251
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Baliova M, Jursky F. Specific glycine to alanine mutation eliminates dynamic interaction of polymeric GlyT1a N-terminus with Coomassie Brilliant Blue G-250. Electrophoresis 2018; 39:1357-1360. [DOI: 10.1002/elps.201700412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Martina Baliova
- Laboratory of Neurobiology; Slovak Academy of Sciences; Institute of Molecular Biology; Bratislava Slovakia
| | - Frantisek Jursky
- Laboratory of Neurobiology; Slovak Academy of Sciences; Institute of Molecular Biology; Bratislava Slovakia
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252
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Lou F, Yang J, Wu S, Perrett S. A co-expression strategy to achieve labeling of individual subunits within a dimeric protein for single molecule analysis. Chem Commun (Camb) 2018. [PMID: 28650509 DOI: 10.1039/c7cc03032k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A generic co-expression strategy for site-specific incorporation of a single donor-acceptor dye pair into any position in a dimeric protein, allowing single molecule FRET study of proteins previously inaccessible to this technique, such as the intrinsically disordered prion N-domain of Ure2 in the context of its globular dimeric C-domain.
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Affiliation(s)
- Fei Lou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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253
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Kasahara K, Shiina M, Higo J, Ogata K, Nakamura H. Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state. Nucleic Acids Res 2018; 46:2243-2251. [PMID: 29309620 PMCID: PMC5861456 DOI: 10.1093/nar/gkx1297] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022] Open
Abstract
Multi-modal interactions are frequently observed in intrinsically disordered regions (IDRs) of proteins upon binding to their partners. In many cases, post-translational modifications in IDRs are accompanied by coupled folding and binding. From both molecular simulations and biochemical experiments with mutational studies, we show that the IDR including a Ser rich region (SRR) of the transcription factor Ets1, just before the DNA-binding core domain, undergoes multi-modal interactions when the SRR is not phosphorylated. In the phosphorylated state, the SRR forms a few specific complex structures with the Ets1 core, covering the recognition helix in the core and drastically reducing the DNA binding affinities as the auto-inhibitory state. The binding kinetics of mutated Ets1 indicates that aromatic residues in the SRR can be substituted with other hydrophobic residues for the interactions with the Ets1 core.
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Affiliation(s)
- Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Noji-higashi 1-1-1, Kusatsu, Shiga 525-8577, Japan
| | - Masaaki Shiina
- Graduate School of Medicine, Yokohama City University, Fuku-ura 3–9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, Osaka 565-0871, Japan
| | - Kazuhiro Ogata
- Graduate School of Medicine, Yokohama City University, Fuku-ura 3–9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, Osaka 565-0871, Japan
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254
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 485] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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255
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Dahal L, Kwan TOC, Shammas SL, Clarke J. pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions. Biophys J 2018; 113:2713-2722. [PMID: 29262364 PMCID: PMC5770965 DOI: 10.1016/j.bpj.2017.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding the detailed mechanism of interaction of intrinsically disordered proteins with their partners is crucial to comprehend their functions in signaling and transcription. Through its interaction with KIX, the disordered pKID region of CREB protein is central in the transcription of cAMP responsive genes, including those involved in long-term memory. Numerous simulation studies have investigated these interactions. Combined with experimental results, these can provide valuable and comprehensive understanding of the mechanisms involved. Here, we probe the transition state of this interaction experimentally through analyzing the kinetic effect of mutating both interface and solvent exposed residues in pKID. We show that very few specific interactions between pKID and KIX are required in the initial binding process. Only a small number of weak interactions are formed at the transition state, including nonnative interactions, and most of the folding occurs after the initial binding event. These properties are consistent with computational results and also the majority of experimental studies of intrinsically disordered protein coupled folding and binding in other protein systems, suggesting that these may be common features.
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Affiliation(s)
- Liza Dahal
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tristan O C Kwan
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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256
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Khare H, Dey D, Madhu C, Senapati D, Raghothama S, Govindaraju T, Ramakumar S. Conformational heterogeneity in tails of DNA-binding proteins is augmented by proline containing repeats. MOLECULAR BIOSYSTEMS 2017; 13:2531-2544. [PMID: 29104984 DOI: 10.1039/c7mb00412e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of 'flexible disorder' and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA)1-4 and (PAKKA)1-4, represent the tails of several bacterial DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone. Analysis of circular variance of backbone dihedral angles indicates alternating regions of relative rigidity and flexibility along the peptide sequence due to prolines. Preferred placement of lysines in the regions of higher backbone flexibility might improve DNA-binding by conformational selection. Our results could be relevant for rational de novo design of disordered peptides.
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Affiliation(s)
- Harshavardhan Khare
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India.
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257
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Dosztányi Z. Prediction of protein disorder based on IUPred. Protein Sci 2017; 27:331-340. [PMID: 29076577 DOI: 10.1002/pro.3334] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Many proteins contain intrinsically disordered regions (IDRs), functional polypeptide segments that in isolation adopt a highly flexible conformational ensemble instead of a single, well-defined structure. Disorder prediction methods, which can discriminate ordered and disordered regions from the amino acid sequence, have contributed significantly to our current understanding of the distinct properties of intrinsically disordered proteins by enabling the characterization of individual examples as well as large-scale analyses of these protein regions. One popular method, IUPred provides a robust prediction of protein disorder based on an energy estimation approach that captures the fundamental difference between the biophysical properties of ordered and disordered regions. This paper reviews the energy estimation method underlying IUPred and the basic properties of the web server. Through an example, it also illustrates how the prediction output can be interpreted in a more complex case by taking into account the heterogeneous nature of IDRs. Various applications that benefited from IUPred to provide improved disorder predictions, complementing domain annotations and aiding the identification of functional short linear motifs are also described here. IUPred is freely available for noncommercial users through the web server (http://iupred.enzim.hu and http://iupred.elte.hu) . The program can also be downloaded and installed locally for large-scale analyses.
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Affiliation(s)
- Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
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258
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Yruela I, Oldfield CJ, Niklas KJ, Dunker AK. Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity. Genome Biol Evol 2017; 9:1248-1265. [PMID: 28430951 PMCID: PMC5434936 DOI: 10.1093/gbe/evx073] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2017] [Indexed: 12/11/2022] Open
Abstract
Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r2 < 0.5), an unbiased and phylogenetically broad analysis shows that organismic complexity is positively and strongly correlated with the total number of TFs, the number of their spliced variants and their total disordered residues content (r2 > 0.8). Furthermore, the correlation between the fraction of disordered residues and cell-type number becomes stronger when confined to the TF families participating in cell cycle, cell size, cell division, cell differentiation, or cell proliferation, and other important developmental processes. The data also indicate that evolutionarily simpler organisms allow for the detection of subtle differences in the conserved IDRs of TFs as well as changes in variable IDRs, which can influence the DNA recognition and multifunctionality of TFs through direct or indirect mechanisms. Although strong correlations cannot be taken as evidence for cause-and-effect relationships, we interpret our data to indicate that increasing TF disorder likely was an important factor contributing to the evolution of organismic complexity and not merely a concurrent unrelated effect of increasing organismic complexity.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Christopher J Oldfield
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
| | - Karl J Niklas
- School of Integrative Plant Science, Cornell University, Ithaca, NY
| | - A Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
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259
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Protein interaction perturbation profiling at amino-acid resolution. Nat Methods 2017; 14:1213-1221. [PMID: 29039417 DOI: 10.1038/nmeth.4464] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022]
Abstract
The identification of genomic variants in healthy and diseased individuals continues to rapidly outpace our ability to functionally annotate these variants. Techniques that both systematically assay the functional consequences of nucleotide-resolution variation and can scale to hundreds of genes are urgently required. We designed a sensitive yeast two-hybrid-based 'off switch' for positive selection of interaction-disruptive variants from complex genetic libraries. Combined with massively parallel programmed mutagenesis and a sequencing readout, this method enables systematic profiling of protein-interaction determinants at amino-acid resolution. We defined >1,000 interaction-disrupting amino acid mutations across eight subunits of the BBSome, the major human cilia protein complex associated with the pleiotropic genetic disorder Bardet-Biedl syndrome. These high-resolution interaction-perturbation profiles provide a framework for interpreting patient-derived mutations across the entire protein complex and thus highlight how the impact of disease variation on interactome networks can be systematically assessed.
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260
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Borkosky SS, Camporeale G, Chemes LB, Risso M, Noval MG, Sánchez IE, Alonso LG, de Prat Gay G. Hidden Structural Codes in Protein Intrinsic Disorder. Biochemistry 2017; 56:5560-5569. [PMID: 28952717 DOI: 10.1021/acs.biochem.7b00721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.
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Affiliation(s)
- Silvia S Borkosky
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gabriela Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Marikena Risso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - María Gabriela Noval
- Department of Microbiology, New York University , Alexandria Center for Life Sciences, New York, New York 10016, United States
| | - Ignacio E Sánchez
- Protein Physiology Laboratory, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Leonardo G Alonso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gonzalo de Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
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261
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Jones MM, Vanyo ST, Visser MB. The C-terminal region of the major outer sheath protein of Treponema denticola inhibits neutrophil chemotaxis. Mol Oral Microbiol 2017; 32:375-389. [PMID: 28296262 PMCID: PMC5585023 DOI: 10.1111/omi.12180] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2017] [Indexed: 12/25/2022]
Abstract
Treponema denticola is an oral spirochete strongly associated with severe periodontal disease. A prominent virulence factor, the major outer sheath protein (Msp), disorients neutrophil chemotaxis by altering the cellular phosphoinositide balance, leading to impairment of downstream chemotactic events including actin rearrangement, Rac1 activation, and Akt activation in response to chemoattractant stimulation. The specific regions of Msp responsible for interactions with neutrophils remain unknown. In this study, we investigated the inhibitory effect of truncated Msp regions on neutrophil chemotaxis and associated signaling pathways. Murine neutrophils were treated with recombinant protein truncations followed by assessment of chemotaxis and associated signal pathway activation. Chemotaxis assays indicate sequences within the C-terminal region; particularly the first 130 amino acids, have the strongest inhibitory effect on neutrophil chemotaxis. Neutrophils incubated with the C-terminal region protein also demonstrated the greatest inhibition of Rac1 activation, increased phosphoinositide phosphatase activity, and decreased Akt activation; orchestrating impairment of chemotaxis. Furthermore, incubation with antibodies specific to only the C-terminal region blocked the Msp-induced inhibition of chemotaxis and denaturing the protein restored Rac1 activation. Msp from the strain OTK, with numerous amino acid substitutions throughout the polypeptide, including the C-terminal region compared with strain 35405, showed increased ability to impair neutrophil chemotaxis. Collectively, these results indicate that the C-terminal region of Msp is the most potent region to modulate neutrophil chemotactic signaling and that specific sequences and structures are likely to be required. Knowledge of how spirochetes dampen the neutrophil response is limited and Msp may represent a novel therapeutic target for periodontal disease.
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Affiliation(s)
- Megan M. Jones
- State University of New York at Buffalo, 3435 Main St, Buffalo, NY 14214, USA
| | - Stephen T. Vanyo
- State University of New York at Buffalo, 3435 Main St, Buffalo, NY 14214, USA
| | - Michelle B. Visser
- State University of New York at Buffalo, 3435 Main St, Buffalo, NY 14214, USA
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262
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Berry IJ, Jarocki VM, Tacchi JL, Raymond BBA, Widjaja M, Padula MP, Djordjevic SP. N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen. Sci Rep 2017; 7:11063. [PMID: 28894154 PMCID: PMC5593965 DOI: 10.1038/s41598-017-11296-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022] Open
Abstract
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.
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Affiliation(s)
- Iain J Berry
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Veronica M Jarocki
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Jessica L Tacchi
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Benjamin B A Raymond
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Michael Widjaja
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia. .,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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263
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Kjaergaard M, Kragelund BB. Functions of intrinsic disorder in transmembrane proteins. Cell Mol Life Sci 2017; 74:3205-3224. [PMID: 28601983 PMCID: PMC11107515 DOI: 10.1007/s00018-017-2562-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding protein disorder.
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Affiliation(s)
- Magnus Kjaergaard
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- The Danish Research Institute of Translational Neuroscience (DANDRITE), Aarhus, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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264
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An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophys J 2017; 113:550-557. [PMID: 28793210 DOI: 10.1016/j.bpj.2017.06.042] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered proteins play important roles throughout biology, yet our understanding of the relationship between their sequences, structural properties, and functions remains incomplete. The dynamic nature of these proteins, however, makes them difficult to characterize structurally. Many disordered proteins can attain both compact and expanded conformations, and the level of expansion may be regulated and important for function. Experimentally, the level of compaction and shape is often determined either by small-angle x-ray scattering experiments or pulsed-field-gradient NMR diffusion measurements, which provide ensemble-averaged estimates of the radius of gyration and hydrodynamic radius, respectively. Often, these experiments are interpreted using molecular simulations or are used to validate them. We here provide, to our knowledge, a new and efficient method to calculate the hydrodynamic radius of a disordered protein chain from a model of its structural ensemble. In particular, starting from basic concepts in polymer physics, we derive a relationship between the radius of gyration of a structure and its hydrodynamic ratio, which in turn can be used, for example, to compare a simulated ensemble of conformations to NMR diffusion measurements. The relationship may also be valuable when using NMR diffusion measurements to restrain molecular simulations.
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265
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Zitouni S, Méchali F, Papin C, Choquet A, Roche D, Baldin V, Coux O, Bonne-Andrea C. The stability of Fbw7α in M-phase requires its phosphorylation by PKC. PLoS One 2017; 12:e0183500. [PMID: 28850619 PMCID: PMC5574586 DOI: 10.1371/journal.pone.0183500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/05/2017] [Indexed: 12/21/2022] Open
Abstract
Fbw7 is a tumor suppressor often deleted or mutated in human cancers. It serves as the substrate-recruiting subunit of a SCF ubiquitin ligase that targets numerous critical proteins for degradation, including oncoproteins and master transcription factors. Cyclin E was the first identified substrate of the SCFFbw7 ubiquitin ligase. In human cancers bearing FBXW7-gene mutations, deregulation of cyclin E turnover leads to its aberrant expression in mitosis. We investigated Fbw7 regulation in Xenopus eggs, which, although arrested in a mitotic-like phase, naturally express high levels of cyclin E. Here, we report that Fbw7α, the only Fbw7 isoform detected in eggs, is phosphorylated by PKC (protein kinase C) at a key residue (S18) in a manner coincident with Fbw7α inactivation. We show that this PKC-dependent phosphorylation and inactivation of Fbw7α also occurs in mitosis during human somatic cell cycles, and importantly is critical for Fbw7α stabilization itself upon nuclear envelope breakdown. Finally, we provide evidence that S18 phosphorylation, which lies within the intrinsically disordered N-terminal region specific to the α-isoform reduces the capacity of Fbw7α to dimerize and to bind cyclin E. Together, these findings implicate PKC in an evolutionarily-conserved pathway that aims to protect Fbw7α from degradation by keeping it transiently in a resting, inactive state.
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Affiliation(s)
- Sihem Zitouni
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Francisca Méchali
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Catherine Papin
- Institut de Génétique Humaine, CNRS, UMR 9002, Université de Montpellier, Montpellier, France
| | - Armelle Choquet
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Université de Montpellier, Montpellier, France
| | - Daniel Roche
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
- Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier, France
| | - Véronique Baldin
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Olivier Coux
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Catherine Bonne-Andrea
- Centre de Recherche de Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
- * E-mail:
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266
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Stürner E, Behl C. The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease. Front Mol Neurosci 2017; 10:177. [PMID: 28680391 PMCID: PMC5478690 DOI: 10.3389/fnmol.2017.00177] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/18/2017] [Indexed: 01/01/2023] Open
Abstract
In neurons, but also in all other cells the complex proteostasis network is monitored and tightly regulated by the cellular protein quality control (PQC) system. Beyond folding of newly synthesized polypeptides and their refolding upon misfolding the PQC also manages the disposal of aberrant proteins either by the ubiquitin-proteasome machinery or by the autophagic-lysosomal system. Aggregated proteins are primarily degraded by a process termed selective macroautophagy (or aggrephagy). One such recently discovered selective macroautophagy pathway is mediated by the multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3). Under acute stress and during cellular aging, BAG3 in concert with the molecular chaperones HSP70 and HSPB8 as well as the ubiquitin receptor p62/SQSTM1 specifically targets aggregation-prone proteins to autophagic degradation. Thereby, BAG3-mediated selective macroautophagy represents a pivotal adaptive safeguarding and emergency system of the PQC which is activated under pathophysiological conditions to ensure cellular proteostasis. Interestingly, BAG3-mediated selective macroautophagy is also involved in the clearance of aggregated proteins associated with age-related neurodegenerative disorders, like Alzheimer’s disease (tau-protein), Huntington’s disease (mutated huntingtin/polyQ proteins), and amyotrophic lateral sclerosis (mutated SOD1). In addition, based on its initial description BAG3 is an anti-apoptotic protein that plays a decisive role in other widespread diseases, including cancer and myopathies. Therefore, in the search for novel therapeutic intervention avenues in neurodegeneration, myopathies and cancer BAG3 is a promising candidate.
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Affiliation(s)
- Elisabeth Stürner
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University MainzMainz, Germany
| | - Christian Behl
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University MainzMainz, Germany
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267
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Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ. Pipeline to Identify Hydroxyproline-Rich Glycoproteins. PLANT PHYSIOLOGY 2017; 174:886-903. [PMID: 28446635 PMCID: PMC5462032 DOI: 10.1104/pp.17.00294] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/21/2017] [Indexed: 05/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signaling, and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive posttranslational modifications (glycosylation), and they have been implicated in many biological functions. HRGPs are evolutionarily ancient, having been isolated from the protein-rich walls of chlorophyte algae to the cellulose-rich walls of embryophytes. Examination of HRGPs in a range of plant species should provide valuable insights into how they have evolved. Commonly divided into the arabinogalactan proteins, extensins, and proline-rich proteins, in reality, a continuum of structures exists within this diverse and heterogenous superfamily. An inability to accurately classify HRGPs leads to inconsistent gene ontologies limiting the identification of HRGP classes in existing and emerging omics data sets. We present a novel and robust motif and amino acid bias (MAAB) bioinformatics pipeline to classify HRGPs into 23 descriptive subclasses. Validation of MAAB was achieved using available genomic resources and then applied to the 1000 Plants transcriptome project (www.onekp.com) data set. Significant improvement in the detection of HRGPs using multiple-k-mer transcriptome assembly methodology was observed. The MAAB pipeline is readily adaptable and can be modified to optimize the recovery of IDPs from other organisms.
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Affiliation(s)
- Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew M Cassin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew Lonsdale
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carolyn J Schultz
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
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268
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D. K, Ramireddy S, P. R, C. S. Expediting dynamics approach to understand the influence of 14-3-3ζ causing metastatic cancer through the interaction of YAP1 and β-TRCP. MOLECULAR BIOSYSTEMS 2017; 13:1981-1992. [DOI: 10.1039/c7mb00271h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 14-3-3ζ protein acts as a molecular switch in regulating the TGF-β pathway, which alters from a tumor suppressor in the early stage of breast cancer to a promoter of metastasis in the late stage.
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Affiliation(s)
- Kamalesh D.
- Department of Integrative Biology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Sriroopreddy Ramireddy
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Raguraman P.
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
| | - Sudandiradoss C.
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore
- India
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269
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VLIEGENTHART JFG. The complexity of glycoprotein-derived glycans. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:64-86. [PMID: 28190870 PMCID: PMC5422628 DOI: 10.2183/pjab.93.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 12/09/2016] [Indexed: 05/31/2023]
Abstract
A brief review is presented of our studies on the structure of glycoprotein-derived glycans. The emphasis is on the introduction of high-resolution 1H-NMR spectroscopy for the unambiguous determination of primary structures. For this purpose, we developed the structural reporter group concept. Structural reporters are defined as unique markers of structural elements in the NMR spectra. Application of this concept led to the discovery of numerous new structures. Furthermore, a number of structures presented in the literature could be corrected. The results are relevant for insight in the various steps in glycan metabolism in health and disease, for the function and mode of action of glycans in vivo and for the interpretation of structural information obtained through other techniques. The strength of the approach is further shown for several highly complex glycoproteins, carrying very heterogeneous and complicated glycans.
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