1
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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2
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Huang WC, Lin WT, Hung MS, Lee JC, Tung CW. Decrypting orphan GPCR drug discovery via multitask learning. J Cheminform 2024; 16:10. [PMID: 38263092 PMCID: PMC10804799 DOI: 10.1186/s13321-024-00806-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
The drug discovery of G protein-coupled receptors (GPCRs) superfamily using computational models is often limited by the availability of protein three-dimensional (3D) structures and chemicals with experimentally measured bioactivities. Orphan GPCRs without known ligands further complicate the process. To enable drug discovery for human orphan GPCRs, multitask models were proposed for predicting half maximal effective concentrations (EC50) of the pairs of chemicals and GPCRs. Protein multiple sequence alignment features, and physicochemical properties and fingerprints of chemicals were utilized to encode the protein and chemical information, respectively. The protein features enabled the transfer of data-rich GPCRs to orphan receptors and the transferability based on the similarity of protein features. The final model was trained using both agonist and antagonist data from 200 GPCRs and showed an excellent mean squared error (MSE) of 0.24 in the validation dataset. An independent test using the orphan dataset consisting of 16 receptors associated with less than 8 bioactivities showed a reasonably good MSE of 1.51 that can be further improved to 0.53 by considering the transferability based on protein features. The informative features were identified and mapped to corresponding 3D structures to gain insights into the mechanism of GPCR-ligand interactions across the GPCR family. The proposed method provides a novel perspective on learning ligand bioactivity within the diverse human GPCR superfamily and can potentially accelerate the discovery of therapeutic agents for orphan GPCRs.
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Affiliation(s)
- Wei-Cheng Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Wei-Ting Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Ming-Shiu Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Jinq-Chyi Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan.
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3
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Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernadó P, Banères JL, Sibille N. Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction. Structure 2023; 31:1394-1406.e7. [PMID: 37669668 DOI: 10.1016/j.str.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
Arrestin-dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR's C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three rhodopsin-like GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR), and the β2-adernergic receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motifs (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transitions appear to favor arrestin-2 binding. Hence, our results suggest a model in which the phosphorylation-dependent structuration of the GPCR C-terminal regions would modulate arrestin binding and therefore signaling outcomes in arrestin-dependent pathways.
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Affiliation(s)
- Myriam Guillien
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Glaécia A N Pereira
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélien Thureau
- HélioBio Section, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91190 Gif-sur-Yvette, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France.
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4
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Manyilov VD, Ilyinsky NS, Nesterov SV, Saqr BMGA, Dayhoff GW, Zinovev EV, Matrenok SS, Fonin AV, Kuznetsova IM, Turoverov KK, Ivanovich V, Uversky VN. Chaotic aging: intrinsically disordered proteins in aging-related processes. Cell Mol Life Sci 2023; 80:269. [PMID: 37634152 PMCID: PMC11073068 DOI: 10.1007/s00018-023-04897-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
The development of aging is associated with the disruption of key cellular processes manifested as well-established hallmarks of aging. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) have no stable tertiary structure that provide them a power to be configurable hubs in signaling cascades and regulate many processes, potentially including those related to aging. There is a need to clarify the roles of IDPs/IDRs in aging. The dataset of 1702 aging-related proteins was collected from established aging databases and experimental studies. There is a noticeable presence of IDPs/IDRs, accounting for about 36% of the aging-related dataset, which is however less than the disorder content of the whole human proteome (about 40%). A Gene Ontology analysis of the used here aging proteome reveals an abundance of IDPs/IDRs in one-third of aging-associated processes, especially in genome regulation. Signaling pathways associated with aging also contain IDPs/IDRs on different hierarchical levels, revealing the importance of "structure-function continuum" in aging. Protein-protein interaction network analysis showed that IDPs present in different clusters associated with different aging hallmarks. Protein cluster with IDPs enrichment has simultaneously high liquid-liquid phase separation (LLPS) probability, "nuclear" localization and DNA-associated functions, related to aging hallmarks: genomic instability, telomere attrition, epigenetic alterations, and stem cells exhaustion. Intrinsic disorder, LLPS, and aggregation propensity should be considered as features that could be markers of pathogenic proteins. Overall, our analyses indicate that IDPs/IDRs play significant roles in aging-associated processes, particularly in the regulation of DNA functioning. IDP aggregation, which can lead to loss of function and toxicity, could be critically harmful to the cell. A structure-based analysis of aging and the identification of proteins that are particularly susceptible to disturbances can enhance our understanding of the molecular mechanisms of aging and open up new avenues for slowing it down.
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Affiliation(s)
- Vladimir D Manyilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia.
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Baraa M G A Saqr
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Guy W Dayhoff
- Department of Chemistry, University of South Florida, Tampa, FL, USA
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Simon S Matrenok
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | | | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612, USA.
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5
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Zhao K, Hua D, Yang C, Wu X, Mao Y, Sheng Y, Sun W, Li Y, Kong X, Li P. Nuclear import of Mas-related G protein-coupled receptor member D induces pathological cardiac remodeling. Cell Commun Signal 2023; 21:181. [PMID: 37488545 PMCID: PMC10364433 DOI: 10.1186/s12964-023-01168-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 05/14/2023] [Indexed: 07/26/2023] Open
Abstract
Alamandine (Ala), a ligand of Mas-related G protein-coupled receptor, member D (MrgD), alleviates angiotensin II (AngII)-induced cardiac hypertrophy. However, the specific physiological and pathological role of MrgD is not yet elucidated. Here, we found that MrgD expression increased under various pathological conditions. Then, MrgD knockdown prevented AngII-induced cardiac hypertrophy and fibrosis via inactivating Gαi-mediacted downstream signaling pathways, including the phosphorylation of p38 (p-P38), while MrgD overexpression induced pathological cardiac remodeling. Next, Ala, like silencing MrgD, exerted its cardioprotective effects by inhibiting Ang II-induced nuclear import of MrgD. MrgD interacted with p-P38 and promoted its entry into the nucleus under Ang II stimulation. Our results indicated that Ala was a blocking ligand of MrgD that inhibited downstream signaling pathway, which unveiled the promising cardioprotective effect of silencing MrgD expression on alleviating cardiac remodeling. Video Abstract.
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Affiliation(s)
- Kun Zhao
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Dongxu Hua
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoguang Wu
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Yukang Mao
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Yanhui Sheng
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Wei Sun
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Yong Li
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
| | - Xiangqing Kong
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China.
| | - Peng Li
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
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6
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Li Y, Qin J, Chen M, Sun N, Tan F, Zhang H, Zou Y, Uversky VN, Liu Y. The Moonlighting Function of Soybean Disordered Methyl-CpG-Binding Domain 10c Protein. Int J Mol Sci 2023; 24:ijms24108677. [PMID: 37240035 DOI: 10.3390/ijms24108677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are multifunctional due to their ability to adopt different structures depending on the local conditions. The intrinsically disordered regions of methyl-CpG-binding domain (MBD) proteins play important roles in regulating growth and development by interpreting DNA methylation patterns. However, whether MBDs have a stress-protective function is far from clear. In this paper, soybean GmMBD10c protein, which contains an MBD and is conserved in Leguminosae, was predicted to be located in the nucleus. It was found to be partially disordered by bioinformatic prediction, circular dichroism and a nuclear magnetic resonance spectral analysis. The enzyme activity assay and SDS-PAGE results showed that GmMBD10c can protect lactate dehydrogenase and a broad range of other proteins from misfolding and aggregation induced by the freeze-thaw process and heat stress, respectively. Furthermore, overexpression of GmMBD10c enhanced the salt tolerance of Escherichia coli. These data validate that GmMBD10c is a moonlighting protein with multiple functions.
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Affiliation(s)
- Yanling Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jiawei Qin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Menglu Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Fangmei Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yongdong Zou
- The Instrumental Analysis Center of Shenzhen University, Shenzhen University, Shenzhen 518060, China
| | - 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 33612, USA
| | - Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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7
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Nicolaides NC, Kontou M, Vasilakis IA, Binou M, Lykopoulou E, Kanaka-Gantenbein C. McCune-Albright Syndrome: A Case Report and Review of Literature. Int J Mol Sci 2023; 24:ijms24108464. [PMID: 37239810 DOI: 10.3390/ijms24108464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
McCune-Albright syndrome (MAS) is a rare sporadic condition defined by the classic triad of fibrous dysplasia of bone, café au lait skin macules, and hyperfunctioning endocrinopathies. The molecular basis of MAS has been ascribed to the post-zygotic somatic gain-of-function mutations in the GNAS gene, which encodes the alpha subunit of G proteins, leading to constitutive activation of several G Protein-Coupled Receptors (GPCRs). The co-occurrence of two of the above-mentioned cardinal clinical manifestations sets the diagnosis at the clinical level. In this case report, we describe a 27-month-old girl who presented with gonadotropin-independent precocious puberty secondary to an estrogen-secreting ovarian cyst, a café au lait skin macule and growth hormone, and prolactin excess, and we provide an updated review of the scientific literature on the clinical features, diagnostic work-up, and therapeutic management of MAS.
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Affiliation(s)
- Nicolas C Nicolaides
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
- Reference Center for Rare Pediatric Endocrine Disorders, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Maria Kontou
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Ioannis-Anargyros Vasilakis
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
- Reference Center for Rare Pediatric Endocrine Disorders, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Maria Binou
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
- Reference Center for Rare Pediatric Endocrine Disorders, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Evangelia Lykopoulou
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Christina Kanaka-Gantenbein
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
- Reference Center for Rare Pediatric Endocrine Disorders, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
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8
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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9
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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10
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Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol 2022; 12:1051487. [PMID: 36505834 PMCID: PMC9730332 DOI: 10.3389/fonc.2022.1051487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small molecule inhibition. However, identifying actionable ASE targets remains challenging due to the uncertainty of its protein product, structure impact, and proteoform (protein isoform) function. Here we argue that an integrated multi-omics profiling strategy can overcome these challenges, allowing us to mine this untapped source of targets for therapeutic development. In this review, we will provide an overview of current multi-omics strategies in characterizing ASEs by utilizing the transcriptome, proteome, and state-of-art algorithms for protein structure prediction. We will discuss limitations and knowledge gaps associated with each technology and informatics analytics. Finally, we will discuss future directions that will enable the full integration of multi-omics data for ASE target discovery.
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Affiliation(s)
- Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States,*Correspondence: Timothy I. Shaw,
| | - Bi Zhao
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Brandon Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Aleksandra Karolak
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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11
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Sudarev VV, Dolotova SM, Bukhalovich SM, Bazhenov SV, Ryzhykau YL, Uversky VN, Bondarev NA, Osipov SD, Mikhailov AE, Kuklina DD, Murugova TN, Manukhov IV, Rogachev AV, Gordeliy VI, Gushchin IY, Kuklin AI, Vlasov AV. Ferritin self-assembly, structure, function, and biotechnological applications. Int J Biol Macromol 2022; 224:319-343. [DOI: 10.1016/j.ijbiomac.2022.10.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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12
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Yang L, Liu D, Wüthrich K. GPCR structural characterization by NMR spectroscopy in solution. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1207-1212. [PMID: 36017890 PMCID: PMC9828178 DOI: 10.3724/abbs.2022106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the human proteome, 826 G-protein-coupled receptors (GPCRs) interact with extracellular stimuli to initiate cascades of intracellular signaling. Determining conformational dynamics and intermolecular interactions are key to understand GPCR function as a basis for drug design. X-ray crystallography and cryo-electron microscopy (cryo-EM) contribute molecular architectures of GPCRs and GPCR-signaling complexes. NMR spectroscopy is complementary by providing information on the dynamics of GPCR structures at physiological temperature. In this review, several NMR approaches in use to probe GPCR dynamics and intermolecular interactions are discussed. The topics include uniform stable-isotope labeling, amino acid residue-selective stable-isotope labeling, site-specific labeling by genetic engineering, the introduction of 19F-NMR probes, and the use of paramagnetic nitroxide spin labels. The unique information provided by NMR spectroscopy contributes to our understanding of GPCR biology and thus adds to the foundations for rational drug design.
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Affiliation(s)
- Lingyun Yang
- iHuman InstituteShanghaiTech UniversityShanghai201210China
| | - Dongsheng Liu
- iHuman InstituteShanghaiTech UniversityShanghai201210China,Correspondence address. Tel: +86-21-20685124; E-mail:
| | - Kurt Wüthrich
- iHuman InstituteShanghaiTech UniversityShanghai201210China,Department of Integrative Structural and Computational BiologyScripps ResearchLa JollaCA92037USA,Institute of Molecular Biology and BiophysicsETH ZürichOtto-Stern-Weg 58093ZürichSwitzerland
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13
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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14
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Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
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Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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15
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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16
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Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs). Sci Rep 2022; 12:8657. [PMID: 35606532 PMCID: PMC9126886 DOI: 10.1038/s41598-022-12731-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
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17
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What Is Parvalbumin for? Biomolecules 2022; 12:biom12050656. [PMID: 35625584 PMCID: PMC9138604 DOI: 10.3390/biom12050656] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/28/2022] Open
Abstract
Parvalbumin (PA) is a small, acidic, mostly cytosolic Ca2+-binding protein of the EF-hand superfamily. Structural and physical properties of PA are well studied but recently two highly conserved structural motifs consisting of three amino acids each (clusters I and II), which contribute to the hydrophobic core of the EF-hand domains, have been revealed. Despite several decades of studies, physiological functions of PA are still poorly known. Since no target proteins have been revealed for PA so far, it is believed that PA acts as a slow calcium buffer. Numerous experiments on various muscle systems have shown that PA accelerates the relaxation of fast skeletal muscles. It has been found that oxidation of PA by reactive oxygen species (ROS) is conformation-dependent and one more physiological function of PA in fast muscles could be a protection of these cells from ROS. PA is thought to regulate calcium-dependent metabolic and electric processes within the population of gamma-aminobutyric acid (GABA) neurons. Genetic elimination of PA results in changes in GABAergic synaptic transmission. Mammalian oncomodulin (OM), the β isoform of PA, is expressed mostly in cochlear outer hair cells and in vestibular hair cells. OM knockout mice lose their hearing after 3–4 months. It was suggested that, in sensory cells, OM maintains auditory function, most likely affecting outer hair cells’ motility mechanisms.
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18
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Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction. Biomolecules 2022; 12:biom12050617. [PMID: 35625550 PMCID: PMC9138321 DOI: 10.3390/biom12050617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Arrestin-dependent pathways are a central component of G protein-coupled receptor (GPCRs) signaling. However, the molecular processes regulating arrestin binding are to be further illuminated, in particular with regard to the structural impact of GPCR C-terminal disordered regions. Here, we used an integrated biophysical strategy to describe the basal conformations of the C-terminal domains of three class A GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR) and the β2-adernergic receptor (β2AR). By doing so, we revealed the presence of transient secondary structures in these regions that are potentially involved in the interaction with arrestin. These secondary structure elements differ from those described in the literature in interaction with arrestin. This suggests a mechanism where the secondary structure conformational preferences in the C-terminal regions of GPCRs could be a central feature for optimizing arrestins recognition.
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19
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Antifeeva IA, Fonin AV, Fefilova AS, Stepanenko OV, Povarova OI, Silonov SA, Kuznetsova IM, Uversky VN, Turoverov KK. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept. Cell Mol Life Sci 2022; 79:251. [PMID: 35445278 PMCID: PMC11073196 DOI: 10.1007/s00018-022-04276-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
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Affiliation(s)
- Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia.
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20
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Kapuganti SK, Bhardwaj A, Kumar P, Bhardwaj T, Nayak N, Uversky VN, Giri R. Role of structural disorder in the multi-functionality of flavivirus proteins. Expert Rev Proteomics 2022; 19:183-196. [PMID: 35655146 DOI: 10.1080/14789450.2022.2085563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION The life cycle of a virus involves interacting with the host cell, entry, hijacking host machinery for viral replication, evading the host's immune system, and releasing mature virions. However, viruses, being small in size, can only harbor a genome large enough to code for the minimal number of proteins required for the replication and maturation of the virions. As a result, many viral proteins are multifunctional machines that do not directly obey the classic structure-function paradigm. Often, such multifunctionality is rooted in intrinsic disorder that allows viral proteins to interact with various cellular factors and remain functional in the hostile environment of different cellular compartments. AREAS COVERED This report covers the classification of flaviviruses, their proteome organization, and the prevalence of intrinsic disorder in the proteomes of different flaviviruses. Further, we have summarized the speculations made about the apparent roles of intrinsic disorder in the observed multifunctionality of flaviviral proteins. EXPERT OPINION Small sizes of viral genomes impose multifunctionality on their proteins, which is dependent on the excessive usage of intrinsic disorder. In fact, intrinsic disorder serves as a universal functional tool, weapon, and armor of viruses and clearly plays an important role in their functionality and evolution.
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Affiliation(s)
| | - Aparna Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Namyashree Nayak
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
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21
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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22
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Abstract Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered. Graphical abstract ![]()
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - 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, 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia, 142290
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23
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Abstract
This mini-review represents a brief, disorder-centric consideration of the interplay between order and disorder in proteins. The goal here is to show that inside the cell, folding, non-folding, and misfolding of proteins are interlinked on multiple levels. This is evidenced by the highly heterogeneous spatio-temporal structural organization of a protein molecule, where one can find differently (dis)ordered components that can undergo local or global order-to-disorder and disorder-to-order transitions needed for functionality. This is further illustrated by the fact that at particular moments of their life, most notably during their synthesis and degradation, all proteins are at least partially disordered. In addition to these intrinsic forms of disorder, proteins are constantly facing extrinsic disorder, which is intrinsic disorder in their functional partners. All this comprises the multileveled protein disorder cycle.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
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24
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Kulkarni P, Behal A, Mohanty A, Salgia R, Nedelcu AM, Uversky VN. Co-opting disorder into order: Intrinsically disordered proteins and the early evolution of complex multicellularity. Int J Biol Macromol 2022; 201:29-36. [PMID: 34998872 DOI: 10.1016/j.ijbiomac.2021.12.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/18/2021] [Accepted: 12/28/2021] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid structures yet play important roles in myriad biological phenomena. A distinguishing feature of IDPs is that they often mediate specific biological outcomes via multivalent weak cooperative interactions with multiple partners. Here, we show that several proteins specifically associated with processes that were key in the evolution of complex multicellularity in the lineage leading to the multicellular green alga Volvox carteri are IDPs. We suggest that, by rewiring cellular protein interaction networks, IDPs facilitated the co-option of ancestral pathways for specialized multicellular functions, underscoring the importance of IDPs in the early evolution of complex multicellularity.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA.
| | - Amita Behal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, Canada.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia.
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25
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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26
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Marzullo L, Turco MC, Uversky VN. What's in the BAGs? Intrinsic disorder angle of the multifunctionality of the members of a family of chaperone regulators. J Cell Biochem 2021; 123:22-42. [PMID: 34339540 DOI: 10.1002/jcb.30123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023]
Abstract
In humans, the family of Bcl-2 associated athanogene (BAG) proteins includes six members characterized by exceptional multifunctionality and engagement in the pathogenesis of various diseases. All of them are capable of interacting with a multitude of often unrelated binding partners. Such binding promiscuity and related functional and pathological multifacetedness cannot be explained or understood within the frames of the classical "one protein-one structure-one function" model, which also fails to explain the presence of multiple isoforms generated for BAG proteins by alternative splicing or alternative translation initiation and their extensive posttranslational modifications. However, all these mysteries can be solved by taking into account the intrinsic disorder phenomenon. In fact, high binding promiscuity and potential to participate in a broad spectrum of interactions with multiple binding partners, as well as a capability to be multifunctional and multipathogenic, are some of the characteristic features of intrinsically disordered proteins and intrinsically disordered protein regions. Such functional proteins or protein regions lacking unique tertiary structures constitute a cornerstone of the protein structure-function continuum concept. The aim of this paper is to provide an overview of the functional roles of human BAG proteins from the perspective of protein intrinsic disorder which will provide a means for understanding their binding promiscuity, multifunctionality, and relation to the pathogenesis of various diseases.
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Affiliation(s)
- Liberato Marzullo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Maria C Turco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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27
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On the specificity of protein-protein interactions in the context of disorder. Biochem J 2021; 478:2035-2050. [PMID: 34101805 PMCID: PMC8203207 DOI: 10.1042/bcj20200828] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.
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28
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Matthees ESF, Haider RS, Hoffmann C, Drube J. Differential Regulation of GPCRs-Are GRK Expression Levels the Key? Front Cell Dev Biol 2021; 9:687489. [PMID: 34109182 PMCID: PMC8182058 DOI: 10.3389/fcell.2021.687489] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of transmembrane receptors and their signal transduction is tightly regulated by GPCR kinases (GRKs) and β-arrestins. In this review, we discuss novel aspects of the regulatory GRK/β-arrestin system. Therefore, we briefly revise the origin of the "barcode" hypothesis for GPCR/β-arrestin interactions, which states that β-arrestins recognize different receptor phosphorylation states to induce specific functions. We emphasize two important parameters which may influence resulting GPCR phosphorylation patterns: (A) direct GPCR-GRK interactions and (B) tissue-specific expression and availability of GRKs and β-arrestins. In most studies that focus on the molecular mechanisms of GPCR regulation, these expression profiles are underappreciated. Hence we analyzed expression data for GRKs and β-arrestins in 61 tissues annotated in the Human Protein Atlas. We present our analysis in the context of pathophysiological dysregulation of the GPCR/GRK/β-arrestin system. This tissue-specific point of view might be the key to unraveling the individual impact of different GRK isoforms on GPCR regulation.
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Affiliation(s)
| | | | - Carsten Hoffmann
- Institut für Molekulare Zellbiologie, CMB – Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
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29
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Biological characterization of ligands targeting the human CC chemokine receptor 8 (CCR8) reveals the biased signaling properties of small molecule agonists. Biochem Pharmacol 2021; 188:114565. [PMID: 33872569 DOI: 10.1016/j.bcp.2021.114565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
The human CC chemokine receptor 8 (CCR8) is a promising drug target for cancer immunotherapy and autoimmune disease. Besides human and viral chemokines, previous studies revealed diverse classes of CCR8-targeting small molecules. We characterized a selection of these CCR8 ligands (hCCL1, vCCL1, ZK756326, AZ6; CCR8 agonists and a naphthalene-sulfonamide-based CCR8 antagonist), in in vitro cell-based assays (hCCL1AF647 binding, calcium mobilization, cellular impedance, cell migration, β-arrestin 1/2 recruitment), and used pharmacological tools to determine G protein-dependent and -independent signaling pathways elicited by these ligands. Our data reveal differences in CCR8-mediated signaling induced by chemokines versus small molecules, which was most pronounced in cell migration studies. Human CCL1 most efficiently induced cell migration whereby Gβγ signaling was indispensable. In contrast, Gβγ signaling did not contribute to cell migration induced by other CCR8 ligands (vCCL1, ZK756326, AZ6). Although all tested CCR8 agonists were full agonists for calcium mobilization, a significant contribution for Gβγ signaling herein was only apparent for human and viral CCL1. Despite both Gαi- and Gαq-signaling regulate intracellular Ca2+-release, cellular impedance experiments showed that CCR8 agonists predominantly induce Gαi-dependent signaling. Finally, small molecule agonists displayed higher efficacy in β-arrestin 1 recruitment, which occurred independently of Gαi signaling. Also in this latter assay, only hCCL1-induced activity was dependent on Gβγ-signaling. Our study provides insight into CCR8 signaling and function and demonstrates differential CCR8 activation by different classes of ligands. This reflects the ability of CCR8 small molecules to evoke different subsets of the receptor's signaling repertoire, which categorizes them as biased agonists.
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Deshpande S, Altermann E, Sarojini V, Lott JS, Lee TV. Structural characterization of a PCP-R didomain from an archaeal nonribosomal peptide synthetase reveals novel interdomain interactions. J Biol Chem 2021; 296:100432. [PMID: 33610550 PMCID: PMC8024701 DOI: 10.1016/j.jbc.2021.100432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that produce a wide range of bioactive peptides, such as siderophores, toxins, and antibacterial and insecticidal agents. NRPSs are dynamic proteins characterized by extensive interdomain communications as a consequence of their assembly-line mode of synthesis. Hence, crystal structures of multidomain fragments of NRPSs have aided in elucidating crucial interdomain interactions that occur during different steps of the NRPS catalytic cycle. One crucial yet unexplored interaction is that between the reductase (R) domain and the peptide carrier protein (PCP) domain. R domains are members of the short-chain dehydrogenase/reductase family and function as termination domains that catalyze the reductive release of the final peptide product from the terminal PCP domain of the NRPS. Here, we report the crystal structure of an archaeal NRPS PCP-R didomain construct. This is the first NRPS R domain structure to be determined together with the upstream PCP domain and is also the first structure of an archaeal NRPS to be reported. The structure reveals that a novel helix-turn-helix motif, found in NRPS R domains but not in other short-chain dehydrogenase/reductase family members, plays a major role in the interface between the PCP and R domains. The information derived from the described PCP-R interface will aid in gaining further mechanistic insights into the peptide termination reaction catalyzed by the R domain and may have implications in engineering NRPSs to synthesize novel peptide products.
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Affiliation(s)
- Sandesh Deshpande
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Eric Altermann
- AgResearch Limited, Food System Integrity, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | | | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - T Verne Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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31
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The G Protein-Coupled Receptor Kinases (GRKs) in Chemokine Receptor-Mediated Immune Cell Migration: From Molecular Cues to Physiopathology. Cells 2021; 10:cells10010075. [PMID: 33466410 PMCID: PMC7824814 DOI: 10.3390/cells10010075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/18/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Although G protein-coupled receptor kinases (GRKs) have long been known to regulate G protein-coupled receptor (GPCR) desensitization, their more recently characterized functions as scaffolds and signalling adapters underscore that this small family of proteins governs a larger array of physiological functions than originally suspected. This review explores how GRKs contribute to the complex signalling networks involved in the migration of immune cells along chemokine gradients sensed by cell surface GPCRs. We outline emerging evidence indicating that the coordinated docking of several GRKs on an active chemokine receptor determines a specific receptor phosphorylation barcode that will translate into distinct signalling and migration outcomes. The guidance cues for neutrophil migration are emphasized based on several alterations affecting GRKs or GPCRs reported to be involved in pathological conditions.
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32
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Elrashdy F, Redwan EM, Uversky VN. Intrinsic disorder perspective of an interplay between the renin-angiotensin-aldosterone system and SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104510. [PMID: 32853823 PMCID: PMC7444473 DOI: 10.1016/j.meegid.2020.104510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
The novel severe acute respiratory syndrome (SARS) coronavirus SARS-CoV-2 walks the planet causing the rapid spread of the CoV disease 2019 (COVID-19) that has especially deleterious consequences for the patients with underlying cardiovascular diseases (CVDs). Entry of the SARS-CoV-2 into the host cell involves interaction of the virus (via the receptor-binding domain (RBD) of its spike glycoprotein) with the membrane-bound form of angiotensin-converting enzyme 2 (ACE2) followed by the virus-ACE2 complex internalization by the cell. Since ACE2 is expressed in various tissues, such as brain, gut, heart, kidney, and lung, and since these organs represent obvious targets for the SARS-CoV-2 infection, therapeutic approaches were developed to either inhibit ACE2 or reduce its expression as a means of prevention of the virus entry into the corresponding host cells. The problem here is that in addition to be a receptor for the SARS-CoV-2 entry into the host cells, ACE2 acts as a key component of the renin-angiotensin-aldosterone system (RAAS) aimed at the generation of a cascade of vasoactive peptides coordinating several physiological processes. In RAAS, ACE2 degrades angiotensin II, which is a multifunctional CVD-promoting peptide hormone and converts it to a heptapeptide angiotensin-(1-7) acting as the angiotensin II antagonist. As protein multifunctionality is commonly associated with the presence of flexible or disordered regions, we analyze here the intrinsic disorder predisposition of major players related to the SARS-CoV-2 - RAAS axis. We show that all considered proteins contain intrinsically disordered regions that might have specific functions. Since intrinsic disorder might play a role in the functionality of query proteins and be related to the COVID-19 pathogenesis, this work represents an important disorder-based outlook of an interplay between the renin-angiotensin-aldosterone system and SARS-CoV-2. It also suggests that consideration of the intrinsic disorder phenomenon should be added to the modern arsenal of means for drug development.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | - Vladimir N Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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33
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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34
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Gadhave K, Gehi BR, Kumar P, Xue B, Uversky VN, Giri R. The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. Cell Mol Life Sci 2020; 77:4163-4208. [PMID: 31894361 PMCID: PMC11104979 DOI: 10.1007/s00018-019-03414-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/17/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of age-related dementia worldwide. Despite more than a century of intensive research, we are not anywhere near the discovery of a cure for this disease or a way to prevent its progression. Among the various molecular mechanisms proposed for the description of the pathogenesis and progression of AD, the amyloid cascade hypothesis, according to which accumulation of a product of amyloid precursor protein (APP) cleavage, amyloid β (Aβ) peptide, induces pathological changes in the brain observed in AD, occupies a unique niche. Although multiple proteins have been implicated in this amyloid cascade signaling pathway, their structure-function relationships are mostly unexplored. However, it is known that two major proteins related to AD pathology, Aβ peptide, and microtubule-associated protein tau belong to the category of intrinsically disordered proteins (IDPs), which are the functionally important proteins characterized by a lack of fixed, ordered three-dimensional structure. IDPs and intrinsically disordered protein regions (IDPRs) play numerous vital roles in various cellular processes, such as signaling, cell cycle regulation, macromolecular recognition, and promiscuous binding. However, the deregulation and misfolding of IDPs may lead to disturbed signaling, interactions, and disease pathogenesis. Often, molecular recognition-related IDPs/IDPRs undergo disorder-to-order transition upon binding to their biological partners and contain specific disorder-based binding motifs, known as molecular recognition features (MoRFs). Knowing the intrinsic disorder status and disorder-based functionality of proteins associated with amyloid cascade signaling pathway may help to untangle the mechanisms of AD pathogenesis and help identify therapeutic targets. In this paper, we have used multiple computational tools to evaluate the presence of intrinsic disorder and MoRFs in 27 proteins potentially relevant to the amyloid cascade signaling pathway. Among these, BIN1, APP, APOE, PICALM, PSEN1 and CD33 were found to be highly disordered. Furthermore, their disorder-based binding regions and associated short linear motifs have also been identified. These findings represent important foundation for the future research, and experimental characterization of disordered regions in these proteins is required to better understand their roles in AD pathogenesis.
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Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | | | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India.
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35
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Van Bibber NW, Haerle C, Khalife R, Dayhoff GW, Uversky VN. Intrinsic Disorder in Human Proteins Encoded by Core Duplicon Gene Families. J Phys Chem B 2020; 124:8050-8070. [PMID: 32880174 DOI: 10.1021/acs.jpcb.0c07676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Segmental duplications (i.e., highly homologous DNA fragments greater than 1 kb in length that are present within a genome at more than one site) are typically found in genome regions that are prone to rearrangements. A noticeable fraction of the human genome (∼5%) includes segmental duplications (or duplicons) that are assumed to play a number of vital roles in human evolution, human-specific adaptation, and genomic instability. Despite their importance for crucial events such as synaptogenesis, neuronal migration, and neocortical expansion, these segmental duplications continue to be rather poorly characterized. Of particular interest are the core duplicon gene (CDG) families, which are replicates sharing common "core" DNA among the randomly attached pieces and which expand along single chromosomes and might harbor newly acquired protein domains. Another important feature of proteins encoded by CDG families is their multifunctionality. Although it seems that these proteins might possess many characteristic features of intrinsically disordered proteins, to the best of our knowledge, a systematic investigation of the intrinsic disorder predisposition of the proteins encoded by core duplicon gene families has not been conducted yet. To fill this gap and to determine the degree to which these proteins might be affected by intrinsic disorder, we analyzed a set of human proteins encoded by the members of 10 core duplicon gene families, such as NBPF, RGPD, GUSBP, PMS2P, SPATA31, TRIM51, GOLGA8, NPIP, TBC1D3, and LRRC37. Our analysis revealed that the vast majority of these proteins are highly disordered, with their disordered regions often being utilized as means for the protein-protein interactions and/or targeted for numerous posttranslational modifications of different nature.
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Affiliation(s)
- Nathan W Van Bibber
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Cornelia Haerle
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Roy Khalife
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 4 Institutskaya St., Pushchino, 142290, Moscow Region, Russia
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36
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Bhopatkar AA, Uversky VN, Rangachari V. Disorder and cysteines in proteins: A design for orchestration of conformational see-saw and modulatory functions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:331-373. [PMID: 32828470 DOI: 10.1016/bs.pmbts.2020.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Being responsible for more than 90% of cellular functions, protein molecules are workhorses in all the life forms. In order to cater for such a high demand, proteins have evolved to adopt diverse structures that allow them to perform myriad of functions. Beginning with the genetically directed amino acid sequence, the classical understanding of protein function involves adoption of hierarchically complex yet ordered structures. However, advances made over the last two decades have revealed that inasmuch as 50% of eukaryotic proteome exists as partially or fully disordered structures. Significance of such intrinsically disordered proteins (IDPs) is further realized from their ability to exhibit multifunctionality, a feature attributable to their conformational plasticity. Among the coded amino acids, cysteines are considered to be "order-promoting" due to their ability to form inter- or intramolecular disulfide bonds, which confer robust thermal stability to the protein structure in oxidizing conditions. The co-existence of order-promoting cysteines with disorder-promoting sequences seems counter-intuitive yet many proteins have evolved to contain such sequences. In this chapter, we review some of the known cysteine-containing protein domains categorized based on the number of cysteines they possess. We show that many protein domains contain disordered sequences interspersed with cysteines. We show that a positive correlation exists between the degree of cysteines and disorder within the sequences that flank them. Furthermore, based on the computational platform, IUPred2A, we show that cysteine-rich sequences display significant disorder in the reduced but not the oxidized form, increasing the potential for such sequences to function in a redox-sensitive manner. Overall, this chapter provides insights into an exquisite evolutionary design wherein disordered sequences with interspersed cysteines enable potential modulatory protein functions under stress and environmental conditions, which thus far remained largely inconspicuous.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, United States; Center of Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, United States.
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37
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Intrinsic Disorder in Tetratricopeptide Repeat Proteins. Int J Mol Sci 2020; 21:ijms21103709. [PMID: 32466138 PMCID: PMC7279152 DOI: 10.3390/ijms21103709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
Among the realm of repeat containing proteins that commonly serve as “scaffolds” promoting protein-protein interactions, there is a family of proteins containing between 2 and 20 tetratricopeptide repeats (TPRs), which are functional motifs consisting of 34 amino acids. The most distinguishing feature of TPR domains is their ability to stack continuously one upon the other, with these stacked repeats being able to affect interaction with binding partners either sequentially or in combination. It is known that many repeat-containing proteins are characterized by high levels of intrinsic disorder, and that many protein tandem repeats can be intrinsically disordered. Furthermore, it seems that TPR-containing proteins share many characteristics with hybrid proteins containing ordered domains and intrinsically disordered protein regions. However, there has not been a systematic analysis of the intrinsic disorder status of TPR proteins. To fill this gap, we analyzed 166 human TPR proteins to determine the degree to which proteins containing TPR motifs are affected by intrinsic disorder. Our analysis revealed that these proteins are characterized by different levels of intrinsic disorder and contain functional disordered regions that are utilized for protein-protein interactions and often serve as targets of various posttranslational modifications.
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Badierah RA, Uversky VN, Redwan EM. Dancing with Trojan horses: an interplay between the extracellular vesicles and viruses. J Biomol Struct Dyn 2020; 39:3034-3060. [DOI: 10.1080/07391102.2020.1756409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Raied A. Badierah
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center ‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’, Pushchino, Moscow Region, Russia
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Hutchings CJ. A review of antibody-based therapeutics targeting G protein-coupled receptors: an update. Expert Opin Biol Ther 2020; 20:925-935. [PMID: 32264722 DOI: 10.1080/14712598.2020.1745770] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION G protein-coupled receptors (GPCRs) play key roles in many biological functions and are linked to many diseases across all therapeutic areas. As such, GPCRs represent a significant opportunity for antibody-based therapeutics. AREAS COVERED The structure of the major GPCR families is summarized in the context of choice of antigen source employed in the drug discovery process and receptor biology considerations which may impact on targeting strategies. An overview of the therapeutic GPCR-antibody target landscape and the diversity of current therapeutic programs is provided along with summary case studies for marketed antibody drugs or those in advanced clinical studies. Antibodies in early clinical studies and the emergence of next-generation modalities are also highlighted. EXPERT OPINION The GPCR-antibody pipeline has progressed significantly with a number of technical developments enabling the successful resolution of some of the challenges previously encountered and this has contributed to the growing interest in antibody-based therapeutics addressing this target class.
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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Gurevich VV. Protein multi-functionality: introduction. Cell Mol Life Sci 2019; 76:4405-4406. [PMID: 31422443 PMCID: PMC11105568 DOI: 10.1007/s00018-019-03271-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 11/28/2022]
Abstract
The five articles in this multi-author review in CMLS provide examples of multi-functionality of proteins belonging to several families. Distinct structural features of proteins suggesting multi-functionality are emphasized: intrinsically disordered elements that can "mold" themselves to fit various binding partners, as well as short linear motifs within larger proteins that perform particular functions. Although only a few protein families are discussed in detail, the conclusions apply to numerous, if not all, proteins. Multi-functionality of virtually every protein implies that the manipulation of its expression levels by over-expression, knockdown, or knockout affects every one of its functions, known and unknown, so that the results of these experiments must be interpreted with this complexity in mind. Particular functions in a multi-functional protein are often fulfilled by identifiable smaller elements that can be expressed separately. Identification of mono-functional elements of a multi-functional protein paves the way to the construction of novel precisely targeted molecular tools for selective manipulation of cellular signaling that can be used for mechanistic studies in cell biology, as well as for therapeutic purposes.
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El Hadidy N, Uversky VN. Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development. Int J Mol Sci 2019; 20:ijms20215260. [PMID: 31652801 PMCID: PMC6862534 DOI: 10.3390/ijms20215260] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
The two-meter-long DNA is compressed into chromatin in the nucleus of every cell, which serves as a significant barrier to transcription. Therefore, for processes such as replication and transcription to occur, the highly compacted chromatin must be relaxed, and the processes required for chromatin reorganization for the aim of replication or transcription are controlled by ATP-dependent nucleosome remodelers. One of the most highly studied remodelers of this kind is the BRG1- or BRM-associated factor complex (BAF complex, also known as SWItch/sucrose non-fermentable (SWI/SNF) complex), which is crucial for the regulation of gene expression and differentiation in eukaryotes. Chromatin remodeling complex BAF is characterized by a highly polymorphic structure, containing from four to 17 subunits encoded by 29 genes. The aim of this paper is to provide an overview of the role of BAF complex in chromatin remodeling and also to use literature mining and a set of computational and bioinformatics tools to analyze structural properties, intrinsic disorder predisposition, and functionalities of its subunits, along with the description of the relations of different BAF complex subunits to the pathogenesis of various human diseases.
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Affiliation(s)
- Nashwa El Hadidy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290 Moscow Region, Russia.
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Wang P, Zhang L, Li H, Wang Y, Zhang S, Liu Z. Characterization of GRP as a functional neuropeptide in basal chordate amphioxus. Int J Biol Macromol 2019; 142:384-394. [PMID: 31593737 DOI: 10.1016/j.ijbiomac.2019.09.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 01/14/2023]
Abstract
Amphioxus belongs to the subphylum cephalochordata, an extant representative of the most basal chordates, whose regulation of endocrine system remains ambiguous. Here we clearly demonstrated the existence of a functional GRP neuropeptide in amphioxus, which was able to interact with GRP receptor, activate both PKC and PKA pathways, increase gh, igf, and vegf expression. We also showed that the transcription level of amphioxus grp was affected by temperature and light, indicating the role of this gene in the regulation of energy balance and circadian rhythms. In addition, the expression of the amphioxus grp was detected in cerebral vesicle that has been proposed to be the homologous organ of vertebrate brain. These data collectively suggested that a functional GRP neuropeptide had already emerged in amphioxus, which provided insights into the evolutionary origin of GRP in chordate and the functional homology between the cerebral vesicle and vertebrate brain.
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Affiliation(s)
- Peng Wang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Liping Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Haoyi Li
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Yunsheng Wang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Zhenhui Liu
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China.
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