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Waseem R, Shamsi A, Khan T, Anwer A, Shahid M, Kazim SN, Hassan MI, Islam A. Characterization of advanced glycation end products and aggregates of irisin: Multispectroscopic and microscopic approaches. J Cell Biochem 2023; 124:156-168. [PMID: 36502526 DOI: 10.1002/jcb.30353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/18/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022]
Abstract
Glycation of proteins leading to the formation of advanced glycation end products (AGEs) has been demonstrated to contribute to the pathogenesis of several diseases. Irisin is a clinically significant protein, putatively involved in obesity, diabetes, and neurological disorders. This study aimed to monitor the methyl-glyoxal (MG) induced AGEs and aggregate formation of irisin, as a function of time, employing multispectroscopic and microscopic approaches. ANS fluorescence suggested a molten globule-like state on Day 6, followed by the formation of irisin AGEs adducts, as confirmed by AGE-specific fluorescence. Glycation of irisin led to aggregate formation, which was characterized by Thioflavin T fluorescence, CD spectroscopy, and microscopic studies. These aggregates were confirmed by exploiting fluorescence microscopy, confocal, and transmission electron microscopy. Molecular docking was performed to determine the crucial residues of irisin involved in irisin-MG interaction. Usually, MG is present in trace amounts as a metabolic by-product in the body, which is found to be elevated in diseased conditions viz. diabetes and Alzheimer's disease. This study characterized the AGEs and aggregates of clinically important protein, irisin; and since MG level has been found to be increased in various pathological conditions, this study provides a clinical perspective. There is a possibility that elevated MG concentrations might glycate irisin resulting in reduced irisin levels as reported in pathological conditions. However, further investigations are required to prove it.
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Affiliation(s)
- Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Tanzeel Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ayesha Anwer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Syed Naqui Kazim
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Mir FM, Bano B. Amyloid aggregation and secondary structure changes of liver cystatin: Acidic denaturation and TFE induced studies. J Biomol Struct Dyn 2022; 40:12506-12515. [PMID: 34488562 DOI: 10.1080/07391102.2021.1971565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A cysteine proteinase inhibitor has been purified by affinity chromatography from the liver of buffalo. Liver cystatin is subjected to incubation at low pH with co-solvent TFE, where we have studied the effect on the conformation, activity and tendency to form aggregates or fibrils. ANS fluorescence was used to study conformational changes. The fibril formation and aggregation was studied using ThT assay, CD, FTIR and fluorescence spectroscopy. At pH 3.0 there was no fibril formation though aggregates were formed but in presence of TFE fibrils appeared. At pH 2.0 and 1.0, TFE induced rapid fibril formation compared to only acid induced state as assessed by Thioflavin T (ThT) fluorescence.TFE stabilized each of the three acid induced intermediates at predenaturational concentrations (20%) and accelerated fibril formation. Solvent conditions had a profound effect on the tendency of liver cystatin to produce fibrils and aggregation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Mustafa Mir
- Department of Biochemistry, faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India.,School of Biotechnology and Graduate school of Biochemistry, Yeungnum University, Gyeongsan, South Korea
| | - Bilqees Bano
- Department of Biochemistry, faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India
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Behjati Hosseini S, Asadzadeh-Lotfabad M, Erfani M, Babayan-Mashhadi F, Mokaberi P, Amiri-Tehranizadeh Z, Saberi MR, Chamani J. A novel vision into the binding behavior of curcumin with human serum albumin-holo transferrin complex: molecular dynamic simulation and multi-spectroscopic perspectives. J Biomol Struct Dyn 2022; 40:11154-11172. [PMID: 34328379 DOI: 10.1080/07391102.2021.1957713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this work, we investigated the simultaneous binding of curcumin (CUR) to human serum albumin (HSA) and human-holo transferrin (HTF) in the roles of binary and ternary systems. The binding affinity and binding site of protein-protein interaction were studied by the methods of multiple spectroscopic and molecular dynamics (MD) simulation. According to the results, the measurements for binding constant of HSA-CUR, HTF-CUR and (HSA-HTF) CUR complexes were observed to be 1.51 × 105, 7.93 × 104 and 1.44 × 105 M-1 respectively. Thermodynamic parameters were considered to be set at three varying temperatures including 298, 303, and 308 K. In conformity to the negative values of ΔH0 and ΔS0 the significant roles of hydrogen binding and van der-Waals forces in the formation of complexes are quiet evident. The binding distance between Trp residues of HSA, HTF and HSA-HTF upon interaction with CUR, were acquired by applying the Förster's theory of non-radioactive energy transfer and reported to be 2.04 nm, 1.78 nm, and 1.86 nm, respectively. In accordance with the conductometry and Resonance light scattering (RLS) results, there were different interaction behaviors among the HSA-HTF complex and CUR in ternary system when being compared to the outcomes of binary system. The secondary structure of all three cases increased as the CUR concentration was intensified, which confirmed the inducement of proteins conformational changes through the application of circular dichroism (CD) technique. The experimental results that were acquired throughout the binding of HSA-CUR, HTF-CUR, and (HSA-HTF) CUR complexes were approved by molecular modeling.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soroush Behjati Hosseini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Maryam Erfani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Fatemeh Babayan-Mashhadi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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Carvacrol protects against carbonyl osmolyte-induced structural modifications and aggregation to serum albumin: Insights from physicochemical and molecular interaction studies. Int J Biol Macromol 2022; 213:663-674. [PMID: 35660040 DOI: 10.1016/j.ijbiomac.2022.05.198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022]
Abstract
The robust use of osmolytes (i.e., polyols and sugars) in the key therapeutic regimens/formulations has questioned their impact beyond the stability of therapeutic proteins as these osmolytes trigger structural alterations into proteins including misfolding and subsequent aggregation into amyloid fibrils. Therefore, the current study is the first to delineate the inhibitory effect of carvacrol (CRV) on the carbonyl osmolyte-induced aggregation as well as structural alterations to the bovine serum albumin (BSA) via a set of physicochemical as well as artificial intelligence (AI)-based molecular docking studies. Our initial findings from physicochemical investigations revealed that CRV exhibits substantial protection to BSA under carbonyl osmolyte stress as evident by the compromised hyperchromicity, Schiff's bases, carbonyl and hydroxymethyl furfural content, reduced fluorescent signals, low Rayleigh scattering and prevention of covalent modifications at Lys and Arg residues. The protection against aggregate formation by CRV was further confirmed through the reduced amyloid-specific congo red absorbance as well as fluorescent signals recorded after adding the fibril-specific extrinsic fluorophore probes (i.e., ThT and ANS). The AI-based molecular docking analysis further revealed that CRV (ΔG: -4.96 kcal/mol) competes with d-fructose (ΔG: -4.40 kcal/mol) to mask the Lys and Arg residues to restrict the osmolyte-mediated protein modifications. In conclusion, CRV exhibits substantial protective impact against carbonyl osmolyte-induced structural alterations and protein misfolding and aggregation.
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Sarmah S, Goswami A, Kumar Belwal V, Singha Roy A. Mitigation of ribose and glyoxal induced glycation, AGEs formation and aggregation of human serum albumin by citrus fruit phytochemicals naringin and naringenin: An insight into their mechanism of action. Food Res Int 2022; 157:111358. [DOI: 10.1016/j.foodres.2022.111358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 11/04/2022]
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Hibino E, Tenno T, Hiroaki H. Relevance of Amorphous and Amyloid-Like Aggregates of the p53 Core Domain to Loss of its DNA-Binding Activity. Front Mol Biosci 2022; 9:869851. [PMID: 35558561 PMCID: PMC9086241 DOI: 10.3389/fmolb.2022.869851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
The anti-oncogenic protein p53 is a transcription factor that prevents tumorigenesis by inducing gene repair proteins or apoptosis under DNA damage. Since the DNA-binding domain of p53 (p53C) is aggregation-prone, the anti-oncogenic function of p53 is often lost in cancer cells. This tendency is rather severe in some tumor-related p53 mutants, such as R175H. In this study, we examined the effect of salts, including KCl and sugars, on the aggregation of p53C by monitoring two distinct aggregates: amorphous-like and amyloid-like. The amorphous aggregates are detectable with 8-(phenylamino)-1-naphthalenesulfonic acid (ANS) fluorescence, whereas the amyloid aggregates are sensitive to thioflavin-T (ThT) fluorescence. We found that KCl inhibited the formation of amorphous aggregates but promoted the formation of amyloid aggregates in a p53C R175H mutant. The salts exhibited different effects against the wild-type and R175H mutants of p53C. However, the ratio of ANS/ThT fluorescence for the wild-type and R175H mutant remained constant. KCl also suppressed the structural transition and loss of the DNA-binding function of p53C. These observations indicate the existence of multiple steps of p53C aggregation, probably coupled with the dissociation of Zn. Notably, amorphous aggregates and amyloid aggregates have distinct properties that could be discriminated by various small additives upon aggregation.
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Affiliation(s)
- Emi Hibino
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
- BeCellBar LLC., Nagoya University, Nagoya, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
- BeCellBar LLC., Nagoya University, Nagoya, Japan
- *Correspondence: Hidekazu Hiroaki,
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Evaluation of interactions between food colorant, tartrazine, and Apo-transferrin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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8
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Mittal C, Kumari A, De I, Singh M, Harsolia R, Yadav JK. Heat treatment of soluble proteins isolated from human cataract lens leads to the formation of non-fibrillar amyloid-like protein aggregates. Int J Biol Macromol 2021; 188:512-522. [PMID: 34333005 DOI: 10.1016/j.ijbiomac.2021.07.158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022]
Abstract
The loss of crystallins solubility with aging and the formation of amyloid-like aggregates is considered the hallmark characteristic of cataract pathology. The present study was carried out to assess the effect of temperature on the soluble lens protein and the formation of protein aggregates with typical amyloid characteristics. The soluble fraction of lens proteins was subjected for heat treatment in the range of 40-60 °C, and the nature of protein aggregates was assessed by using Congo red (CR), thioflavin T (ThT), and 8-anilinonaphthalene-1-sulfonic acid (ANS) binding assays, circular dichroism (CD), Fourier-transform infrared (FT-IR) spectroscopy, and transmission electron microscopy (TEM). The heat-treated protein samples displayed a substantial bathochromic shift (≈15 nm) in the CR's absorption maximum (λmax) and increased ThT and ANS binding. The heat treatment of lens soluble proteins results in the formation of nontoxic, β-sheet rich, non-fibrillar, protein aggregates similar to the structures evident in the insoluble fraction of proteins isolated from the cataractous lens. The data obtained from the present study suggest that the exposure of soluble lens proteins to elevated temperature leads to the formation of non-fibrillar aggregates, establishing the role of amyloid in the heat-induced augmentation of cataracts pathology.
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Affiliation(s)
- Chandrika Mittal
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ashwani Kumari
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Indranil De
- Institute of Nano Science and Technology, Mohali 160062, Punjab, India
| | - Manish Singh
- Institute of Nano Science and Technology, Mohali 160062, Punjab, India
| | - Ramswaroop Harsolia
- Department of Ophthalmology, Jawaharlal Nehru Medical College and Hospital, Ajmer, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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Li J, Gao G, Tang X, Yu M, He M, Sun T. Isomeric Effect of Nano-Inhibitors on Aβ 40 Fibrillation at The Nano-Bio Interface. ACS APPLIED MATERIALS & INTERFACES 2021; 13:4894-4904. [PMID: 33486955 DOI: 10.1021/acsami.0c21906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical and physical properties of nanobio interface substantially affect the conformational transitions of adjacent biomolecules. Previous studies have reported the chiral effect and charge effect of nanobio interface on the misfolding, aggregation, and fibrillation of amyloid protein. However, the isomeric effect of nanobio interface on protein/peptides amyloidosis is still unclear. Here, three isomeric nanobio interfaces were designed and fabricated based on the same sized gold nanoclusters (AuNCs) modified with 4-mercaptobenzoic acid (p-MBA), 3-mercaptobenzoic acid (m-MBA), and 2-mercaptobenzoic acid (o-MBA). Then three isomeric AuNCs were employed as models to explore the isomeric effect on the misfolding, aggregation, and fibrillation of Aβ40 at nanobio interfaces. Site-specific replacement experiments on the basis of theoretical analysis revealed the possible mechanism of Aβ40 interacting with isomeric ligands of AuNCs at the nanobio interfaces. The distance and orientation of -COOH group from the surface of AuNCs can affect the electrostatic interaction between isomeric ligands and the positively charged residues (R5, K16, and K28) of Aβ40, which may affect the inhibition efficiency of isomeric AuNCs on protein amyloidosis. Actually, the amyloid fibrillation kinetics results together with atomic force microscope (AFM) images, dynamic light scattering (DLS) results and circular dichroism (CD) spectra indeed proved that all the three isomeric AuNCs could inhibit the misfolding, aggregation and fibrillation of Aβ40 in a dose-dependent manner, and the inhibition efficiency was definitely different from each other. The inhibition efficiency of o-MBA-AuNCs was higher than that of m-MBA-AuNCs and p-MBA-AuNCs at the same dosage. These results provide an insight for isomeric effect at nanobio interfaces, and open an avenue for structure-based nanodrug design target Alzheimer's disease (AD) and even other protein conformational diseases.
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Affiliation(s)
- Jianhang Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
| | - Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
| | - Xintong Tang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
| | - Meng Yu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
| | - Meng He
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, No.122 Luoshi Road, Wuhan 430070, China
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Mohammadi S, Khajeh K, Taghdir M, Ranjbar B. An experimental investigation on the influence of various buffer concentrations, osmolytes and gold nanoparticles on lysozyme: Spectroscopic and calorimetric study. Int J Biol Macromol 2021; 172:162-169. [PMID: 33412205 DOI: 10.1016/j.ijbiomac.2020.12.208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 11/27/2022]
Abstract
Considering importance and several industrial applications of lysozyme, including natural antibiotic and preservative, identifier for the diagnosis of diseases, and extraction purposes, its reversibility and stability studies can be very important. In this paper, the role that buffer and osmolytes concentrations play on the thermodynamic stability of lysozyme denaturation process, that is a new simple and inexpensive method, was evaluated by Nano-DSC III, far- and near-UV CD and fluorescence techniques. In thermal denaturation study, RI and ΔG of protein increased from 25.62% to 58.82% and 48.87 to 63.63 kJ mol-1 with the increment of buffer and osmolytes concentrations, respectively. These changes showed a significant increase of 129.59% in RI and 28.16% in ΔG. The effect of buffer and osmolytes concentrations on the secondary and tertiary structures of protein was also investigated. The results indicated that increment of buffer and osmolytes concentrations increase rigidity and thermodynamic stability of protein. Also, structure of protein may be changed by its interaction with GNPs. Hence, interaction of lysozyme with GNPs was studied at the buffer and osmolytes concentrations that gives the maximum RI and ΔG, respectively. The results showed that molten globule-like state was formed by lysozyme in the presence of GNPs.
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Affiliation(s)
- Soraya Mohammadi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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Protective actions of bioactive flavonoids chrysin and luteolin on the glyoxal induced formation of advanced glycation end products and aggregation of human serum albumin: In vitro and molecular docking analysis. Int J Biol Macromol 2020; 165:2275-2285. [PMID: 33058977 DOI: 10.1016/j.ijbiomac.2020.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022]
Abstract
The post-translational modification of proteins by nonenzymatic glycation (NEG) and the accumulation of AGEs are the two underlying factors associated with the long-term pathogenesis in diabetes. Glyoxal (GO) is a reactive intermediate which has the ability to modify proteins and generate AGEs at a faster rate. Human serum albumin (HSA) being the most abundant serum protein has a higher chance to be modified by NEG. The key objective of the present study is to investigate the potency of chrysin and luteolin as antiglycating and antifibrillating agents in the GO-mediated glycation and fibril formation of HSA. AGEs formation were confirmed from the absorption and fluorescence spectral measurements. Both the flavonoids were able to quench the AGEs fluorescence intensity in vitro indicating the antiglycating nature of the molecules. The formation of fibrils in the GO-modified HSA was confirmed by the Thioflavin T (ThT) fluorescence assay and the flavonoids were found to exihibit the antifibrillation properties in vitro. Docking results suggested that both the flavonoids interact with various amino acid residues of subdomain IIA including glycation prone lysines and arginines via non-covalent forces and further stabilized the structure of HSA, which further explains their mechanisms of action as antiglycating and antifibrillating agents.
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Zhang C, Zhang J, Rao H, Yang J, Wang X, Peng X. Investigation on the interaction of brazilin with bovine serum albumin using multi-spectroscopic and computational methods: Exploring the binding mechanism and inhibitory effect on amyloid aggregation. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Comparative study of the protein denaturing ability of different organic cosolvents. Int J Biol Macromol 2020; 160:880-888. [DOI: 10.1016/j.ijbiomac.2020.05.260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
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Hasan S, Isar M, Naeem A. Macromolecular crowding stabilises native structure of α-chymotrypsinogen-A against hexafluoropropanol-induced aggregates. Int J Biol Macromol 2020; 164:3780-3788. [PMID: 32835802 DOI: 10.1016/j.ijbiomac.2020.08.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Cell interior is extremely congested with tightly packed biological macromolecules that exerts macromolecular crowding effect, influencing biophysical properties of proteins. To have a deeper insight into it we studied consequences of crowding on aggregation susceptibility and structural stability of α-chymotrypsinogen-A, pro-enzyme of serine protease family, upon addition of co-solvent reported to exert stress on polypeptides crafting favourable conditions for aggregation. Hexafluoropropan-2-ol (HFIP), a fluorinated alcohol caused structural disruption at 5% v/v unveiled by reduced intrinsic intensity and blue shifted ANS spectra. Significantly enhanced, red-shifted ThT and Congo red spectra sustained conformational changes concomitant with aggregation. FTIR and CD results confirmed transition of native structure to non-native extended, cross-linked beta-sheets. Transmission electron micrographs visibly exhibited incidence of amorphous aggregates. Macromolecular crowding, typically mimicked by concentrated solutions of dextran 70, was noticeably witnessed to defend conformational stability under denaturing condition. The native structure was retained maximally in presence of 100 mg/ml followed by 200 and 300 mg/ml dextran indicating concentration dependent deceleration of aggregate formation. It can be established that explicit consideration of crowding effects using relevant range of inert crowding agents must be a requisite for presumptions on intracellular conformational behaviour of proteins deduced from in vitro experiments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Mohd Isar
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India.
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Mangiagalli M, Carvalho H, Natalello A, Ferrario V, Pennati ML, Barbiroli A, Lotti M, Pleiss J, Brocca S. Diverse effects of aqueous polar co-solvents on Candida antarctica lipase B. Int J Biol Macromol 2020; 150:930-940. [DOI: 10.1016/j.ijbiomac.2020.02.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 02/04/2023]
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16
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Luo Z, Gao G, Ma Z, Liu Q, Gao X, Tang X, Gao Z, Li C, Sun T. Cichoric acid from witloof inhibit misfolding aggregation and fibrillation of hIAPP. Int J Biol Macromol 2020; 148:1272-1279. [PMID: 31759017 DOI: 10.1016/j.ijbiomac.2019.10.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The misfolding, aggregation and fibrillation of human islet amyloid polypeptide (hIAPP) has been acknowledged as a hallmark event in type-II diabetes. Hence, inhibiting the misfolding, aggregation and fibrillation of hIAPP have been accepted as a vital factor to treat the disease. Here cichoric acid was extracted from witloof to explore its inhibition effects on misfolding, aggregation and fibrillation of hIAPP. Thioflavin-T (ThT) fluorescence assay, dynamic light scattering (DLS) and atomic force microscopy (AFM) images showed that cichoric acid inhibited the aggregation and fibrillation of hIAPP in a dosage-dependent manner. Circular dichroism (CD) spectra showed that cichoric acid inhibited the misfolding of hIAPP from unfolded to β-sheet. Molecular docking and further experiments revealed interactions between hIAPP and cichoric acid. Cichoric acid could bind to K1 and R11 of hIAPP via electrostatic interaction. In addition, cichoric acid could form π-π stacking with hIAPP residues F15 and F23. These interactions inhibited the misfolding, aggregation and fibrillation of hIAPP. These results, together with cichoric acid's good cytocompatibility and significant protective effects in hIAPP lesioned cell models, not only showed that cichoric acid could be used to fight against amyloidosis, but also brought a new perspective for Chinese herbal medicine as natural compound's medical potential.
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Affiliation(s)
- Zhuoying Luo
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China.
| | - Zhongjie Ma
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Qian Liu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Xiaobing Gao
- General Hospital of Central Theater Command, Wuhan 430070, China
| | - Xintong Tang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Zhenxing Gao
- Affiliated Cancer Hospital &Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou 510000, China
| | - Chaoyang Li
- Affiliated Cancer Hospital &Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou 510000, China.
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China.
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Samykannu G, Vijayababu P, Antonyraj CB, Narayanan S. Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach. Biochem Biophys Rep 2019; 21:100693. [PMID: 31872081 PMCID: PMC6911951 DOI: 10.1016/j.bbrep.2019.100693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/03/2019] [Accepted: 10/02/2019] [Indexed: 11/14/2022] Open
Abstract
Outer membrane proteins were playing a crucial role on the several functions controlled by cell membranes even though they are not naturally expressed at higher levels. In order to obtain biologically active protein, the denaturation of these inclusion bodies must be optimized using chaotropic agents. Hence, this study focuses on improving the yield of Outer Membrane Protease (PgtE) from Salmonella enterica serotype Typhi (S. Typhi) using chaotropes and additives. Denaturation methods were tried with various pH, detergents, and reducing agents were used to optimize the solubility of PgtE with biologically active form. Due to the aggregation, we failed to achieve the maximum yield of PgtE. Consequently, we predicted 9 Aggregation Prone Regions (APRs) in PgtE, which are mutated by known structural Gatekeepers. We calculated the Aggregation Index (AI) of PgtE with 10 mM of aspartic acid as an additive in optimized buffer. In addition, the mutations at specific positions within the protein structure can act as APRs suppressors without affecting protein stability with CABS flex dynamics. The multiple sequence analysis demonstrate that aspartic acid is appropriate denaturing additive for other Gram-negative pathogens of Omptin family.
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Affiliation(s)
- Gopinath Samykannu
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | - Princy Vijayababu
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | | | - Sundarabaalaji Narayanan
- Structural Biology Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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Shait Mohammed MR, Ahmad V, Ahmad A, Tabrez S, Choudhry H, Zamzami MA, Bakhrebah MA, Ahmad A, Wasi S, Mukhtar H, Khan MI. Prospective of nanoscale metal organic frameworks [NMOFs] for cancer therapy. Semin Cancer Biol 2019; 69:129-139. [PMID: 31866477 DOI: 10.1016/j.semcancer.2019.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/16/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022]
Abstract
Nano metal organic frameworks (NMOFs) belong to the group of nanoporous materials. Over the decades, the conducted researches explored the area for the potential applications of NMOFs in areas like biomedical, chemical engineering and materials science. Recently, NMOFs have been explored for their potential use in cancer diagnosis and therapeutics. The excellent physico-chemical features of NMOFs also make them a potential candiadate to facilitate drug design, delivery and storage against cancer cells. In this review, we have explored the characterstic features, synthesis methods, NMOFs based drug delivery, diagnosis and imaging in various cancer types. In addition to this, we have also pondered on the stability and toxicological concerns of NMOFs. Despite, a significant research has been done for the potential use of NMOFs in cancer diagonostic and therapeutics, more information regarding the stability, in-vivo clearance, toxicology, and pharmacokinetics is still needed to ehnace the use of NMOFs in cancer diagonostic and therapeutics.
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Affiliation(s)
| | - Varish Ahmad
- Health Information Technology Department,Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research Center (KFMRC), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammed A Bakhrebah
- Life Science and Environmental Research Institute (KFMRC), King Abdulaziz City of Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Aftab Ahmad
- Health Information Technology Department,Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Samina Wasi
- College of Medicine, Department of Biochemistry, Imam Abdul Rahman Bin Faisal Uuniversity, Dammam, Saudi Arabia
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin, Madison, 4385 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706, USA
| | - Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Khalilzadeh B, Rashidi M, Soleimanian A, Tajalli H, Kanberoglu GS, Baradaran B, Rashidi MR. Development of a reliable microRNA based electrochemical genosensor for monitoring of miR-146a, as key regulatory agent of neurodegenerative disease. Int J Biol Macromol 2019; 134:695-703. [DOI: 10.1016/j.ijbiomac.2019.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
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Characterization of methylglyoxal induced advanced glycation end products and aggregates of human transferrin: Biophysical and microscopic insight. Int J Biol Macromol 2019; 138:718-724. [PMID: 31351151 DOI: 10.1016/j.ijbiomac.2019.07.140] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 11/24/2022]
Abstract
Protein aggregation and glycation is gaining increased attention in recent times as protein aggregates and advanced glycation end products (AGEs) play a pivotal role in many disorders. The purpose of our study was to have an insight into AGEs and aggregates formation of human transferrin (hTF) in the presence of methylglyoxal (MG) employing intrinsic, ANS, Thioflavin T fluorescence, circular dichroism (CD) spectroscopy, docking studies and microscopy. In our study, effect of varying concentration of MG was observed on hTF retorting multispectroscopic, in silico and microscopic approach. Intrinsic fluorescence showed an increase in fluorescence of hTF in presence of MG. The obtained AGEs of hTF in the presence of MG were characterized with respect to fluorescence of AGEs specific adducts. Further, aggregates of hTF were characterized employing ThT fluorescence, transmission electron microscopy (TEM) and fluorescence microscopy. Fluorescence microscopy and TEM confirmed the presence of hTF aggregates in the presence of 50 mM MG; aggregates to be globular in nature. Molecular docking was also employed highlighting the important residues playing a pivotal role in this interaction. Thus, our study characterized the AGEs and aggregates of clinically important protein, hTF; level of MG increases in various pathological conditions giving our study clinical perspective.
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Es-haghi A, Jahedi Moghaddam M, Shahpasand K. Role of Pre-molten Globule Structure in Protein Amyloid Fibril Formation. AVICENNA JOURNAL OF MEDICAL BIOCHEMISTRY 2019. [DOI: 10.34172/ajmb.2019.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The conversion of a protein from its native conformation to the pathogenic form is a critical event in the pathogenesis of several neurodegenerative disorders such as Alzheimer’s (AD), Parkinson’s, and Huntington’s diseases, along with type II diabetic mellitus. Although there are several reports on the mechanism of protein aggregation, the actual conformation playing a part in the pathogenicity is yet unclear. Accordingly, the present study summarizes the early pathogenic conformation resulting in several protein aggregations. It is well-documented that a pre-molten globule (MG) structure appears at the early stages of some proteins. Pre-MG is one of the intermediate structures, which is formed during some protein unfolding processes. In addition, it is shown that the pre-molten structure is more flexible than the mature MG one and thus, protein easily rearranges to form amyloid fibrils in this conformation. Therefore, protein aggregation is halted by preventing the pre-MG structure. The strategy of protein aggregation prevention has profound implications in fighting the devastating disorder.
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Affiliation(s)
- Ali Es-haghi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Centre of Education, Culture and Research, Tehran, Iran
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23
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Manivel P, Parthiban M, Ilanchelian M. Exploring the binding mechanism between methylene blue and ovalbumin using spectroscopic analyses and computational simulations. J Biomol Struct Dyn 2019; 38:1838-1847. [DOI: 10.1080/07391102.2019.1618734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Perumal Manivel
- Department of Chemistry, Bharathiar University, Coimbatore, Tamil Nadu, India
- Electro Organic Division, Central Electrochemical Research Institute, Karaikudi, Tamil Nadu, India
| | - Marimuthu Parthiban
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku, Finland
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Hemamalini R, Khare SK. Halophilic lipase does forms catalytically active aggregates: Evidence from Marinobacter sp. EMB5 lipase (LipEMB5). Int J Biol Macromol 2018; 119:172-179. [DOI: 10.1016/j.ijbiomac.2018.07.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/12/2018] [Accepted: 07/14/2018] [Indexed: 10/28/2022]
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25
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Wlodarczyk SR, Custódio D, Pessoa A, Monteiro G. Influence and effect of osmolytes in biopharmaceutical formulations. Eur J Pharm Biopharm 2018; 131:92-98. [DOI: 10.1016/j.ejpb.2018.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/28/2018] [Accepted: 07/22/2018] [Indexed: 02/05/2023]
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26
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Khan MV, Zakariya SM, Khan RH. Protein folding, misfolding and aggregation: A tale of constructive to destructive assembly. Int J Biol Macromol 2018; 112:217-229. [DOI: 10.1016/j.ijbiomac.2018.01.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/04/2018] [Accepted: 01/14/2018] [Indexed: 12/20/2022]
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27
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Mondal S, Biswas B, Nandy T, Singh PC. Understanding the Role of Hydrophobic Terminal in the Hydrogen Bond Network of the Aqueous Mixture of 2,2,2-Trifluoroethanol: IR, Molecular Dynamics, Quantum Chemical as Well as Atoms in Molecules Studies. J Phys Chem B 2018; 122:6616-6626. [DOI: 10.1021/acs.jpcb.8b04365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biswajit Biswas
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tonima Nandy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Chunhui H, Dilin X, Ke Z, Jieyi S, Sicheng Y, Dapeng W, Qinwen W, Wei C. A11-positive β-amyloid Oligomer Preparation and Assessment Using Dot Blotting Analysis. J Vis Exp 2018:57592. [PMID: 29889206 PMCID: PMC6101355 DOI: 10.3791/57592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
β-amyloid (Aβ) is a hydrophobic peptide with an intrinsic tendency to self-assemble into aggregates. Among various aggregates, Aβ oligomer is widely accepted as the leading neurotoxin in the progress of Alzheimer's disease (AD) and is considered to be the crucial event in the pathogenesis of AD. Therefore, Aβ oligomer inhibitors might prevent neurodegeneration and have the potential to be developed as disease-modifying treatments of AD. However, different formation protocols of Aβ oligomer might lead to oligomers with different characteristics. Moreover, there are not many methods to effectively screen Aβ1-42 oligomer inhibitors. An A11 antibody can react with a subset of toxic Aβ1-42 oligomer with anti-parallel β-sheet structures. In this protocol, we describe how to prepare an A11-positive Aβ1-42 oligomer-rich sample from a synthetic Aβ1-42 peptide in vitro and to evaluate relative amounts of A11-positive Aβ1-42 oligomer in samples by a dot blotting analysis using A11 and Aβ1-42-specific 6E10 antibodies. Using this protocol, inhibitors of A11-positive Aβ1-42 oligomer can also be screened from semi-quantitative experimental results.
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Affiliation(s)
- Huang Chunhui
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University
| | - Xu Dilin
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University
| | - Zhang Ke
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University
| | - Shentu Jieyi
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University
| | - Yan Sicheng
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University
| | - Wu Dapeng
- School of Materials Science and Chemical Engineering, Ningbo University
| | - Wang Qinwen
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University
| | - Cui Wei
- Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University;
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Khan MV, Zaman M, Chandel TI, Siddiqui MK, Ajmal MR, Abdelhameed AS, Khan RH. Cationic surfactant mediated fibrillogenesis in bovine liver catalase: a biophysical approach. J Biomol Struct Dyn 2017; 36:2543-2557. [DOI: 10.1080/07391102.2017.1363085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Tajalli Ilm Chandel
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Khursheed Siddiqui
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Rehan Ajmal
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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30
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Khan MV, Ishtikhar M, Siddiqui MK, Zaman M, Chandel TI, Majid N, Ajmal MR, Abdelhameed AS, Shahein YE, Khan RH. Biophysical insight reveals tannic acid as amyloid inducer and conformation transformer from amorphous to amyloid aggregates in Concanavalin A (ConA). J Biomol Struct Dyn 2017; 36:1261-1273. [DOI: 10.1080/07391102.2017.1318718] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Ishtikhar
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Khursheed Siddiqui
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Tajalli Ilm Chandel
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Nabeela Majid
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Rehan Ajmal
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Yasser E. Shahein
- Molecular Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Cairo, Egypt
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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Dammers C, Reiss K, Gremer L, Lecher J, Ziehm T, Stoldt M, Schwarten M, Willbold D. Pyroglutamate-Modified Amyloid-β(3-42) Shows α-Helical Intermediates before Amyloid Formation. Biophys J 2017; 112:1621-1633. [PMID: 28445753 PMCID: PMC5406372 DOI: 10.1016/j.bpj.2017.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 01/15/2023] Open
Abstract
Pyroglutamate-modified amyloid-β (pEAβ) has been described as a relevant Aβ species in Alzheimer's-disease-affected brains, with pEAβ (3-42) as a dominant isoform. Aβ (1-40) and Aβ (1-42) have been well characterized under various solution conditions, including aqueous solutions containing trifluoroethanol (TFE). To characterize structural properties of pEAβ (3-42) possibly underlying its drastically increased aggregation propensity compared to Aβ (1-42), we started our studies in various TFE-water mixtures and found striking differences between the two Aβ species. Soluble pEAβ (3-42) has an increased tendency to form β-sheet-rich structures compared to Aβ (1-42), as indicated by circular dichroism spectroscopy data. Kinetic assays monitored by thioflavin-T show drastically accelerated aggregation leading to large fibrils visualized by electron microscopy of pEAβ (3-42) in contrast to Aβ (1-42). NMR spectroscopy was performed for backbone and side-chain chemical-shift assignments of monomeric pEAβ (3-42) in 40% TFE solution. Although the difference between pEAβ (3-42) and Aβ (1-42) is purely N-terminal, it has a significant impact on the chemical environment of >20% of the total amino acid residues, as revealed by their NMR chemical-shift differences. Freshly dissolved pEAβ (3-42) contains two α-helical regions connected by a flexible linker, whereas the N-terminus remains unstructured. We found that these α-helices act as a transient intermediate to β-sheet and fibril formation of pEAβ (3-42).
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Affiliation(s)
- Christina Dammers
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Kerstin Reiss
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Lothar Gremer
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Justin Lecher
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tamar Ziehm
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Matthias Stoldt
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Melanie Schwarten
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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Khan MV, Ishtikhar M, Rabbani G, Zaman M, Abdelhameed AS, Khan RH. Polyols (Glycerol and Ethylene glycol) mediated amorphous aggregate inhibition and secondary structure restoration of metalloproteinase-conalbumin (ovotransferrin). Int J Biol Macromol 2016; 94:290-300. [PMID: 27744055 PMCID: PMC7112414 DOI: 10.1016/j.ijbiomac.2016.10.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/24/2022]
Abstract
Conalbumin aggregates at 65 °C and denaturation occur at above this temperature. The nature of aggregates was identified as amorphous. The polyols inhibits the aggregation of conalbumin via protecting the secondary structure. Glycerol is found to be more protective than ethylene glycol.
Under physical or chemical stress, proteins tend to form aggregates either highly ordered (amyloid) or unordered (amorphous) causing many pathological disorders in human and loss of proteins functionality in both laboratory conditions and industries during production and storage at commercial level. We investigated the effect of increasing temperature on Conalbumin (CA) and induced aggregation at 65 °C. The enhanced Thioflavin T (ThT) and ANS (1-anilinonaphtalene 8-sulfonic acid) fluorescence intensity, show no shift on Congo red binding, additionally, transmission and scanning electron microscopy (TEM) (SEM) reveal amorphous morphology of the aggregate. Our investigation clearly demonstrated that polyols namely Glycerol (GL) and Ethylene glycol (EG) are so staunch to inhibit amorphous aggregates via restoring secondary conformation. Addition of polyols (15% GL and 35% EG) significantly decrease the turbidity, Rayleigh scattering ThT and ANS fluorescence intensity. The dynamic light scattering (DLS) data show that hydrodynamic radii (Rh) of the aggregates is ∼20 times higher than native CA while nearly similar for GL and EG protected CA due to condensation of core size with little difference.
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Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohd Ishtikhar
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Gulam Rabbani
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Ajmal MR, Abdelhameed AS, Alam P, Khan RH. Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 159:199-208. [PMID: 26851488 DOI: 10.1016/j.saa.2016.01.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/15/2016] [Accepted: 01/23/2016] [Indexed: 06/05/2023]
Abstract
In the current study we have investigated the interaction of newly approved kinase inhibitors namely Cabozantinib (CBZ) and Tofacitinib (TFB) with human Alpha-1 acid glycoprotein (AAG) under simulated physiological conditions using fluorescence quenching measurements, circular dichroism, dynamic light scattering and molecular docking methods. CBZ and TFB binds to AAG with significant affinity and the calculated binding constant for the drugs lie in the order of 10(4). With the increase in temperature the binding constant values decreased for both CBZ and TFB. The fluorescence resonance energy transfer (FRET) from AAG to CBZ and TFB suggested the fluorescence intensity of AAG was quenched by the two studied drugs via the formation of a non-fluorescent complex in the static manner. The molecular distance r value calculated from FRET is around 2 nm for both drugs, fluorescence spectroscopy data was employed for the study of thermodynamic parameters, standard Gibbs free energy change at 300 K was calculated as -5.234 kcal mol(-1) for CBZ-AAG interaction and -6.237 kcal mol(-1) for TFB-AAG interaction, standard enthalpy change and standard entropy change for CBZ-AAG interaction are -9.553 kcal mol(-1) and -14.618 cal mol(-1) K(-1) respectively while for AAG-TFB interaction, standard enthalpy and standard entropy change was calculated as 4.019 kcal mol(-1) and 7.206 cal mol(-1) K(-1) respectively. Protein binding of the two drugs caused the tertiary structure alterations. Dynamic light scattering measurements demonstrated the reduction in the hydrodynamic radii of the protein. Furthermore molecular docking results suggested the Hydrophobic interaction and hydrogen bonding were the interactive forces in the binding process of CBZ to AAG while in case of TFB only hydrophobic interactions were found to be involved, overlap of the binding site for two studied drugs on the AAG molecule was revealed by docking results.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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Zaman M, Chaturvedi SK, Zaidi N, Qadeer A, Chandel TI, Nusrat S, Alam P, Khan RH. DNA induced aggregation of stem bromelain; a mechanistic insight. RSC Adv 2016. [DOI: 10.1039/c6ra01079b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Negatively charged species such as nucleic acids have commonly been found to be associated with the proteinaceous deposits in the tissues of patients with amyloid diseases.
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Affiliation(s)
- Masihuz Zaman
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | | | - Nida Zaidi
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Atiyatul Qadeer
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Tajalli Ilm Chandel
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Saima Nusrat
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh-202002
- India
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Dammers C, Gremer L, Reiß K, Klein AN, Neudecker P, Hartmann R, Sun N, Demuth HU, Schwarten M, Willbold D. Structural Analysis and Aggregation Propensity of Pyroglutamate Aβ(3-40) in Aqueous Trifluoroethanol. PLoS One 2015; 10:e0143647. [PMID: 26600248 PMCID: PMC4658145 DOI: 10.1371/journal.pone.0143647] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/06/2015] [Indexed: 12/23/2022] Open
Abstract
A hallmark of Alzheimer's disease (AD) is the accumulation of extracellular amyloid-β (Aβ) plaques in the brains of patients. N-terminally truncated pyroglutamate-modified Aβ (pEAβ) has been described as a major compound of Aβ species in senile plaques. pEAβ is more resistant to degradation, shows higher toxicity and has increased aggregation propensity and β-sheet stabilization compared to non-modified Aβ. Here we characterized recombinant pEAβ(3-40) in aqueous trifluoroethanol (TFE) solution regarding its aggregation propensity and structural changes in comparison to its non-pyroglutamate-modified variant Aβ(1-40). Secondary structure analysis by circular dichroism spectroscopy suggests that pEAβ(3-40) shows an increased tendency to form β-sheet-rich structures in 20% TFE containing solutions where Aβ(1-40) forms α-helices. Aggregation kinetics of pEAβ(3-40) in the presence of 20% TFE monitored by thioflavin-T (ThT) assay showed a typical sigmoidal aggregation in contrast to Aβ(1-40), which lacks ThT positive structures under the same conditions. Transmission electron microscopy confirms that pEAβ(3-40) aggregated to large fibrils and high molecular weight aggregates in spite of the presence of the helix stabilizing co-solvent TFE. High resolution NMR spectroscopy of recombinantly produced and uniformly isotope labeled [U-15N]-pEAβ(3-40) in TFE containing solutions indicates that the pyroglutamate formation affects significantly the N-terminal region, which in turn leads to decreased monomer stability and increased aggregation propensity.
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Affiliation(s)
- Christina Dammers
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Lothar Gremer
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Kerstin Reiß
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Antonia N. Klein
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Philipp Neudecker
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Rudolf Hartmann
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Na Sun
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Drug Design and Target Validation, 06120, Halle (Saale), Germany
| | - Melanie Schwarten
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- * E-mail:
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Non-fluorinated cosolvents: A potent amorphous aggregate inducer of metalloproteinase-conalbumin (ovotransferrin). Int J Biol Macromol 2015; 78:417-28. [DOI: 10.1016/j.ijbiomac.2015.04.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
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