1
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Reyes-Serratos E, Ramielle L. Santos J, Puttagunta L, Lewis SJ, Watanabe M, Gonshor A, Buck R, Befus AD, Marcet-Palacios M. Identification and characterization of calcium binding protein, spermatid-associated 1 (CABS1)# in selected human tissues and fluids. PLoS One 2024; 19:e0301855. [PMID: 38753592 PMCID: PMC11098423 DOI: 10.1371/journal.pone.0301855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/22/2024] [Indexed: 05/18/2024] Open
Abstract
Calcium binding protein, spermatid associated 1 (CABS1) is a protein most widely studied in spermatogenesis. However, mRNA for CABS1 has been found in numerous tissues, albeit with little information about the protein. Previously, we identified CABS1 mRNA and protein in human salivary glands and provided evidence that in humans CABS1 contains a heptapeptide near its carboxyl terminus that has anti-inflammatory activities. Moreover, levels of an immunoreactive form of CABS1 were elevated in psychological stress. To more fully characterize human CABS1 we developed additional polyclonal and monoclonal antibodies to different sections of the protein and used these antibodies to characterize CABS1 in an overexpression cell lysate, human salivary glands, saliva, serum and testes using western blot, immunohistochemistry and bioinformatics approaches exploiting the Gene Expression Omnibus (GEO) database. CABS1 appears to have multiple molecular weight forms, consistent with its recognition as a structurally disordered protein, a protein with structural plasticity. Interestingly, in human testes, its cellular distribution differs from that in rodents and pigs, and includes Leydig cells, primary spermatogonia, Sertoli cells and developing spermatocytes and spermatids, Geodata suggests that CABS1 is much more widely distributed than previously recognized, including in the urogenital, gastrointestinal and respiratory tracts, as well as in the nervous system, immune system and other tissues. Much remains to be learned about this intriguing protein.
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Affiliation(s)
- Eduardo Reyes-Serratos
- Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Joy Ramielle L. Santos
- Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Lakshmi Puttagunta
- Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen J. Lewis
- Departments of Pediatrics and Pharmacology, Rainbow Babies and Children’s Hospital, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
| | - Mechiko Watanabe
- Departments of Pediatrics and Pharmacology, Rainbow Babies and Children’s Hospital, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
- Division of Pediatric Cardiology, Department of Pediatrics, Rainbow Babies and Children’s Hospital, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
| | | | - Robert Buck
- GB Diagnostics, Montreal, Quebec, Canada
- GB Diagnostics, Albuquerque, New Mexico, United States of America
| | - A. Dean Befus
- Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Marcelo Marcet-Palacios
- Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Northern Alberta Institute of Technology, Edmonton, Alberta, Canada
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2
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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: 14] [Impact Index Per Article: 7.0] [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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3
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Gao M, Li P, Su Z, Huang Y. Topological frustration leading to backtracking in a coupled folding-binding process. Phys Chem Chem Phys 2022; 24:2630-2637. [PMID: 35029261 DOI: 10.1039/d1cp04927e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in all species. Their discovery challenges the traditional "sequence-structure-function" paradigm of protein science because IDPs play important roles in various biological processes without preformed folded structures. Bioinformatic analysis reveals that the intrinsically conformational disorder of IDPs as well as their conformational transition upon binding to their targets is encoded by their amino acid sequences. The rRNase domain of colicin E3 and the immunity protein Im3 are a pair of proteins involved in bacterial survival. While the N-terminal segment and the central segment of E3 make comparable intermolecular contacts with Im3 in the bound state, binding of E3 with Im3 is dominantly triggered by the central segment of E3. In this work, to further investigate the binding mechanism of disordered E3 with Im3, we performed systematic free energy and transition path analysis through coarse-grained molecular dynamics simulations. We observed backtracking of the N-terminal segment of E3 in the binding process, whose occurrence depends on salt concentration. Conformational analysis revealed that initial binding of the N-terminal segment of E3 to Im3 usually leads to misorientation of a central hairpin of E3 on Im3, which generates topological frustration and results in backtracking of the N-terminal segment. Our results not only provide deeper mechanistic insights into the coupled folding-binding process of the E3/Im3 complex, but also suggest that topological frustration could be present in the coupled folding-binding process of IDPs and play an important role in regulating the binding transition pathways.
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Affiliation(s)
- Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Ping Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
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4
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Marcet-Palacios M, Reyes-Serratos E, Gonshor A, Buck R, Lacy P, Befus AD. Structural and posttranslational analysis of human calcium-binding protein, spermatid-associated 1. J Cell Biochem 2020; 121:4945-4958. [PMID: 32692864 DOI: 10.1002/jcb.29824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 06/23/2020] [Indexed: 12/31/2022]
Abstract
Recently, we detected a novel biomarker in human saliva called calcium-binding protein, spermatid-associated 1 (CABS1). CABS1 protein had previously been described only in testis, and little was known of its characteristics other than it was considered a structurally disordered protein. Levels of human CABS1 (hCABS1) in saliva correlate with stress, whereas smaller sized forms of hCABS1 in saliva are associated with resilience to stress. Interestingly, hCABS1 also has an anti-inflammatory peptide sequence near its carboxyl terminus, similar to that of a rat prohormone, submandibular rat 1. We performed phylogenetic and sequence analysis of hCABS1. We found that from 72 CABS1 sequences currently annotated in the National Center for Biotechnology Information protein database, only 14 contain the anti-inflammatory domain "TxIFELL," all of which are primates. We performed structural unfoldability analysis using PONDER and FoldIndex and discovered three domains that are highly disordered. Predictions of three-dimensional structure of hCABS1 using RaptorX, IonCom, and I-TASSER software agreed with these findings. Predicted neutrophil elastase cleavage density also correlated with hCABS1 regions of high structural disorder. Ligand binding prediction identified Ca2+ , Mg2+ , Zn2+ , leucine, and thiamine pyrophosphate, a pattern observed in enzymes associated with energy metabolism and mitochondrial localization. These new observations on hCABS1 raise intriguing questions about the interconnection between the autonomic nervous system, stress, and the immune system. However, the precise molecular mechanisms involved in the complex biology of hCABS1 remain unclear. We provide a detailed in silico analysis of relevant aspects of the structure and function of hCABS1 and postulate extracellular and intracellular roles.
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Affiliation(s)
- Marcelo Marcet-Palacios
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Northern Alberta Institute of Technology, Biological Sciences, Edmonton, Alberta, Canada
| | - Eduardo Reyes-Serratos
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
| | | | - Robert Buck
- Fluids iQ Inc., Ottawa, Ontario, Canada
- GB Diagnostics, Kingman, Arizona
| | - Paige Lacy
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
| | - A D Befus
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
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5
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Rajab IM, Hart PC, Potempa LA. How C-Reactive Protein Structural Isoforms With Distinctive Bioactivities Affect Disease Progression. Front Immunol 2020; 11:2126. [PMID: 33013897 PMCID: PMC7511658 DOI: 10.3389/fimmu.2020.02126] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
C-reactive protein (CRP) is a widely known, hepatically synthesized protein whose blood levels change rapidly and pronouncedly in response to any tissue damaging event associated with an inflammatory response. The synthesis and secretion of CRP is stimulated by interleukin-6, an early pleiotropic cytokine released by macrophages, endothelial, and other cells that are activated when localized normal tissue structures are compromised by trauma or disease. Serum CRP levels can change rapidly and robustly from 10-100-fold within 6–72 h of any tissue damaging event. Elevated blood levels correlate with the onset and extent of both activated inflammation and the acute phase biochemical response to the tissue insult. Because its functional bioactivity as the prototypic acute phase reactant has eluded clear definition for decades, diagnosticians of various conditions and diseases use CRP blood levels as a simple index for ongoing inflammation. In many pathologies, which involves many different tissues, stages of disease, treatments, and responses to treatments, its interpretive diagnostic value requires a deeper understanding of the localized tissue processes and events that contribute signals which regulate protective or pathological host defense bioactivities. This report presents concepts that describe how local tissue activation events can lead to a non-proteolytic, conformational rearrangement of CRP into a unique isoform with distinctive solubility, antigenicity, binding reactivities and bioactivities from that protein widely known and measured in serum. By describing factors that control the expression, tissue localization, half-life and pro-inflammatory amplification activity of this CRP isoform, a unifying explanation for the diagnostic significance of CRP measurement in disease is advanced.
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Affiliation(s)
- Ibraheem M Rajab
- Roosevelt University College of Pharmacy, Schaumburg, IL, United States
| | - Peter C Hart
- Roosevelt University College of Pharmacy, Schaumburg, IL, United States
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6
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Yang J, Zeng Y, Liu Y, Gao M, Liu S, Su Z, Huang Y. Electrostatic interactions in molecular recognition of intrinsically disordered proteins. J Biomol Struct Dyn 2019; 38:4883-4894. [DOI: 10.1080/07391102.2019.1692073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jing Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yifan Zeng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yunfei Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
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7
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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8
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Olins DE, Olins AL. Epichromatin and chromomeres: a 'fuzzy' perspective. Open Biol 2019; 8:rsob.180058. [PMID: 29875200 PMCID: PMC6030114 DOI: 10.1098/rsob.180058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Abstract
'Epichromatin', the surface of chromatin beneath the interphase nuclear envelope (NE) or at the surface of mitotic chromosomes, was discovered by immunostaining with a specific bivalent mouse monoclonal anti-nucleosome antibody (mAb PL2-6). 'Chromomeres', punctate chromatin particles approximately 200-300 nm in diameter, identified throughout the interphase chromatin and along mitotic chromosomes, were observed by immunostaining with the monovalent papain-derived Fab fragments of bivalent PL2-6. The specific target for PL2-6 appears to include the nucleosome acidic patch. Thus, within the epichromatin and chromomeric regions, this epitope is 'exposed'. Considering that histones possess unstructured 'tails' (i.e. intrinsically disordered peptide regions, IDPR), our perception of these chromatin regions becomes more 'fuzzy' (less defined). We suggest that epichromatin cationic tails facilitate interactions with anionic components of NE membranes. We also suggest that the unstructured histone tails (especially, histone H1 tails), with their presumed promiscuous binding, establish multivalent binding that stabilizes each chromomere as a unit of chromatin higher order structure. We propose an 'unstructured stability' hypothesis, which postulates that the stability of epichromatin and chromomeres (as well as other nuclear chromatin structures) is a consequence of the collective contributions of numerous weak histone IDPR binding interactions arising from the multivalent nucleosome, analogous to antibody avidity.
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Affiliation(s)
- Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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9
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Abstract
The past few years have resulted in an increased awareness and recognition of the prevalence and roles of intrinsically disordered proteins and protein regions (IDPs and IDRs, respectively) in synaptic vesicle trafficking and exocytosis and in overall synaptic organization. IDPs and IDRs constitute a class of proteins and protein regions that lack stable tertiary structure, but nevertheless retain biological function. Their significance in processes such as cell signaling is now well accepted, but their pervasiveness and importance in other areas of biology are not as widely appreciated. Here, we review the prevalence and functional roles of IDPs and IDRs associated with the release and recycling of synaptic vesicles at nerve terminals, as well as with the architecture of these terminals. We hope to promote awareness, especially among neuroscientists, of the importance of this class of proteins in these critical pathways and structures. The examples discussed illustrate some of the ways in which the structural flexibility conferred by intrinsic protein disorder can be functionally advantageous in the context of cellular trafficking and synaptic function.
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Affiliation(s)
- David Snead
- From the Department of Biochemistry, Weill Cornell Medicine, New York, New York 10021
| | - David Eliezer
- From the Department of Biochemistry, Weill Cornell Medicine, New York, New York 10021
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10
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The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease. Biochem Soc Trans 2017; 44:1185-1200. [PMID: 27911701 PMCID: PMC5095923 DOI: 10.1042/bst20160172] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
Abstract
In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence–structure–function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function. I will then discuss molecular principles by which regulatory mechanisms, such as alternative splicing and asymmetric localization of transcripts that encode disordered regions, can increase the functional versatility of proteins. Finally, I will discuss how disordered regions contribute to human disease and the emergence of cellular complexity during organismal evolution.
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11
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Olsen JG, Teilum K, Kragelund BB. Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness. Cell Mol Life Sci 2017; 74:3175-3183. [PMID: 28597296 PMCID: PMC5533869 DOI: 10.1007/s00018-017-2560-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not, by themselves, fold into a compact globular structure. They are extremely dynamic and flexible, and are typically involved in signalling and transduction of information through binding to other macromolecules. The reason for their existence may lie in their malleability, which enables them to bind several different partners with high specificity. In addition, their interactions with other macromolecules can be regulated by a variable amount of chemically diverse post-translational modifications. Four kinetically and energetically different types of complexes between an IDP and another macromolecule are reviewed: (1) simple two-state binding involving a single binding site, (2) avidity, (3) allovalency and (4) fuzzy binding; the last three involving more than one site. Finally, a qualitative definition of fuzzy binding is suggested, examples are provided, and its distinction to allovalency and avidity is highlighted and discussed.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
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12
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Singh S, Bowman GR. Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS. J Chem Theory Comput 2017; 13:1509-1517. [PMID: 28282132 PMCID: PMC5934993 DOI: 10.1021/acs.jctc.6b01181] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric (i.e., long-range) communication within proteins is crucial for many biological processes, such as the activation of signaling cascades in response to specific stimuli. However, the physical basis for this communication remains unclear. Existing computational methods for identifying allostery focus on the role of concerted structural changes, but recent experimental work demonstrates that disorder is also an important factor. Here, we introduce the Correlation of All Rotameric and Dynamical States (CARDS) framework for quantifying correlations between both the structure and disorder of different regions of a protein. To quantify disorder, we draw inspiration from methods for quantifying "dynamic heterogeneity" from chemical physics to classify segments of a dihedral's time evolution as being in either ordered or disordered regimes. To demonstrate the utility of this approach, we apply CARDS to the Catabolite Activator Protein (CAP), a transcriptional activator that is regulated by Cyclic Adenosine MonoPhosphate (cAMP) binding. We find that CARDS captures allosteric communication between the two cAMP-Binding Domains (CBDs). Importantly, CARDS reveals that this coupling is dominated by disorder-mediated correlations, consistent with NMR experiments that establish allosteric coupling between the CBDs occurs without a concerted structural change. CARDS also recapitulates an enhanced role for disorder in the communication between the DNA-Binding Domains (DBDs) and CBDs in the S62F variant of CAP. Finally, we demonstrate that using CARDS to find communication hotspots identifies regions of CAP that are in allosteric communication without foreknowledge of their identities. Therefore, we expect CARDS to be of great utility for both understanding and predicting allostery.
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Affiliation(s)
- Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO
- Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO
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Banerjee R. Introduction to the Thematic Minireview Series on Intrinsically Disordered Proteins. J Biol Chem 2016; 291:6679-80. [PMID: 26851284 DOI: 10.1074/jbc.r116.719930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this thematic minireview series, the JBC presents six exciting articles on low complexity or intrinsically disordered proteins (IDPs). The dynamical and fluctuating structures of IDPs or of disordered regions within proteins result in virtually all of their primary sequence being exposed, at least at some time, to potential interacting partners. Their structural versatility underlies their often wide functional repertoires, which is further expanded by post-translational modifications. Given these characteristics, it is not surprising that IDPs serve as important hubs in signaling networks, scaffolding multivalent interactions. They are also important for organizing membrane-less protein organelles. This collection of reviews discusses biophysical approaches for studying IDPs and illuminates their importance to critical functions such as cell cycle control, transcription, and translation, as well as their regulation via cellular input signals.
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Affiliation(s)
- Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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Hiramatsu A, Kobayashi N, Osawa N. Properties of Two Inhibitors of Plant Virus Infection from Fruiting Bodies of Lentinus edodes and from Leaves of Yucca recurvifolia Salisb. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/00021369.1987.10868096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Akira Hiramatsu
- Laboratory of Agricultural Chemicals, Faculty of Agriculture, Ibaraki University, Ami-machi, Inashiki-gun, Ibaraki 300–03, Japan
| | - Norifumi Kobayashi
- Laboratory of Agricultural Chemicals, Faculty of Agriculture, Ibaraki University, Ami-machi, Inashiki-gun, Ibaraki 300–03, Japan
| | - Naofumi Osawa
- Laboratory of Agricultural Chemicals, Faculty of Agriculture, Ibaraki University, Ami-machi, Inashiki-gun, Ibaraki 300–03, Japan
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