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Boyer NR, Tokmina-Lukaszewska M, Bueno Batista M, Mus F, Dixon R, Bothner B, Peters JW. Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system. Proc Natl Acad Sci U S A 2023; 120:e2302732120. [PMID: 37459513 PMCID: PMC10372690 DOI: 10.1073/pnas.2302732120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ54-dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL-NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph, Azotobacter vinelandii.
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Affiliation(s)
- Nathaniel R. Boyer
- Institute of Biological Chemistry, Washington State University, Pullman, WA99164
| | | | - Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA99164
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73019
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA99164
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73019
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McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Li C, Attanayake K, Valentine SJ, Li P. Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization. Anal Chem 2020; 92:2492-2502. [PMID: 31940176 PMCID: PMC7318871 DOI: 10.1021/acs.analchem.9b03983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.
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Affiliation(s)
- Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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