol Russ 2021; 14:86-100. [PMID: 36950318 PMCID: PMC10026998 DOI: 10.11621/pir.2021.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 02/06/2021] [Indexed: 11/23/2022] Open
Abstract
Background Spearman's law of diminishing returns (SLODR) states that intercorrelations between scores on tests of intellectual abilities were higher when the data set was comprised of subjects with lower intellectual abilities and vice versa. After almost a hundred years of research, this trend has only been detected on average. Objective To determine whether the very different results were obtained due to variations in scaling and the selection of subjects. Design We used three methods for SLODR detection based on moderated factor analysis (MFCA) to test real data and three sets of simulated data. Of the latter group, the first one simulated a real SLODR effect. The second one simulated the case of a different density of tasks of varying difficulty; it did not have a real SLODR effect. The third one simulated a skewed selection of respondents with different abilities and also did not have a real SLODR effect. We selected the simulation parameters so that the correlation matrix of the simulated data was similar to the matrix created from the real data, and all distributions had similar skewness parameters (about -0.3). Results The results of MFCA are contradictory and we cannot clearly distinguish by this method the dataset with real SLODR from datasets with similar correlation structure and skewness, but without a real SLODR effect. The results allow us to conclude that when effects like SLODR are very subtle and can be identified only with a large sample, then features of the psychometric scale become very important, because small variations of scale metrics may lead either to masking of real SLODR or to false identification of SLODR.
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Affiliation(s)
| | | | | | - Dmitriy V. Ushakov
- Lomonosov Moscow State University, Moscow, Russia
- Institute of Psychology of Russian Academy of Sciences, Moscow, Russia
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15
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Cunha Bustamante-Filho I, Renato Menegassi S, Ribas Pereira G, Dias Salton G, Mosena Munari F, Roberto Schneider M, Costa Mattos R, Otávio Jardim Barcellos J, Pereira Laurino J, Obino Cirne-Lima E, Inês Mascarenhas Jobim M. Bovine seminal plasma osteopontin: Structural modelling, recombinant expression and its relationship with semen quality. Andrologia 2020; 53:e13905. [PMID: 33225455 DOI: 10.1111/and.13905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/13/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022] Open
Abstract
Osteopontin (OPN) is a multifunctional phosphoprotein that has been linked to fertility in bulls. However, the exact mechanism by which OPN contributes to fertilisation is yet unknown. The biotechnological use of OPN in bovine reproduction is promising but some gaps remain unfilled. The present work aimed: (a) to verify whether the seminal plasma OPN is associated with seminal traits and a standard breeding soundness exam; (b) to predict OPN interactions with integrins, CD44 and glycosaminoglycans through molecular docking; and (c) to develop a protocol for recombinant expression of OPN from vesicular gland cDNA. Ejaculates from top ranked bulls had higher amounts of seminal plasma OPN in comparison with bulls classified as questionable (p < .01). The structural modelling and molecular docking predictions indicated that bovine OPN binds to heparin disaccharide, hyaluronic acid and hyaluronan. In addition, docking studies described the binding complexes of OPN with CD44 and the integrin heterodimers α5β1 and αVβ3. Finally, expression of rOPN-6His was successfully obtained after 3 hr of induction with 0.5 mM IPTG at 37°C and a denaturing purification protocol resulted in efficiently purified recombinant OPN. The present results contribute to the development of biotechnological uses of OPN as a biomarker in bovine reproduction.
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Affiliation(s)
- Ivan Cunha Bustamante-Filho
- Laboratório de Biotecnologia, Universidade do Vale do Taquari - UNIVATES, Lajeado, RS, Brazil.,Departamento de Ciência Animal, PPG Zootecnia - NESPRO, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Gene Center, Ludwig-Maximilians Universität München, Munich, Bayern, Germany
| | - Silvio Renato Menegassi
- Departamento de Ciência Animal, PPG Zootecnia - NESPRO, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriel Ribas Pereira
- Laboratório de Biotecnologia, Universidade do Vale do Taquari - UNIVATES, Lajeado, RS, Brazil
| | - Gabrielle Dias Salton
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Fernanda Mosena Munari
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Rodrigo Costa Mattos
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Júlio Otávio Jardim Barcellos
- Departamento de Ciência Animal, PPG Zootecnia - NESPRO, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jomar Pereira Laurino
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Elizabeth Obino Cirne-Lima
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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16
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Baudin M, Schreiber KJ, Martin EC, Petrescu AJ, Lewis JD. Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity. Plant J 2020; 101:352-370. [PMID: 31557357 DOI: 10.1111/tpj.14547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 05/26/2023]
Abstract
NLR (nucleotide-binding [NB] leucine-rich repeat [LRR] receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly modulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor-like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana that allowed us to demonstrate that ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modelling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions modulate ZAR1 activity. We identified determinants required for the formation of the ZARCC oligomer and its activity. Lastly, we characterized intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, USA
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17
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Clyde M, Pipe A, Reid R, Els C, Tulloch H. A bidirectional path analysis model of smoking cessation self-efficacy and concurrent smoking status: impact on abstinence outcomes. Addict Biol 2019; 24:1034-1043. [PMID: 30088695 DOI: 10.1111/adb.12647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/04/2018] [Accepted: 05/27/2018] [Indexed: 11/28/2022]
Abstract
Self-efficacy is routinely associated with abstinence in the addictions literature, and is a major component relapse-prevention models. The magnitude of this relationship has been brought into question following equivocal results in studies controlling for concurrent smoking status. The aim of our study was to clarify the relationship between cessation self-efficacy, smoking status, and cessation outcomes in a cohort of treatment-seeking smokers. Smokers participating in the FLEX trial, a randomized trial investigating the efficacy of three pharmacologic treatments for smoking cessation, completed questionnaires assessing cessation self-efficacy at baseline and at weeks 1, 3, 5 and 10 post-target quit date; smoking status was verified using expired carbon monoxide. Structural models were fit in order to ascertain the relationship between cessation self-efficacy and concurrent smoking at each time-point, and to assess the association between cessation self-efficacy, smoking and seven-day point prevalence smoking status at week 10. A total of 737 treatment-seeking smokers participated. In our path model, self-efficacy and smoking status at all time points were associated with week 10 abstinence (except week 3 self-efficacy), after controlling these values' previous time-points. All direct pathways between cessation self-efficacy and smoking were also significant, supporting a bidirectional relationship. Our results support a bidirectional and reciprocal relationship between cessation self-efficacy and concurrent smoking behavior; participants with higher confidence were more likely to be smoke-free, and concurrent smoking status predicted levels of confidence over the ensuing weeks. Both measures were associated with week 10 abstinence. Our results indicate that while correlated, both cessation self-efficacy and current smoking behavior during a cessation attempt are important independent markers of ultimate cessation success.
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Affiliation(s)
- Matthew Clyde
- Prevention and Rehabilitation Centre; University of Ottawa Heart Institute; Ottawa Ontario Canada
- Department of Psychology; University of Ottawa; Ottawa Ontario Canada
| | - Andrew Pipe
- Prevention and Rehabilitation Centre; University of Ottawa Heart Institute; Ottawa Ontario Canada
- Department of Medicine; University of Ottawa; Ottawa Ontario Canada
| | - Robert Reid
- Prevention and Rehabilitation Centre; University of Ottawa Heart Institute; Ottawa Ontario Canada
- Department of Medicine; University of Ottawa; Ottawa Ontario Canada
| | - Charl Els
- Department of Psychiatry; University of Alberta; Edmonton Alberta Canada
| | - Heather Tulloch
- Prevention and Rehabilitation Centre; University of Ottawa Heart Institute; Ottawa Ontario Canada
- Department of Psychology; University of Ottawa; Ottawa Ontario Canada
- Department of Medicine; University of Ottawa; Ottawa Ontario Canada
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18
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Frolikova M, Manaskova-Postlerova P, Cerny J, Jankovicova J, Simonik O, Pohlova A, Secova P, Antalikova J, Dvorakova-Hortova K. CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization. Int J Mol Sci 2018; 19:ijms19041236. [PMID: 29671763 PMCID: PMC5979608 DOI: 10.3390/ijms19041236] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
Proteins CD9 and CD81 are members of the tetraspanin superfamily and were detected in mammalian sperm, where they are suspected to form an active tetraspanin web and to participate in sperm–egg membrane fusion. The importance of these two proteins during the early stages of fertilization is supported by the complete sterility of CD9/CD81 double null female mice. In this study, the putative mechanism of CD9/CD81 involvement in tetraspanin web formation in sperm and its activity prior to fertilization was addressed. Confocal microscopy and colocalization assay was used to determine a mutual CD9/CD81 localization visualised in detail by super-resolution microscopy, and their interaction was address by co-immunoprecipitation. The species-specific traits in CD9 and CD81 distribution during sperm maturation were compared between mice and humans. A mutual position of CD9/CD81 is shown in human spermatozoa in the acrosomal cap, however in mice, CD9 and CD81 occupy a distinct area. During the acrosome reaction in human sperm, only CD9 is relocated, compared to the relocation of both proteins in mice. The structural modelling of CD9 and CD81 homologous and possibly heterologous network formation was used to propose their lateral Cis as well as Trans interactions within the sperm membrane and during sperm–egg membrane fusion.
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Affiliation(s)
- Michaela Frolikova
- Group of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
| | - Pavla Manaskova-Postlerova
- Group of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic.
| | - Jiri Cerny
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
| | - Jana Jankovicova
- Laboratory of Reproductive Physiology, Institute of Animal Biochemistry and Genetics Centre of Biosciences Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia.
| | - Ondrej Simonik
- Group of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic.
| | - Alzbeta Pohlova
- Group of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague, Czech Republic.
| | - Petra Secova
- Laboratory of Reproductive Physiology, Institute of Animal Biochemistry and Genetics Centre of Biosciences Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia.
| | - Jana Antalikova
- Laboratory of Reproductive Physiology, Institute of Animal Biochemistry and Genetics Centre of Biosciences Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia.
| | - Katerina Dvorakova-Hortova
- Group of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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19
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Wemheuer B, Wemheuer F, Meier D, Billerbeck S, Giebel HA, Simon M, Scherber C, Daniel R. Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea. Microorganisms 2017; 5:microorganisms5040068. [PMID: 29113091 PMCID: PMC5748577 DOI: 10.3390/microorganisms5040068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/16/2022] Open
Abstract
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.
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Affiliation(s)
- Bernd Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Franziska Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Dimitri Meier
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Christoph Scherber
- Institute of Landscape Ecology, University of Muenster, Heisenbergstr. 2, D-48149 Muenster, Germany.
| | - Rolf Daniel
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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21
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Tuukkanen AT, Spilotros A, Svergun DI. Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons. IUCrJ 2017; 4:518-528. [PMID: 28989709 PMCID: PMC5619845 DOI: 10.1107/s2052252517008740] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/12/2017] [Indexed: 05/26/2023]
Abstract
Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct low-resolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects. In addition, utilizing high-flux synchrotron facilities, time-resolved SAXS allows analysis of kinetic processes over time ranges from microseconds to hours. Dedicated bioSAXS beamlines now offer fully automated data-collection and analysis pipelines, where analysis and modelling is conducted on the fly. This enables SAXS to be employed as a high-throughput method to rapidly screen various sample conditions and additives. The growing SAXS user community is supported by developments in data and model archiving and quality criteria. This review illustrates the latest developments in SAXS, in particular highlighting time-resolved applications aimed at flexible and evolving systems.
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Affiliation(s)
- Anne T. Tuukkanen
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alessandro Spilotros
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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22
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Asteris PG, Douvika MG, Apostolopoulou M, Moropoulou A. Seismic and Restoration Assessment of Monumental Masonry Structures. Materials (Basel) 2017; 10:E895. [PMID: 28767073 DOI: 10.3390/ma10080895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/13/2017] [Accepted: 07/20/2017] [Indexed: 11/29/2022]
Abstract
Masonry structures are complex systems that require detailed knowledge and information regarding their response under seismic excitations. Appropriate modelling of a masonry structure is a prerequisite for a reliable earthquake-resistant design and/or assessment. However, modelling a real structure with a robust quantitative (mathematical) representation is a very difficult, complex and computationally-demanding task. The paper herein presents a new stochastic computational framework for earthquake-resistant design of masonry structural systems. The proposed framework is based on the probabilistic behavior of crucial parameters, such as material strength and seismic characteristics, and utilizes fragility analysis based on different failure criteria for the masonry material. The application of the proposed methodology is illustrated in the case of a historical and monumental masonry structure, namely the assessment of the seismic vulnerability of the Kaisariani Monastery, a byzantine church that was built in Athens, Greece, at the end of the 11th to the beginning of the 12th century. Useful conclusions are drawn regarding the effectiveness of the intervention techniques used for the reduction of the vulnerability of the case-study structure, by means of comparison of the results obtained.
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23
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Franke D, Petoukhov MV, Konarev PV, Panjkovich A, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh NR, Franklin JM, Jeffries CM, Svergun DI. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J Appl Crystallogr 2017; 50:1212-1225. [PMID: 28808438 PMCID: PMC5541357 DOI: 10.1107/s1600576717007786] [Citation(s) in RCA: 953] [Impact Index Per Article: 136.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022] Open
Abstract
Developments and improvements of the ATSAS software suite (versions 2.5–2.8) for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described. ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- D Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - M V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.,Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky prospect 31, 119071 Moscow, and N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Kosygina street 4, 119991 Moscow, Russian Federation
| | - P V Konarev
- Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', ploshchad Kurchatova 1, 123182 Moscow, Russian Federation
| | - A Panjkovich
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A Tuukkanen
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - H D T Mertens
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - N R Hajizadeh
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - J M Franklin
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - C M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - D I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
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24
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Agarwal A, Mudgil Y, Pandey S, Fartyal D, Reddy MK. Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development. Bioinformation 2017; 12:416-419. [PMID: 28358146 PMCID: PMC5357570 DOI: 10.6026/97320630012416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants.
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Affiliation(s)
- Aakrati Agarwal
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India;; Plant Molecular Biology Lab, Department of Botany, University of Delhi, New Delhi, India
| | - Yashwanti Mudgil
- Plant Molecular Biology Lab, Department of Botany, University of Delhi, New Delhi, India
| | - Saurabh Pandey
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Dhirendra Fartyal
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Malireddy K Reddy
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
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25
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Xu Y, Muhamadali H, Sayqal A, Dixon N, Goodacre R. Partial Least Squares with Structured Output for Modelling the Metabolomics Data Obtained from Complex Experimental Designs: A Study into the Y-Block Coding. Metabolites 2016; 6:metabo6040038. [PMID: 27801817 PMCID: PMC5192444 DOI: 10.3390/metabo6040038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022] Open
Abstract
Partial least squares (PLS) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. PLS is typically employed as either a regression model (PLS-R) or a classification model (PLS-DA). However, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. Such data often cannot be considered as a “pure” regression or a classification problem. Nevertheless, these data have often still been treated as a regression or classification problem and this could lead to ambiguous results. In this study, we investigated the feasibility of designing a hybrid target matrix Y that better reflects the experimental design than simple regression or binary class membership coding commonly used in PLS modelling. The new design of Y coding was based on the same principle used by structural modelling in machine learning techniques. Two real metabolomics datasets were used as examples to illustrate how the new Y coding can improve the interpretability of the PLS model compared to classic regression/classification coding.
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Affiliation(s)
- Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
| | - Ali Sayqal
- School of Chemistry, Umm Al-Qura University, Al Taif Road, Mecca 24382, Saudi Arabia.
| | - Neil Dixon
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
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26
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Cheng S, Gutmann B, Zhong X, Ye Y, Fisher MF, Bai F, Castleden I, Song Y, Song B, Huang J, Liu X, Xu X, Lim BL, Bond CS, Yiu SM, Small I. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J 2016; 85:532-47. [PMID: 26764122 DOI: 10.1111/tpj.13121] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/05/2016] [Indexed: 05/02/2023]
Abstract
The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.plantppr.com) that provides open access to these resources for the community.
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Affiliation(s)
- Shifeng Cheng
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
| | | | - Yongtao Ye
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Mark F Fisher
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Ian Castleden
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
| | - Yue Song
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Boon L Lim
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, Australia
| | - Siu-Ming Yiu
- HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009, Australia
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Davare MA, Vellore NA, Wagner JP, Eide CA, Goodman JR, Drilon A, Deininger MW, O'Hare T, Druker BJ. Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors. Proc Natl Acad Sci U S A 2015; 112:E5381-90. [PMID: 26372962 DOI: 10.1073/pnas.1515281112] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Oncogenic ROS1 fusion proteins are molecular drivers in multiple malignancies, including a subset of non-small cell lung cancer (NSCLC). The phylogenetic proximity of the ROS1 and anaplastic lymphoma kinase (ALK) catalytic domains led to the clinical repurposing of the Food and Drug Administration (FDA)-approved ALK inhibitor crizotinib as a ROS1 inhibitor. Despite the antitumor activity of crizotinib observed in both ROS1- and ALK-rearranged NSCLC patients, resistance due to acquisition of ROS1 or ALK kinase domain mutations has been observed clinically, spurring the development of second-generation inhibitors. Here, we profile the sensitivity and selectivity of seven ROS1 and/or ALK inhibitors at various levels of clinical development. In contrast to crizotinib's dual ROS1/ALK activity, cabozantinib (XL-184) and its structural analog foretinib (XL-880) demonstrate a striking selectivity for ROS1 over ALK. Molecular dynamics simulation studies reveal structural features that distinguish the ROS1 and ALK kinase domains and contribute to differences in binding site and kinase selectivity of the inhibitors tested. Cell-based resistance profiling studies demonstrate that the ROS1-selective inhibitors retain efficacy against the recently reported CD74-ROS1(G2032R) mutant whereas the dual ROS1/ALK inhibitors are ineffective. Taken together, inhibitor profiling and stringent characterization of the structure-function differences between the ROS1 and ALK kinase domains will facilitate future rational drug design for ROS1- and ALK-driven NSCLC and other malignancies.
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28
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Petoukhov MV, Svergun DI. Ambiguity assessment of small-angle scattering curves from monodisperse systems. ACTA ACUST UNITED AC 2015; 71:1051-8. [PMID: 25945570 DOI: 10.1107/s1399004715002576] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/06/2015] [Indexed: 01/09/2023]
Abstract
A novel approach is presented for an a priori assessment of the ambiguity associated with spherically averaged single-particle scattering. The approach is of broad interest to the structural biology community, allowing the rapid and model-independent assessment of the inherent non-uniqueness of three-dimensional shape reconstruction from scattering experiments on solutions of biological macromolecules. One-dimensional scattering curves recorded from monodisperse systems are nowadays routinely utilized to generate low-resolution particle shapes, but the potential ambiguity of such reconstructions remains a major issue. At present, the (non)uniqueness can only be assessed by a posteriori comparison and averaging of repetitive Monte Carlo-based shape-determination runs. The new a priori ambiguity measure is based on the number of distinct shape categories compatible with a given data set. For this purpose, a comprehensive library of over 14,000 shape topologies has been generated containing up to seven beads closely packed on a hexagonal grid. The computed scattering curves rescaled to keep only the shape topology rather than the overall size information provide a `scattering map' of this set of shapes. For a given scattering data set, one rapidly obtains the number of neighbours in the map and the associated shape topologies such that in addition to providing a quantitative ambiguity measure the algorithm may also serve as an alternative shape-analysis tool. The approach has been validated in model calculations on geometrical bodies and its usefulness is further demonstrated on a number of experimental X-ray scattering data sets from proteins in solution. A quantitative ambiguity score (a-score) is introduced to provide immediate and convenient guidance to the user on the uniqueness of the ab initio shape reconstruction from the given data set.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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29
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Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI. New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 2012; 45:342-350. [PMID: 25484842 PMCID: PMC4233345 DOI: 10.1107/s0021889812007662] [Citation(s) in RCA: 1350] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/20/2012] [Indexed: 11/26/2022] Open
Abstract
New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.
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Affiliation(s)
- Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexander V. Shkumatov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Michal Gajda
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Gorba
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Petr V. Konarev
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
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Puizdar V, Zajc T, Žerovnik E, Renko M, Pieper U, Eswar N, Šali A, Dolenc I, Turk V. Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein. Biol Chem 2012; 393:177-86. [PMID: 22718633 PMCID: PMC4111641 DOI: 10.1515/hsz-2011-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 12/19/2011] [Indexed: 11/15/2022]
Abstract
Cathepsin E splice variant 2 appears in a number of gastric carcinomas. Here we report detecting this variant in HeLa cells using polyclonal antibodies and biotinylated inhibitor pepstatin A. An overexpression of GFP fusion proteins of cathepsin E and its splice variant within HEK-293T cells was performed to show their localization. Their distribution under a fluorescence microscope showed that they are colocalized. We also expressed variants 1 and 2 of cathepsins E, with propeptide and without it, in Escherichia coli. After refolding from the inclusion bodies, the enzymatic activity and circular dichroism spectra of the splice variant 2 were compared to those of the wild-type mature active cathepsins E. While full-length cathepsin E variant 1 is activated at acid pH, the splice variant remains inactive. In contrast to the active cathepsin E, the splice variant 2 predominantly assumes β-sheet structure, prone to oligomerization, at least under in vitro conditions, as shown by atomic force microscopy as shallow disk-like particles. A comparative structure model of splice variant 2 was computed based on its alignment to the known structure of cathepsin E intermediate (Protein Data Bank code 1TZS) and used to rationalize its conformational properties and loss of activity.
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Affiliation(s)
- Vida Puizdar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Tajana Zajc
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Miha Renko
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Narayanan Eswar
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Andrej Šali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences at UCSF, Department of Pharmaceutical Chemistry, University of California, San Francisco, UCSF MC 2552, Byers Hall, 1700 4th Street, Suite 503 B, San Francisco, CA 94158, USA
| | - Iztok Dolenc
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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Abstract
The multi-subunit vacuolar-type H(+)-ATPase consists of a V(1) domain (A-H subunits) catalyzing ATP hydrolysis and a V(0) domain (a, c, c', c", d, e) responsible for H(+) translocation. The mammalian V(0) d subunit is one of the least-well characterized, and its function and position within the pump are still unclear. It has two different forms encoded by separate genes, d1 being ubiquitous while d2 is predominantly expressed at the cell surface in kidney and osteoclast. To determine whether it forms part of the pump's central stalk as suggested by bacterial A-ATPase studies, or is peripheral as hypothesized from a yeast model, we investigated both human d subunit isoforms. In silico structural modelling demonstrated that human d1 and d2 are structural orthologues of bacterial subunit C, despite poor sequence identity. Expression studies of d1 and d2 showed that each can pull down the central stalk's D and F subunits from human kidney membrane, and in vitro studies using D and F further showed that the interactions between these proteins and the d subunit is direct. These data indicate that the d subunit in man is centrally located within the pump and is thus important in its rotary mechanism.
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Affiliation(s)
- Annabel N. Smith
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Richard W. Francis
- Cambridge Institute for Medical Research, University of Cambridge, Box 139 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY UK
| | - Sara L. Sorrell
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Fiona E. Karet
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Box 139 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY UK
- Division of Renal Medicine, University of Cambridge, Cambridge, UK
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