1351
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Roberts S, Dzuricky M, Chilkoti A. Elastin-like polypeptides as models of intrinsically disordered proteins. FEBS Lett 2015; 589:2477-86. [PMID: 26325592 PMCID: PMC4599720 DOI: 10.1016/j.febslet.2015.08.029] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 01/01/2023]
Abstract
Elastin-like polypeptides (ELPs) are a class of stimuli-responsive biopolymers inspired by the intrinsically disordered domains of tropoelastin that are composed of repeats of the VPGXG pentapeptide motif, where X is a "guest residue". They undergo a reversible, thermally triggered lower critical solution temperature (LCST) phase transition, which has been utilized for a variety of applications including protein purification, affinity capture, immunoassays, and drug delivery. ELPs have been extensively studied as protein polymers and as biomaterials, but their relationship to other disordered proteins has heretofore not been established. The biophysical properties of ELPs that lend them their unique material behavior are similar to the properties of many intrinsically disordered proteins (IDP). Their low sequence complexity, phase behavior, and elastic properties make them an interesting "minimal" artificial IDP, and the study of ELPs can hence provide insights into the behavior of other more complex IDPs. Motivated by this emerging realization of the similarities between ELPs and IDPs, this review discusses the biophysical properties of ELPs, their biomedical utility, and their relationship to other disordered polypeptide sequences.
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1352
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Lemonidis K, Sanchez-Perez MC, Chamberlain LH. Identification of a Novel Sequence Motif Recognized by the Ankyrin Repeat Domain of zDHHC17/13 S-Acyltransferases. J Biol Chem 2015; 290:21939-50. [PMID: 26198635 PMCID: PMC4571948 DOI: 10.1074/jbc.m115.657668] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Indexed: 11/06/2022] Open
Abstract
S-Acylation is a major post-translational modification affecting several cellular processes. It is particularly important for neuronal functions. This modification is catalyzed by a family of transmembrane S-acyltransferases that contain a conserved zinc finger DHHC (zDHHC) domain. Typically, eukaryote genomes encode for 7-24 distinct zDHHC enzymes, with two members also harboring an ankyrin repeat (AR) domain at their cytosolic N termini. The AR domain of zDHHC enzymes is predicted to engage in numerous interactions and facilitates both substrate recruitment and S-acylation-independent functions; however, the sequence/structural features recognized by this module remain unknown. The two mammalian AR-containing S-acyltransferases are the Golgi-localized zDHHC17 and zDHHC13, also known as Huntingtin-interacting proteins 14 and 14-like, respectively; they are highly expressed in brain, and their loss in mice leads to neuropathological deficits that are reminiscent of Huntington's disease. Here, we report that zDHHC17 and zDHHC13 recognize, via their AR domain, evolutionary conserved and closely related sequences of a [VIAP][VIT]XXQP consensus in SNAP25, SNAP23, cysteine string protein, Huntingtin, cytoplasmic linker protein 3, and microtubule-associated protein 6. This novel AR-binding sequence motif is found in regions predicted to be unstructured and is present in a number of zDHHC17 substrates and zDHHC17/13-interacting S-acylated proteins. This is the first study to identify a motif recognized by AR-containing zDHHCs.
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Affiliation(s)
- Kimon Lemonidis
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Maria C Sanchez-Perez
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Luke H Chamberlain
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
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1353
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Oshokoya OO, JiJi RD. “Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”. Anal Chim Acta 2015; 892:59-68. [DOI: 10.1016/j.aca.2015.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/11/2015] [Indexed: 01/25/2023]
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1354
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Minkiewicz P, Darewicz M, Iwaniak A, Sokołowska J, Starowicz P, Bucholska J, Hrynkiewicz M. Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. Int J Mol Sci 2015; 16:20748-73. [PMID: 26340620 PMCID: PMC4613229 DOI: 10.3390/ijms160920748] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/18/2015] [Accepted: 08/24/2015] [Indexed: 02/06/2023] Open
Abstract
A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment containing two or three amino acid residues, may occur in many protein sequences. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept.
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Affiliation(s)
- Piotr Minkiewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Małgorzata Darewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Anna Iwaniak
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Jolanta Sokołowska
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Piotr Starowicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Justyna Bucholska
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Monika Hrynkiewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
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1355
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Mantsyzov AB, Shen Y, Lee JH, Hummer G, Bax A. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data. JOURNAL OF BIOMOLECULAR NMR 2015; 63. [PMID: 26219516 PMCID: PMC4577467 DOI: 10.1007/s10858-015-9971-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ((15)N, (13)C(α), and (13)C'), six types of J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JCαN and (1)JCαN), as well as the (15)N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.
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Affiliation(s)
- Alexey B Mantsyzov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russian Federation, 119991
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung Ho Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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1356
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Kurotani A, Sakurai T. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae. Int J Mol Sci 2015; 16:19812-35. [PMID: 26307970 PMCID: PMC4581327 DOI: 10.3390/ijms160819812] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 12/23/2022] Open
Abstract
Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.
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Affiliation(s)
- Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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1357
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Dickmanns A, Kehlenbach RH, Fahrenkrog B. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 320:171-233. [PMID: 26614874 DOI: 10.1016/bs.ircmb.2015.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
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1358
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Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies. Int J Mol Sci 2015; 16:19040-54. [PMID: 26287166 PMCID: PMC4581285 DOI: 10.3390/ijms160819040] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022] Open
Abstract
The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.
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1359
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Tusnády GE, Dobson L, Tompa P. Disordered regions in transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2839-48. [PMID: 26275590 DOI: 10.1016/j.bbamem.2015.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 11/18/2022]
Abstract
The functions of transmembrane proteins in living cells are widespread; they range from various transport processes to energy production, from cell-cell adhesion to communication. Structurally, they are highly ordered in their membrane-spanning regions, but may contain disordered regions in the cytosolic and extra-cytosolic parts. In this study, we have investigated the disordered regions in transmembrane proteins by a stringent definition of disordered residues on the currently available largest experimental dataset, and show a significant correlation between the spatial distributions of positively charged residues and disordered regions. This finding suggests a new role of disordered regions in transmembrane proteins by providing structural flexibility for stabilizing interactions with negatively charged head groups of the lipid molecules. We also find a preference of structural disorder in the terminal--as opposed to loop--regions in transmembrane proteins, and survey the respective functions involved in recruiting other proteins or mediating allosteric signaling effects. Finally, we critically compare disorder prediction methods on our transmembrane protein set. While there are no major differences between these methods using the usual statistics, such as per residue accuracies, Matthew's correlation coefficients, etc.; substantial differences can be found regarding the spatial distribution of the predicted disordered regions. We conclude that a predictor optimized for transmembrane proteins would be of high value to the field of structural disorder.
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Affiliation(s)
- Gábor E Tusnády
- Institute of Enzymology, RCNS, HAS, Magyar Tudósok körútja 2, 1117 Budapest, Hungary.
| | - László Dobson
- Institute of Enzymology, RCNS, HAS, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Peter Tompa
- Institute of Enzymology, RCNS, HAS, Magyar Tudósok körútja 2, 1117 Budapest, Hungary; VIB Structural Biology Research Center, VUB, Building E, Pleinlaan 2, 1050 Brussels, Belgium
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1360
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Gupta G, Lim L, Song J. NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics. PLoS One 2015; 10:e0134823. [PMID: 26258523 PMCID: PMC4530887 DOI: 10.1371/journal.pone.0134823] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its “complete insolubility”, the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48–100) or the full-length NS2B (1–130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48–100;Δ77–84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection.
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Affiliation(s)
- Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore, Singapore
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1361
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Pan K, Zhong Q. Amyloid-like fibrils formed from intrinsically disordered caseins: physicochemical and nanomechanical properties. SOFT MATTER 2015; 11:5898-904. [PMID: 26112282 DOI: 10.1039/c5sm01037c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Amyloid-like fibrils are studied because of their significance in understanding pathogenesis and creating functional materials. Amyloid-like fibrils have been studied by heating globular proteins at acidic conditions. In the present study, intrinsically disordered α-, β-, and κ-caseins were studied to form amyloid-like fibrils at pH 2.0 and 90 °C. No fibrils were observed for α-caseins, and acid hydrolysis was found to be the rate-limiting step of fibrillation of β- and κ-caseins. An increase of β-sheet structure was observed after fibrillation. Nanomechanic analysis of long amyloid-like fibrils using peak-force quantitative nanomechanical atomic force microscopy showed the lowest and highest Young's modulus for β-casein (2.35 ± 0.29 GPa) and κ-casein (4.14 ± 0.66 GPa), respectively. The dispersion with β-casein fibrils had a viscosity more than 10 and 5 times higher than those of κ-casein and β-lactoglobulin, respectively, at 0.1 s(-1) at comparable concentrations. The current findings may assist not only the understanding of amyloid fibril formation but also the development of novel functional materials from disordered proteins.
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Affiliation(s)
- Kang Pan
- Department of Food Science and Technology, University of Tennessee in Knoxville, USA.
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1362
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Xu Y, Zhang H, Nguyen VTM, Angelopoulos N, Nunes J, Reid A, Buluwela L, Magnani L, Stebbing J, Giamas G. LMTK3 Represses Tumor Suppressor-like Genes through Chromatin Remodeling in Breast Cancer. Cell Rep 2015; 12:837-49. [PMID: 26212333 DOI: 10.1016/j.celrep.2015.06.073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 01/23/2023] Open
Abstract
LMTK3 is an oncogenic receptor tyrosine kinase (RTK) implicated in various types of cancer, including breast, lung, gastric, and colorectal cancer. It is localized in different cellular compartments, but its nuclear function has not been investigated so far. We mapped LMTK3 binding across the genome using ChIP-seq and found that LMTK3 binding events are correlated with repressive chromatin markers. We further identified KRAB-associated protein 1 (KAP1) as a binding partner of LMTK3. The LMTK3/KAP1 interaction is stabilized by PP1α, which suppresses KAP1 phosphorylation specifically at LMTK3-associated chromatin regions, inducing chromatin condensation and resulting in transcriptional repression of LMTK3-bound tumor suppressor-like genes. Furthermore, LMTK3 functions at distal regions in tethering the chromatin to the nuclear periphery, resulting in H3K9me3 modification and gene silencing. In summary, we propose a model where a scaffolding function of nuclear LMTK3 promotes cancer progression through chromatin remodeling.
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Affiliation(s)
- Yichen Xu
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hua Zhang
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Van Thuy Mai Nguyen
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Nicos Angelopoulos
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Joao Nunes
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alistair Reid
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Laki Buluwela
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Luca Magnani
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
| | - Justin Stebbing
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Georgios Giamas
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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1363
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Suss O, Reichmann D. Protein plasticity underlines activation and function of ATP-independent chaperones. Front Mol Biosci 2015; 2:43. [PMID: 26284255 PMCID: PMC4516975 DOI: 10.3389/fmolb.2015.00043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/13/2015] [Indexed: 12/31/2022] Open
Abstract
One of the key issues in biology is to understand how cells cope with protein unfolding caused by changes in their environment. Self-protection is the natural immediate response to any sudden threat and for cells the critical issue is to prevent aggregation of existing proteins. Cellular response to stress is therefore indistinguishably linked to molecular chaperones, which are the first line of defense and function to efficiently recognize misfolded proteins and prevent their aggregation. One of the major protein families that act as cellular guards includes a group of ATP-independent chaperones, which facilitate protein folding without the consumption of ATP. This review will present fascinating insights into the diversity of ATP-independent chaperones, and the variety of mechanisms by which structural plasticity is utilized in the fine-tuning of chaperone activity, as well as in crosstalk within the proteostasis network. Research into this intriguing class of chaperones has introduced new concepts of stress response to a changing cellular environment, and paved the way to uncover how this environment affects protein folding.
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Affiliation(s)
- Ohad Suss
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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1364
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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1365
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Aït-Bara S, Carpousis AJ. RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs. Mol Microbiol 2015; 97:1021-135. [PMID: 26096689 DOI: 10.1111/mmi.13095] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/29/2022]
Abstract
Ribonuclease E (RNase E) of Escherichia coli, which is the founding member of a widespread family of proteins in bacteria and chloroplasts, is a fascinating enzyme that still has not revealed all its secrets. RNase E is an essential single-strand specific endoribonuclease that is involved in the processing and degradation of nearly every transcript in E. coli. A striking enzymatic property is a preference for substrates with a 5' monophosphate end although recent work explains how RNase E can overcome the protection afforded by the 5' triphosphate end of a primary transcript. Other features of E. coli RNase E include its interaction with enzymes involved in RNA degradation to form the multienzyme RNA degradosome and its localization to the inner cytoplasmic membrane. The N-terminal catalytic core of the RNase E protomer associates to form a tetrameric holoenzyme. Each RNase E protomer has a large C-terminal intrinsically disordered (ID) noncatalytic region that contains sites for interactions with protein components of the RNA degradosome as well as RNA and phospholipid bilayers. In this review, RNase E homologs have been classified into five types based on their primary structure. A recent analysis has shown that type I RNase E in the γ-proteobacteria forms an orthologous group of proteins that has been inherited vertically. The RNase E catalytic core and a large ID noncatalytic region containing an RNA binding motif and a membrane targeting sequence are universally conserved features of these orthologs. Although the ID noncatalytic region has low composition and sequence complexity, it is possible to map microdomains, which are short linear motifs that are sites of interaction with protein and other ligands. Throughout bacteria, the composition of the multienzyme RNA degradosome varies with species, but interactions with exoribonucleases (PNPase, RNase R), glycolytic enzymes (enolase, aconitase) and RNA helicases (DEAD-box proteins, Rho) are common. Plasticity in RNA degradosome composition is due to rapid evolution of RNase E microdomains. Characterization of the RNase E-PNPase interaction in α-proteobacteria, γ-proteobacteria and cyanobacteria suggests that it arose independently several times during evolution, thus conferring an advantage in control and coordination of RNA processing and degradation.
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Affiliation(s)
- Soraya Aït-Bara
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte, Institut, National de la Santé et de la Recherche Médicale & Université d'Auvergne, Clermont-Ferrand, 63001, France
| | - Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100, Centre National de la Recherche Scientifique et Université de Toulouse 3, Toulouse, 31062, France
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1366
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Popelka H, Klionsky DJ. Post-translationally-modified structures in the autophagy machinery: an integrative perspective. FEBS J 2015; 282:3474-88. [PMID: 26108642 DOI: 10.1111/febs.13356] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/11/2015] [Accepted: 06/19/2015] [Indexed: 01/10/2023]
Abstract
Autophagy is a self-cleaning process that occurs at a constitutive basal level, and is upregulated in response to stress. Macroautophagy (hereafter autophagy) is the most robust type of autophagy, where cargo (specific or nonspecific) is engulfed within a double-membrane structure termed an autophagosome. This process needs to be tightly regulated to maintain normal cellular homeostasis and prevent dysfunction; therefore, a fuller knowledge of the mechanisms of autophagy regulation is crucial for understanding the entire pathway. The autophagy-related proteins are the primary components that carry out autophagy. Many of these proteins are conserved from yeast to humans. A number of significant discoveries with regard to protein functional domains, protein-protein interactions or post-translational modifications of proteins involved in autophagy have been reported in parallel with, or followed by, solving the NMR or crystal structures of autophagy proteins or their protein domains. In the present review, we summarize structural insights gathered to date on the proteins of the autophagy machinery that are modulated by a post-translational modification, specifically phosphorylation, acetylation, ubiquitination and/or SUMOylation. For each protein, we link the reported results with information on the propensity of the corresponding amino acid sequence toward order/disorder. This integrative approach yields a comprehensive overview for each post-translationally modified protein, and also reveals areas for further investigation.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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1367
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Podzimska-Sroka D, O'Shea C, Gregersen PL, Skriver K. NAC Transcription Factors in Senescence: From Molecular Structure to Function in Crops. PLANTS (BASEL, SWITZERLAND) 2015; 4:412-48. [PMID: 27135336 PMCID: PMC4844398 DOI: 10.3390/plants4030412] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 02/08/2023]
Abstract
Within the last decade, NAC transcription factors have been shown to play essential roles in senescence, which is the focus of this review. Transcriptome analyses associate approximately one third of Arabidopsis NAC genes and many crop NAC genes with senescence, thereby implicating NAC genes as important regulators of the senescence process. The consensus DNA binding site of the NAC domain is used to predict NAC target genes, and protein interaction sites can be predicted for the intrinsically disordered transcription regulatory domains of NAC proteins. The molecular characteristics of these domains determine the interactions in gene regulatory networks. Emerging local NAC-centered gene regulatory networks reveal complex molecular mechanisms of stress- and hormone-regulated senescence and basic physiological steps of the senescence process. For example, through molecular interactions involving the hormone abscisic acid, Arabidopsis NAP promotes chlorophyll degradation, a hallmark of senescence. Furthermore, studies of the functional rice ortholog, OsNAP, suggest that NAC genes can be targeted to obtain specific changes in lifespan control and nutrient remobilization in crop plants. This is also exemplified by the wheat NAM1 genes which promote senescence and increase grain zinc, iron, and protein content. Thus, NAC genes are promising targets for fine-tuning senescence for increased yield and quality.
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Affiliation(s)
- Dagmara Podzimska-Sroka
- Department of Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, Slagelse DK-4200, Denmark.
| | - Charlotte O'Shea
- Department of Biology, University of Copenhagen, 5 Ole Maaloesvej, Copenhagen DK-2200, Denmark.
| | - Per L Gregersen
- Department of Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, Slagelse DK-4200, Denmark.
| | - Karen Skriver
- Department of Biology, University of Copenhagen, 5 Ole Maaloesvej, Copenhagen DK-2200, Denmark.
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1368
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Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 2015. [PMID: 26217327 PMCID: PMC4498126 DOI: 10.3389/fmicb.2015.00696] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Ryan O Schenck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Stephanie N Lawler
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
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1369
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Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci 2015; 16:15743-60. [PMID: 26184172 PMCID: PMC4519922 DOI: 10.3390/ijms160715743] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an "indirect/reflected" detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR). This approach employs a "chimeric membrane protein"-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding)-fold domain (named NfeDC domain), connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.
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Affiliation(s)
- Natsuko Goda
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0046, Japan.
| | - Yohta Kuwahara
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | - Takeshi Tenno
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hidekazu Hiroaki
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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1370
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Badasyan A, Mamasakhlisov YS, Podgornik R, Parsegian VA. Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins. J Chem Phys 2015; 143:014102. [DOI: 10.1063/1.4923292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Artem Badasyan
- Materials Research Laboratory, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia
| | - Yevgeni Sh. Mamasakhlisov
- Department of Molecular Physics, Yerevan State University, A. Manougian St. 1, 0025 Yerevan, Armenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA
| | - V. Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003-9337, USA
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1371
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Keeler AB, Schreiner D, Weiner JA. Protein Kinase C Phosphorylation of a γ-Protocadherin C-terminal Lipid Binding Domain Regulates Focal Adhesion Kinase Inhibition and Dendrite Arborization. J Biol Chem 2015; 290:20674-20686. [PMID: 26139604 DOI: 10.1074/jbc.m115.642306] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Indexed: 11/06/2022] Open
Abstract
The γ-protocadherins (γ-Pcdhs) are a family of 22 adhesion molecules with multiple critical developmental functions, including the proper formation of dendritic arbors by forebrain neurons. The γ-Pcdhs bind to and inhibit focal adhesion kinase (FAK) via a constant C-terminal cytoplasmic domain shared by all 22 proteins. In cortical neurons lacking the γ-Pcdhs, aberrantly high activity of FAK and of PKC disrupts dendrite arborization. Little is known, however, about how γ-Pcdh function is regulated by other factors. Here we show that PKC phosphorylates a serine residue situated within a phospholipid binding motif at the shared γ-Pcdh C terminus. Western blots using a novel phospho-specific antibody against this site suggest that a portion of γ-Pcdh proteins is phosphorylated in the cortex in vivo. We find that PKC phosphorylation disrupts both phospholipid binding and the γ-Pcdh inhibition of (but not binding to) FAK. Introduction of a non-phosphorylatable (S922A) γ-Pcdh construct into wild-type cortical neurons significantly increases dendrite arborization. This same S922A construct can also rescue dendrite arborization defects in γ-Pcdh null neurons cell autonomously. Consistent with these data, introduction of a phosphomimetic (S/D) γ-Pcdh construct or treatment with a PKC activator reduces dendrite arborization in wild-type cortical neurons. Together, these data identify a novel mechanism through which γ-Pcdh control of a signaling pathway important for dendrite arborization is regulated.
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Affiliation(s)
- Austin B Keeler
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242; Neuroscience Graduate Program, The University of Iowa, Iowa City, Iowa 52242
| | - Dietmar Schreiner
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242; Neuroscience Graduate Program, The University of Iowa, Iowa City, Iowa 52242.
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1372
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Raj B, Blencowe B. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron 2015; 87:14-27. [DOI: 10.1016/j.neuron.2015.05.004] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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1373
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Sammak S, Zinzalla G. Targeting protein-protein interactions (PPIs) of transcription factors: Challenges of intrinsically disordered proteins (IDPs) and regions (IDRs). PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:41-6. [PMID: 26126425 DOI: 10.1016/j.pbiomolbio.2015.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022]
Abstract
In this review we discuss recent progress in targeting the protein-protein interactions made by oncogenic transcription factors. We particularly focus on the challenges posed by the prevalence of intrinsically disordered regions in this class of protein and the strategies being used to overcome them.
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Affiliation(s)
- Susan Sammak
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden
| | - Giovanna Zinzalla
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden.
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1374
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The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding. PLoS Genet 2015; 11:e1005251. [PMID: 26107960 PMCID: PMC4480970 DOI: 10.1371/journal.pgen.1005251] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/28/2015] [Indexed: 12/18/2022] Open
Abstract
The lineage factor Foxp3 is essential for the development and maintenance of regulatory T cells, but little is known about the mechanisms involved. Here, we demonstrate that an N-terminal proline-rich interaction region is crucial for Foxp3’s function. Subdomains within this key region link Foxp3 to several independent mechanisms of transcriptional regulation. Our study suggests that Foxp3, even in the absence of its DNA-binding forkhead domain, acts as a bridge between DNA-binding interaction partners and proteins with effector function permitting it to regulate a large number of genes. We show that, in one such mechanism, Foxp3 recruits class I histone deacetylases to the promoters of target genes, counteracting activation-induced histone acetylation and thereby suppressing their expression. The suppressive activity of regulatory T cells provides the immune system with a mechanism to prevent detrimental immune responses, such as autoimmunity, attack of the beneficial commensal microbiota and rejection of the fetus. Intriguingly, expression of a single lineage factor Foxp3 is sufficient to completely reprogram T cells from a pro-inflammatory to a suppressive phenotype. Here, we show that Foxp3 alters the expression of thousands of genes through several independent mechanisms. In many cases, its own ability to bind to DNA appears to be dispensable, but rather it binds indirectly to the DNA by interaction with other transcription factors. Foxp3 then in turn recruits other proteins that affect gene expression through chromatin modification. For example, Foxp3 indirectly binds to the IL-2 promoter via interaction with the transcriptional activators c-Rel, AML-1 and NFAT. This leads to the Foxp3 mediated recruitment of class I histone deacetylases HDAC1, 2 and 3, which in turn counteracts the activation-induced hyper-acetylation of the promoter, thereby switching the gene off. In a way, Foxp3 hijacks pre-existing regulatory mechanism to reverse the transcriptional expression status of the target gene. By dissecting Foxp3 on a molecular level, we also show that this is only one of several independent mechanism utilised by Foxp3.
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1375
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Entropic clocks in the service of electrical signaling: ‘Ball and chain’ mechanisms for ion channel inactivation and clustering. FEBS Lett 2015; 589:2441-7. [DOI: 10.1016/j.febslet.2015.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 12/19/2022]
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1376
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Berlow RB, Dyson HJ, Wright PE. Functional advantages of dynamic protein disorder. FEBS Lett 2015; 589:2433-40. [PMID: 26073260 DOI: 10.1016/j.febslet.2015.06.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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1377
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Latysheva NS, Flock T, Weatheritt RJ, Chavali S, Babu MM. How do disordered regions achieve comparable functions to structured domains? Protein Sci 2015; 24:909-22. [PMID: 25752799 PMCID: PMC4456105 DOI: 10.1002/pro.2674] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The traditional structure to function paradigm conceives of a protein's function as emerging from its structure. In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. In this review, we provide a brief overview of how IDRs can perform similar functions to structured proteins, focusing especially on the formation of protein complexes and assemblies and the mediation of regulated conformational changes. In addition to highlighting instances of such functional equivalence, we explain how differences in the biological and physicochemical properties of IDRs allow them to expand the functional and regulatory repertoire of proteins. We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases.
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Affiliation(s)
| | - Tilman Flock
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | | | - Sreenivas Chavali
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
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1378
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Zhu L, Brangwynne CP. Nuclear bodies: the emerging biophysics of nucleoplasmic phases. Curr Opin Cell Biol 2015; 34:23-30. [PMID: 25942753 DOI: 10.1016/j.ceb.2015.04.003] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/16/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that low complexity/disordered protein motifs and repetitive binding domains drive assembly of droplets of nuclear RNA/protein by promoting nucleoplasmic phase separation. Nucleation and maturation of these structures is regulated by, and may in turn affect, factors including post-translational modifications, protein concentration, transcriptional activity, and chromatin state. Here we present a concise review of these exciting recent advances, and discuss current and future challenges in understanding the assembly, regulation, and function of nuclear RNA/protein bodies.
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Affiliation(s)
- Lian Zhu
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA.
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1379
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Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015; 16:153. [PMID: 25968230 PMCID: PMC4427981 DOI: 10.1186/s12859-015-0592-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/23/2015] [Indexed: 12/03/2022] Open
Abstract
Background Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. Results Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. Conclusions DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons.
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Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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1380
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Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015. [PMID: 25968230 DOI: 10.1186/s12859‐015‐0592‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. RESULTS Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. CONCLUSIONS DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons .
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Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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1381
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Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. J Am Chem Soc 2015; 137:6245-53. [DOI: 10.1021/jacs.5b00235] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- David Winogradoff
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Ignacia Echeverria
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Davit A. Potoyan
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | - Garegin A. Papoian
- Chemical
Physics Program and ‡Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology, University of Maryland, College
Park, Maryland 20742, United States
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1382
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Vassall KA, Jenkins AD, Bamm VV, Harauz G. Thermodynamic Analysis of the Disorder-to-α-Helical Transition of 18.5-kDa Myelin Basic Protein Reveals an Equilibrium Intermediate Representing the Most Compact Conformation. J Mol Biol 2015; 427:1977-92. [DOI: 10.1016/j.jmb.2015.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
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1383
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Smithers B, Oates ME, Gough J. Splice junctions are constrained by protein disorder. Nucleic Acids Res 2015; 43:4814-22. [PMID: 25934802 PMCID: PMC4446445 DOI: 10.1093/nar/gkv407] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/15/2015] [Indexed: 01/23/2023] Open
Abstract
We have discovered that positions of splice junctions in genes are constrained by the tolerance for disorder-promoting amino acids in the translated protein region. It is known that efficient splicing requires nucleotide bias at the splice junction; the preferred usage produces a distribution of amino acids that is disorder-promoting. We observe that efficiency of splicing, as seen in the amino-acid distribution, is not compromised to accommodate globular structure. Thus we infer that it is the positions of splice junctions in the gene that must be under constraint by the local protein environment. Examining exonic splicing enhancers found near the splice junction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode disordered protein regions than exons encoding structured regions. Thus we also conclude that local protein features constrain efficient splicing more in structure than in disorder.
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Affiliation(s)
- Ben Smithers
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Matt E Oates
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Julian Gough
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
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1384
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Rani P, Biswas P. Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins. J Phys Chem B 2015; 119:10858-67. [DOI: 10.1021/jp511961c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Pooja Rani
- Department of Chemistry, University of Delhi, Delhi - 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi - 110007, India
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1385
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Abstract
Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 consists of two tethered domains: a WW domain for substrate binding, and a catalytic domain for peptidyl-prolyl isomerase (PPIase) activity. Pin1 accelerates the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs within proteins regulating the cell cycle and neuronal development. The early x-ray (Ranganathan et al. 1997; Verdecia et al. 2000) and solution NMR studies (Bayer et al. 2003; Jacobs et al. 2003) of Pin1 indicated inter- and intradomain motion. We became interested in exploring how such motions might affect interdomain communication, using NMR. Our accumulated results indicate substrate binding to Pin1 WW domain changes the intra/inter domain mobility, thereby altering substrate activity in the distal PPIase domain catalytic site. Thus, Pin1 shows evidence of dynamic allostery, in the sense of Cooper and Dryden (Cooper and Dryden 1984). We highlight our results supporting this conclusion, and summarize them via a simple speculative model of conformational selection.
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1386
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Larion M, Miller B, Brüschweiler R. Conformational heterogeneity and intrinsic disorder in enzyme regulation: Glucokinase as a case study. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1011008. [PMID: 28232887 DOI: 10.1080/21690707.2015.1011008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 12/14/2014] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
Abstract
Many human proteins are predicted to contain intrinsically disordered regions (IDRs), yet their occurrence in enzymes is notably rare. Human pancreatic glucokinase (GCK) is one of a small, but growing number of enzymes shown to possess an IDR. In this commentary, we summarize the results of recent biophysical studies that provide evidence for a functionally significant disorder-order transition within the IDR of GCK during the enzyme's catalytic cycle. High-resolution NMR studies indicate that kinetic cooperativity in GCK results from glucose-mediated millisecond conformational dynamics within the structurally heterogeneous and partially disordered small domain of this monomeric enzyme, whereby the precise timescale of these motions is critical for the manifestation of the kinetic cooperativity effect. GCK provides an excellent case study for understanding how structural and dynamic alterations within an IDR enable novel regulatory mechanisms. These studies also establish GCK as a model system for investigating the functional consequences of disorder and conformational heterogeneity in enzymatic systems in general.
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Affiliation(s)
- Mioara Larion
- Department of Chemistry and Biochemistry; The Ohio State University ; Columbus, OH USA
| | - Brian Miller
- Department of Chemistry and Biochemistry; Florida State University ; Tallahassee, FL USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry; The Ohio State University; Columbus, OH USA; The Campus Chemical Instrument Center; The Ohio State University; Columbus, OH USA
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1387
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Papadakos G, Sharma A, Lancaster LE, Bowen R, Kaminska R, Leech AP, Walker D, Redfield C, Kleanthous C. Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein–Protein Interaction. J Am Chem Soc 2015; 137:5252-5. [DOI: 10.1021/ja512607r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Grigorios Papadakos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amit Sharma
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna E. Lancaster
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Rebecca Bowen
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Andrew P. Leech
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Daniel Walker
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8AT, United Kingdom
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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1388
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Miraula M, Ciurli S, Zambelli B. Intrinsic disorder and metal binding in UreG proteins from Archae hyperthermophiles: GTPase enzymes involved in the activation of Ni(II) dependent urease. J Biol Inorg Chem 2015; 20:739-55. [PMID: 25846143 DOI: 10.1007/s00775-015-1261-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/20/2015] [Indexed: 02/03/2023]
Abstract
Urease is a Ni(II) enzyme present in every domain of life, in charge for nitrogen recycling through urea hydrolysis. Its activity requires the presence of two Ni(II) ions in the active site. These are delivered by the concerted action of four accessory proteins, named UreD, UreF, UreG and UreE. This process requires protein flexibility at different levels and some disorder-to-order transition events that coordinate the mechanism of protein-protein interaction. In particular, UreG, the GTPase in charge of nucleotide hydrolysis required for urease activation, presents a significant degree of intrinsic disorder, existing as a conformational ensemble featuring characteristics that recall a molten globule. Here, the folding properties of UreG were explored in Archaea hyperthermophiles, known to generally feature significantly low level of structural disorder in their proteome. UreG proteins from Methanocaldococcus jannaschii (Mj) and Metallosphaera sedula (Ms) were structurally and functionally analyzed by integrating circular dichroism, NMR, light scattering and enzymatic assays. Metal-binding properties were studied using isothermal titration calorimetry. The results indicate that, as the mesophilic counterparts, both proteins contain a significant amount of secondary structure but maintain a flexible fold and a low GTPase activity. As opposed to other UreGs, secondary structure is lost at high temperatures (68 and 75 °C, respectively) with an apparent two-state mechanism. Both proteins bind Zn(II) and Ni(II), with affinities two orders of magnitude higher for Zn(II) than for Ni(II). No major modifications of the average conformational ensemble are observed, but binding of Zn(II) yields a more compact dimeric form in MsUreG.
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Affiliation(s)
- Manfredi Miraula
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
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1389
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Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr Opin Struct Biol 2015; 32:102-12. [PMID: 25863585 DOI: 10.1016/j.sbi.2015.03.008] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using polymer physics theories.
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1390
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Alternative splicing modulates Kv channel clustering through a molecular ball and chain mechanism. Nat Commun 2015; 6:6488. [DOI: 10.1038/ncomms7488] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 02/02/2015] [Indexed: 01/22/2023] Open
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1391
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Cobbert JD, DeMott C, Majumder S, Smith EA, Reverdatto S, Burz DS, McDonough KA, Shekhtman A. Caught in action: selecting peptide aptamers against intrinsically disordered proteins in live cells. Sci Rep 2015; 5:9402. [PMID: 25801767 PMCID: PMC4371151 DOI: 10.1038/srep09402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) or unstructured segments within proteins play an important role in cellular physiology and pathology. Low cellular concentration, multiple binding partners, frequent post-translational modifications and the presence of multiple conformations make it difficult to characterize IDP interactions in intact cells. We used peptide aptamers selected by using the yeast-two-hybrid scheme and in-cell NMR to identify high affinity binders to transiently structured IDP and unstructured segments at atomic resolution. Since both the selection and characterization of peptide aptamers take place inside the cell, only physiologically relevant conformations of IDPs are targeted. The method is validated by using peptide aptamers selected against the prokaryotic ubiquitin-like protein, Pup, of the mycobacterium proteasome. The selected aptamers bind to distinct sites on Pup and have vastly different effects on rescuing mycobacterial proteasome substrate and on the survival of the Bacille-Calmette-Guèrin, BCG, strain of M. bovis. This technology can be applied to study the elusive action of IDPs under near physiological conditions.
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Affiliation(s)
| | | | | | - Eric A Smith
- Wadsworth Center, NY State Department of Health, Albany, NY
| | | | - David S Burz
- Department of Chemistry, University at Albany, Albany, NY
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1392
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Abstract
NMR spectroscopy and ITC have recently been combined to demonstrate how phosphorylation of the intrinsically disordered eukaryotic translation initiation factor 4E-binding protein 2 (4E-BP2) induces folding into a stable three-dimensional structure. The classical structure-function paradigm is inverted, with phosphorylation-induced folding inhibiting binding to the eukaryotic translation initiation factor 4E (eIF4E) and thereby contributing to regulation of the interaction.
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Affiliation(s)
- Guillaume Bouvignies
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38027 Grenoble (France); CEA, DSV, IBS, 71 Avenue des Martyrs, 38027 Grenoble (France); CNRS, IBS, 71 Avenue des Martyrs, 38027 Grenoble (France)
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1393
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Abstract
Intrinsically disordered proteins (IDPs) are important components of the cellular signalling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signalling. These proteins participate in the assembly of signalling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles. Experimental, computational and bioinformatic analyses combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread roles in biological processes.
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1394
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Astro V, de Curtis I. Plasma membrane-associated platforms: Dynamic scaffolds that organize membrane-associated events. Sci Signal 2015; 8:re1. [DOI: 10.1126/scisignal.aaa3312] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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1395
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Goda N, Matsuo N, Tenno T, Ishino S, Ishino Y, Fukuchi S, Ota M, Hiroaki H. An optimized N pro-based method for the expression and purification of intrinsically disordered proteins for an NMR study. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1011004. [PMID: 28232886 DOI: 10.1080/21690707.2015.1011004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an emerging concept. IDPs have high flexibility in their polypeptide chains, lacking a stable 3-dimensional structure. Because of the difficulty in performing X-ray crystallography for IDPs, nuclear magnetic resonance (NMR) spectroscopy is the first choice for atomic-level investigation of their nature. Given that isotopically labeled IDP samples are necessary for NMR study, a robust and cost-effective protocol for bacterial expression and purification of IDP is also needed. We employed the Npro (EDDIE)-autoprotease fusion protein system. Although IDPs are believed to be readily degraded by endogenous proteases when expressed in Escherichia coli, Npro-fused IDPs showed excellent resistance to degradation. Seven IDPs of uncharacterized function sampled from the human genome as well as 3 constructs from IDP regions derived from human FancM and Thermococcus kodakarensis Hef were prepared. We improved the protocol of refolding of Npro (EDDIE) to use dialysis, which is convenient for subsequent purification using reversed-phase (RP) HPLC. The method is robust and widely applicable to any IDP sample, promoting the acquisition of experimental data for IDPs in a high-throughput manner.
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Affiliation(s)
- Natsuko Goda
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; These authors equally contributed to the work
| | - Naoki Matsuo
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; These authors equally contributed to the work
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; The Structural Biology Research Center and Division of Biological Science; Graduate School of Science; Nagoya University; Furocho, Nagoya, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology; Graduate School of Bioresource and Bioenvironmental Sciences and Faculty of Agriculture; Kyushu University ; Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology; Graduate School of Bioresource and Bioenvironmental Sciences and Faculty of Agriculture; Kyushu University ; Fukuoka, Japan
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology ; Maebashi, Japan
| | - Motonori Ota
- Department of Complex Systems Science; Graduate School of Information Sciences; Nagoya University ; Nagoya, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; The Structural Biology Research Center and Division of Biological Science; Graduate School of Science; Nagoya University; Furocho, Nagoya, Japan
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1396
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Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Exp Biol Med (Maywood) 2015; 240:351-60. [PMID: 25710931 PMCID: PMC4436281 DOI: 10.1177/1535370214566558] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.
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Affiliation(s)
- Emma Joy Dodson
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Vered Fishbain-Yoskovitz
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
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1397
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Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 2015; 16:155-66. [PMID: 25693131 DOI: 10.1038/nrm3951] [Citation(s) in RCA: 604] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-coding RNA genes and is globally regulated by Mediator - a large, conformationally flexible protein complex with a variable subunit composition (for example, a four-subunit cyclin-dependent kinase 8 module can reversibly associate with it). These biochemical characteristics are fundamentally important for Mediator's ability to control various processes that are important for transcription, including the organization of chromatin architecture and the regulation of Pol II pre-initiation, initiation, re-initiation, pausing and elongation. Although Mediator exists in all eukaryotes, a variety of Mediator functions seem to be specific to metazoans, which is indicative of more diverse regulatory requirements.
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Affiliation(s)
- Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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1398
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Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) ORF57 protein (also known as mRNA transcript accumulation (Mta)) is a potent posttranscriptional regulator essential for the efficient expression of KSHV lytic genes and productive KSHV replication. ORF57 possesses numerous activities that promote the expression of viral genes, including the three major functions of enhancement of RNA stability, promotion of RNA splicing, and stimulation of protein translation. The multifunctional nature of ORF57 is driven by its ability to interact with an array of cellular cofactors. These interactions are required for the formation of ORF57-containing ribonucleoprotein complexes at specific binding sites in the target transcripts, referred as Mta-responsive elements (MREs). Understanding of the ORF57 protein conformation has led to the identification of two structurally-distinct domains within the ORF57 polypeptide: an unstructured intrinsically disordered N-terminal domain and a structured α-helix-rich C-terminal domain. The distinct structures of the domains serve as the foundation for their unique binding affinities: the N-terminal domain mediates ORF57 interactions with cellular cofactors and target RNAs, and the C-terminal domain mediates ORF57 homodimerization. In addition, each domain has been found to contribute to the stability of ORF57 protein in infected cells by counteracting caspase- and proteasome-mediated degradation pathways. Together, these new findings provide insight into the function and biological properties of ORF57 in the KSHV life cycle and pathogenesis.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, USA.
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, USA.
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1399
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Gibbs EB, Showalter SA. Quantitative biophysical characterization of intrinsically disordered proteins. Biochemistry 2015; 54:1314-26. [PMID: 25631161 DOI: 10.1021/bi501460a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) are broadly defined as protein regions that do not cooperatively fold into a spatially or temporally stable structure. Recent research strongly supports the hypothesis that a conserved functional role for structural disorder renders IDPs uniquely capable of functioning in biological processes such as cellular signaling and transcription. Recently, the frequency of application of rigorous mechanistic biochemistry and quantitative biophysics to disordered systems has increased dramatically. For example, the launch of the Protein Ensemble Database (pE-DB) demonstrates that the potential now exists to refine models for the native state structure of IDPs using experimental data. However, rigorous assessment of which observables place the strongest and least biased constraints on those ensembles is now needed. Most importantly, the past few years have seen strong growth in the number of biochemical and biophysical studies attempting to connect structural disorder with function. From the perspective of equilibrium thermodynamics, there is a clear need to assess the relative significance of hydrophobic versus electrostatic forces in IDP interactions, if it is possible to generalize at all. Finally, kinetic mechanisms that invoke conformational selection and/or induced fit are often used to characterize coupled IDP folding and binding, although application of these models is typically built upon thermodynamic observations. Recently, the reaction rates and kinetic mechanisms of more intrinsically disordered systems have been tested through rigorous kinetic experiments. Motivated by these exciting advances, here we provide a review and prospectus for the quantitative study of IDP structure, thermodynamics, and kinetics.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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1400
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Uversky VN. Functional roles of transiently and intrinsically disordered regions within proteins. FEBS J 2015; 282:1182-9. [DOI: 10.1111/febs.13202] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 12/16/2022]
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 FL USA
- Department of Biological Science; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
- Laboratory of Structural Dynamics; Stability and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St Petersburg Russia
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