51
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Liu X, Chen J. Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields. J Chem Theory Comput 2019; 15:4708-4720. [PMID: 31241933 DOI: 10.1021/acs.jctc.9b00397] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular dynamics simulations using physics-based atomistic force fields have been increasingly used to characterize the heterogeneous structural ensembles of intrinsically disordered proteins (IDPs). To evaluate the accuracy of the latest atomistic explicit-solvent force fields in modeling larger IDPs with nontrivial structural features, we focus on the 61-residue N-terminal transactivation domain (TAD) of tumor suppressor p53, an important protein in cancer biology that has been extensively studied, and abundant experimental data is available for evaluation of simulated ensembles. We performed extensive replica exchange with solute tempering simulations, in excess of 1.0 μs/replica, to generate disordered structural ensembles of p53-TAD using six latest explicit solvent protein force fields. Multiple local and long-range structural properties, including chain dimension, residual secondary structures, and transient long-range contacts, were analyzed and compared against available experimental data. The results show that IDPs such as p53-TAD remain highly challenging for atomistic simulations due to conformational complexity and difficulty in achieving adequate convergence. Structural ensembles of p53-TAD generated using various force fields differ significantly from each other. The a99SB-disp force field demonstrates the best agreement with experimental data at all levels and proves to be suitable for simulating unbound p53-TAD and how its conformational properties may be modulated by phosphorylation and other cellular signals or cancer-associated mutations. Feasibility of such detailed structural characterization is a key step toward establishing the sequence-disordered ensemble-function-disease relationship of p53 and other biologically important IDPs.
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52
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Zhao L, Ouyang Y, Li Q, Zhang Z. Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation. J Biomol Struct Dyn 2019; 38:2613-2623. [DOI: 10.1080/07391102.2019.1637784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Likun Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Ouyang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhuqing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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53
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Hartlmüller C, Spreitzer E, Göbl C, Falsone F, Madl T. NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:305-317. [PMID: 31297688 PMCID: PMC6692294 DOI: 10.1007/s10858-019-00248-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/11/2019] [Indexed: 05/12/2023]
Abstract
In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach.
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 87548, Garching, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Christoph Göbl
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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54
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Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
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55
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Zhu S, Liu W, Ding HF, Cui H, Yang L. BMP4 and Neuregulin regulate the direction of mouse neural crest cell differentiation. Exp Ther Med 2019; 17:3883-3890. [PMID: 31007733 PMCID: PMC6468403 DOI: 10.3892/etm.2019.7439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
The neural crest is a transient embryonic tissue that initially generates neural crest stem cells, which then migrate throughout the body to give rise to a variety of mature tissues. It was proposed that the fate of neural crest cells is gradually determined via environmental cues from the surrounding tissues. In the present study, neural crest cells were isolated and identified from mouse embryos. Bone morphogenetic protein 4 (BMP4) and Neuregulin (NRG) were employed to induce the differentiation of neural crest cells. Treatment with BMP4 revealed neuron-associated differentiation; cells treated with NRG exhibited differentiation into the Schwann cell lineage, a type of glia. Soft agar clonogenic and neurosphere formation assays were conducted to investigate the effects of N-Myc (MYCN) overexpression in neural crest cells; the number of colonies and neurospheres notably increased after 14 days. These findings demonstrated that the direction of cell differentiation may be affected by altering the factors present in the surrounding environment. In addition, MYCN may serve a key role in regulating neural crest cell differentiation.
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Affiliation(s)
- Shunqin Zhu
- School of Life Sciences, Southwest University, Chongqing 400715, P.R. China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, P.R. China
| | - Wanhong Liu
- School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P.R. China
| | - Han-Fei Ding
- Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, P.R. China
| | - Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, P.R. China
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56
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Kinetic and thermodynamic effects of phosphorylation on p53 binding to MDM2. Sci Rep 2019; 9:693. [PMID: 30679555 PMCID: PMC6345774 DOI: 10.1038/s41598-018-36589-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/15/2018] [Indexed: 02/03/2023] Open
Abstract
p53 is frequently mutated in human cancers. Its levels are tightly regulated by the E3 ubiquitin ligase MDM2. The complex between MDM2 and p53 is largely formed by the interaction between the N-terminal domain of MDM2 and the N-terminal transactivation (TA) domain of p53 (residues 15–29). We investigated the kinetic and thermodynamic basis of the MDM2/p53 interaction by using wild-type and mutant variants of the TA domain. We focus on the effects of phosphorylation at positions Thr18 and Ser20 including their substitution with phosphomimetics. Conformational propensities of the isolated peptides were investigated using in silico methods and experimentally by circular dichroism and 1H-NMR in aqueous solution. Both experimental and computational analyses indicate that the p53 peptides are mainly disordered in aqueous solution, with evidence of nascent helix around the Ser20-Leu25 region. Both phosphorylation and the phosphomimetics at Thr18 result in a decrease in the binding affinity by ten- to twenty-fold when compared to the wild-type. Phosphorylation and phosphomimetics at Ser20 result in a smaller decrease in the affinity. Mutation of Lys24 and Leu25 also disrupts the interaction. Our results may be useful for further development of peptide-based drugs targeting the MDM2/p53 interaction.
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57
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Rehman AU, Rahman MU, Arshad T, Chen HF. Allosteric Modulation of Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:335-357. [PMID: 31707710 DOI: 10.1007/978-981-13-8719-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The allosteric property of globular proteins is applauded as their intrinsic ability to regulate distant sites, and this property further plays a critical role in a wide variety of cellular regulatory mechanisms. Recent advancements and studies have revealed the manifestation of allostery in intrinsically disordered proteins or regions as allosteric sites present within or mediated by IDP/IDRs facilitates the signaling interactions for various biological mechanisms which would otherwise be impossible for globular proteins to regulate. This thematic review has highlighted the biological outcomes that can be achieved by the mechanism of allosteric regulation of intrinsically disordered proteins or regions. The similar mechanism has been implemented on Adenovirus 5 early region 1A and tumor apoptosis protein p53 in correspondence with other partners in binary and ternary complexes, which are the subject of the current review. Both these proteins regulate once they bind to their partners, consequently, forming either a binary or a ternary complex. Allosteric regulation by IDPs is currently a subject undergoing intense study, and the ongoing research work will ensure a better understanding of precision and efficiency of cellular regulation by them. Allosteric regulation mechanism can also be researched by intrinsically disordered protein-specific force field.
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Affiliation(s)
- Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Center for Bioinformation Technology, Shanghai, China.
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58
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Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19113614. [PMID: 30445805 PMCID: PMC6275026 DOI: 10.3390/ijms19113614] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.
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59
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Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 2018; 115:E11302-E11310. [PMID: 30420502 DOI: 10.1073/pnas.1814051115] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic resolution characterization of the full-length p53 tetramer has been hampered by its size and the presence of extensive intrinsically disordered regions at both the N and C termini. As a consequence, the structural characteristics and dynamics of the disordered regions are poorly understood within the context of the intact p53 tetramer. Here we apply trans-intein splicing to generate segmentally 15N-labeled full-length p53 constructs in which only the resonances of the N-terminal transactivation domain (NTAD) are visible in NMR spectra, allowing us to observe this region of p53 with unprecedented detail within the tetramer. The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD). Chemical-shift changes and paramagnetic spin-labeling experiments reveal that the amphipathic AD1 and AD2 motifs of the NTAD interact with the DNA-binding surface of the DBD through primarily electrostatic interactions. Importantly, this interaction inhibits binding of nonspecific DNA to the DBD while having no effect on binding to a specific p53 recognition element. We conclude that the NTAD:DBD interaction functions to enhance selectivity toward target genes by inhibiting binding to nonspecific sites in genomic DNA. This work provides some of the highest-resolution data on the disordered N terminus of the nearly 180-kDa full-length p53 tetramer and demonstrates a regulatory mechanism by which the N terminus of p53 transiently interacts with the DBD to enhance target site discrimination.
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60
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Kim DH, Han KH. PreSMo Target-Binding Signatures in Intrinsically Disordered Proteins. Mol Cells 2018; 41:889-899. [PMID: 30352491 PMCID: PMC6199570 DOI: 10.14348/molcells.2018.0192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions. The discovery of IDPs has destroyed the classical structure-function paradigm in protein science, 3-D structure = function, because IDPs even without well-folded 3-D structures are still capable of performing important biological functions and furthermore are associated with fatal diseases such as cancers, neurodegenerative diseases and viral pandemics. Pre-structured motifs (PreSMos) refer to transient local secondary structural elements present in the target-unbound state of IDPs. During the last two decades PreSMos have been steadily acknowledged as the critical determinants for target binding in dozens of IDPs. To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution. Here we present a brief developmental history of PreSMos and describe their common characteristics. We also provide a list of newly discovered PreSMos along with their functional relevance.
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Affiliation(s)
- Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141,
Korea
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61
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Borcherds WM, Daughdrill GW. Using NMR Chemical Shifts to Determine Residue-Specific Secondary Structure Populations for Intrinsically Disordered Proteins. Methods Enzymol 2018; 611:101-136. [PMID: 30471686 PMCID: PMC8130511 DOI: 10.1016/bs.mie.2018.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein disorder is a pervasive phenomenon in biology and a natural consequence of polymer evolution that facilitates cell signaling by organizing sites for posttranslational modifications and protein-protein interactions into arrays of short linear motifs that can be rearranged by RNA splicing. Disordered proteins are missing the long-range nonpolar interactions that form tertiary structures, but they often contain regions with residual secondary structure that are stabilized by protein binding. NMR spectroscopy is uniquely suited to detect residual secondary structure in a disordered protein and it can provide atomic resolution data on the structure and dynamics of disordered protein interaction sites. Here we describe how backbone chemical shifts are used for assigning residual secondary structure in disordered proteins and discuss some of the tools available for estimating secondary structure populations with a focus on disordered proteins containing different levels of alpha helical secondary structure which are stabilized by protein binding.
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Affiliation(s)
- Wade M Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
| | - Gary W Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States.
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62
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Li C, Clark LVT, Zhang R, Porebski BT, McCoey JM, Borg NA, Webb GI, Kass I, Buckle M, Song J, Woolfson A, Buckle AM. Structural Capacitance in Protein Evolution and Human Diseases. J Mol Biol 2018; 430:3200-3217. [PMID: 30111491 DOI: 10.1016/j.jmb.2018.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism that we term "structural capacitance," which results in the de novo generation of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opposed to gradualistic canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Liah V T Clark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rory Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julia M McCoey
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Amai Proteins, Prof. A. D. Bergman 2B, Suite 212, Rehovot 7670504, Israel
| | - Malcolm Buckle
- LBPA, ENS Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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63
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Chen J, Wang J, Pang L, Zhu W. Inhibiting mechanism of small molecule toward the p53-MDM2 interaction: A molecular dynamic exploration. Chem Biol Drug Des 2018; 92:1763-1777. [DOI: 10.1111/cbdd.13345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/01/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Jianzhong Chen
- School of Science; Shandong Jiaotong University; Jinan China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Laixue Pang
- School of Science; Shandong Jiaotong University; Jinan China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
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64
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Kim DH, Wright A, Han KH. An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor. BMB Rep 2018; 50:522-527. [PMID: 28946939 PMCID: PMC5683822 DOI: 10.5483/bmbrep.2017.50.10.152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 01/30/2023] Open
Abstract
A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ~70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity. We carried out heteronuclear multi-dimensional NMR experiments on hGR tau1c in a more physiological aqueous buffer solution and found that it forms three helices that are ~30% pre-populated. Since pre-populated helices in several TADs were shown to be key elements for transcriptional activity, the three pre-formed helices in hGR tau1c delineated in this study should be critical determinants of the transcriptional activity of hGR. The presence of pre-structured helices in hGR tau1c strongly suggests that the existence of pre-structured motifs in target-unbound TADs is a very broad phenomenon.
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Affiliation(s)
- Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Anthony Wright
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Nano and Bioinformatics, University of Science and Technology, Daejeon 34113, Korea
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65
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p53-Autophagy-Metastasis Link. Cancers (Basel) 2018; 10:cancers10050148. [PMID: 29783720 PMCID: PMC5977121 DOI: 10.3390/cancers10050148] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Abstract
The tumor suppressor p53 as the “guardian of the genome” plays an essential role in numerous signaling pathways that control the cell cycle, cell death and in maintaining the integrity of the human genome. p53, depending on the intracellular localization, contributes to the regulation of various cell death pathways, including apoptosis, autophagy and necroptosis. Accumulated evidence suggests that this function of p53 is closely involved in the process of cancer development. Here, present knowledge concerning a p53-autophagy-metastasis link, as well as therapeutic approaches that influence this link, are discussed.
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66
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Du Z, Yu J, Li F, Deng L, Wu F, Huang X, Bergstrand J, Widengren J, Dong C, Ren J. In Situ Monitoring of p53 Protein and MDM2 Protein Interaction in Single Living Cells Using Single-Molecule Fluorescence Spectroscopy. Anal Chem 2018; 90:6144-6151. [DOI: 10.1021/acs.analchem.8b00473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | | | | | | | | | - Jan Bergstrand
- Experimental Biomolecular
Physics, Department of Applied Physics, Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - Jerker Widengren
- Experimental Biomolecular
Physics, Department of Applied Physics, Royal Institute of Technology, Stockholm, 106 91, Sweden
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67
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Ouyang Y, Zhao L, Zhang Z. Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00067k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.
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Affiliation(s)
- Yanhua Ouyang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Likun Zhao
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Zhuqing Zhang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
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68
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Betancor-Fernández I, Timson DJ, Salido E, Pey AL. Natural (and Unnatural) Small Molecules as Pharmacological Chaperones and Inhibitors in Cancer. Handb Exp Pharmacol 2018; 245:155-190. [PMID: 28993836 DOI: 10.1007/164_2017_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations causing single amino acid exchanges can dramatically affect protein stability and function, leading to disease. In this chapter, we will focus on several representative cases in which such mutations affect protein stability and function leading to cancer. Mutations in BRAF and p53 have been extensively characterized as paradigms of loss-of-function/gain-of-function mechanisms found in a remarkably large fraction of tumours. Loss of RB1 is strongly associated with cancer progression, although the molecular mechanisms by which missense mutations affect protein function and stability are not well known. Polymorphisms in NQO1 represent a remarkable example of the relationships between intracellular destabilization and inactivation due to dynamic alterations in protein ensembles leading to loss of function. We will review the function of these proteins and their dysfunction in cancer and then describe in some detail the effects of the most relevant cancer-associated single amino exchanges using a translational perspective, from the viewpoints of molecular genetics and pathology, protein biochemistry and biophysics, structural, and cell biology. This will allow us to introduce several representative examples of natural and synthetic small molecules applied and developed to overcome functional, stability, and regulatory alterations due to cancer-associated amino acid exchanges, which hold the promise for using them as potential pharmacological cancer therapies.
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Affiliation(s)
- Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, 18071, Spain.
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69
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C-terminal region of human p53 attenuates buffalo p53 N-terminal-specific transactivation of p21 promoter by modulating tetramerization of the protein. Mol Cell Biochem 2017; 443:101-110. [PMID: 29147811 DOI: 10.1007/s11010-017-3214-7] [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: 06/02/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
Here, we have studied in p53 null H1299 lung carcinoma cells, the dominant-negative effect of human p53 (h-p53) on buffalo p53 (b-p53) induced nuclear transactivation-dependent function. Recently, we have isolated and cloned the full-length cDNA of buffalo p53. Buffalo and human p53 proteins exhibit a high degree of structural and functional similarities. In transiently transfected H1299 cell line b-p53 appeared to be more sensitive to Mdm2-mediated degradation as compared to h-p53, although its ability to transactivate p21 promoter was stronger than that of the human counterpart. This higher transactivation ability of b-p53 was lost in the presence of h-p53 suggesting, a dominant-negative effect of h-p53 on b-p53's transactivation of p21 promoter. Both human and buffalo p53 proteins could hetero-oligomerize but the b-p53 could tetramerize much faster than the h-p53. A chimeric cDNA construct of human p53 was made where the 1-260 bp N-terminus was replaced with buffalo p53 counterpart and expressed in H1299 cell line. The tetramerization ability of the chimeric p53 protein was comparable to that of h-p53. Properties of b-p53 like stronger p21 transactivation and super sensitivity to Mdm2 mediated degradation were lacking in the chimeric protein. Thus, it is suggested that faster ability of tetramerization as well as higher transactivation property of buffalo p53 is determined by the interplay of N- and C-terminal domains through macromolecular interactions.
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70
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Yadahalli S, Li J, Lane DP, Gosavi S, Verma CS. Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations. Sci Rep 2017; 7:15600. [PMID: 29142290 PMCID: PMC5688104 DOI: 10.1038/s41598-017-15930-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022] Open
Abstract
The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. Complementing earlier observations, the current study suggests that the p53 peptides largely follow the ‘conformational selection’ paradigm in their recognition of and complexation by MDM2 while the 12/1 peptides likely undergo some element of conformational selection but are mostly driven by ‘binding induced folding’. This hypothesis is further supported by pulling simulations that pull the peptides away from their bound states with MDM2. This data extends the earlier mechanisms proposed to rationalize the entropically driven binding of the p53 set and the enthalpically driven binding of the 12/1 set. Using our hypothesis, we suggest mutations to the 12/1 peptide that increase its helicity in simulations and may, in turn, shift the binding towards conformational selection. In summary, understanding the conformational landscapes of the MDM2-binding peptides may suggest new peptide designs with bespoke binding mechanisms.
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Affiliation(s)
- Shilpa Yadahalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India.,Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Manipal University, Madhav Nagar, Manipal, 576104, India.,p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Jianguo Li
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore, 168751, Singapore
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 11758, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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71
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Zhu S, Khatun R, Lento C, Sheng Y, Wilson DJ. Enhanced Binding Affinity via Destabilization of the Unbound State: A Millisecond Hydrogen–Deuterium Exchange Study of the Interaction between p53 and a Pleckstrin Homology Domain. Biochemistry 2017; 56:4127-4133. [DOI: 10.1021/acs.biochem.7b00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shaolong Zhu
- Department
of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Rahima Khatun
- Department
of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department
of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Yi Sheng
- Department
of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department
of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre
for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
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72
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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73
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Liu Y, Wu J, Sun N, Tu C, Shi X, Cheng H, Liu S, Li S, Wang Y, Zheng Y, Uversky VN. Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles. J Proteome Res 2017; 16:2393-2409. [PMID: 28525284 DOI: 10.1021/acs.jproteome.6b01045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R0mm and R15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R0mm and R15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R0mm and R15mm, respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.
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Affiliation(s)
- Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Jiahui Wu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo , 285 Kapoor Hall, Buffalo, New York14260, United States
| | - Xiaoying Shi
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Hua Cheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Simu Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Shuiming Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yong Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Yizhi Zheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University , Nanhai Ave 3688, Shenzhen, Guangdong 518060, China
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard MDC07, Tampa, Florida 33612, United States
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences , Institutskaya str., 7, Pushchino, Moscow region 142290, Russia
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74
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Landau KS, Na I, Schenck RO, Uversky VN. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. Asian J Androl 2017; 18:662-72. [PMID: 27453073 PMCID: PMC5000786 DOI: 10.4103/1008-682x.184999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease.
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Affiliation(s)
- Kevin S Landau
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ryan O Schenck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia,
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75
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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76
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Lee C, Kim DH, Lee SH, Su J, Han KH. Structural investigation on the intrinsically disordered N-terminal region of HPV16 E7 protein. BMB Rep 2017; 49:431-6. [PMID: 27418281 PMCID: PMC5070730 DOI: 10.5483/bmbrep.2016.49.8.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 11/28/2022] Open
Abstract
Human papillomavirus (HPV) is the major cause of cervical cancer, a deadly threat to millions of females. The early oncogene product (E7) of the high-risk HPV16 is the primary agent associated with HPV-related cervical cancers. In order to understand how E7 contributes to the transforming activity, we investigated the structural features of the flexible N-terminal region (46 residues) of E7 by carrying out N-15 heteronuclear NMR experiments and replica exchange molecular dynamics simulations. Several NMR parameters as well as simulation ensemble structures indicate that this intrinsically disordered region of E7 contains two transient (10-20% populated) helical pre-structured motifs that overlap with important target binding moieties such as an E2F-mimic motif and a pRb-binding LXCXE segment. Presence of such target-binding motifs in HPV16 E7 provides a reasonable explanation for its promiscuous target-binding behavior associated with its transforming activity. [BMB Reports 2016; 49(8): 431-436]
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Affiliation(s)
- Chewook Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Do-Hyoung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Si-Hyung Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jiulong Su
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141; Department of Bioinformatics, University of Science and Technology, Daejeon 34113, Korea
| | - Kyou-Hoon Han
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141; Department of Bioinformatics, University of Science and Technology, Daejeon 34113, Korea
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77
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Raj N, Attardi LD. The Transactivation Domains of the p53 Protein. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026047. [PMID: 27864306 DOI: 10.1101/cshperspect.a026047] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The p53 tumor suppressor is a transcriptional activator, with discrete domains that participate in sequence-specific DNA binding, tetramerization, and transcriptional activation. Mutagenesis and reporter studies have delineated two distinct activation domains (TADs) and specific hydrophobic residues within these TADs that are critical for their function. Knockin mice expressing p53 mutants with alterations in either or both of the two TADs have revealed that TAD1 is critical for responses to acute DNA damage, whereas both TAD1 and TAD2 participate in tumor suppression. Biochemical and structural studies have identified factors that bind either or both TADs, including general transcription factors (GTFs), chromatin modifiers, and negative regulators, helping to elaborate a model through which p53 activates transcription. Posttranslational modifications (PTMs) of the p53 TADs through phosphorylation also regulate TAD activity. Together, these studies on p53 TADs provide great insight into how p53 serves as a tumor suppressor.
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Affiliation(s)
- Nitin Raj
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
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78
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Kim D, Lee C, Lee S, Kim K, Han JJ, Cha E, Lim J, Cho Y, Hong S, Han K. The Mechanism of p53 Rescue by SUSP4. Angew Chem Int Ed Engl 2016; 56:1278-1282. [DOI: 10.1002/anie.201607819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Do‐Hyoung Kim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Chewook Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Si‐Hyung Lee
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Kyung‐Tae Kim
- Molecular Epidemology Branch Research Institute National Cancer Center 323 Ilsandong-gu, Goyang-si Gyeonggi-do 10408 Korea
| | - Joan J. Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- College of Human Medicine Michigan State University East Lansing MI 48824 USA
| | - Eun‐Ji Cha
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ji‐Eun Lim
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
| | - Ye‐Jin Cho
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
| | - Seung‐Hee Hong
- Division of Food Science and Culinary Art, Food and Nutrition Major Shinhan University 95 Hoam-ro, Uijeongbu-si Gyeonggi-do 11644 Korea
| | - Kyou‐Hoon Han
- Genome Editing Research Center Korea Research Institute of Bioscience and Biotechnology 125, Gwahak-ro, Yuseong-gu Daejeon 34141 Korea
- Department of Bioinformatics University of Science and Technology 217, Gajeong-ro, Yuseong-gu Daejoen 34113 Korea
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79
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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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80
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Abstract
The p53 tumor suppressor is highly regulated at the level of protein degradation and transcriptional activity. The key players of the pathway, p53, MDM2, and MDMX are present at multiple conformational states that are responsive to regulation by post-translational modifications and protein-protein interactions. The structures of major functional domains of these proteins have been determined, but the mechanisms of several intrinsically disordered regions remain unclear despite their critical roles in signaling and regulation. Recent studies suggest that these disordered regions function in part by dynamic intra molecular interactions with the structured domains to regulate p53 DNA binding, MDM2 ubiquitin E3 ligase activity, and MDMX-p53 binding. These findings provide new insight on how p53 is controlled by various stress signals, and suggest potential targets for the search of allosteric regulators of the p53 pathway.
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Affiliation(s)
- Jiandong Chen
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
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81
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Rehman Z, Sadia H, Fahim A, Niazi UHK, Azam MZ. Mutational analysis and interactions of HBV preS1 with asialoglycoprotein receptor. Future Virol 2016. [DOI: 10.2217/fvl-2016-0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: The mutations in preS1 of a large envelop protein of HBV may have profound implications in HBV receptor binding to hepatocytes and subsequent entry of the virus into host cells. Aims: This study aimed to identify the mutations in preS1 region and the receptor binding interactions of preS1 with hepatocytes. Methods: The mutations were searched through direct sequencing of the preS1 region. Sequence analysis was done through ClustalX and Jalview. Ab initio modeling of preS1 was done through Rosetta and QUARK followed by glycosylation of best model of preS1. Finally the interactions of preS1 with ASGPR was studied using PatchDock and analysis was done using MOE and pyMol. Results: Sequence comparison revealed changes in the preS1 region. Ab initio modeling results showed that preS1 is an overall unstructured protein with the presence of three structural motifs. Docking of preS1 with asialoglycoprotein receptor showed mostly hydrophobic interactions. Conclusion: In conclusion, preS1 sequences from Pakistani isolates were found to be 90% conserved and the predicted structure of preS1 was near to native structure.
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Affiliation(s)
- Zaira Rehman
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology, Islamabad, Pakistan
| | - Hajra Sadia
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology, Islamabad, Pakistan
| | - Ammad Fahim
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology, Islamabad, Pakistan
| | - Umer HK Niazi
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion, Wales SY23 3FG, UK
| | - Muhammad Z Azam
- National Institute of Liver & Gastrointestinal Diseases, Dow University of Health Sciences, Karachi, Pakistan
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82
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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept. Int J Mol Sci 2016; 17:ijms17111874. [PMID: 27834926 PMCID: PMC5133874 DOI: 10.3390/ijms17111874] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/10/2023] Open
Abstract
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based hetero-tetramers, and is able to interact with many binding partners. It contains numerous posttranslational modifications, has several isoforms generated by alternative splicing, alternative promoter usage or alternative initiation of translation, and is commonly mutated in different cancers. Therefore, p53 serves as an important illustration of the protein structure–function continuum concept, where the generation of multiple proteoforms by various mechanisms defines the ability of this protein to have a multitude of structurally and functionally different states. Considering p53 in the light of a proteoform-based structure–function continuum represents a non-canonical and conceptually new contemplation of structure, regulation, and functionality of this important protein.
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83
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Xie M, Hansen AL, Yuan J, Brüschweiler R. Residue-Specific Interactions of an Intrinsically Disordered Protein with Silica Nanoparticles and their Quantitative Prediction. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:24463-24468. [PMID: 28337243 PMCID: PMC5358802 DOI: 10.1021/acs.jpcc.6b08213] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Elucidation of the driving forces that govern interactions between nanoparticles and intrinsically disordered proteins (IDP) is important for the understanding of the effect of nanoparticles in living systems and for the design of new nanoparticle-based assays to monitor health and combat disease. The quantitative interaction profile of the intrinsically disordered transactivation domain of p53 and its mutants with anionic silica nanoparticles is reported at atomic resolution using nuclear magnetic spin relaxation experiments. These profiles are analyzed with a novel interaction model that is based on a quantitative nanoparticle affinity scale separately derived for the 20 natural amino acids. The results demonstrate how the interplay of attractive and repulsive Coulomb interactions with hydrophobic effects is responsible for the sequence-dependent binding of a disordered protein to nanoparticles.
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Affiliation(s)
- Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jiaqi Yuan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
- To whom correspondence should be addressed: Rafael Brüschweiler, Ph.D., Department of Chemistry and Biochemistry, CBEC building, The Ohio State University, Columbus, Ohio 43210, , Tel. 614-688-2083
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84
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Costa DCF, de Oliveira GAP, Cino EA, Soares IN, Rangel LP, Silva JL. Aggregation and Prion-Like Properties of Misfolded Tumor Suppressors: Is Cancer a Prion Disease? Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023614. [PMID: 27549118 DOI: 10.1101/cshperspect.a023614] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Prion diseases are disorders that share several characteristics that are typical of many neurodegenerative diseases. Recently, several studies have extended the prion concept to pathological aggregation in malignant tumors involving misfolded p53, a tumor-suppressor protein. The aggregation of p53 and its coaggregation with p53 family members, p63 and p73, have been shown. Certain p53 mutants exert a dominant-negative regulatory effect on wild-type (WT) p53. The basis for this dominant-negative effect is that amyloid-like mutant p53 converts WT p53 into an aggregated species, leading to a gain-of-function (GoF) phenotype and the loss of its tumor-suppressor function. Recently, it was shown that p53 aggregates can be internalized by cells and can coaggregate with endogenous p53, corroborating the prion-like properties of p53 aggregates. The prion-like behavior of oncogenic p53 mutants provides an explanation for its dominant-negative and GoF properties, including the high metastatic potential of cancer cells carrying p53 mutations. The inhibition of p53 aggregation appears to represent a promising target for therapeutic intervention in patients with malignant tumors.
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Affiliation(s)
- Danielly C F Costa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto de Nutrição, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550-013, Brazil
| | - Guilherme A P de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Elio A Cino
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Iaci N Soares
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Luciana P Rangel
- Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil Instituto Nacional de Ciência e Tecnologia (INCT) de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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85
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Tompa P, Han KH, Bokor M, Kamasa P, Tantos Á, Fritz B, Kim DH, Lee C, Verebélyi T, Tompa K. Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment. BMB Rep 2016; 49:497-501. [PMID: 27418282 PMCID: PMC5227142 DOI: 10.5483/bmbrep.2016.49.9.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/18/2016] [Accepted: 03/26/2016] [Indexed: 11/28/2022] Open
Abstract
Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501].
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Affiliation(s)
- Peter Tompa
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Kyou-Hoon Han
- Genome Editing Research Center, Division of Biomedical Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141
- Department of Nano & Bioinformatics, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest H-1525, Hungary
| | - Pawel Kamasa
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest H-1525, Hungary
| | - Ágnes Tantos
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Beáta Fritz
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Do-Hyoung Kim
- Genome Editing Research Center, Division of Biomedical Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141
| | - Chewook Lee
- Genome Editing Research Center, Division of Biomedical Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141
| | - Tamás Verebélyi
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest H-1525, Hungary
| | - Kálmán Tompa
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest H-1525, Hungary
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86
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Scholes NS, Weinzierl ROJ. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions. PLoS Comput Biol 2016; 12:e1004935. [PMID: 27175900 PMCID: PMC4866707 DOI: 10.1371/journal.pcbi.1004935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/21/2016] [Indexed: 12/13/2022] Open
Abstract
Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators.
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Affiliation(s)
- Natalie S. Scholes
- Imperial College London, Department of Life Sciences, London, United Kingdom
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87
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Laptenko O, Shiff I, Freed-Pastor W, Zupnick A, Mattia M, Freulich E, Shamir I, Kadouri N, Kahan T, Manfredi J, Simon I, Prives C. The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Mol Cell 2016; 57:1034-1046. [PMID: 25794615 DOI: 10.1016/j.molcel.2015.02.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/23/2014] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
Abstract
DNA binding by numerous transcription factors including the p53 tumor suppressor protein constitutes a vital early step in transcriptional activation. While the role of the central core DNA binding domain (DBD) of p53 in site-specific DNA binding has been established, the contribution of the sequence-independent C-terminal domain (CTD) is still not well understood. We investigated the DNA-binding properties of a series of p53 CTD variants using a combination of in vitro biochemical analyses and in vivo binding experiments. Our results provide several unanticipated and interconnected findings. First, the CTD enables DNA binding in a sequence-dependent manner that is drastically altered by either its modification or deletion. Second, dependence on the CTD correlates with the extent to which the p53 binding site deviates from the canonical consensus sequence. Third, the CTD enables stable formation of p53-DNA complexes to divergent binding sites via DNA-induced conformational changes within the DBD itself.
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Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Idit Shiff
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Will Freed-Pastor
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Andrew Zupnick
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Melissa Mattia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ella Freulich
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Inbal Shamir
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Noam Kadouri
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Tamar Kahan
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - James Manfredi
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel.
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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88
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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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89
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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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90
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Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein. Proc Natl Acad Sci U S A 2016; 113:E1853-62. [PMID: 26976603 DOI: 10.1073/pnas.1602487113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An important component of the activity of p53 as a tumor suppressor is its interaction with the transcriptional coactivators cyclic-AMP response element-binding protein (CREB)-binding protein (CBP) and p300, which activate transcription of p53-regulated stress response genes and stabilize p53 against ubiquitin-mediated degradation. The highest affinity interactions are between the intrinsically disordered N-terminal transactivation domain (TAD) of p53 and the TAZ1 and TAZ2 domains of CBP/p300. The NMR spectra of simple binary complexes of the TAZ1 and TAZ2 domains with the p53TAD suffer from exchange broadening, but innovations in construct design and isotopic labeling have enabled us to obtain high-resolution structures using fusion proteins, uniformly labeled in the case of the TAZ2-p53TAD fusion and segmentally labeled through transintein splicing for the TAZ1-p53TAD fusion. The p53TAD is bipartite, with two interaction motifs, termed AD1 and AD2, which fold to form short amphipathic helices upon binding to TAZ1 and TAZ2 whereas intervening regions of the p53TAD remain flexible. Both the AD1 and AD2 motifs bind to hydrophobic surfaces of the TAZ domains, with AD2 making more extensive hydrophobic contacts consistent with its greater contribution to the binding affinity. Binding of AD1 and AD2 is synergistic, and structural studies performed with isolated motifs can be misleading. The present structures of the full-length p53TAD complexes demonstrate the versatility of the interactions available to an intrinsically disordered domain containing bipartite interaction motifs and provide valuable insights into the structural basis of the affinity changes that occur upon stress-related posttranslational modification.
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91
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Coffill CR, Lee AP, Siau JW, Chee SM, Joseph TL, Tan YS, Madhumalar A, Tay BH, Brenner S, Verma CS, Ghadessy FJ, Venkatesh B, Lane DP. The p53-Mdm2 interaction and the E3 ligase activity of Mdm2/Mdm4 are conserved from lampreys to humans. Genes Dev 2016; 30:281-92. [PMID: 26798135 PMCID: PMC4743058 DOI: 10.1101/gad.274118.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/14/2015] [Indexed: 01/09/2023]
Abstract
Here, Coffill et al. characterize Tp53, Tp63, and Tp73 in a jawless vertebrate, the Japanese lamprey, as well as the Mdm2 and Mdm4 genes using genome analysis. Functional analysis reveals conservation of p63 and p73 compared with p53, which shows substantial variability within the C-terminal and N-terminal domains, and that lamprey Mdm2 degrades human p53 with great efficiency; however, this interaction is not inhibited by currently available small molecule inhibitors of the human HDM2 protein. The extant jawless vertebrates, represented by lampreys and hagfish, are the oldest group of vertebrates and provide an interesting genomic evolutionary pivot point between invertebrates and jawed vertebrates. Through genome analysis of one of these jawless vertebrates, the Japanese lamprey (Lethenteron japonicum), we identified all three members of the important p53 transcription factor family—Tp53, Tp63, and Tp73—as well as the Mdm2 and Mdm4 genes. These genes and their products are significant cellular regulators in human cancer, and further examination of their roles in this most distant vertebrate relative sheds light on their origin and coevolution. Their important role in response to DNA damage has been highlighted by the discovery of multiple copies of the Tp53 gene in elephants. Expression of lamprey p53, Mdm2, and Mdm4 proteins in mammalian cells reveals that the p53–Mdm2 interaction and the Mdm2/Mdm4 E3 ligase activity existed in the common ancestor of vertebrates and have been conserved for >500 million years of vertebrate evolution. Lamprey Mdm2 degrades human p53 with great efficiency, but this interaction is not blocked by currently available small molecule inhibitors of the human HDM2 protein, suggesting utility of lamprey Mdm2 in the study of the human p53 signaling pathway.
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Affiliation(s)
- Cynthia R Coffill
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore 138648
| | - Alison P Lee
- Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673
| | - Jia Wei Siau
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore 138648
| | - Sharon M Chee
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore 138648
| | | | - Yaw Sing Tan
- Bioinformatics Institute, A*STAR, Singapore 138671
| | - Arumugam Madhumalar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Boon-Hui Tay
- Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673
| | - Sydney Brenner
- Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673; Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR, Singapore 138671; School of Biological Sciences, Nanyang Technological University, Singapore 637551; Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Farid J Ghadessy
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore 138648
| | - Byrappa Venkatesh
- Institute of Molecular and Cellular Biology, A*STAR, Singapore 138673; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - David P Lane
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore 138648
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92
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Abstract
Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC)
- Brussels
- Belgium
- Vrije Universiteit Brussel
- Brussels
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93
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Chattopadhyay S, Ajani H, Basu G. Effect of introducing aib in a designed helical inhibitor of hdm2-p53 interaction: A molecular dynamics study. Biopolymers 2015; 106:51-61. [PMID: 26537425 DOI: 10.1002/bip.22761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/15/2015] [Accepted: 11/01/2015] [Indexed: 11/09/2022]
Abstract
Although p53 is an intrinsically disordered protein, upon binding to Hdm2, a short stretch (residues 19-25) comprising the binding epitope assumes a helical backbone. Because the allowed conformational space of α-aminoisobutyric acid (Aib) is restricted to only the helical basin, Aib-containing helical mimics of p53 (binding epitope) are expected to inhibit interaction between p53 and Hdm2 with a much stronger affinity than the wild type p53 peptide (binding epitope), due to the entropic advantage associated with Aib. However, the IC50 values for the disruption of p53-Hdm2 interaction by Aib-p53 peptides and wild type p53 peptide were found to be comparable (J. Peptide Res. 2002, 60:88-94). To understand why incorporation of Aib didn't substantially increase Hdm2 affinity of Aib-p53 peptides, a series of molecular dynamics simulations were performed. It was found that despite stabilizing a helical backbone in the unbound state, the Aib residues in Aib-p53 peptide arrested two functionally important side-chains (F19 and W23) in non-productive conformations, resulting in relative side-chain orientations of the binding triad F19-W23-L26 incompatible with the bound conformation. Therefore, although a Aib-induced pre-formed helical peptide backbone in the unbound state is expected to favor binding, the locked side-chain orientations of the binding triad in non-productive modes would disfavor binding. This study shows that when using Aib to design functionally important helical peptides, care must be taken to consider potential interactions between side-chains of neighboring residues and Aib in the unbound state.
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Affiliation(s)
- Sarbani Chattopadhyay
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Haresh Ajani
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.,National Institute of Pharmaceutical Education and Research, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
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94
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Aït-Bara S, Carpousis AJ. RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs. Mol Microbiol 2015; 97:1021-135. [PMID: 26096689 DOI: 10.1111/mmi.13095] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/29/2022]
Abstract
Ribonuclease E (RNase E) of Escherichia coli, which is the founding member of a widespread family of proteins in bacteria and chloroplasts, is a fascinating enzyme that still has not revealed all its secrets. RNase E is an essential single-strand specific endoribonuclease that is involved in the processing and degradation of nearly every transcript in E. coli. A striking enzymatic property is a preference for substrates with a 5' monophosphate end although recent work explains how RNase E can overcome the protection afforded by the 5' triphosphate end of a primary transcript. Other features of E. coli RNase E include its interaction with enzymes involved in RNA degradation to form the multienzyme RNA degradosome and its localization to the inner cytoplasmic membrane. The N-terminal catalytic core of the RNase E protomer associates to form a tetrameric holoenzyme. Each RNase E protomer has a large C-terminal intrinsically disordered (ID) noncatalytic region that contains sites for interactions with protein components of the RNA degradosome as well as RNA and phospholipid bilayers. In this review, RNase E homologs have been classified into five types based on their primary structure. A recent analysis has shown that type I RNase E in the γ-proteobacteria forms an orthologous group of proteins that has been inherited vertically. The RNase E catalytic core and a large ID noncatalytic region containing an RNA binding motif and a membrane targeting sequence are universally conserved features of these orthologs. Although the ID noncatalytic region has low composition and sequence complexity, it is possible to map microdomains, which are short linear motifs that are sites of interaction with protein and other ligands. Throughout bacteria, the composition of the multienzyme RNA degradosome varies with species, but interactions with exoribonucleases (PNPase, RNase R), glycolytic enzymes (enolase, aconitase) and RNA helicases (DEAD-box proteins, Rho) are common. Plasticity in RNA degradosome composition is due to rapid evolution of RNase E microdomains. Characterization of the RNase E-PNPase interaction in α-proteobacteria, γ-proteobacteria and cyanobacteria suggests that it arose independently several times during evolution, thus conferring an advantage in control and coordination of RNA processing and degradation.
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Affiliation(s)
- Soraya Aït-Bara
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte, Institut, National de la Santé et de la Recherche Médicale & Université d'Auvergne, Clermont-Ferrand, 63001, France
| | - Agamemnon J Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100, Centre National de la Recherche Scientifique et Université de Toulouse 3, Toulouse, 31062, France
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95
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Dogan J, Jonasson J, Andersson E, Jemth P. Binding Rate Constants Reveal Distinct Features of Disordered Protein Domains. Biochemistry 2015; 54:4741-50. [DOI: 10.1021/acs.biochem.5b00520] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jakob Dogan
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Josefin Jonasson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Eva Andersson
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Per Jemth
- Department
of Medical Biochemistry
and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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96
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Rehman Z, Fahim A, Sadia H. Deciphering the mystery of hepatitis B virus receptors: A historical perspective. Virusdisease 2015; 26:97-104. [PMID: 26396975 DOI: 10.1007/s13337-015-0260-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 06/25/2015] [Indexed: 12/22/2022] Open
Abstract
Hepatitis B virus is one of the major reasons of viral hepatitis with an estimated 350 million infected patients worldwide. Although, the virus was discovered and cloned more than three decades ago, its entry mechanism has still been in investigation. Numerous potential candidates have been proposed and investigated rigorously to reveal HBV entry mechanism and to unveil the first door of viral entry to hepatocytes. This review provides a short account of role of receptors for entry of HBV into hepatocytes. The viral preS1 region of large surface protein is involved in the attachment of HBV to hepatocytes. The putative attachment site of HBV is located at amino acids 21-47 of preS1. So far, several proteins have been proposed to interact with these different regions of the preS1 domain which includes human immunoglobulin A receptor, glyceraldehyde-3-phosphate dehydrogenase, interleukin-6, a 31-kDa protein, HBV binding factor, asialoglycoprotein receptor, nascent polypeptide-associated complex α polypeptide, lipoprotein lipase, hepatocyte-associated heparan sulfate proteoglycans, glucose-regulated protein 75. However, none of them have appeared to be generally accepted as a true receptor for the virus until recently when sodium taurocholate cotransporting polypeptide identified as HBV entry receptor. Current review provides scientific historical perspective of various candidates known to be interacting with preS1 of HBV for their possible role in viral entry.
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Affiliation(s)
- Zaira Rehman
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
| | - Ammad Fahim
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
| | - Hajra Sadia
- Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
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97
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Zhan YA, Ytreberg FM. The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans. Arch Biochem Biophys 2015; 575:22-9. [PMID: 25840370 PMCID: PMC5444545 DOI: 10.1016/j.abb.2015.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/11/2022]
Abstract
The cis and trans conformations of the Xaa-Pro (Xaa: any amino acid) peptide bond are thermodynamically stable while other peptide bonds strongly prefer trans. The effect of proline cis-trans isomerization on protein binding has not been thoroughly investigated. In this study, computer simulations were used to calculate the absolute binding affinity for a p53 peptide (residues 17-29) to MDM2 for both cis and trans isomers of the p53 proline in position 27. Results show that the cis isomer of p53(17-29) binds more weakly to MDM2 than the trans isomer, and that this is primarily due to the difference in the free energy cost associated with the loss of conformational entropy of p53(17-29) when it binds to MDM2. The population of cis p53(17-29) was estimated to be 0.8% of the total population in the bound state. The stronger binding of trans p53(17-29) to MDM2 compared to cis may leave a minimal level of p53 available to respond to cellular stress. This study demonstrates that it is feasible to estimate the absolute binding affinity for an intrinsically disordered protein fragment binding to an ordered protein that are in good agreement with experimental results.
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Affiliation(s)
- Yingqian Ada Zhan
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - F Marty Ytreberg
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States; Department of Physics, University of Idaho, Moscow, ID, United States.
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98
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de Oliveira GAP, Rangel LP, Costa DC, Silva JL. Misfolding, Aggregation, and Disordered Segments in c-Abl and p53 in Human Cancer. Front Oncol 2015; 5:97. [PMID: 25973395 PMCID: PMC4413674 DOI: 10.3389/fonc.2015.00097] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/10/2015] [Indexed: 01/31/2023] Open
Abstract
The current understanding of the molecular mechanisms that lead to cancer is not sufficient to explain the loss or gain of function in proteins related to tumorigenic processes. Among them, more than 100 oncogenes, 20-30 tumor-suppressor genes, and hundreds of genes participating in DNA repair and replication have been found to play a role in the origins of cancer over the last 25 years. The phosphorylation of serine, threonine, or tyrosine residues is a critical step in cellular growth and development and is achieved through the tight regulation of protein kinases. Phosphorylation plays a major role in eukaryotic signaling as kinase domains are found in 2% of our genes. The deregulation of kinase control mechanisms has disastrous consequences, often leading to gains of function, cell transformation, and cancer. The c-Abl kinase protein is one of the most studied targets in the fight against cancer and is a hotspot for drug development because it participates in several solid tumors and is the hallmark of chronic myelogenous leukemia. Tumor suppressors have the opposite effects. Their fundamental role in the maintenance of genomic integrity has awarded them a role as the guardians of DNA. Among the tumor suppressors, p53 is the most studied. The p53 protein has been shown to be a transcription factor that recognizes and binds to specific DNA response elements and activates gene transcription. Stress triggered by ionizing radiation or other mutagenic events leads to p53 phosphorylation and cell-cycle arrest, senescence, or programed cell death. The p53 gene is the most frequently mutated gene in cancer. Mutations in the DNA-binding domain are classified as class I or class II depending on whether substitutions occur in the DNA contact sites or in the protein core, respectively. Tumor-associated p53 mutations often lead to the loss of protein function, but recent investigations have also indicated gain-of-function mutations. The prion-like aggregation of mutant p53 is associated with loss-of-function, dominant-negative, and gain-of-function effects. In the current review, we focused on the most recent insights into the protein structure and function of the c-Abl and p53 proteins that will provide us guidance to understand the loss and gain of function of these misfolded tumor-associated proteins.
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Affiliation(s)
- Guilherme A. P. de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana P. Rangel
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielly C. Costa
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jerson L. Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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99
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Ganguly D, Chen J. Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations. PLoS Comput Biol 2015; 11:e1004247. [PMID: 25897952 PMCID: PMC4405366 DOI: 10.1371/journal.pcbi.1004247] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles. Tumor suppressor p53 is the most frequently mutated protein in human cancers. Clinical studies have suggested that the type of p53 mutation can be linked to cancer prognosis, response to drug treatment, and patient survival. It is thus crucial to understand the molecular basis of p53 inactivation by various types of mutations, so as to understand the biological outcomes and assess potential cancer intervention strategies. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in an implicit solvent protein force field. The calculated ensembles are in quantitative agreement with several types of existing NMR data on the wild-type protein and the K24N mutant. The results suggest that, while all sequences sample a similar set of conformational substates, cancer mutants could introduce both local and long-range structural modulations and in turn perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The study also reveals important limitations in implicit solvent for simulations of disordered proteins like p53-TAD.
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Affiliation(s)
- Debabani Ganguly
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- Indian Institute of Engineering Science and Technology, Shibpur Howrah, India
- * E-mail: (DG); (JC)
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail: (DG); (JC)
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100
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Frege T, Uversky VN. Intrinsically disordered proteins in the nucleus of human cells. Biochem Biophys Rep 2015; 1:33-51. [PMID: 29124132 PMCID: PMC5668563 DOI: 10.1016/j.bbrep.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the disordered nuclear proteins.
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Affiliation(s)
- Telma Frege
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- GenomeNext LLC, 175 South 3rd Street, Suite 200, Columbus OH 43215, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer׳s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Correspondence to: Department of Molecular, Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC07, Tampa, FL 33612, USA. Tel.: +1 813 974 5816; fax: +1 813 974 7357.
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