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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [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] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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Si H, Yan W, Jun S, Hongyu M, Xia Z, Kuan W, Cunchao Z. Modulation of cecal microbiota and fecal metabolism in mice by walnut protein. Food Funct 2024; 15:1689-1704. [PMID: 38251959 DOI: 10.1039/d3fo04403c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Walnut meal is a by-product of walnut oil pressing, in which the protein content is more than 40%, which is an excellent food raw material, but at present, it is basically used as animal feed or discarded, which results in a great waste of resources, and its modulating effect on the intestinal microbiota is not clear. In this study, we used supercritically extracted walnut meal as a raw material, prepared walnut meal isolate protein (WP) by alkaline extraction and acid precipitation, and systematically analyzed its structure by Fourier infrared spectroscopy (FTIR), Raman spectroscopy (Raman), and scanning electron microscopy (SEM); meanwhile, we explored the effects of WP on the cecal bacterial flora and fecal metabolites of mice by microbiological and metabolomic techniques. The results showed that the protein content of WP prepared using alkaline extraction and acid precipitation was as high as 83.7%, in which arginine and glutamic acid were abundant, and it has the potential to be used as a raw material for weight-loss meal replacement food; FTIR and Raman analyses showed that the absorption peaks of WP's characteristic functional groups were obvious, and that the content of the α-helix and β-fold in the secondary structure was greater than 30%, which indicated that it was structurally stable; differential scanning calorimetry (DSC) and SEM analyses showed that WP is a typical spherical particle, its denaturation temperature is 73.6 °C, and it has good thermal stability. Supplementation of WP significantly altered the composition of the intestinal flora in mice, with an increase in beneficial bacteria and a decrease in harmful bacteria; the strongest modulation of the intestinal flora was achieved by altering the composition of the intestinal flora and by increasing the number of Akkermansia (p < 0.01), which consequently affects the function of the microbiota. Based on LC-MS metabolomic results, we identified a total of 87 WP-regulated metabolites, mainly enriched in the bile secretion pathway, which had the highest relevance, followed by benzoxazine biosynthesis. In summary, walnut protein is an important plant protein and has a positive impact on intestinal health, which may provide new ideas for the development of functional foods.
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Affiliation(s)
- Huang Si
- Yunnan Agricultural University, China.
| | - Wang Yan
- Yunnan Agricultural University, China.
| | - Sheng Jun
- Yunnan Agricultural University, China.
- Yunnan Province Characteristic Resources Food Biofabrication Engineering Research Center, China.
| | - Mu Hongyu
- Yunnan Agricultural University, China.
| | - Zhang Xia
- Yunnan Agricultural University, China.
| | - Wu Kuan
- Yunnan Agricultural University, China.
| | - Zhao Cunchao
- Yunnan Agricultural University, China.
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, China.
- Yunnan Province Characteristic Resources Food Biofabrication Engineering Research Center, China.
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Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
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Menezes TM, Seabra G, Neves JL. Molecular Recognition Study toward the Mitochondrial Electron Transport Chain Inhibitor Mubritinib and Human Serum Albumin. Mol Pharm 2023; 20:4021-4030. [PMID: 37382244 DOI: 10.1021/acs.molpharmaceut.3c00187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The ability to bind plasma proteins helps in comprehending relevant aspects related to the pharmacological properties of many drugs. Despite the vital role of the drug mubritinib (MUB) in the prophylaxis of various diseases, its interaction with carrier proteins still needs to be clarified. The present work focuses on the interaction between MUB and Human serum albumin (HSA), investigated by employing multispectroscopic, biochemical, and molecular docking approaches. The results reveal that MUB has quenched HSA intrinsic fluorescence (following a static mechanism) by attaching very close (r = 6.76 Å) and with moderate affinity (Kb ≈ 104 M-1) to the protein site I (mainly by H-bonds, hydrophobic and Van der Waals forces). On one side, the HSA-MUB interaction has been accompanied by a slight disturbance in the HSA chemical environment (around the Trp residue) and protein secondary structure modifications. On another side, MUB competitively inhibits HSA esterase-like activity, which is very similar to other Tyrosine kinase inhibitors, and evidence that protein functional alterations have been triggered by MUB interaction. In summary, all of the presented observations can shed light on diverse pharmacological factors associated with drug administration.
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Affiliation(s)
- Thais Meira Menezes
- Unidade Acadêmica Cabo de Santo Agostinho (UACSA), Universidade Federal Rural de Pernambuco, Recife 54518-430, Brazil
| | - Gustavo Seabra
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32603, United States
| | - Jorge Luiz Neves
- Departamento de Química Fundamental (DQF), Universidade Federal de Pernambuco, Recife 50670-901, Brazil
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Lin HJL, Parkinson DH, Holman JC, Thompson WC, Anderson CNK, Hadfield M, Ames S, Zuniga Pina NR, Bowden JN, Quinn C, Hansen LD, Price JC. Modification of the structural stability of human serum albumin in rheumatoid arthritis. PLoS One 2023; 18:e0271008. [PMID: 36930604 PMCID: PMC10022781 DOI: 10.1371/journal.pone.0271008] [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] [Received: 06/20/2022] [Accepted: 12/29/2022] [Indexed: 03/18/2023] Open
Abstract
Differential scanning calorimetry (DSC) can indicate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes result from either concentration changes or altered thermal stabilities for 7-10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA and the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes observed in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of some fraction of the human serum albumin (HSA) proteins in the sample. By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.
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Affiliation(s)
- Hsien-Jung L. Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - David H. Parkinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - J. Connor Holman
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - W. Chad Thompson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Christian N. K. Anderson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Marcus Hadfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Stephen Ames
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Nathan R. Zuniga Pina
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Jared N. Bowden
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Colette Quinn
- Applications Lab, TA Instruments, Lindon, Utah, United States of America
| | - Lee D. Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - John C. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
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Linciano S, Moro G, Zorzi A, Angelini A. Molecular analysis and therapeutic applications of human serum albumin-fatty acid interactions. J Control Release 2022; 348:115-126. [PMID: 35643382 DOI: 10.1016/j.jconrel.2022.05.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/16/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
Abstract
Human serum albumin (hSA) is the major carrier protein for fatty acids (FAs) in plasma. Its ability to bind multiple FA moieties with moderate to high affinity has inspired the use of FA conjugation as a safe and natural platform to generate long-lasting therapeutics with enhanced pharmacokinetic properties and superior efficacy. In this frame, the choice of the FA is crucial and a comprehensive elucidation of the molecular interactions of FAs with hSA cannot be left out of consideration. To this intent, we report here a comparative analysis of the binding mode of different FA moieties with hSA. The choice among different albumin-binding FAs and how this influence the pharmacokinetics properties of a broad spectrum of therapeutic molecules will be discussed including a critical description of some clinically relevant FA conjugated therapeutics.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Giulia Moro
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; AXES Research Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Alessandro Zorzi
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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Eskew MW, Benight AS. Equivalence of the transition heat capacities of proteins and DNA. Biochem Biophys Res Commun 2022; 597:98-101. [PMID: 35134611 DOI: 10.1016/j.bbrc.2022.01.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023]
Abstract
It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.
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Affiliation(s)
- Matthew W Eskew
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA.
| | - Albert S Benight
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA; Department of Physics, Portland State University, Portland, OR, USA
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