1
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 DOI: 10.1021/acs.chemrev.3c00850] [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: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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2
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Nikolsky KS, Kulikova LI, Petrovskiy DV, Rudnev VR, Malsagova KA, Kaysheva AL. Analysis of Structural Changes in the Protein near the Phosphorylation Site. Biomolecules 2023; 13:1564. [PMID: 38002246 PMCID: PMC10668964 DOI: 10.3390/biom13111564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/26/2023] Open
Abstract
Modification of the protein after synthesis (PTM) often affects protein function as supported by numerous studies. However, there is no consensus about the degree of structural protein changes after modification. For phosphorylation of serine, threonine, and tyrosine, which is a common PTM in the biology of living organisms, we consider topical issues related to changes in the geometric parameters of a protein (Rg, RMSD, Cα displacement, SASA). The effect of phosphorylation on protein geometry was studied both for the whole protein and at the local level (i.e., in different neighborhoods of the modification site). Heterogeneity in the degree of protein structural changes after phosphorylation was revealed, which allowed for us to isolate a group of proteins having pronounced local structural changes in the neighborhoods of up to 15 amino acid residues from the modification site. This is a comparative study of protein structural changes in neighborhoods of 3-15 amino acid residues from the modified site. Amino acid phosphorylation in proteins with pronounced local changes caused switching from the inactive functional state to the active one.
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Affiliation(s)
| | | | | | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, Biobanking Group, Pogodinskaya, 10, 119121 Moscow, Russia; (K.S.N.); (L.I.K.); (D.V.P.); (V.R.R.); (A.L.K.)
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3
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Bobalova J, Strouhalova D, Bobal P. Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14825-14837. [PMID: 37792446 PMCID: PMC10591476 DOI: 10.1021/acs.jafc.3c00886] [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: 02/16/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023]
Abstract
Post-translational modifications (PTMs) of biomacromolecules can be useful for understanding the processes by which a relatively small number of individual genes in a particular genome can generate enormous biological complexity in different organisms. The proteomes of barley and the brewing process were investigated by different techniques. However, their diverse and complex PTMs remain understudied. As standard analytical approaches have limitations, innovative analytical approaches need to be developed and applied in PTM studies. To make further progress in this field, it is necessary to specify the sites of modification, as well as to characterize individual isoforms with increased selectivity and sensitivity. This review summarizes advances in the PTM analysis of barley proteins, particularly those involving mass spectrometric detection. Our focus is on monitoring phosphorylation, glycation, and glycosylation, which critically influence functional behavior in metabolism and regulation in organisms.
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Affiliation(s)
- Janette Bobalova
- Institute
of Analytical Chemistry of the CAS, v. v. i., Veveri 97, Brno 602 00, Czech Republic
| | - Dana Strouhalova
- Institute
of Analytical Chemistry of the CAS, v. v. i., Veveri 97, Brno 602 00, Czech Republic
| | - Pavel Bobal
- Masaryk
University, Department of Chemical Drugs,
Faculty of Pharmacy, Palackeho
1946/1, Brno 612 00, Czech Republic
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4
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Morse PT, Pérez-Mejías G, Wan J, Turner AA, Márquez I, Kalpage HA, Vaishnav A, Zurek MP, Huettemann PP, Kim K, Arroum T, De la Rosa MA, Chowdhury DD, Lee I, Brunzelle JS, Sanderson TH, Malek MH, Meierhofer D, Edwards BFP, Díaz-Moreno I, Hüttemann M. Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Nat Commun 2023; 14:4166. [PMID: 37443314 PMCID: PMC10345088 DOI: 10.1038/s41467-023-39820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Inmaculada Márquez
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Philipp P Huettemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, IL, 60439, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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5
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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6
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Liang B, Zhu Y, Shi W, Ni C, Tan B, Tang S. SARS-CoV-2 Spike Protein Post-Translational Modification Landscape and Its Impact on Protein Structure and Function via Computational Prediction. RESEARCH (WASHINGTON, D.C.) 2023; 6:0078. [PMID: 36930770 PMCID: PMC10013967 DOI: 10.34133/research.0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
To elucidate the role of post-translational modifications (PTMs) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein's structure and virulence, we generated a high-resolution map of 87 PTMs using liquid chromatography with tandem mass spectrometry data on the extracted spike protein from SARS-CoV-2 virions and then reconstituted its structure heterogeneity caused by PTMs. Nonetheless, Alphafold2, a high-accuracy artificial intelligence tool to perform protein structure prediction, relies solely on primary amino acid sequence, whereas the impact of PTM, which often modulates critical protein structure and function, is much ignored. To overcome this challenge, we proposed the mutagenesis approach-an in silico, site-directed amino acid substitution to mimic the influence of PTMs on protein structure due to altered physicochemical properties in the post-translationally modified amino acids-and then reconstituted the spike protein's structure from the substituted sequences by Alphafold2. For the first time, the proposed method revealed predicted protein structures resulting from PTMs, a problem that Alphafold2 has yet to address. As an example, we performed computational analyses of the interaction of the post-translationally modified spike protein with its host factors such as angiotensin-converting enzyme 2 to illuminate binding affinity. Mechanistically, this study suggested the structural analysis of post-translationally modified protein via mutagenesis and deep learning. To summarize, the reconstructed spike protein structures showed that specific PTMs can be used to modulate host factor binding, guide antibody design, and pave the way for new therapeutic targets. The code and Supplementary Materials are freely available at https://github.com/LTZHKUSTGZ/SARS-CoV-2-spike-protein-PTM.
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Affiliation(s)
- Buwen Liang
- The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Yiying Zhu
- Analysis Center, Chemistry Department, Tsinghua University, Beijing, China
| | - Wenhao Shi
- Analysis Center, Chemistry Department, Tsinghua University, Beijing, China
| | - Can Ni
- The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Bowen Tan
- The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Shaojun Tang
- The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China.,The Hong Kong University of Science and Technology, Hong Kong SAR, China
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7
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Morosky P, Comyns C, Nunes LGA, Chung CZ, Hoffmann PR, Söll D, Vargas-Rodriguez O, Krahn N. Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins. Front Mol Biosci 2023; 10:1096261. [PMID: 36762212 PMCID: PMC9902344 DOI: 10.3389/fmolb.2023.1096261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein's function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε-acetyl-l-lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.
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Affiliation(s)
- Pearl Morosky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Cody Comyns
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Lance G. A. Nunes
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Peter R. Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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8
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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9
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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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10
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Yu H, Feng J, Zhong F, Wu Y. Chemical Modification for the "off-/on" Regulation of Enzyme Activity. Macromol Rapid Commun 2022; 43:e2200195. [PMID: 35482602 DOI: 10.1002/marc.202200195] [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: 02/28/2022] [Revised: 04/14/2022] [Indexed: 11/07/2022]
Abstract
Enzymes with excellent catalytic performance play important roles in living organisms. Advances in strategies for enzyme chemical modification have enabled powerful strategies for exploring and manipulating enzyme functions and activities. Based on the development of chemical enzyme modifications, incorporating external stimuli-responsive features-for example, responsivity to light, voltage, magnetic force, pH, temperature, redox activity, and small molecules-into a target enzyme to turn "on" and "off" its activity has attracted much attention. The ability to precisely control enzyme activity using different approaches would greatly expand the chemical biology toolbox for clarification and detection of signal transduction and in vivo enzyme function and significantly promote enzyme-based disease therapy. This review summarizes the methods available for chemical enzyme modification mainly for the off-/on control of enzyme activity and particularly highlights the recent progress regarding the applications of this strategy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huaibin Yu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Jiayi Feng
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Fangrui Zhong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Yuzhou Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
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11
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Mikkelsen JH, Gustafsson MBF, Skrydstrup T, Jensen KB. Selective N-Terminal Acylation of Peptides and Proteins with Tunable Phenol Esters. Bioconjug Chem 2022; 33:625-633. [PMID: 35320668 DOI: 10.1021/acs.bioconjchem.2c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Selective modification of peptides and proteins is of foremost importance for the development of biopharmaceuticals and exploring biochemical pathways, as well as other applications. Here, we present a study on the development of a general and easily applicable selective method for N-terminal acylation of biomolecules, applying a new type of phenol esters. Key to the success was the development of highly tunable phenol activators bearing in the ortho-position, sulfonic acid or sulfonamide, acting as a steric shield for hydrolysis, and electron-withdrawing groups in the other ortho- and para-position for controlling the reactivity of the activated phenol esters. A library of heptapeptides, testing all 20 natural amino acids positioned at the N-terminal, were acylated in a selective manner at the N-terminus. The majority showed high conversion and excellent Nα-selectivity. Several biologically relevant biomolecules, including DesB30 insulin and human growth hormone, could also be modified at the N-terminal in a highly selective way, exemplified by either a fluorophore or a fatty acid sidechain. Finally, taking advantage of the possibility to accurately adjust the reactivity of the phenol esters, we present a potential strategy for the construction of dual active biopharmaceuticals through the employment of a bifunctional acylation linker and demonstrate its use in the creation of a GLP-1 insulin analogue, coupled through the lysine residue of GLP-1 and the N-terminal PheB1 amine of DesB30 insulin.
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Affiliation(s)
- Jesper H Mikkelsen
- Global Research Technologies, Novo Nordisk Research Park, 2760 Måløv, Denmark.,Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Troels Skrydstrup
- Carbon Dioxide Activation Center (CADIAC), Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kim B Jensen
- Global Research Technologies, Novo Nordisk Research Park, 2760 Måløv, Denmark
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12
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King DT, Serrano-Negrón JE, Zhu Y, Moore CL, Shoulders MD, Foster LJ, Vocadlo DJ. Thermal Proteome Profiling Reveals the O-GlcNAc-Dependent Meltome. J Am Chem Soc 2022; 144:3833-3842. [PMID: 35230102 PMCID: PMC8969899 DOI: 10.1021/jacs.1c10621] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Posttranslational modifications alter the biophysical properties of proteins and thereby influence cellular physiology. One emerging manner by which such modifications regulate protein functions is through their ability to perturb protein stability. Despite the increasing interest in this phenomenon, there are few methods that enable global interrogation of the biophysical effects of posttranslational modifications on the proteome. Here, we describe an unbiased proteome-wide approach to explore the influence of protein modifications on the thermodynamic stability of thousands of proteins in parallel. We apply this profiling strategy to study the effects of O-linked N-acetylglucosamine (O-GlcNAc), an abundant modification found on hundreds of proteins in mammals that has been shown in select cases to stabilize proteins. Using this thermal proteomic profiling strategy, we identify a set of 72 proteins displaying O-GlcNAc-dependent thermostability and validate this approach using orthogonal methods targeting specific proteins. These collective observations reveal that the majority of proteins influenced by O-GlcNAc are, surprisingly, destabilized by O-GlcNAc and cluster into distinct macromolecular complexes. These results establish O-GlcNAc as a bidirectional regulator of protein stability and provide a blueprint for exploring the impact of any protein modification on the meltome of, in principle, any organism.
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Affiliation(s)
- Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jesús E Serrano-Negrón
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yanping Zhu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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13
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Hall ML, Givens S, Santosh N, Iacovino M, Kyba M, Ogle BM. Laminin 411 mediates endothelial specification via multiple signaling axes that converge on β-catenin. Stem Cell Reports 2022; 17:569-583. [PMID: 35120622 PMCID: PMC9039757 DOI: 10.1016/j.stemcr.2022.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/24/2022] Open
Abstract
The extracellular matrix (ECM) provides essential cues to promote endothelial specification during tissue development in vivo; correspondingly, ECM is considered essential for endothelial differentiation outside of the body. However, systematic studies to assess the precise contribution of individual ECM proteins to endothelial differentiation have not been conducted. Further, the multi-component nature of differentiation protocols makes it challenging to study the underlying mechanisms by which the ECM contributes to cell fate. In this study, we determined that Laminin 411 alone increases endothelial differentiation of induced pluripotent stem cells over collagen I or Matrigel. The effect of ECM was shown to be independent of vascular endothelial growth factor (VEGF) binding capacity. We also show that ECM-guided endothelial differentiation is dependent on activation of focal adhesion kinase (FAK), integrin-linked kinase (ILK), Notch, and β-catenin pathways. Our results indicate that ECM contributes to endothelial differentiation through multiple avenues, which converge at the expression of active β-catenin.
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Affiliation(s)
- Mikayla L Hall
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sophie Givens
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Natasha Santosh
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Michelina Iacovino
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Lillehei Heart Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Brenda M Ogle
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, 7-130 Nils Hasselmo Hall, 312 Church St. SE, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Lillehei Heart Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Institute for Engineering in Medicine, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA.
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14
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Nissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh B, Sun Z, Ghantasala S, Chetanya C, Shenoy SV, Moritz RL, Goswami M, Srivastava S. Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita. J Proteome Res 2021; 21:420-437. [PMID: 34962809 DOI: 10.1021/acs.jproteome.1c00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteomics has enormous applications in human and animal research. However, proteomic studies in fisheries science are quite scanty particularly for economically important species. Few proteomic studies have been carried out in model fish species, but comprehensive proteomics of aquaculture species are still scarce. This study aimed to perform a comprehensive organ-based protein profiling of important tissue samples for one of the most important aquaculture species,Labeo rohita.Deep proteomic profiling of 17 histologically normal tissues, blood plasma, and embryo provided mass-spectrometric evidence for 8498 proteins at 1% false discovery rate that make up about 26% of the total annotated protein-coding sequences in Rohu. Tissue-wise expression analysis was performed, and the presence of several biologically important proteins was also verified using a targeted proteomic approach. We identified the global post-translational modifications (PTMs) in terms of acetylation (N-terminus and lysine), methylation (N-terminus, lysine, and arginine), and phosphorylation (serine, threonine, and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal has been developed for an overall landscape of protein expression across the studied tissues of Labeo rohita (www.fishprot.org). This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Biplab Ghosh
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Saicharan Ghantasala
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chetanya Chetanya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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15
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Siraj A, Lim DY, Tayara H, Chong KT. UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites. Genes (Basel) 2021; 12:genes12050717. [PMID: 34064731 PMCID: PMC8151217 DOI: 10.3390/genes12050717] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
Protein ubiquitylation is an essential post-translational modification process that performs a critical role in a wide range of biological functions, even a degenerative role in certain diseases, and is consequently used as a promising target for the treatment of various diseases. Owing to the significant role of protein ubiquitylation, these sites can be identified by enzymatic approaches, mass spectrometry analysis, and combinations of multidimensional liquid chromatography and tandem mass spectrometry. However, these large-scale experimental screening techniques are time consuming, expensive, and laborious. To overcome the drawbacks of experimental methods, machine learning and deep learning-based predictors were considered for prediction in a timely and cost-effective manner. In the literature, several computational predictors have been published across species; however, predictors are species-specific because of the unclear patterns in different species. In this study, we proposed a novel approach for predicting plant ubiquitylation sites using a hybrid deep learning model by utilizing convolutional neural network and long short-term memory. The proposed method uses the actual protein sequence and physicochemical properties as inputs to the model and provides more robust predictions. The proposed predictor achieved the best result with accuracy values of 80% and 81% and F-scores of 79% and 82% on the 10-fold cross-validation and an independent dataset, respectively. Moreover, we also compared the testing of the independent dataset with popular ubiquitylation predictors; the results demonstrate that our model significantly outperforms the other methods in prediction classification results.
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Affiliation(s)
- Arslan Siraj
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
| | - Dae Yeong Lim
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.)
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.)
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16
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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17
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Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
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18
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Josephson B, Fehl C, Isenegger PG, Nadal S, Wright TH, Poh AWJ, Bower BJ, Giltrap AM, Chen L, Batchelor-McAuley C, Roper G, Arisa O, Sap JBI, Kawamura A, Baldwin AJ, Mohammed S, Compton RG, Gouverneur V, Davis BG. Light-driven post-translational installation of reactive protein side chains. Nature 2020; 585:530-537. [PMID: 32968259 DOI: 10.1038/s41586-020-2733-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) greatly expand the structures and functions of proteins in nature1,2. Although synthetic protein functionalization strategies allow mimicry of PTMs3,4, as well as formation of unnatural protein variants with diverse potential functions, including drug carrying5, tracking, imaging6 and partner crosslinking7, the range of functional groups that can be introduced remains limited. Here we describe the visible-light-driven installation of side chains at dehydroalanine residues in proteins through the formation of carbon-centred radicals that allow C-C bond formation in water. Control of the reaction redox allows site-selective modification with good conversions and reduced protein damage. In situ generation of boronic acid catechol ester derivatives generates RH2C• radicals that form the native (β-CH2-γ-CH2) linkage of natural residues and PTMs, whereas in situ potentiation of pyridylsulfonyl derivatives by Fe(II) generates RF2C• radicals that form equivalent β-CH2-γ-CF2 linkages bearing difluoromethylene labels. These reactions are chemically tolerant and incorporate a wide range of functionalities (more than 50 unique residues/side chains) into diverse protein scaffolds and sites. Initiation can be applied chemoselectively in the presence of sensitive groups in the radical precursors, enabling installation of previously incompatible side chains. The resulting protein function and reactivity are used to install radical precursors for homolytic on-protein radical generation; to study enzyme function with natural, unnatural and CF2-labelled post-translationally modified protein substrates via simultaneous sensing of both chemo- and stereoselectivity; and to create generalized 'alkylator proteins' with a spectrum of heterolytic covalent-bond-forming activity (that is, reacting diversely with small molecules at one extreme or selectively with protein targets through good mimicry at the other). Post-translational access to such reactions and chemical groups on proteins could be useful in both revealing and creating protein function.
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Affiliation(s)
- Brian Josephson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlie Fehl
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Simon Nadal
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tom H Wright
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Adeline W J Poh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ben J Bower
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew M Giltrap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
| | - Lifu Chen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Grace Roper
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Oluwatobi Arisa
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeroen B I Sap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew J Baldwin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Richard G Compton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronique Gouverneur
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- The Rosalind Franklin Institute, Harwell, UK.
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19
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Wang ZA, Cole PA. The Chemical Biology of Reversible Lysine Post-translational Modifications. Cell Chem Biol 2020; 27:953-969. [PMID: 32698016 PMCID: PMC7487139 DOI: 10.1016/j.chembiol.2020.07.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 07/01/2020] [Indexed: 12/31/2022]
Abstract
Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," "erasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA.
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20
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Zheng Q, Maksimovic I, Upad A, Guber D, David Y. Synthesis of an Alkynyl Methylglyoxal Probe to Investigate Nonenzymatic Histone Glycation. J Org Chem 2020; 85:1691-1697. [PMID: 31875401 DOI: 10.1021/acs.joc.9b02504] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methylglyoxal (MGO) is a reactive dicarbonyl metabolite that modifies histones in vivo and induces changes in chromatin structure and function. Here we report the synthesis and application of a chemical probe for investigating MGO-glycation. A two-step synthesis of a Cu-click compatible alkynyl oxoaldehyde probe (AlkMGO) via sequential Dess-Martin and Riley oxidations is presented. This synthesis elevates the accessibility and utility of an important tool for tracking, enriching, and studying MGO-glycation to aid in understanding its underlying biochemical functions.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Igor Maksimovic
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Tri-Institutional Ph.D. Program in Chemical Biology , New York , New York 10065 , United States
| | - Akhil Upad
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - David Guber
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Department of Chemistry , City University of New York, Hunter College , New York , New York 10065 , United States
| | - Yael David
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Tri-Institutional Ph.D. Program in Chemical Biology , New York , New York 10065 , United States.,Department of Pharmacology , Weill Cornell Medicine , New York , New York 10065 , United States.,Department of Physiology, Biophysics and Systems Biology , Weill Cornell Medicine , New York , New York 10065 , United States
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21
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Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Biochem Soc Trans 2018; 46:1381-1392. [PMID: 30287510 DOI: 10.1042/bst20180488] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 01/08/2023]
Abstract
Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FIS). This approach allowed us to identify a total of 101 unique PTMs in the 11 independent proteomic studies covered in this review. Combined with structural and genetic information on these proteins, we describe potential effects of these modifications (perturbed DNA-binding, structural integrity or interaction with other proteins) on their function.
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22
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Affiliation(s)
- Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
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