1
|
Sharma IM, Rappé MC, Addepalli B, Grabow WW, Zhuang Z, Abeysirigunawardena SC, Limbach PA, Jaeger L, Woodson SA. A metastable rRNA junction essential for bacterial 30S biogenesis. Nucleic Acids Res 2019; 46:5182-5194. [PMID: 29850893 PMCID: PMC6007441 DOI: 10.1093/nar/gky120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/13/2018] [Indexed: 12/26/2022] Open
Abstract
Tertiary sequence motifs encode interactions between RNA helices that create the three-dimensional structures of ribosomal subunits. A Right Angle motif at the junction between 16S helices 5 and 6 (J5/6) is universally conserved amongst small subunit rRNAs and forms a stable right angle in minimal RNAs. J5/6 does not form a right angle in the mature ribosome, suggesting that this motif encodes a metastable structure needed for ribosome biogenesis. In this study, J5/6 mutations block 30S ribosome assembly and 16S maturation in Escherichia coli. Folding assays and in-cell X-ray footprinting showed that J5/6 mutations favor an assembly intermediate of the 16S 5' domain and prevent formation of the central pseudoknot. Quantitative mass spectrometry revealed that mutant pre-30S ribosomes lack protein uS12 and are depleted in proteins uS5 and uS2. Together, these results show that impaired folding of the J5/6 right angle prevents the establishment of inter-domain interactions, resulting in global collapse of the 30S structure observed in electron micrographs of mutant pre-30S ribosomes. We propose that the J5/6 motif is part of a spine of RNA helices that switch conformation at distinct stages of assembly, linking peripheral domains with the 30S active site to ensure the integrity of 30S biogenesis.
Collapse
Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Mollie C Rappé
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Balasubrahmanyam Addepalli
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | | - Patrick A Limbach
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| |
Collapse
|
2
|
Bloszies CS, Fiehn O. Using untargeted metabolomics for detecting exposome compounds. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2018.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
3
|
Gombar R, Pitcher TE, Lewis JA, Auld J, Vacratsis PO. Proteomic characterization of seminal plasma from alternative reproductive tactics of Chinook salmon ( Oncorhynchus tswatchysha ). J Proteomics 2017; 157:1-9. [DOI: 10.1016/j.jprot.2017.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/24/2017] [Accepted: 01/28/2017] [Indexed: 12/11/2022]
|
4
|
Qi Q, Yan G, Deng C, Zhang X. A novel protocol for enzymatic digestion based on covalent binding by protein immobilization. Anal Bioanal Chem 2016; 408:8437-8445. [PMID: 27757514 DOI: 10.1007/s00216-016-9964-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/04/2016] [Accepted: 09/20/2016] [Indexed: 11/30/2022]
Abstract
The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed. Proteins can be completely denatured and immobilized on the surface of functional materials by covalent binding to form a monolayer. Subsequently, varieties of denaturants or contaminants would be removed thoroughly by washing. To achieve fast immobilization and high digestion efficiency, different functional materials and denaturants were selected. Compared with traditional in-solution digestion, the method achieved a prominent increase in identified peptides numbers and sequence coverage of proteins. Data analysis also showed that covalent binding could evidently decrease enzymatic missed cleavage for various protein sequences. Furthermore, possible peptide losses due to covalent binding were also investigated. Also, it has been proved to be efficient for complex biological sample digestion. Graphical abstract Workflow of the IPD method, including protein denaturation, immobilization, digestion, and identification.
Collapse
Affiliation(s)
- Qian Qi
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
5
|
Ye H, Wang L, Zhu L, Sun D, Luo X, Wang H, Wang G, Hao H. Stepped collisional energy MS(All) : an analytical approach for optimal MS/MS acquisition of complex mixture with diverse physicochemical properties. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:328-341. [PMID: 27194517 DOI: 10.1002/jms.3751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
The analysis of complex mixtures is becoming increasingly important in various fields, such as nutrition, medicinal plants and metabolomics. The components contained in such complex mixtures are always characterized with diverse physiochemical properties that pose a major challenge during the optimization of various parameters using liquid chromatography-mass spectrometer (LC-MS). The parameter 'CE energy' that is normally set at a fixed value with a moderate range of CE spread during data-dependent acquisition (DDA) analysis, a prevalent approach for untargeted identification, often fails to generate sufficient MS/MS fragment ions for untargeted identification of components from complex mixtures. Here we developed a simple and generally applicable acquisition method named stepped MS(All) (sMS(All) ) in this study, aiming to obtain optimal MS/MS spectra for identification of chemically diverse compounds from complex mixtures. sMS(All) collects serial MS(All) scans acquired at low CE to gradually ramped-up high CE values in a cycle that conventional DDA scans cannot afford. The resultant MS/MS spectra of each compound were compared and evaluated among serial MS(All) scans, and the optimal spectra were used for identification. An untargeted data analysis strategy was then employed to analyze these optimal MS/MS spectra by searching common diagnostic ions and connecting the diagnostic ion families into a network via bridging components. This sMS(All) -based route enables identification of 71 natural products from a herbal preparation, whereas only 53 out of 71 compounds were identified using the classical DDA approach. Therefore, the sMS(All) -based approach is expected to find its wide applications for characterization of vastly diverse compounds with no priori knowledge from various complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Lin Wang
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Lin Zhu
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Di Sun
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Xiaozhuo Luo
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Hong Wang
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Guangji Wang
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 21009, China
| |
Collapse
|
6
|
Silveira JA, Michelmann K, Ridgeway ME, Park MA. Fundamentals of Trapped Ion Mobility Spectrometry Part II: Fluid Dynamics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:585-595. [PMID: 26864793 DOI: 10.1007/s13361-015-1310-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 06/05/2023]
Abstract
Trapped ion mobility spectrometry (TIMS) is a new high resolution (R up to ~300) separation technique that utilizes an electric field to hold ions stationary against a moving gas. Recently, an analytical model for TIMS was derived and, in part, experimentally verified. A central, but not yet fully explored, component of the model involves the fluid dynamics at work. The present study characterizes the fluid dynamics in TIMS using simulations and ion mobility experiments. Results indicate that subsonic laminar flow develops in the analyzer, with pressure-dependent gas velocities between ~120 and 170 m/s measured at the position of ion elution. One of the key philosophical questions addressed is: how can mobility be measured in a dynamic system wherein the gas is expanding and its velocity is changing? We noted previously that the analytically useful work is primarily done on ions as they traverse the electric field gradient plateau in the analyzer. In the present work, we show that the position-dependent change in gas velocity on the plateau is balanced by a change in pressure and temperature, ultimately resulting in near position-independent drag force. That the drag force, and related variables, are nearly constant allows for the use of relatively simple equations to describe TIMS behavior. Nonetheless, we derive a more comprehensive model, which accounts for the spatial dependence of the flow variables. Experimental resolving power trends were found to be in close agreement with the theoretical dependence of the drag force, thus validating another principal component of TIMS theory.
Collapse
Affiliation(s)
| | | | - Mark E Ridgeway
- Bruker Daltonics, 40 Manning Road, Billerica, MA, 01821, USA
| | - Melvin A Park
- Bruker Daltonics, 40 Manning Road, Billerica, MA, 01821, USA.
| |
Collapse
|
7
|
Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
Collapse
Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | | | | |
Collapse
|
8
|
Distler U, Kuharev J, Tenzer S. Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics. Expert Rev Proteomics 2014; 11:675-84. [DOI: 10.1586/14789450.2014.971114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|