1
|
Panagiotopoulos AA, Kalyvianaki K, Tsodoulou PK, Darivianaki MN, Dellis D, Notas G, Daskalakis V, Theodoropoulos PA, Panagiotidis CΑ, Castanas E, Kampa M. Recognition motifs for importin 4 [(L)PPRS(G/P)P] and importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation. Comput Struct Biotechnol J 2022; 20:5952-5961. [PMID: 36382187 PMCID: PMC9646746 DOI: 10.1016/j.csbj.2022.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/21/2023] Open
Abstract
Nuclear translocation of large proteins is mediated through karyopherins, carrier proteins recognizing specific motifs of cargo proteins, known as nuclear localization signals (NLS). However, only few NLS signals have been reported until now. In the present work, NLS signals for Importins 4 and 5 were identified through an unsupervised in silico approach, followed by experimental in vitro validation. The sequences LPPRS(G/P)P and KP(K/Y)LV were identified and are proposed as recognition motifs for Importins 4 and 5 binding, respectively. They are involved in the trafficking of important proteins into the nucleus. These sequences were validated in the breast cancer cell line T47D, which expresses both Importins 4 and 5. Elucidating the complex relationships of the nuclear transporters and their cargo proteins is very important in better understanding the mechanism of nuclear transport of proteins and laying the foundation for the development of novel therapeutics, targeting specific importins.
Collapse
Affiliation(s)
| | - Konstantina Kalyvianaki
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece
| | - Paraskevi K. Tsodoulou
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Maria N. Darivianaki
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Dimitris Dellis
- National Infrastructures for Research and Technology, Athens 11523, Greece
| | - George Notas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | | | - Christos Α. Panagiotidis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece,Corresponding authors.
| | - Marilena Kampa
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71013, Greece,Corresponding authors.
| |
Collapse
|
2
|
Khan MQ, Mubeen H, Khan ZQ, Masood A, Zafar A, Wattoo JI, Nisa AU. Computational insights into missense mutations in HTT gene causing Huntington's disease and its interactome networks. Ir J Med Sci 2022:10.1007/s11845-022-03043-5. [PMID: 35829908 DOI: 10.1007/s11845-022-03043-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Huntington's disease is a rare neurodegenerative illness of the central nervous system that is inherited in an autosomal dominant pattern. Mutant huntingtin protein is produced as a result of enlargement of CAG repeat in the N-terminal of the polyglutamine tract. AIM OF THE STUDY Herein, we aim to investigate the mutations and their effects on the HTT gene and its genetic variants. Additionally, the protein-protein interaction of HTT with other proteins and receptor-ligand interaction with the three-dimensional structure of huntingtin protein were identified. METHODS A comprehensive analysis of the HTT interactome and protein-ligand interaction has been carried out to provide a global picture of structure-function analysis of huntingtin protein. Mutations were analyzed and mutation verification tools were used to check the effect of mutation on protein function. RESULTS The results showed, mutations in a single gene are not only responsible for causing a particular disease but may also cause other hereditary disorders as well. Moreover, the modification at the nucleotide level also cause the change in the specific amino acid which may disrupt the function of HTT and its interacting proteins contributing in disease pathogenesis. Furthermore, the interaction between MECP2 and BDNF lowers the rate of transcriptional activity. Molecular docking further confirmed the strong interaction between MECP2 and BDNF with highest affinity. Amino acid residues of the HTT protein, involved in the interaction with tetrabenazine were N912, Y890, G2385, and V2320. These findings proved, tetrabenazine as one of the potential therapeutic agent for treatment of Huntington's disease. CONCLUSION These results give further insights into the genetics of Huntington's disease for a better understanding of disease models which will be beneficial for the future therapeutic studies.
Collapse
Affiliation(s)
| | - Hira Mubeen
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan.
| | | | - Ammara Masood
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Asma Zafar
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Javed Iqbal Wattoo
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Alim Un Nisa
- Pakistan Council of Scientific and Industrial Research, Lahore, Pakistan
| |
Collapse
|
3
|
In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. Int J Mol Sci 2021; 22:ijms22063214. [PMID: 33809947 PMCID: PMC8004120 DOI: 10.3390/ijms22063214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Huntington’s disease is a rare neurodegenerative and autosomal dominant disorder. HD is caused by a mutation in the gene coding for huntingtin (Htt). The result is the production of a mutant Htt with an abnormally long polyglutamine repeat that leads to pathological Htt aggregates. Although the structure of human Htt has been determined, albeit at low resolution, its functions and how they are performed are largely unknown. Moreover, there is little information on the structure and function of Htt in other organisms. The comparison of Htt homologs can help to understand if there is a functional conservation of domains in the evolution of Htt in eukaryotes. In this work, through a computational approach, Htt homologs from lower eukaryotes have been analysed, identifying ordered domains and modelling their structure. Based on the structural models, a putative function for most of the domains has been predicted. A putative C. elegans Htt-like protein has also been analysed following the same approach. The results obtained support the notion that this protein is a orthologue of human Htt.
Collapse
|
4
|
Carbo M, Brandi V, Pascarella G, Staid DS, Colotti G, Polticelli F, Ilari A, Morea V. Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy. Int J Mol Med 2019; 44:2223-2233. [PMID: 31638189 PMCID: PMC6844632 DOI: 10.3892/ijmm.2019.4373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/19/2019] [Indexed: 11/15/2022] Open
Abstract
Huntington's disease (HD) is a lethal neurodegenerative disorder for which no cure is available yet. It is caused by abnormal expansion of a CAG triplet in the gene encoding the huntingtin protein (Htt), with consequent expansion of a polyglutamine repeat in mutated Htt (mHtt). This makes mHtt highly unstable and aggregation prone. Soluble mHtt is linked to cytotoxicity and neurotoxicity, whereas mHtt aggregates are thought to be neuroprotective. While Htt and mHtt are ubiquitously expressed throughout the brain and peripheral tissues, HD is characterized by selective degradation of the corpus striatum, without notable alterations in peripheral tissues. Screening for mRNAs preferentially expressed in rodent striatum led to the discovery of a GTP binding protein homologous to Ras family members. Due to these features, the newly discovered protein was termed Ras Homolog Enriched in Striatum (RHES). The aetiological role of RHES in HD has been ascribed to its small ubiquitin-like modifier (SUMO)-E3 ligase function. RHES sumoylates mHtt with higher efficiency than wild-type Htt, thereby protecting mHtt from degradation and increasing the amounts of the soluble form. Although RHES is an attractive target for HD treatment, essential information about protein structure and function are still missing. With the aim of investigating RHES 3D structure and function, bioinformatic analyses and molecular modelling have been performed in the present study, based on which, RHES regions predicted to be involved in the interaction with mHtt or the SUMO-E2 ligase Ubc9 have been identified. These regions have been used to design peptides aimed at inhibiting RHES interactions and, therefore, mHtt sumoylation; in turn, these peptides will be used to develop small molecule inhibitors by both rational design and virtual screening of large compound libraries. Once identified, RHES sumoylation inhibitors may open the road to the development of therapeutic agents against the severe, and currently untreatable, HD.
Collapse
Affiliation(s)
- Miriam Carbo
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University, I‑00185 Rome, Italy
| | - Valentina Brandi
- Department of Sciences, Roma Tre University, I‑00159 Rome, Italy
| | - Gianmarco Pascarella
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University, I‑00185 Rome, Italy
| | - David Sasah Staid
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University, I‑00185 Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology of The National Research Council of Italy, I‑00185 Rome, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, I‑00159 Rome, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of The National Research Council of Italy, I‑00185 Rome, Italy
| | - Veronica Morea
- Institute of Molecular Biology and Pathology of The National Research Council of Italy, I‑00185 Rome, Italy
| |
Collapse
|
5
|
Maiuri T, Suart CE, Hung CLK, Graham KJ, Barba Bazan CA, Truant R. DNA Damage Repair in Huntington's Disease and Other Neurodegenerative Diseases. Neurotherapeutics 2019; 16:948-956. [PMID: 31364066 PMCID: PMC6985310 DOI: 10.1007/s13311-019-00768-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent genome-wide association studies of Huntington's disease (HD) primarily highlighted genes involved in DNA damage repair mechanisms as modifiers of age at onset and disease severity, consistent with evidence that more DNA repair genes are being implicated in late age-onset neurodegenerative diseases. This provides an exciting opportunity to advance therapeutic development in HD, as these pathways have already been under intense investigation in cancer research. Also emerging are the roles of other polyglutamine disease proteins in DNA damage repair mechanisms. A potential universal trigger of oxidative DNA damage shared in these late age-onset diseases is the increase of reactive oxygen species (ROS) in human aging, defining an age-related mechanism that has defied other hypotheses of neurodegeneration. We discuss the potential commonality of DNA damage repair pathways in HD and other neurodegenerative diseases. Potential targets for therapy that may prove beneficial across many of these diseases are also identified, defining nodes in the ataxia telangiectasia-mutated (ATM) complex, mismatch repair, and poly ADP-ribose polymerases (PARPs).
Collapse
Affiliation(s)
- T Maiuri
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C E Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C L K Hung
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - K J Graham
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C A Barba Bazan
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - R Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada.
| |
Collapse
|