1
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Bello-Madruga R, Torrent Burgas M. The limits of prediction: Why intrinsically disordered regions challenge our understanding of antimicrobial peptides. Comput Struct Biotechnol J 2024; 23:972-981. [PMID: 38404711 PMCID: PMC10884422 DOI: 10.1016/j.csbj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/10/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Antimicrobial peptides (AMPs) are molecules found in most organisms, playing a vital role in innate immune defense against pathogens. Their mechanism of action involves the disruption of bacterial cell membranes, causing leakage of cellular contents and ultimately leading to cell death. While AMPs typically lack a defined structure in solution, they often assume a defined conformation when interacting with bacterial membranes. Given this structural flexibility, we investigated whether intrinsically disordered regions (IDRs) with AMP-like properties could exhibit antimicrobial activity. We tested 14 peptides from different IDRs predicted to have antimicrobial activity and found that nearly all of them did not display the anticipated effects. These peptides failed to adopt a defined secondary structure and had compromised membrane interactions, resulting in a lack of antimicrobial activity. We hypothesize that evolutionary constraints may prevent IDRs from folding, even in membrane-like environments, limiting their antimicrobial potential. Moreover, our research reveals that current antimicrobial predictors fail to accurately capture the structural features of peptides when dealing with intrinsically unstructured sequences. Hence, the results presented here may have far-reaching implications for designing and improving antimicrobial strategies and therapies against infectious diseases.
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Affiliation(s)
- Roberto Bello-Madruga
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marc Torrent Burgas
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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2
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Herrera MG, Amundarain MJ, Dörfler PW, Dodero VI. The Celiac-Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model. Angew Chem Int Ed Engl 2024; 63:e202317552. [PMID: 38497459 DOI: 10.1002/anie.202317552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
Celiac disease (CeD) is an autoimmune disorder triggered by gluten proteins, affecting approximately 1 % of the global population. The 33-mer deamidated gliadin peptide (DGP) is a metabolically modified wheat-gluten superantigen for CeD. Here, we demonstrate that the 33-mer DGP spontaneously assembles into oligomers with a diameter of approximately 24 nm. The 33-mer DGP oligomers present two main secondary structural motifs-a major polyproline II helix and a minor β-sheet structure. Importantly, in the presence of 33-mer DGP oligomers, there is a statistically significant increase in the permeability in the gut epithelial cell model Caco-2, accompanied by the redistribution of zonula occludens-1, a master tight junction protein. These findings provide novel molecular and supramolecular insights into the impact of 33-mer DGP in CeD and highlight the relevance of gliadin peptide oligomerization.
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Affiliation(s)
- Maria G Herrera
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, C1428EG, Argentina
| | - Maria J Amundarain
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Philipp W Dörfler
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Veronica I Dodero
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
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3
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Badreldin M, Salas-Ambrosio P, Bourasseau S, Lecommandoux S, Harrisson S, Bonduelle C. Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides. Biomacromolecules 2024; 25:3033-3043. [PMID: 38652289 DOI: 10.1021/acs.biomac.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.
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Affiliation(s)
- Mostafa Badreldin
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Pedro Salas-Ambrosio
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Sylvain Bourasseau
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | | | - Simon Harrisson
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Colin Bonduelle
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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4
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Tang NC, Su JC, Shmidov Y, Kelly G, Deshpande S, Sirohi P, Peterson N, Chilkoti A. Synthetic intrinsically disordered protein fusion tags that enhance protein solubility. Nat Commun 2024; 15:3727. [PMID: 38697982 PMCID: PMC11066018 DOI: 10.1038/s41467-024-47519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jonathan C Su
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parul Sirohi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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5
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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6
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Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Hilditch AT, Romanyuk A, Cross SJ, Obexer R, McManus JJ, Woolfson DN. Assembling membraneless organelles from de novo designed proteins. Nat Chem 2024; 16:89-97. [PMID: 37710047 PMCID: PMC10774119 DOI: 10.1038/s41557-023-01321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.
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Affiliation(s)
- Alexander T Hilditch
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Andrey Romanyuk
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Stephen J Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Richard Obexer
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Jennifer J McManus
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
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8
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Dagher SF, Vaishnav A, Stanley CB, Meilleur F, Edwards BFP, Bruno-Bárcena JM. Structural analysis and functional evaluation of the disordered ß-hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis. Front Bioeng Biotechnol 2023; 11:1291245. [PMID: 38162180 PMCID: PMC10755861 DOI: 10.3389/fbioe.2023.1291245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1-110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region's impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%-97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | | | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Brian F. P. Edwards
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | - José M. Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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9
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Snyder A, Ryan VH, Hawrot J, Lawton S, Ramos DM, Qi YA, Johnson K, Reed X, Johnson NL, Kollasch AW, Duffy M, VandeVrede L, Cochran JN, Miller BL, Toro C, Bielekova B, Yokoyama JS, Marks DS, Kwan JY, Cookson MR, Ward ME. An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome. Res Sq 2023:rs.3.rs-3462973. [PMID: 37886540 PMCID: PMC10602153 DOI: 10.21203/rs.3.rs-3462973/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
As genetic testing has become more accessible and affordable, variants of uncertain significance (VUS) are increasingly identified, and determining whether these variants play causal roles in disease is a major challenge. The known disease-associated Annexin A11 (ANXA11) mutations result in ANXA11 aggregation, alterations in lysosomal-RNA granule co-trafficking, and TDP-43 mis-localization and present as amyotrophic lateral sclerosis or frontotemporal dementia. We identified a novel VUS in ANXA11 (P93S) in a kindred with corticobasal syndrome and unique radiographic features that segregated with disease. We then queried neurodegenerative disorder clinic databases to identify the phenotypic spread of ANXA11 mutations. Multi-modal computational analysis of this variant was performed and the effect of this VUS on ANXA11 function and TDP-43 biology was characterized in iPSC-derived neurons. Single-cell sequencing and proteomic analysis of iPSC-derived neurons and microglia were used to determine the multiomic signature of this VUS. Mutations in ANXA11 were found in association with clinically diagnosed corticobasal syndrome, thereby establishing corticobasal syndrome as part of ANXA11 clinical spectrum. In iPSC-derived neurons expressing mutant ANXA11, we found decreased colocalization of lysosomes and decreased neuritic RNA as well as decreased nuclear TDP-43 and increased formation of cryptic exons compared to controls. Multiomic assessment of the P93S variant in iPSC-derived neurons and microglia indicates that the pathogenic omic signature in neurons is modest compared to microglia. Additionally, omic studies reveal that immune dysregulation and interferon signaling pathways in microglia are central to disease. Collectively, these findings identify a new pathogenic variant in ANXA11, expand the range of clinical syndromes caused by ANXA11 mutations, and implicate both neuronal and microglia dysfunction in ANXA11 pathophysiology. This work illustrates the potential for iPSC-derived cellular models to revolutionize the variant annotation process and provides a generalizable approach to determining causality of novel variants across genes.
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Affiliation(s)
- Allison Snyder
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - James Hawrot
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Sydney Lawton
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - Y Andy Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - Kory Johnson
- Intramural Bioinformatics, National Institute of Neurological Disorders and Stroke
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | | | | | - Megan Duffy
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging
| | - Lawren VandeVrede
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | | | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section, National Institute of Allergy and Infectious Disease
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston
| | - Justin Y Kwan
- Office of the Clinical Director, National Institute of Neurological Disorders and Stroke
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
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10
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Belli V, Maiello D, Di Lorenzo C, Furia M, Vicidomini R, Turano M. New Insights into Dyskerin-CypA Interaction: Implications for X-Linked Dyskeratosis Congenita and Beyond. Genes (Basel) 2023; 14:1766. [PMID: 37761906 PMCID: PMC10531313 DOI: 10.3390/genes14091766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The highly conserved family of cyclophilins comprises multifunctional chaperones that interact with proteins and RNAs, facilitating the dynamic assembly of multimolecular complexes involved in various cellular processes. Cyclophilin A (CypA), the predominant member of this family, exhibits peptidyl-prolyl cis-trans isomerase activity. This enzymatic function aids with the folding and activation of protein structures and often serves as a molecular regulatory switch for large multimolecular complexes, ensuring appropriate inter- and intra-molecular interactions. Here, we investigated the involvement of CypA in the nucleus, where it plays a crucial role in supporting the assembly and trafficking of heterogeneous ribonucleoproteins (RNPs). We reveal that CypA is enriched in the nucleolus, where it colocalizes with the pseudouridine synthase dyskerin, the catalytic component of the multifunctional H/ACA RNPs involved in the modification of cellular RNAs and telomere stability. We show that dyskerin, whose mutations cause the X-linked dyskeratosis (X-DC) and the Hoyeraal-Hreidarsson congenital ribosomopathies, can directly interact with CypA. These findings, together with the remark that substitution of four dyskerin prolines are known to cause X-DC pathogenic mutations, lead us to indicate this protein as a CypA client. The data presented here suggest that this chaperone can modulate dyskerin activity influencing all its partecipated RNPs.
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Affiliation(s)
- Valentina Belli
- Istituto Nazionale Tumori—IRCSS—Fondazione G. Pascale, 80131 Naples, Italy;
| | - Daniela Maiello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
| | - Concetta Di Lorenzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Maria Furia
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
| | - Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mimmo Turano
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
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11
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Tatsubo D, Suyama K, Sakamoto N, Tomohara K, Taniguchi S, Maeda I, Nose T. Determining the Sequence Dependency of Self-Assembly of Elastin-Like Peptides Using Short Peptide Analogues with Shuffled Repetitive Sequences. Biochemistry 2023; 62:2559-2570. [PMID: 37540116 DOI: 10.1021/acs.biochem.3c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Synthetic elastin-like peptides (ELPs) that possess characteristic tropoelastin-derived hydrophobic repetitive sequences, such as (VPGVG)n, exhibit thermoresponsive reversible self-assembly. Although their thermoresponsive properties have been well-studied, the sequence-dependent and structural requirements for self-assembly remain ambiguous. In particular, it is still unclear whether the amino acid sequences derived from tropoelastin are necessary for self-assembly. In this study, 11 sequence-shuffled ELP analogues based on (FPGVG)5, which is a previously developed short ELP (sELP), were designed to elucidate the sequence-dependent and structural requirements for their self-assembly. Among them, eight shuffled peptides exhibited self-assembling properties, whereas the other three peptides were difficult to dissolve in water. Structural analyses revealed that the structural characteristics of the three insoluble peptides were different from those of their thermoresponsive analogues. Furthermore, the secondary structures of the peptide analogues possessing the self-assembly abilities were different from each other. These results suggest that the potential for self-assembly and water solubility of sELPs depend on the primary structure in each repeated unit. Moreover, several shuffled analogues exhibited more potent self-assembling properties than the original (FPGVG)5, indicating that shorter ELPs can be obtained using their novel motifs as repetitive units. We also observed that the presence of Pro-Gly sequence in the repeating units was advantageous in terms of peptide solubility. Although further analysis will be necessary to elucidate the molecular mechanism underlying the self-assembly of these sELPs, this study provides insights into the relationship between the amino acid sequence and the self-assembling ability of the peptides for developing new sELPs for various applications.
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Affiliation(s)
- Daiki Tatsubo
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Naoki Sakamoto
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Keisuke Tomohara
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Suguru Taniguchi
- Department of Physics and Information Technology, Kyushu Institute of Technology, Iizuka 820-8502, Fukuoka, Japan
| | - Iori Maeda
- Department of Physics and Information Technology, Kyushu Institute of Technology, Iizuka 820-8502, Fukuoka, Japan
| | - Takeru Nose
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
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12
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Schiavina M, Konrat R, Ceccolini I, Mateos B, Konrat R, Felli IC, Pierattelli R. Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation. J Magn Reson 2023; 354:107539. [PMID: 37632987 DOI: 10.1016/j.jmr.2023.107539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Intrinsically disordered proteins (IDPs) are significantly enriched in proline residues, which can populate specific local secondary structural elements called PPII helices, characterized by small packing densities. Proline is often thought to promote disorder, but it can participate in specific π·CH interactions with aromatic side chains resulting in reduced conformational flexibilities of the polypeptide. Differential local motional dynamics are relevant for the stabilization of preformed structural elements and can serve as nucleation sites for the establishment of long-range interactions. NMR experiments to probe the dynamics of proline ring systems would thus be highly desirable. Here we present a pulse scheme based on 13C detection to quantify dipole-dipole cross-correlated relaxation (CCR) rates at methylene CH2 groups in proline residues. Applying 13C-CON detection strategy provides exquisite spectral resolution allowing applications also to high molecular weight IDPs even in conditions approaching the physiological ones. The pulse scheme is illustrated with an application to the 220 amino acids long protein Osteopontin, an extracellular cytokine involved in inflammation and cancer progression, and a construct in which three proline-aromatic sequence patches have been mutated.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ruth Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Irene Ceccolini
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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13
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Redl I, Fisicaro C, Dutton O, Hoffmann F, Henderson L, Owens BJ, Heberling M, Paci E, Tamiola K. ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers. NAR Genom Bioinform 2023; 5:lqad041. [PMID: 37138579 PMCID: PMC10150328 DOI: 10.1093/nargab/lqad041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/07/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are important for a broad range of biological functions and are involved in many diseases. An understanding of intrinsic disorder is key to develop compounds that target IDPs. Experimental characterization of IDPs is hindered by the very fact that they are highly dynamic. Computational methods that predict disorder from the amino acid sequence have been proposed. Here, we present ADOPT (Attention DisOrder PredicTor), a new predictor of protein disorder. ADOPT is composed of a self-supervised encoder and a supervised disorder predictor. The former is based on a deep bidirectional transformer, which extracts dense residue-level representations from Facebook's Evolutionary Scale Modeling library. The latter uses a database of nuclear magnetic resonance chemical shifts, constructed to ensure balanced amounts of disordered and ordered residues, as a training and a test dataset for protein disorder. ADOPT predicts whether a protein or a specific region is disordered with better performance than the best existing predictors and faster than most other proposed methods (a few seconds per sequence). We identify the features that are relevant for the prediction performance and show that good performance can already be gained with <100 features. ADOPT is available as a stand-alone package at https://github.com/PeptoneLtd/ADOPT and as a web server at https://adopt.peptone.io/.
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Affiliation(s)
- Istvan Redl
- Peptone Ltd, 370 Grays Inn Road, London WC1X 8BB, UK
| | | | - Oliver Dutton
- Peptone Ltd, 370 Grays Inn Road, London WC1X 8BB, UK
| | - Falk Hoffmann
- Peptone Ltd, 370 Grays Inn Road, London WC1X 8BB, UK
| | | | | | | | - Emanuele Paci
- Peptone Ltd, 370 Grays Inn Road, London WC1X 8BB, UK
- Department of Physics and Astronomy ‘Augusto Righi’, University of Bologna, 40127 Bologna, Italy
| | - Kamil Tamiola
- To whom correspondence should be addressed. Tel: +41 79 609 7333;
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14
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Abstract
There are over 100 computational predictors of intrinsic disorder. These methods predict amino acid-level propensities for disorder directly from protein sequences. The propensities can be used to annotate putative disordered residues and regions. This unit provides a practical and holistic introduction to the sequence-based intrinsic disorder prediction. We define intrinsic disorder, explain the format of computational prediction of disorder, and identify and describe several accurate predictors. We also introduce recently released databases of intrinsic disorder predictions and use an illustrative example to provide insights into how predictions should be interpreted and combined. Lastly, we summarize key experimental methods that can be used to validate computational predictions. © 2023 Wiley Periodicals LLC.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia
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15
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Sołtys K, Ożyhar A. Phase separation propensity of the intrinsically disordered AB region of human RXRβ. Cell Commun Signal 2023; 21:92. [PMID: 37143076 PMCID: PMC10157963 DOI: 10.1186/s12964-023-01113-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/25/2023] [Indexed: 05/06/2023] Open
Abstract
RXRβ is one of three subtypes of human retinoid X receptor (RXR), a transcription factor that belongs to the nuclear receptor superfamily. Its expression can be detected in almost all tissues. In contrast to other subtypes - RXRα and RXRγ - RXRβ has the longest and unique N-terminal sequence called the AB region, which harbors a ligand-independent activation function. In contrast to the functional properties of this sequence, the molecular properties of the AB region of human RXRβ (AB_hRXRB) have not yet been characterized. Here, we present a systematic biochemical and biophysical analysis of recombinant AB_hRXRB, along with in silico examinations, which demonstrate that AB_hRXRB exhibits properties of a coil-like intrinsically disordered region. AB_hRXRB possesses a flexible structure that is able to adopt a more ordered conformation under the influence of different environmental factors. Interestingly, AB_hRXRB promotes the formation of liquid-liquid phase separation (LLPS), a phenomenon previously observed for the AB region of another human subtype of RXR - RXRγ (AB_hRXRG). Although both AB regions seem to be similar in terms of their ability to induce phase separation, they clearly differ in the sensitivity to factors driving and regulating LLPS. This distinct LLPS response to environmental factors driven by the unique amino acid compositions of AB_hRXRB and AB_hRXRG can be significant for the specific modulation of the transcriptional activation of target genes by different subtypes of RXR. Video Abstract.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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16
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Gaeta IM, Tyska MJ. BioID2 screening identifies KIAA1671 as an EPS8 proximal factor that marks sites of microvillus growth. Mol Biol Cell 2023; 34:ar31. [PMID: 36790915 PMCID: PMC10092648 DOI: 10.1091/mbc.e22-11-0498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Microvilli are defining morphological features of the apical surfaces in diverse epithelial tissues. To develop our understanding of microvillus biogenesis, we used a biotin proximity-labeling approach to uncover new molecules enriched near EPS8, a well-studied marker of the microvillus distal tip compartment. Mass spectrometry of biotinylated hits identified KIAA1671, a large (∼200 kDa), disordered, and previously uncharacterized protein. Based on immunofluorescent staining and expression of fluorescent protein-tagged constructs, we found that KIAA1671 localizes to the base of the brush border in native intestinal tissue and polarized epithelial-cell culture models, as well as dynamic actin-rich structures in unpolarized, nonepithelial cell types. Live imaging also revealed that during the early stages of microvillar growth, KIAA1671 colocalizes with EPS8 in diffraction-limited puncta. However, once elongation of the core bundle begins, these two factors separate, with EPS8 tracking the distal end and KIAA1671 remaining behind at the base of the structure. These results suggest that KIAA1671 cooperates with EPS8 and potentially other assembly factors to initiate growth of microvilli on the apical surface. These findings offer new details on how transporting epithelial cells builds the brush border and may inform our understanding of how apical specializations are assembled in other epithelial contexts.
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Affiliation(s)
- Isabella M Gaeta
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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17
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Amundarain MJ, Vietri A, Dodero VI, Costabel MD. IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides. J Phys Chem B 2023; 127:2407-2417. [PMID: 36884001 DOI: 10.1021/acs.jpcb.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The 33-mer gliadin peptide and its deamidated metabolite, 33-mer DGP, are the immunodominant peptides responsible for the adaptive immune response in celiac disease (CD). CD is a complex autoimmune chronic disorder triggered by gluten ingestion that affects the small intestine and affects ∼1% of the global population. The 33-mers are polyproline II-rich (PPII) and intrinsically disordered peptides (IDPs), whose structures remain elusive. We sampled the conformational ensembles of both 33-mer peptides via molecular dynamics simulations employing two force fields (FFs) (Amber ff03ws and Amber ff99SB-disp) specifically validated for other IDPs. Our results show that both FFs allow the extensive exploration of the conformational landscape, which was not possible with the standard FF GROMOS53A6 reported before. Clustering analysis of the trajectories showed that the five largest clusters (78-88% of the total structures) present elongated, semielongated, and curved conformations in both FFs. Large average radius of gyration and solvent-exposed surfaces characterized these structures. While the structures sampled are similar, the Amber ff99SB-disp trajectories explored folded conformations with a higher probability. In addition, PPII secondary structure was preserved throughout the trajectories (58-73%) together with a non-negligible content of β structures (11-23%), in agreement with previous experimental results. This work represents the initial step in studying further the interaction of these peptides with other biologically relevant molecules, which could lead to finally disclose the molecular events that lead to CD.
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Affiliation(s)
- María J Amundarain
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Agustín Vietri
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Verónica I Dodero
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Marcelo D Costabel
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
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18
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Basu S, Chakravarty D, Hou Q, Uversky VN. Editorial: From the hydrophobic core to the globular-disorder interface: New challenges and insights into protein design. Front Mol Biosci 2023; 10:1151676. [PMID: 36814642 PMCID: PMC9939879 DOI: 10.3389/fmolb.2023.1151676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Affiliation(s)
- Sankar Basu
- Department of Microbiology, Asutosh College, University of Calcutta, Kolkata, India,*Correspondence: Sankar Basu, ; Vladimir N. Uversky,
| | - Devlina Chakravarty
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States
| | - Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States,*Correspondence: Sankar Basu, ; Vladimir N. Uversky,
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19
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Raicu AM, Kadiyala D, Niblock M, Jain A, Yang Y, Bird KM, Bertholf K, Seenivasan A, Siddiq M, Arnosti DN. The Cynosure of CtBP: Evolution of a Bilaterian Transcriptional Corepressor. Mol Biol Evol 2023; 40:msad003. [PMID: 36625090 PMCID: PMC9907507 DOI: 10.1093/molbev/msad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Evolution of sequence-specific transcription factors clearly drives lineage-specific innovations, but less is known about how changes in the central transcriptional machinery may contribute to evolutionary transformations. In particular, transcriptional regulators are rich in intrinsically disordered regions that appear to be magnets for evolutionary innovation. The C-terminal Binding Protein (CtBP) is a transcriptional corepressor derived from an ancestral lineage of alpha hydroxyacid dehydrogenases; it is found in mammals and invertebrates, and features a core NAD-binding domain as well as an unstructured C-terminus (CTD) of unknown function. CtBP can act on promoters and enhancers to repress transcription through chromatin-linked mechanisms. Our comparative phylogenetic study shows that CtBP is a bilaterian innovation whose CTD of about 100 residues is present in almost all orthologs. CtBP CTDs contain conserved blocks of residues and retain a predicted disordered property, despite having variations in the primary sequence. Interestingly, the structure of the C-terminus has undergone radical transformation independently in certain lineages including flatworms and nematodes. Also contributing to CTD diversity is the production of myriad alternative RNA splicing products, including the production of "short" tailless forms of CtBP in Drosophila. Additional diversity stems from multiple gene duplications in vertebrates, where up to five CtBP orthologs have been observed. Vertebrate lineages show fewer major modifications in the unstructured CTD, possibly because gene regulatory constraints of the vertebrate body plan place specific constraints on this domain. Our study highlights the rich regulatory potential of this previously unstudied domain of a central transcriptional regulator.
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Affiliation(s)
- Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
| | - Dhruva Kadiyala
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Madeline Niblock
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | | | - Yahui Yang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kalynn M Bird
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kayla Bertholf
- Biochemistry and Molecular Biology Program, College of Wooster
| | - Akshay Seenivasan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Mohammad Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - David N Arnosti
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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20
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Gingerich MA, Liu X, Chai B, Pearson GL, Vincent MP, Stromer T, Zhu J, Sidarala V, Renberg A, Sahu D, Klionsky DJ, Schnell S, Soleimanpour SA. An intrinsically disordered protein region encoded by the human disease gene CLEC16A regulates mitophagy. Autophagy 2023; 19:525-543. [PMID: 35604110 PMCID: PMC9851259 DOI: 10.1080/15548627.2022.2080383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CLEC16A regulates mitochondrial health through mitophagy and is associated with over 20 human diseases. However, the key structural and functional regions of CLEC16A, and their relevance for human disease, remain unknown. Here, we report that a disease-associated CLEC16A variant lacks a C-terminal intrinsically disordered protein region (IDPR) that is critical for mitochondrial quality control. IDPRs comprise nearly half of the human proteome, yet their mechanistic roles in human disease are poorly understood. Using carbon detect NMR, we find that the CLEC16A C terminus lacks secondary structure, validating the presence of an IDPR. Loss of the CLEC16A C-terminal IDPR in vivo impairs mitophagy, mitochondrial function, and glucose-stimulated insulin secretion, ultimately causing glucose intolerance. Deletion of the CLEC16A C-terminal IDPR increases CLEC16A ubiquitination and degradation, thus impairing assembly of the mitophagy regulatory machinery. Importantly, CLEC16A stability is dependent on proline bias within the C-terminal IDPR, but not amino acid sequence order or charge. Together, we elucidate how an IDPR in CLEC16A regulates mitophagy and implicate pathogenic human gene variants that disrupt IDPRs as novel contributors to diabetes and other CLEC16A-associated diseases.Abbreviations : CAS: carbon-detect amino-acid specific; IDPR: intrinsically disordered protein region; MEFs: mouse embryonic fibroblasts; NMR: nuclear magnetic resonance.
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Affiliation(s)
- Morgan A. Gingerich
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xueying Liu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Biaoxin Chai
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Gemma L. Pearson
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Michael P. Vincent
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tracy Stromer
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Jie Zhu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Vaibhav Sidarala
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Aaron Renberg
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Debashish Sahu
- BioNMR Core Facility, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Scott A. Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Medicine Service, Endocrinology and Metabolism Section, VA Ann Arbor Health Care System, Ann Arbor, MI, USA,CONTACT Scott A. Soleimanpour Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Wall Street, Brehm Tower Room, Ann Arbor, MI, USA
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21
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Pintado-Grima C, Santos J, Iglesias V, Manglano-Artuñedo Z, Pallarès I, Ventura S. Exploring cryptic amyloidogenic regions in prion-like proteins from plants. Front Plant Sci 2023; 13:1060410. [PMID: 36726678 PMCID: PMC9885169 DOI: 10.3389/fpls.2022.1060410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Prion-like domains (PrLDs) are intrinsically disordered regions (IDRs) of low sequence complexity with a similar composition to yeast prion domains. PrLDs-containing proteins have been involved in different organisms' regulatory processes. Regions of moderate amyloid propensity within IDRs have been shown to assemble autonomously into amyloid fibrils. These sequences tend to be rich in polar amino acids and often escape from the detection of classical bioinformatics screenings that look for highly aggregation-prone hydrophobic sequence stretches. We defined them as cryptic amyloidogenic regions (CARs) and recently developed an integrated database that collects thousands of predicted CARs in IDRs. CARs seem to be evolutionary conserved among disordered regions because of their potential to stablish functional contacts with other biomolecules. Here we have focused on identifying and characterizing CARs in prion-like proteins (pCARs) from plants, a lineage that has been poorly studied in comparison with other prionomes. We confirmed the intrinsic amyloid potential for a selected pCAR from Arabidopsis thaliana and explored functional enrichments and compositional bias of pCARs in plant prion-like proteins.
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Affiliation(s)
- Carlos Pintado-Grima
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaime Santos
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Valentín Iglesias
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Barcelona Institute for Global Health, Barcelona Centre for International Health Research (ISGlobal, Hospital Clínic-Universitat de Barcelona), Barcelona, Spain
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zoe Manglano-Artuñedo
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarès
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
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22
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Ehm T, Shinar H, Jacoby G, Meir S, Koren G, Segal Asher M, Korpanty J, Thompson MP, Gianneschi NC, Kozlov MM, Azoulay-Ginsburg S, Amir RJ, Rädler JO, Beck R. Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles. Biomacromolecules 2023; 24:98-108. [PMID: 36469950 PMCID: PMC9832477 DOI: 10.1021/acs.biomac.2c00866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions. Yet, the possible sequence variations and their influence on the self-assembly structures are vast and have hardly been explored. Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alter the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induce enzymatically activated phase transitions. These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with the desired properties.
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Affiliation(s)
- Tamara Ehm
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Shinar
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Guy Jacoby
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sagi Meir
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gil Koren
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Merav Segal Asher
- The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Joanna Korpanty
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew P. Thompson
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States,Department
of Materials Science & Engineering, Department of Biomedical Engineering
and Department of Pharmacology, Northwestern
University, Evanston, Illinois 60208, United States
| | - Michael M. Kozlov
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Salome Azoulay-Ginsburg
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roey J. Amir
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel,The
ADAMA Center for Novel Delivery Systems in Crop Protection, Tel Aviv University, Tel Aviv 6997801, Israel,Email
| | - Joachim O. Rädler
- Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany,
| | - Roy Beck
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,
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23
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Lee KE, Procopio R, Pulido JS, Gunton KB. Initial Investigations of Intrinsically Disordered Regions in Inherited Retinal Diseases. Int J Mol Sci 2023; 24:ijms24021060. [PMID: 36674574 PMCID: PMC9861917 DOI: 10.3390/ijms24021060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/16/2022] [Accepted: 12/30/2022] [Indexed: 01/08/2023] Open
Abstract
Intrinsically disordered regions (IDRs) are protein regions that are unable to fold into stable tertiary structures, enabling their involvement in key signaling and regulatory functions via dynamic interactions with diverse binding partners. An understanding of IDRs and their association with biological function may help elucidate the pathogenesis of inherited retinal diseases (IRDs). The main focus of this work was to investigate the degree of disorder in 14 proteins implicated in IRDs and their relationship with the number of pathogenic missense variants. Metapredict, an accurate, high-performance predictor that reproduces consensus disorder scores, was used to probe the degree of disorder as a function of the amino acid sequence. Publicly available data on gnomAD and ClinVar was used to analyze the number of pathogenic missense variants. We show that proteins with an over-representation of missense variation exhibit a high degree of disorder, and proteins with a high amount of disorder tolerate a higher degree of missense variation. These proteins also exhibit a lower amount of pathogenic missense variants with respect to total missense variants. These data suggest that protein function may be related to the overall level of disorder and could be used to refine variant interpretation in IRDs.
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Affiliation(s)
- Karen E. Lee
- Pediatric Ophthalmology & Adult Strabismus Service, Wills Eye Hospital, 840 Walnut Street, Philadelphia, PA 19107, USA
| | - Rebecca Procopio
- Pediatric Ophthalmology & Adult Strabismus Service, Wills Eye Hospital, 840 Walnut Street, Philadelphia, PA 19107, USA
| | - Jose S. Pulido
- Retina Service, Wills Eye Hospital and Mid Atlantic Retina, 840 Walnut Street, Philadelphia, PA 19107, USA
- Department of Translational Ophthalmology, Wills Eye Hospital, 840 Walnut Street, Philadelphia, PA 19107, USA
- Correspondence:
| | - Kammi B. Gunton
- Pediatric Ophthalmology & Adult Strabismus Service, Wills Eye Hospital, 840 Walnut Street, Philadelphia, PA 19107, USA
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24
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PANAGOPOULOS IOANNIS, ANDERSEN KRISTIN, GORUNOVA LUDMILA, HOGNESTAD HANNEREGINE, PEDERSEN THOMASDAHL, LOBMAIER INGVILD, MICCI FRANCESCA, HEIM SVERRE. Chromosome Translocation t(10;19)(q26;q13) in a CIC-sarcoma. In Vivo 2023; 37:57-69. [PMID: 36593014 PMCID: PMC9843759 DOI: 10.21873/invivo.13054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIM CIC-sarcomas are characterized by rearrangements of the capicua transcriptional repressor (CIC) gene on chromosome subband 19q13.2, generating chimeras in which CIC is the 5'-end partner. Most reported CIC-sarcomas have been detected using PCR amplifications together with Sanger sequencing, high throughput sequencing, and fluorescence in situ hybridization (FISH). Only a few CIC-rearranged tumors have been characterized cytogenetically. Here, we describe the cytogenetic and molecular genetic features of a CIC-sarcoma carrying a t(10;19)(q26;q13), a chromosomal rearrangement not previously detected in such neoplasms. MATERIALS AND METHODS A round cell sarcoma removed from the right thigh of a 57-year-old man was investigated by G-banding cytogenetics, FISH, PCR and Sanger sequencing. RESULTS The tumor cells had three cytogenetically related clones with the translocations t(9;18)(q22;q21) and t(10;19)(q26;q13) common to all of them. FISH with a BAC probe containing the CIC gene hybridized to the normal chromosome 19, to der(10)t(10;19), and to der(19)t(10;19). PCR using tumor cDNA as template together with Sanger sequencing detected two CIC::DUX4 fusion transcripts which both had a stop TAG codon immediately after the fusion point. Both transcripts are predicted to encode truncated CIC polypeptides lacking the carboxy terminal part of the native protein. This missing part is crucial for CIC's DNA binding capacity and interaction with other proteins. CONCLUSION In addition to demonstrating that CIC rearrangement in sarcomas can occur via the microscopically visible translocation t(10;19)(q26;q13), the findings in the present case provide evidence that the missing part in CIC-truncated proteins has important functions whose loss may be important in tumorigenesis.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - KRISTIN ANDERSEN
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - LUDMILA GORUNOVA
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | | | | | - FRANCESCA MICCI
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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25
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Kouros CE, Makri V, Ouzounis CA, Chasapi A. Disease association and comparative genomics of compositional bias in human proteins. F1000Res 2023; 12:198. [PMID: 37082000 PMCID: PMC10111144.2 DOI: 10.12688/f1000research.129929.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 04/25/2023] Open
Abstract
Background: The evolutionary rate of disordered protein regions varies greatly due to the lack of structural constraints. So far, few studies have investigated the presence/absence patterns of compositional bias, indicative of disorder, across phylogenies in conjunction with human disease. In this study, we report a genome-wide analysis of compositional bias association with disease in human proteins and their taxonomic distribution. Methods: The human genome protein set provided by the Ensembl database was annotated and analysed with respect to both disease associations and the detection of compositional bias. The Uniprot Reference Proteome dataset, containing 11297 proteomes was used as target dataset for the comparative genomics of a well-defined subset of the Human Genome, including 100 characteristic, compositionally biased proteins, some linked to disease. Results: Cross-evaluation of compositional bias and disease-association in the human genome reveals a significant bias towards biased regions in disease-associated genes, with charged, hydrophilic amino acids appearing as over-represented. The phylogenetic profiling of 17 disease-associated, proteins with compositional bias across 11297 proteomes captures characteristic taxonomic distribution patterns. Conclusions: This is the first time that a combined genome-wide analysis of compositional bias, disease-association and taxonomic distribution of human proteins is reported, covering structural, functional, and evolutionary properties. The reported framework can form the basis for large-scale, follow-up projects, encompassing the entire human genome and all known gene-disease associations.
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Affiliation(s)
- Christos E. Kouros
- BCCB-AIIA, School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vasiliki Makri
- BCCB-AIIA, School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos A. Ouzounis
- BCCB-AIIA, School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
- BCPL, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Anastasia Chasapi
- BCPL, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
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26
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Kondratyev MS, Rudnev VR, Nikolsky KS, Petrovsky DV, Kulikova LI, Malsagova KA, Stepanov AA, Kopylov AT, Kaysheva AL. In Silico Study of the Interactions of Anle138b Isomer, an Inhibitor of Amyloid Aggregation, with Partner Proteins. Int J Mol Sci 2022; 23. [PMID: 36555748 DOI: 10.3390/ijms232416096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Herein, we aimed to highlight current "gaps" in the understanding of the potential interactions between the Anle138b isomer ligand, a promising agent for clinical research, and the intrinsically disordered alpha-synuclein protein. The presence of extensive unstructured areas in alpha-synuclein determines its existence in the cell of partner proteins, including the cyclophilin A chaperone, which prevents the aggregation of alpha-synuclein molecules that are destructive to cell life. Using flexible and cascaded molecular docking techniques, we aimed to expand our understanding of the molecular architecture of the protein complex between alpha-synuclein, cyclophilin A and the Anle138b isomer ligand. We demonstrated the possibility of intricate complex formation under cellular conditions and revealed that the main interactions that stabilize the complex are hydrophobic and involve hydrogen.
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27
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Pal S, Udgaonkar JB. Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form. J Mol Biol 2022; 434:167854. [PMID: 36228749 DOI: 10.1016/j.jmb.2022.167854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen-deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research, Pune, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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28
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Manukian S, Lindberg GE, Punch E, Mudiyanselage SPD, Gage MJ. pH-Dependent Compaction of the Intrinsically Disordered Poly-E Motif in Titin. Biology 2022; 11:1302. [PMID: 36138781 PMCID: PMC9495361 DOI: 10.3390/biology11091302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
The conformational sensitivity of intrinsically disordered proteins to shifts in pH due to their high degree of charged residues has been recognized for well over a decade. However, the role of the non-ionizable residues in this pH sensitivity remains poorly understood. Our lab has been investigating the pH sensitivity of the poly-E motifs of the PEVK region of the muscle protein titin, which provides an ideal model system to explore this question. Using a series of 15-amino acid peptides derived from one of the poly-E motif sequences, we have investigated the role of side-chain chemistry in the conformational flexibility of this region. Our results demonstrate that aromatic side chains and proline content are the two variables that most influence pH sensitivity. The introduction of aromatic side chains resulted in a more collapsed structure, even at pH 7, while the removal of prolines resulted in a higher degree of pH sensitivity. These results highlight the importance of considering the impact of non-ionizable residues on IDP function, especially when considering the impact of pH on conformational flexibility.
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29
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Babu M, Favretto F, Rankovic M, Zweckstetter M. Peptidyl Prolyl Isomerase A Modulates the Liquid-Liquid Phase Separation of Proline-Rich IDPs. J Am Chem Soc 2022; 144:16157-16163. [PMID: 36018855 PMCID: PMC9460772 DOI: 10.1021/jacs.2c07149] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and the action of molecular chaperones are tightly connected. An important class of molecular chaperones are peptidyl prolyl isomerases, which enhance the cis/trans-isomerization of proline. However, little is known about the impact of peptidyl prolyl isomerases on the LLPS of IDPs, which often contain many prolines. Here, we demonstrate that the most ubiquitous peptidyl prolyl isomerase, peptidyl prolyl isomerase A (PPIA), concentrates inside liquid-like droplets formed by the Alzheimer's disease-associated protein tau, as well as inside RNA-induced coacervates of a proline-arginine dipeptide repeat protein. We further show that the recruitment of PPIA into the IDP droplets triggers their dissolution and return to a single mixed phase. NMR-based binding and proline isomerization studies provide insights into the mechanism of LLPS modulation. Together, the results establish a regulatory role of proline isomerases on the liquid-liquid phase separation of proline-rich IDPs.
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Affiliation(s)
- Maria Babu
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Von-Siebold Straße 3a, Göttingen, 37075, Germany
| | - Filippo Favretto
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Von-Siebold Straße 3a, Göttingen, 37075, Germany
| | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, 37077, Germany
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Von-Siebold Straße 3a, Göttingen, 37075, Germany.,Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, 37077, Germany
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30
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Suyama K, Shimizu M, Maeda I, Nose T. Flexible customization of the self-assembling abilities of short elastin-like peptide Fn analogs by substituting N-terminal amino acids. Biopolymers 2022; 113:e23521. [PMID: 35830538 DOI: 10.1002/bip.23521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/20/2022] [Accepted: 07/01/2022] [Indexed: 11/06/2022]
Abstract
Elastin-like peptides (ELPs) are thermoresponsive biopolymers inspired by the characteristic repetitive sequences of natural elastin. As ELPs exhibit temperature-dependent reversible self-assembly, they are expected to be biocompatible thermoresponsive materials for drug delivery carriers. One of the most widely studied ELPs in this field is the repetitive pentapeptide, (VPGXG)n . We previously reported that phenylalanine-containing ELP (Fn) analogs, in which the former Val residue of the repetitive sequence (VPGVG)n is replaced by Phe, show coacervation with a short chain length (n = 5). Owing to their short sequences, Fn analogs are easily modified in amino acid sequences via simple chemical synthesis, and are useful for investigating the relationship between peptide sequences and temperature responsiveness. In this study, we developed Fn analogs by replacing Phe residue(s) with other amino acids or introducing another amino acid at the N-terminus. The temperature responsiveness of the Fn analogs changed drastically with the substitution of a single Phe residue, suggesting that aromatic amino acids play an important role in their self-assembly. In addition, the self-assembling ability of Fn was enhanced by increasing the bulkiness of the N-terminal amino acids. Therefore, the N-terminal residue was considered to be important for hydrophobicity-induced intermolecular interactions between the peptides during coacervation.
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Affiliation(s)
- Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
| | - Marin Shimizu
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Iori Maeda
- Department of Physics and Information Technology, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan.,Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, Japan
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31
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Bezerra RP, Conniff AS, Uversky VN. Comparative study of structures and functional motifs in lectins from the commercially important photosynthetic microorganisms. Biochimie 2022; 201:63-74. [PMID: 35839918 DOI: 10.1016/j.biochi.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/17/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Photosynthetic microorganisms, specifically cyanobacteria and microalgae, can synthesize a vast array of biologically active molecules, such as lectins, that have great potential for various biotechnological and biomedical applications. However, since the structures of these proteins are not well established, likely due to the presence of intrinsically disordered regions, our ability to better understand their functionality is hampered. We embarked on a study of the carbohydrate recognition domain (CRD), intrinsically disordered regions (IDRs), amino acidic composition, as well as and functional motifs in lectins from cyanobacteria of the genus Arthrospira and microalgae Chlorella and Dunaliella genus using a combination of bioinformatics techniques. This search revealed the presence of five distinctive CRD types differently distributed between the genera. Most CRDs displayed a group-specific distribution, except to C. sorokiniana possessing distinctive CRD probably due to its specific lifestyle. We also found that all CRDs contain short IDRs. Bacterial lectin of Arthrospira prokarionte showed lower intrinsic disorder and proline content when compared to the lectins from the eukaryotic microalgae (Chlorella and Dunaliella). Among the important functions predicted in all lectins were several specific motifs, which directly interacts with proteins involved in the cell-cycle control and which may be used for pharmaceutical purposes. Since the aforementioned properties of each type of lectin were investigated in silico, they need experimental confirmation. The results of our study provide an overview of the distribution of CRD, IDRs, and functional motifs within lectin from the commercially important microalgae.
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Affiliation(s)
- Raquel P Bezerra
- Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco-UFRPE, Dom Manoel de Medeiros Ave, Recife, PE, 52171-900, Brazil.
| | - Amanda S Conniff
- Department of Medical Engineering, Morsani College of Medicine and College of Engineering, University of South Florida, Tampa, FL, 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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32
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Chen X, Mirazee JM, Skorupka KA, Matsuo H, Youkharibache P, Taylor N, Walters KJ. The CD8α hinge is intrinsically disordered with a dynamic exchange that includes proline cis-trans isomerization. J Magn Reson 2022; 340:107234. [PMID: 35617919 PMCID: PMC9237829 DOI: 10.1016/j.jmr.2022.107234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
T cells engineered to express artificial chimeric antigen receptors (CARs) that selectively target tumor-specific antigens or deleterious cell types offer transformative therapeutic possibilities. CARs contain an N-terminal extracellular antigen recognition domain, C-terminal intracellular signal transduction domains, and connecting hinge and transmembrane regions, each of which have been varied to optimize targeting and minimize toxicity. We find that a CD22-targeting CAR harboring a CD8α hinge (H) exhibits greater cytotoxicity against a low antigen density CD22+ leukemia as compared to an equivalent CAR with a CD28 H. We therefore studied the biophysical and dynamic properties of the CD8α H by nuclear magnetic resonance (NMR) spectroscopy. We find that a large region of the CD8α H undergoes dynamic chemical exchange between distinct and observable states. This exchanging region contains proline residues dispersed throughout the sequence that undergo cis-trans isomerization. Up to four signals of differing intensity are observed, with the most abundantly populated being intrinsically disordered and with all prolines in the trans isomerization state. The lesser populated states all contain cis prolines and evidence of local structural motifs. Altogether, our data suggest that the CD8α H lacks long-range structural order but has local structural motifs that transiently exchange with a dominant disordered state. We propose that structural plasticity and local structural motifs promoted by cis proline states within the CD8α H are important for relaying and amplifying antigen-binding effects to the transmembrane and signal transduction domains.
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Affiliation(s)
- Xiang Chen
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Justin M Mirazee
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Katarzyna A Skorupka
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA.
| | - Kylie J Walters
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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33
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Zhao B, Kurgan L. Compositional Bias of Intrinsically Disordered Proteins and Regions and Their Predictions. Biomolecules 2022; 12:888. [PMID: 35883444 PMCID: PMC9313023 DOI: 10.3390/biom12070888] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Intrinsically disordered regions (IDRs) carry out many cellular functions and vary in length and placement in protein sequences. This diversity leads to variations in the underlying compositional biases, which were demonstrated for the short vs. long IDRs. We analyze compositional biases across four classes of disorder: fully disordered proteins; short IDRs; long IDRs; and binding IDRs. We identify three distinct biases: for the fully disordered proteins, the short IDRs and the long and binding IDRs combined. We also investigate compositional bias for putative disorder produced by leading disorder predictors and find that it is similar to the bias of the native disorder. Interestingly, the accuracy of disorder predictions across different methods is correlated with the correctness of the compositional bias of their predictions highlighting the importance of the compositional bias. The predictive quality is relatively low for the disorder classes with compositional bias that is the most different from the “generic” disorder bias, while being much higher for the classes with the most similar bias. We discover that different predictors perform best across different classes of disorder. This suggests that no single predictor is universally best and motivates the development of new architectures that combine models that target specific disorder classes.
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34
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Weninger G, Pochechueva T, El Chami D, Luo X, Kohl T, Brandenburg S, Urlaub H, Guan K, Lenz C, Lehnart SE. Calpain cleavage of Junctophilin-2 generates a spectrum of calcium-dependent cleavage products and DNA-rich NT 1-fragment domains in cardiomyocytes. Sci Rep 2022; 12:10387. [PMID: 35725601 PMCID: PMC9209451 DOI: 10.1038/s41598-022-14320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Calpains are calcium-activated neutral proteases involved in the regulation of key signaling pathways. Junctophilin-2 (JP2) is a Calpain-specific proteolytic target and essential structural protein inside Ca2+ release units required for excitation-contraction coupling in cardiomyocytes. While downregulation of JP2 by Calpain cleavage in heart failure has been reported, the precise molecular identity of the Calpain cleavage sites and the (patho-)physiological roles of the JP2 proteolytic products remain controversial. We systematically analyzed the JP2 cleavage fragments as function of Calpain-1 versus Calpain-2 proteolytic activities, revealing that both Calpain isoforms preferentially cleave mouse JP2 at R565, but subsequently at three additional secondary Calpain cleavage sites. Moreover, we identified the Calpain-specific primary cleavage products for the first time in human iPSC-derived cardiomyocytes. Knockout of RyR2 in hiPSC-cardiomyocytes destabilized JP2 resulting in an increase of the Calpain-specific cleavage fragments. The primary N-terminal cleavage product NT1 accumulated in the nucleus of mouse and human cardiomyocytes in a Ca2+-dependent manner, closely associated with euchromatic chromosomal regions, where NT1 is proposed to function as a cardio-protective transcriptional regulator in heart failure. Taken together, our data suggest that stabilizing NT1 by preventing secondary cleavage events by Calpain and other proteases could be an important therapeutic target for future studies.
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Affiliation(s)
- Gunnar Weninger
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany.,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany.,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany.,Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Tatiana Pochechueva
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany.,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany.,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany
| | - Dana El Chami
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany.,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany.,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany
| | - Xiaojing Luo
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, 01307, Dresden, Germany
| | - Tobias Kohl
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany.,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany.,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC2067), University of Göttingen, 37073, Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, 37075, Göttingen, Germany
| | - Sören Brandenburg
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany.,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany.,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC2067), University of Göttingen, 37073, Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, 37075, Göttingen, Germany
| | - Henning Urlaub
- Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany.,Proteomanalyse, Department of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, 01307, Dresden, Germany
| | - Christof Lenz
- Proteomanalyse, Department of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany. .,Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Stephan E Lehnart
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Str. 42a, 37075, Göttingen, Germany. .,Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075, Göttingen, Germany. .,Collaborative Research Center SFB1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, 37073, Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC2067), University of Göttingen, 37073, Göttingen, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site, 37075, Göttingen, Germany.
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35
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Kosinski LJ, Aviles NR, Gomez K, Masel J. Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful. Genome Biol Evol 2022; 14:evac085. [PMID: 35668555 PMCID: PMC9210321 DOI: 10.1093/gbe/evac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 11/15/2022] Open
Abstract
Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from non-coding DNA. Proteins are more likely to be born from non-coding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to "first, do no harm", we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent dataset of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.
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Affiliation(s)
- Luke J Kosinski
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, USA
| | - Nathan R Aviles
- Graduate Interdisciplinary Program in Statistics, University of Arizona, Tucson, USA
| | - Kevin Gomez
- Graduate Interdisciplinary Program in Applied Math, University of Arizona, Tucson, USA
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
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36
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Szabó CL, Szabó B, Sebák F, Bermel W, Tantos A, Bodor A. The Disordered EZH2 Loop: Atomic Level Characterization by 1H N- and 1H α-Detected NMR Approaches, Interaction with the Long Noncoding HOTAIR RNA. Int J Mol Sci 2022; 23:6150. [PMID: 35682829 DOI: 10.3390/ijms23116150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023] Open
Abstract
The 96-residue-long loop of EZH2 is proposed to play a role in the interaction with long non-coding RNAs (lncRNAs) and to contribute to EZH2 recruitment to the chromatin. However, molecular details of RNA recognition have not been described so far. Cellular studies have suggested that phosphorylation of the Thr345 residue localized in this loop influences RNA binding; however, no mechanistic explanation has been offered. To address these issues, a systematic NMR study was performed. As the 1HN-detected NMR approach presents many challenges under physiological conditions, our earlier developed, as well as improved, 1Hα-detected experiments were used. As a result of the successful resonance assignment, the obtained chemical shift values indicate the highly disordered nature of the EZH2 loop, with some nascent helical tendency in the Ser407–Ser412 region. Further investigations conducted on the phosphomimetic mutant EZH2T345D showed that the mutation has only a local effect, and that the loop remains disordered. On the other hand, the mutation influences the cis/trans Pro346 equilibrium. Interactions of both the wild-type and the phosphomimetic mutant with the lncRNA HOTAIR140 (1–140 nt) highlight that the Thr367–Ser375 region is affected. This segment does not resemble any of the previously reported RNA-binding motifs, therefore the identified binding region is unique. As no structural changes occur in the EZH2 loop upon RNA binding, we can consider the protein–RNA interaction as a “fuzzy” complex.
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37
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Hilt S, Liu R, Maezawa I, Rojalin T, Aung HH, Budamagunta M, Slez R, Gong Q, Carney RP, Voss JC. Novel Stilbene-Nitroxyl Hybrid Compounds Display Discrete Modulation of Amyloid Beta Toxicity and Structure. Front Chem 2022; 10:896386. [PMID: 35720993 PMCID: PMC9204515 DOI: 10.3389/fchem.2022.896386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Several neurodegenerative diseases are driven by misfolded proteins that assemble into soluble aggregates. These "toxic oligomers" have been associated with a plethora of cellular dysfunction and dysregulation, however the structural features underlying their toxicity are poorly understood. A major impediment to answering this question relates to the heterogeneous nature of the oligomers, both in terms of structural disorder and oligomer size. This not only complicates elucidating the molecular etiology of these disorders, but also the druggability of these targets as well. We have synthesized a class of bifunctional stilbenes to modulate both the conformational toxicity within amyloid beta oligomers (AβO) and the oxidative stress elicited by AβO. Using a neuronal culture model, we demonstrate this bifunctional approach has the potential to counter the molecular pathogenesis of Alzheimer's disease in a powerful, synergistic manner. Examination of AβO structure by various biophysical tools shows that each stilbene candidate uniquely alters AβO conformation and toxicity, providing insight towards the future development of structural correctors for AβO. Correlations of AβO structural modulation and bioactivity displayed by each provides insights for future testing in vivo. The multi-target activity of these hybrid molecules represents a highly advantageous feature for disease modification in Alzheimer's, which displays a complex, multifactorial etiology. Importantly, these novel small molecules intervene with intraneuronal AβO, a necessary feature to counter the cycle of dysregulation, oxidative stress and inflammation triggered during the earliest stages of disease progression.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Izumi Maezawa
- M.I.N.D. Institute and Department of Pathology and Laboratory Medicine, University of California, Davis, Davis, CA, United States
| | - Tatu Rojalin
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - Hnin H. Aung
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
- Research Division, California Air Resource Board, Sacramento, CA, United States
| | - Madhu Budamagunta
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Ryan Slez
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Randy P. Carney
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - John C. Voss
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Paramag Biosciences Inc., Davis, CA, United States
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38
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Kılınç E, Can Timucin A, Selim Cinaroglu S, Timucin E. Modeling and dynamical analysis of the full-length structure of factor XII with zinc. J Mol Model 2022; 28:129. [PMID: 35469101 DOI: 10.1007/s00894-022-05113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Zinc (II), the second most abundant transition metal in blood, binds to the initiator of the contact pathway, factor XII (FXII). This binding induces conformational changes in the structure of FXII eventually leading to its activation. Despite many in vitro and in vivo studies on zinc-mediated activation of FXII, its molecular mechanism remains elusive mainly due to absence of a full-length structural model of FXII. To this end, this study investigated the role of zinc in the structure and dynamics of the full-length structure FXII that was obtained through molecular modeling. We have used four structural templates covering more than 70% of the FXII sequence and the remaining interconnecting regions were built by loop modeling. The resulting full-length structure of FXII contained disordered regions, but in comparison to the AlphaFold (AF) prediction, our full-length model represented a more realistic structure because of the disordered regions which were modeled to yield a more compact full-length structure in our model than the AF structure. Other than the disordered regions, our model and AF prediction were highly similar. The resulting full-length FXII structure was used to generate different systems representing the zinc-bound form (holo). Further to assess the contribution of the disulfide bridges, we also analyzed the apo and holo FXII structures with oxidized or reduced cysteine side-chains. Simulations suggested zinc binding conferred rigidity to the structure, particularly to the light chain of FXII. Zinc binding alone was sufficient to limit the backbone flexibility while 15 disulfide bonds, which were scattered throughout the structure, made a less significant contribution to the backbone rigidity. Altogether our results provide insights into the first realistic full-length structure of FXII focusing on the impact of structural zinc and disulfide bridges in the dynamics of this structure.
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Affiliation(s)
- Evren Kılınç
- Department of Biophysics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | - Ahmet Can Timucin
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | | | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey.
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39
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Popelka H, Uversky VN. Theater in the Self-Cleaning Cell: Intrinsically Disordered Proteins or Protein Regions Acting with Membranes in Autophagy. Membranes 2022; 12:457. [PMID: 35629783 PMCID: PMC9143426 DOI: 10.3390/membranes12050457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally diverse components including membranes are essential. The autophagy pathway builds, de novo, a membrane organelle, the autophagosome, using carefully orchestrated interactions between proteins and lipid bilayers. Here, we discuss molecular mechanisms related to the protein disorder-based interactions of the autophagy machinery with membranes. We describe not only membrane binding phenomenon, but also examples of membrane remodeling processes including membrane tethering, bending, curvature sensing, and/or fragmentation of membrane organelles such as the endoplasmic reticulum, which is an important membrane source as well as cargo for autophagy. Summary of the current state of knowledge presented here will hopefully inspire new studies. A profound understanding of the autophagic protein–membrane interface is essential for advancements in therapeutic interventions against major human diseases, in which autophagy is involved including neurodegeneration, cancer as well as cardiovascular, metabolic, infectious, musculoskeletal, and other disorders.
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40
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Wilson CJ, Choy WY, Karttunen M. AlphaFold2: A Role for Disordered Protein/Region Prediction? Int J Mol Sci 2022; 23:4591. [PMID: 35562983 DOI: 10.3390/ijms23094591] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 01/27/2023] Open
Abstract
The development of AlphaFold2 marked a paradigm-shift in the structural biology community. Herein, we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that AlphaFold2 performs well at discriminating disordered regions, but also note that the disorder predictor one constructs from an AlphaFold2 structure determines accuracy. In particular, a naïve, but non-trivial assumption that residues assigned to helices, strands, and H-bond stabilized turns are likely ordered and all other residues are disordered results in a dramatic overestimation in disorder; conversely, the predicted local distance difference test (pLDDT) provides an excellent measure of residue-wise disorder. Furthermore, by employing molecular dynamics (MD) simulations, we note an interesting relationship between the pLDDT and secondary structure, that may explain our observations and suggests a broader application of the pLDDT for characterizing the local dynamics of intrinsically disordered proteins and regions (IDPs/IDRs).
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41
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Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are proteins or protein-domains that do not have a single native structure, rather, they are a class of flexible peptides that can rapidly adopt multiple conformations. IDPs are quite abundant, and their dynamic characteristics provide unique advantages for various biological processes. The field of “unstructured biology” has emerged, in part, because of numerous computational studies that had identified the unique characteristics of IDPs and IDRs. The package ‘idpr’, short for Intrinsically Disordered Proteins in R, implements several R functions that match the established characteristics of IDPs to protein sequences of interest. This includes calculations of residue composition, charge-hydropathy relationships, and predictions of intrinsic disorder. Additionally, idpr integrates several amino acid substitution matrices and calculators to supplement IDP-based workflows. Overall, idpr aims to integrate tools for the computational analysis of IDPs within R, facilitating the analysis of these important, yet under-characterized, proteins. The idpr package can be downloaded from Bioconductor (https://bioconductor.org/packages/idpr/).
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Affiliation(s)
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- * E-mail:
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42
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Bianchi G, Mangiagalli M, Barbiroli A, Longhi S, Grandori R, Santambrogio C, Brocca S. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules 2022; 12:biom12040561. [PMID: 35454150 PMCID: PMC9031945 DOI: 10.3390/biom12040561] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge patterning on the average compactness and shape of three model IDPs with different proline content. We model IDP ensemble conformations as ellipsoids, whose size and shape are calculated by combining data from size-exclusion chromatography and native mass spectrometry. For each model IDP, we analyzed the wild-type protein and two synthetic variants with permuted positions of charged residues, where positive and negative amino acids are either evenly distributed or segregated. We found that charge clustering induces remodeling of the conformational ensemble, promoting compaction and/or increasing spherical shape. Our data illustrate that the average shape and volume of the ensembles depend on the charge distribution. The potential effect of other factors, such as chain length, number of proline residues, and secondary structure content, is also discussed. This methodological approach is a straightforward way to model IDP average conformation and decipher the salient sequence attributes influencing IDP structural properties.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Alberto Barbiroli
- Departement of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy;
| | - Sonia Longhi
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, 13288 Marseille, France;
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (G.B.); (M.M.); (R.G.)
- Correspondence: (C.S.); (S.B.); Tel.: +39-02-6448-3363 (C.S.); +39-02-6448-3518 (S.B.)
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Bonde AC, Hansen SR, Johansson E, Bjelke JR, Lund J. Site‐specific functional roles of the Factor X activation peptide in the intrinsic tenase‐mediated Factor X activation. FEBS Lett 2022; 596:1567-1575. [DOI: 10.1002/1873-3468.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/21/2022] [Accepted: 02/12/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Amalie Carnbring Bonde
- Research & Early Development Novo Nordisk A/S 2760 Måløv Denmark
- Department of Molecular Biology and Genetics Aarhus University Denmark
| | | | - Eva Johansson
- Research & Early Development Novo Nordisk A/S 2760 Måløv Denmark
| | - Jais Rose Bjelke
- Research & Early Development Novo Nordisk A/S 2760 Måløv Denmark
| | - Jacob Lund
- Research & Early Development Novo Nordisk A/S 2760 Måløv Denmark
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44
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Medvedev KE, Pei J, Grishin NV. DisEnrich: database of enriched regions in human dark proteome. Bioinformatics 2022; 38:1870-1876. [PMID: 35094056 PMCID: PMC8963327 DOI: 10.1093/bioinformatics/btac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Intrinsically disordered proteins (IDPs) are involved in numerous processes crucial for living organisms. Bias in amino acid composition of these proteins determines their unique biophysical and functional features. Distinct intrinsically disordered regions (IDRs) with compositional bias play different important roles in various biological processes. IDRs enriched in particular amino acids in human proteome have not been described consistently. RESULTS We developed DisEnrich-the database of human proteome IDRs that are significantly enriched in particular amino acids. Each human protein is described using Gene Ontology (GO) function terms, disorder prediction for the full-length sequence using three methods, enriched IDR composition and ranks of human proteins with similar enriched IDRs. Distribution analysis of enriched IDRs among broad functional categories revealed significant overrepresentation of R- and Y-enriched IDRs in metabolic and enzymatic activities and F-enriched IDRs in transport. About 75% of functional categories contain IDPs with IDRs significantly enriched in hydrophobic residues that are important for protein-protein interactions. AVAILABILITY AND IMPLEMENTATION The database is available at http://prodata.swmed.edu/DisEnrichDB/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Jimin Pei
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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45
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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46
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Sebák F, Ecsédi P, Bermel W, Luy B, Nyitray L, Bodor A. Selective
1
H
α
NMR Methods Reveal Functionally Relevant Proline
cis/trans
Isomers in Intrinsically Disordered Proteins: Characterization of Minor Forms, Effects of Phosphorylation, and Occurrence in Proteome. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fanni Sebák
- Eötvös Loránd University Institute of Chemistry Pázmány Péter s. 1/a 1117 Budapest Hungary
- Semmelweis University Doctoral School of Pharmaceutical Sciences Üllői út 26 1085 Budapest Hungary
| | - Péter Ecsédi
- Eötvös Loránd University Department of Biochemistry Pázmány Péter s. 1/c 1117 Budapest Hungary
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Burkhard Luy
- KIT-Institut für Organische Chemie IBG4—Magnetische Resonanz Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - László Nyitray
- Eötvös Loránd University Department of Biochemistry Pázmány Péter s. 1/c 1117 Budapest Hungary
| | - Andrea Bodor
- Eötvös Loránd University Institute of Chemistry Pázmány Péter s. 1/a 1117 Budapest Hungary
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Rani M, Siddiqi RA, Singh G, Kumar R, Sogi DS, Gill BS. Comparative evaluation of gliadins from four extraction protocols using advanced analytical techniques. Int J Biol Macromol 2021; 193:1114-1123. [PMID: 34715206 DOI: 10.1016/j.ijbiomac.2021.10.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 10/20/2022]
Abstract
Gliadin, a major component of gluten, is known to trigger celiac disease; therefore, its extraction is important to study its properties as well as its presence in gluten-free products. Four gliadin extraction procedures Osborne (1924), Weiss (1993), Wallace (1989) and DuPont (2005), were investigated on six wheat cultivars using advanced analytical techniques such as dynamic light scattering (DLS), X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Higher zeta potential of extracted gliadin was observed in DuPont (23.53-27), followed by Weiss (16.17-20.80), Osborne (16.17-20.13), and Wallace (14.60-19.47). Particle Z-average size (15.74-184.83 nm) was found to have an inverse relationship with the Polydispersity index (0.17-184.83). The surface morphological structure of TEM studies revealed the compact globular particle arrangement of gliadin, besides rod-shaped arrangement, was also found in DuPont and Wallace extracted gliadin. XRD pattern of gliadin exposed the crystalline domain at 44.1°, 37.8°, and 10.4° diffraction peaks. The d-spacing obtained from XRD and TEM-SAED analysis supports the presence of crystalline domains in gliadin apart from the amorphous domain. The insight obtained from this work will provide a better understanding of morphology and other properties of the same protein extracted with different extraction procedures.
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Affiliation(s)
- Monika Rani
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Raashid Ahmad Siddiqi
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Gurbir Singh
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Ravish Kumar
- Department of Physics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Dalbir Singh Sogi
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Balmeet Singh Gill
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar, Punjab, India.
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Rani M, Sogi DS, Gill BS. Characterization of gliadin, secalin and hordein fractions using analytical techniques. Sci Rep 2021; 11:23135. [PMID: 34848764 DOI: 10.1038/s41598-021-02099-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 10/01/2021] [Indexed: 11/12/2022] Open
Abstract
Prolamins, alcohol soluble storage proteins of the Triticeae tribe of Gramineae family, are known as gliadin, secalin and hordein in wheat, rye and barley respectively. Prolamins were extracted from fifteen cultivars using DuPont protocol to study their physiochemical, morphological and structural characteristics. SDS-PAGE of prolamins showed well resolved low molecular weight proteins with significant amount of albumin and globulin as cross-contaminant. The β-sheet (32.72–37.41%) and β-turn (30.36–37.91%) were found higher in gliadins, while α-helix (20.32–28.95%) and random coil (9.05–10.28%) in hordeins. The high colloidal stability as depicted by zeta-potential was observed in gliadins (23.5–27.0 mV) followed secalins (11.2–16.6 mV) and hordeins (4.1–7.8 mV). Surface morphology by SEM illustrated the globular particle arrangement in gliadins, sheet like arrangement in secalins and stacked flaky particle arrangement in hordeins fraction. TEM studies showed that secalin and hordein fractions were globular in shape while gliadins in addition to globular structure also possessed rod-shaped particle arrangement. XRD pattern of prolamin fractions showed the ordered crystalline domain at 2θ values of 44.1°, 37.8° and 10.4°. The extracted prolamins fractions showed amorphous as well as crystalline structures as revealed by XRD and TEM analysis. Space saving hexagonal molecular symmetry was also observed in TEM molecular arrangement of prolamins which has profound application in development of plant-based polymers and fibres.
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Vakilian M. A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis. Clin Immunol 2021; 234:108896. [PMID: 34848356 DOI: 10.1016/j.clim.2021.108896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022]
Abstract
Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.
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Affiliation(s)
- Mehrdad Vakilian
- Department of Cell Biology, Genetics and Physiology, University of Malaga (UMA), The Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain.
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Pinet L, Assrir N, van Heijenoort C. Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs. Biomolecules 2021; 11:1690. [PMID: 34827688 DOI: 10.3390/biom11111690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022] Open
Abstract
ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features.
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