1
|
Schey GL, Hildebrandt ER, Wang Y, Diwan S, Passetti HA, Potts GW, Sprague-Getsy AM, Leoni ER, Kuebler TS, Sham YY, Hougland JL, Beese LS, Schmidt WK, Distefano MD. Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase. Int J Mol Sci 2024; 25:5324. [PMID: 38791363 PMCID: PMC11121372 DOI: 10.3390/ijms25105324] [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: 02/03/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.
Collapse
Affiliation(s)
- Garrett L. Schey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - You Wang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; (Y.W.); (L.S.B.)
| | - Safwan Diwan
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Holly A. Passetti
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Gavin W. Potts
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Andrea M. Sprague-Getsy
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (A.M.S.-G.); (J.L.H.)
| | - Ethan R. Leoni
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - Taylor S. Kuebler
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA; (T.S.K.); (Y.Y.S.)
| | - Yuk Y. Sham
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA; (T.S.K.); (Y.Y.S.)
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (A.M.S.-G.); (J.L.H.)
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Lorena S. Beese
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; (Y.W.); (L.S.B.)
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - Mark D. Distefano
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| |
Collapse
|
2
|
Quantification of Farnesylated Progerin in Hutchinson-Gilford Progeria Patient Cells by Mass Spectrometry. Int J Mol Sci 2022; 23:ijms231911733. [PMID: 36233036 PMCID: PMC9569443 DOI: 10.3390/ijms231911733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare fatal disorder characterized by premature aging and death at a median age of 14.5 years. The most common cause of HGPS (affecting circa 90% of patients) is a de novo heterozygous synonymous single-base substitution (c.1824C>T; p.G608G) in the LMNA gene that results in the accumulation of progerin, an aberrant form of lamin A that, unlike mature lamin A, remains permanently farnesylated. The ratio of progerin to mature lamin A correlates with disease severity in HGPS patients, and can be used to assess the effectiveness of therapies aimed at lessening aberrant splicing or progerin farnesylation. We recently showed that the endogenous content of lamin A and progerin can be measured by mass spectrometry (MS), providing an alternative to immunological methods, which lack the necessary specificity and quantitative accuracy. Here, we present the first non-immunological method that reliably quantifies the levels of wild-type lamin A and farnesylated progerin in cells from HGPS patients. This method, which is based on a targeted MS approach and the use of isotope-labeled internal standards, could be applied in ongoing clinical trials evaluating the efficacy of drugs that inhibit progerin farnesylation.
Collapse
|
3
|
Fang Z, Chowdhury SM. Dual-Stage Neutral Loss Tandem Mass Spectrometric Strategy for Confident Identification of Protein Prenylation. Anal Chem 2021; 93:13169-13176. [PMID: 34558911 DOI: 10.1021/acs.analchem.1c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein prenylation is an important post-translational modification that regulates protein interactions, localizations, and signaling pathways in normal functioning of eukaryotic cells. It is also a critical step in the oncogenic developments of various cancers. Direct identification of native protein prenylation by mass spectrometry (MS) has been challenging due to high hydrophobicity and the lack of an efficient enrichment technique. Prior MS studies of prenylation revealed that prenyl peptides readily generate high-intensity fragments after neutral loss of the prenyl group (R group), and more recent investigation of oxidized prenyl peptides discovered more consistent neutral loss of the oxidized prenyl group (RSOH group). Here, a dual-stage neutral loss MS3 (DS-NLMS3)-based strategy is therefore developed by combining both gas-phase cleavable properties of the prenyl thioether bond and mono-oxidized thioether to improve the large-scale identification of prenylation. Both neutral losses can individually and distinctively confirm the prenylation type in MS2 and the sequence of the prenyl peptide upon targeted MS3 fragmentation. This dual-faceted NLMS3 strategy significantly improves the confidence in the identification of protein prenylation from large-scale samples, which enables the unambiguous identification of prenylated sites of the spiked low-abundance farnesyl peptide and native prenyl proteins from mouse macrophage cells, even without prior enrichment during sample preparation. The ease of incorporating this strategy into the prenylation study workflow and minimum disruption to the biological lipidome are advantageous for unraveling unknown native protein prenylation and further developments in profiling and quantifying prenylome.
Collapse
Affiliation(s)
- Zixiang Fang
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| |
Collapse
|
4
|
Zacharias AO, Fang Z, Rahman A, Talukder A, Cornelius S, Chowdhury SM. Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks. J Sep Sci 2020; 44:310-322. [DOI: 10.1002/jssc.202000930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Adway O. Zacharias
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Zixiang Fang
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Aurchie Rahman
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Akash Talukder
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| |
Collapse
|
5
|
Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL. Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS. Mol Cell Proteomics 2020; 19:1005-1016. [PMID: 32284353 PMCID: PMC7261820 DOI: 10.1074/mcp.ra120.001944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/19/2020] [Indexed: 01/16/2023] Open
Abstract
Posttranslational modifications play a critical and diverse role in regulating cellular activities. Despite their fundamentally important role in cellular function, there has been no report to date of an effective generalized approach to the targeting, extraction, and characterization of the critical c-terminal regions of natively prenylated proteins. Various chemical modification and metabolic labeling strategies in cell culture have been reported. However, their applicability is limited to cell culture systems and does not allow for analysis of tissue samples. The chemical characteristics (hydrophobicity, low abundance, highly basic charge) of many of the c-terminal regions of prenylated proteins have impaired the use of standard proteomic workflows. In this context, we sought a direct approach to the problem in order to examine these proteins in tissue without the use of labeling. Here we demonstrate that prenylated proteins can be captured on chromatographic resins functionalized with mixed disulfide functions. Protease treatment of resin-bound proteins using chymotryptic digestion revealed peptides from many known prenylated proteins. Exposure of the protease-treated resin to reducing agents and hydro organic mixtures released c-terminal peptides with intact prenyl groups along with other enzymatic modifications expected in this protein family. Database and search parameters were selected to allow for c-terminal modifications unique to these molecules such as CAAX box processing and c-terminal methylation. In summary, we present a direct approach to enrich and obtain information at a molecular level of detail about prenylation of proteins from tissue and cell extracts using high-performance LC-MS without the need for metabolic labeling and derivatization.
Collapse
Affiliation(s)
- James A Wilkins
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158.
| | - Krista Kaasik
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| | - Robert J Chalkley
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| | - Alma L Burlingame
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| |
Collapse
|
6
|
Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL. Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk. Proc Natl Acad Sci U S A 2018; 115:4140-4145. [PMID: 29610327 PMCID: PMC5910823 DOI: 10.1073/pnas.1716122115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations of the KRAS gene are found in human cancers with high frequency and result in the constitutive activation of its protein products. This leads to aberrant regulation of downstream pathways, promoting cell survival, proliferation, and tumorigenesis that drive cancer progression and negatively affect treatment outcomes. Here, we describe a workflow that can detect and quantify mutation-specific consequences of KRAS biochemistry, namely linked changes in posttranslational modifications (PTMs). We combined immunoaffinity enrichment with detection by top-down mass spectrometry to discover and quantify proteoforms with or without the Gly13Asp mutation (G13D) specifically in the KRAS4b isoform. The workflow was applied first to isogenic KRAS colorectal cancer (CRC) cell lines and then to patient CRC tumors with matching KRAS genotypes. In two cellular models, a direct link between the knockout of the mutant G13D allele and the complete nitrosylation of cysteine 118 of the remaining WT KRAS4b was observed. Analysis of tumor samples quantified the percentage of mutant KRAS4b actually present in cancer tissue and identified major differences in the levels of C-terminal carboxymethylation, a modification critical for membrane association. These data from CRC cells and human tumors suggest mechanisms of posttranslational regulation that are highly context-dependent and which lead to preferential production of specific KRAS4b proteoforms.
Collapse
Affiliation(s)
- Ioanna Ntai
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Luca Fornelli
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Caroline J DeHart
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Josiah E Hutton
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Peter F Doubleday
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Richard D LeDuc
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Alexandra J van Nispen
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Ryan T Fellers
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| | - Gordon Whiteley
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892
| | - Neil L Kelleher
- Department of Chemistry, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208;
- Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208
| |
Collapse
|
7
|
Brioschi M, Martinez Fernandez A, Banfi C. Exploring the biochemistry of the prenylome and its role in disease through proteomics: progress and potential. Expert Rev Proteomics 2017; 14:515-528. [PMID: 28521569 DOI: 10.1080/14789450.2017.1332998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential. Areas covered: This review attempts to summarize the basic aspects of prenylation integrating them with biological functions in diseases and giving an account of the current status of prenylation inhibitors as potential therapeutics. We also summarize the methodologies for the characterization of this modification. Expert commentary: The growing body of evidence suggesting an important role of prenylation in diseases and the subsequent development of inhibitors of the enzymes responsible for this modification lead to the urgent need to identify the full spectrum of prenylated proteins that are altered in the disease or affected by drugs. Proteomic tools to analyze prenylated proteins are recently emerging, thanks to the advancement in the field of mass spectrometry coupled to enrichment strategies.
Collapse
|
8
|
Lindemann C, Thomanek N, Hundt F, Lerari T, Meyer HE, Wolters D, Marcus K. Strategies in relative and absolute quantitative mass spectrometry based proteomics. Biol Chem 2017; 398:687-699. [DOI: 10.1515/hsz-2017-0104] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/28/2017] [Indexed: 11/15/2022]
Abstract
Abstract
Quantitative mass spectrometry approaches are used for absolute and relative quantification in global proteome studies. To date, relative and absolute quantification techniques are available that differ in quantification accuracy, proteome coverage, complexity and robustness. This review focuses on most common relative or absolute quantification strategies exemplified by three experimental studies. A label-free relative quantification approach was performed for the investigation of the membrane proteome of sensory cilia to the depth of olfactory receptors in Mus musculus. A SILAC-based relative quantification approach was successfully applied for the identification of core components and transient interactors of the peroxisomal importomer in Saccharomyces cerevisiae. Furthermore, AQUA using stable isotopes was exemplified to unraveling the prenylome influenced by novel prenyltransferase inhibitors. Characteristic enrichment and fragmentation strategies for a robust quantification of the prenylome are also summarized.
Collapse
|
9
|
Bhawal RP, Shahinuzzaman ADA, Chowdhury SM. Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:704-707. [PMID: 27785692 DOI: 10.1007/s13361-016-1503-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 06/06/2023]
Abstract
Farnesylation and geranylgeranylation are the two types of prenyl modification of proteins. Prenylated peptides are highly hydrophobic and their abundances in biological samples are low. In this report, we studied the oxidized prenylated peptides by electrospray ionization mass spectrometry and identified them by collision-induced dissociation (CID) and electron-transfer dissociation (ETD) tandem mass spectrometry. Modified prenyl peptides were generated utilizing strong and low strength oxidizing agents to selectively oxidize and epoxidize cysteine sulfur and prenyl side chain. We selected three peptides with prenyl motifs and synthesized their prenylated versions. The detailed characteristic fragmentations of oxidized and epoxidized farnesylated and geranylgeranylated peptides were studied side by side with two popular fragmentation techniques. CID and ETD mass spectrometry clearly distinguished the modified version of these peptides. ETD mass spectrometry provided sequence information of the highly labile modified prenyl peptides and showed different characteristic fragmentations compared with CID. A detailed fragmentation of modified geranylgeranylated peptides was compared by CID and ETD mass spectrometry for the first time. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Ruchika P Bhawal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, USA
| | - A D A Shahinuzzaman
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, USA.
| |
Collapse
|
10
|
Hentschel A, Zahedi RP, Ahrends R. Protein lipid modifications--More than just a greasy ballast. Proteomics 2016; 16:759-82. [PMID: 26683279 DOI: 10.1002/pmic.201500353] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/24/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022]
Abstract
Covalent lipid modifications of proteins are crucial for regulation of cellular plasticity, since they affect the chemical and physical properties and therefore protein activity, localization, and stability. Most recently, lipid modifications on proteins are increasingly attracting important regulatory entities in diverse signaling events and diseases. In all cases, the lipid moiety of modified proteins is essential to allow water-soluble proteins to strongly interact with membranes or to induce structural changes in proteins that are critical for elemental processes such as respiration, transport, signal transduction, and motility. Until now, roughly about ten lipid modifications on different amino acid residues are described at the UniProtKB database and even well-known modifications are underrepresented. Thus, it is of fundamental importance to develop a better understanding of this emerging and so far under-investigated type of protein modification. Therefore, this review aims to give a comprehensive and detailed overview about enzymatic and nonenzymatic lipidation events, will report their role in cellular biology, discuss their relevancy for diseases, and describe so far available bioanalytical strategies to analyze this highly challenging type of modification.
Collapse
Affiliation(s)
- Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| |
Collapse
|
11
|
ZHANG XQ, CHEN C, FANG CY, LU HJ. Progress of Analytical Methods for Protein Cysteine Post-translational Modifications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60974-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Rimmer MA, Artigues A, Nadeau OW, Villar MT, Vasquez-Montes V, Carlson GM. Mass Spectrometric Analysis of Surface-Exposed Regions in the Hexadecameric Phosphorylase Kinase Complex. Biochemistry 2015; 54:6887-95. [PMID: 26551836 DOI: 10.1021/acs.biochem.5b00682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphorylase kinase (PhK) is a 1.3 MDa (αβγδ)4 enzyme complex, in which αβγδ protomers associate in D2 symmetry to form two large octameric lobes that are interconnected by four bridges. The approximate locations of the subunits have been mapped in low-resolution cryo-electron microscopy structures of the complex; however, the disposition of the subunits within the complex remains largely unknown. We have used partial proteolysis and chemical footprinting in combination with high-resolution mass spectrometry to identify surface-exposed regions of the intact nonactivated and phospho-activated conformers. In addition to the known interaction of the γ subunit's C-terminal regulatory domain with the δ subunit (calmodulin), our exposure results indicate that the catalytic core of γ may also anchor to the PhK complex at the bottom backside of its C-terminal lobe facing away from the active site cleft. Exposed loops on the α and β regulatory subunits within the complex occur at regions overlapping with tissue-specific alternative RNA splice sites and regulatory phosphorylatable domains. Their phosphorylation alters the surface exposure of α and β, corroborating previous biophysical and biochemical studies that detected phosphorylation-dependent conformational changes in these subunits; however, for the first time, specific affected regions have been identified.
Collapse
Affiliation(s)
- Mary Ashley Rimmer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Maria T Villar
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Gerald M Carlson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| |
Collapse
|
13
|
Bhawal RP, Sadananda SC, Bugarin A, Laposa B, Chowdhury SM. Mass Spectrometry Cleavable Strategy for Identification and Differentiation of Prenylated Peptides. Anal Chem 2015; 87:2178-86. [DOI: 10.1021/ac503794s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ruchika P. Bhawal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Sandhya C. Sadananda
- Department
of Computer Science, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Alejandro Bugarin
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Brian Laposa
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| |
Collapse
|
14
|
Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. TRANSLATIONAL BIOINFORMATICS 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
15
|
Abstract
Protein palmitoylation describes the post-translational fatty acyl thioesterification of cellular cysteine residues and is critical for the localization, trafficking, and compartmentalization of a large number of membrane proteins. This labile thioester modification facilitates a dynamic acylation cycle that directionally traffics key signaling complexes, receptors, and channels to select membrane compartments. Chemical enrichment and advanced mass spectrometry-based proteomics methods have highlighted a pervasive role for palmitoylation across all eukaryotes, including animals, plants, and parasites. Emerging chemical tools promise to open new avenues to study the enzymes, substrates, and dynamics of this distinct post-translational modification.
Collapse
Affiliation(s)
- Christopher T.M.B. Tom
- Program in Chemical Biology and Department
of Chemistry, University of Michigan, 930
N. University Avenue, Ann
Arbor, Michigan 48109, United States
| | - Brent R. Martin
- Program in Chemical Biology and Department
of Chemistry, University of Michigan, 930
N. University Avenue, Ann
Arbor, Michigan 48109, United States
| |
Collapse
|