751
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Sequence-Based Prediction of Fuzzy Protein Interactions. J Mol Biol 2020; 432:2289-2303. [DOI: 10.1016/j.jmb.2020.02.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/31/2022]
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752
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Fu X, Cai L, Zeng X, Zou Q. StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. Bioinformatics 2020; 36:3028-3034. [DOI: 10.1093/bioinformatics/btaa131] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 12/19/2022] Open
Abstract
Abstract
Motivation
Cell-penetrating peptides (CPPs) are a vehicle for transporting into living cells pharmacologically active molecules, such as short interfering RNAs, nanoparticles, plasmid DNAs and small peptides, thus offering great potential as future therapeutics. Existing experimental techniques for identifying CPPs are time-consuming and expensive. Thus, the prediction of CPPs from peptide sequences by using computational methods can be useful to annotate and guide the experimental process quickly. Many machine learning-based methods have recently emerged for identifying CPPs. Although considerable progress has been made, existing methods still have low feature representation capabilities, thereby limiting further performance improvements.
Results
We propose a method called StackCPPred, which proposes three feature methods on the basis of the pairwise energy content of the residue as follows: RECM-composition, PseRECM and RECM–DWT. These features are used to train stacking-based machine learning methods to effectively predict CPPs. On the basis of the CPP924 and CPPsite3 datasets with jackknife validation, StackDPPred achieved 94.5% and 78.3% accuracy, which was 2.9% and 5.8% higher than the state-of-the-art CPP predictors, respectively. StackCPPred can be a powerful tool for predicting CPPs and their uptake efficiency, facilitating hypothesis-driven experimental design and accelerating their applications in clinical therapy.
Availability and implementation
Source code and data can be downloaded from https://github.com/Excelsior511/StackCPPred.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Lijun Cai
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
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753
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Sadar MD. Discovery of drugs that directly target the intrinsically disordered region of the androgen receptor. Expert Opin Drug Discov 2020; 15:551-560. [PMID: 32100577 DOI: 10.1080/17460441.2020.1732920] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Intrinsically disordered proteins (IDPs) and regions (IDRs) lack stable three-dimensional structure making drug discovery challenging. A validated therapeutic target for diseases such as prostate cancer is the androgen receptor (AR) which has a disordered amino-terminal domain (NTD) that contains all of its transcriptional activity. Drug discovery against the AR-NTD is of intense interest as a potential treatment for disease such as advanced prostate cancer that is driven by truncated constitutively active splice variants of AR that lack the C-terminal ligand-binding domain (LBD).Areas covered: This article presents an overview of the relevance of AR and its intrinsically disordered NTD as a drug target. AR structure and approaches to blocking AR transcriptional activity are discussed. The discovery of small molecules, including the libraries used, proven binders to the AR-NTD, and site of interaction of these small molecules in the AR-NTD are presented along with discussion of the Phase I clinical trial.Expert opinion: The lack of drugs in the clinic that directly bind IDPs/IDRs reflects the difficulty of targeting these proteins and obtaining specificity. However, it may also point to an inappropriateness of too closely borrowing concepts and resources from drug discovery to folded proteins.
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Affiliation(s)
- Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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754
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Dey A, Sen S, Uversky VN, Maulik U. Structural facets of POU2F1 in light of the functional annotations and sequence-structure patterns. J Biomol Struct Dyn 2020; 39:1093-1105. [PMID: 32081083 DOI: 10.1080/07391102.2020.1733092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
POU domain class 2 homebox 1 or POU2F1 is broadly known as an important transcription factor. Due to its association with different types of malignancies, POU2F1 became one of the key factors in pancancer analysis. However, in spite of considering this protein as a potential drug target, none of the drug targeting POU2F1 has been designed as of yet due to the extreme structural flexibility of this protein. In this article, we have proposed a three-level comprehensive framework for understanding the structural conservation and co-variation of POU2F1. First, a gene regulatory network based on the normal and pathological functions of POU2F1 has been created for better understanding the strong association between POU2F1 deregulation and cancers. After that, based on the evolutionary sequence space analysis, the comparative sequence dynamics of the protein members of POU domain family has been studied mostly between non-human and human species. Subsequently, the reciprocity effect of the residual co-variation has been identified through direct coupling analysis. Along with that, the structure of POU2F1 has been analyzed depending on quality assessment and normal mode-based structure network. Comparing the sequence and structure space information, the most significant set of residues viz., 3, 9, 13, 17, 20, 21, 28, 35, and 36 have been identified as structural facet for function. This study demonstrates that the structural malleability of POU2F1 serves as one of the prime reason behind its functional multiplicity in terms of protein moonlighting. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashmita Dey
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Sagnik Sen
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Vladimir N Uversky
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ujjwal Maulik
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
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755
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Schultzhaus Z, Romsdahl J, Chen A, Tschirhart T, Kim S, Leary D, Wang Z. The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure. Environ Microbiol 2020; 22:1310-1326. [PMID: 32011087 DOI: 10.1111/1462-2920.14936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 01/21/2023]
Abstract
The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses and is used as a model for understanding the diverse roles of melanin in fungi. Here, we describe the extent of resistance of E. dermatitidis to acute γ-radiation exposure and the major mechanisms it uses to recover from this stress. We find that melanin does not protect E. dermatitidis from γ-radiation. Instead, environmental factors such as nutrient availability, culture age and culture density are much greater determinants of cell survival after exposure. We also observe a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation and DNA repair, and is unaffected by the presence of melanin. Together, these results suggest that the ability of E. dermatitidis to survive γ-radiation exposure is determined by the prior and the current metabolic state of the cells as well as DNA repair mechanisms, and that small changes in these conditions can lead to large effects in radiation resistance, which should be taken into account when understanding how diverse fungi recover from this unique stress.
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Affiliation(s)
- Zachary Schultzhaus
- National Research Council Postdoctoral Research Associate, National Research Laboratory, Washington, DC, USA
| | - Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, National Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Tanya Tschirhart
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Seongwon Kim
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Dagmar Leary
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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756
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Trushina NI, Mulkidjanian AY, Brandt R. The microtubule skeleton and the evolution of neuronal complexity in vertebrates. Biol Chem 2020; 400:1163-1179. [PMID: 31116700 DOI: 10.1515/hsz-2019-0149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022]
Abstract
The evolution of a highly developed nervous system is mirrored by the ability of individual neurons to develop increased morphological complexity. As microtubules (MTs) are crucially involved in neuronal development, we tested the hypothesis that the evolution of complexity is driven by an increasing capacity of the MT system for regulated molecular interactions as it may be implemented by a higher number of molecular players and a greater ability of the individual molecules to interact. We performed bioinformatics analysis on different classes of components of the vertebrate neuronal MT cytoskeleton. We show that the number of orthologs of tubulin structure proteins, MT-binding proteins and tubulin-sequestering proteins expanded during vertebrate evolution. We observed that protein diversity of MT-binding and tubulin-sequestering proteins increased by alternative splicing. In addition, we found that regions of the MT-binding protein tau and MAP6 displayed a clear increase in disorder extent during evolution. The data provide evidence that vertebrate evolution is paralleled by gene expansions, changes in alternative splicing and evolution of coding sequences of components of the MT system. The results suggest that in particular evolutionary changes in tubulin-structure proteins, MT-binding proteins and tubulin-sequestering proteins were prominent drivers for the development of increased neuronal complexity.
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Affiliation(s)
- Nataliya I Trushina
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastraße 7, D-49076 Osnabrück, Germany.,A.N. Belozersky Institute of Physico-Chemical Biology and School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Center for Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Institute of Cognitive Science, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
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757
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Changes in hydrophobicity mainly promotes the aggregation tendency of ALS associated SOD1 mutants. Int J Biol Macromol 2020; 145:904-913. [PMID: 31669277 DOI: 10.1016/j.ijbiomac.2019.09.181] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
Protein misfolding and aggregation due to mutations, are associated with fatal neurodegenerative disorders. The mutations in Cu/Zn superoxide dismutase (SOD1) causing its misfolding and aggregation are found linked to the motor neuron disorder, amyotrophic lateral sclerosis. Since the mutations are scattered throughout SOD1 structure, determining the exact molecular mechanism underlying the ALS pathology remains unresolved. In this study, we have investigated the major molecular factors that mainly contribute to SOD1 destabilization, intrinsic disorder, and misfolding using sequence and structural information. We have analysed 153 ALS causing SOD1 point mutants for aggregation tendency using four different aggregation prediction tools, viz., Aggrescan3D (A3D), CamSol, GAP and Zyggregator. Our results suggest that 74-79 mutants are susceptible to aggregation, due to distorted native interactions originated at the mutation site. Majority of the aggregation prone mutants are located in the buried regions of SOD1 molecule. Further, the mutations at the hydrophobic amino acids primarily promote the aggregation tendency of SOD1 protein through different destabilizing mechanisms including changes in hydrophobic free energy, loss of electrostatic interactions in the protein's surface and loss of hydrogen bonds that bridges the protein core and surface.
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758
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Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020; 22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.
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Affiliation(s)
| | | | - Jiaqi Zhou
- Huazhong University of Science and Technology
| | - Ying Shi
- Huazhong University of Science and Technology
| | - Chen Ruan
- Huazhong University of Science and Technology
| | - Yiran Tu
- Huazhong University of Science and Technology
| | - Lan Yao
- Huazhong University of Science and Technology
| | - Di Peng
- Huazhong University of Science and Technology
| | - Yu Xue
- Huazhong University of Science and Technology
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759
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Lee Y, Baumhardt JM, Pei J, Chook YM, Grishin NV. pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. Bioinformatics 2020; 36:961-963. [PMID: 31504173 PMCID: PMC8496372 DOI: 10.1093/bioinformatics/btz657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/01/2019] [Accepted: 08/20/2019] [Indexed: 08/05/2023] Open
Abstract
MOTIVATION The consensus pattern of Nuclear Export Signal (NES) is a short sequence motif that is commonly identified in protein sequences, whether the motif acts as an NES (true positive) or not (false positive). Finding more plausible NES functioning regions among the vast array of consensus-matching segments would provide an interesting resource for further experimental validation. Better defined NES should also allow meaningful mapping of cancer-related mutation positions, leading to plausible explanations for the relationship between nuclear export and disease. RESULTS Possible NES candidate regions are extracted from the cancer-related human reference proteome. Extracted NES are scored for reliability by combining sequence-based and structure-based approaches. The confidently identified NES candidate motifs were checked for overlap with cancer-related mutation positions annotated in the COSMIC database. Among the ∼700 cancer-related sequences in the COSMIC Cancer Gene Census, 178 sequences are predicted to have possible NES motifs containing cancer-related mutations at their key positions. These lists are organized into our database (pCRM1exportome), and other protein sequences in the human reference proteome can also be retrieved by their UniProt IDs. AVAILABILITY AND IMPLEMENTATION The database is freely available at http://prodata.swmed.edu/pCRM1exportome. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Nick V Grishin
- Department of Biophysics, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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760
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Kim H, Yen L, Wongpalee SP, Kirshner JA, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, Jacobsen SE. The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction. Mol Cell 2020; 75:700-710.e6. [PMID: 31442422 DOI: 10.1016/j.molcel.2019.07.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/28/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022]
Abstract
Microrchidia (MORC) ATPases are critical for gene silencing and chromatin compaction in multiple eukaryotic systems, but the mechanisms by which MORC proteins act are poorly understood. Here, we apply a series of biochemical, single-molecule, and cell-based imaging approaches to better understand the function of the Caenorhabditis elegans MORC-1 protein. We find that MORC-1 binds to DNA in a length-dependent but sequence non-specific manner and compacts DNA by forming DNA loops. MORC-1 molecules diffuse along DNA but become static as they grow into foci that are topologically entrapped on DNA. Consistent with the observed MORC-1 multimeric assemblies, MORC-1 forms nuclear puncta in cells and can also form phase-separated droplets in vitro. We also demonstrate that MORC-1 compacts nucleosome templates. These results suggest that MORCs affect genome structure and gene silencing by forming multimeric assemblages to topologically entrap and progressively loop and compact chromatin.
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Affiliation(s)
- HyeongJun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Linda Yen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Somsakul P Wongpalee
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jessica A Kirshner
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Nicita Mehta
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Yan Xue
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Steve E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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761
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Broekelmann TJ, Bodmer NK, Mecham RP. Identification of the growth factor-binding sequence in the extracellular matrix protein MAGP-1. J Biol Chem 2020; 295:2687-2697. [PMID: 31988245 DOI: 10.1074/jbc.ra119.010540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Microfibril-associated glycoprotein-1 (MAGP-1) is a component of vertebrate extracellular matrix (ECM) microfibrils that, together with the fibrillins, contributes to microfibril function. Many of the phenotypes associated with MAGP-1 gene inactivation are consistent with dysregulation of the transforming growth factor β (TGFβ)/bone morphogenetic protein (BMP) signaling system. We have previously shown that full-length MAGP-1 binds active TGFβ-1 and some BMPs. The work presented here further defines the growth factor-binding domain of MAGP-1. Using recombinant domains and synthetic peptides, along with surface plasmon resonance analysis to measure the kinetics of the MAGP-1-TGFβ-1 interaction, we localized the TGFβ- and BMP-binding site in MAGP-1 to a 19-amino acid-long, highly acidic sequence near the N terminus. This domain was specific for binding active, but not latent, TGFβ-1. Growth factor activity experiments revealed that TGFβ-1 retains signaling activity when complexed with MAGP-1. Furthermore, when bound to fibrillin, MAGP-1 retained the ability to interact with TGFβ-1, and active TGFβ-1 did not bind fibrillin in the absence of MAGP-1. The absence of MAGP was sufficient to raise the amount of total TGFβ stored in the ECM of cultured cells, suggesting that the MAGPs compete with the TGFβ large latent complex for binding to microfibrils. Together, these results indicate that MAGP-1 plays an active role in TGFβ signaling in the ECM.
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Affiliation(s)
- Thomas J Broekelmann
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Nicholas K Bodmer
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Robert P Mecham
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110.
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762
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Mandaci SY, Caliskan M, Sariaslan MF, Uversky VN, Coskuner‐Weber O. Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α‐synuclein on simulation techniques and force field parameters. Chem Biol Drug Des 2020; 96:659-667. [DOI: 10.1111/cbdd.13662] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/14/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Sunay Y. Mandaci
- Molecular Biotechnology Turkish‐German University Istanbul Turkey
| | - Murat Caliskan
- Molecular Biotechnology Turkish‐German University Istanbul Turkey
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine USF Health Byrd Alzheimer's Research Institute Morsani College of Medicine University of South Florida Tampa FL USA
- Laboratory of New Methods in Biology Institute for Biological Instrumentation of the Russian Academy of Sciences Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” Pushchino Russia
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763
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Transit of Procaspase-9 towards its activation. New mechanistic insights from molecular dynamics simulations. J Mol Model 2020; 26:24. [PMID: 31927634 DOI: 10.1007/s00894-019-4285-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 12/20/2019] [Indexed: 10/25/2022]
Abstract
Caspases are cysteine proteases that perform a wide variety of roles in lethal intracellular signaling and cell-death regulation. Caspase-9, the primary initiator caspase of the intrinsic apoptotic pathway, is produced as a scarcely active zymogen (Procaspase-9). Here, we describe, for the first time, at the atomistic level, conformational changes which might be correlated to the activation of Procaspase-9. Molecular dynamics simulations performed at two temperatures (310 and 410 K) provide insights about the conformational space and the time-course evolution of the geometrical and structural characteristics of Procaspase-9. At both temperatures studied, the extremal globular domains of the protein approach each other, contracting the disordered region. In both temperatures, the compact conformations hide more than 40 nm2 (about 20% of the total solvent-accessible surface area), and their radius of gyration are reduced by about 40% from the original values. At each temperature, the pathway of contraction is different, as well as the compact structures reached. In consequence, the network of stabilizing interactions at the final conformations is dissimilar. Both final conformations were evaluated in their structural compatibility with the activation models described so far. In this work, we describe mechanistically how and why the activation of Procaspase-9 is favored by apoptosome recruitment via the Caspase Activation Recruitment Domain (CARD), as it has been proposed recently by in vitro experiments.
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764
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Reddy ST, Uversky VN, Costa-Filho AJ. Nucleation-dependent amyloid fibrillation of human GRASP55 in aqueous solution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:133-143. [DOI: 10.1007/s00249-019-01419-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/22/2022]
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765
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Bhopatkar AA, Uversky VN, Rangachari V. Granulins modulate liquid-liquid phase separation and aggregation of the prion-like C-terminal domain of the neurodegeneration-associated protein TDP-43. J Biol Chem 2020; 295:2506-2519. [PMID: 31911437 DOI: 10.1074/jbc.ra119.011501] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) has emerged as a key player in many neurodegenerative pathologies, including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Hallmarks of both FTLD and ALS are the toxic cytoplasmic inclusions of the prion-like C-terminal fragments of TDP-43 CTD (TDP-43 C-terminal domain), formed upon proteolytic cleavage of full-length TDP-43 in the nucleus and subsequent transport to the cytoplasm. Both full-length TDP-43 and its CTD are also known to form stress granules by coacervating with RNA in the cytoplasm during stress and may be involved in these pathologies. Furthermore, mutations in the PGRN gene, leading to haploinsufficiency and diminished function of progranulin (PGRN) protein, are strongly linked to FTLD and ALS. Recent reports have indicated that proteolytic processing of PGRN to smaller protein modules called granulins (GRNs) contributes to FTLD and ALS progression, with specific GRNs exacerbating TDP-43-induced cytotoxicity. Here we investigated the interactions between the proteolytic products of both TDP-43 and PGRN. Based on structural disorder and charge distributions, we hypothesized that GRN-3 and GRN-5 could interact with the TDP-43 CTD. We show that, under both reducing and oxidizing conditions, GRN-3 and GRN-5 interact with and differentially modulate TDP-43 CTD aggregation and/or liquid-liquid phase separation in vitro GRN-3 promoted insoluble aggregates of the TDP-43 CTD while GRN-5 mediated liquid-liquid phase separation. These results constitute the first observation of an interaction between GRNs and TDP-43, suggesting a mechanism by which attenuated PGRN function could lead to familial FTLD or ALS.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406.
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766
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Nunez-Castilla J, Siltberg-Liberles J. An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins. Methods Mol Biol 2020; 2141:147-177. [PMID: 32696356 DOI: 10.1007/978-1-0716-0524-0_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We present an easy protocol for evolutionary analysis of proteins, with an emphasis on studying the evolutionary dynamics of disordered regions. Using the p53 protein family as an example, we provide a guide for finding homologous sequences in a database and refining a dataset before constructing the evolutionary context by building a phylogenetic tree. We show how a multiple sequence alignment and phylogeny for a protein family can be further partitioned into smaller datasets in order to investigate the changes in disorder content across the phylogeny. Based on the evolutionary context, we also investigate site-specific conservation of disorder. Last, we address how to evaluate the evolutionary dynamics of disorder-to-order transitions.
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Affiliation(s)
- Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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767
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Abstract
Intrinsically disordered proteins (IDPs) can adopt a range of conformations from globules to swollen coils. This large range of conformational preferences for different IDPs raises the question of how conformational preferences are encoded by sequence. Global compositional features of a sequence such as the fraction of charged residues and the net charge per residue engender certain conformational biases. However, more specific sequence features such as the patterning of oppositely charged residues, expansion driving residues, or residues that can undergo posttranslational modifications can also influence the conformational ensembles of an IDP. Here, we outline how to calculate important global compositional features and patterning metrics that can be used to classify IDPs into different conformational classes and predict relative changes in conformation for sequences with the same amino acid composition. Although increased effort has been devoted to determining conformational properties of IDPs in recent years, quantitative predictions of conformation directly from sequence remain difficult and often inaccurate. Thus, if quantitative predictions of conformational properties are desired, then sequence-specific simulations must be performed.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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768
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Ginell GM, Holehouse AS. Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER. Methods Mol Biol 2020; 2141:103-126. [PMID: 32696354 DOI: 10.1007/978-1-0716-0524-0_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intrinsically disordered proteins and protein regions are ubiquitous across eukaryotic proteomes where they play a range of functional roles. Unlike folded proteins, IDRs lack a well-defined native state but exist in heterogeneous ensembles of conformations. In the absence of a defined native state, structure-guided mutations to test specific mechanistic hypotheses are generally not possible. Despite this, the use of mutations to alter sequence properties has become a relatively common approach for teasing out the relationship between sequence, ensemble, and function. A key step in designing informative mutants is the ability to identify specific sequence features that may reveal an interpretable response if perturbed. Here, we provide guidance on using the CIDER and localCIDER tools for amino acid sequence analysis, with a focus on building intuition with respect to the most commonly described features.
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Affiliation(s)
- Garrett M Ginell
- Graduate Program in Biochemistry, Biophysics, and Structural Biology, Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.,Center for the Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Center for the Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA. .,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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769
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Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) are commonly found in all proteomes analyzed so far. These proteins/regions are subject to numerous posttranslational modifications (PTMs) and alternative splicing, are involved in a wide range of cellular functions, and often facilitate protein-protein interactions (PPIs). Some of these proteins contain molecular recognition features (MoRFs), which are IDRs that bind to partner proteins and undergo disorder-to-order transitions. Although many IDPs/IDRs can fold upon binding, a large fraction of these proteins are known to maintain significant amounts of disorder in their bound states. Being well-recognized interaction specialists, IDPs/IDRs can participate in one-to-many and many-to-one interactions, where one IDP/IDR binds to multiple partners potentially gaining very different structures in the bound state, or where multiple unrelated IDPs/IDRs bind to one partner. As a result, IDPs frequently serve as hubs (i.e., proteins with many links) in complex PPI networks. The goal of this chapter is to describe computational and bioinformatics tools that can be used to look at the disorder status of proteins within a given PPI network and also to gain some knowledge on the disorder-based functionality of the members of this network. To this end, description is provided for some of the use of UniProt and DisProt databases, several databases generating PPI networks (BioGRID, IntAct, DIP, MINT, HPRD, APID, KEGG, and STRING), Composition profiler, some tools for the per-residue disorder predictions (PONDR® VLXT, PONDR® VL3, PONDR® VSL2, PONDR-FIT, and IUPred), binary disorder classifiers CH-plot and CDF-plot and their combined CH-CDF analysis, web-based tools for the visualization of disorder distribution in a query protein (D2P2 and MobiDB), as well as some tools for evaluation disorder-based functionality of proteins (ANCHOR, MoRFpred, DEPP, and ModPred).
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. .,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. .,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
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770
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Ganguli S, Shah A, Hamid A, Singh A, Palakurti R, Bhandari R. A high energy phosphate jump - From pyrophospho-inositol to pyrophospho-serine. Adv Biol Regul 2020; 75:100662. [PMID: 31668836 DOI: 10.1016/j.jbior.2019.100662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg2+-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.
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Affiliation(s)
- Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Aisha Hamid
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Ravichand Palakurti
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India.
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771
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Abstract
Short linear motifs (SLiMs) are important mediators of interactions between intrinsically disordered regions of proteins and their interaction partners. Here, we detail instructions for the computational prediction of SLiMs in disordered protein regions, using the main tools of the SLiMSuite package: (1) SLiMProb identifies and calculates enrichment of predefined motifs in a set of proteins; (2) SLiMFinder predicts SLiMs de novo in a set of proteins, accounting for evolutionary relationships; (3) QSLiMFinder increases SLiMFinder sensitivity by focusing SLiM prediction on a specific query protein/region; (4) CompariMotif compares predicted SLiMs to known SLiMs or other SLiM predictions to identify common patterns. For each tool, command-line and online server examples are provided. Detailed notes provide additional advice on different applications of SLiMSuite, including batch running of multiple datasets and conservation masking using alignments of predicted orthologues.
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772
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Akbarian M, Yousefi R, Farjadian F, Uversky VN. Insulin fibrillation: toward strategies for attenuating the process. Chem Commun (Camb) 2020; 56:11354-11373. [DOI: 10.1039/d0cc05171c] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The environmental factors affecting the rate of insulin fibrillation. The factors are representative.
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Affiliation(s)
- Mohsen Akbarian
- Pharmaceutical Sciences Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
| | - Reza Yousefi
- Protein Chemistry Laboratory
- Department of Biology
- College of Sciences
- Shiraz University
- Shiraz
| | - Fatemeh Farjadian
- Pharmaceutical Sciences Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Health Byrd Alzheimer's Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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773
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Gouw M, Alvarado-Valverde J, Čalyševa J, Diella F, Kumar M, Michael S, Van Roey K, Dinkel H, Gibson TJ. How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. Methods Mol Biol 2020; 2141:73-102. [PMID: 32696353 DOI: 10.1007/978-1-0716-0524-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few years, it has become apparent that approximately 35% of the human proteome consists of intrinsically disordered regions. Many of these disordered regions are rich in short linear motifs (SLiMs) which mediate protein-protein interactions. Although these motifs are short and often partially conserved, they are involved in many important aspects of protein function, including cleavage, targeting, degradation, docking, phosphorylation, and other posttranslational modifications. The Eukaryotic Linear Motif resource (ELM) was established over 15 years ago as a repository to store and catalogue the scientific discoveries of motifs. Each motif in the database is annotated and curated manually, based on the experimental evidence gathered from publications. The entries themselves are submitted to ELM by filling in two annotation templates designed for motif class and motif instance annotation. In this protocol, we describe the steps involved in annotating new motifs and how to submit them to ELM.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Holger Dinkel
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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774
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King SM, Patel-King RS. The outer dynein arm assembly factor CCDC103 forms molecular scaffolds through multiple self-interaction sites. Cytoskeleton (Hoboken) 2019; 77:25-35. [PMID: 31858719 DOI: 10.1002/cm.21591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/03/2019] [Accepted: 12/13/2019] [Indexed: 11/07/2022]
Abstract
CCDC103 is a small protein with unusual biophysical properties that is required for outer dynein arm assembly on ciliary axonemes. Mutations in both human and zebrafish CCDC103 proteins lead to primary ciliary dyskinesia. Previous studies revealed that this protein can oligomerize and appears to be arrayed along the entire length of the ciliary axoneme. CCDC103 also binds purified microtubules directly and indeed stabilizes them. Here we use biochemical approaches to identify two regions of CCDC103 that mediate self-interaction. In both cases, these associations are stable to heating in the presence of detergent and are not disrupted by strong reducing agents. One interaction region consists of a 27-residue inherently disorder segment that can mediate heat/detergent-resistant dimerization when attached to unrelated monomeric proteins. The second interface includes the C-terminal RPAP3_C alpha helical domain. Our data suggest that CCDC103 can form an unconventional polymer and we propose models for how the monomers might be organized. We also use molecular modeling of the RPAP3_C domain to determine the structural consequences of the pathogenic H154P mutation found in human PCD patients.
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Affiliation(s)
- Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT
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775
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Barik A, Katuwawala A, Hanson J, Paliwal K, Zhou Y, Kurgan L. DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server. J Mol Biol 2019; 432:3379-3387. [PMID: 31870849 DOI: 10.1016/j.jmb.2019.12.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/07/2019] [Accepted: 12/15/2019] [Indexed: 01/06/2023]
Abstract
Computational predictions of the intrinsic disorder and its functions are instrumental to facilitate annotation for the millions of unannotated proteins. However, access to these predictors is fragmented and requires substantial effort to find them and to collect and combine their results. The DEPICTER (DisorderEd PredictIon CenTER) server provides first-of-its-kind centralized access to 10 popular disorder and disorder function predictions that cover protein and nucleic acids binding, linkers, and moonlighting regions. It automates the prediction process, runs user-selected methods on the server side, visualizes the results, and outputs all predictions in a consistent and easy-to-parse format. DEPICTER also includes two accurate consensus predictors of disorder and disordered protein binding. Empirical tests on an independent (low similarity) benchmark dataset reveal that the computational tools included in DEPICTER generate accurate predictions that are significantly better than the results secured using sequence alignment. The DEPICTER server is freely available at http://biomine.cs.vcu.edu/servers/DEPICTER/.
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Affiliation(s)
- Amita Barik
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA; Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Akila Katuwawala
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Jack Hanson
- Signal Processing Laboratory, Griffith University, Brisbane, QLD, 4122, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, Griffith University, Brisbane, QLD, 4122, Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, 4222, Australia; Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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776
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François-Moutal L, Perez-Miller S, Scott DD, Miranda VG, Mollasalehi N, Khanna M. Structural Insights Into TDP-43 and Effects of Post-translational Modifications. Front Mol Neurosci 2019; 12:301. [PMID: 31920533 PMCID: PMC6934062 DOI: 10.3389/fnmol.2019.00301] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Transactive response DNA binding protein (TDP-43) is a key player in neurodegenerative diseases. In this review, we have gathered and presented structural information on the different regions of TDP-43 with high resolution structures available. A thorough understanding of TDP-43 structure, effect of modifications, aggregation and sites of localization is necessary as we develop therapeutic strategies targeting TDP-43 for neurodegenerative diseases. We discuss how different domains as well as post-translational modification may influence TDP-43 overall structure, aggregation and droplet formation. The primary aim of the review is to utilize structural insights as we develop an understanding of the deleterious behavior of TDP-43 and highlight locations of established and proposed post-translation modifications. TDP-43 structure and effect on localization is paralleled by many RNA-binding proteins and this review serves as an example of how structure may be modulated by numerous compounding elements.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - David D Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Victor G Miranda
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Niloufar Mollasalehi
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
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777
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Nakamura T, Fahmi M, Tanaka J, Seki K, Kubota Y, Ito M. Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico. Int J Mol Sci 2019; 20:E6290. [PMID: 31847093 PMCID: PMC6940844 DOI: 10.3390/ijms20246290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.
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Affiliation(s)
- Takahiro Nakamura
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Jun Tanaka
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Kaito Seki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Yukihiro Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan;
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan;
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778
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Millard PS, Weber K, Kragelund BB, Burow M. Specificity of MYB interactions relies on motifs in ordered and disordered contexts. Nucleic Acids Res 2019; 47:9592-9608. [PMID: 31400117 PMCID: PMC6765112 DOI: 10.1093/nar/gkz691] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/18/2019] [Accepted: 08/08/2019] [Indexed: 02/05/2023] Open
Abstract
Physical interactions between members of the MYB and bHLH transcription factor (TF) families regulate many important biological processes in plants. Not all reported MYB–bHLH interactions can be explained by the known binding sites in the R3 repeat of the MYB DNA-binding domain. Noteworthy, most of the sequence diversity of MYB TFs lies in their non-MYB regions, which contain orphan small subgroup-defining motifs not yet linked to molecular functions. Here, we identified the motif mediating interaction between MYB TFs from subgroup 12 and their bHLH partners. Unlike other known MYB–bHLH interactions, the motif locates to the centre of the predicted disordered non-MYB region. We characterised the core motif, which enabled accurate prediction of previously unknown bHLH-interacting MYB TFs in Arabidopsis thaliana, and we confirmed its functional importance in planta. Our results indicate a correlation between the MYB–bHLH interaction affinity and the phenotypic output controlled by the TF complex. The identification of an interaction motif outside R3 indicates that MYB–bHLH interactions must have arisen multiple times, independently and suggests many more motifs of functional relevance to be harvested from subgroup-specific studies.
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Affiliation(s)
- Peter S Millard
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.,Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Konrad Weber
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.,Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.,Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
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779
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Prestel A, Wichmann N, Martins JM, Marabini R, Kassem N, Broendum SS, Otterlei M, Nielsen O, Willemoës M, Ploug M, Boomsma W, Kragelund BB. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cell Mol Life Sci 2019; 76:4923-4943. [PMID: 31134302 PMCID: PMC6881253 DOI: 10.1007/s00018-019-03150-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/16/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a potential drug target. Its binding partners carry a short linear motif (SLiM) known as the PCNA-interacting protein-box (PIP-box), but sequence-divergent motifs have been reported to bind to the same binding pocket. To investigate how PCNA accommodates motif diversity, we assembled a set of 77 experimentally confirmed PCNA-binding proteins and analyzed features underlying their binding affinity. Combining NMR spectroscopy, affinity measurements and computational analyses, we corroborate that most PCNA-binding motifs reside in intrinsically disordered regions, that structure preformation is unrelated to affinity, and that the sequence-patterns that encode binding affinity extend substantially beyond the boundaries of the PIP-box. Our systematic multidisciplinary approach expands current views on PCNA interactions and reveals that the PIP-box affinity can be modulated over four orders of magnitude by positive charges in the flanking regions. Including the flanking regions as part of the motif is expected to have broad implications, particularly for interpretation of disease-causing mutations and drug-design, targeting DNA-replication and -repair.
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Affiliation(s)
- Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Nanna Wichmann
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Joao M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Riccardo Marabini
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Noah Kassem
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian S Broendum
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, 3800, Australia
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Olaf Nielsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Finsen Laboratory, Biotechnology Research Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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780
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Staufner C, Peters B, Wagner M, Alameer S, Barić I, Broué P, Bulut D, Church JA, Crushell E, Dalgıç B, Das AM, Dick A, Dikow N, Dionisi-Vici C, Distelmaier F, Bozbulut NE, Feillet F, Gonzales E, Hadzic N, Hauck F, Hegarty R, Hempel M, Herget T, Klein C, Konstantopoulou V, Kopajtich R, Kuster A, Laass MW, Lainka E, Larson-Nath C, Leibner A, Lurz E, Mayr JA, McKiernan P, Mention K, Moog U, Mungan NO, Riedhammer KM, Santer R, Palafoll IV, Vockley J, Westphal DS, Wiedemann A, Wortmann SB, Diwan GD, Russell RB, Prokisch H, Garbade SF, Kölker S, Hoffmann GF, Lenz D. Defining clinical subgroups and genotype–phenotype correlations in NBAS-associated disease across 110 patients. Genet Med 2019; 22:610-621. [DOI: 10.1038/s41436-019-0698-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
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781
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Matos CO, Passos YM, do Amaral MJ, Macedo B, Tempone MH, Bezerra OCL, Moraes MO, Almeida MS, Weber G, Missailidis S, Silva JL, Uversky VN, Pinheiro AS, Cordeiro Y. Liquid-liquid phase separation and fibrillation of the prion protein modulated by a high-affinity DNA aptamer. FASEB J 2019; 34:365-385. [PMID: 31914616 DOI: 10.1096/fj.201901897r] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023]
Abstract
Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events associated with the onset of transmissible spongiform encephalopathies (TSEs). Experimental evidence supports the role of nucleic acids (NAs) in assisting this conversion. Here, we asked whether PrP undergoes liquid-liquid phase separation (LLPS) and if this process is modulated by NAs. To this end, two 25-mer DNA aptamers, A1 and A2, were selected against the globular domain of recombinant murine PrP (rPrP90-231) using SELEX methodology. Multiparametric structural analysis of these aptamers revealed that A1 adopts a hairpin conformation. Aptamer binding caused partial unfolding of rPrP90-231 and modulated its ability to undergo LLPS and fibrillate. In fact, although free rPrP90-231 phase separated into large droplets, aptamer binding increased the number of droplets but noticeably reduced their size. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced formation of amyloid fibrils on the surface of the droplets. We show here that PrP undergoes LLPS, and that the PrP interaction with NAs modulates phase separation and promotes PrP fibrillation in a NA structure and concentration-dependent manner. These results shed new light on the roles of NAs in PrP misfolding and TSEs.
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Affiliation(s)
- Carolina O Matos
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yulli M Passos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana J do Amaral
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Macedo
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus H Tempone
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ohanna C L Bezerra
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Milton O Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcius S Almeida
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gerald Weber
- Department of Physics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sotiris Missailidis
- Institute of Technology in Immunobiologics (Bio-Manguinhos), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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782
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Muta H, So M, Sakurai K, Kardos J, Naiki H, Goto Y. Amyloid Formation under Complicated Conditions in Which β 2-Microglobulin Coexists with Its Proteolytic Fragments. Biochemistry 2019; 58:4925-4934. [PMID: 31724398 DOI: 10.1021/acs.biochem.9b00917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid formation in vivo occurs under complicated conditions in which various amyloidogenic and non-amyloidogenic components coexist, often under crowding. Controversy surrounds the role of additional components under complicated conditions. They have been suggested to accelerate amyloid formation because molecular crowding or interactions with additives increase effective concentrations and, thus, break the supersaturation of amyloidogenic proteins. On the other hand, cellular crowding conditions with various heterogeneous components may retard or prevent amyloid formation because they impede homologous amyloidogenic associations. To elucidate the roles of these additional components, we examined the amyloid formation of β2-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis, with a simplified model system in which intact β2m and its proteolytic peptides coexist. Among the nine proteolytic peptides of β2m produced in vitro with lysyl endopeptidase, the 22-residue K3 peptide is highly amyloidogenic. The amyloid formation of the K3 peptide, which occurred with a lag time of 1 h at pH 2 and 37 °C, was significantly retarded by the coexistence of β2m or a mixture of the proteolytic digests. To identify the sites of inhibitory interactions, we performed paramagnetic relaxation enhancement measurements using spin-labeled K3 and uniformly 15N-labeled β2m with nuclear magnetic resonance detection. The results revealed that K3 interacted weakly with a broad cluster of the hydrophobic residues of β2m, which accommodated the residues located in some distant sequence, leading to competitive inhibition. The results showed that relatively weak and broad interactions formed a nonproductive complex, implying a role for heterogeneous interactions under complicated conditions.
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Affiliation(s)
- Hiroya Muta
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Masatomo So
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Kazumasa Sakurai
- Institute of Advanced Technology , Kindai University , Wakayama 649-6493 , Japan
| | - Jozsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry , Eötvös Loránd University , Pázmány P. sétány 1/C , Budapest 1117 , Hungary
| | - Hironobu Naiki
- Faculty of Medical Sciences , University of Fukui , Fukui 910-1193 , Japan
| | - Yuji Goto
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
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783
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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784
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Folding perspectives of an intrinsically disordered transactivation domain and its single mutation breaking the folding propensity. Int J Biol Macromol 2019; 155:1359-1372. [PMID: 31733244 DOI: 10.1016/j.ijbiomac.2019.11.111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/01/2019] [Accepted: 11/12/2019] [Indexed: 12/23/2022]
Abstract
Transcriptional regulation is a critical facet of cellular development controlled by numerous transcription factors, among which are E-proteins (E2A, HEB, and E2-2) that play important roles in lymphopoiesis. For example, primary hematopoietic cells immortalisation is promoted by interaction of the conserved PCET motif consisting of the Leu-X-X-Leu-Leu (LXXLL) and Leu-Asp-Phe-Ser (LDFS) sequences of the transactivation domains (AD1) of E-proteins with the KIX domain of CBP/p300 transcriptional co-activators. Earlier, it was shown that the LXXLL motif is essential for the PCET-KIX interaction driven by the PCET helical transition. In this study, we analyzed the dehydration-driven gain of helicity in the conserved region (residues 11-28) of the AD1 domain of E-protein. Particularly, we showed that AD1 structure was dramatically affected by alcohols, but was insensitive to changes in pH or the presence of osmolytes sarcosine and taurine, or high polyethylene glycol (PEG) concentrations and DOPC Liposomes. These structure-forming effects of solvents were almost completely absent in the case of L21P AD1 mutant characterized by weakened interaction with KIX. This indicates that KIX interaction-induced AD1 ordering is driven by PCET motif dehydration. The L21P mutation-caused loss of molecular recognition function of AD1 is due to the mutation-induced disruption of the AD1 helical propensity.
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785
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Song H, Guo Z, Hu X, Qian L, Miao F, Zhang X, Chen J. Evolutionary balance between LRR domain loss and young NBS-LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner. BMC Genomics 2019; 20:844. [PMID: 31722670 PMCID: PMC6852974 DOI: 10.1186/s12864-019-6212-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance genes that are involved in response to various pathogens. RESULTS We identified 713 full-length NBS-LRRs in A. hypogaea cv. Tifrunner. Genetic exchange events occurred on NBS-LRRs in A. hypogaea cv. Tifrunner, which were detected in the same subgenomes and also found in different subgenomes. Relaxed selection acted on NBS-LRR proteins and LRR domains in A. hypogaea cv. Tifrunner. Using quantitative trait loci (QTL), we found that NBS-LRRs were involved in response to late leaf spot, tomato spotted wilt virus, and bacterial wilt in A. duranensis (2 NBS-LRRs), A. ipaensis (39 NBS-LRRs), and A. hypogaea cv. Tifrunner (113 NBS-LRRs). In A. hypogaea cv. Tifrunner, 113 NBS-LRRs were classified as 75 young and 38 old NBS-LRRs, indicating that young NBS-LRRs were involved in response to disease after tetraploidization. However, compared to A. duranensis and A. ipaensis, fewer LRR domains were found in A. hypogaea cv. Tifrunner NBS-LRR proteins, partly explaining the lower disease resistance of the cultivated peanut. CONCLUSIONS Although relaxed selection acted on NBS-LRR proteins and LRR domains, LRR domains were preferentially lost in A. hypogaea cv. Tifrunner compared to A. duranensis and A. ipaensis. The QTL results suggested that young NBS-LRRs were important for resistance against diseases in A. hypogaea cv. Tifrunner. Our results provid insight into the greater susceptibility of A. hypogaea cv. Tifrunner to disease compared to A. duranensis and A. ipaensis.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China.
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaohui Hu
- Shandong Peanut Research Institute, Qingdao, China
| | - Lang Qian
- Dalian Academy of Agricultural Sciences, Dalian, China
| | - Fuhong Miao
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao, China.
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786
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Fagerberg E, Lenton S, Skepö M. Evaluating Models of Varying Complexity of Crowded Intrinsically Disordered Protein Solutions Against SAXS. J Chem Theory Comput 2019; 15:6968-6983. [DOI: 10.1021/acs.jctc.9b00723] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Samuel Lenton
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, 223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, 223 70 Lund, Sweden
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787
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Fahmi M, Yasui G, Seki K, Katayama S, Kaneko-Kawano T, Inazu T, Kubota Y, Ito M. In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. Int J Mol Sci 2019; 20:ijms20225593. [PMID: 31717404 PMCID: PMC6888432 DOI: 10.3390/ijms20225593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 12/28/2022] Open
Abstract
Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which has multiple functions such as binding to methylated DNA or interacting with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We investigated the evolution and molecular features of MeCP2, CDKL5, and FOXG1 and their binding partners using phylogenetic profiling to gain a better understanding of their similarities. We also predicted the structural order-disorder propensity and assessed the evolutionary rates per site of MeCP2, CDKL5, and FOXG1 to investigate the relationships between disordered structure and other related properties with RTT. Here, we provide insight to the structural characteristics, evolution and interaction landscapes of those three proteins. We also uncovered the disordered structure properties and evolution of those proteins which may provide valuable information for the development of therapeutic strategies of RTT.
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Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Gen Yasui
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Kaito Seki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Syouichi Katayama
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Takako Kaneko-Kawano
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Tetsuya Inazu
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;
- Correspondence:
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788
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Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. Int J Mol Sci 2019; 20:ijms20215460. [PMID: 31683980 PMCID: PMC6862064 DOI: 10.3390/ijms20215460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that take into account the particular biological and biophysical properties of MSF complexes. Here, we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current protein structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.
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789
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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790
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Sequential, Structural and Functional Properties of Protein Complexes Are Defined by How Folding and Binding Intertwine. J Mol Biol 2019; 431:4408-4428. [DOI: 10.1016/j.jmb.2019.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/10/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
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791
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Zimmermann MT, Williams MM, Klee EW, Lomberk GA, Urrutia R. Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers. Proteins 2019; 87:904-916. [PMID: 31152607 PMCID: PMC6790107 DOI: 10.1002/prot.25752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022]
Abstract
Heterochromatin protein 1α (HP1α) is a protein that mediates cancer-associated processes in the cell nucleus. Proteomic experiments, reported here, demonstrate that HP1α complexes with importin α (IMPα), a protein necessary for its nuclear transport. This data is congruent with Simple Linear Motif (SLiM) analyses that identify an IMPα-binding motif within the linker that joins the two globular domains of this protein. Using molecular modeling and dynamics simulations, we develop a model of the IMPα-HP1α complex and investigate the impact of phosphorylation and genomic variants on their interaction. We demonstrate that phosphorylation of the HP1α linker likely regulates its association with IMPα, which has implications for HP1α access to the nucleus, where it functions. Cancer-associated genomic variants do not abolish the interaction of HP1α but instead lead to rearrangements where the variant proteins maintain interaction with IMPα, but with less specificity. Combined, this new mechanistic insight bears biochemical, cell biological, and biomedical relevance.
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Affiliation(s)
- Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
- Clinical and Translational Sciences InstituteMedical College of WisconsinMilwaukeeWisconsin
| | - Monique M. Williams
- Department of BiochemistryMayo ClinicRochesterMinnesota
- Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Eric W. Klee
- Department of BiochemistryMayo ClinicRochesterMinnesota
- Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Gwen A. Lomberk
- Division of Research, Department of SurgeryMedical College of WisconsinMilwaukeeWisconsin
- Department of Pharmacology and ToxicologyMedical College of WisconsinMilwaukeeWisconsin
- Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
| | - Raul Urrutia
- Division of Research, Department of SurgeryMedical College of WisconsinMilwaukeeWisconsin
- Genomic Science and Precision Medicine Center (GSPMC)Medical College of WisconsinMilwaukeeWisconsin
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsin
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792
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The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality. J Mol Biol 2019; 431:4959-4977. [PMID: 31634467 DOI: 10.1016/j.jmb.2019.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
The rabies and Ebola viruses recruit the highly conserved host protein LC8 for their own reproductive success. In vivo knockouts of the LC8 recognition motif within the rabies virus phosphoprotein (RavP) result in completely nonlethal viral infections. In this work, we examine the molecular role LC8 plays in viral lethality. We show that RavP and LC8 colocalize in rabies infected cells, and that LC8 interactions are essential for efficient viral polymerase functionality. NMR, SAXS, and molecular modeling demonstrate that LC8 binding to a disordered linker adjacent to an endogenous dimerization domain results in restrictions in RavP domain orientations. The resulting ensemble structure of RavP-LC8 tetrameric complex is similar to that of a related virus phosphoprotein that does not bind LC8, suggesting that with RavP, LC8 binding acts as a switch to induce a more active conformation. The high conservation of the LC8 motif in Lyssavirus phosphoproteins and its presence in other analogous proteins such as the Ebola virus VP35 evinces a broader purpose for LC8 in regulating downstream phosphoprotein functions vital for viral replication.
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793
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Analysis of Heterodimeric "Mutual Synergistic Folding"-Complexes. Int J Mol Sci 2019; 20:ijms20205136. [PMID: 31623284 PMCID: PMC6829572 DOI: 10.3390/ijms20205136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.
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794
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Katuwawala A, Oldfield CJ, Kurgan L. Accuracy of protein-level disorder predictions. Brief Bioinform 2019; 21:1509-1522. [DOI: 10.1093/bib/bbz100] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/22/2019] [Accepted: 07/15/2019] [Indexed: 01/15/2023] Open
Abstract
Abstract
Experimental annotations of intrinsic disorder are available for 0.1% of 147 000 000 of currently sequenced proteins. Over 60 sequence-based disorder predictors were developed to help bridge this gap. Current benchmarks of these methods assess predictive performance on datasets of proteins; however, predictions are often interpreted for individual proteins. We demonstrate that the protein-level predictive performance varies substantially from the dataset-level benchmarks. Thus, we perform first-of-its-kind protein-level assessment for 13 popular disorder predictors using 6200 disorder-annotated proteins. We show that the protein-level distributions are substantially skewed toward high predictive quality while having long tails of poor predictions. Consequently, between 57% and 75% proteins secure higher predictive performance than the currently used dataset-level assessment suggests, but as many as 30% of proteins that are located in the long tails suffer low predictive performance. These proteins typically have relatively high amounts of disorder, in contrast to the mostly structured proteins that are predicted accurately by all 13 methods. Interestingly, each predictor provides the most accurate results for some number of proteins, while the best-performing at the dataset-level method is in fact the best for only about 30% of proteins. Moreover, the majority of proteins are predicted more accurately than the dataset-level performance of the most accurate tool by at least four disorder predictors. While these results suggests that disorder predictors outperform their current benchmark performance for the majority of proteins and that they complement each other, novel tools that accurately identify the hard-to-predict proteins and that make accurate predictions for these proteins are needed.
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Affiliation(s)
- Akila Katuwawala
- Department of Computer Science, Virginia Commonwealth University, USA
- Department of Computer Science, Virginia Commonwealth University, USA
| | - Christopher J Oldfield
- Department of Computer Science, Virginia Commonwealth University, USA
- Department of Computer Science, Virginia Commonwealth University, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, USA
- Department of Computer Science, Virginia Commonwealth University, USA
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795
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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796
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Bösl K, Ianevski A, Than TT, Andersen PI, Kuivanen S, Teppor M, Zusinaite E, Dumpis U, Vitkauskiene A, Cox RJ, Kallio-Kokko H, Bergqvist A, Tenson T, Merits A, Oksenych V, Bjørås M, Anthonsen MW, Shum D, Kaarbø M, Vapalahti O, Windisch MP, Superti-Furga G, Snijder B, Kainov D, Kandasamy RK. Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis. Front Immunol 2019; 10:2186. [PMID: 31636628 PMCID: PMC6787150 DOI: 10.3389/fimmu.2019.02186] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/29/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are one of the major causes of acute and chronic infectious diseases and thus a major contributor to the global burden of disease. Several studies have shown how viruses have evolved to hijack basic cellular pathways and evade innate immune response by modulating key host factors and signaling pathways. A collective view of these multiple studies could advance our understanding of virus-host interactions and provide new therapeutic perspectives for the treatment of viral diseases. Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes. Network and bioinformatics analyses showed how viruses with small genomes efficiently achieve the maximal effect by targeting multifunctional and highly connected host proteins with a high occurrence of disordered regions. We also identified the core cellular process subnetworks that are targeted by all the viruses. Integration with functional RNA interference (RNAi) datasets showed that a large proportion of the targets are required for viral replication. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Altogether, these orthogonal datasets could serve as a platform for hypothesis generation and follow-up studies to broaden our understanding of the viral evasion landscape.
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Affiliation(s)
- Korbinian Bösl
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thoa T Than
- Institut Pasteur Korea, Seongnam, South Korea
| | - Petter I Andersen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Suvi Kuivanen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Mona Teppor
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Uga Dumpis
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Astra Vitkauskiene
- Department of Laboratory Medicine, Lithuanian University of Health Science, Kaunas, Lithuania
| | - Rebecca J Cox
- Department of Clinical Science, Influenza Centre, University of Bergen, Bergen, Norway
| | - Hannimari Kallio-Kokko
- Department of Virology and Immunology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Anders Bergqvist
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marit W Anthonsen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - David Shum
- Institut Pasteur Korea, Seongnam, South Korea
| | - Mari Kaarbø
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Olli Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Berend Snijder
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Richard K Kandasamy
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, United States
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797
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Millard PS, Kragelund BB, Burow M. R2R3 MYB Transcription Factors - Functions outside the DNA-Binding Domain. TRENDS IN PLANT SCIENCE 2019; 24:934-946. [PMID: 31358471 DOI: 10.1016/j.tplants.2019.07.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 05/20/2023]
Abstract
Several transcription factor (TF) families, including the MYB family, regulate a wide array of biological processes. TFs contain DNA-binding domains (DBDs) and regulatory regions; although information on protein structure is scarce for plant MYB TFs, various in silico methods suggest that the non-MYB regions contain extensive intrinsically disordered regions (IDRs). Although IDRs do not fold into stable globular structures, they comprise functional regions including interaction motifs, and recent research has shown that IDRs perform crucial biological roles. We map here domain organization, disorder predictions, and functional regions across the entire Arabidopsis thaliana R2R3 MYB TF family, and highlight where an increased research focus will be necessary to shape a new understanding of structure-function relationships in plant TFs.
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Affiliation(s)
- Peter S Millard
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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798
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Draceni Y, Pechmann S. Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis. Proc Natl Acad Sci U S A 2019; 116:20009-20014. [PMID: 31527276 PMCID: PMC6778244 DOI: 10.1073/pnas.1904611116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation and degradation. Failure and decline of protein homeostasis are directly associated with conditions of aging and aging-related neurodegeneration. However, it is not clear what tips the balance of protein homeostasis and leads to onset of aging and diseases. Here, using a comparative genomics approach we report general principles of maintaining protein homeostasis across the eukaryotic tree of life. Expanding a previous study of 16 eukaryotes to the quantitative analysis of 216 eukaryotic genomes, we find a strong correlation between the composition of eukaryotic chaperone networks and genome complexity that is distinct for different species kingdoms. Organisms with pronounced phenotypes clearly buck this trend. Northobranchius furzeri, the shortest-lived vertebrate and a widely used model for fragile protein homeostasis, is found to be chaperone limited while Heterocephalus glaber as the longest-lived rodent and thus an especially robust organism is characterized by above-average numbers of chaperones. Strikingly, the relative size of chaperone networks is found to generally correlate with longevity in Metazoa. Our results thus indicate that the balance in protein homeostasis may be a key variable in explaining organismal robustness.
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Affiliation(s)
- Yasmine Draceni
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Sebastian Pechmann
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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799
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Manguy J, Shields DC. Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190939. [PMID: 31824707 PMCID: PMC6837221 DOI: 10.1098/rsos.190939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Milk alpha-, beta- and kappa-casein proteins assemble into casein micelles in breast epithelial cells. The glycomacropeptide (GMP) tails of kappa-casein that extend from the surface of the micelle are key to assembly and aggregation. Aggregation is triggered by stomach pepsin cleavage of GMP from para-kappa-casein (PKC). While one casein micelle model emphasizes the importance of hydrophobic interactions, another focuses on polar residues. We performed an evolutionary analysis of kappa-casein primary sequence and predicted features that potentially impact on protein interactions. We noted more rapid change in the earlier period (166 to 60 Ma). Pepsin and plasmin cleavage sites were avoided in the GMP, which may partly explain its amino acid composition. Short tandem repeats have led to modest expansions of PKC, and to large GMP expansions, suggesting the GMP is less length constrained. Amino acid compositional constraints were assessed across species. Polarity and hydrophobicity properties were insufficient to explain differences between PKC and GMP. Among polar residues, threonine dominates the GMP, compared to serine, probably reflecting its preference for O-glycosylation over phosphorylation. Glutamine, enriched in the bovine PQ-rich region, is not positionally conserved in other species. Among hydrophobic residues, isoleucine is clearly preferred over leucine in the GMP, and patches of hydrophobicity are not markedly positionally conserved. PKC tyrosine and charged residues showed stronger conservation of position, suggesting a role for pi-interactions, seen in other structurally dynamic protein membraneless assemblies. Independent acquisitions of cysteines are consistent with a trend of increasing stabilization of multimers by covalent disulphide bonds, over evolutionary time. In conclusion, kappa-casein compositional and positional constraints appear to be influenced by modification preferences, protease evasion and protein-protein interactions.
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Affiliation(s)
- Jean Manguy
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C. Shields
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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800
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Marijan D, Tse R, Elliott K, Chandhok S, Luo M, Lacroix E, Audas TE. Stress-specific aggregation of proteins in the amyloid bodies. FEBS Lett 2019; 593:3162-3172. [PMID: 31512750 DOI: 10.1002/1873-3468.13597] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 12/26/2022]
Abstract
Physiological amyloid aggregation occurs within the nuclei of stress-treated cells. These structures, termed Amyloid bodies (A-bodies), assemble through the rapid accumulation of proteins into dense membrane-less organelles, which possess the same biophysical properties as plaques observed in many amyloid-based diseases. Here, we demonstrate that A-body proteomic compositions vary significantly between stimuli, as constituent proteins can be sequestered by one or more stressors. Stimulus exposure alone was insufficient to induce aggregation, demonstrating that this pathway is not regulated solely by stress-induced conformational changes of the A-body targets. We propose that different environmental conditions induce the formation of A-body subtypes containing distinct protein residents. This selective immobilization of proteins may have evolved as a finely tuned mechanism for surviving divergent stressors.
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Affiliation(s)
- Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Ronnie Tse
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Keenan Elliott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Monica Luo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
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