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Seefelder M, Kochanek S, Klein FAC. ProteinCoLoc streamlines Bayesian analysis of colocalization in microscopic images. Sci Rep 2024; 14:13277. [PMID: 38858475 PMCID: PMC11164984 DOI: 10.1038/s41598-024-63884-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
Colocalization, the spatial overlap of molecular entities, is often key to support their involvement in common functions. Existing colocalization tools, however, face limitations, particularly because of their basic statistical analysis and their low-throughput manual entry processes making them unsuitable for automation and potentially introducing bias. These shortcomings underscore the need for user-friendly tools streamlining colocalization assessments and enabling their robust and automated quantitative analyses. We have developed ProteinCoLoc, an innovative software designed for automated high-throughput colocalization analyses and incorporating advanced statistical features such as Bayesian modelling, automatic background detection and localised correlation analysis. ProteinCoLoc rationalises colocalization assessments without manual input, comes with a user-friendly graphical user interface and provides various analytics allowing to study and locally quantify colocalization. This easy-to-use application presents numerous advantages, including a direct comparison with controls employing a Bayesian model and the analysis of local correlation patterns, while reducing hands-on time through automatic background detection. The software was validated while studying the colocalization pattern of two proteins forming a stable complex: the huntingtin protein (HTT) and its partner huntingtin-associated protein 40 (HAP40). Our results showcase the software's capacity to quantitatively assess colocalizations. ProteinCoLoc is available both as a Julia package and as a compiled software ( https://github.com/ma-seefelder/ProteinCoLoc ).
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany.
| | - Stefan Kochanek
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany
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2
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Alteen MG, Deme JC, Alvarez CP, Loppnau P, Hutchinson A, Seitova A, Chandrasekaran R, Silva Ramos E, Secker C, Alqazzaz M, Wanker EE, Lea SM, Arrowsmith CH, Harding RJ. Delineation of functional subdomains of Huntingtin protein and their interaction with HAP40. Structure 2023; 31:1121-1131.e6. [PMID: 37390814 PMCID: PMC10527579 DOI: 10.1016/j.str.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
The huntingtin (HTT) protein plays critical roles in numerous cellular pathways by functioning as a scaffold for its many interaction partners and HTT knock out is embryonic lethal. Interrogation of HTT function is complicated by the large size of this protein so we studied a suite of structure-rationalized subdomains to investigate the structure-function relationships within the HTT-HAP40 complex. Protein samples derived from the subdomain constructs were validated using biophysical methods and cryo-electron microscopy, revealing they are natively folded and can complex with validated binding partner, HAP40. Derivatized versions of these constructs enable protein-protein interaction assays in vitro, with biotin tags, and in cells, with luciferase two-hybrid assay-based tags, which we use in proof-of-principle analyses to further interrogate the HTT-HAP40 interaction. These open-source biochemical tools enable studies of fundamental HTT biochemistry and biology, will aid the discovery of macromolecular or small-molecule binding partners and help map interaction sites across this large protein.
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Affiliation(s)
- Matthew G Alteen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; POINT Biopharma, 22 St Clair Avenue E Suite 1201, Toronto, ON M4T 2S3, Canada
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Claudia P Alvarez
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; SCIEX, 71 Four Valley Dr, Vaughan, ON L4K 4V8, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Renu Chandrasekaran
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Mona Alqazzaz
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Seefelder M, Klein FAC, Landwehrmeyer B, Fernández-Busnadiego R, Kochanek S. Huntingtin and Its Partner Huntingtin-Associated Protein 40: Structural and Functional Considerations in Health and Disease. J Huntingtons Dis 2022; 11:227-242. [PMID: 35871360 PMCID: PMC9484127 DOI: 10.3233/jhd-220543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the discovery of the mutation causing Huntington’s disease (HD) in 1993, it has been debated whether an expanded polyglutamine (polyQ) stretch affects the properties of the huntingtin (HTT) protein and thus contributes to the pathological mechanisms responsible for HD. Here we review the current knowledge about the structure of HTT, alone (apo-HTT) or in a complex with Huntingtin-Associated Protein 40 (HAP40), the influence of polyQ-length variation on apo-HTT and the HTT-HAP40 complex, and the biology of HAP40. Phylogenetic analyses suggest that HAP40 performs essential functions. Highlighting the relevance of its interaction with HTT, HAP40 is one of the most abundant partners copurifying with HTT and is rapidly degraded, when HTT levels are reduced. As the levels of both proteins decrease during disease progression, HAP40 could also be a biomarker for HD. Whether declining HAP40 levels contribute to disease etiology is an open question. Structural studies have shown that the conformation of apo-HTT is less constrained but resembles that adopted in the HTT-HAP40 complex, which is exceptionally stable because of extensive interactions between HAP40 and the three domains of HTT. The complex— and to some extent apo-HTT— resists fragmentation after limited proteolysis. Unresolved regions of apo-HTT, constituting about 25% of the protein, are the main sites of post-translational modifications and likely have major regulatory functions. PolyQ elongation does not substantially alter the structure of HTT, alone or when associated with HAP40. Particularly, polyQ above the disease length threshold does not induce drastic conformational changes in full-length HTT. Therefore, models of HD pathogenesis stating that polyQ expansion drastically alters HTT properties should be reconsidered.
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Affiliation(s)
| | | | | | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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Zhang L, Kang H, Perez-Aguilar JM, Zhou R. Possible Co-Evolution of Polyglutamine and Polyproline in Huntingtin Protein: Proline-Rich Domain as Transient Folding Chaperone. J Phys Chem Lett 2022; 13:6331-6341. [PMID: 35796410 DOI: 10.1021/acs.jpclett.2c01184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Huntington's disease is an inherited neurodegenerative disorder caused by the overduplication of CAG repeats in the Huntingtin gene. Recent findings revealed that among the orthologs, the expansion of CAG repeats (polyQ) in the Huntingtin gene occurs in tandem with the duplication of CCG repeats (polyP). However, the molecular mechanism of this possible co-evolution remains unknown. We examined the structures of Huntingtin exon 1 (HttEx1) from six species along with five designed mutants. We found that the polyP segments "chaperone" the rest of the HttEx1 by forming ad hoc polyP binding grooves. Such a process elongates the otherwise poorly solvated polyQ domain, while modulating its secondary structure propensity from β-strands to α-helices. This chaperoning effect is achieved mostly through transient hydrogen bond interactions between polyP and the rest of HttEx1, resulting in a striking golden ratio of ∼2:1 between the chain lengths of polyQ and polyP.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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Harding RJ, Deme JC, Hevler JF, Tamara S, Lemak A, Cantle JP, Szewczyk MM, Begeja N, Goss S, Zuo X, Loppnau P, Seitova A, Hutchinson A, Fan L, Truant R, Schapira M, Carroll JB, Heck AJR, Lea SM, Arrowsmith CH. Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1. Commun Biol 2021; 4:1374. [PMID: 34880419 PMCID: PMC8654980 DOI: 10.1038/s42003-021-02895-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Huntington's disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. We demonstrate in vivo and in cell models that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 Å cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The exon 1 region of HTT is dynamic but shows greater conformational variety in the polyglutamine expanded mutant than wildtype exon 1. Our data provide a foundation for future functional and drug discovery studies targeting Huntington's disease and illuminate the structural consequences of HTT polyglutamine expansion.
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Affiliation(s)
- Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jeffrey P Cantle
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, 98225, USA
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nola Begeja
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Siobhan Goss
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core of NCI, National Institutes of Health, Frederick, MD, 21701, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey B Carroll
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, 98225, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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Huntingtin Ubiquitination Mechanisms and Novel Possible Therapies to Decrease the Toxic Effects of Mutated Huntingtin. J Pers Med 2021; 11:jpm11121309. [PMID: 34945781 PMCID: PMC8709430 DOI: 10.3390/jpm11121309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/24/2022] Open
Abstract
Huntington Disease (HD) is a dominant, lethal neurodegenerative disorder caused by the abnormal expansion (>35 copies) of a CAG triplet located in exon 1 of the HTT gene encoding the huntingtin protein (Htt). Mutated Htt (mHtt) easily aggregates, thereby inducing ER stress that in turn leads to neuronal injury and apoptosis. Therefore, both the inhibition of mHtt aggregate formation and the acceleration of mHtt degradation represent attractive strategies to delay HD progression, and even for HD treatment. Here, we describe the mechanism underlying mHtt degradation by the ubiquitin–proteasome system (UPS), which has been shown to play a more important role than the autophagy–lysosomal pathway. In particular, we focus on E3 ligase proteins involved in the UPS and detail their structure–function relationships. In this framework, we discuss the possible exploitation of PROteolysis TArgeting Chimeras (PROTACs) for HD therapy. PROTACs are heterobifunctional small molecules that comprise two different ligands joined by an appropriate linker; one of the ligands is specific for a selected E3 ubiquitin ligase, the other ligand is able to recruit a target protein of interest, in this case mHtt. As a consequence of PROTAC binding, mHtt and the E3 ubiquitin ligase can be brought to a relative position that allows mHtt to be ubiquitinated and, ultimately, allows a reduction in the amount of mHtt in the cell.
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Seefelder M, Kochanek S. A meta-analysis of transcriptomic profiles of Huntington's disease patients. PLoS One 2021; 16:e0253037. [PMID: 34111223 PMCID: PMC8191979 DOI: 10.1371/journal.pone.0253037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Description of robust transcriptomic alterations in Huntington’s disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0% of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinson’s (PD) and Alzheimer’s disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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Huang B, Guo Q, Niedermeier ML, Cheng J, Engler T, Maurer M, Pautsch A, Baumeister W, Stengel F, Kochanek S, Fernández-Busnadiego R. Pathological polyQ expansion does not alter the conformation of the Huntingtin-HAP40 complex. Structure 2021; 29:804-809.e5. [PMID: 33909994 DOI: 10.1016/j.str.2021.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 01/12/2023]
Abstract
The abnormal amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington's disease (HD). At the protein level, this translates into the expansion of a polyglutamine (polyQ) stretch located at the HTT N terminus, which renders HTT aggregation prone by unknown mechanisms. Here we investigated the effects of polyQ expansion on HTT in a complex with its stabilizing interaction partner huntingtin-associated protein 40 (HAP40). Surprisingly, our comprehensive biophysical, crosslinking mass spectrometry and cryo-EM experiments revealed no major differences in the conformation of HTT-HAP40 complexes of various polyQ length, including 17QHTT-HAP40 (wild type), 46QHTT-HAP40 (typical polyQ length in HD patients), and 128QHTT-HAP40 (extreme polyQ length). Thus, HTT polyQ expansion does not alter the global conformation of HTT when associated with HAP40.
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Affiliation(s)
- Bin Huang
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany
| | - Qiang Guo
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Marie L Niedermeier
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Tatjana Engler
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany
| | - Melanie Maurer
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riß, Germany
| | - Alexander Pautsch
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riß, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
| | - Stefan Kochanek
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany.
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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Kastano K, Mier P, Andrade-Navarro MA. The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. Int J Mol Sci 2021; 22:1727. [PMID: 33572172 PMCID: PMC7915032 DOI: 10.3390/ijms22041727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Low complexity regions (LCRs) are very frequent in protein sequences, generally having a lower propensity to form structured domains and tending to be much less evolutionarily conserved than globular domains. Their higher abundance in eukaryotes and in species with more cellular types agrees with a growing number of reports on their function in protein interactions regulated by post-translational modifications. LCRs facilitate the increase of regulatory and network complexity required with the emergence of organisms with more complex tissue distribution and development. Although the low conservation and structural flexibility of LCRs complicate their study, evolutionary studies of proteins across species have been used to evaluate their significance and function. To investigate how to apply this evolutionary approach to the study of LCR function in protein-protein interactions, we performed a detailed analysis for Huntingtin (HTT), a large protein that is a hub for interaction with hundreds of proteins, has a variety of LCRs, and for which partial structural information (in complex with HAP40) is available. We hypothesize that proteins RASA1, SYN2, and KAT2B may compete with HAP40 for their attachment to the core of HTT using similar LCRs. Our results illustrate how evolution might favor the interplay of LCRs with domains, and the possibility of detecting multiple modes of LCR-mediated protein-protein interactions with a large hub such as HTT when enough protein interaction data is available.
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Affiliation(s)
| | | | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany; (K.K.); (P.M.)
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