1
|
Wagner WJ, Moyle AB, Wagner ND, Rempel DL, Gross ML. Evaluating Chemical Footprinting-Induced Perturbation of Protein Higher Order Structure. Anal Chem 2024; 96:9693-9703. [PMID: 38815160 PMCID: PMC11238718 DOI: 10.1021/acs.analchem.4c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Specific amino acid footprinting mass spectrometry (MS) is an increasingly utilized method for elucidating protein higher order structure (HOS). It does this by adding to certain amino acid residues a mass tag, whose reaction extent depends on solvent accessibility and microenvironment of the protein. Unlike reactive free radicals and carbenes, these specific footprinters react slower than protein unfolding. Thus, their footprinting, under certain conditions, provokes structural changes to the protein, leading to labeling on non-native structures. It is critical to establish conditions (i.e., reagent concentrations, time of reaction) to ensure that the structure of the protein following footprinting remains native. Here, we compare the efficacy of five methods in assessing protein HOS following footprinting at the intact protein level and then further localize the perturbation at the peptide level. Three are MS-based methods that provide dose-response plot analysis, evaluation of Poisson distributions of precursor and products, and determination of the average number of modifications. These MS-based methods reliably and effectively indicate HOS perturbation at the intact protein level, whereas spectroscopic methods (circular dichroism (CD) and dynamic light scattering (DLS)) are less sensitive in monitoring subtle HOS perturbation caused by footprinting. Evaluation of HOS at the peptide level indicates regions that are sensitive to localized perturbations. Peptide-level analysis also provides higher resolution of the HOS perturbation, and we recommend using it for future footprinting studies. Overall, this work shows conclusive evidence for HOS perturbation caused by footprinting. Implementation of quality control workflows can identify conditions to avoid the perturbation, for footprinting, allowing accurate and reliable identification of protein structural changes that accompany, for example, ligand interactions, mutations, and changes in solution environment.
Collapse
Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| |
Collapse
|
2
|
Jeneske HJ, Chun CKY, Koulicoff LA, Hene SR, Vipham J, O'Quinn TG, Zumbaugh MD, Chao MD. Effect of accelerated aging on shelf-stability, product loss, sensory and biochemical characteristics in 2 lower quality beef cuts. Meat Sci 2024; 213:109513. [PMID: 38608338 DOI: 10.1016/j.meatsci.2024.109513] [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: 09/29/2023] [Revised: 02/26/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
The aim of this study was to determine the impact of accelerated aging (AA) on shelf stability, product loss, sensory and biochemical characteristics of 2 lower quality beef cuts. Triceps brachii (TB) and semimembranosus (SM) were collected and fabricated from 10 USDA Choice beef carcasses and assigned to 1 of 6 treatments: 3 d cooler aged (control), 21 d cooler aged, AA 49 °C for 2 h, AA 49 °C for 3 h, AA 54 °C for 2 h, and AA 54 °C for 3 h. The results showed that AA can decrease APC counts on steak surface and in purge and redness, but increase lightness and product loss of the steaks (P < 0.01). Lower shear force was also found for AA steaks compared to those from the control (P < 0.01), with the AA 54 °C treatments being comparable to 21 d cooler aging. However, the trained sensory panel determined AA steaks were less juicy and flavorful than those from the control and 21 d cooler aged samples (P < 0.05). There was no off-flavor detected in AA steaks though lipid oxidation was higher in AA samples than those in the control steaks (P < 0.01). The AA treatments stimulated cathepsin activity (P < 0.05), which may have enhanced the solubilization of stromal proteins and led to a different troponin-T degradation pattern compared to those from the 21 d aged samples (P < 0.01). Although AA is an economical and time-efficient method to increase tenderness of lower-quality beef cuts, further research is needed to determine strategies to mitigate the decrease in juiciness from AA treatments.
Collapse
Affiliation(s)
- Haley J Jeneske
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Colin K Y Chun
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Larissa A Koulicoff
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Sara R Hene
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Jessie Vipham
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Travis G O'Quinn
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Morgan D Zumbaugh
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA
| | - Michael D Chao
- Kansas State University, Department of Animal Sciences and Industry, Manhattan, KS 66506, USA.
| |
Collapse
|
3
|
Ahmed I, Das N, Islam AKMM, Plaisier JR, Parisse P, Bal JK. Interfacial Interactions of a Myoglobin/DOPC Hybrid System at the Air-Water Interface and Its Physicochemical Properties. ACS OMEGA 2023; 8:30199-30212. [PMID: 37636970 PMCID: PMC10448488 DOI: 10.1021/acsomega.3c02909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023]
Abstract
In the present study, the intermolecular interactions between a water-insoluble phospholipid (DOPC) and water-soluble protein (myoglobin) and the interaction among themselves were investigated at the air-water interface using the Langmuir and Langmuir-Blodgett techniques. The effects of changes in physicochemical factors, like pH and temperature, on these interactions were also examined. Surface pressure-molecular area (π-A) isotherms of the DOPC monolayer at the air-water interface, with and without myoglobin (Myo) revealed the evolution of various physical properties, such as elastic, thermodynamic, and hysteric properties, in response to changes in subphase pH and temperature. With the increment of subphase pH from 5 to 7 at a fixed temperature (20 °C), the DOPC isotherm expanded, and the in-plane elasticity (CS-1) decreased, but no significant presence of hysteresis was encountered in either of the pH values. On the other hand, a diminution of temperature (from 20 to 5 °C) leads to an expansion of monolayers yielding low elasticity and significant hysteresis. The incorporation of Myo molecules within the DOPC monolayer decreased the CS-1 value of the DOPC monolayer. Such a decrement in CS-1 was also encountered while increasing the pH and decreasing the temperature (T) of the subphase in the absence of Myo. Systematic expansion of DOPC isotherm and increased hysteric area with the increase in Myo proportion were observed and the atomic force microscopy (AFM) observations suggested a strong conjugation between Myo and DOPC in the mixed monolayer. The denaturation effect of Myo molecules was studied using AFM at different temperatures. Furthermore, the Myo molecules were found to be most surface active at pH = 7, which is very close to its isoelectric point. These observations come up with the interaction mechanism between biomolecules under dynamically varied conditions.
Collapse
Affiliation(s)
- Ikbal Ahmed
- Department
of Physics, Aliah University, Kolkata 700160, India
- International
Centre for Theoretical Sciences, Tata Institute
of Fundamental Research, Bengaluru 560089, India
| | - Nilanjan Das
- Abhedananda
Mahavidyalaya, University of Burdwan, Sainthia 731234, India
| | | | - Jasper Rikkert Plaisier
- Elettra-Sincrotrone
Trieste S.C.p.A., S.S.
14 Km 163,5 in Area Science Park, Basovizza, Trieste 34149, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone
Trieste S.C.p.A., S.S.
14 Km 163,5 in Area Science Park, Basovizza, Trieste 34149, Italy
- Istituto
Officina dei Materiali—Consiglio Nazionale delle Ricerche, S.S. 14 Km 163,5 in Area Science
Park, Basovizza, Trieste 34149, Italy
| | - Jayanta Kumar Bal
- Abhedananda
Mahavidyalaya, University of Burdwan, Sainthia 731234, India
| |
Collapse
|
4
|
Gent L, Schwalbe EC, Procopio N. The impact of maceration on the 'Osteo-ome'; a pilot investigation. J Proteomics 2023; 271:104754. [PMID: 36243311 DOI: 10.1016/j.jprot.2022.104754] [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: 03/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
The bone proteome, i.e., the 'osteo-ome', is a rich source of information for forensic studies. There have been advances in the study of biomolecule biomarkers for age-at-death (AAD) and post-mortem interval (PMI) estimations, by looking at changes in protein abundance and post-translational modifications (PTMs) at the peptide level. However, the extent to which other post-mortem factors alter the proteome, including 'maceration' procedures adopted in human taphonomy facilities (HTFs) to clean bones for osteological collections, is poorly understood. This pilot study aimed to characterise the impact of these 'cleaning' methods for de-fleshing skeletons on bone biomolecules, and therefore, what further impact this may have on putative biomarkers in future investigations. Three specific maceration procedures, varying in submersion time (one week or two days) and water temperature (55 °C or 87 °C) were conducted on six bovid tibiae from three individual bovines; the proteome of fresh and macerated bones of each individual was compared. The maceration at 87 °C for two days had the greatest proteomic impact, decreasing protein relative abundances and inducing specific PTMs. Overall, these results suggest that routinely-employed maceration procedures are harsh, variable and potentially threaten the viability of discovering new forensic biomarkers in macerated skeletal remains. SIGNIFICANCE: For the first time, the application of bone proteomics in understanding maceration procedures was conducted to help address the risks for experimental confounding associated with this post-mortem cleaning technique. This pilot study demonstrates that recent advances in biomarker discovery for post-mortem interval and age-at-death estimation using bone proteomics has potential for confounding by differing and destructive bone-cleaning methods.
Collapse
Affiliation(s)
- Luke Gent
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK; School of Natural Sciences, University of Central Lancashire, PR1 2HE Preston, UK
| | - Edward C Schwalbe
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK
| | - Noemi Procopio
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST Newcastle Upon Tyne, UK; School of Natural Sciences, University of Central Lancashire, PR1 2HE Preston, UK.
| |
Collapse
|
5
|
Triyannanto E, Febrisiantosa A, Kusumaningrum A, Amri AF, Fauziah S, Sulistyono EP, Dewandaru BM, Nurhikmat A, Susanto A. The Quality Characteristics of Ready-to-Eat Empal Gentong affected by
meat pre-cooking. Food Sci Anim Resour 2021; 42:557-565. [PMID: 35855270 PMCID: PMC9289804 DOI: 10.5851/kosfa.2021.e70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 11/06/2022] Open
Abstract
The purpose of this research was to examine the effectiveness of pre-cooking
treatments on the quality characteristics of ready-to-eat (RTE) empal gentong.
Raw beef meat was pre-cooked in water bath at 90°C for 0 min (C), 10 min
(T1), 20 min (T2), and 30 min (T3) prior to retorting process at 121°C
and pressure at 70,000 Pa. Results showed that pre-cooking treatments in all
treated samples could reduce fat contents in empal gentong’s meat by
0.02% (T1), 0.28% (T2), and 1.13% (T3) respectively.
Highest precooking time tends to increase the pH and CIE a* values. However, CIE
b* values, water holding capacity, and sensory analysis were not affected by
pre-cooking duration which must have been affected by sterilization process
after pre-cooking. In conclusion, pre-cooking treatment before sterilization in
producing empal gentong is a probable technique to reduce its fat content and
improve its physical quality. A specific treatment at 90°C for 10 min is
recommended to achieve optimum quality of RTE empal gentong’s meat.
Collapse
Affiliation(s)
- Endy Triyannanto
- Department of Animal Products Technology,
Animal Science Faculty, Universitas Gadjah Mada, Yogyakarta
55281, Indonesia
| | - Andi Febrisiantosa
- Research Centre for Food Technology and
Processing, National Research and Innovation Agency,
Gunungkidul, Yogyakarta 55861, Indonesia
- Corresponding author: Andi
Febrisiantosa, Research Centre for Food Technology and Processing, National
Research and Innovation Agency, Gunungkidul, Yogyakarta 55861, Indonesia, Tel:
+62-274-392570, Fax: +62-274-391168, E-mail:
| | - Annisa Kusumaningrum
- Research Centre for Food Technology and
Processing, National Research and Innovation Agency,
Gunungkidul, Yogyakarta 55861, Indonesia
| | - Aldicky Faizal Amri
- Research Centre for Food Technology and
Processing, National Research and Innovation Agency,
Gunungkidul, Yogyakarta 55861, Indonesia
| | - Safna Fauziah
- Department of Animal Products Technology,
Animal Science Faculty, Universitas Gadjah Mada, Yogyakarta
55281, Indonesia
| | - Eki Prilla Sulistyono
- Department of Animal Products Technology,
Animal Science Faculty, Universitas Gadjah Mada, Yogyakarta
55281, Indonesia
| | - Bayu Murti Dewandaru
- Department of Animal Products Technology,
Animal Science Faculty, Universitas Gadjah Mada, Yogyakarta
55281, Indonesia
| | - Asep Nurhikmat
- Research Centre for Food Technology and
Processing, National Research and Innovation Agency,
Gunungkidul, Yogyakarta 55861, Indonesia
| | - Agus Susanto
- Research Centre for Food Technology and
Processing, National Research and Innovation Agency,
Gunungkidul, Yogyakarta 55861, Indonesia
| |
Collapse
|
6
|
Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [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
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
Collapse
Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| |
Collapse
|
7
|
Russo D, Garvey CJ, Wurm FR, Teixeira J. Conformation of Myoglobin-Poly(Ethyl Ethylene Phosphate) Conjugates Probed by SANS: Correlation with Polymer Grafting Density and Interaction. Macromol Biosci 2021; 21:e2000356. [PMID: 33393176 DOI: 10.1002/mabi.202000356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Indexed: 01/07/2023]
Abstract
One can take advantage of the influence of a polymer conjugated with a protein to control the thermal stability and the deployment of the protein. Here, the structural properties are reported of the protein-polymer conjugate myoglobin (Mb)-poly(ethyl ethylene phosphate) (PEEP) in the native and unfolded conformations, in order to understand the respective roles of the protein and of the polymer size in the stability of the conjugate. The effect is also investigated of the grafting density of the linear biodegradable polyphosphoesters covalently attached to the protein. It is observed that, while the conjugation process at room temperature does not modify the secondary and tertiary structure of the Mb, the unfolding process, as a function of temperature, depends on the grafting density. Small angle neutron scattering reveals that, at room temperature, conjugation does not alter the size of the native protein and that the thickness of the polymer shell around the protein increases as a function of grafting density and of polymer molecular weight. The denatured form of all conjugates is described by an unfolded chain and a correlation length due to the presence of local stiffness.
Collapse
Affiliation(s)
- Daniela Russo
- Consiglio Nazionale delle Ricerche & Istituto Officina dei Materiali c/o Institut Laue Langevin, Grenoble, 38042, France.,Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - Christopher J Garvey
- Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW, 2234, Australia.,Lund Institute for Advanced Neutron and X-ray Science, Lund, 20503, Sweden.,Biofilm-Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Frederick R Wurm
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, Mainz, 55128, Germany
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, Gif-sur-Yvette, Cedex, 91191, France
| |
Collapse
|
8
|
Begun A, Molochkov A, Niemi AJ. Protein tertiary structure and the myoglobin phase diagram. Sci Rep 2019; 9:10819. [PMID: 31346242 PMCID: PMC6658483 DOI: 10.1038/s41598-019-47317-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
We develop an effective theory approach to investigate the phase properties of globular proteins. Instead of interactions between individual atoms or localized interaction centers, the approach builds directly on the tertiary structure of a protein. As an example we construct the phase diagram of (apo)myoglobin with temperature (T) and acidity (pH) as the thermodynamical variables. We describe how myoglobin unfolds from the native folded state to a random coil when temperature and acidity increase. We confirm the presence of two molten globule folding intermediates, and we predict an abrupt transition between the two when acidity changes. When temperature further increases we find that the abrupt transition line between the two molten globule states terminates at a tricritical point, where the helical structures fade away. Our results also suggest that the ligand entry and exit is driven by large scale collective motions that destabilize the myoglobin F-helix.
Collapse
Affiliation(s)
- Alexander Begun
- Laboratory of Physics of Living Matter, Far Eastern Federal University, 690950, Sukhanova 8, Vladivostok, Russia
| | - Alexander Molochkov
- Laboratory of Physics of Living Matter, Far Eastern Federal University, 690950, Sukhanova 8, Vladivostok, Russia
| | - Antti J Niemi
- Laboratory of Physics of Living Matter, Far Eastern Federal University, 690950, Sukhanova 8, Vladivostok, Russia.
- Nordita, Stockholm University, Roslagstullsbacken 23, SE-106 91, Stockholm, Sweden.
- Institut Denis Poisson, CNRS UMR 7013, Parc de Grandmont, F37200, Tours, France.
- Department of Physics, Beijing Institute of Technology, Haidian District, Beijing, 100081, People's Republic of China.
| |
Collapse
|
9
|
Jiang Z, You L, Dou W, Sun T, Xu P. Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study. Polymers (Basel) 2019; 11:polym11020282. [PMID: 30960266 PMCID: PMC6419079 DOI: 10.3390/polym11020282] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field. The characteristic time when the jump occurs in the time evolution curves of root mean square deviation (RMSD) and radius of gyration Rg decreases with increasing electric strength, which demonstrates the rapidly conformational transition that occurs. The number of intra-protein hydrogen bonds, which is the key factor for stabilizing the protein structure, is related to the overall size of the protein. The value of the dipole moment and characteristic time are both influenced by the strength, but are independent of the direction of the external field. The protein sample becomes rotated with the electric field direction. These conclusions provide a theoretical realization of understanding the protein conformational transition in an electric field and the guidance for anticipative applications.
Collapse
Affiliation(s)
- Zhouting Jiang
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Le You
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Wenhui Dou
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, No. 318 Liuhe Road, Hangzhou 310023, China.
| | - Peng Xu
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| |
Collapse
|
10
|
Kossowska D, Kwak K, Cho M. Do Osmolytes Impact the Structure and Dynamics of Myoglobin? Molecules 2018; 23:E3189. [PMID: 30513982 PMCID: PMC6321238 DOI: 10.3390/molecules23123189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 11/16/2022] Open
Abstract
Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes' protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct interaction of osmolytes with proteins (water replacement hypothesis), and an indirect interaction (vitrification hypothesis). Here, to investigate these two possible mechanisms, we studied myoglobin-osmolyte systems using FTIR, UV-vis, CD, and femtosecond IR pump-probe spectroscopy. Interestingly, noticeable changes are observed in both the lifetime of the CO stretch of CO-bound myoglobin and the spectra of UV-vis, CD, and FTIR upon addition of the osmolytes. In addition, the temperature-dependent CD studies reveal that the protein's thermal stability depends on molecular structure, hydrogen-bonding ability, and size of osmolytes. We anticipate that the present experimental results provide important clues about the complicated and intricate mechanism of osmolyte effects on protein structure and dynamics in a crowded cellular environment.
Collapse
Affiliation(s)
- Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea.
- Department of Chemistry, Korea University, Seoul 136-713, Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea.
| |
Collapse
|
11
|
Kohn EM, Lee JY, Calabro A, Vaden TD, Caputo GA. Heme Dissociation from Myoglobin in the Presence of the Zwitterionic Detergent N, N-Dimethyl- N-Dodecylglycine Betaine: Effects of Ionic Liquids. Biomolecules 2018; 8:biom8040126. [PMID: 30380655 PMCID: PMC6315634 DOI: 10.3390/biom8040126] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/24/2023] Open
Abstract
We have investigated myoglobin protein denaturation using the zwitterionic detergent Empigen BB (EBB, N,N-Dimethyl-N-dodecylglycine betaine). A combination of absorbance, fluorescence, and circular dichroism spectroscopic measurements elucidated the protein denaturation and heme dissociation from myoglobin. The results indicated that Empigen BB was not able to fully denature the myoglobin structure, but apparently can induce the dissociation of the heme group from the protein. This provides a way to estimate the heme binding free energy, ΔGdissociation. As ionic liquids (ILs) have been shown to perturb the myoglobin protein, we have investigated the effects of the ILs 1-butyl-3-methylimidazolium chloride (BMICl), 1-ethyl-3-methylimidazolium acetate (EMIAc), and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF4) in aqueous solution on the ΔGdissociation values. Absorbance experiments show the ILs had minimal effect on ΔGdissociation values when compared to controls. Fluorescence and circular dichroism data confirm the ILs have no effect on heme dissociation, demonstrating that low concentrations ILs do not impact the heme dissociation from the protein and do not significantly denature myoglobin on their own or in combination with EBB. These results provide important data for future studies of the mechanism of IL-mediated protein stabilization/destabilization and biocompatibility studies.
Collapse
Affiliation(s)
- Eric M Kohn
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Bantivoglio Honors College, Rowan University, Glassboro, NJ 08028, USA.
| | - Joshua Y Lee
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Bantivoglio Honors College, Rowan University, Glassboro, NJ 08028, USA.
| | - Anthony Calabro
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
- Department of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA.
| |
Collapse
|
12
|
Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. Sci Rep 2017; 7:4552. [PMID: 28674401 PMCID: PMC5495787 DOI: 10.1038/s41598-017-04689-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/18/2017] [Indexed: 11/23/2022] Open
Abstract
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting <SASA> measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use <SASA> measurements from HR-HRPF to differentiate molecular models of high accuracy (<3 Å backbone RMSD) from models of lower accuracy (>4 Å backbone RMSD). The ability of <SASA> data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of <SASA> data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.
Collapse
|
13
|
Moriyama Y, Takeda K. Secondary Structural Changes of Intact and Disulfide Bridges-Cleaved Human Serum Albumins in Thermal Denaturation up to 130°C – Additive Effects of Sodium Dodecyl Sulfate on the Changes. J Oleo Sci 2017; 66:521-529. [DOI: 10.5650/jos.ess16228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yoshiko Moriyama
- Department of Applied Chemistry and Biotechnology, Okayama University of Science
| | - Kunio Takeda
- Department of Applied Chemistry and Biotechnology, Okayama University of Science
| |
Collapse
|
14
|
Peng X, Sieradzan AK, Niemi AJ. Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach. Phys Rev E 2016; 94:062405. [PMID: 28085346 DOI: 10.1103/physreve.94.062405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 11/07/2022]
Abstract
The Landau-Ginzburg-Wilson paradigm is applied to model the low-temperature crystallographic Cα backbone structure of sperm whale myoglobin. The Glauber protocol is employed to simulate its response to an increase in ambient temperature. The myoglobin is found to unfold from its native state by a succession of α-helical intermediates, fully in line with the observed folding and unfolding patterns in denaturation experiments. In particular, a molten globule intermediate is identified with experimentally correct attributes. A detailed, experimentally testable contact map is constructed to characterize the specifics of the unfolding pathway, including the formation of long-range interactions. The results reveal how the unfolding process of a protein is driven by the interplay between, and a successive melting of, its modular secondary structure components.
Collapse
Affiliation(s)
- Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Antti J Niemi
- Department of Physics and Astronomy, Uppsala University, P. O. Box 803, S-75108, Uppsala, Sweden.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.,Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081, People's Republic of China
| |
Collapse
|
15
|
Silverstein TP, Kirk SR, Meyer SC, Holman KLM. Myoglobin structure and function: A multiweek biochemistry laboratory project. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 43:181-8. [PMID: 25726810 DOI: 10.1002/bmb.20845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/02/2014] [Indexed: 05/25/2023]
Abstract
We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin.
Collapse
Affiliation(s)
| | - Sarah R Kirk
- Department of Chemistry, Willamette University, Salem, Oregon, 97301
| | - Scott C Meyer
- Department of Chemistry, Willamette University, Salem, Oregon, 97301
| | | |
Collapse
|
16
|
Takeda K, Moriyama Y. Kinetic Aspects of Surfactant-Induced Structural Changes of Proteins-Unsolved Problems of Two-State Model for Protein Denaturation-. J Oleo Sci 2015; 64:1143-58. [DOI: 10.5650/jos.ess15157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kunio Takeda
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science
| | - Yoshiko Moriyama
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science
| |
Collapse
|
17
|
Amadei A, Marracino P. Theoretical–computational modelling of the electric field effects on protein unfolding thermodynamics. RSC Adv 2015. [DOI: 10.1039/c5ra15605j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper we present a general theoretical–computational approach to model the protein unfolding thermodynamics response to intense electric fields.
Collapse
Affiliation(s)
- A. Amadei
- Dipartimento di Scienze e Tecnologie Chimiche
- Università degli studi di Roma Tor Vergata
- 00031 Rome
- Italy
| | - P. Marracino
- Dipartimento di Ingegneria dell'Informazione
- Elettronica e Telecomunicazioni
- Sapienza Universitaà di Roma
- 00184 Rome
- Italy
| |
Collapse
|
18
|
Kumar A, Venkatesu P. Does the stability of proteins in ionic liquids obey the Hofmeister series? Int J Biol Macromol 2013; 63:244-53. [PMID: 24211268 DOI: 10.1016/j.ijbiomac.2013.10.031] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022]
Abstract
Understanding the behavior of Hofmeister anions of ionic liquids (ILs) on protein stability helps to shed light on how the anions interact with proteins in aqueous solution and is a long standing object for chemistry and biochemistry. Ions effects play a major role in understanding the physicochemical and biological phenomenon that undertakes the protein folding/unfolding and refolding process. Despite the generality of these effects, our understanding of ions at the molecular-level is still limited. This review offers a tour through past successful investigations and presents a challenge in current research in the field to reassess the possibilities of ions and to apply new strategies. This review highlights on the stability behavior of the proteins and also comparisons of our past research work in the Hofmeister series of ILs. Furthermore, we specifically focus on the critical discussion on the recent findings with existing results and their implications, along with our understanding of the Hofmeister series of anions of ILs on biomolecular stability. A detailed examination of the difference between selective proteins can provide a better understanding of the molecular mechanism of protein folding/unfolding in the presence of the Hofmeister series of ions of ILs.
Collapse
Affiliation(s)
- Awanish Kumar
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | | |
Collapse
|
19
|
Krokhotin A, Niemi AJ, Peng X. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics. J Chem Phys 2013; 138:175101. [PMID: 23656161 DOI: 10.1063/1.4801330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.
Collapse
Affiliation(s)
- Andrey Krokhotin
- Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala, Sweden.
| | | | | |
Collapse
|
20
|
Moriyama Y, Kondo N, Takeda K. Secondary structural changes of homologous proteins, lysozyme and α-lactalbumin, in thermal denaturation up to 130 °C and sodium dodecyl sulfate (SDS) effects on these changes: comparison of thermal stabilities of SDS-induced helical structures in these proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16268-16273. [PMID: 23110666 DOI: 10.1021/la3035598] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The thermal stability of two homologous proteins, lysozyme and α-lactalbumin, was examined by circular dichroism. The present study clearly showed two different aspects between the homologous proteins: (1) the original helices of lysozyme and α-lactalbumin were unchanged at heat treatments up to 60 and 40 °C, respectively, indicating a higher thermal stability of lysozyme, and (2) upon cooling to 25 °C, the original helices of lysozyme were never reformed after they were once disrupted, while those of α-lactalbumin, disrupted at a particular temperature range between 40 and 60 °C, were completely reformed. In addition, the structural changes were also examined in the coexistence of sodium dodecyl sulfate (SDS), which induced the formation of helical structures in these proteins at 25 °C. A distinct difference appeared in the thermal stabilities of the SDS-induced helices. All of the SDS-induced helices of lysozyme were disrupted below 60 °C, while those of α-lactalbumin at 10 mM SDS were unchanged up to 130 °C. A similarity was also fixed. Not only the SDS-induced helices but also the original helices of the two proteins were reformed upon cooling to 25 °C after the thermal denaturation below 100 °C in the coexistence of 10 mM SDS.
Collapse
Affiliation(s)
- Yoshiko Moriyama
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Okayama 700-0005, Japan
| | | | | |
Collapse
|
21
|
Sankaranarayanan K, Dhathathreyan A, Krägel J, Miller R. Interfacial viscoelasticity of myoglobin at air/water and air/solution interfaces: role of folding and clustering. J Phys Chem B 2012; 116:895-902. [PMID: 22176527 DOI: 10.1021/jp2100733] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This study describes the folding and organization of myoglobin (Mb) at the solution/air interface at different pH values of 2.5, 3.5, 5.5, 7.5, and 8.5. Dynamic surface tension and the associated dilational and shear viscoelasticity for Mb at these pH's have been studied using a sinusoidal surface compression and expansion for frequencies ranging from 0.01 to 0.4 Hz. The changes in dilational viscosity, elasticity, and fluorescence lifetime measurements have been related to the conformational changes of the protein films at the interface. It is observed that while acid-induced denaturation of the protein does not lead to large changes in dilational properties, the shear properties on the other hand are strongly influenced by it, and the protein behaves like a shear-thickening fluid. At higher pH, particularly at the isoelectric point, Mb is pseudoplastic indicating an increase in the shear viscosity. These results are strongly suggestive of formation of hydrophobic clusters at the protein-buffer interface because of the change in the overall charge distributions.
Collapse
|
22
|
Moriyama Y, Razali A, Tanaka M, Takeda K. Protein structural change in a mixed system of ionic and zwitterionic surfactants. J Oleo Sci 2011; 60:229-36. [PMID: 21502723 DOI: 10.5650/jos.60.229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The secondary structure of bovine serum albumin (BSA) in the binary surfactant system of anionic sodium dodecyl sulfate (SDS) and zwitterionic N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (DDAPS) was examined at 25°C. The helicity of BSA decreased from 66% to 55% in a solution of DDAPS alone and decreased to 50% in a solution of SDS alone. However, the late addition of DDAPS reformed the helical structure of BSA, which was initially disrupted by SDS. The reformation required higher DDAPS concentrations as the initial SDS concentration increased. A maximum helicity of 63% was attained by this reformation. On the other hand, the helical structure of the protein, which was first affected by DDAPS denaturation, was also reformed to the same degree by the late addition of certain amounts of SDS. Although attention was paid to the additive order of these two surfactants to BSA, the final helicity of the protein depended on the final concentrations of these two surfactants, irrespective of the additive order. These phenomena may be attributed to the predominance of mixed micelle formation over complex formation between BSA and the two surfactants below the mixing ratio of DDAPS ([DDAPS]/([DDAPS]+[SDS])) of 0.95. The predominance of the mixed micelle formation distinctly appeared in mixing ratios between 0.50 and 0.75. In this range, the mixed micelle formation accompanied the removal of dodecyl sulfate (DS) ions bound to BSA upon the late addition of DDAPS to the BSA-SDS mixture, whereas, upon the late addition of SDS to the BSA-DDAPS mixture, the mixed micelle formation was accelerated by the coexistence of DDAPS which disturbed the binding of DS ions to the protein.
Collapse
Affiliation(s)
- Yoshiko Moriyama
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Kita-ku, Okayama, Japan
| | | | | | | |
Collapse
|
23
|
Hassan N, Maldonado-Valderrama J, Gunning AP, Morris VJ, Ruso JM. Surface Characterization and AFM Imaging of Mixed Fibrinogen−Surfactant Films. J Phys Chem B 2011; 115:6304-11. [DOI: 10.1021/jp200835j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Natalia Hassan
- Soft Matter and Molecular Biophysics
Group, Department of Applied Physics University of Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela,
Spain
| | | | - A. Patrick Gunning
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, U.K
| | - Victor J. Morris
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, U.K
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics
Group, Department of Applied Physics University of Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela,
Spain
| |
Collapse
|