1
|
Piedl KN, Arcoria PJ, Etzkorn FA. Misacylation of tRNA with Ser-Pro Dipeptide for In Vitro Transcription-Translation. Curr Protoc 2024; 4:e1010. [PMID: 38516989 PMCID: PMC10963037 DOI: 10.1002/cpz1.1010] [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] [Indexed: 03/23/2024]
Abstract
Serine-proline (Ser-Pro) backbone-modified dipeptide analogues are powerful tools to investigate the role of cis-trans isomerization in the regulation of the cell cycle and transcription. These studies have previously been limited to synthetic peptides, whose synthesis is a challenge for larger peptides due to the compounding yield loss incurred in each step. We now introduce a method for the aminoacylation of tRNA with dipeptides and dipeptide analogs to permit the installation of cis- and trans-locked Ser-Pro analogues into full-length proteins. To that end, we synthesized the 3,5-dinitrobenzyl (DNB)-activated esters of a native Ser-Pro dipeptide and its cis- and trans-locked alkene analogs. Murakami et al. created the DNB flexizyme (dFx), a ribozyme that acylates tRNA with DNB esters of amino acids to permit unnatural amino acids to be incorporated into proteins. A tRNA from yeast that recognizes the amber stop codon, along with the dFx flexizyme, were generated by in vitro transcription with T7 RNA polymerase. dFx was used to successfully catalyze the chemical misacylation of truncated amber tRNA with the Ser-Pro-DNB activated dipeptide. This method allows the introduction of non-native Ser-Pro dipeptide mimics into full-length proteins by in vitro transcription-translation. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 3,5-dinitrobenzyl activated esters of Ser-Pro Basic Protocol 2: Preparation of truncated amber tRNA Basic Protocol 3: Acylation of amber-tRNA by the dFx flexizyme Basic Protocol 4: PAGE electrophoresis of tRNASerPro.
Collapse
Affiliation(s)
- Karla N Piedl
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | - Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia
| | | |
Collapse
|
2
|
Arcoria PJ, Etzkorn FA. A fluoro-alkene mimic of Gly- trans-Pro produces a stable collagen triple helix. Org Biomol Chem 2023; 21:4039-4051. [PMID: 37114339 DOI: 10.1039/d3ob00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
We report the first experimental evidence for a fluoro-alkene amide isostere participating in n→π* donation, which stabilizes the collagen triple helix. Of the three amide positions in canonical collagen-like peptides, Gly-Pro, Pro-Hyp, and Hyp-Gly, triple helix stability stands to benefit from substitution of only the isomerizable 3° Gly-Pro amide bond with a trans-locked fluoro-alkene. A (Z)-fluoro-alkene isostere of Gly-trans-Pro was synthesized, and its effect on the thermostability of a collagen-like peptide triple helix was measured. The mixture of enantiomers, Boc-Gly-Ψ[(Z)CFC]-L/D-Pro-OH, was synthesized in 8 steps with 27% overall yield, and the Fmoc-Gly-Ψ[(Z)CFC]-L/D-Pro-Hyp-OBn diastereomers were separated. The Gly-Ψ[(Z)CFC]-Pro isostere installed in a collagen-like peptide forms a stable triple helix. By CD, the thermal melting (Tm) value of the fluoro-alkene peptide was +42.2 ± 0.4 °C, and the Tm value of the control peptide was +48.4 ± 0.5 °C, a difference in stability of ΔTm -6.2 °C. Deshielding of the fluorine nucleus in the 19F NMR spectra is evidence of a stabilizing n→π* electronic interaction.
Collapse
Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA.
| | | |
Collapse
|
3
|
Zhang Z, Hu B, Joseph J, Wang Y, Mao J, Zhang H, Ma Q, Zhang Y, Wang J. Stable H-bond networks are crucial for selective CDK4 inhibition revealed from comprehensive in silico investigation. Comput Biol Chem 2022; 99:107699. [DOI: 10.1016/j.compbiolchem.2022.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
|
4
|
Arcoria PJ, Ware RI, Makwana SV, Troya D, Etzkorn FA. Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic Collagen. J Phys Chem B 2021; 126:217-228. [PMID: 34968406 DOI: 10.1021/acs.jpcb.1c09180] [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
Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
Collapse
Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rachel I Ware
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sunny V Makwana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Diego Troya
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Felicia A Etzkorn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
5
|
Zhao H, Li S, Wang G, Zhao W, Zhang D, Wang F, Li W, Sun L. Study of the mechanism by which dinaciclib induces apoptosis and cell cycle arrest of lymphoma Raji cells through a CDK1-involved pathway. Cancer Med 2019; 8:4348-4358. [PMID: 31207099 PMCID: PMC6675732 DOI: 10.1002/cam4.2324] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 01/02/2023] Open
Abstract
Objective This study aimed to identify and evaluate the mechanism by which apoptosis and cell cycle arrest were induced by dinaciclib in lymphoma Raji cells. Methods The colony formation assay was used to detect cell proliferation of Raji cells. Cell cycle arrest and cell apoptosis were determined by flow cytometry and TUNEL assays, respectively. Protein expression related to the Raji cell state was evaluated by Western blot. The Raji/Dinaciclib drug‐resistant cell line was established, where the regulating functions of CDK1‐involved pathway were verified. In addition, the effect of dinaciclib in vivo was examined in orthotopically implanted tumors in nude mice. Results Cell apoptosis was induced, and DNA synthesis ability was decreased in a time‐dependent manner in dinaciclib‐treated lymphoma Raji cells. Furthermore, the cell cycle was found to be blocked in the G2/M Phase. Further study indicated that CDK1‐involved pathway played a key regulatory role in this process. It was revealed by cell transfection that the expression of cell cycle proteins was downregulated after treatment with dinaciclib through a CDK1‐involved pathway, which eventually led to apoptosis. Knockdown of CDK1 restored the sensitivity of the Raji/Dinaciclib cells to dinaciclib. Xenograft model of nude mice showed that dinaciclib treatment in vivo could effectively inhibit tumor growth, consistent with the experiment results mentioned before. Conclusion In this study, we clarified the mechanisms through which dinaciclib induces Raji cell apoptosis and blocks the cell cycle through a CDK1‐involved pathway, which supported that dinaciclib had potential values in the treatment of lymphoma.
Collapse
Affiliation(s)
- Huayan Zhao
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guannan Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wugan Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dandan Zhang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fang Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wencai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Sun
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
6
|
Properties of the Amide Bond Involving Proline 4,5-methanologues: an Experimental and Theoretical Study. Isr J Chem 2016. [DOI: 10.1002/ijch.201600106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
7
|
Mayfield JE, Burkholder NT, Zhang YJ. Dephosphorylating eukaryotic RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:372-87. [PMID: 26779935 DOI: 10.1016/j.bbapap.2016.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/20/2022]
Abstract
The phosphorylation state of the C-terminal domain of RNA polymerase II is required for the temporal and spatial recruitment of various factors that mediate transcription and RNA processing throughout the transcriptional cycle. Therefore, changes in CTD phosphorylation by site-specific kinases/phosphatases are critical for the accurate transmission of information during transcription. Unlike kinases, CTD phosphatases have been traditionally neglected as they are thought to act as passive negative regulators that remove all phosphate marks at the conclusion of transcription. This over-simplified view has been disputed in recent years and new data assert the active and regulatory role phosphatases play in transcription. We now know that CTD phosphatases ensure the proper transition between different stages of transcription, balance the distribution of phosphorylation for accurate termination and re-initiation, and prevent inappropriate expression of certain genes. In this review, we focus on the specific roles of CTD phosphatases in regulating transcription. In particular, we emphasize how specificity and timing of dephosphorylation are achieved for these phosphatases and consider the various regulatory factors that affect these dynamics.
Collapse
Affiliation(s)
- Joshua E Mayfield
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nathaniel T Burkholder
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
8
|
Mayfield JE, Fan S, Wei S, Zhang M, Li B, Ellington AD, Etzkorn FA, Zhang YJ. Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. ACS Chem Biol 2015; 10:2405-14. [PMID: 26332362 DOI: 10.1021/acschembio.5b00296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using novel, direct, and quantitative chemical tools. We determine the proline isomeric preference of three CTD phosphatases: Ssu72 as cis-proline specific, Scp1 and Fcp1 as strongly trans-preferred. Due to this inherent characteristic, these phosphatases respond differently to enzymes that catalyze the isomerization of proline, like Ess1/Pin1. We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. This leads to diversified phosphorylation states of CTD in vitro and in cells. We provide the chemical tools to investigate proline isomerization and its ability to selectively enhance signaling in transcription and other biological contexts.
Collapse
Affiliation(s)
- Joshua E. Mayfield
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Shuang Fan
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shuo Wei
- 1 Cancer
Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Mengmeng Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bing Li
- Department
of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines
Boulevard, Dallas, Texas 75390, United States
| | - Andrew D. Ellington
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yan Jessie Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|