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Turilli-Ghisolfi ES, Lualdi M, Fasano M. Ligand-Based Regulation of Dynamics and Reactivity of Hemoproteins. Biomolecules 2023; 13:683. [PMID: 37189430 PMCID: PMC10135655 DOI: 10.3390/biom13040683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
Hemoproteins include several heme-binding proteins with distinct structure and function. The presence of the heme group confers specific reactivity and spectroscopic properties to hemoproteins. In this review, we provide an overview of five families of hemoproteins in terms of dynamics and reactivity. First, we describe how ligands modulate cooperativity and reactivity in globins, such as myoglobin and hemoglobin. Second, we move on to another family of hemoproteins devoted to electron transport, such as cytochromes. Later, we consider heme-based reactivity in hemopexin, the main heme-scavenging protein. Then, we focus on heme-albumin, a chronosteric hemoprotein with peculiar spectroscopic and enzymatic properties. Eventually, we analyze the reactivity and dynamics of the most recently discovered family of hemoproteins, i.e., nitrobindins.
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Affiliation(s)
| | | | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, 22100 Como, Italy
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2
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Structural and evolutionary analysis unveil functional adaptations in the promiscuous behavior of serum albumins. Biochimie 2022; 197:113-120. [DOI: 10.1016/j.biochi.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022]
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3
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Martinez Del Rio C, Gutiérrez-Guerrero YT. An Evolutionary Remedy for an Abominable Physiological Mystery: Benign Hyperglycemia in Birds. J Mol Evol 2020; 88:715-719. [PMID: 33164119 DOI: 10.1007/s00239-020-09970-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 01/11/2023]
Abstract
Relative to other vertebrates, birds have unusually high blood glucose levels. In humans, the hyperglycemia observed in birds would be associated with diabetes mellitus and the non-enzymatic glycation of proteins, which leads to the accumulation of advanced glycation products and to a plethora of microvascular pathologies. How do birds avoid the negative effects of hyperglycemia? Anthony-Regnitz et al. (J Mol Evol 88: 653-661, 2020) discovered that birds might have evolved glycation-resistant proteins. Serum albumin is an important multifunctional protein susceptible to glycation. Anthony-Regnitz et al. (J Mol Evol 88: 653-661, 2020) found that chicken albumin is resistant to glycation relative to bovine serum albumin. Protein glycation takes place primarily in lysine residues, which are less abundant in chicken than in bovine serum albumin. A multispecies comparison of serum albumin sequences revealed lower numbers of lysine residues in birds than in mammals. Benign hyperglycemia is a shared derived trait of birds and glycation resistance mechanisms appear to have accompanied its evolution. The evolution of benign hyperglycemia in birds coincided with a genomic upheaval that included the loss of important genes, including the one that codes for GLUT4, the transporter responsible for insulin-dependent glucose transport in other vertebrates' insulin-sensitive cells. This loss seems to have resulted in the remodeling of the insulin-signaling pathway in bird tissues. Avian hyperglycemia has been considered a mystery for a long time. Although we remain ignorant of its origins and its repercussions for the physiology of birds, the discovery of resistance to glycation in bird serum albumin offers a path forward to solve this mystery.
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Affiliation(s)
| | - Yocelyn T Gutiérrez-Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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4
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Shityakov S, Fischer A, Su KP, Hussein AA, Dandekar T, Broscheit J. Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species. ACS OMEGA 2020; 5:25543-25551. [PMID: 33073080 PMCID: PMC7557242 DOI: 10.1021/acsomega.0c01295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 05/09/2023]
Abstract
The interaction between the main carrier (serum albumin, SA) of endogenous and exogenous compounds in the bloodstream of different species (human, bovine, canine, rat, rabbit, and sheep) and a general anesthetic agent (propofol, PR) was investigated using an experimental technique (high-performance liquid chromatography) and computational methods (molecular docking, molecular dynamics, sequence, and phylogenetic analyses). The obtained results revealed the differences in the PR binding affinity to various homologous forms of this protein with reliable statistics (R 2 = 0.9 and p-value < 0.005), correlating with the evolutionary relationships among SAs from different species. Additionally, the protein conformational changes (root-mean-square deviation ≈ 1.0 Å) and amino acid conservation of binding sites in protein domains were detected, contributing to the SA-PR binding modes. Overall, the outcomes from this study might provide a novel methodology to assess protein-ligand interactions and to gain some interesting insights into drug pharmacokinetics and pharmacodynamics to explain its variations among different species.
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Affiliation(s)
- Sergey Shityakov
- Department
of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 40402, Taiwan
- Department
of Bioinformatics, Würzburg University, Würzburg 97074, Germany
- College
of Medicine, China Medical University, Taichung 404, Taiwan
- . Phone: +49-931-318-4550. Fax: +49-931-318-4552
| | - Anneli Fischer
- Department
of Anesthesia and Critical Care, Würzburg
University Hospital, Würzburg 97080, Germany
| | - Kuan-Pin Su
- Department
of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 40402, Taiwan
- College
of Medicine, China Medical University, Taichung 404, Taiwan
| | - Aqeel A. Hussein
- Faculty
of Dentistry, University of Al-Ameed, 56001 Karbala, Iraq
- Department
of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Thomas Dandekar
- Department
of Bioinformatics, Würzburg University, Würzburg 97074, Germany
- Phone: +49 (0)931 31-84551. Fax: +49-931-318-4552
| | - Jens Broscheit
- Department
of Anesthesia and Critical Care, Würzburg
University Hospital, Würzburg 97080, Germany
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5
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Hazarika Z, Jha AN. Computational Analysis of the Silver Nanoparticle-Human Serum Albumin Complex. ACS OMEGA 2020; 5:170-178. [PMID: 31956763 PMCID: PMC6963898 DOI: 10.1021/acsomega.9b02340] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Drug delivery in excess concentrations and at not-specified sites inside the human body adversely affects the body and gives rise to other diseases. Several methods have been developed to deliver the drugs in required amounts and at specific targets. Nanoparticle-mediated drug delivery is one such approach and has gained success at primary levels. The effect of nanoparticles on the human body needs important apprehension, and it has been unraveled by assessing the protein-nanoparticle interactions. Here, we have measured the impact of silver nanoparticles (AgNPs) on the human serum albumin (HSA) structure and function with the help of all-atom molecular dynamics simulations (MDS). HSA is a transport protein, and any change in the structure may obstruct its function. The post MD analyses showed that the NP interacts with HSA and the conjugated system got stabilized with time evolution of trajectories. The present investigation confirms that the AgNP interacts with HSA without affecting its tertiary and secondary structures and in turn the protein function as well. AgNP application is recommended in transporting conjugated drug molecules as it has no adverse effect on serum proteins. Since HSA is present in the circulatory system, it may open various applications of AgNPs in the biomedical field.
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6
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Ruxolitinib binding to human serum albumin: bioinformatics, biochemical and functional characterization in JAK2V617F + cell models. Sci Rep 2019; 9:16379. [PMID: 31704999 PMCID: PMC6841977 DOI: 10.1038/s41598-019-52852-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Ruxolitinib is a type I JAK inhibitor approved by FDA for targeted therapy of Philadelphia-negative myeloproliferative neoplasms (MPNs), all characterized by mutations activating the JAK2/STAT signaling pathway. Treatment with ruxolitinib improves constitutional symptoms and splenomegaly. However, patients can become resistant to treatment and chronic therapy has only a mild effect on molecular/pathologic remissions. Drugs interaction with plasma proteins, i.e. human serum albumin (HSA), is an important factor affecting the intensity and duration of their pharmacological actions. Here, the ruxolitinib recognition by the fatty acid binding sites (FAs) 1, 6, 7, and 9 of HSA has been investigated from the bioinformatics, biochemical and/or biological viewpoints. Docking simulations indicate that ruxolitinib binds to multiple sites of HSA. Ruxolitinib binds to the FA1 and FA7 sites of HSA with high affinity (Kr = 3.1 μM and 4.6 μM, respectively, at pH 7.3 and 37.0 °C). Moreover, HSA selectively blocks, in a dose dependent manner, the cytotoxic activity of ruxolitinib in JAK2V617F+ cellular models for MPN, in vitro. Furthermore this event is accompanied by changes in the cell cycle, p27Kip1 and cyclin D3 levels, and JAK/STAT signaling. Given the high plasma concentration of HSA, ruxolitinib trapping may be relevant in vivo.
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Polticelli F, Leboffe L, Tortosa V, Trezza V, Fanali G, Fasano M, Ascenzi P. Cantharidin inhibits competitively heme-Fe(III) binding to the FA1 site of human serum albumin. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Fabio Polticelli
- Department of Sciences; Roma Tre University; Roma Italy
- National Institute of Nuclear Physics, Roma Tre Section; Rome Italy
| | - Loris Leboffe
- Department of Sciences; Roma Tre University; Roma Italy
| | | | | | | | - Mauro Fasano
- Department of Science and High Technology; University of Insubria; Busto Arsizio Varese Italy
- Neuroscience Research Center; University of Insubria; Busto Arsizio Varese Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy; Roma Tre University; Roma Italy
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8
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di Masi A, Trezza V, Leboffe L, Ascenzi P. Human plasma lipocalins and serum albumin: Plasma alternative carriers? J Control Release 2016; 228:191-205. [PMID: 26951925 DOI: 10.1016/j.jconrel.2016.02.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/14/2023]
Abstract
Lipocalins are an evolutionarily conserved family of proteins that bind and transport a variety of exogenous and endogenous ligands. Lipocalins share a conserved eight anti-parallel β-sheet structure. Among the different lipocalins identified in humans, α-1-acid glycoprotein (AGP), apolipoprotein D (apoD), apolipoprotein M (apoM), α1-microglobulin (α1-m) and retinol-binding protein (RBP) are plasma proteins. In particular, AGP is the most important transporter for basic and neutral drugs, apoD, apoM, and RBP mainly bind endogenous molecules such as progesterone, pregnenolone, bilirubin, sphingosine-1-phosphate, and retinol, while α1-m binds the heme. Human serum albumin (HSA) is a monomeric all-α protein that binds endogenous and exogenous molecules like fatty acids, heme, and acidic drugs. Changes in the plasmatic levels of lipocalins and HSA are responsible for the onset of pathological conditions associated with an altered drug transport and delivery. This, however, does not necessary result in potential adverse effects in patients because many drugs can bind both HSA and lipocalins, and therefore mutual compensatory binding mechanisms can be hypothesized. Here, molecular and clinical aspects of ligand transport by plasma lipocalins and HSA are reviewed, with special attention to their role as alterative carriers in health and disease.
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Affiliation(s)
- Alessandra di Masi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy; Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy.
| | - Viviana Trezza
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Loris Leboffe
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy; Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy
| | - Paolo Ascenzi
- Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy; Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy
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9
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Andreeva AM, Lamas NE, Serebryakova MV, Ryabtseva IP, Bolshakov VV. Reorganization of low-molecular-weight fraction of plasma proteins in the annual cycle of cyprinidae. BIOCHEMISTRY (MOSCOW) 2015; 80:208-18. [PMID: 25756535 DOI: 10.1134/s0006297915020078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Reorganization of the low-molecular-weight fraction of cyprinid plasma was analyzed using various electrophoretic techniques (disc electrophoresis, electrophoresis in polyacrylamide concentration gradient, in polyacrylamide with urea, and in SDS-polyacrylamide). The study revealed coordinated changes in the low-molecular-weight protein fractions with seasonal dynamics and related reproductive rhythms of fishes. We used cultured species of the Cyprinidae family with sequenced genomes for the detection of these interrelations in fresh-water and anadromous cyprinid species. The common features of organization of fish low-molecular-weight plasma protein fractions made it possible to make reliable identification of their proteins. MALDI mass-spectrometry analysis revealed the presence of the same proteins (hemopexin, apolipoproteins, and serpins) in the low-molecular-weight plasma fraction in wild species and cultured species with sequenced genomes (carp, zebrafish). It is found that the proteins of the first two classes are organized as complexes made of protein oligomers. Stoichiometry of these complexes changes in concordance with the seasonal and reproductive rhythms.
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Affiliation(s)
- A M Andreeva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia.
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10
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Heel T, McIntosh JA, Dodani SC, Meyerowitz JT, Arnold FH. Non-natural olefin cyclopropanation catalyzed by diverse cytochrome P450s and other hemoproteins. Chembiochem 2014; 15:2556-62. [PMID: 25294253 DOI: 10.1002/cbic.201402286] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 11/12/2022]
Abstract
Recent work has shown that engineered variants of cytochrome P450BM3 (CYP102A1) efficiently catalyze non-natural reactions, including carbene and nitrene transfer reactions. Given the broad substrate range of natural P450 enzymes, we set out to explore if this diversity could be leveraged to generate a broad panel of new catalysts for olefin cyclopropanation (i.e., carbene transfer). Here, we took a step towards this goal by characterizing the carbene transfer activities of four new wild-type P450s that have different native substrates. All four were active and exhibited a range of product selectivities in the model reaction: cyclopropanation of styrene by using ethyl diazoacetate (EDA). Previous work on P450BM3 demonstrated that mutation of the axial coordinating cysteine, universally conserved among P450 enzymes, to a serine residue, increased activity for this non-natural reaction. The equivalent mutation in the selected P450s was found to activate carbene transfer chemistry both in vitro and in vivo. Furthermore, serum albumins complexed with hemin were also found to be efficient in vitro cyclopropanation catalysts.
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Affiliation(s)
- Thomas Heel
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125 (USA)
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11
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Imatinib binding to human serum albumin modulates heme association and reactivity. Arch Biochem Biophys 2014; 560:100-12. [DOI: 10.1016/j.abb.2014.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/25/2014] [Accepted: 07/02/2014] [Indexed: 01/09/2023]
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12
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Malik A, Al-Senaidy A, Skrzypczak-Jankun E, Jankun J. Isolation and characterization of serum albumin from Camelus dromedarius.. Exp Ther Med 2013; 6:519-524. [PMID: 24137219 PMCID: PMC3786902 DOI: 10.3892/etm.2013.1145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 05/29/2013] [Indexed: 11/06/2022] Open
Abstract
Serum albumin constitutes 35–50 mg/ml of plasma proteins and performs various physiological activities including the regulation of osmotic pressure on blood, maintaining buffering of the blood pH, carrying different fatty acids and other small molecules, such as bilirubin, hormones, drugs and metal ions, as well as participating in immunological responses. Serum albumin is an extensively used protein in biotechnological and pharmaceutical industries. The camel (Camelus dromedarius) is well tailored to successfully survive in extremely hot and dry climates. Plasma osmolality in the camel increases during water-deprived conditions. In such circumstances serum albumin is crucial in the regulation of blood pressure. The study of biochemical, biophysical and immunological aspects of camel serum albumin (CSA) are likely to provide molecular insights into camel physiology and may render it an alternative to human serum albumin (HSA) and bovine serum albumin (BSA) in all cases. However, these proteins are currently not available or cannot be utilized due to a variety of considerations. In this study, 12 mg of highly pure CSA was obtained from 1 ml plasma. Coomassie Brilliant Blue staining of SDS-PAGE yielded one band and RP-HPLC results revealed a single sharp peak, indicating homogenous preparation of the CSA. The charge/mass ratio and surface hydrophobicity of the CSA was similar to that of BSA. Mass spectrometry analysis of the purified protein confirmed the identity of CSA.
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Affiliation(s)
- Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Sciences, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
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Ascenzi P, di Masi A, Leboffe L, Alberio T, Fanali G, Fasano M. Molecular phylogenetic analyses of albuminoids reveal the molecular evolution of allosteric properties. IUBMB Life 2013; 65:544-9. [DOI: 10.1002/iub.1164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/21/2013] [Indexed: 11/07/2022]
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Bujacz A. Structures of bovine, equine and leporine serum albumin. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1278-89. [PMID: 22993082 DOI: 10.1107/s0907444912027047] [Citation(s) in RCA: 517] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/14/2012] [Indexed: 02/23/2023]
Abstract
Serum albumin first appeared in early vertebrates and is present in the plasma of all mammals. Its canonical structure supported by a conserved set of disulfide bridges is maintained in all mammalian serum albumins and any changes in sequence are highly correlated with evolution of the species. Previous structural investigations of mammalian serum albumins have only concentrated on human serum albumin (HSA), most likely as a consequence of crystallization and diffraction difficulties. Here, the crystal structures of serum albumins isolated from bovine, equine and leporine blood plasma are reported. The structure of bovine serum albumin (BSA) was determined at 2.47 Å resolution, two crystal structures of equine serum albumin (ESA) were determined at resolutions of 2.32 and 2.04 Å, and that of leporine serum albumin (LSA) was determined at 2.27 Å resolution. These structures were compared in detail with the structure of HSA. The ligand-binding pockets in BSA, ESA and LSA revealed different amino-acid compositions and conformations in comparison to HSA in some cases; however, much more significant differences were observed on the surface of the molecules. BSA, which is one of the most extensively utilized proteins in laboratory practice and is used as an HSA substitute in many experiments, exhibits only 75.8% identity compared with HSA. The higher resolution crystal structure of ESA highlights the binding properties of this protein because it includes several bound compounds from the crystallization solution that provide additional structural information about potential ligand-binding pockets.
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Affiliation(s)
- Anna Bujacz
- Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
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