1
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Malone M, Maeyama A, Ogden N, Perry KN, Kramer A, Bates C, Marble C, Orlando R, Rausch A, Smeraldi C, Lowey C, Fees B, Dyson HJ, Dorrell M, Kast-Woelbern H, Jansma AL. The effect of phosphorylation efficiency on the oncogenic properties of the protein E7 from high-risk HPV. Virus Res 2024; 348:199446. [PMID: 39127239 DOI: 10.1016/j.virusres.2024.199446] [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: 06/12/2024] [Revised: 07/27/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
The Human papillomavirus (HPV) causes tumors in part by hijacking the host cell cycle and forcing uncontrolled cellular division. While there are >200 genotypes of HPV, 15 are classified as high-risk and have been shown to transform infected cells and contribute to tumor formation. The remaining low-risk genotypes are not considered oncogenic and result in benign skin lesions. In high-risk HPV, the oncoprotein E7 contributes to the dysregulation of cell cycle regulatory mechanisms. High-risk E7 is phosphorylated in cells at two conserved serine residues by Casein Kinase 2 (CK2) and this phosphorylation event increases binding affinity for cellular proteins such as the tumor suppressor retinoblastoma (pRb). While low-risk E7 possesses similar serine residues, it is phosphorylated to a lesser degree in cells and has decreased binding capabilities. When E7 binding affinity is decreased, it is less able to facilitate complex interactions between proteins and therefore has less capability to dysregulate the cell cycle. By comparing E7 protein sequences from both low- and high-risk HPV variants and using site-directed mutagenesis combined with NMR spectroscopy and cell-based assays, we demonstrate that the presence of two key nonpolar valine residues within the CK2 recognition sequence, present in low-risk E7, reduces serine phosphorylation efficiency relative to high-risk E7. This results in significant loss of the ability of E7 to degrade the retinoblastoma tumor suppressor protein, thus also reducing the ability of E7 to increase cellular proliferation and reduce senescence. This provides additional insight into the differential E7-mediated outcomes when cells are infected with high-risk verses low-risk HPV. Understanding these oncogenic differences may be important to developing targeted treatment options for HPV-induced cancers.
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Affiliation(s)
- Madison Malone
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Ava Maeyama
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Naomi Ogden
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Kayla N Perry
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Andrew Kramer
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Caleb Bates
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Camryn Marble
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Ryan Orlando
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Amy Rausch
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Caleb Smeraldi
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Connor Lowey
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Bronson Fees
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA
| | - Michael Dorrell
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA
| | - Heidi Kast-Woelbern
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA.
| | - Ariane L Jansma
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, 92126, CA, USA.
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2
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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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3
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Dyson HJ. Vital for Viruses: Intrinsically Disordered Proteins. J Mol Biol 2023; 435:167860. [PMID: 37330280 PMCID: PMC10656058 DOI: 10.1016/j.jmb.2022.167860] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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4
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Bhardwaj T, Kumar P, Giri R. Investigating the conformational dynamics of Zika virus NS4B protein. Virology 2022; 575:20-35. [PMID: 36037701 DOI: 10.1016/j.virol.2022.08.005] [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: 12/15/2021] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Zika virus (ZIKV) NS4B protein is a membranotropic multifunctional protein. Despite its versatile functioning, its topology and dynamics are not entirely understood. There is no X-ray or cryo-EM structure available for any flaviviral NS4B full-length protein. In this study, we have investigated the structural dynamics of full-length ZIKV NS4B protein through 3D structure models using molecular dynamics simulations and experimental techniques. Also, we employed a reductionist approach to understand the dynamics of NS4B protein where we studied its N-terminal (residues 1-38), C-terminal (residues 194-251), and cytosolic (residues 131-169) regions in isolation in addition to the full-length protein. Further, using a series of circular dichroism spectroscopic experiments, we validate the cytosolic region as an intrinsically disordered protein region. The microsecond-long all atoms molecular dynamics and replica-exchange simulations complement the experimental observations. Furthermore, we have also studied the NS4B proteins C-terminal regions of four other flaviviruses viz. DENV2, JEV, WNV, and YFV through microsecond simulations to characterize their behaviour in presence and absence of lipid membranes. There are significant differences observed in the conformations of other flavivirus NS4B C-terminal regions in comparison to ZIKV NS4B. Lastly, we have proposed a ZIKV NS4B protein model illustrating its putative topology consisting of various membrane-spanning and non-membranous regions.
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Affiliation(s)
- Taniya Bhardwaj
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India.
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5
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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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6
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2. Biomolecules 2022; 12:631. [PMID: 35625559 PMCID: PMC9139003 DOI: 10.3390/biom12050631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%-lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer shell) among all CoVs. This is likely to be responsible for the higher contagiousness of SARS-CoV-2 and Omicron, since hard outer shell protects the virion from salivary/mucosal antimicrobial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan-Hu-1 strain closely related to pangolin-CoVs. M, being evolutionarily conserved in COVID-19, is most ideal for COVID-19 phylogenetic study. Omicron may have been hiding among burrowing animals (e.g., pangolins) that provide optimal evolutionary environments for attenuation and increase shell hardness, which is essential for fecal-oral-respiratory transmission via buried feces. Incoming data support SDM e.g., the presence of fewer infectious particles in the lungs than in the bronchi upon infection.
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Affiliation(s)
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia
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Prediction of Intrinsically Disordered Proteins Using Machine Learning Based on Low Complexity Methods. ALGORITHMS 2022. [DOI: 10.3390/a15030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Prediction of intrinsic disordered proteins is a hot area in the field of bio-information. Due to the high cost of evaluating the disordered regions of protein sequences using experimental methods, we used a low-complexity prediction scheme. Sequence complexity is used in this scheme to calculate five features for each residue of the protein sequence, including the Shannon entropy, the Topo-logical entropy, the Permutation entropy and the weighted average values of two propensities. Particularly, this is the first time that permutation entropy has been applied to the field of protein sequencing. In addition, in the data preprocessing stage, an appropriately sized sliding window and a comprehensive oversampling scheme can be used to improve the prediction performance of our scheme, and two ensemble learning algorithms are also used to verify the prediction results before and after. The results show that adding permutation entropy improves the performance of the prediction algorithm, in which the MCC value can be improved from the original 0.465 to 0.526 in our scheme, proving its universality. Finally, we compare the simulation results of our scheme with those of some existing schemes to demonstrate its effectiveness.
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8
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Shamilov R, Robinson VL, Aneskievich BJ. Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder. Int J Mol Sci 2021; 22:ijms22157912. [PMID: 34360678 PMCID: PMC8348711 DOI: 10.3390/ijms22157912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Epidermal keratinocyte proteins include many with an eccentric amino acid content (compositional bias), atypical ultrastructural fate (built-in protease sensitivity), or assembly visible at the light microscope level (cytoplasmic granules). However, when considered through the looking glass of intrinsic disorder (ID), these apparent oddities seem quite expected. Keratinocyte proteins with highly repetitive motifs are of low complexity but high adaptation, providing polymers (e.g., profilaggrin) for proteolysis into bioactive derivatives, or monomers (e.g., loricrin) repeatedly cross-linked to self and other proteins to shield underlying tissue. Keratohyalin granules developing from liquid–liquid phase separation (LLPS) show that unique biomolecular condensates (BMC) and proteinaceous membraneless organelles (PMLO) occur in these highly customized cells. We conducted bioinformatic and in silico assessments of representative keratinocyte differentiation-dependent proteins. This was conducted in the context of them having demonstrated potential ID with the prospect of that characteristic driving formation of distinctive keratinocyte structures. Intriguingly, while ID is characteristic of many of these proteins, it does not appear to guarantee LLPS, nor is it required for incorporation into certain keratinocyte protein condensates. Further examination of keratinocyte-specific proteins will provide variations in the theme of PMLO, possibly recognizing new BMC for advancements in understanding intrinsically disordered proteins as reflected by keratinocyte biology.
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Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA;
| | - Victoria L. Robinson
- Department of Molecular and Cellular Biology, College of Liberal Arts & Sciences, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA;
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
- Correspondence: ; Tel.: +1-860-486-3053
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9
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Aarthy M, Singh SK. Interpretations on the Interaction between Protein Tyrosine Phosphatase and E7 Oncoproteins of High and Low-Risk HPV: A Computational Perception. ACS OMEGA 2021; 6:16472-16487. [PMID: 34235319 PMCID: PMC8246469 DOI: 10.1021/acsomega.1c01619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/08/2021] [Indexed: 05/17/2023]
Abstract
The most prevalent and common sexually transmitted infection is caused by human papillomavirus (HPV) among sexually active women. Numerous genotypes of HPV are available, among which the major oncoproteins E6 and E7 lead to the progression of cervical cancer. The E7 oncoprotein interacts with cytoplasmic tumor suppressor protein PTPN14, which is the key regulator of cellular growth control pathways effecting the reduction of steady-state level. Disrupting the interaction between the tumor suppressor and the oncoprotein is vital to cease the development of cancer. Hence, the mechanism of interaction between E7 and tumor suppressor is explored through protein-protein and protein-ligand binding along with the conformational stability studies. The obtained results state that the LXCXE domain of HPV E7 of high and low risks binds with the tumor suppressor protein. Also, the small molecules bind in the interface of E7-PTPN14 that disrupts the interaction between the tumor suppressor and oncoprotein. These results were further supported by the dynamics simulation stating the stability over the bounded complex and the energy maintained during postdocking as well as postdynamics calculations. These observations possess an avenue in the drug discovery that leads to further validation and also proposes a potent drug candidate to treat cervical cancer caused by HPV.
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10
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Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins. J Proteome Res 2021; 20:2704-2713. [PMID: 33719450 DOI: 10.1021/acs.jproteome.1c00011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Much of our understanding of proteins and proteomes comes from the traditional protein structure-function paradigm. However, in the last 2 decades, both computational and experimental studies have provided evidence that a large fraction of functional proteomes across different domains of life consists of intrinsically disordered proteins, thus triggering a quest to unravel and decipher protein intrinsic disorder. Unlike structured/ordered proteins, intrinsically disordered proteins/regions (IDPs/IDRs) do not possess a well-defined structure under physiological conditions and exist as highly dynamic conformational ensembles. In spite of this peculiarity, these proteins have crucial roles in cell signaling and regulation. To date, studies on the abundance and function of IDPs/IDRs in viruses are rather limited. To fill this gap, we carried out an extensive and thorough bioinformatics analysis of 283 000 proteins from 6108 reference viral proteomes. We analyzed protein intrinsic disorder from multiple perspectives, such as abundance of IDPs/IDRs across diverse virus types, their functional annotations, and subcellular localization in taxonomically divergent hosts. We show that the content of IDPs/IDRs in viral proteomes varies broadly as a function of virus genome types and taxonomically divergent hosts. We have combined the two most commonly used and accurate IDP predictors' results with charge-hydropathy (CH) versus cumulative distribution function (CDF) plots to categorize the viral proteins according to their IDR content and physicochemical properties. Mapping of gene ontology on the disorder content of viral proteins reveals that IDPs are primarily involved in key virus-host interactions and host antiviral immune response downregulation, which are reinforced by the post-translational modifications tied to disorder-enriched viral proteins. The present study offers detailed insights into the prevalence of the intrinsic disorder in viral proteomes and provides appealing targets for the design of novel therapeutics.
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Affiliation(s)
- Naveen Kumar
- Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.,Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Aix Marseille Université, CNRS, 13288 Marseille, France
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sandeep Bhatia
- Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
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Hosoya Y, Ohkanda J. Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. Molecules 2021; 26:2118. [PMID: 33917117 PMCID: PMC8067799 DOI: 10.3390/molecules26082118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid-liquid phase separations-which critically involve both intermolecular interactions between IDPs and their posttranslational modification-are analyzed to understand the potential of IDPs as new drug targets.
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Affiliation(s)
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano 399-4598, Japan;
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12
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Shrestha UR, Smith JC, Petridis L. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations. Commun Biol 2021; 4:243. [PMID: 33623120 PMCID: PMC7902620 DOI: 10.1038/s42003-021-01759-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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Affiliation(s)
- Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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13
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Alshehri MA, Manee MM, Alqahtani FH, Al-Shomrani BM, Uversky VN. On the Prevalence and Potential Functionality of an Intrinsic Disorder in the MERS-CoV Proteome. Viruses 2021; 13:v13020339. [PMID: 33671602 PMCID: PMC7926987 DOI: 10.3390/v13020339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/14/2022] Open
Abstract
Middle East respiratory syndrome is a severe respiratory illness caused by an infectious coronavirus. This virus is associated with a high mortality rate, but there is as of yet no effective vaccine or antibody available for human immunity/treatment. Drug design relies on understanding the 3D structures of viral proteins; however, arriving at such understanding is difficult for intrinsically disordered proteins, whose disorder-dependent functions are key to the virus’s biology. Disorder is suggested to provide viral proteins with highly flexible structures and diverse functions that are utilized when invading host organisms and adjusting to new habitats. To date, the functional roles of intrinsically disordered proteins in the mechanisms of MERS-CoV pathogenesis, transmission, and treatment remain unclear. In this study, we performed structural analysis to evaluate the abundance of intrinsic disorder in the MERS-CoV proteome and in individual proteins derived from the MERS-CoV genome. Moreover, we detected disordered protein binding regions, namely, molecular recognition features and short linear motifs. Studying disordered proteins/regions in MERS-CoV could contribute to unlocking the complex riddles of viral infection, exploitation strategies, and drug development approaches in the near future by making it possible to target these important (yet challenging) unstructured regions.
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Affiliation(s)
- Manal A. Alshehri
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Manee M. Manee
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Fahad H. Alqahtani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Badr M. Al-Shomrani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
- Correspondence: (B.M.A.-S.); (V.N.U.)
| | - 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
- Correspondence: (B.M.A.-S.); (V.N.U.)
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14
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Gupta MN, Roy I. Drugs, host proteins and viral proteins: how their promiscuities shape antiviral design. Biol Rev Camb Philos Soc 2020; 96:205-222. [PMID: 32918378 DOI: 10.1111/brv.12652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
The reciprocal nature of drug specificity and target specificity implies that the same is true for their respective promiscuities. Protein promiscuity has two broadly different types of footprint in drug design. The first is relaxed specificity of binding sites for substrates, inhibitors, effectors or cofactors. The second involves protein-protein interactions of regulatory processes such as signal transduction and transcription, and here protein intrinsic disorder plays an important role. Both viruses and host cells exploit intrinsic disorder for their survival, as do the design and discovery programs for antivirals. Drug action, strictly speaking, always relies upon promiscuous activity, with drug promiscuity enlarging its scope. Drug repurposing searches for additional promiscuity on the part of both the drug and the target in the host. Understanding the subtle nuances of these promiscuities is critical in the design of novel and more effective antivirals.
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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
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160062, India
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15
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Bhardwaj T, Saumya KU, Kumar P, Sharma N, Gadhave K, Uversky VN, Giri R. Japanese encephalitis virus - exploring the dark proteome and disorder-function paradigm. FEBS J 2020; 287:3751-3776. [PMID: 32473054 DOI: 10.1111/febs.15427] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/26/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
Japanese encephalitis virus (JEV) is one of the major causes of viral encephalitis all around the globe. Approximately 3 billion people in endemic areas are at risk of Japanese encephalitis. To develop a wholistic understanding of the viral proteome, it is important to investigate both its ordered and disordered proteins. However, the functional and structural significance of disordered regions in the JEV proteome has not been systematically investigated as of yet. To fill this gap, we used here a set of bioinformatics tools to analyze the JEV proteome for the predisposition of its proteins for intrinsic disorder and for the presence of the disorder-based binding regions (also known as molecular recognition features, MoRFs). We also analyzed all JEV proteins for the presence of the probable nucleic acid-binding (DNA and RNA) sites. The results of these computational studies are experimentally validated using JEV capsid protein as an illustrative example. In agreement with bioinformatic analysis, we found that the N-terminal region of the JEV capsid (residues 1-30) is intrinsically disordered. We showed that this region is characterized by the temperature response typical for highly disordered proteins. Furthermore, we have experimentally shown that this disordered N-terminal domain of a capsid protein has a noticeable 'gain-of-structure' potential. In addition, using DOPS liposomes, we demonstrated the presence of pronounced membrane-mediated conformational changes in the N-terminal region of JEV capsid. In our view, this disorder-centric analysis would be helpful for a better understanding of the JEV pathogenesis.
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Affiliation(s)
- Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, India
| | - Kumar Udit Saumya
- School of Basic Sciences, Indian Institute of Technology Mandi, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, India
| | - Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 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', Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, India
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16
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Kumar A, Rathi E, Hariharapura RC, Kini SG. Is viral E6 oncoprotein a viable target? A critical analysis in the context of cervical cancer. Med Res Rev 2020; 40:2019-2048. [PMID: 32483862 DOI: 10.1002/med.21697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022]
Abstract
An understanding of the pathology of cervical cancer (CC) mediated by E6/E7 oncoproteins of high-risk human papillomavirus (HPV) was developed by late 80's. But if we look at the present scenario, not a single drug could be developed to inhibit these oncoproteins and in turn, be used specifically for the treatment of CC. The readers are advised not to presume the "viability of E6 protein" as mentioned in the title relates to just druggability of E6. The viability aspect will cover almost everything a researcher should know to develop E6 inhibitors until the preclinical stage. Herein, we have analysed the achievements and shortcomings of the scientific community in the last four decades in targeting HPV E6 against CC. Role of all HPV proteins has been briefly described for better perspective with a little detailed discussion of the role of E6. We have reviewed the articles from 1985 onward, reporting in vitro inhibition of E6. Recently, many computational studies have reported potent E6 inhibitors and these have also been reviewed. Subsequently, a critical analysis has been reported to cover the in vitro assay protocols and in vivo models to develop E6 inhibitors. A paragraph has been devoted to the role of public policy to fight CC employing vaccines and whether the vaccine against HPV has quenched the zeal to develop drugs against it. The review concludes with the challenges and the way forward.
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Affiliation(s)
- Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Raghu Chandrashekar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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17
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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18
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Bahramabadi R, Dabiri S, Iranpour M, Kazemi Arababadi M. TLR4: An Important Molecule Participating in Either Anti-Human Papillomavirus Immune Responses or Development of Its Related Cancers. Viral Immunol 2019; 32:417-423. [PMID: 31721657 DOI: 10.1089/vim.2019.0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It has been reported that human papillomavirus (HPV) is a main cause of cervical cancer. Immune system plays key roles in the HPV infection clearance. Additionally, the roles played by immune responses in development of cancers have been documented previously. Toll-like receptors (TLRs) are the main surface or intravesicular receptors driving innate immunity, which either participate in the fight against infectious agents or participate in the progression of cancers. Thus, it has been hypothesized that the molecules may be part of the HPV/cancers puzzle. TLR4 is a unique member of TLRs family that uses both well-known TLRs related intracellular signaling pathways. Furthermore, the roles played by TLR4 against several viruses and also their related complications, such as tumors, have been demonstrated. Thus, it has been hypothesized that TLR4 may play a key role in HPV infection and its related complications. This review article collected the information regarding the mentioned plausible roles by TLR4.
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Affiliation(s)
- Reza Bahramabadi
- Pathology and Stem Cell Research Center, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Pathology and Stem Cell Research Center, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryam Iranpour
- Pathology and Stem Cell Research Center, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Kazemi Arababadi
- Immunology of Infectious Diseases Research Centre, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Department of Laboratory Sciences, Faculty of Paramedicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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19
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Zika and Flavivirus Shell Disorder: Virulence and Fetal Morbidity. Biomolecules 2019; 9:biom9110710. [PMID: 31698857 PMCID: PMC6920988 DOI: 10.3390/biom9110710] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV) was first discovered in 1947 in Africa. Since then, sporadic ZIKV infections of humans have been reported in Africa and Asia. For a long time, this virus was mostly unnoticed due to its mild symptoms and low fatality rates. However, during the 2015-2016 epidemic in Central and South America, when millions of people were infected, it was discovered that ZIKV causes microcephaly in the babies of mothers infected during pregnancy. An examination of the M and C proteins of the ZIKV shell using the disorder predictor PONDR VLXT revealed that the M protein contains relatively high disorder levels comparable only to those of the yellow fever virus (YFV). On the other hand, the disorder levels in the C protein are relatively low, which can account for the low case fatality rate (CFR) of this virus in contrast to the more virulent YFV, which is characterized by high disorder in its C protein. A larger variation was found in the percentage of intrinsic disorder (PID) in the C protein of various ZIKV strains. Strains of African lineage are characterized by higher PIDs. Using both in vivo and in vitro experiments, laboratories have also previously shown that strains of African origin have a greater potential to inflict higher fetal morbidity than do strains of Asian lineage, with dengue-2 virus (DENV-2) having the least potential. Strong correlations were found between the potential to inflict fetal morbidity and shell disorder in ZIKV (r2 = 0.9) and DENV-2 (DENV-2 + ZIKV, r2 = 0.8). A strong correlation between CFR and PID was also observed when ZIKV was included in an analysis of sets of shell proteins from a variety of flaviviruses (r2 = 0.8). These observations have potential implications for antiviral vaccine development and for the design of cancer therapeutics in terms of developing therapeutic viruses that penetrate hard-to-reach organs.
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Affiliation(s)
- Gerard Kian-Meng Goh
- Goh’s BioComputing, Singapore 548957, Singapore
- Correspondence: ; Tel.: +65-8648-5440
| | - A. Keith Dunker
- Center for Computational Biology, Indiana and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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20
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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21
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Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Front Mol Biosci 2019; 6:64. [PMID: 31475155 PMCID: PMC6705226 DOI: 10.3389/fmolb.2019.00064] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell physiology, such as signal transduction and transcription, as well as pathological states, including Alzheimer's, Parkinson's, and Huntington's disease. Unlike their globular counterparts that are defined by a few structures and free energy minima, IDP/IDR comprise a large ensemble of rapidly interconverting structures and a corresponding free energy landscape characterized by multiple minima. This aspect has precluded the use of structural biological techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR) for resolving their structures. Instead, low-resolution techniques, such as small-angle X-ray or neutron scattering (SAXS/SANS), have become a mainstay in characterizing coarse features of the ensemble of structures. These are typically complemented with NMR data if possible or computational techniques, such as atomistic molecular dynamics, to further resolve the underlying ensemble of structures. However, over the past 10–15 years, it has become evident that the classical, pairwise-additive force fields that have enjoyed a high degree of success for globular proteins have been somewhat limited in modeling IDP/IDR structures that agree with experiment. There has thus been a significant effort to rehabilitate these models to obtain better agreement with experiment, typically done by optimizing parameters in a piecewise fashion. In this work, we take a different approach by optimizing a set of force field parameters simultaneously, using machine learning to adapt force field parameters to experimental SAXS scattering profiles. We demonstrate our approach in modeling three biologically IDP ensembles based on experimental SAXS profiles and show that our optimization approach significantly improve force field parameters that generate ensembles in better agreement with experiment.
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Affiliation(s)
- Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Utsab R Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Arvind Ramanathan
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States
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22
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Lyngdoh D, Shukla H, Sonkar A, Anupam R, Tripathi T. Portrait of the Intrinsically Disordered Side of the HTLV-1 Proteome. ACS OMEGA 2019; 4:10003-10018. [PMID: 31460093 PMCID: PMC6648719 DOI: 10.1021/acsomega.9b01017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack an ordered 3D structure. These proteins contain one or more intrinsically disordered protein regions (IDPRs). IDPRs interact promiscuously with other proteins, which leads to their structural transition from a disordered to an ordered state. Such interaction-prone regions of IDPs are known as molecular recognition features. Recent studies suggest that IDPs provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion within the host cells. In the present study, we evaluated the prevalence of IDPs and IDPRs in human T lymphotropic virus type 1 (HTLV-1) proteome. We also investigated the presence of MoRF regions in the structural and nonstructural proteins of HTLV-1. We found abundant IDPRs in HTLV-1 bZIP factor, p30, Rex, and structural nucleocapsid p15 proteins, which are involved in diverse functions such as virus proliferation, mRNA export, and genomic RNA binding. Our study analyzed the HTLV-1 proteome with the perspective of intrinsic disorder identification. We propose that the intrinsic disorder analysis of HTLV-1 proteins may form the basis for the development of protein disorder-based drugs.
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Affiliation(s)
- Denzelle
L. Lyngdoh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rajaneesh Anupam
- Department
of Biotechnology, Dr. Harisingh Gour Central
University, Sagar 470003, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- E-mail: , . Phone: +91-364-2722141. Fax: +91-364-2550108
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23
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The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions. Sci Rep 2019; 9:5822. [PMID: 30967564 PMCID: PMC6456579 DOI: 10.1038/s41598-019-41925-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
When present, structural disorder makes it very challenging to characterise the conformational properties of proteins. This is particularly the case of proteins, such as the oncogene protein E7 of human papillomavirus type 16, which contain both ordered and disordered domains, and that can populate monomeric and oligomeric states under physiological conditions. Nuclear magnetic resonance (NMR) spectroscopy is emerging as a powerful method to study these complex systems, most notably in combination with molecular dynamics simulations. Here we use NMR chemical shifts and residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations to determine the free energy landscape of E7. This landscape reveals a complex interplay between a folded but highly dynamical C-terminal domain and a disordered N-terminal domain that forms transient secondary and tertiary structures, as well as an equilibrium between a high-populated (98%) dimeric state and a low-populated (2%) monomeric state. These results provide compelling evidence of the complex conformational heterogeneity associated with the behaviour and interactions of this disordered protein associated with disease.
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24
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Redwan EM, AlJaddawi AA, Uversky VN. Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). Cell Mol Life Sci 2019; 76:577-608. [PMID: 30443749 PMCID: PMC7079808 DOI: 10.1007/s00018-018-2968-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022]
Abstract
Infection by the Alkhurma virus (ALKV) leading to the Alkhurma hemorrhagic fever is a common thread in Saudi Arabia, with no efficient treatment or prevention available as of yet. Although the rational drug design traditionally uses information on known 3D structures of viral proteins, intrinsically disordered proteins (i.e., functional proteins that do not possess unique 3D structures), with their multitude of disorder-dependent functions, are crucial for the biology of viruses. Here, viruses utilize disordered regions in their invasion of the host organisms and in hijacking and repurposing of different host systems. Furthermore, the ability of viruses to efficiently adjust and accommodate to their hostile habitats is also intrinsic disorder-dependent. However, little is currently known on the level of penetrance and functional utilization of intrinsic disorder in the ALKV proteome. To fill this gap, we used here multiple computational tools to evaluate the abundance of intrinsic disorder in the ALKV genome polyprotein. We also analyzed the peculiarities of intrinsic disorder predisposition of the individual viral proteins, as well as human proteins known to be engaged in interaction with the ALKV proteins. Special attention was paid to finding a correlation between protein functionality and structural disorder. To the best of our knowledge, this work represents the first systematic study of the intrinsic disorder status of ALKV proteome and interactome.
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Affiliation(s)
- Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Abdullah A AlJaddawi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, 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, Pushchino, 142290, Moscow Region, Russia.
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25
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Deryusheva E, Nemashkalova E, Galloux M, Richard C, Eléouët J, Kovacs D, Belle K, Tompa P, Uversky V, Permyakov S. Does Intrinsic Disorder in Proteins Favor Their Interaction with Lipids? Proteomics 2019; 19:e1800098. [DOI: 10.1002/pmic.201800098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 12/09/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Evgenia Deryusheva
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
| | - Ekaterina Nemashkalova
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
| | - Marie Galloux
- VIM, INRAUniversité Paris‐Saclay Jouy‐en‐Josas 78350 France
| | | | | | - Denis Kovacs
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
| | - Karo Belle
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
| | - Peter Tompa
- VIB, Structural Biology Research CenterVrije Universiteit Brussel Brussels 1050 Belgium
- Institute of EnzymologyResearch Centre for Natural Sciences of the Hungarian Academy of Sciences Budapest 1117 Hungary
| | - Vladimir Uversky
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteMorsani College of MedicineUniversity of South Florida Tampa FL 33612 USA
| | - Sergei Permyakov
- Russian Academy of SciencesInstitute for Biological Instrumentation Pushchino Moscow Region 142290 Russia
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26
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Liu Z, Teng L, Gao L, Wang H, Su Y, Li J. The role of eukaryotic translation initiation factor 5A-1 (eIF5A-1) gene in HPV 16 E6 induces cell growth in human cervical squamous carcinoma cells. Biochem Biophys Res Commun 2018; 504:6-12. [PMID: 30170728 DOI: 10.1016/j.bbrc.2018.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022]
Abstract
Human Papillomavirus (HPV) is considered as the major risk factor for the development and progression of cervical cancer. The high expression of HPV 16 E6 may be the causative factor for induction and maintenance of the transformed phenotype. These oncoproteins would interact with several intracellular proteins, such as eukaryotic translation initiation factor 5A-1 (eIF5A-1) that is essential for proliferation of eukaryotic cells. Our study explored the expression level of HPV 16 E6 and eIF5A-1 in human cervical squamous carcinoma samples and the adjacent non-cancerous cervix samples. Both C33a cells and SiHa cells transfected with a vector encoding HPV 16 E6 resulted in increase of eIF5A-1 expression level and enhancement of viability, migration and proliferation of these cells, furthermore, these effects in both C33a cells and SiHa cells could be abrogated by treatment with eIF5A-1 small-interfering RNA (siRNA) or the specific inhibitors ciclopirox (CPX) that was used to inhibit the function of eIF5A-1 via blocking the main enzymes deoxyhypusine hydroxylase (DOHH). Our results support that the silencing the eIF5A-1 gene or blocking the DOHH could induce the apoptosis of HPV 16 E6-infected cervical carcinoma cells. Thus might provide a new approach to preventing and treating cervical cancer.
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Affiliation(s)
- Zhu Liu
- Department of Clinical Laboratory, Traditional Chinese Medical Hospital of Huangdao District, Qingdao, China
| | - Lichen Teng
- Department of Clinical Laboratory, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Lingjuan Gao
- Department of Gynecology, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital North Branch, Nanjing, China
| | - Huiyan Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Yajuan Su
- Department of Clinical Laboratory, The Affiliated Cancer Hospital, Harbin Medical University, Harbin, China.
| | - Jingbo Li
- Department of Gynecology, The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital North Branch, Nanjing, China.
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27
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Tarakhovsky A, Prinjha RK. Drawing on disorder: How viruses use histone mimicry to their advantage. J Exp Med 2018; 215:1777-1787. [PMID: 29934321 PMCID: PMC6028506 DOI: 10.1084/jem.20180099] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/24/2018] [Accepted: 06/07/2018] [Indexed: 12/16/2022] Open
Abstract
Humans carry trillions of viruses that thrive because of their ability to exploit the host. In this exploitation, viruses promote their own replication by suppressing the host antiviral response and by inducing changes in host biosynthetic processes, often with extremely small genomes of their own. In the review, we discuss the phenomenon of histone mimicry by viral proteins and how this mimicry allows the virus to dial in to the cell's transcriptional processes and establish a cell state that promotes infection. We suggest that histone mimicry is part of a broader viral strategy to use intrinsic protein disorder as a means to overcome the size limitations of its own genome and to maximize its impact on host protein networks. In particular, we discuss how intrinsic protein disorder may enable viral proteins to interfere with phase-separated host protein condensates, including those that contribute to chromatin-mediated control of gene expression.
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Affiliation(s)
- Alexander Tarakhovsky
- Laboratory of the Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY
| | - Rab K Prinjha
- Epigenetics DPU, Oncology and Immuno-inflammation TA Units, GlaxoSmithKline Medicines Research Centre, Stevenage, England, UK
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Aarthy M, Kumar D, Giri R, Singh SK. E7 oncoprotein of human papillomavirus: Structural dynamics and inhibitor screening study. Gene 2018. [DOI: 10.1016/j.gene.2018.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains. Cell Biochem Biophys 2018; 76:411-431. [PMID: 29511990 PMCID: PMC7090660 DOI: 10.1007/s12013-018-0839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
The number of fatalities and economic losses caused by the Ebola virus infection across the planet culminated in the havoc that occurred between August and November 2014. However, little is known about the molecular protein profile of this devastating virus. This work represents a thorough bioinformatics analysis of the regularities of charge distribution (polar profiles) in two groups of proteins and their functional domains associated with Ebola virus disease: Ebola virus proteins and Human proteins interacting with Ebola virus. Our analysis reveals that a fragment exists in each of these proteins—one named the “functional domain”—with the polar profile similar to the polar profile of the protein that contains it. Each protein is formed by a group of short sub-sequences, where each fragment has a different and distinctive polar profile and where the polar profile between adjacent short sub-sequences changes orderly and gradually to coincide with the polar profile of the whole protein. When using the charge distribution as a metric, it was observed that it effectively discriminates the proteins from their functional domains. As a counterexample, the same test was applied to a set of synthetic proteins built for that purpose, revealing that any of the regularities reported here for the Ebola virus proteins and human proteins interacting with Ebola virus were not present in the synthetic proteins. Our results indicate that the polar profile of each protein studied and its corresponding functional domain are similar. Thus, when building each protein from its functional domai—adding one amino acid at a time and plotting each time its polar profile—it was observed that the resulting graphs can be divided into groups with similar polar profiles.
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Tamarozzi ER, Giuliatti S. Understanding the Role of Intrinsic Disorder of Viral Proteins in the Oncogenicity of Different Types of HPV. Int J Mol Sci 2018; 19:ijms19010198. [PMID: 29315236 PMCID: PMC5796147 DOI: 10.3390/ijms19010198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/06/2018] [Accepted: 01/07/2018] [Indexed: 12/21/2022] Open
Abstract
Intrinsic disorder is very important in the biological function of several proteins, and is directly linked to their foldability during interaction with their targets. There is a close relationship between the intrinsically disordered proteins and the process of carcinogenesis involving viral pathogens. Among these pathogens, we have highlighted the human papillomavirus (HPV) in this study. HPV is currently among the most common sexually transmitted infections, besides being the cause of several types of cancer. HPVs are divided into two groups, called high- and low-risk, based on their oncogenic potential. The high-risk HPV E6 protein has been the target of much research, in seeking treatments against HPV, due to its direct involvement in the process of cell cycle control. To understand the role of intrinsic disorder of the viral proteins in the oncogenic potential of different HPV types, the structural characteristics of intrinsically disordered regions of high and low-risk HPV E6 proteins were analyzed. In silico analyses of primary sequences, prediction of tertiary structures, and analyses of molecular dynamics allowed the observation of the behavior of such disordered regions in these proteins, thereby proving a direct relationship of structural variation with the degree of oncogenicity of HPVs. The results obtained may contribute to the development of new therapies, targeting the E6 oncoprotein, for the treatment of HPV-associated diseases.
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Affiliation(s)
- Elvira Regina Tamarozzi
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo, Sao Paulo 14049-900, Brazil.
| | - Silvana Giuliatti
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo, Sao Paulo 14049-900, Brazil.
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Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. Int J Mol Sci 2017; 18:ijms18122761. [PMID: 29257115 PMCID: PMC5751360 DOI: 10.3390/ijms18122761] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs.
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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Shen-Gunther J, Wang Y, Lai Z, Poage GM, Perez L, Huang THM. Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix. BMC Genomics 2017; 18:231. [PMID: 28288568 PMCID: PMC5348809 DOI: 10.1186/s12864-017-3612-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the reference method of choice for clinical diagnostics. However, for samples with multiple HPV infections, genotype identification is singular and occasionally imprecise or indeterminable due to overlapping chromatograms. Our aim was to explore and compare HPV metagenomes in abnormal cervical cytology by deep sequencing for correlation with disease states. RESULTS Low- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples were DNA extracted for PCR-amplification of the HPV E6/E7 genes. HPV+ samples were sequenced by dideoxy and deep methods. Deep sequencing revealed ~60% of all samples (n = 72) were multi-HPV infected. Among LSIL samples (n = 43), 27 different genotypes were found. The 3 dominant (most abundant) genotypes were: HPV-39, 11/43 (26%); -16, 9/43 (21%); and -35, 4/43 (9%). Among HSIL (n = 29), 17 HPV genotypes were identified; the 3 dominant genotypes were: HPV-16, 21/29 (72%); -35, 4/29 (14%); and -39, 3/29 (10%). Phylogenetically, type-specific E6/E7 genetic distances correlated with carcinogenic potential. Species diversity analysis between LSIL and HSIL revealed loss of HPV diversity and domination by HPV-16 in HSIL samples. CONCLUSIONS Deep sequencing resolves HPV genotype composition within multi-infected cervical cytology. Biodiversity analysis reveals loss of diversity and gain of dominance by carcinogenic genotypes in high-grade cytology. Metagenomic profiles may therefore serve as a biomarker of disease severity and a population surveillance tool for emerging genotypes.
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Affiliation(s)
- Jane Shen-Gunther
- Department of Clinical Investigation, Brooke Army Medical Center, Gynecologic Oncology & Clinical Investigation, 3698 Chambers Pass, Fort Sam Houston, TX 78234 USA
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Graham M. Poage
- Department of Clinical Investigation, Brooke Army Medical Center, Gynecologic Oncology & Clinical Investigation, 3698 Chambers Pass, Fort Sam Houston, TX 78234 USA
| | - Luis Perez
- Department of Clinical Investigation, Brooke Army Medical Center, Gynecologic Oncology & Clinical Investigation, 3698 Chambers Pass, Fort Sam Houston, TX 78234 USA
| | - Tim H. M. Huang
- Department of Molecular Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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Russo A, Manna SL, Novellino E, Malfitano AM, Marasco D. Molecular signaling involving intrinsically disordered proteins in prostate cancer. Asian J Androl 2017; 18:673-81. [PMID: 27212129 PMCID: PMC5000787 DOI: 10.4103/1008-682x.181817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigations on cellular protein interaction networks (PINs) reveal that proteins that constitute hubs in a PIN are notably enriched in Intrinsically Disordered Proteins (IDPs) compared to proteins that constitute edges, highlighting the role of IDPs in signaling pathways. Most IDPs rapidly undergo disorder-to-order transitions upon binding to their biological targets to perform their function. Conformational dynamics enables IDPs to be versatile and to interact with a broad range of interactors under normal physiological conditions where their expression is tightly modulated. IDPs are involved in many cellular processes such as cellular signaling, transcriptional regulation, and splicing; thus, their high-specificity/low-affinity interactions play crucial roles in many human diseases including cancer. Prostate cancer (PCa) is one of the leading causes of cancer-related mortality in men worldwide. Therefore, identifying molecular mechanisms of the oncogenic signaling pathways that are involved in prostate carcinogenesis is crucial. In this review, we focus on the aspects of cellular pathways leading to PCa in which IDPs exert a primary role.
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Affiliation(s)
- Anna Russo
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Anna Maria Malfitano
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134 Naples, Italy
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Zambelli B, Uversky VN, Ciurli S. Nickel impact on human health: An intrinsic disorder perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1714-1731. [DOI: 10.1016/j.bbapap.2016.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 01/26/2023]
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Yacoub HA, Elazzazy AM, Mahmoud MM, Baeshen MN, Al-Maghrabi OA, Alkarim S, Ahmed ES, Almehdar HA, Uversky VN. Chicken cathelicidins as potent intrinsically disordered biocides with antimicrobial activity against infectious pathogens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:8-24. [PMID: 27328070 DOI: 10.1016/j.dci.2016.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
This study was performed to identify the expression patterns of the cathelicidin genes in a local chicken breed and to evaluate the antimicrobial activities of the cathelicidin peptides against pathogenic bacteria. This analysis revealed that the coding regions of CATH-1, -2, and -3 genes contain 447 bp, 465 bp, and 456 bp, respectively, and encode proteins of 148, 154, 151 amino acids, respectively. The complete amino acid sequences of the cathelicidin peptides are similar to those found in Meleagris gallopavo, Phasianus colchicus, and Coturnix coturnix, and show high sequence identity to their Columba livia and Anas platyrhynchos counterparts. In contrast, these avian peptides shared a very low sequence identity with the mammalian cathelicidins. The analysis further revealed that the cathelicidin genes are expressed in various organ and tissues. We also show that the CATH peptides 1, 2, 3 and their amide-modified structures possess potent antimicrobial activities against both Gram-positive and Gram-negative pathogens, with these bacteria being affected to different extents. The antimicrobial activities of the peptides are slightly lower than those of their amide analogs. Computational analysis revealed that pre-pro-cathelicidins are hybrid proteins that contain ordered domains and functional intrinsically disordered regions. Furthermore, high structural and sequence variability of mature cathelicidins is a strong indication of their rather disordered nature. It is likely that intrinsic disorder is needed for the multifarious functionality of these antimicrobial peptides. Our analyses indicated that cathelicidin peptides require further study to better understand their full potentials in the treatment of diseases in both humans and animals. The data obtained for synthetic avian peptides will help elucidating of their potential applications in the pharmaceutical industry.
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Affiliation(s)
- Haitham A Yacoub
- Biological Sciences Department, Faculty of Science, University of Jeddah, P.O. Box 80203, Jeddah, Saudi Arabia; Cell Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, P.O. Box 12622, Gizza, Egypt.
| | - Ahmed M Elazzazy
- Biological Sciences Department, Faculty of Science, University of Jeddah, P.O. Box 80203, Jeddah, Saudi Arabia; Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries, National Research Centre, Dokki, P.O. Box 12622, Gizza, Egypt.
| | - Maged M Mahmoud
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; Department of Molecular Genetics and Enzymology, Davison of Human Genetics and Genome Research, National Research Centre, Dokki, P.O. Box 12622, Gizza, Egypt
| | - Mohamed Nabih Baeshen
- Biological Sciences Department, Faculty of Science, University of Jeddah, P.O. Box 80203, Jeddah, Saudi Arabia; Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Omar A Al-Maghrabi
- Biological Sciences Department, Faculty of Science, University of Jeddah, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Saleh Alkarim
- Embryonic Stem Cell Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Ekram S Ahmed
- Cell Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, P.O. Box 12622, Gizza, Egypt
| | - Hussein A Almehdar
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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Charon J, Theil S, Nicaise V, Michon T. Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation. MOLECULAR BIOSYSTEMS 2016; 12:634-52. [PMID: 26699268 DOI: 10.1039/c5mb00677e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs.
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Affiliation(s)
- Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Sébastien Theil
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Valérie Nicaise
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
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Illiano E, Demurtas OC, Massa S, Di Bonito P, Consalvi V, Chiaraluce R, Zanotto C, De Giuli Morghen C, Radaelli A, Venuti A, Franconi R. Production of functional, stable, unmutated recombinant human papillomavirus E6 oncoprotein: implications for HPV-tumor diagnosis and therapy. J Transl Med 2016; 14:224. [PMID: 27465494 PMCID: PMC4963926 DOI: 10.1186/s12967-016-0978-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-risk human papillomaviruses (HR-HPVs) types 16 and 18 are the main etiological agents of cervical cancer, with more than 550,000 new cases each year worldwide. HPVs are also associated with other ano-genital and head-and-neck tumors. The HR-HPV E6 and E7 oncoproteins are responsible for onset and maintenance of the cell transformation state, and they represent appropriate targets for development of diagnostic and therapeutic tools. METHODS The unmutated E6 gene from HPV16 and HPV18 and from low-risk HPV11 was cloned in a prokaryotic expression vector for expression of the Histidine-tagged E6 protein (His6-E6), according to a novel procedure. The structural properties were determined using circular dichroism and fluorescence spectroscopy. His6-E6 oncoprotein immunogenicity was assessed in a mouse model, and its functionality was determined using in vitro GST pull-down and protein degradation assays. RESULTS The His6-tagged E6 proteins from HPV16, HPV18, and HPV11 E6 genes, without any further modification in the amino-acid sequence, were produced in bacteria as soluble and stable molecules. Structural analyses of HPV16 His6-E6 suggests that it maintains correct folding and conformational properties. C57BL/6 mice immunized with HPV16 His6-E6 developed significant humoral immune responses. The E6 proteins from HPV16, HPV18, and HPV11 were purified according to a new procedure, and investigated for protein-protein interactions. HR-HPV His6-E6 bound p53, the PDZ1 motif from MAGI-1 proteins, the human discs large tumor suppressor, and the human ubiquitin ligase E6-associated protein, thus suggesting that it is biologically active. The purified HR-HPV E6 proteins also targeted the MAGI-3 and p53 proteins for degradation. CONCLUSIONS This new procedure generates a stable, unmutated HPV16 E6 protein, which maintains the E6 properties in in vitro binding assays. This will be useful for basic studies, and for development of diagnostic kits and immunotherapies in preclinical mouse models of HPV-related tumorigenesis.
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Affiliation(s)
- Elena Illiano
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy.,Laboratory of Biomedical Technologies (SSPT-TECS-TEB), Department for Sustainability, Division of Health Protection Technologies, Italian National Agency for New Technologies, Energy and the Environment (ENEA), 'Casaccia' Research Centre, Via Anguillarese 301, 00123, Rome, Italy
| | - Olivia Costantina Demurtas
- Laboratory of Biotechnology (SSPT-BIOAG-BIOTEC), Department for Sustainability, Division Biotechnology and Agroindustry, Italian National Agency for New Technologies, Energy and the Environment (ENEA), 'Casaccia' Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Silvia Massa
- Laboratory of Biotechnology (SSPT-BIOAG-BIOTEC), Department for Sustainability, Division Biotechnology and Agroindustry, Italian National Agency for New Technologies, Energy and the Environment (ENEA), 'Casaccia' Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore Sanità, Viale Regina Elena 299, 00185, Rome, Italy
| | - Valerio Consalvi
- 'A. Rossi Fanelli' Department of Biochemical Sciences, University of Rome 'La Sapienza', P.le Aldo Moro 5, 00185, Rome, Italy
| | - Roberta Chiaraluce
- 'A. Rossi Fanelli' Department of Biochemical Sciences, University of Rome 'La Sapienza', P.le Aldo Moro 5, 00185, Rome, Italy
| | - Carlo Zanotto
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy
| | - Carlo De Giuli Morghen
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy.,Catholic University 'Our Lady of Good Counsel', Tirana, Albania
| | - Antonia Radaelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy.,Cellular and Molecular Pharmacology Section, CNR Institute of Neurosciences, University of Milan, 20129, Milan, Italy
| | - Aldo Venuti
- HPV-UNIT, Ridait Department, Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Rosella Franconi
- Laboratory of Biomedical Technologies (SSPT-TECS-TEB), Department for Sustainability, Division of Health Protection Technologies, Italian National Agency for New Technologies, Energy and the Environment (ENEA), 'Casaccia' Research Centre, Via Anguillarese 301, 00123, Rome, Italy.
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Uversky VN. Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis. Biopolymers 2016; 99:870-87. [PMID: 23754493 PMCID: PMC7161862 DOI: 10.1002/bip.22298] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal‐like structure in a functional protein. The two only places for conformational ensembles of under‐folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under‐folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms–functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under‐folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under‐folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under‐folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under‐folded proteins, the different categories of under‐foldedness are differently encoded in protein amino acid sequences. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 870–887, 2013.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
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Goh GKM, Dunker AK, Uversky VN. Detection of links between Ebola nucleocapsid and virulence using disorder analysis. MOLECULAR BIOSYSTEMS 2016; 11:2337-44. [PMID: 26086270 DOI: 10.1039/c5mb00240k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The underlying reasons for the differences in the virulence of various types of Ebola virus (EBOV) remain unknown. Comparison of the percentage of disorder (PID) in nucleocapsid proteins VP30 and NP reveals high correlation between nucleocapsid PIDs and the case-fatality rates of EBOV. The higher disorder of these proteins is likely to be needed for more efficient multiplication of virus copies via more efficient viral RNA transcription and more promiscuous protein binding potential. This is important for the more efficient assistance of nucleocapsid in viral particle budding and of the assembly and mobility of viral proteins across the host membrane and within the cytoplasm. A more comprehensive knowledge of the molecular mechanisms of EBOV virulence would also lead to new and more effective strategies in vaccine development.
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Yacoub HA, Al-Maghrabi OA, Ahmed ES, Uversky VN. Abundance and functional roles of intrinsic disorder in the antimicrobial peptides of the NK-lysin family. J Biomol Struct Dyn 2016; 35:836-856. [DOI: 10.1080/07391102.2016.1164077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Haitham A. Yacoub
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Omar A. Al-Maghrabi
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ekram S. Ahmed
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Vladimir N. Uversky
- Faculty of Sciences, Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Burger VM, Nolasco DO, Stultz CM. Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum. J Biol Chem 2016; 291:6706-13. [PMID: 26851282 PMCID: PMC4807258 DOI: 10.1074/jbc.r115.692590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The traditional view of the structure-function paradigm is that a protein's function is inextricably linked to a well defined, three-dimensional structure, which is determined by the protein's primary amino acid sequence. However, it is now accepted that a number of proteins do not adopt a unique tertiary structure in solution and that some degree of disorder is required for many proteins to perform their prescribed functions. In this review, we highlight how a number of protein functions are facilitated by intrinsic disorder and introduce a new protein structure taxonomy that is based on quantifiable metrics of a protein's disorder.
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Affiliation(s)
- Virginia M Burger
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Diego O Nolasco
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Collin M Stultz
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and the Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
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Meng F, Badierah RA, Almehdar HA, Redwan EM, Kurgan L, Uversky VN. Unstructural biology of the dengue virus proteins. FEBS J 2015; 282:3368-94. [DOI: 10.1111/febs.13349] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 06/01/2015] [Accepted: 06/15/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Fanchi Meng
- Department of Electrical and Computer Engineering; University of Alberta; Edmonton Alberta Canada
| | - Reaid A. Badierah
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Hussein A. Almehdar
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Elrashdy M. Redwan
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
- 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 Egypt
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering; University of Alberta; Edmonton Alberta Canada
| | - Vladimir N. Uversky
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Laboratory of Structural Dynamics, Stability and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St Petersburg Russia
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Chebaro Y, Ballard AJ, Chakraborty D, Wales DJ. Intrinsically disordered energy landscapes. Sci Rep 2015; 5:10386. [PMID: 25999294 PMCID: PMC4441119 DOI: 10.1038/srep10386] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022] Open
Abstract
Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such 'intrinsically disordered' landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an α-helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.
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Affiliation(s)
- Yassmine Chebaro
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - Andrew J Ballard
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
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Marasco D, Scognamiglio PL. Identification of inhibitors of biological interactions involving intrinsically disordered proteins. Int J Mol Sci 2015; 16:7394-412. [PMID: 25849651 PMCID: PMC4425024 DOI: 10.3390/ijms16047394] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few "hot spots", thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.
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Affiliation(s)
- Daniela Marasco
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
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Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) ORF57 protein (also known as mRNA transcript accumulation (Mta)) is a potent posttranscriptional regulator essential for the efficient expression of KSHV lytic genes and productive KSHV replication. ORF57 possesses numerous activities that promote the expression of viral genes, including the three major functions of enhancement of RNA stability, promotion of RNA splicing, and stimulation of protein translation. The multifunctional nature of ORF57 is driven by its ability to interact with an array of cellular cofactors. These interactions are required for the formation of ORF57-containing ribonucleoprotein complexes at specific binding sites in the target transcripts, referred as Mta-responsive elements (MREs). Understanding of the ORF57 protein conformation has led to the identification of two structurally-distinct domains within the ORF57 polypeptide: an unstructured intrinsically disordered N-terminal domain and a structured α-helix-rich C-terminal domain. The distinct structures of the domains serve as the foundation for their unique binding affinities: the N-terminal domain mediates ORF57 interactions with cellular cofactors and target RNAs, and the C-terminal domain mediates ORF57 homodimerization. In addition, each domain has been found to contribute to the stability of ORF57 protein in infected cells by counteracting caspase- and proteasome-mediated degradation pathways. Together, these new findings provide insight into the function and biological properties of ORF57 in the KSHV life cycle and pathogenesis.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, USA.
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, USA.
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Dolan PT, Roth AP, Xue B, Sun R, Dunker AK, Uversky VN, LaCount DJ. Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions. Protein Sci 2014; 24:221-35. [PMID: 25424537 DOI: 10.1002/pro.2608] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/19/2014] [Indexed: 12/18/2022]
Abstract
Viral proteins bind to numerous cellular and viral proteins throughout the infection cycle. However, the mechanisms by which viral proteins interact with such large numbers of factors remain unknown. Cellular proteins that interact with multiple, distinct partners often do so through short sequences known as molecular recognition features (MoRFs) embedded within intrinsically disordered regions (IDRs). In this study, we report the first evidence that MoRFs in viral proteins play a similar role in targeting the host cell. Using a combination of evolutionary modeling, protein-protein interaction analyses and forward genetic screening, we systematically investigated two computationally predicted MoRFs within the N-terminal IDR of the hepatitis C virus (HCV) Core protein. Sequence analysis of the MoRFs showed their conservation across all HCV genotypes and the canine and equine Hepaciviruses. Phylogenetic modeling indicated that the Core MoRFs are under stronger purifying selection than the surrounding sequence, suggesting that these modules have a biological function. Using the yeast two-hybrid assay, we identified three cellular binding partners for each HCV Core MoRF, including two previously characterized cellular targets of HCV Core (DDX3X and NPM1). Random and site-directed mutagenesis demonstrated that the predicted MoRF regions were required for binding to the cellular proteins, but that different residues within each MoRF were critical for binding to different partners. This study demonstrated that viruses may use intrinsic disorder to target multiple cellular proteins with the same amino acid sequence and provides a framework for characterizing the binding partners of other disordered regions in viral and cellular proteomes.
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Affiliation(s)
- Patrick T Dolan
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907
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Morgenfeld M, Lentz E, Segretin ME, Alfano EF, Bravo-Almonacid F. Translational fusion and redirection to thylakoid lumen as strategies to enhance accumulation of human papillomavirus E7 antigen in tobacco chloroplasts. Mol Biotechnol 2014; 56:1021-31. [PMID: 24981330 DOI: 10.1007/s12033-014-9781-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Human papillomavirus (HPV) is the causal agent of cervical cancer, one of the most common causes of death in women worldwide, and its E7 antigen is the major candidate for a therapeutic vaccine. The large scale production of E7 by molecular farming that would lead to the development of a safe and inexpensive vaccine is impaired by its low accumulation level in the plant cell. To enhance antigen production in the plastids, two alternative strategies were carried out: the expression of E7 as a translational fusion to β-glucuronidase enzyme and redirection of E7 into the thylakoid lumen. The use of the β-glucuronidase as a partner protein turned out to be a successful strategy, antigen expression levels were enhanced between 30 and 40 times relative to unfused E7. Moreover, best accumulation, albeit at a high metabolic cost that compromised biomass production, was obtained redirecting E7 into the thylakoid lumen by the incorporation of the N-terminal transit peptide, Str. Following this approach lumenal E7 production exceeded the stromal by two orders of magnitude. Our results highlight the relevance of exploring different strategies to improve recombinant protein stability for certain transgenes in order to exploit potential advantages of recombinant protein accumulation in chloroplasts.
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Affiliation(s)
- Mauro Morgenfeld
- Instituto de Ingeniería Genética y Biología Molecular "Dr, Hector Torres" (INGEBI-CONICET), Vuelta de Obligado 2490, C.C 1428ADN, Ciudad Autónoma de Buenos Aires, Argentina
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Chen ZL, Su YJ, Zhang HL, Gu PQ, Gao LJ. The role of the globular heads of the C1q receptor in HPV-16 E2-induced human cervical squamous carcinoma cell apoptosis via a mitochondria-dependent pathway. J Transl Med 2014; 12:286. [PMID: 25288439 PMCID: PMC4194366 DOI: 10.1186/s12967-014-0286-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022] Open
Abstract
Background Human papillomavirus type-16 (HPV-16) E2 protein acts as a transcriptional modulator and plays a key role in regulating many biological responses. The purpose of this study was to investigate the relationship between HPV-16 E2, the receptor for the globular heads of human C1q (gC1qR) gene expression, mitochondrial dysfunction and apoptosis regulation in human cervical squamous carcinoma cells (C33a and SiHa). Methods HPV-16 E2 and gC1qR expression was examined using real-time PCR and western blot analysis. Apoptosis in C33a and SiHa cells was assessed by flow cytometry. Mitochondrial function was detected via ROS generation, the amount of cytosolic Ca2+, and changes in the mitochondrial membrane potential (Δψm). Results The expression of the HPV-16 E2 and gC1qR gene significantly decreased in human cervical squamous carcinoma samples relative to the non-cancerous cervix samples. C33a and SiHa cells that were transfected with a vector encoding HPV-16 E2 displayed significantly increased gC1qR gene expression and mitochondrial dysfunction as well as an up-regulation of cellular apoptosis, which was abrogated by the addition of gC1qR small-interfering RNA (siRNA). Conclusions These data support a mechanism whereby gC1qR plays an important role in HPV-16 E2-induced human cervical squamous carcinoma cell apoptosis via a mitochondria-dependent pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0286-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Ping-qing Gu
- State Key Laboratory of Reproductive Medicine, Department of Clinical Laboratory, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China.
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Redwan EM, Uversky VN, El-Fakharany EM, Al-Mehdar H. Potential lactoferrin activity against pathogenic viruses. C R Biol 2014; 337:581-95. [PMID: 25282173 DOI: 10.1016/j.crvi.2014.08.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/10/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Lactoferrin (LF) is an 80-kDa globular glycoprotein with high affinity for metal ions, particularly for iron. This protein possesses many biological functions, including the binding and release of iron and serves as one of the important components of the innate immune system, where it acts as a potent inhibitor of several pathogens. LF has efficacious antibacterial and antiviral activities against a wide range of Gram-positive and Gram-negative bacteria and against both naked and enveloped DNA and RNA viruses. In its antiviral pursuit, LF acts predominantly at the acute phase of the viral infection or even at the intracellular stage, as in hepatitis C virus infection. LF inhibits the entry of viral particles into host cells, either by direct attachment to the viral particles or by blocking their cellular receptors. This wide range of activities may be attributed to the capacity of LF to bind iron and its ability to interfere with the cellular receptors of both hosts and pathogenic microbes.
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Affiliation(s)
- Elrashdy M Redwan
- Biology Department, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, New Borg EL-Arab 21394, Alexandria, Egypt.
| | - Vladimir N Uversky
- Biology Department, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; 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, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
| | - Esmail M El-Fakharany
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, New Borg EL-Arab 21394, Alexandria, Egypt.
| | - Hussein Al-Mehdar
- Biology Department, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia.
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