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Benedetti R, Di Crosta M, D’Orazi G, Cirone M. Post-Translational Modifications (PTMs) of mutp53 and Epigenetic Changes Induced by mutp53. BIOLOGY 2024; 13:508. [PMID: 39056701 PMCID: PMC11273943 DOI: 10.3390/biology13070508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Wild-type (wt) p53 and mutant forms (mutp53) play a key but opposite role in carcinogenesis. wtP53 acts as an oncosuppressor, preventing oncogenic transformation, while mutp53, which loses this property, may instead favor this process. This suggests that a better understanding of the mechanisms activating wtp53 while inhibiting mutp53 may help to design more effective anti-cancer treatments. In this review, we examine possible PTMs with which both wt- and mutp53 can be decorated and discuss how their manipulation could represent a possible strategy to control the stability and function of these proteins, focusing in particular on mutp53. The impact of ubiquitination, phosphorylation, acetylation, and methylation of p53, in the context of several solid and hematologic cancers, will be discussed. Finally, we will describe some of the recent studies reporting that wt- and mutp53 may influence the expression and activity of enzymes responsible for epigenetic changes such as acetylation, methylation, and microRNA regulation and the possible consequences of such changes.
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Affiliation(s)
- Rossella Benedetti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Michele Di Crosta
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Gabriella D’Orazi
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio”, 66013 Chieti, Italy
| | - Mara Cirone
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
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2
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Zhang N, Wu J, Zheng Q. Chemical proteomics approaches for protein post-translational modification studies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141017. [PMID: 38641087 DOI: 10.1016/j.bbapap.2024.141017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The diversity and dynamics of proteins play essential roles in maintaining the basic constructions and functions of cells. The abundance of functional proteins is regulated by the transcription and translation processes, while the alternative splicing enables the same gene to generate distinct protein isoforms of different lengths. Beyond the transcriptional and translational regulations, post-translational modifications (PTMs) are able to further expand the diversity and functional scope of proteins. PTMs have been shown to make significant changes in the surface charges, structures, activation states, and interactome of proteins. Due to the functional complexity, highly dynamic nature, and low presence percentage, the study of protein PTMs remains challenging. Here we summarize and discuss the major chemical biology tools and chemical proteomics approaches to enrich and investigate the protein PTM of interest.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Jinghua Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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3
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Rajczewski A, Ndreu L, Vryonidis E, Hurben AK, Jamshidi S, Griffin TJ, Törnqvist MÅ, Tretyakova NY, Karlsson I. Mass Spectrometry-Based Strategies for Assessing Human Exposure Using Hemoglobin Adductomics. Chem Res Toxicol 2023; 36:2019-2030. [PMID: 37963067 PMCID: PMC10731639 DOI: 10.1021/acs.chemrestox.3c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Hemoglobin (Hb) adducts are widely used in human biomonitoring due to the high abundance of hemoglobin in human blood, its reactivity toward electrophiles, and adducted protein stability for up to 120 days. In the present paper, we compared three methods of analysis of hemoglobin adducts: mass spectrometry of derivatized N-terminal Val adducts, mass spectrometry of N-terminal adducted hemoglobin peptides, and limited proteolysis mass spectrometry . Blood from human donors was incubated with a selection of contact allergens and other electrophiles, after which hemoglobin was isolated and subjected to three analysis methods. We found that the FIRE method was able to detect and reliably quantify N-terminal adducts of acrylamide, acrylic acid, glycidic acid, and 2,3-epoxypropyl phenyl ether (PGE), but it was less efficient for 2-methyleneglutaronitrile (2-MGN) and failed to detect 1-chloro-2,4-dinitrobenzene (DNCB). By contrast, bottom-up proteomics was able to determine the presence of adducts from all six electrophiles at both the N-terminus and reactive hemoglobin side chains. Limited proteolysis mass spectrometry, studied for four contact allergens (three electrophiles and a metal salt), was able to determine the presence of covalent hemoglobin adducts with one of the three electrophiles (DNCB) and coordination complexation with the nickel salt. Together, these approaches represent complementary tools in the study of the hemoglobin adductome.
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Affiliation(s)
- Andrew
T. Rajczewski
- Department
of Biochemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Lorena Ndreu
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Efstathios Vryonidis
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Alexander K. Hurben
- Department
of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Sara Jamshidi
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Timothy J. Griffin
- Department
of Biochemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | | | - Natalia Y. Tretyakova
- Department
of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Isabella Karlsson
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
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4
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Krois AS, Park S, Martinez-Yamout MA, Dyson HJ, Wright PE. Mapping Interactions of the Intrinsically Disordered C-Terminal Regions of Tetrameric p53 by Segmental Isotope Labeling and NMR. Biochemistry 2022; 61:2709-2719. [PMID: 36380579 PMCID: PMC9788666 DOI: 10.1021/acs.biochem.2c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The C-terminal region of the tumor suppressor protein p53 contains three domains, nuclear localization signal (NLS), tetramerization domain (TET), and C-terminal regulatory domain (CTD), which are essential for p53 function. Characterization of the structure and interactions of these domains within full-length p53 has been limited by the overall size and flexibility of the p53 tetramer. Using trans-intein splicing, we have generated full-length p53 constructs in which the C-terminal region is isotopically labeled with 15N for NMR analysis, allowing us to obtain atomic-level information on the C-terminal domains in the context of the full-length protein. Resonances of NLS and CTD residues have narrow linewidths, showing that these regions are largely solvent-exposed and dynamically disordered, whereas resonances from the folded TET are broadened beyond detection. Two regions of the CTD, spanning residues 369-374 and 381-388 and with high lysine content, make dynamic and sequence-independent interactions with DNA in regions that flank the p53 recognition element. The population of DNA-bound states increases as the length of the flanking regions is extended up to approximately 20 base pairs on either side of the recognition element. Acetylation of K372, K373, and K382, using a construct of the transcriptional coactivator CBP containing the TAZ2 and acetyltransferase domains, inhibits interaction of the CTD with DNA. This work provides high-resolution insights into the behavior of the intrinsically disordered C-terminal regions of p53 within the full-length tetramer and the molecular basis by which the CTD mediates DNA binding and specificity.
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Affiliation(s)
- Alexander S Krois
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Sangho Park
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California92037, United Sates
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5
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Shell DJ, Rectenwald JM, Buttery PH, Johnson RL, Foley CA, Guduru SKR, Uguen M, Rubiano JS, Zhang X, Li F, Norris-Drouin JL, Axtman M, Brian Hardy P, Vedadi M, Frye SV, James LI, Pearce KH. Discovery of hit compounds for methyl-lysine reader proteins from a target class DNA-encoded library. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:428-439. [PMID: 36272689 DOI: 10.1016/j.slasd.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
Methyl-lysine (Kme) reader domains are prevalent in chromatin regulatory proteins which bind post-translational modification sites to recruit repressive and activating factors; therefore, these proteins play crucial roles in cellular signaling and epigenetic regulation. Proteins that contain Kme domains are implicated in various diseases, including cancer, making them attractive therapeutic targets for drug and chemical probe discovery. Herein, we report on expanding the utility of a previously reported, Kme-focused DNA-encoded library (DEL), UNCDEL003, as a screening tool for hit discovery through the specific targeting of Kme reader proteins. As an efficient method for library generation, focused DELs are designed based on structural and functional features of a specific class of proteins with the intent of novel hit discovery. To broadly assess the applicability of our library, UNCDEL003 was screened against five diverse Kme reader protein domains (53BP1 TTD, KDM7B JmjC-PHD, CDYL2 CD, CBX2 CD, and LEDGF PWWP) with varying structures and functions. From these screening efforts, we identified hit compounds which contain unique chemical scaffolds distinct from previously reported ligands. The selected hit compounds were synthesized off-DNA and confirmed using primary and secondary assays and assessed for binding selectivity. Hit compounds from these efforts can serve as starting points for additional development and optimization into chemical probes to aid in further understanding the functionality of these therapeutically relevant proteins.
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Affiliation(s)
- Devan J Shell
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justin M Rectenwald
- School of Medicine, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peter H Buttery
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca L Johnson
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline A Foley
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiva K R Guduru
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mélanie Uguen
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juanita Sanchez Rubiano
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xindi Zhang
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jacqueline L Norris-Drouin
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Axtman
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - P Brian Hardy
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephen V Frye
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I James
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth H Pearce
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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6
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Chatterjee C, Singh SK. Peptide and protein chemistry approaches to study the tumor suppressor protein p53. Org Biomol Chem 2022; 20:5500-5509. [PMID: 35786742 PMCID: PMC10112546 DOI: 10.1039/d2ob00902a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tumor suppressor and master gene regulator protein p53 has been the subject of intense investigation for several decades due to its mutation in about half of all human cancers. However, mechanistic studies of p53 in cells are complicated by its many dynamic binding partners and heterogeneous post-translational modifications. The design of therapeutics that rescue p53 functions in cells requires a mechanistic understanding of its protein-protein interactions in specific protein complexes and identifying changes in p53 activity by diverse post-translational modifications. This review highlights the important roles that peptide and protein chemistry have played in biophysical and biochemical studies aimed at elucidating p53 regulation by several key binding partners. The design of various peptide inhibitors that rescue p53 function in cells and new opportunities in targeting p53-protein interactions are discussed. In addition, the review highlights the importance of a protein semisynthesis approach to comprehend the role of site-specific PTMs in p53 regulation.
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Affiliation(s)
- Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sumeet K Singh
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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7
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Zavileyskiy L, Bunik V. Regulation of p53 Function by Formation of Non-Nuclear Heterologous Protein Complexes. Biomolecules 2022; 12:biom12020327. [PMID: 35204825 PMCID: PMC8869670 DOI: 10.3390/biom12020327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 01/10/2023] Open
Abstract
A transcription factor p53 is activated upon cellular exposure to endogenous and exogenous stresses, triggering either homeostatic correction or cell death. Depending on the stress level, often measurable as DNA damage, the dual outcome is supported by p53 binding to a number of regulatory and metabolic proteins. Apart from the nucleus, p53 localizes to mitochondria, endoplasmic reticulum and cytosol. We consider non-nuclear heterologous protein complexes of p53, their structural determinants, regulatory post-translational modifications and the role in intricate p53 functions. The p53 heterologous complexes regulate the folding, trafficking and/or action of interacting partners in cellular compartments. Some of them mainly sequester p53 (HSP proteins, G6PD, LONP1) or its partners (RRM2B, PRKN) in specific locations. Formation of other complexes (with ATP2A2, ATP5PO, BAX, BCL2L1, CHCHD4, PPIF, POLG, SOD2, SSBP1, TFAM) depends on p53 upregulation according to the stress level. The p53 complexes with SIRT2, MUL1, USP7, TXN, PIN1 and PPIF control regulation of p53 function through post-translational modifications, such as lysine acetylation or ubiquitination, cysteine/cystine redox transformation and peptidyl-prolyl cis-trans isomerization. Redox sensitivity of p53 functions is supported by (i) thioredoxin-dependent reduction of p53 disulfides, (ii) inhibition of the thioredoxin-dependent deoxyribonucleotide synthesis by p53 binding to RRM2B and (iii) changed intracellular distribution of p53 through its oxidation by CHCHD4 in the mitochondrial intermembrane space. Increasing knowledge on the structure, function and (patho)physiological significance of the p53 heterologous complexes will enable a fine tuning of the settings-dependent p53 programs, using small molecule regulators of specific protein–protein interactions of p53.
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Affiliation(s)
- Lev Zavileyskiy
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Victoria Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119991 Moscow, Russia
- Correspondence:
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8
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Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations. Protein J 2022; 41:27-43. [PMID: 35099676 DOI: 10.1007/s10930-022-10041-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
p53, a tumor suppressor protein, is essential for preventing cancer development. Enhancing our understanding of the human p53 function and its modifications in carcinogenesis will aid in developing more highly effective strategies for cancer prevention and treatment. In this study, we have modeled five human p53 forms, namely, inactive, distal-active, proximal-active, distal-Arg175His mutant, and proximal-Arg175His mutant forms. These forms have been investigated using Gaussian accelerated molecular dynamics (GaMD) simulations in OPC water model at physiological temperature and pH. Our observations, obtained throughout [Formula: see text] of production run, are in good agreement with the relevant results in the classical molecular dynamics (MD) studies. Therefore, GaMD method is more economic and efficient method than the classical MD method for studying biomolecular systems. The featured dynamics of the five human p53-DBD forms include noticeable conformational changes of L1 and [Formula: see text]-[Formula: see text] loops as well as [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] turns. We have identified two clusters that represent two distinct conformational states in each p53-DBD form. The free-energy profiles of these clusters demonstrate the flexibility of the protein to undergo a conformational transition between the two clusters. We have predicted two out of seven possible druggability pockets on the clusters of the Arg175His forms. These two druggability pockets are near the mutation site and are expected to be actual pockets, which will be helpful for the compound clinical progression studies.
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9
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Šoštarić N, van Noort V. Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PLoS Comput Biol 2021; 17:e1008988. [PMID: 33979327 PMCID: PMC8143416 DOI: 10.1371/journal.pcbi.1008988] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/24/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond. Proteins are a diverse set of biological molecules responsible for numerous functions within cells, such as obtaining energy from food or transport of small molecules, and many processes rely on interactions of specific proteins. Moreover, a single protein may acquire different roles depending on cellular requirements and as a response to changes in the environment. A commonly used way to quickly change protein’s function or activity is by introducing small chemical modifications on specific locations within the protein. These modifications can cause the protein to interact in a more or less stable way with other proteins. We have previously developed a computational pipeline for predicting the effect of modifications on interactions of proteins, and in this work we apply it to all yeast proteins with known structures. We find differences in effects on the binding for different types of modifications. Importantly, we demonstrate that the modifications far from the interaction interface also significantly contribute to binding due to their impact on protein’s shape, which is often neglected by other methods. This work contributes to our understanding of the modulation of protein interactions in yeast due to modifications, while our widely applicable method will allow similar investigations in other organisms.
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Affiliation(s)
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
- Leiden University, Institute of Biology Leiden, Leiden, The Netherlands
- * E-mail:
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10
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Design and Construction of a Focused DNA-Encoded Library for Multivalent Chromatin Reader Proteins. Molecules 2020; 25:molecules25040979. [PMID: 32098353 PMCID: PMC7070942 DOI: 10.3390/molecules25040979] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and function, and consequently cellular phenotype, is regulated in part by a network of chromatin-modifying enzymes that place post-translational modifications (PTMs) on histone tails. These marks serve as recruitment sites for other chromatin regulatory complexes that ‘read’ these PTMs. High-quality chemical probes that can block reader functions of proteins involved in chromatin regulation are important tools to improve our understanding of pathways involved in chromatin dynamics. Insight into the intricate system of chromatin PTMs and their context within the epigenome is also therapeutically important as misregulation of this complex system is implicated in numerous human diseases. Using computational methods, along with structure-based knowledge, we have designed and constructed a focused DNA-Encoded Library (DEL) containing approximately 60,000 compounds targeting bi-valent methyl-lysine (Kme) reader domains. Additionally, we have constructed DNA-barcoded control compounds to allow optimization of selection conditions using a model Kme reader domain. We anticipate that this target-class focused approach will serve as a new method for rapid discovery of inhibitors for multivalent chromatin reader domains.
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11
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018; 17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023] Open
Abstract
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.
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Affiliation(s)
- Nikolina Šoštarić
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Technical University of Berlin, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium; Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.
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12
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Wawrzynow B, Zylicz A, Zylicz M. Chaperoning the guardian of the genome. The two-faced role of molecular chaperones in p53 tumor suppressor action. Biochim Biophys Acta Rev Cancer 2018; 1869:161-174. [DOI: 10.1016/j.bbcan.2017.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022]
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13
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Furth N, Aylon Y, Oren M. p53 shades of Hippo. Cell Death Differ 2018; 25:81-92. [PMID: 28984872 PMCID: PMC5729527 DOI: 10.1038/cdd.2017.163] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/15/2017] [Accepted: 08/30/2017] [Indexed: 12/11/2022] Open
Abstract
The three p53 family members, p53, p63 and p73, are structurally similar and share many biochemical activities. Yet, along with their common fundamental role in protecting genomic fidelity, each has acquired distinct functions related to diverse cell autonomous and non-autonomous processes. Similar to the p53 family, the Hippo signaling pathway impacts a multitude of cellular processes, spanning from cell cycle and metabolism to development and tumor suppression. The core Hippo module consists of the tumor-suppressive MST-LATS kinases and oncogenic transcriptional co-effectors YAP and TAZ. A wealth of accumulated data suggests a complex and delicate regulatory network connecting the p53 and Hippo pathways, in a highly context-specific manner. This generates multiple layers of interaction, ranging from interdependent and collaborative signaling to apparent antagonistic activity. Furthermore, genetic and epigenetic alterations can disrupt this homeostatic network, paving the way to genomic instability and cancer. This strengthens the need to better understand the nuances that control the molecular function of each component and the cross-talk between the different components. Here, we review interactions between the p53 and Hippo pathways within a subset of physiological contexts, focusing on normal stem cells and development, as well as regulation of apoptosis, senescence and metabolism in transformed cells.
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Affiliation(s)
- Noa Furth
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot, Israel
| | - Yael Aylon
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute, POB 26, 234 Herzl Street, Rehovot 7610001, Israel. Tel: +972 89342358; Fax: +972 89346004; E-mail: or
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute, POB 26, 234 Herzl Street, Rehovot 7610001, Israel. Tel: +972 89342358; Fax: +972 89346004; E-mail: or
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14
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Sullivan KD, Galbraith MD, Andrysik Z, Espinosa JM. Mechanisms of transcriptional regulation by p53. Cell Death Differ 2017; 25:133-143. [PMID: 29125602 PMCID: PMC5729533 DOI: 10.1038/cdd.2017.174] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/19/2022] Open
Abstract
p53 is a transcription factor that suppresses tumor growth through regulation of dozens of target genes with diverse biological functions. The activity of this master transcription factor is inactivated in nearly all tumors, either by mutations in the TP53 locus or by oncogenic events that decrease the activity of the wild-type protein, such as overexpression of the p53 repressor MDM2. However, despite decades of intensive research, our collective understanding of the p53 signaling cascade remains incomplete. In this review, we focus on recent advances in our understanding of mechanisms of p53-dependent transcriptional control as they relate to five key areas: (1) the functionally distinct N-terminal transactivation domains, (2) the diverse regulatory roles of its C-terminal domain, (3) evidence that p53 is solely a direct transcriptional activator, not a direct repressor, (4) the ability of p53 to recognize many of its enhancers across diverse chromatin environments, and (5) mechanisms that modify the p53-dependent transcriptional program in a context-dependent manner.
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Affiliation(s)
- Kelly D Sullivan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zdenek Andrysik
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80203, USA
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15
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Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F. Protein function machinery: from basic structural units to modulation of activity. Curr Opin Struct Biol 2016; 42:67-74. [PMID: 27865209 DOI: 10.1016/j.sbi.2016.10.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/29/2022]
Abstract
Contemporary protein structure is a result of the trade off between the laws of physics and the evolutionary selection. The polymer nature of proteins played a decisive role in establishing the basic structural and functional units of soluble proteins. We discuss how these elementary building blocks work in the hierarchy of protein domain structure, co-translational folding, as well as in enzymatic activity and molecular interactions. Next, we consider modulators of the protein function, such as intermolecular interactions, disorder-to-order transitions, and allosteric signaling, acting via interference with the protein's structural dynamics. We also discuss the post-translational modifications, which is a complementary intricate mechanism evolved for regulation of protein functions and interactions. In conclusion, we assess an anticipated contribution of discussed topics to the future advancements in the field.
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Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117579, Singapore.
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Zejun Zheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Singapore
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16
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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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17
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Hashiguchi A, Komatsu S. Posttranslational Modifications and Plant-Environment Interaction. Methods Enzymol 2016; 586:97-113. [PMID: 28137579 DOI: 10.1016/bs.mie.2016.09.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Posttranslational modifications (PTMs) of proteins such as phosphorylation and ubiquitination are crucial for controlling protein stability, localization, and conformation. Genetic information encoded in DNA is transcribed, translated, and increases its complexity by multiple PTMs. Conformational change introduced by PTMs affects interacting partners of each proteins and their downstream signaling; therefore, PTMs are the major level of modulations of total outcome of living cells. Plants are living in harsh environment that requires unremitting physiological modulation to survive, and the plant response to various environment stresses is regulated by PTMs of proteins. This review deals with the novel knowledge of PTM-focused proteomic studies on various life conditions. PTMs are focused that mediate plant-environment interaction such as stress perception, protein homeostasis, control of energy shift, and defense by immune system. Integration of diverse signals on a protein via multiple PTMs is discussed as well, considering current situation where signal integration became an emerging area approached by systems biology into account.
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Affiliation(s)
- A Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - S Komatsu
- National Institute of Crop Science, NARO, Tsukuba, Japan.
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18
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Laptenko O, Tong DR, Manfredi J, Prives C. The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein. Trends Biochem Sci 2016; 41:1022-1034. [PMID: 27669647 DOI: 10.1016/j.tibs.2016.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 01/22/2023]
Abstract
The p53 tumor suppressor is a transcription factor (TF) that exerts antitumor functions through its ability to regulate the expression of multiple genes. Within the p53 protein resides a relatively short unstructured C-terminal domain (CTD) that remarkably participates in virtually every aspect of p53 performance as a TF. Because these aspects are often interdependent and it is not always possible to dissect them experimentally, there has been a great deal of controversy about the CTD. In this review we evaluate the significance and key features of this interesting region of p53 and its impact on the many aspects of p53 function in light of previous and more recent findings.
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Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - David R Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James Manfredi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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19
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A Chromatin-Focused siRNA Screen for Regulators of p53-Dependent Transcription. G3-GENES GENOMES GENETICS 2016; 6:2671-8. [PMID: 27334938 PMCID: PMC4978920 DOI: 10.1534/g3.116.031534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The protein product of the Homo sapiens TP53 gene is a transcription factor (p53) that regulates the expression of genes critical for the response to DNA damage and tumor suppression, including genes involved in cell cycle arrest, apoptosis, DNA repair, metabolism, and a number of other tumorigenesis-related pathways. Differential transcriptional regulation of these genes is believed to alter the balance between two p53-dependent cell fates: cell cycle arrest or apoptosis. A number of previously identified p53 cofactors covalently modify and alter the function of both the p53 protein and histone proteins. Both gain- and loss-of-function mutations in chromatin modifiers have been strongly implicated in cancer development; thus, we sought to identify novel chromatin regulatory proteins that affect p53-dependent transcription and the balance between the expression of pro-cell cycle arrest and proapoptotic genes. We utilized an siRNA library designed against predicted chromatin regulatory proteins, and identified known and novel chromatin-related factors that affect both global p53-dependent transcription and gene-specific regulators of p53 transcriptional activation. The results from this screen will serve as a comprehensive resource for those interested in further characterizing chromatin and epigenetic factors that regulate p53 transcription.
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20
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Joerger AC, Fersht AR. The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches. Annu Rev Biochem 2016; 85:375-404. [DOI: 10.1146/annurev-biochem-060815-014710] [Citation(s) in RCA: 363] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany;
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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21
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Noh KM, Allis CD, Li H. Reading between the Lines: "ADD"-ing Histone and DNA Methylation Marks toward a New Epigenetic "Sum". ACS Chem Biol 2016; 11:554-63. [PMID: 26596909 DOI: 10.1021/acschembio.5b00830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covalent modifications of both DNA and histones act in concert to define the landscape of our epigenome. In this review, we explore the interconnections between histone and DNA modifications by focusing on a conserved chromatin-binding regulatory domain, the ATRX-DNMT3-DNMT3L (ADD) domain. New studies show that the ADD domain is capable of sensing, and therefore integrating, the status of multiple histone modifications. This in turn dictates the in vivo localization or allosteric regulation of the full-length ADD-containing protein and its ability to function in downstream chromatin remodeling events. Strategies to re-engineer the ADD "reader pocket" in the de novo DNA methyltransferase DNMT3A such that it redirects this "writer" to new genomic loci proved useful in understanding important biological downstream consequences of mis-targeting of DNA methylation via altered reading of histone marks. Combined with genome-editing tools, this approach stands as a poof-of-principle and will be broadly applicable to the elucidation of epigenetic networks that have been altered by "reader" mutations, either artificially or as naturally occurs in some human diseases.
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Affiliation(s)
- Kyung-Min Noh
- European Molecular Biology Laboratory, Genome Biology
Unit, 69117 Heidelberg, Germany
| | - C. David Allis
- Laboratory
of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, United States
| | - Haitao Li
- MOE
Key Laboratory of Protein Sciences, Center for Structural Biology,
Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, P.R. China
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22
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Huang X, Zhang S, Qi H, Wang Z, Chen HW, Shao J, Shen J. JMJD5 interacts with p53 and negatively regulates p53 function in control of cell cycle and proliferation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2286-95. [DOI: 10.1016/j.bbamcr.2015.05.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/12/2015] [Accepted: 05/22/2015] [Indexed: 01/05/2023]
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