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Javanshad R, Panth R, Venter AR. Effects of Amino Acid Additives on Protein Stability during Electrothermal Supercharging in ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:151-157. [PMID: 38078777 DOI: 10.1021/jasms.3c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The surprising formation of highly charged protein ions from aqueous ammonium bicarbonate solution is a fascinating phenomenon referred to as electrothermal supercharging (ETS). Although the precise mechanism involved is not clearly understood, previous studies predominantly suggest that ETS is due to native protein destabilization in the presence of bicarbonate anion inside the electrospray ionization droplets under high temperatures and spray voltages. To evaluate existing hypotheses surrounding the underlying mechanism of ETS, the effects of several additives on protein charging under ETS conditions were investigated. The changes in the protein charge state distributions were compared by measuring the ratios between the intensities of highest intensity charge states of native and unfolded protein envelopes and shifts in the lowest and highest observed charge states. This study demonstrated that source temperature plays a more important role in ETS compared to spray voltage, especially when using a nebulized microelectrospray ionization source. Moreover, the effect of amino acids on ETS were generally in good agreement with the extensive literature available on the stabilization or destabilization of proteins by these additives in bulk solution. Among the natural amino acids, protein supercharging was significantly reduced by proline and glycine; however, imidazole provided the highest degree of noncovalent complex stabilization against ETS, outperforming the amino acids. Overall, our study shows that the simple addition of stabilizing reagents such as proline and imidazole can reduce the extent of apparent protein unfolding and supercharging in ammonium bicarbonate solution and provide evidence against the roles of charge depletion and thermal unfolding during ETS.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Rajendra Panth
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
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Bajaj M, Muddassir M, Choi B, Singh P, Park JB, Singh S, Yadav M, Kumar R, Eom K, Sharma D. Single-molecule analysis of osmolyte-mediated nanomechanical unfolding behavior of a protein domain. Int J Biol Macromol 2023; 253:126849. [PMID: 37717878 DOI: 10.1016/j.ijbiomac.2023.126849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
The small organic molecules, known as osmolytes being ubiquitously present in different cell types, affect protein folding, stability and aggregation. However, it is unknown how the osmolytes affect the nanomechanical unfolding behavior of protein domain. Here, we show the osmolyte-dependent mechanical unfolding properties of protein titin immunoglobulin-27 (I27) domain using an atomic force microscopy (AFM)-based single-molecule force spectroscopy. We found that amines and methylamines improved the mechanical stability of I27 domain, whereas polyols had no effect. Interestingly, glycine betaine (GB) or trimethylamine-N-oxide (TMAO) increased the average unfolding force of the protein domain. The kinetic parameters analyzed at single-molecule level reveal that stabilizing effect of osmolytes is due to a decrease in the unfolding rate constant of I27, which was confirmed by molecular dynamics simulations. Our study reveals different effects that diverse osmolytes have on the mechanical properties of the protein, and suggests the potential use of osmolytes in modulating the mechanical stability of proteins required for various nano-biotechnological applications.
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Affiliation(s)
- Manish Bajaj
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Mohd Muddassir
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Digial Bio R&D Center, Mediazen, Seoul 07789, Republic of Korea
| | - Priyanka Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Jong Bum Park
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Surjeet Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Manisha Yadav
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Rajesh Kumar
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Deepak Sharma
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Academy of Scientific & Innovative Research, India.
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Ó'Fágáin C, Colliton K. Storage and Lyophilization of Pure Proteins. Methods Mol Biol 2023; 2699:421-475. [PMID: 37647008 DOI: 10.1007/978-1-0716-3362-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This chapter outlines empirical procedures for the storage of pure proteins with preservation of high levels of biological activity. It describes simple and workable means of preventing microbial contamination and proteolytic degradation and the use of various types of stabilizing additives. It sets out the principles of lyophilization (a complex process comprising freezing, primary drying, and secondary drying stages, otherwise known as freeze-drying). There follows a general procedure for the use of lyophilizer apparatus with emphasis on best practice and on pitfalls to avoid. The use of modulated differential scanning calorimetry to measure the glass transition temperature, a key parameter in the design and successful operation of lyophilization processes, is described. This chapter concludes with brief summaries of interesting recent work in the field.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| | - Keith Colliton
- Pfizer Ireland Pharmaceuticals, Grange Castle Business Park, Dublin, Ireland
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Azizah M, Pohnert G. Orchestrated Response of Intracellular Zwitterionic Metabolites in Stress Adaptation of the Halophilic Heterotrophic Bacterium Pelagibaca bermudensis. Mar Drugs 2022; 20:727. [PMID: 36422005 PMCID: PMC9695272 DOI: 10.3390/md20110727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 12/01/2023] Open
Abstract
Osmolytes are naturally occurring organic compounds that protect cells against various forms of stress. Highly polar, zwitterionic osmolytes are often used by marine algae and bacteria to counteract salinity or temperature stress. We investigated the effect of several stress conditions including different salinities, temperatures, and exposure to organic metabolites released by the alga Tetraselmis striata on the halophilic heterotrophic bacterium Pelagibaca bermudensis. Using ultra-high-performance liquid chromatography (UHPLC) on a ZIC-HILIC column and high-resolution electrospray ionization mass spectrometry, we simultaneously detected and quantified the eleven highly polar compounds dimethylsulfoxonium propionate (DMSOP), dimethylsulfoniopropionate (DMSP), gonyol, cysteinolic acid, ectoine, glycine betaine (GBT), carnitine, sarcosine, choline, proline, and 4-hydroxyproline. All compounds are newly described in P. bermudensis and potentially involved in physiological functions essential for bacterial survival under variable environmental conditions. We report that adaptation to various forms of stress is accomplished by adjusting the pattern and amount of the zwitterionic metabolites.
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Affiliation(s)
- Muhaiminatul Azizah
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, D-07743 Jena, Germany
| | - Georg Pohnert
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstrasse 8, D-07743 Jena, Germany
- MPG Fellow Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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Dutta S, Khan NS, Bose K, Poddar NK. A comparative in silico study to detect the effect of food-additives on metabolic protein and its perturbations compensated by osmolytes. Int J Biol Macromol 2022; 216:179-192. [PMID: 35780921 DOI: 10.1016/j.ijbiomac.2022.06.152] [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: 04/06/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022]
Abstract
Since its inception, food additive has been an integral part of the food processing industry with various commercial roles. Besides its advantages, various studies have already highlighted its long-term adverse effects on human health. However, in terms of protein structures and functions, the innate mechanism that triggers these effects has not been elucidated in previously reported studies. Our work takes an in silico approach to delve into structural implications resulting from these additives with three well studied metabolic proteins-lysozyme, bovine serum albumin (BSA) and ribonuclease A. Three classes of food additives- synthetic color, preservatives, and phosphate-containing, are taken here to understand their effects on the aforementioned metabolic proteins. Conventional molecular docking and dynamics (MD) studies reveal that these additives induce significant structural perturbations. Among them, carmoisine brings about the most secondary structural changes for lysozyme and ribonuclease A, whereas sodium tripolyphosphate affects BSA the most. To restore the secondary structural loss, we further examine the roles of osmolytes through cross-docking and higher timescale MD simulations. These studies unravel that application of osmolytes like raffinose and trehalose triggers structural restoration for BSA, lysozyme and ribonuclease A, and highlight their roles as co-formulants to alleviate the adverse effects of food additives.
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Affiliation(s)
- Shubhankar Dutta
- Integrated Biophysics and Structural Biology Lab, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Noor Saba Khan
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh 243123, India
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
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Heying M, Lam K, Richardson AD, Canepa J, Wilkinson SP. Cavity-based free energy analysis of osmolyte effects on protein denaturation. Phys Chem Chem Phys 2022; 24:5394-5403. [DOI: 10.1039/d1cp04460e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental measurements of the thermal effects of the same osmolytes on two different globular proteins, C-reactive protein (CRP) and tumor necrosis factor alpha (TNFα), have shown that quantifying the change...
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