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Costantino A, Pham LBT, Barbieri L, Calderone V, Ben‐Nissan G, Sharon M, Banci L, Luchinat E. Controlling the incorporation of fluorinated amino acids in human cells and its structural impact. Protein Sci 2024; 33:e4910. [PMID: 38358125 PMCID: PMC10868450 DOI: 10.1002/pro.4910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Fluorinated aromatic amino acids (FAAs) are promising tools when studying protein structure and dynamics by NMR spectroscopy. The incorporation FAAs in mammalian expression systems has been introduced only recently. Here, we investigate the effects of FAAs incorporation in proteins expressed in human cells, focusing on the probability of incorporation and its consequences on the 19 F NMR spectra. By combining 19 F NMR, direct MS and x-ray crystallography, we demonstrate that the probability of FAA incorporation is only a function of the FAA concentration in the expression medium and is a pure stochastic phenomenon. In contrast with the MS data, the x-ray structures of carbonic anhydrase II reveal that while the 3D structure is not affected, certain positions lack fluorine, suggesting that crystallization selectively excludes protein molecules featuring subtle conformational modifications. This study offers a predictive model of the FAA incorporation efficiency and provides a framework for controlling protein fluorination in mammalian expression systems.
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Affiliation(s)
- Azzurra Costantino
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Lan B. T. Pham
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Letizia Barbieri
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
| | - Vito Calderone
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Gili Ben‐Nissan
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Michal Sharon
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lucia Banci
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Enrico Luchinat
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
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2
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Pham LB, Costantino A, Barbieri L, Calderone V, Luchinat E, Banci L. Direct Expression of Fluorinated Proteins in Human Cells for 19F In-Cell NMR Spectroscopy. J Am Chem Soc 2023; 145:1389-1399. [PMID: 36604341 PMCID: PMC9853860 DOI: 10.1021/jacs.2c12086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In-cell NMR spectroscopy is a powerful approach to study protein structure and function in the native cellular environment. It provides precious insights into the folding, maturation, interactions, and ligand binding of important pharmacological targets directly in human cells. However, its widespread application is hampered by the fact that soluble globular proteins often interact with large cellular components, causing severe line broadening in conventional heteronuclear NMR experiments. 19F NMR can overcome this issue, as fluorine atoms incorporated in proteins can be detected by simple background-free 1D NMR spectra. Here, we show that fluorinated amino acids can be easily incorporated in proteins expressed in human cells by employing a medium switch strategy. This straightforward approach allows the incorporation of different fluorinated amino acids in the protein of interest, reaching fluorination efficiencies up to 60%, as confirmed by mass spectrometry and X-ray crystallography. The versatility of the approach is shown by performing 19F in-cell NMR on several proteins, including those that would otherwise be invisible by 1H-15N in-cell NMR. We apply the approach to observe the interaction between an intracellular target, carbonic anhydrase 2, and its inhibitors, and to investigate how the formation of a complex between superoxide dismutase 1 and its chaperone CCS modulates the interaction of the chaperone subunit with the cellular environment.
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Affiliation(s)
- Lan B.
T. Pham
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Azzurra Costantino
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Vito Calderone
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, 47521Cesena, Italy,
| | - Lucia Banci
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy,
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3
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Luchinat E, Barbieri L, Cremonini M, Pennestri M, Nocentini A, Supuran CT, Banci L. Determination of intracellular protein-ligand binding affinity by competition binding in-cell NMR. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1270-1281. [PMID: 34605430 PMCID: PMC8489230 DOI: 10.1107/s2059798321009037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Structure-based drug development suffers from high attrition rates due to the poor activity of lead compounds in cellular and animal models caused by low cell penetrance, off-target binding or changes in the conformation of the target protein in the cellular environment. The latter two effects cause a change in the apparent binding affinity of the compound, which is indirectly assessed by cellular activity assays. To date, direct measurement of the intracellular binding affinity remains a challenging task. In this work, in-cell NMR spectroscopy was applied to measure intracellular dissociation constants in the nanomolar range by means of protein-observed competition binding experiments. Competition binding curves relative to a reference compound could be retrieved either from a series of independent cell samples or from a single real-time NMR bioreactor run. The method was validated using a set of sulfonamide-based inhibitors of human carbonic anhydrase II with known activity in the subnanomolar to submicromolar range. The intracellular affinities were similar to those obtained in vitro, indicating that these compounds selectively bind to the intracellular target. In principle, the approach can be applied to any soluble intracellular target that gives rise to measurable chemical shift changes upon ligand binding.
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Affiliation(s)
- Enrico Luchinat
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Pennestri
- Pharmaceutical Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, United Kingdom
| | - Alessio Nocentini
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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4
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Novel hypervalent iodine catalyzed synthesis of α-sulfonoxy ketones: Biological activity and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130492] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Wang L, Sparacino-Watkins CE, Wang J, Wajih N, Varano P, Xu Q, Cecco E, Tejero J, Soleimani M, Kim-Shapiro DB, Gladwin MT. Carbonic anhydrase II does not regulate nitrite-dependent nitric oxide formation and vasodilation. Br J Pharmacol 2019; 177:898-911. [PMID: 31658361 DOI: 10.1111/bph.14887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Although it has been reported that bovine carbonic anhydrase CAII is capable of generating NO from nitrite, the function and mechanism of CAII in nitrite-dependent NO formation and vascular responses remain controversial. We tested the hypothesis that CAII catalyses NO formation from nitrite and contributes to nitrite-dependent inhibition of platelet activation and vasodilation. EXPERIMENT APPROACH The role of CAII in enzymatic NO generation was investigated by measuring NO formation from the reaction of isolated human and bovine CAII with nitrite using NO photolysis-chemiluminescence. A CAII-deficient mouse model was used to determine the role of CAII in red blood cell mediated nitrite reduction and vasodilation. KEY RESULTS We found that the commercially available purified bovine CAII exhibited limited and non-enzymatic NO-generating reactivity in the presence of nitrite with or without addition of the CA inhibitor dorzolamide; the NO formation was eliminated with purification of the enzyme. There was no significant detectable NO production from the reaction of nitrite with recombinant human CAII. Using a CAII-deficient mouse model, there were no measurable changes in nitrite-dependent vasodilation in isolated aorta rings and in vivo in CAII-/- , CAII+/- , and wild-type mice. Moreover, deletion of the CAII gene in mice did not block nitrite reduction by red blood cells and the nitrite-NO-dependent inhibition of platelet activation. CONCLUSION AND IMPLICATIONS These studies suggest that human, bovine and mouse CAII are not responsible for nitrite-dependent NO formation in red blood cells, aorta, or the systemic circulation.
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Affiliation(s)
- Ling Wang
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Courtney E Sparacino-Watkins
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jun Wang
- Hubei University of Technology, Wuhan, P. R. China
| | - Nadeem Wajih
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina
| | - Paul Varano
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Qinzi Xu
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eric Cecco
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jesús Tejero
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Daniel B Kim-Shapiro
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina.,Translational Science Center, Wake Forest University, Winston-Salem, North Carolina
| | - Mark T Gladwin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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6
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Rozbeský D, Rosůlek M, Kukačka Z, Chmelík J, Man P, Novák P. Impact of Chemical Cross-Linking on Protein Structure and Function. Anal Chem 2018; 90:1104-1113. [DOI: 10.1021/acs.analchem.7b02863] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Rozbeský
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
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7
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Uygun M, Karagözler AA, Denizli A. Molecularly imprinted cryogels for carbonic anhydrase purification from bovine erythrocyte. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2014; 42:128-37. [DOI: 10.3109/21691401.2013.864663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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8
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Dupont A, Chwastyniak M, Beseme O, Guihot AL, Drobecq H, Amouyel P, Pinet F. Application of saturation dye 2D-DIGE proteomics to characterize proteins modulated by oxidized low density lipoprotein treatment of human macrophages. J Proteome Res 2008; 7:3572-82. [PMID: 18549265 DOI: 10.1021/pr700683s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Macrophages are believed to play a crucial role in atherogenesis and atherosclerotic plaque progression, mainly through their role in the accumulation of large amounts of cholesteryl ester and foam cell formation after the uptake into the arterial intima of oxidized LDL (oxLDL) particles known to be proatherogenic. The aim of this study was to use a differential proteomic approach to identify the response of human monocyte-derived macrophages after treatment with oxLDL for 24 h. Mass spectrometry analysis (MALDI-TOF) of 2D-DIGE gels made it possible to identify 9 intracellular and 3 secreted proteins that were up-regulated, 11 intracellular and 1 secreted proteins that were down-regulated, and 2 secreted proteins that were induced. This methodological approach not only confirmed the differential expression levels of proteins known to be regulated by oxLDL in macrophages, such as catalase and pyruvate kinase, but also identified oxLDL modulation of other proteins for the first time, including heat shock proteins (HSP) and Actin cytoskeletal proteins. Semiquantitative Western blot confirmed their role. The HSPs identified included heat shock cognate 71 kDa protein (Hsc70), 75 kDa glucose-regulated protein (GRP75), heat shock 70 kDa protein (Hsp70), and 60 kDa (Hsp60) proteins. These highly conserved intracellular protein chaperones, commonly seen in atherosclerotic plaques, appear to participate in protection against cellular stress. Interestingly, oxLDL also modulated several F-Actin capping proteins involved in Actin polymerization and motility: gelsolin, CapG, and CapZ. In conclusion, we have demonstrated the effects of oxLDL in the modulation of several proteins in human macrophages and established a functional profile of the human macrophage during the atherosclerotic process.
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Affiliation(s)
- Annabelle Dupont
- INSERM, U744, Lille, France, Institut Pasteur de Lille, Lille, France
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9
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Soyut H, Beydemir S, Hisar O. Effects of some metals on carbonic anhydrase from brains of rainbow trout. Biol Trace Elem Res 2008; 123:179-90. [PMID: 18288451 DOI: 10.1007/s12011-008-8108-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 12/18/2007] [Accepted: 01/21/2008] [Indexed: 01/16/2023]
Abstract
Carbonic anhydrase (CA) enzyme was purified from rainbow trout brain by Sepharose-4B-L: -tyrosine-sulfanilamide affinity chromatography. The enzyme was obtained with a specific activity of 2,275 EU mg(-1) and a yield of 22.5%. The sample obtained from the affinity column was used for kinetic properties and inhibition studies. Both optimum and stable pH were found as 9.0 in 1 M Tris-SO(4) at 4 degrees C, respectively. To check the purity and subunit molecular weight of enzyme, sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis was performed, and MW was found as approximately 29.0 kDa. The molecular weight of native enzyme was estimated to be approximately 27.3 kDa by gel filtration chromatography. The purified enzyme had apparent K (m),V (max), and k (cat) as follows: 0.92 mM, 0.207 micromol.min(-1) and 43.6 s(-1) for p-nitrophenylacetate. The inhibitory effects of Co(II), Cu(II), Zn(II), Ag(I), and Cd(II) on CA enzyme activity were determined using the esterase method under in vitro conditions at low concentrations of the corresponding metals. The obtained IC(50) values, which cause 50% inhibition on in vitro enzyme activity, were 0.05, 30, 0.31, 159, and 82.5 mM for cobalt, copper, zinc, silver, and cadmium, respectively. K ( i ) values were also calculated from Linewaever-Burk plots for these substances as 0.014, 27.68, 2.15, 193.86, and 94.18 for cobalt, copper, zinc, silver, and cadmium, respectively; it was determined that cobalt, silver and cadmium inhibited the enzyme competitively, copper inhibited noncompetitively while zinc inhibited the enzyme uncompetitively.
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Affiliation(s)
- Hakan Soyut
- Department of Chemistry, Science and Arts Faculty, Atatürk University, 25240, Erzurum, Turkey
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10
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Magnani R, Nayak NR, Mazarei M, Dirk LMA, Houtz RL. Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase. J Biol Chem 2007; 282:27857-64. [PMID: 17635932 DOI: 10.1074/jbc.m702069200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rubisco large subunit methyltransferase (PsLSMT) is a SET domain protein responsible for the trimethylation of Lys-14 in the large subunit of Rubisco. The polypeptide substrate specificity determinants for pea Rubisco large subunit methyltransferase were investigated using a fusion protein construct between the first 23 amino acids from the large subunit of Rubisco and human carbonic anhydrase II. A total of 40 conservative and non-conservative amino acid substitutions flanking the target Lys-14 methylation site (positions P(-3) to P(+3)) were engineered in the fusion protein. The catalytic efficiency (k(cat)/K(m)) of PsLSMT was determined using each of the substitutions and a polypeptide consensus recognition sequence deduced from the results. The consensus sequence, represented by X-(Gly/Ser)-(Phe/Tyr)-Lys-(Ala/Lys/Arg)-(Gly/Ser)-pi, where X is any residue, Lys is the methylation site, and pi is any aromatic or hydrophobic residue, was used to predict potential alternative substrates for PsLSMT. Four chloroplast-localized proteins were identified including gamma-tocopherol methyltransferase (gamma-TMT). In vitro methylation assays using PsLSMT and a bacterially expressed form of gamma-TMT from Perilla frutescens confirmed recognition and methylation of gamma-TMT by PsLSMT in vitro. RNA interference-mediated knockdown of the PsLSMT homologue (NtLSMT) in transgenic tobacco plants resulted in a 2-fold decrease of alpha-tocopherol, the product of gamma-TMT. The results demonstrate the efficacy of consensus sequence-driven identification of alternative substrates for PsLSMT as well as identification of functional attributes of protein methylation catalyzed by LSMT.
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Affiliation(s)
- Roberta Magnani
- Department of Horticulture, Plant Physiology/Biochemistry/Molecular Biology Program, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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11
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Rahimi Y, Shrestha S, Deo SK. Metal Affinity-Based Purification of a Red Fluorescent Protein. Chromatographia 2007. [DOI: 10.1365/s10337-007-0177-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Kang JH, Kim HT, Choi MS, Lee WH, Huh TL, Park YB, Moon BJ, Kwon OS. Proteome analysis of human monocytic THP-1 cells primed with oxidized low-density lipoproteins. Proteomics 2006; 6:1261-73. [PMID: 16402358 DOI: 10.1002/pmic.200500290] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Native low-density lipoprotein (LDL) and oxidized LDL (oxLDL) possess a wide variety of biological properties, and play a central role in atherogenesis. In this study, we used a proteomic analysis of human monocyte THP-1 cells induced with oxLDL or with LDL, to identify proteins potentially involved in atherosclerotic processes. Of the 2500 proteins detected, 93 were differentially expressed as a result of priming with LDL or oxLDL. The proteins were unambiguously identified by comparing the masses of their tryptic peptides with those of all known proteins using MALDI-TOF MS and the NCBI database. The largest differences in expression were observed for vimentin (94-fold increase), meningioma-expressed antigen 6 (48-fold increase), serine/threonine protein phosphatase 2A (40-fold increase), and beta-1,3-galactosyltransferase (15-fold increase). In contrast, the abundance of an unnamed protein product and phosphogluconate dehydrogenase decreased 30-fold and 25-fold, respectively. The expression of some selected proteins was confirmed by Western blot and RT-PCR analyses. The proteins identified in this study are attractive candidates for further biomarker research. This description of the altered protein profiles induced by oxLDL in human monocytes will support functional studies of the macrophage-derived foam cells involved in the pathogenesis of atherosclerosis.
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Affiliation(s)
- Jeong Han Kang
- Department of Biochemistry, Kyungpook National University, Daegu, Korea
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13
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Jude KM, Banerjee AL, Haldar MK, Manokaran S, Roy B, Mallik S, Srivastava DK, Christianson DW. Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity. J Am Chem Soc 2006; 128:3011-8. [PMID: 16506782 PMCID: PMC2527509 DOI: 10.1021/ja057257n] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.
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Affiliation(s)
- Kevin M. Jude
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Abir L. Banerjee
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Manas K. Haldar
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sumathra Manokaran
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Bidhan Roy
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sanku Mallik
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - D. K. Srivastava
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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