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Ploch-Jankowska A. Spectroscopic Analysis of the Effect of Ibuprofen Degradation Products on the Interaction between Ibuprofen and Human Serum Albumin. Curr Protein Pept Sci 2024; 25:492-506. [PMID: 38351694 DOI: 10.2174/0113892037284277240126094716] [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: 11/11/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) are one of the most commonly used groups of medicinal compounds in the world. The wide access to NSAIDs and the various ways of storing them due to their easy accessibility often entail the problem with the stability and durability resulting from the exposure of drugs to external factors. The aim of the research was to evaluate in vitro the mechanism of competition between ibuprofen (IBU) and its degradation products, i.e., 4'-isobutylacetophenone (IBAP) and (2RS)-2-(4- formylphenyl)propionic acid (FPPA) during transport in a complex with fatted (HSA) and defatted (dHSA) human serum albumin. METHODS The research was carried out using spectroscopic techniques, such as spectrophotometry, infrared spectroscopy and nuclear magnetic resonance spectroscopy. RESULTS The comprehensive application of spectroscopic techniques allowed, among others, for the determination of the binding constant, the number of classes of binding sites and the cooperativeness constant of the analyzed systems IBU-(d)HSA, IBU-(d)HSA-FPPA, IBU-(d)HSA-IBAP; the determination of the effect of ibuprofen and its degradation products on the secondary structure of albumin; identification and assessment of interactions between ligand and albumin; assessment of the impact of the presence of fatty acids in the structure of albumin and the measurement temperature on the binding of IBU, IBAP and FPPA to (d)HSA. CONCLUSION The conducted research allowed us to conclude that the presence of ibuprofen degradation products and the increase in their concentration significantly affect the formation of the IBU-albumin complex and thus, the value of the association constant of the drug, changing the concentration of its free fraction in the blood plasma. It was also found that the presence of an ibuprofen degradation product in a complex with albumin affects its secondary structure.
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Affiliation(s)
- Anna Ploch-Jankowska
- Department of Pharmacy and Ecological Chemistry, Institute of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
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Usoltsev D, Sitnikova V, Kajava A, Uspenskaya M. Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions. Biomolecules 2019; 9:biom9080359. [PMID: 31409012 PMCID: PMC6723850 DOI: 10.3390/biom9080359] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022] Open
Abstract
Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.
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Affiliation(s)
- Dmitrii Usoltsev
- Department of Applied Optics, ITMO University, 49 Kronverksky Pr., St.-Petersburg 197101, Russia
| | - Vera Sitnikova
- Department of Applied Optics, ITMO University, 49 Kronverksky Pr., St.-Petersburg 197101, Russia.
- International Research Institute of Bioengineering, ITMO University, 49 Kronverksky Pr., 197101 St.-Petersburg, Russia.
| | - Andrey Kajava
- International Research Institute of Bioengineering, ITMO University, 49 Kronverksky Pr., 197101 St.-Petersburg, Russia
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Universit Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
| | - Mayya Uspenskaya
- Department of Applied Optics, ITMO University, 49 Kronverksky Pr., St.-Petersburg 197101, Russia
- International Research Institute of Bioengineering, ITMO University, 49 Kronverksky Pr., 197101 St.-Petersburg, Russia
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Mazoni I, Borro LC, Jardine JG, Yano IH, Salim JA, Neshich G. Study of specific nanoenvironments containing α-helices in all-α and (α+β)+(α/β) proteins. PLoS One 2018; 13:e0200018. [PMID: 29990352 PMCID: PMC6039001 DOI: 10.1371/journal.pone.0200018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/18/2018] [Indexed: 12/02/2022] Open
Abstract
Protein secondary structure elements (PSSEs) such as α-helices, β-strands, and turns are the primary building blocks of the tertiary protein structure. Our primary interest here is to reveal the characteristics of the nanoenvironment formed by both PSSEs and their surrounding amino acid residues (AARs), which might contribute to the general understanding of how proteins fold. The characteristics of such nanoenvironments must be specific to each secondary structure element, and we have set our goal here to gather the fullest possible description of the α-helical nanoenvironment. In general, this postulate (the existence of specific nanoenvironments for specific protein substructures/neighbourhoods/regions with distinct functionality) was already successfully explored and confirmed for some protein regions, such as protein-protein interfaces and enzyme catalytic sites. Consequently, PSSEs were the obvious next choice for additional work for further evidence showing that specific nanoenvironments (having characteristics fully describable by means of structural and physical chemical descriptors) do exist for the corresponding and determined intraprotein regions. The nanoenvironment of α-helices (nEoαH) is defined as any region of the protein where this secondary structure element type is detected. The nEoαH, therefore, includes not only the α-helix amino acid residues but also the residues immediately around the α-helix. The hypothesis that motivated this work is that it might in fact be possible to detect a postulated "signal" or "signature" that distinguishes the specific location of α-helices. This "signal" must be discernible by tracking differences in the values of physical, chemical, physicochemical, structural and geometric descriptors immediately before (or after) the PSSE from those in the region along the α-helices. The search for this specific nanoenvironment "signal" was made possible by aligning previously selected α-helices of equal length. Afterward, we calculated the average value, standard deviation and mean square error at each aligned residue position for each selected descriptor. We applied Student's t-test, the Kolmogorov-Smirnov test and MANOVA statistical tests to the dataset constructed as described above, and the results confirmed that the hypothesized "signal"/"signature" is both existing/identifiable and capable of distinguishing the presence of an α-helix inside the specific nanoenvironment, contextualized as a specific region within the whole protein. However, such conclusion might rarely be reached if only one descriptor is considered at a time. A more accurate signal with broader coverage is achieved only if one applies multivariate analysis, which means that several descriptors (usually approximately 10 descriptors) should be considered at the same time. To a limited extent (up to a maximum of 15% of cases), such conclusion is also possible with only a single descriptor, and the conclusion is also possible in general for up to 50-80% of cases when no less than 5 nonlinear descriptors are selected and considered. Using all the descriptors considered in this work, provided all assumptions about data characteristics for this analysis are met, multivariate analysis regularly reached a coverage and accuracy above 90%. Understanding how secondary structure elements are formed and maintained within a protein structure could enable a more detailed understanding of how proteins reach their final 3D structure and consequently, their function. Likewise, this knowledge may also improve the tools used to determine how good a structure is by means of comparing the "signal" around a selected PSSE with the one obtained from the best (resolution and quality wise) protein structures available.
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Affiliation(s)
- Ivan Mazoni
- Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Luiz César Borro
- Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - José Augusto Salim
- Research Center on Biodiversity and Computing, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Goran Neshich
- Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
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Li J, Zhang H, Yang C, Li Y, Dai Z. An overview of osteocalcin progress. J Bone Miner Metab 2016; 34:367-79. [PMID: 26747614 DOI: 10.1007/s00774-015-0734-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/22/2015] [Indexed: 12/20/2022]
Abstract
An increasing amount of data indicate that osteocalcin is an endocrine hormone which regulates energy metabolism, male fertility and brain development. However, the detailed functions and mechanism of osteocalcin are not well understood and conflicting results have been obtained from researchers worldwide. In the present review, we summarize the progress of osteocalcin studies over the past 40 years, focusing on the structure of carboxylated and undercarboxylated osteocalcin, new functions and putative receptors, the role of osteocalcin in bone remodeling, specific expression and regulation in osteoblasts, and new indices for clinical studies. The complexity of osteocalcin in completely, uncompletely and non-carboxylated forms may account for the discrepancies in its tertiary structure and clinical results. Moreover, the extensive expression of osteocalcin and its putative receptor GPRC6A imply that there are new physiological functions and mechanisms of action of osteocalcin to be explored. New discoveries related to osteocalcin function will assist its potential clinical application and physiological theory, but comprehensive investigations are required.
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Affiliation(s)
- Jinqiao Li
- China Astronaut Research and Training Center, State Key Lab of Space Medicine Fundamentals and Application, P.O.Box 1053-23#, No. 26, Beijing Road, Haidian District, Beijing, 100094, China
| | - Hongyu Zhang
- China Astronaut Research and Training Center, State Key Lab of Space Medicine Fundamentals and Application, P.O.Box 1053-23#, No. 26, Beijing Road, Haidian District, Beijing, 100094, China
| | - Chao Yang
- China Astronaut Research and Training Center, State Key Lab of Space Medicine Fundamentals and Application, P.O.Box 1053-23#, No. 26, Beijing Road, Haidian District, Beijing, 100094, China
| | - Yinghui Li
- China Astronaut Research and Training Center, State Key Lab of Space Medicine Fundamentals and Application, P.O.Box 1053-23#, No. 26, Beijing Road, Haidian District, Beijing, 100094, China
| | - Zhongquan Dai
- China Astronaut Research and Training Center, State Key Lab of Space Medicine Fundamentals and Application, P.O.Box 1053-23#, No. 26, Beijing Road, Haidian District, Beijing, 100094, China.
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Abstract
Calmodulin (CaM) is a highly conserved calcium-binding protein consisting of two homologous domains, each of which contains two EF-hands, that is known to bind well over 300 proteins and peptides. In most cases the (Ca(2+))(4-)form of CaM leads to the activation of a key regulatory enzyme or protein in a myriad of biological processes. Using the nitroxide spin-labeling reagent, 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyl oxyl, bovine brain CaM was modified at 2-3 methionines with retention of activity as judged by the activation of cyclic nucleotide phosphodiesterase. X-band electron paramagnetic resonance (EPR) spectroscopy was used to measure the spectral changes upon addition of Ca(2+) to the apo-form of spin-labeled protein. A significant loss of spectral intensity, arising primarily from reductions in the heights of the low, intermediate, and high field peaks, accompanied Ca(2+) binding. The midpoint of the Ca(2+)-mediated transition determined by EPR occurred at a higher Ca(2+) concentration than that measured with circular dichroic spectroscopy and enzyme activation. Recent data have indicated that the transition from the apo-state of CaM to the fully saturated form, [(Ca(2+))(4-)CaM], contains a compact intermediate corresponding to [(Ca(2+))(2-)CaM], and the present results suggest that the spin probes are reporting on Ca(2+) binding to the last two sites in the N-terminal domain, i.e. for the [(Ca(2+))(2)-CaM] → [(Ca(2+))(4-)CaM] transition in which the compact structure becomes more extended. EPR of CaM, spin-labeled at methionines, offers a different approach for studying Ca(2+)-mediated conformational changes and may emerge as a useful technique for monitoring interactions with target proteins.
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Affiliation(s)
- Paula B Bowman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
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Zou Y, Ma G. A new criterion to evaluate water vapor interference in protein secondary structural analysis by FTIR spectroscopy. Int J Mol Sci 2014; 15:10018-33. [PMID: 24901531 PMCID: PMC4100137 DOI: 10.3390/ijms150610018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 01/14/2023] Open
Abstract
Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample's absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band.
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Affiliation(s)
- Ye Zou
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
| | - Gang Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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Zinnel NF, Russell DH. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification. Anal Chem 2014; 86:4791-8. [PMID: 24754452 DOI: 10.1021/ac403929u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.
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Affiliation(s)
- Nathanael F Zinnel
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
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Malashkevich VN, Almo SC, Dowd TL. X-ray crystal structure of bovine 3 Glu-osteocalcin. Biochemistry 2013; 52:8387-92. [PMID: 24138653 DOI: 10.1021/bi4010254] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 3 Glu form of osteocalcin (3 Glu-OCN) is increased in serum during low vitamin K intake or oral anticoagulant use (warfarin). Previous reports using circular dichroism show it is less structured than 3 Gla Ca²⁺-osteocalcin and does not bind strongly to bone mineral. Recent studies have suggested a role for 3 Glu-OCN as a potential regulator of glucose metabolism. A G-protein-coupled receptor, GPRC6a, found in the pancreas and testes was identified as the putative osteocalcin receptor. The purpose of this study is to determine the high-resolution structure of bovine 3 Glu-OCN, using X-ray crystallography, to understand molecular interactions with mineral and the GPRC6a receptor. Diffraction quality crystals of thermally decarboxylated bovine osteocalcin were grown, and the crystal structure was determined to 1.88 Å resolution. The final refined structure contained residues 17-47 and, like 3 Gla Ca²⁺-OCN, consisted of three α-helices surrounding a hydrophobic core, a C23-C29 disulfide bond between two of the helices, and no bound Ca²⁺. Thus, the helical structure of 3 Glu-OCN is Ca²⁺-independent but similar to that of 3 Gla Ca²⁺-OCN. A reduced level of mineral binding could result from a lower number of Ca²⁺ coordinating ligands on 3 Glu-OCN. The structure suggests the GPRC6a receptor may respond to helical osteocalcin and will aid in providing molecular mechanistic insight into the role of 3 Glu-OCN in glucose homeostasis.
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Affiliation(s)
- Vladimir N Malashkevich
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
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Filipe V, Hawe A, Carpenter JF, Jiskoot W. Analytical approaches to assess the degradation of therapeutic proteins. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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