1
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Wang J, Yu J, Copeland L, Wang S. Revisiting the Formation of Starch-Monoglyceride-Protein Complexes: Effects of Octenyl Succinic Anhydride Modification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19033-19044. [PMID: 37997356 DOI: 10.1021/acs.jafc.3c07269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Starch-lipid-protein complexes are attracting increasing attention due to their unique structure and low enzymatic digestibility. However, the mechanisms underlying the formation of these ternary complexes, especially those with monoglycerides as the lipid component, remain unclear. In the present study, potato starch or octenyl succinic anhydride (OSA)-modified potato starch (OSAPS), various monoglycerides (MGs), and beta-lactoglobulin (βLG) were used in model systems to characterize the formation, structure, and in vitro digestibility of the respective ternary complexes. Colorimetry and live/dead staining assays demonstrated that the OSAPS had good biocompatibility. Experimental data and molecular dynamics simulations showed that both unmodified potato starch and OSAPS formed starch-lipid-protein complexes with MGs and βLG. Of the two types of starch, OSA formed a greater amount of the more stable type II V-crystallites in complexes, which had greater resistance to in vitro enzymic digestion. This study demonstrated for the first time that starch can interact with MGs and βLG to form ternary complexes and that OSA esterification of starch promoted the formation of more complexes than unmodified starch.
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Affiliation(s)
- Jinwei Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- Food Laboratory of Zhongyuan, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jinglin Yu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Les Copeland
- School of Life and Environmental Sciences, The University of Sydney, Camperdown 2006, New South Wales, Australia
| | - Shujun Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- School of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, 300457, China
- Food Laboratory of Zhongyuan, Tianjin University of Science & Technology, Tianjin 300457, China
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2
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Sebők-Nagy K, Kóta Z, Kincses A, Fazekas ÁF, Dér A, László Z, Páli T. Spin-Label Electron Paramagnetic Resonance Spectroscopy Reveals Effects of Wastewater Filter Membrane Coated with Titanium Dioxide Nanoparticles on Bovine Serum Albumin. Molecules 2023; 28:6750. [PMID: 37836593 PMCID: PMC10574081 DOI: 10.3390/molecules28196750] [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: 08/11/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The accumulation of proteins in filter membranes limits the efficiency of filtering technologies for cleaning wastewater. Efforts are ongoing to coat commercial filters with different materials (such as titanium dioxide, TiO2) to reduce the fouling of the membrane. Beyond monitoring the desired effect of the retention of biomolecules, it is necessary to understand what the biophysical changes are in water-soluble proteins caused by their interaction with the new coated filter membranes, an aspect that has received little attention so far. Using spin-label electron paramagnetic resonance (EPR), aided with native fluorescence spectroscopy and dynamic light scattering (DLS), here, we report the changes in the structure and dynamics of bovine serum albumin (BSA) exposed to TiO2 (P25) nanoparticles or passing through commercial polyvinylidene fluoride (PVDF) membranes coated with the same nanoparticles. We have found that the filtering process and prolonged exposure to TiO2 nanoparticles had significant effects on different regions of BSA, and denaturation of the protein was not observed, neither with the TiO2 nanoparticles nor when passing through the TiO2-coated filter membranes.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Zoltán Kóta
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - András Kincses
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Ákos Ferenc Fazekas
- Department of Biosystems Engineering, Faculty of Engineering, University of Szeged, 6725 Szeged, Hungary; (Á.F.F.); (Z.L.)
| | - András Dér
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Zsuzsanna László
- Department of Biosystems Engineering, Faculty of Engineering, University of Szeged, 6725 Szeged, Hungary; (Á.F.F.); (Z.L.)
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
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3
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Raczyńska A, Kapica P, Papaj K, Stańczak A, Shyntum D, Spychalska P, Byczek-Wyrostek A, Góra A. Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity. PLoS One 2023; 18:e0280776. [PMID: 36827335 PMCID: PMC9956002 DOI: 10.1371/journal.pone.0280776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/09/2023] [Indexed: 02/25/2023] Open
Abstract
The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.g., tunnel entrances) were excluded from the analysis to concentrate rather on non-obvious surface residues. From a set of 130 surface residues, twenty-six were proposed as a promising improvement of enzyme performance. Eventually, based on rational selection and filtering out the potentially unstable mutants, a small library of ten mutants was proposed to validate the possibility of fine-tuning the LinB protein. Nearly half of the predicted mutant structures showed improved activity towards the selected substrates, which demonstrates that the proposed approach could be applied to identify non-obvious yet beneficial mutations for enzyme performance especially when obvious locations have already been explored.
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Affiliation(s)
- Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Agnieszka Stańczak
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Divine Shyntum
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patrycja Spychalska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
- * E-mail:
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4
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Khalil M, Serale N, Diab F, Baldini F, Portincasa P, Lupidi G, Vergani L. Beneficial Effects of Carvacrol on In Vitro Models of Metabolically-Associated Liver Steatosis and Endothelial Dysfunction: A Role for Fatty Acids in Interfering with Carvacrol Binding to Serum Albumin. Curr Med Chem 2022; 29:5113-5129. [PMID: 35366761 DOI: 10.2174/0929867329666220401103643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 11/22/2022]
Abstract
Background:
Carvacrol, a plant phenolic monoterpene, is largely employed as
food additive and phytochemical.
Objective:
We aimed to assess the lipid lowering and protective effects of carvacrol in
vitro using cellular models of hepatic steatosis and endothelial dysfunction. We also investigated if and how the binding of carvacrol to albumin, the physiological transporter
for small compounds in the blood, might be altered by the presence of high levels of fatty
acids (FAs).
Methods:
Hepatic FaO cells treated with exogenous FAs mimic hepatosteatosis; endothelial HECV cells exposed to hydrogen peroxide are a model of endothelial dysfunction. In
these models, we measured spectrophotometrically lipid accumulation and release,
lipoperoxidation, free radical production, and nitric oxide release before and after treatment with carvacrol. The carvacrol binding to albumin in the presence or absence of high
levels of FAs was assessed by absorption and emission spectroscopies.
Results:
Carvacrol counteracted lipid accumulation and oxidative stress in hepatocytes
and protected endothelial cells from oxidative stress and dysfunction. Moreover, high levels of FAs reduced the binding of carvacrol to albumin.
Conclusion:
The results suggest the good potential of carvacrol in ameliorating dysfunction of hepatic and endothelial cells in vitro. High levels of circulating FAs might compete with carvacrol for binding to albumin thus influencing its transport and bio-distribution.
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Affiliation(s)
- Mohamad Khalil
- Clinica Medica “A. Murri”, Dept. of Biomedical Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, Italy
| | - Nadia Serale
- Clinica Medica “A. Murri”, Dept. of Biomedical Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, Italy
| | - Farah Diab
- Department of Earth, Environment and Life Sciences (DISTAV), University
of Genova, Corso Europa 26, 16132, Haly
| | - Francesca Baldini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia,
Genoa, Italy
| | - Piero Portincasa
- Clinica Medica “A. Murri”, Dept. of Biomedical Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, Italy
| | - Giulio Lupidi
- School of Pharmacy, University of Camerino, Camerino, Italy
| | - Laura Vergani
- Department of Earth, Environment and Life Sciences (DISTAV), University
of Genova, Corso Europa 26, 16132, Haly
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5
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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6
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Chen T, Sun T, Bian Y, Pei Y, Feng F, Chi H, Li Y, Tang X, Sang S, Du C, Chen Y, Chen Y, Sun H. The Design and Optimization of Monomeric Multitarget Peptides for the Treatment of Multifactorial Diseases. J Med Chem 2022; 65:3685-3705. [DOI: 10.1021/acs.jmedchem.1c01456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Tianyu Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yaoyao Bian
- College of Acupuncture and Massage, College of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Feng Feng
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Heng Chi
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Yuan Li
- Department of Pharmaceutical Engineering, Jiangsu Food and Pharmaceuticals Science College, Huaian 223005, People’s Republic of China
| | - Xu Tang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Shenghu Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Chenxi Du
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Ying Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
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7
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Pacheco-Garcia JL, Loginov D, Rizzuti B, Vankova P, Neira JL, Kavan D, Mesa-Torres N, Guzzi R, Man P, Pey AL. A single evolutionarily divergent mutation determines the different FAD-binding affinities of human and rat NQO1 due to site-specific phosphorylation. FEBS Lett 2021; 596:29-41. [PMID: 34817874 DOI: 10.1002/1873-3468.14238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022]
Abstract
The phosphomimetic mutation S82D in the cancer-associated, FAD-dependent human NADP(H):quinone oxidoreductase 1 (hNQO1) causes a decrease in flavin-adenine dinucleotide-binding affinity and intracellular stability. We test in this work whether the evolutionarily recent neutral mutation R80H in the vicinity of S82 may alter the strong functional effects of S82 phosphorylation through electrostatic interactions. We show using biophysical and bioinformatic analyses that the reverse mutation H80R prevents the effects of S82D phosphorylation on hNQO1 by modulating the local stability. Consistently, in rat NQO1 (rNQO1) which contains R80, the effects of phosphorylation were milder, resembling the behaviour found in hNQO1 when this residue was humanized in rNQO1 (by the R80H mutation). Thus, apparently neutral and evolutionarily divergent mutations may determine the functional response of mammalian orthologues towards phosphorylation.
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Affiliation(s)
| | - Dmitry Loginov
- Institute of Microbiology of the Czech Academy of Sciences, BioCeV, Praha, Czech Republic
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, Rende, Italy.,Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), Zaragoza, Spain
| | - Pavla Vankova
- Institute of Biotechnology of the Czech Academy of Sciences, BioCeV, Vestec, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jose L Neira
- Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), Zaragoza, Spain.,Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, BioCeV, Praha, Czech Republic
| | - Noel Mesa-Torres
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Spain
| | - Rita Guzzi
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, Rende, Italy.,Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, BioCeV, Praha, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Spain
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8
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Belinskaia DA, Goncharov NV. Theoretical and Practical Aspects of Albumin Esterase Activity. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020030036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Cho J, Park J, Kim S, Kim JC, Tae G, Jin MS, Kwon I. Intramolecular distance in the conjugate of urate oxidase and fatty acid governs FcRn binding and serum half-life in vivo. J Control Release 2020; 321:49-58. [DOI: 10.1016/j.jconrel.2020.01.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/18/2020] [Indexed: 12/17/2022]
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10
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The Minimal Effect of Linker Length for Fatty Acid Conjugation to a Small Protein on the Serum Half-Life Extension. Biomedicines 2020; 8:biomedicines8050096. [PMID: 32357510 PMCID: PMC7277390 DOI: 10.3390/biomedicines8050096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 01/20/2023] Open
Abstract
Conjugation of serum albumin or one of its ligands (such as fatty acid) has been an effective strategy to prolong the serum half-lives of drugs via neonatal Fc receptor (FcRn)–mediated recycling of albumin. So far, fatty acid (FA) has been effective in prolonging the serum half-lives for therapeutic peptides and small proteins, but not for large therapeutic proteins. Very recently, it was reported a large protein conjugated to FA competes with the binding of FcRn with serum albumin, leading to limited serum half-life extension, because primary FA binding sites in serum albumin partially overlap with FcRn binding sites. In order to prevent such competition, longer linkers between FA and the large proteins were required. Herein, we hypothesized that small proteins do not cause substantial competition for FcRn binding to albumin, resulting in the extended serum half-life. Using a small protein (28 kDa), we investigated whether the intramolecular distance in FA-protein conjugate affects the FcRn binding with albumin and serum half-life using linkers with varying lengths. Unlike with the FA-conjugated large protein, all FA-conjugated small proteins with different linkers exhibited comparable the FcRn binding to albumin and extended serum half-life.
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11
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Prakash TP, Mullick AE, Lee RG, Yu J, Yeh ST, Low A, Chappell AE, Østergaard ME, Murray S, Gaus HJ, Swayze EE, Seth PP. Fatty acid conjugation enhances potency of antisense oligonucleotides in muscle. Nucleic Acids Res 2020; 47:6029-6044. [PMID: 31127296 PMCID: PMC6614804 DOI: 10.1093/nar/gkz354] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/19/2019] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Enhancing the functional uptake of antisense oligonucleotide (ASO) in the muscle will be beneficial for developing ASO therapeutics targeting genes expressed in the muscle. We hypothesized that improving albumin binding will facilitate traversal of ASO from the blood compartment to the interstitium of the muscle tissues to enhance ASO functional uptake. We synthesized structurally diverse saturated and unsaturated fatty acid conjugated ASOs with a range of hydrophobicity. The binding affinity of ASO fatty acid conjugates to plasma proteins improved with fatty acid chain length and highest binding affinity was observed with ASO conjugates containing fatty acid chain length from 16 to 22 carbons. The degree of unsaturation or conformation of double bond appears to have no influence on protein binding or activity of ASO fatty acid conjugates. Activity of fatty acid ASO conjugates correlated with the affinity to albumin and the tightest albumin binder exhibited the highest activity improvement in muscle. Palmitic acid conjugation increases ASO plasma Cmax and improved delivery of ASO to interstitial space of mouse muscle. Conjugation of palmitic acid improved potency of DMPK, Cav3, CD36 and Malat-1 ASOs (3- to 7-fold) in mouse muscle. Our approach provides a foundation for developing more effective therapeutic ASOs for muscle disorders.
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Affiliation(s)
| | - Adam E Mullick
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Richard G Lee
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Jinghua Yu
- Ionis Pharmaceuticals, Medicinal Chemistry, USA
| | - Steve T Yeh
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Audrey Low
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | | | | | - Sue Murray
- Antisense Drug Discovery, 2855 Gazelle Ct., Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals, Medicinal Chemistry, USA
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12
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Ryberg LA, Sønderby P, Bukrinski JT, Harris P, Peters GHJ. Investigations of Albumin–Insulin Detemir Complexes Using Molecular Dynamics Simulations and Free Energy Calculations. Mol Pharm 2019; 17:132-144. [DOI: 10.1021/acs.molpharmaceut.9b00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Line A. Ryberg
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pernille Sønderby
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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13
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Warfarin increases thermal resistance of albumin through stabilization of the protein lobe that includes its binding site. Arch Biochem Biophys 2019; 676:108123. [DOI: 10.1016/j.abb.2019.108123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 01/11/2023]
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14
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Cheng P, Liu D, Chee PX, Yang D, Long D. Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein. Biophys J 2019; 117:239-246. [PMID: 31301805 DOI: 10.1016/j.bpj.2019.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/19/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
Structural dynamics of fatty acid binding proteins (FABPs), which accommodate poorly soluble ligands in the internalized binding cavities, are intimately related to their function. Recently, local unfolding of the α-helical cap in a variant of human intestinal FABP (IFABP) has been shown to correlate with the kinetics of ligand association, shedding light on the nature of the critical conformational reorganization. Yet, the physical origin and mechanism of the functionally relevant transient unfolding remain elusive. Here, we investigate the intrinsic structural instability of the second helix (αII) of IFABP in comparison with other segments of the protein using hydrogen-exchange NMR spectroscopy, microsecond molecular dynamics simulations, and enhanced sampling techniques. Although tertiary interactions positively contribute to the stability of helices in IFABP, the intrinsic unfolding tendency of αII is encoded in its primary sequence and can be described by the Lifson-Roig theory in the absence of tertiary interactions. The unfolding pathway of αII in intact proteins involves an on-pathway intermediate state that is characterized with the fraying of the last helical turn, captured by independent enhanced sampling methods. The simulations in this work, combined with hydrogen-exchange NMR data, provide new, to our knowledge, atomistic insights into the functional local unfolding of FABPs.
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Affiliation(s)
- Peng Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Pin Xuan Chee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China.
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15
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Lappano R, Mallet C, Rizzuti B, Grande F, Galli GR, Byrne C, Broutin I, Boudieu L, Eschalier A, Jacquot Y, Maggiolini M. The Peptide ERα17p Is a GPER Inverse Agonist that Exerts Antiproliferative Effects in Breast Cancer Cells. Cells 2019; 8:cells8060590. [PMID: 31207943 PMCID: PMC6627388 DOI: 10.3390/cells8060590] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The inhibition of the G protein-coupled estrogen receptor (GPER) offers promising perspectives for the treatment of breast tumors. A peptide corresponding to part of the hinge region/AF2 domain of the human estrogen receptor α (ERα17p, residues 295–311) exerts anti-proliferative effects in various breast cancer cells including those used as triple negative breast cancer (TNBC) models. As preliminary investigations have evoked a role for the GPER in the mechanism of action of this peptide, we focused our studies on this protein using SkBr3 breast cancer cells, which are ideal for GPER evaluation. ERα17p inhibits cell growth by targeting membrane signaling. Identified as a GPER inverse agonist, it co-localizes with GPER and induces the proteasome-dependent downregulation of GPER. It also decreases the level of pEGFR (phosphorylation of epidermal growth factor receptor), pERK1/2 (phosphorylation of extracellular signal-regulated kinase), and c-fos. ERα17p is rapidly distributed in mice after intra-peritoneal injection and is found primarily in the mammary glands. The N-terminal PLMI motif, which presents analogies with the GPER antagonist PBX1, reproduces the effect of the whole ERα17p. Thus, this motif seems to direct the action of the entire peptide, as highlighted by docking and molecular dynamics studies. Consequently, the tetrapeptide PLMI, which can be claimed as the first peptidic GPER disruptor, could open new avenues for specific GPER modulators.
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Affiliation(s)
- Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Christophe Mallet
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Giulia Raffaella Galli
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Cillian Byrne
- Laboratoire des Biomolécules (LBM), CNRS-UMR 7203, Sorbonne University, Ecole Normale Supérieure, 75252 Paris Cedex 05, France.
| | - Isabelle Broutin
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS-UMR 8038, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75270 Paris Cedex 06, France.
| | - Ludivine Boudieu
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Alain Eschalier
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Yves Jacquot
- Laboratoire des Biomolécules (LBM), CNRS-UMR 7203, Sorbonne University, Ecole Normale Supérieure, 75252 Paris Cedex 05, France.
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
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16
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Neira JL, Correa J, Rizzuti B, Santofimia-Castaño P, Abian O, Velázquez-Campoy A, Fernandez-Megia E, Iovanna JL. Dendrimers as Competitors of Protein–Protein Interactions of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1. Biomacromolecules 2019; 20:2567-2576. [DOI: 10.1021/acs.biomac.9b00378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Neira
- Instituto de Biología
Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Juan Correa
- Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, La Coruña, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS
Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and
Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Olga Abian
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Eduardo Fernandez-Megia
- Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, La Coruña, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and
Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
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17
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Pantoja-Uceda D, Neira JL, Contreras LM, Manton CA, Welch DR, Rizzuti B. The isolated C-terminal nuclear localization sequence of the breast cancer metastasis suppressor 1 is disordered. Arch Biochem Biophys 2019; 664:95-101. [PMID: 30707944 DOI: 10.1016/j.abb.2019.01.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 02/02/2023]
Abstract
BRMS1 is a 246-residue-long protein belonging to the family of metastasis suppressors. It is a predominantly nuclear protein, although it can also function in the cytoplasm. At its C terminus, it has a region that is predicted to be a nuclear localization sequence (NLS); this region, NLS2, is necessary for metastasis suppression. We have studied in vitro and in silico the conformational preferences in aqueous solution of a peptide (NLS2-pep) that comprises the NLS2 of BRMS1, to test whether it has a preferred conformation that could be responsible for its function. Our spectroscopic (far-UV circular dichroism, DOSY-NMR and 2D-NMR) and computational (all-atom molecular dynamics) results indicate that NLS2-pep was disordered in aqueous solution. Furthermore, it did not acquire a structure even when experiments were performed in a more hydrophobic environment, such as the one provided by 2,2,2-trifluoroethanol (TFE). The hydrodynamic radius of the peptide in water was identical to that of a random-coil sequence, in agreement with both our molecular simulations and other theoretical predictions. Thus, we suggest that NLS2 is a disordered region, with non pre-formed structure, that participates in metastasis suppression.
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Affiliation(s)
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBSC-CSIC-BIFI, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Lellys M Contreras
- Center for Environmental Biology and Chemistry Research, Facultad Experimental de Ciencias y Tecnología, Universidad de Carabobo, 2001, Valencia, Venezuela
| | - Christa A Manton
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Danny R Welch
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA; The University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036, Rende, Italy.
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18
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The C Terminus of the Ribosomal-Associated Protein LrtA Is an Intrinsically Disordered Oligomer. Int J Mol Sci 2018; 19:ijms19123902. [PMID: 30563168 PMCID: PMC6321479 DOI: 10.3390/ijms19123902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/01/2023] Open
Abstract
The 191-residue-long LrtA protein of Synechocystis sp. PCC 6803 is involved in post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family, intervening in protein synthesis. The protein consists of two domains: The N-terminal region (N-LrtA, residues 1–101), which is common to all the members of the HPF, and seems to be well-folded; and the C-terminal region (C-LrtA, residues 102–191), which is hypothesized to be disordered. In this work, we studied the conformational preferences of isolated C-LrtA in solution. The protein was disordered, as shown by computational modelling, 1D-1H NMR, steady-state far-UV circular dichroism (CD) and chemical and thermal denaturations followed by fluorescence and far-UV CD. Moreover, at physiological conditions, as indicated by several biochemical and hydrodynamic techniques, isolated C-LrtA intervened in a self-association equilibrium, involving several oligomerization reactions. Thus, C-LrtA was an oligomeric disordered protein.
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19
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Medina-Carmona E, Rizzuti B, Martín-Escolano R, Pacheco-García JL, Mesa-Torres N, Neira JL, Guzzi R, Pey AL. Phosphorylation compromises FAD binding and intracellular stability of wild-type and cancer-associated NQO1: Insights into flavo-proteome stability. Int J Biol Macromol 2018; 125:1275-1288. [PMID: 30243998 DOI: 10.1016/j.ijbiomac.2018.09.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/30/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
Over a quarter million of protein phosphorylation sites have been identified so far, although the effects of site-specific phosphorylation on protein function and stability, as well as their possible impact in the phenotypic manifestation in genetic diseases are vastly unknown. We investigated here the effects of phosphorylating S82 in human NADP(H):quinone oxidoreductase 1, a representative example of disease-associated flavoprotein in which protein stability is coupled to the intracellular flavin levels. Additionally, the cancer-associated P187S polymorphism causes inactivation and destabilization of the enzyme. By using extensive in vitro and in silico characterization of phosphomimetic S82D mutations, we showed that S82D locally affected the flavin binding site of the wild-type (WT) and P187S proteins thus altering flavin binding affinity, conformational stability and aggregation propensity. Consequently, the phosphomimetic S82D may destabilize the WT protein intracellularly by promoting the formation of the degradation-prone apo-protein. Noteworthy, WT and P187S proteins respond differently to the phosphomimetic mutation in terms of intracellular stability, further supporting differences in molecular recognition of these two variants by the proteasomal degradation pathway. We propose that phosphorylation could have critical consequences on stability and function of human flavoproteins, important for our understanding of genotype-phenotype relationships in their related genetic diseases.
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Affiliation(s)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rubén Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, 18071 Granada, Spain
| | | | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009 Zaragoza, Spain
| | - Rita Guzzi
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy; Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain.
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20
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Zhai Y, Deng P, Wang X, Zhang C, Gan R, Gan N, Sun Q, Li H. Interaction mechanism of olaparib binding to human serum albumin investigated with NMR relaxation data and computational methods. RSC Adv 2018; 8:31555-31563. [PMID: 35548207 PMCID: PMC9085917 DOI: 10.1039/c8ra05330h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/02/2018] [Indexed: 11/21/2022] Open
Abstract
The interaction mechanism between olaparib (OLA) and human serum albumin (HSA) has been investigated using experimental and computational techniques. An NMR relaxation approach based on the analysis of proton selective and non-selective spin-lattice relaxation rates at different temperatures can provide quantitative information about the affinity index and the thermodynamic equilibrium constant of the OLA-HSA system. The affinity index and the thermodynamic equilibrium constant decreased as temperature increased, indicating that the interactions between OLA and HSA could be weakened as temperature increased. Molecular docking and dynamics simulations revealed that OLA stably bound to subdomain II (site 1), and OLA could induce the conformational and micro-environmental changes in HSA. CD results suggested that α-helix content decreased after OLA was added, demonstrating that OLA affected the secondary structure of HSA.
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Affiliation(s)
- Yuanming Zhai
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Pengchi Deng
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Xiaoyan Wang
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Ruixue Gan
- School of Chemical Engineering, Sichuan University Chengdu 610065 China
| | - Na Gan
- School of Chemical Engineering, Sichuan University Chengdu 610065 China
| | - Qiaomei Sun
- School of Chemical Engineering, Sichuan University Chengdu 610065 China
| | - Hui Li
- School of Chemical Engineering, Sichuan University Chengdu 610065 China
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21
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Contreras LM, Sevilla P, Cámara-Artigas A, Hernández-Cifre JG, Rizzuti B, Florencio FJ, Muro-Pastor MI, García de la Torre J, Neira JL. The Cyanobacterial Ribosomal-Associated Protein LrtA from Synechocystis sp. PCC 6803 Is an Oligomeric Protein in Solution with Chameleonic Sequence Properties. Int J Mol Sci 2018; 19:ijms19071857. [PMID: 29937518 PMCID: PMC6073757 DOI: 10.3390/ijms19071857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/25/2022] Open
Abstract
The LrtA protein of Synechocystis sp. PCC 6803 intervenes in cyanobacterial post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family of proteins, involved in protein synthesis. In this work, we studied the conformational preferences and stability of isolated LrtA in solution. At physiological conditions, as shown by hydrodynamic techniques, LrtA was involved in a self-association equilibrium. As indicated by Nuclear Magnetic Resonance (NMR), circular dichroism (CD) and fluorescence, the protein acquired a folded, native-like conformation between pH 6.0 and 9.0. However, that conformation was not very stable, as suggested by thermal and chemical denaturations followed by CD and fluorescence. Theoretical studies of its highly-charged sequence suggest that LrtA had a Janus sequence, with a context-dependent fold. Our modelling and molecular dynamics (MD) simulations indicate that the protein adopted the same fold observed in other members of the HPF family (β-α-β-β-β-α) at its N-terminal region (residues 1–100), whereas the C terminus (residues 100–197) appeared disordered and collapsed, supporting the overall percentage of overall secondary structure obtained by CD deconvolution. Then, LrtA has a chameleonic sequence and it is the first member of the HPF family involved in a self-association equilibrium, when isolated in solution.
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Affiliation(s)
- Lellys M Contreras
- Center for Environmental Biology and Chemistry Research, Facultad Experimental de Ciencias y Tecnología, Universidad de Carabobo, 2001 Valencia, Venezuela.
| | - Paz Sevilla
- Facultad de Farmacia, Departamento de Química Física II, Universidad Complutense de Madrid, 28040 Madrid, Spain.
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, 04120 Almería, Spain.
| | | | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | - María Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | | | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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22
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Evoli S, Mobley DL, Guzzi R, Rizzuti B. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations. Phys Chem Chem Phys 2018; 18:32358-32368. [PMID: 27854368 DOI: 10.1039/c6cp05680f] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow's drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.
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Affiliation(s)
- Stefania Evoli
- Department of Physics, University of Calabria, 87036 Rende, Italy
| | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, USA
| | - Rita Guzzi
- Department of Physics, University of Calabria, 87036 Rende, Italy and CNISM Unit, University of Calabria, 87036 Rende, Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
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23
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Guglielmelli A, Rizzuti B, Guzzi R. Stereoselective and domain-specific effects of ibuprofen on the thermal stability of human serum albumin. Eur J Pharm Sci 2017; 112:122-131. [PMID: 29158196 DOI: 10.1016/j.ejps.2017.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/31/2017] [Accepted: 11/16/2017] [Indexed: 12/20/2022]
Abstract
Ibuprofen is one of the most used anti-inflammatory drugs, and it is transported in the blood by human serum albumin, a major plasmatic protein with a peculiar adaptability in the binding of several different ligands. We have characterized the interaction between albumin and ibuprofen, either in racemic mixture, or in the S(+) and R(-) enantiomeric forms, by using differential scanning calorimetry, attenuated total reflectance Fourier transform infrared spectroscopy, and molecular dynamics simulation. The results show that increasing concentrations of ibuprofen (up to sixfold drug/protein molar ratio) improve the protein resistance to thermal unfolding without altering the secondary structure. Deconvolution of the calorimetric thermal profiles at different albumin/ibuprofen molar ratios demonstrates a selective stability of the protein domains where the binding sites of the drug are localized. At the highest ibuprofen concentration, the melting temperature increased by about 10°C with respect to the drug-free protein, whereas the unfolding enthalpy maintains an almost constant value. Furthermore, the degree of protein stabilization depends upon the chirality of the drug, and the R(-) enantiomer is more effective compared to the S(+) form. The stability is supported by molecular dynamics simulations, showing that ibuprofen maintains a stable coordination in the most favorable binding sites, leading to a more compact protein structure at high temperature. The overall results attest that the binding of ibuprofen determines on albumin a stereoselective and domain-specific stabilization with a predominantly entropic character, contributing to clarify significant aspects of the molecular mechanism of protein/drug interaction.
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Affiliation(s)
- Alexa Guglielmelli
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rita Guzzi
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy.
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24
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Arnold WR, Baylon JL, Tajkhorshid E, Das A. Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase. Biochemistry 2016; 55:6969-6980. [PMID: 27992998 DOI: 10.1021/acs.biochem.6b01037] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 (CYP) 2J2 is the primary epoxygenase in the heart and is responsible for the epoxidation of arachidonic acid (AA), an ω-6 polyunsaturated fatty acid (PUFA), into anti-inflammatory epoxide metabolites. It also epoxidizes other PUFAs such as docosahexaenoic acid (DHA), linoleic acid (LA), and eicosapentaenoic acid (EPA). Herein, we have performed detailed thermodynamic and kinetic analyses to determine how DHA, LA, and EPA modulate the metabolism of AA by CYP2J2. We use the Nanodisc system to stabilize CYP2J2 and its redox partner, CYP reductase (CPR). We observe that DHA strongly inhibits CYP2J2-mediated AA metabolism, LA only moderately inhibits AA metabolism, and EPA exhibits insignificant inhibition. We also characterized the binding of these molecules using ebastine competitive binding assays and show that DHA binds significantly tighter to CYP2J2 than AA, EPA, or LA. Furthermore, we utilize a combined approach of molecular dynamics (MD) simulations and docking to predict key residues mediating the tight binding of DHA. We show that although all the tested fatty acids form similar contacts to the active site residues, the affinity of DHA for CYP2J2 is tighter because of the interaction of DHA with residues Arg-321, Thr-318, and Ser-493. To demonstrate the importance of these residues in binding, we mutated these residues to make two mutant variants, CYP2J2-T318A and CYP2J2-T318V/S493A. Both mutant variants showed weaker binding than the wild type (WT) to DHA and AA; DHA inhibition of AA was also mitigated in the mutants compared to the WT. Therefore, using a combined experimental and MD simulation approach, we establish that CYP2J2 inhibition of AA metabolism by DHA, EPA, and LA is asymmetric because of tighter binding of DHA to select residues in the active site.
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Affiliation(s)
- William R Arnold
- Department of Comparative Biosciences, ‡Department of Biochemistry, §Center for Biophysics and Quantitative Biology, ∥Beckman Institute for Advanced Science and Technology, and ⊥Neuroscience Program, Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Javier L Baylon
- Department of Comparative Biosciences, ‡Department of Biochemistry, §Center for Biophysics and Quantitative Biology, ∥Beckman Institute for Advanced Science and Technology, and ⊥Neuroscience Program, Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Comparative Biosciences, ‡Department of Biochemistry, §Center for Biophysics and Quantitative Biology, ∥Beckman Institute for Advanced Science and Technology, and ⊥Neuroscience Program, Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Aditi Das
- Department of Comparative Biosciences, ‡Department of Biochemistry, §Center for Biophysics and Quantitative Biology, ∥Beckman Institute for Advanced Science and Technology, and ⊥Neuroscience Program, Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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25
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Stirpe A, Pantusa M, Rizzuti B, De Santo MP, Sportelli L, Bartucci R, Guzzi R. Resveratrol induces thermal stabilization of human serum albumin and modulates the early aggregation stage. Int J Biol Macromol 2016; 92:1049-1056. [DOI: 10.1016/j.ijbiomac.2016.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/03/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
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Yang H, Huang Y, He J, Li S, Tang B, Li H. Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies. Arch Biochem Biophys 2016; 606:81-9. [PMID: 27457418 DOI: 10.1016/j.abb.2016.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 12/11/2022]
Abstract
In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA.
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Affiliation(s)
- Hongqin Yang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yanmei Huang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jiawei He
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Shanshan Li
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Bin Tang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Hui Li
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China.
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Bhattacharya S, Das A, Bagchi A. In-silico structural analysis of E509K mutation in LARGE and T192M mutation in Alpha Dystroglycan in the inhibition of glycosylation of Alpha Dystroglycan by LARGE. Comput Biol Chem 2016; 64:313-321. [PMID: 27565399 DOI: 10.1016/j.compbiolchem.2016.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/19/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
Abstract
Impaired glycosylation of cellular receptor Alpha Dystroglycan (α-DG) leads to dystroglycanopathy. Glycoprotein α-DG is the receptor protein in the Dystrophin Associated Protein Complex (DAPC), a macromolecular gathering on muscle cell membrane to form a bridge between extracellular matrix (ECM) and cellular actin cytoskeleton. Proper glycosylation of α-DG is mediated by the glycosylating enzyme LARGE. Mutations either in α-DG or in LARGE lead to improper glycosylations of α-DG thereby hampering the formation of final Laminin binding form α-DG resulting in dystroglycanopathy. In our current work, we explored the structural changes associated with the presence of mutations in α-DG as well as in the enzyme LARGE. We further extended our research to understand the effect of the mutations onto protein-enzyme interactions. Moreover, since LARGE transfers the sugar moiety (glucuronic acid; GlcA) onto α-DG, we tried to analyze what effect the mutation in LARGE confers on this enzyme ligand interaction. This work for the first time addressed the molecular changes occurring in the structures α-DG, LARGE and their interactions and shed lights on the as yet poorly understood mechanism behind the dystroglycanopathy onset.
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Affiliation(s)
- Simanti Bhattacharya
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
| | - Amit Das
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
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