1
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Archapraditkul C, Janon K, Japrung D, Pongprayoon P. Structural and dynamic properties of urinary human serum albumin fragments: a molecular dynamics study. J Biomol Struct Dyn 2024; 42:7532-7540. [PMID: 37526205 DOI: 10.1080/07391102.2023.2240426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
A microalbuminuria level acts as a good index to screen and monitor diabetes and renal failure. However, the urinary albumin loss after sample preservation and storage is the major bottleneck to obtain the accurate microalbuminuria test. Such loss is due to the rapid albumin fragmentation by urinary proteases. Some fragments were suggested to be bioactive biomarkers of diabetes and renal disease, but no structural and dynamical properties of albumin fragments are available. Thus, in this work, the structural and dynamical properties of reported albumin fragments are revealed using molecular dynamics simulations. The properties of nine fragments (F1-F9) discovered recently were studied at the real pH conditions of urine samples (pH 4.5, 7 and 8). The complete loss of secondary structure is found in short fragments (F1-F6), while large-sized polypeptides (F7-F9) can somehow maintain their folds. Especially, F8 (subdomain IIIB) is the most stable fragment. The difference in histidine protonation states has no impact on the structural stability of albumin fragments. The ability of F8 (subdomain IIIB) to maintain its stability and folds suggests it as an alternative albumin biomarker in urine. An insight obtained here will become the fundamental importance for understanding clinical assays for albumin detection, sample stability and peptidomics analysis of urine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chanya Archapraditkul
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Kanokwan Janon
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prapasiri Pongprayoon
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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2
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Anjo SI, He Z, Hussain Z, Farooq A, McIntyre A, Laughton CA, Carvalho AN, Finelli MJ. Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers. Antioxidants (Basel) 2024; 13:681. [PMID: 38929122 PMCID: PMC11200609 DOI: 10.3390/antiox13060681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Oxidation-reduction post-translational modifications (redox-PTMs) are chemical alterations to amino acids of proteins. Redox-PTMs participate in the regulation of protein conformation, localization and function, acting as signalling effectors that impact many essential biochemical processes in the cells. Crucially, the dysregulation of redox-PTMs of proteins has been implicated in the pathophysiology of numerous human diseases, including neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. This review aims to highlight the current gaps in knowledge in the field of redox-PTMs biology and to explore new methodological advances in proteomics and computational modelling that will pave the way for a better understanding of the role and therapeutic potential of redox-PTMs of proteins in neurodegenerative diseases. Here, we summarize the main types of redox-PTMs of proteins while providing examples of their occurrence in neurodegenerative diseases and an overview of the state-of-the-art methods used for their detection. We explore the potential of novel computational modelling approaches as essential tools to obtain insights into the precise role of redox-PTMs in regulating protein structure and function. We also discuss the complex crosstalk between various PTMs that occur in living cells. Finally, we argue that redox-PTMs of proteins could be used in the future as diagnosis and prognosis biomarkers for neurodegenerative diseases.
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Affiliation(s)
- Sandra I. Anjo
- CNC-Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-517 Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Zhicheng He
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zohaib Hussain
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Aruba Farooq
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alan McIntyre
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Charles A. Laughton
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andreia Neves Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Mattéa J. Finelli
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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Kadlecová Z, Sevriugina V, Lysáková K, Rychetský M, Chamradová I, Vojtová L. Liposomes Affect Protein Release and Stability of ITA-Modified PLGA-PEG-PLGA Hydrogel Carriers for Controlled Drug Delivery. Biomacromolecules 2024; 25:67-76. [PMID: 38135465 PMCID: PMC10777393 DOI: 10.1021/acs.biomac.3c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Fat grafting, a key regenerative medicine technique, often requires repeat procedures due to high-fat reabsorption and volume loss. Addressing this, a novel drug delivery system uniquely combines a thermosensitive, FDA-approved hydrogel (itaconic acid-modified PLGA-PEG-PLGA copolymer) with FGF2-STAB, a stable fibroblast growth factor 2 with a 21-day stability, far exceeding a few hours of wild-type FGF2's stability. Additionally, the growth factor was encapsulated in "green" liposomes prepared via the Mozafari method, ensuring pH protection. The system, characterized by first-order FGF2-STAB release, employs green chemistry for biocompatibility, bioactivity, and eco-friendliness. The liposomes, with diameters of 85.73 ± 3.85 nm and 68.6 ± 2.2% encapsulation efficiency, allowed controlled FGF2-STAB release from the hydrogel compared to the unencapsulated FGF2-STAB. Yet, the protein compromised the carrier's hydrolytic stability. Prior tests were conducted on model proteins human albumin (efficiency 80.8 ± 3.2%) and lysozyme (efficiency 81.0 ± 2.7%). This injectable thermosensitive system could advance reconstructive medicine and cosmetic procedures.
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Affiliation(s)
- Zuzana Kadlecová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova
656/123, 612 00 Brno, Czech Republic
| | - Veronika Sevriugina
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova
656/123, 612 00 Brno, Czech Republic
| | - Klára Lysáková
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova
656/123, 612 00 Brno, Czech Republic
| | - Matěj Rychetský
- Faculty
of Chemistry, Brno University of Technology, Purkyňova 464, 612 00 Brno, Czech Republic
| | - Ivana Chamradová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova
656/123, 612 00 Brno, Czech Republic
| | - Lucy Vojtová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova
656/123, 612 00 Brno, Czech Republic
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Azeem K, Ahmed M, Uddin A, Singh S, Patel R, Abid M. Comparative investigation on interaction between potent antimalarials and human serum albumin using multispectroscopic and computational approaches. LUMINESCENCE 2023; 38:2018-2033. [PMID: 37654050 DOI: 10.1002/bio.4590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
This study performed a comparative investigation to explore the interaction mechanisms between two potential antimalarial compounds, JMI 346 and JMI 105, and human serum albumin (HSA), a vital carrier protein responsible for maintaining important biological functions. Our aim was to assess the pharmacological efficiency of these compounds while comprehensively analyzing their impact on the dynamic behavior and overall stability of the protein. A comprehensive array of multispectroscopic techniques, including UV-Vis. spectroscopy, steady-state fluorescence analysis, synchronous fluorescence spectroscopy, three-dimensional fluorescence and circular dichroism spectroscopy, docking studies, and molecular dynamics simulations, were performed to probe the intricate details of the interaction between the compounds and HSA. Our results revealed that both JMI 346 and JMI 105 exhibited promising pharmacological effectiveness within the context of malaria therapy. However, JMI 346 was found to exhibit a significantly higher affinity and only minor altered impact on HSA, suggesting a more favorable interaction with the protein on the dynamic behavior and overall stability of the protein in comparison to JMI 105. Further studies can build on these results to optimize the drug-protein interaction and enable the development of more potent and targeted antimalarial treatments.
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Affiliation(s)
- Kashish Azeem
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mofieed Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rajan Patel
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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5
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Zou GY, Wen Y, Bi F, Chen S, Yu YL, Wang JH. A "dual-key-and-lock" ratiometric fluorescent probe with biocompatibility and selectivity for imaging vicinal dithiol proteins. Chem Commun (Camb) 2023; 59:1785-1788. [PMID: 36722873 DOI: 10.1039/d2cc06422g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
TMR-TPE, a ratiometric fluorescent probe, was reported for the imaging of vicinal dithiol proteins (VDPs) in living cells. Profiting from the "dual-key-and-lock" design, TMR-TPE solves the toxicity problem of VDP probes (98% cell viability at 50 μM) and avoids the interference of small thiols (up to 10 mM GSH). The change of VDPs during drug-induced liver injury was monitored for the first time using TMR-TPE.
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Affiliation(s)
- Guang-Yue Zou
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Yun Wen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Fan Bi
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
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6
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Smardz P, Sieradzan AK, Krupa P. Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment. J Phys Chem B 2022; 126:6240-6249. [PMID: 35975925 PMCID: PMC9421896 DOI: 10.1021/acs.jpcb.2c04718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Disulfide bonds are covalent bonds that connect nonlocal fragments of proteins, and they are unique post-translational modifications of proteins. They require the oxidizing environment to be stable, which occurs for example during oxidative stress; however, in a cell the reductive environment is maintained, lowering their stability. Despite many years of research on disulfide bonds, their role in the protein life cycle is not fully understood and seems to strictly depend on a system or process in which they are involved. In this article, coarse-grained UNited RESidue (UNRES), and all-atom Assisted Model Building with Energy Refinement (AMBER) force fields were applied to run a series of steered molecular dynamics (SMD) simulations of one of the most studied, but still not fully understood, proteins─ribonuclease A (RNase A). SMD simulations were performed to study the mechanical stability of RNase A in different oxidative-reductive environments. As disulfide bonds (and any other covalent bonds) cannot break/form in any classical all-atom force field, we applied additional restraints between sulfur atoms of reduced cysteines which were able to mimic the breaking of the disulfide bonds. On the other hand, the coarse-grained UNRES force field enables us to study the breaking/formation of the disulfide bonds and control the reducing/oxidizing environment owing to the presence of the designed distance/orientation-dependent potential. This study reveals that disulfide bonds have a strong influence on the mechanical stability of RNase A only in a highly oxidative environment. However, the local stability of the secondary structure seems to play a major factor in the overall stability of the protein. Both our thermal unfolding and mechanical stretching studies show that the most stable disulfide bond is Cys65-Cys72. The breaking of disulfide bonds Cys26-Cys84 and Cys58-Cys110 is associated with large force peaks. They are structural bridges, which are mostly responsible for stabilizing the RNase A conformation, while the presence of the remaining two bonds (Cys65-Cys72 and Cys40-Cys95) is most likely connected with the enzymatic activity rather than the structural stability of RNase A in the cytoplasm. Our results prove that disulfide bonds are indeed stabilizing fragments of the proteins, but their role is strongly redox environment-dependent.
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Affiliation(s)
- Pamela Smardz
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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7
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Farrugia A, Mori F. Therapeutic solutions of human albumin - The possible effect of process-induced molecular alterations on clinical efficacy and safety. J Pharm Sci 2022; 111:1292-1308. [PMID: 35276228 DOI: 10.1016/j.xphs.2022.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/14/2022]
Abstract
Human albumin solutions were developed as therapeutic during the Second World War to address blood loss due to battlefield injury. This indication was based on the recognition that albumin provided most of the oncotic capacity of human plasma. For the succeeding sixty years, this formed the basis for the use of albumin in traumatology and emergency medicine. In more recent times, the pharmacological properties arising from albumin's complex structure have become a focus of attention by clinical researchers. In particular, albumin, through anti-inflammatory and anti-oxidant properties, has been proposed as an agent for the treatment of sepsis, cirrhosis and other inflammatory states. Some evidence for these indications has accrued from a number of small clinical trials and observational studies. These studies have not been confirmed in other large trials. Together with other investigators, we have shown that the process of plasma fractionation results in alterations in the structure of albumin, including those parts of the molecule involved in anti-oxidant and anti-inflammatory effects. Albumin products from diverse manufacturers show heterogeneity in their ability to address these effects. In this article, we review the historical development of albumin solutions, pointing out the variations in fractionation chemistries which different manufacturers have adopted. We suggest ways by which the manufacturing processes have contributed to variations in the physico-chemical properties of molecule. We review the outcomes of clinical studies assessing the role of albumin in ameliorating conditions such as sepsis and cirrhosis, and we speculate as to the extent which heterogeneity in the products may have contributed to variable clinical outcomes. Finally, we argue for a change in the perception of the plasma product industry and its regulatory overseers. Historically, albumin has been viewed as a generic commodity, with different preparations being interchangeable in their clinical application. We suggest that this implied biosimilarity is not necessarily applicable for different albumin solutions. The use of albumin, in indications other than its historical role as a plasma expander, can only be validated by clinical investigation of each separate albumin product.
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Affiliation(s)
- Albert Farrugia
- Faculty of Health and Medical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Perth, Australia.
| | - Filippo Mori
- Kedrion S.p.A., Research and Innovation Department, Via di Fondovalle, Loc., Bolognana 55027, Gallicano (LU), Italy
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8
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Perera NLD, Miksovska J, O'Shea KE. Elucidation of specific binding sites and extraction of toxic Gen X from HSA employing cyclodextrin. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127765. [PMID: 34838360 DOI: 10.1016/j.jhazmat.2021.127765] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The presence of per and poly-fluoroalkyl substances (PFAS), commonly referred to as forever chemicals, in aquatic systems is a serious global health problem. While the remediation of PFAS from aqueous media has been extensively investigated, their interactions with and removal from biological systems have received far less attention. We report herein structural alterations to human serum albumin (HSA) upon addition of perfluoro(2-methyl-3-oxahexanoic) acid (Gen X) monitored by changes to the fluorescence and circular dichroism (CD) spectra of HSA. The equilibrium association constant for Gen X binding to HSA is 7( ± 1) × 103 M-1 determined from changes in HSA fluorescence emission data during titration. Site-specific HSA binding fluorophores, 8-anilinonaphthalene-1-sulfonic acid (1,8-ANS), warfarin and dansyl-L-proline were used to investigate the specific binding sites of Gen X on HSA. A competitive displacement study yields association constants for Gen X to HSA at the 1,8-ANS, warfarin, and dansyl-L-proline binding sites to be 6.25 ( ± 0.5) × 104 M-1, 1.1 × 106 M-1, and 2.5( ± 0.2) × 109 M-1 respectively. Addition of β-cyclodextrin (β-CD) and heptakis(6-deoxy-6-amino)-β-cyclodextrin heptahydrochloride to the HSA:Gen X complex leads to the effective extraction of Gen X from the complex with the return of HSA in its native form. Gen X also leads to displacement of site-specific binding fluorophores bound to HSA, while subsequent addition of β-CD extracts Gen X from HSA with the return of the characteristic fluorescence of the HSA bound site-specific agent. These results illustrate the strong and specific binding sites of Gen X on HSA and demonstrate the principles for the potential application of β-CD for the remediation of PFAS from biological systems.
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Affiliation(s)
- N L Dilani Perera
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th street, Miami, FL 33199, United States
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th street, Miami, FL 33199, United States
| | - Kevin E O'Shea
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th street, Miami, FL 33199, United States.
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9
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Wang S, Ou X, Yi M, Li J. Spontaneous desorption of protein from self-assembled monolayer (SAM)-coated gold nanoparticles induced by high temperature. Phys Chem Chem Phys 2022; 24:2363-2370. [PMID: 35018922 DOI: 10.1039/d1cp04000f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nonspecific binding of proteins with nanomaterials (NMs) is a dynamic reversible process including both protein adsorption and desorption parts, which is crucial for controlled release of protein drug loaded by nanocarriers. The nonspecific binding of proteins is susceptible to high temperature, whereas its underlying mechanism still remains elusive. Here, the binding behavior of human serum albumin (HSA) with an amino-terminated self-assembled monolayer (SAM)-coated gold (111) surface was investigated by using molecular dynamics (MD) simulations. HSA binds to the SAM surface through salt bridges at 300 K. As the temperature increases to 350 K, HSA maintains its native structure, while the salt bridges largely diminish owing to the considerable lateral diffusion of HSA on the SAM. Moreover, the interfacial water located between HSA and the SAM gets increased and prevents the reformation of the salt bridges of HSA with the SAM, which reduces the binding affinity of HSA. And HSA eventually desorbs from the SAM. The depiction of thermally induced spontaneous protein desorption enriches our understanding of reversible binding behavior of protein with NMs, and may provide new insights into the controlled release of protein drugs delivered by using nanocarriers under the regulation of high temperature.
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Affiliation(s)
- Shuai Wang
- College of informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Xinwen Ou
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China.
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
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10
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Awang T, Niramitranon J, Japrung D, Saparpakorn P, Pongprayoon P. Investigating the binding affinities of fructose and galactose to human serum albumin: simulation studies. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1922687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tadsanee Awang
- Department of Chemistry, Kasetsart University, Bangkok, Thailand
| | - Jitti Niramitranon
- Department of Computer Engineering, Kasetsart University, Bangkok, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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11
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Mollahosseini A, Abdelrasoul A. Molecular dynamics simulation for membrane separation and porous materials: A current state of art review. J Mol Graph Model 2021; 107:107947. [PMID: 34126546 DOI: 10.1016/j.jmgm.2021.107947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 01/29/2023]
Abstract
Computational frameworks have been under specific attention within the last two decades. Molecular Dynamics (MD) simulations, identical to the other computational approaches, try to address the unknown question, lighten the dark areas of unanswered questions, to achieve probable explanations and solutions. Owing to their complex microporous structure on one side and the intricate biochemical nature of various materials used in the structure, separative membrane materials possess peculiar degrees of complications. More notably, as nanocomposite materials are often integrated into separative membranes, thin-film nanocomposites and porous separative nanocomposite materials could possess an additional level of complexity with regard to the nanoscale interactions brought to the structure. This critical review intends to cover the recent methods used to assess membranes and membrane materials. Incorporation of MD in membrane technology-related fields such as desalination, fuel cell-based energy production, blood purification through hemodialysis, etc., were briefly covered. Accordingly, this review could be used to understand the current extent of MD applications for separative membranes. The review could also be used as a guideline to use the proper MD implementation within the related fields.
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Affiliation(s)
- Arash Mollahosseini
- Department of Chemical and Biological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, Saskatchewan, S7N 5A9, Canada
| | - Amira Abdelrasoul
- Department of Chemical and Biological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, Saskatchewan, S7N 5A9, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, Saskatchewan, S7N 5A9, Canada.
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12
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Thermodynamic and anticancer properties of inorganic zinc oxide nanoparticles synthesized through co-precipitation method. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115602] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Ganorkar K, Mukherjee S, Singh P, Ghosh SK. Stabilization of a potential anticancer thiosemicarbazone derivative in Sudlow site I of human serum albumin: In vitro spectroscopy coupled with molecular dynamics simulation. Biophys Chem 2021; 269:106509. [PMID: 33302053 DOI: 10.1016/j.bpc.2020.106509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022]
Abstract
Human Serum Albumin (HSA) is the most important protein in human blood plasma and can acts as a major transporting agent for various drug molecules with flexible binding interaction. To elucidate the interaction of a newly designed potential anticancer thiosemicarbazone based luminophore (E)-1-(4-(diethylamino)-2-hydroxybenzylidene)-4,4-dimethyl-thiosemicarbazide (DAHTS) with HSA under physiological condition, in vitro optical spectroscopic experiments viz UV-Vis absorption, steady state fluorescence, fluroscence anisotropy, time resolved fluorscence (TRF) and cicular dichroism (CD) spectroscopy have been scrutinised. The experimental findings have been corroborated with in silico molecular docking analysis and Molecular Dynamics (MD) simulation. The spectroscopic results demonstrated that the conventionally anion-favouring Sudlow site I of HSA copiously adapt neutral DAHTS molecule with moderate binding affinity. The mean fluorescence lifetime of the sole tryptophan (Trp-214) present in the macromolecule experiences an appreciable diminution with an increase in concentration of the synthesized molecule. DAHTS localize itself close to Trp-214 within subdomain IIA (Sudlow site I) and surrounded by multiple hydrophobic amino acid residues (Val-235, Val-231, Ala-229, Phe-228, Val-325, Phe-326, Leu-327, Met-329, Phe-330, Leu-331, Tyr-332, Leu-346, Leu-347, Val-482, Leu-349, Ala-350, Ala-210, Trp-214, Ala- 213 and Val-216) in HSA. The distinct fluorescence lifetime, diverse pathways and changing rate of population indicates that the rotamerisation of Trp-214 residue is controlled by the guest molecule. Sudlow site I of HSA behaves flexibly and induces an allosteric modulation in the macromolecule resulting a minor deformation in the protein secondary structure as observed in CD (observed 11% change of α-helix content) as well as in MD simulation. The integrated multi-spectroscopic research described herein provides several important information about the binding interaction of a thiosemicarbazone Schiff base with HSA, which can be very significant for thiosemicarbazone based drug designing for academia as well as industry.
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Affiliation(s)
- Kapil Ganorkar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Soham Mukherjee
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Piyush Singh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Sujit Kumar Ghosh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India.
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Azman NA, Nguyen TX, Kah JCY. Dynamics of Human Serum Albumin Corona Formation on Gold Nanorods with Different Surface Ligands In Silico. J Phys Chem B 2021; 125:1181-1195. [PMID: 33476152 DOI: 10.1021/acs.jpcb.0c09236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interaction between human serum albumin (HSA) and nanoparticles (NPs) to form HSA corona has widely been studied since endogenous functions of albumin are highly attractive for drug delivery. However, a full understanding of the molecular dynamics and factors behind the formation of HSA corona, including interactions between HSA and different surface ligands and between neighboring HSA molecules, resulting in conformational change of HSA is presently lacking. Here, we assembled 14 HSA molecules around gold nanorods (AuNRs) with different surface chemistries (bare gold surface, cetyltrimethylammonium bromide (CTAB), polystyrene sulfonate (PSS), and polydiallyldimethylammonium chloride (PDADMAC)) in silico and examined the dynamics of HSA corona formation using coarse-grained molecular dynamics for 300 ns of simulation. We observed that PDADMAC, being more flexible than PSS, resulted in all HSA molecules moving toward AuNR-PDADMAC, while the instability of CTAB on AuNR resulted in fewer HSA molecules moving toward AuNR-CTAB compared to AuNR-PSS. HSA molecules around AuNR-PDADMAC also exhibited the largest conformational change in terms of their radius of gyration (Rg) and root mean square deviation (RMSD). In the absence of surface ligands, HSA molecules around the bare AuNR were susceptible to steric hindrance with conformational change observed in terms of their RMSD but not their Rg unlike that of HSA molecules around AuNR-PDADMAC. The insights gained from the inclusion of neighboring HSA molecules in the simulation of corona formation could be more representative than examining a single adsorbed HSA molecule on AuNRs with different surface passivations.
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Affiliation(s)
- Nurul Ain Azman
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
| | - Thanh Xuan Nguyen
- Department of Mechanical Engineering, Vietnamese-German University, Le Lai Street, Hoa Phu Ward, Binh Duong New City 75114, Binh Duong Province, Vietnam
| | - James Chen Yong Kah
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
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15
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Mahdavi M, Fattahi A, Nouranian S. Doxorubicin Stability and Retention on PEGylated Graphene Oxide Nanocarriers Adjacent to Human Serum Albumin. ACS APPLIED BIO MATERIALS 2020; 3:7646-7653. [DOI: 10.1021/acsabm.0c00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mina Mahdavi
- Department of Chemical Engineering, The University of Mississippi, University, Mississippi 38677, United States
| | - Ali Fattahi
- Center for Applied NanoBioscience and Medicine, College of Medicine−Phoenix, The University of Arizona, Phoenix, Arizona 85004, United States
- Whitespace Enterprises, 1305 W Auto Drive, Tempe, Arizona 85284, United States
| | - Sasan Nouranian
- Department of Chemical Engineering, The University of Mississippi, University, Mississippi 38677, United States
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16
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Blum MM, Richter A, Siegert M, Thiermann H, John H. Adduct of the blistering warfare agent sesquimustard with human serum albumin and its mass spectrometric identification for biomedical verification of exposure. Anal Bioanal Chem 2020; 412:7723-7737. [PMID: 32902690 PMCID: PMC7550388 DOI: 10.1007/s00216-020-02917-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/25/2020] [Indexed: 11/24/2022]
Abstract
Apart from the well-known sulfur mustard (SM), additional sulfur-containing blistering chemical warfare agents exist. Sesquimustard (Q) is one of them and five times more blistering than SM. It is a common impurity in mustard mixtures and regularly found in old munitions but can also be used in pure form. Compared to the extensive literature on SM, very little experimental data is available on Q and no protein biomarkers of exposure have been reported. We herein report for the first time the adduct of Q with the nucleophilic Cys34 residue of human serum albumin (HSA) formed in vitro and introduce two novel bioanalytical procedures for detection. After proteolysis of this HSA adduct catalyzed either by pronase or by proteinase K, two biomarkers were identified by high-resolution tandem mass spectrometry (MS/HR MS), namely a dipeptide and a tripeptide, both alkylated at their Cys residue, which we refer to as HETETE-CP and HETETE-CPF. HETETE represents the Q-derived thio-alkyl moiety bearing a terminal hydroxyl group: "hydroxyethylthioethylthioethyl." Targeting both peptide markers from plasma, a micro liquid chromatography-electrospray ionization tandem mass spectrometry method working in the selected reaction monitoring mode (μLC-ESI MS/MS SRM) was developed and validated as well suited for the verification of exposure to Q. Fulfilling the quality criteria defined by the Organisation for the Prohibition of Chemical Weapons, the novel methods enable the detection of exposure to Q alone or in mixtures with SM. We further report on the relative reactivity of Q compared to SM. Based on experiments making use of partially deuterated Q as the alkylating agent, we rule out a major role for six-membered ring sulfonium ions as relevant reactive species in the alkylation of Cys34. Furthermore, the results of molecular dynamics simulations are indicative that the protein environment around Cys34 allows adduct formation with elongated but not bulky molecules such as Q, and identify important hydrogen bonding interactions and hydrophobic contacts. Graphical abstract.
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Affiliation(s)
- Marc-Michael Blum
- Blum - Scientific Services, Björnsonweg 70d, 22587, Hamburg, Germany
| | - Annika Richter
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Markus Siegert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Harald John
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.
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17
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Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H 1. J Comput Aided Mol Des 2020; 34:1045-1062. [PMID: 32572668 DOI: 10.1007/s10822-020-00328-8] [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: 05/09/2020] [Accepted: 06/18/2020] [Indexed: 02/02/2023]
Abstract
Cetirizine, a major metabolite of hydroxyzine, became a marketed second-generation H1 antihistamine that is orally active and has a rapid onset of action, long duration of effects and a very good safety record at recommended doses. The approved drug is a racemic mixture of (S)-cetirizine and (R)-cetirizine, the latter being the levorotary enantiomer that also exists in the market as a third-generation, non-sedating and highly selective antihistamine. Both enantiomers bind tightly to the human histamine H1 receptor (hH1R) and behave as inverse agonists but the affinity and residence time of (R)-cetirizine are greater than those of (S)-cetirizine. In blood plasma, cetirizine exists in the zwitterionic form and more than 90% of the circulating drug is bound to human serum albumin (HSA), which acts as an inactive reservoir. Independent X-ray crystallographic work has solved the structure of the hH1R:doxepin complex and has identified two drug-binding sites for cetirizine on equine serum albumin (ESA). Given this background, we decided to model a membrane-embedded hH1R in complex with either (R)- or (S)-cetirizine and also the complexes of both ESA and HSA with these two enantiomeric drugs to analyze possible differences in binding modes between enantiomers and also among targets. The ensuing molecular dynamics simulations in explicit solvent and additional computational chemistry calculations provided structural and energetic information about all of these complexes that is normally beyond current experimental possibilities. Overall, we found very good agreement between our binding energy estimates and extant biochemical and pharmacological evidence. A much higher degree of solvent exposure in the cetirizine-binding site(s) of HSA and ESA relative to the more occluded orthosteric binding site in hH1R is translated into larger positional fluctuations and considerably lower affinities for these two nonspecific targets. Whereas it is demonstrated that the two known pockets in ESA provide enough stability for cetirizine binding, only one such site does so in HSA due to a number of amino acid replacements. At the histamine-binding site in hH1R, the distinct interactions established between the phenyl and chlorophenyl moieties of the two enantiomers with the amino acids lining up the pocket and between their free carboxylates and Lys179 in the second extracellular loop account for the improved pharmacological profile of (R)-cetirizine.
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18
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Photothermally enhanced photodynamic therapy based on glutathione-responsive pheophorbide a-conjugated gold nanorod formulations for cancer theranostic applications. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.01.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Ashkezari AZ, Jolfaei NA, Jolfaei NA, Hekmatifar M, Toghraie D, Sabetvand R, Rostami S. Calculation of the thermal conductivity of human serum albumin (HSA) with equilibrium/non-equilibrium molecular dynamics approaches. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 188:105256. [PMID: 31841788 DOI: 10.1016/j.cmpb.2019.105256] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Human serum albumin (HSA) controls the flow of numerous chemical structures and molecules in the cardiovascular system. So, thermal conductivity of this atomic compound is important in medicinal applications. METHODS In this work, the thermal conductivity of HSA is calculated with equilibrium/non-equilibrium molecular dynamic approaches. In these methods each HSA molecule is exactly represented by C, N, O and S atoms and their implemented dreiding potential. Finally by using Green-Kubo and Fourier's law the thermal conductivity of HSA/H2O mixture is calculated. RESULTS Our calculated rates for thermal conductivity via equilibrium/non-equilibrium molecular dynamics methods are 0.496 W/m K and 0.448 W/m K, respectively. The calculated thermal conductivity for this structure was very close to the thermal conductivity calculated for water molecules which were reported by other research groups. Furthermore our simulated structures show that thermal conductivity of HAS/H2O mixtures has inverse relation with HAS molecules numbers and temperature of simulated atomic structures. CONCLUSIONS Comparing thermal conductivity from equilibrium/non-equilibrium molecular dynamics methods for HAS/H2O shows that EMD and NEMD results are reliable and EMD calculated results are higher than NEMD results.
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Affiliation(s)
| | | | - Niyusha Adavoodi Jolfaei
- Department of pharmaceutical sciences, KLE college of Pharmacy, 2nd block, Rajajinagar, Bengaluru, Karnatka, India
| | - Maboud Hekmatifar
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Roozbeh Sabetvand
- Department of Energy Engineering and Physics, Faculty of Condensed Matter Physics, Amirkabir University of Technology, Tehran, Iran
| | - Sara Rostami
- Laboratory of Magnetism and Magnetic Materials, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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20
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Jahangirizadeh Z, Taghdir M. Tuning the active site dynamic properties and substrate affinity in Pseudomonas aeruginosa elastase by Cys270–Cys297 disulfide bond. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Hassanian M, Aryapour H, Goudarzi A, Javan MB. Are zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods. J Biomol Struct Dyn 2020; 39:330-335. [PMID: 31994452 DOI: 10.1080/07391102.2019.1711189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With due attention to adsorption of proteins on the nanoparticles surface and the formation of nanoparticle-protein corona, investigation of nanoparticles toxicity on the structure of proteins is important. Therefore, this work was done to evaluate toxicity of Zinc oxide nanoparticles (ZnO NPs) on the structure of human serum albumin (HSA) through in vitro and in silico studies. First, ZnO NPs were synthesized using hydrothermal method and their size and morphology were determined by SEM and TEM methods and then to study its toxicity on the HSA structure were used UV-Vis and fluorescence spectroscopy. Also, in order to investigate interaction mechanism of ZnO NP with HSA at the atomistic level was used molecular dynamics (MD) simulation. The obtained images from SEM and TEM showed that ZnO NPs were nanosheet with size of less than 40 nm. The results of spectroscopic studies showed ZnO NPs lead to significant conformational changes in the protein's absorption and emission spectra. Moreover, MD results indicated the minor structure changes in HSA due to interaction with ZnO NP during the 100 ns simulation, and the formation of nanoparticle-protein corona complex is mainly because of electrostatic interactions between charge groups of HSA and ZnO NP.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Marziyeh Hassanian
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Alireza Goudarzi
- Department of Polymer Engineering, Faculty of Engineering, Golestan University, Gorgan, Iran
| | - Masoud Bezi Javan
- Department of Physics, Faculty of Science, Golestan University, Gorgan, Iran
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22
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Hazarika Z, Jha AN. Computational Analysis of the Silver Nanoparticle-Human Serum Albumin Complex. ACS OMEGA 2020; 5:170-178. [PMID: 31956763 PMCID: PMC6963898 DOI: 10.1021/acsomega.9b02340] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Drug delivery in excess concentrations and at not-specified sites inside the human body adversely affects the body and gives rise to other diseases. Several methods have been developed to deliver the drugs in required amounts and at specific targets. Nanoparticle-mediated drug delivery is one such approach and has gained success at primary levels. The effect of nanoparticles on the human body needs important apprehension, and it has been unraveled by assessing the protein-nanoparticle interactions. Here, we have measured the impact of silver nanoparticles (AgNPs) on the human serum albumin (HSA) structure and function with the help of all-atom molecular dynamics simulations (MDS). HSA is a transport protein, and any change in the structure may obstruct its function. The post MD analyses showed that the NP interacts with HSA and the conjugated system got stabilized with time evolution of trajectories. The present investigation confirms that the AgNP interacts with HSA without affecting its tertiary and secondary structures and in turn the protein function as well. AgNP application is recommended in transporting conjugated drug molecules as it has no adverse effect on serum proteins. Since HSA is present in the circulatory system, it may open various applications of AgNPs in the biomedical field.
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23
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Zhao L, Bai F, Chen F, Guo M, Gan L, Zhang H, Fang J. A β-allyl carbamate fluorescent probe for vicinal dithiol proteins. Chem Commun (Camb) 2020; 56:2857-2860. [DOI: 10.1039/c9cc09841k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An unprecedented β-allyl carbamate fluorescent probe for vicinal dithiol proteins (VDPs) was developed. The favourable properties of the probe make it a useful tool for tracing the global changes of VDPs in living systems.
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Affiliation(s)
- Lanning Zhao
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- China
| | - Feifei Bai
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- China
| | - Fan Chen
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- China
| | - Menghuan Guo
- School of Pharmacy Lanzhou University
- Lanzhou
- China
| | - Lu Gan
- Department of Radiation Medicine
- Institute of Modern Physics
- Chinese Academy of Sciences
- Lanzhou
- China
| | - Hong Zhang
- Department of Radiation Medicine
- Institute of Modern Physics
- Chinese Academy of Sciences
- Lanzhou
- China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- China
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24
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Munasinghe A, Mathavan A, Mathavan A, Lin P, Colina CM. PEGylation within a confined hydrophobic cavity of a protein. Phys Chem Chem Phys 2019; 21:25584-25596. [PMID: 31720639 DOI: 10.1039/c9cp04387j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The conjugation of polyethylene glycol (PEG) to proteins, known as PEGylation, has increasingly been employed to expand the efficacy of therapeutic drugs. Recently, research has emphasized the effect of the conjugation site on protein-polymer interactions. In this study, we performed atomistic molecular dynamics (MD) simulations of lysine 116 PEGylated bovine serum albumin (BSA) to illustrate how conjugation near a hydrophobic pocket affects the conjugate's dynamics and observed altered low mode vibrations in the protein. MD simulations were performed for a total of 1.5 μs for each PEG chain molecular mass from 2 to 20 kDa. Analysis of preferential PEG-BSA interactions showed that polymer behavior was also affected as proximity to the attractive protein surface patches promoted interactions in small (2 kDa) PEG chains, while the confined environment of the conjugation site reduced the expected BSA surface coverage when the polymer molecular mass increased to 10 kDa. This thorough analysis of PEG-BSA interactions and polymer dynamics increases the molecular understanding of site-specific PEGylation and enhances the use of protein-polymer conjugates as therapeutics.
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Affiliation(s)
- Aravinda Munasinghe
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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25
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Jaunet-Lahary T, Vercauteren DP, Fleury F, Laurent AD. Computational simulations determining disulfonic stilbene derivative bioavailability within human serum albumin. Phys Chem Chem Phys 2019; 20:18020-18030. [PMID: 29931001 DOI: 10.1039/c8cp00704g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Disulfonic stilbene (DS) derivatives are a member of the large family of compounds widely employed in medicine and biology as modulators for membrane transporters or inhibitors of a protein involved in DNA repair. They constitute interesting compounds that have not yet been investigated within the bioavailability framework. No crystallographic structures exist involving such compounds embedded in the most common drug carrier, human serum albumin (HSA). The present work studies, for the first time, the physico-chemical features driving the inclusion of three DS derivatives (amino, nitro and acetamido, named DADS, DNDS and DATDS, respectively) within the four common HSA binding sites using combined molecular docking and molecular dynamics simulations. A careful analysis of each ligand within each of the studied binding sites is carried out, highlighting specific interactions and key residues playing a role in stabilizing the ligand within each pocket. The comparison between DADS, DNDS and DATDS reveals that depending on the binding site, the conclusions are rather different. For instance, the IB binding site shows a specificity to DADS compounds while IIIA is the most favorable site for DNDS and DATDS.
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Affiliation(s)
- Titouan Jaunet-Lahary
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
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26
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Scavenging of hydrated electron by HSA or Ligand/HSA adduct: Pulse radiolysis study. Radiat Phys Chem Oxf Engl 1993 2018. [DOI: 10.1016/j.radphyschem.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Hildebrand N, Wei G, Köppen S, Colombi Ciacchi L. Simulated and experimental force spectroscopy of lysozyme on silica. Phys Chem Chem Phys 2018; 20:19595-19605. [PMID: 30009290 DOI: 10.1039/c8cp03747g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The force spectra of proteins detaching from oxide surfaces measured by atomic force microscopy (AFM) often present complex patterns of peaks, which are difficult to correlate with individual bond-breaking events at the atomic scale. In this work we rationalize experimental AFM force spectra of hen-egg-white lysozyme detaching from silica by means of all-atom steered molecular dynamics (SMD) simulations. In particular, we demonstrate that the native tertiary structure of lysozyme is preserved if, and only if, its four intramolecular disulfide bridges are intact. Otherwise, the protein pulled off the surface undergoes severe unfolding, which is well captured by SMD simulations in explicit solvent. Implicit solvent simulations, on the contrary, wrongly predict protein unfolding even in the presence of S-S bridges, due to the lack of additional structural stabilization provided by the water's hydrogen-bond network within and surrounding the protein. On the basis of our combined experimental and theoretical findings, we infer that the rugged force spectra characteristic of lysozyme/silica interfaces are not due to the successive breaking of internal disulfide bonds leading to partial unfolding events. Rather, they reflect the detachment of several molecules bound to the same AFM tip, each anchored to the surface via multiple hydrogen and ionic bonds.
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Affiliation(s)
- Nils Hildebrand
- Hybrid Materials Interfaces Group, Faculty Production Engineering, Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany.
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28
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Zhang Q, Zhou M, Zhao L, Jiang H, Yang H. Dynamic States of the Ligand-Free Class A G Protein-Coupled Receptor Extracellular Side. Biochemistry 2018; 57:4767-4775. [PMID: 29999306 DOI: 10.1021/acs.biochem.8b00146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G protein-coupled receptors (GPCRs) make up the largest family of drug targets. The second extracellular loop (ECL2) and extracellular end of the third transmembrane helix (TM3) are basic structural elements of the GPCR ligand binding site. Currently, the disulfide bond between the two conserved cysteines in the ECL2 and TM3 is considered to be a basic GPCR structural feature. This disulfide bond has a significant effect on receptor dynamics and ligand binding. Here, molecular dynamics simulations and experimental results show that the two cysteines are distant from one another in the highest-population conformational state of ligand-free class A GPCRs and do not form a disulfide bond, indicating that the dynamics of the GPCR extracellular side are different from our conventional understanding. These surprising dynamics should have important effects on the drug binding process. On the basis of the two distinct ligand-free states, we suggest two kinetic processes for binding of ligands to GPCRs. These results challenge our commonly held beliefs regarding both GPCR structural features and ligand binding.
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Affiliation(s)
- Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai 200241 , China
| | - Mang Zhou
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Lifen Zhao
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Hualiang Jiang
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Huaiyu Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai 200241 , China
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29
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Choi J, Lee SE, Park JS, Kim SY. Gold nanorod-photosensitizer conjugates with glutathione-sensitive linkages for synergistic cancer photodynamic/photothermal therapy. Biotechnol Bioeng 2018; 115:1340-1354. [DOI: 10.1002/bit.26536] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Jongseon Choi
- Graduate School of Energy Science and Technology; Chungnam National University; Daejeon Korea
| | - Sang-Eun Lee
- Department of Physical Pharmacy; College of Pharmacy; Chungnam National University; Daejeon Korea
| | - Jeong-Sook Park
- Department of Physical Pharmacy; College of Pharmacy; Chungnam National University; Daejeon Korea
| | - So Yeon Kim
- Graduate School of Energy Science and Technology; Chungnam National University; Daejeon Korea
- Department of Chemical Engineering Education; College of Education; Chungnam National University; Daejeon Korea
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30
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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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31
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Atamas N, Bardik V, Bannikova A, Grishina O, Lugovskoi E, Lavoryk S, Makogonenko Y, Korolovych V, Nerukh D, Paschenko V. The effect of water dynamics on conformation changes of albumin in pre-denaturation state: photon correlation spectroscopy and simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Naldi M, Baldassarre M, Domenicali M, Bartolini M, Caraceni P. Structural and functional integrity of human serum albumin: Analytical approaches and clinical relevance in patients with liver cirrhosis. J Pharm Biomed Anal 2017; 144:138-153. [PMID: 28465079 DOI: 10.1016/j.jpba.2017.04.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 02/08/2023]
Abstract
Human serum albumin (HSA) is the most abundant circulating plasma protein. Besides a significant contribution to the osmotic pressure, it is also involved in the fine regulation of many other physiological processes, including the balance of the redox state, the inflammatory and/or immunological responses, and the pharmacokinetic and pharmacodynamics of many drugs. Growing evidence suggests that HSA undergoes structural and functional damage in diseases characterized by an enhanced systemic inflammatory response and oxidative stress, as it occurs in chronic liver disease. Based on their clinical relevance, this review provides a summary of the most common post-translational modifications affecting HSA structural integrity and functions and their clinical relevance in the field of liver disease. The review also provides a critical description of the analytical approaches employed for the investigation of conformational alterations and the identification/quantitation of specific post-translational modifications affecting HSA. Finally, the analytical methods available for the assessment of two of the most clinically relevant non-oncotic properties of HSA, namely the binding capacity and the antioxidant activity, are critically reviewed. Among the available techniques particular attention is given to those proposed for the in vitro and in vivo investigation of structurally modified albumin.
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Affiliation(s)
- Marina Naldi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126, Italy; Center for Applied Biomedical Research (C.R.B.A.), S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy
| | - Maurizio Baldassarre
- Center for Applied Biomedical Research (C.R.B.A.), S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138, Italy
| | - Marco Domenicali
- Center for Applied Biomedical Research (C.R.B.A.), S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138, Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126, Italy
| | - Paolo Caraceni
- Center for Applied Biomedical Research (C.R.B.A.), S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138, Italy.
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Abstract
The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.
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Affiliation(s)
- Qing Shao
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, 27695, USA.
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34
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Awang T, Wiriyatanakorn N, Saparpakorn P, Japrung D, Pongprayoon P. Understanding the effects of two bound glucose in Sudlow site I on structure and function of human serum albumin: theoretical studies. J Biomol Struct Dyn 2016; 35:781-790. [DOI: 10.1080/07391102.2016.1160841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tadsanee Awang
- Faculty of Science, Department of Chemistry, Prince of Songkla University, Hatyai, Songkla 90112, Thailand
| | - Nuttapon Wiriyatanakorn
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Patchreenart Saparpakorn
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
| | - Prapasiri Pongprayoon
- Faculty of Science, Department of Chemistry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Nanotechnology and its Applications in Chemical, Food and Agricultural Industries, Kasetsart University, Bangkok 10900, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Kasetsart University, Bangkok 10900, Thailand
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35
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Fehér K, Timári I, Rákosi K, Szolomájer J, Illyés TZ, Bartok A, Varga Z, Panyi G, Tóth GK, Kövér KE. Probing pattern and dynamics of disulfide bridges using synthesis and NMR of an ion channel blocker peptide toxin with multiple diselenide bonds. Chem Sci 2016; 7:2666-2673. [PMID: 28660039 PMCID: PMC5477041 DOI: 10.1039/c5sc03995a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/17/2015] [Indexed: 12/28/2022] Open
Abstract
Anuroctoxin (AnTx), a 35-amino-acid scorpion toxin containing four disulfide bridges, is a high affinity blocker of the voltage-gated potassium channel Kv1.3, but also blocks Kv1.2. To improve potential therapeutic use of the toxin, we have designed a double substituted analog, [N17A/F32T]-AnTx, which showed comparable Kv1.3 affinity to the wild-type peptide, but also a 2500-fold increase in the selectivity for Kv1.3 over Kv1.2. In the present study we have achieved the chemical synthesis of a Sec-analog in which all cysteine (Cys) residues have been replaced by selenocysteine (Sec) forming four diselenide bonds. To the best of our knowledge this is the first time to replace, by chemical synthesis, all disulfide bonds with isosteric diselenides in a peptide/protein. Gratifyingly, the key pharmacological properties of the Sec-[N17A/F32T]-AnTx are retained since the peptide is functionally active. We also propose here a combined experimental and theoretical approach including NOE- and 77Se-based NMR supplemented by MD simulations for conformational and dynamic characterization of the Sec-[N17A/F32T]-AnTx. Using this combined approach allowed us to attain unequivocal assignment of all four diselenide bonds and supplemental MD simulations allowed characterization of the conformational dynamics around each disulfide/diselenide bridge.
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Affiliation(s)
- Krisztina Fehér
- Department of Inorganic and Analytical Chemistry , University of Debrecen , Egyetem tér 1 , H-4032 , Debrecen , Hungary .
- Department of Organic and Macromolecular Chemistry , Ghent University , Kringslaan 281 S4 , 9000 , Ghent , Belgium
| | - István Timári
- Department of Inorganic and Analytical Chemistry , University of Debrecen , Egyetem tér 1 , H-4032 , Debrecen , Hungary .
| | - Kinga Rákosi
- Department of Medical Chemistry , University of Szeged , Dóm tér 8 , H-6720 , Szeged , Hungary .
| | - János Szolomájer
- Department of Medical Chemistry , University of Szeged , Dóm tér 8 , H-6720 , Szeged , Hungary .
| | - Tünde Z Illyés
- Department of Organic Chemistry , University of Debrecen , Egyetem tér 1 , H-4032 , Debrecen , Hungary
| | - Adam Bartok
- Department of Biophysics and Cell Biology , University of Debrecen , Egyetem tér 1 , H-4012 , Debrecen , Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology , University of Debrecen , Egyetem tér 1 , H-4012 , Debrecen , Hungary
- MTA-DE-NAP B Ion Channel Structure-Function Research Group , Egyetem tér 1 , H-4032 , Debrecen , Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology , University of Debrecen , Egyetem tér 1 , H-4012 , Debrecen , Hungary
- MTA-DE Cell Biology and Signaling Research Group , University of Debrecen , Egyetem tér 1 , H-4032 , Debrecen , Hungary
| | - Gábor K Tóth
- Department of Medical Chemistry , University of Szeged , Dóm tér 8 , H-6720 , Szeged , Hungary .
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry , University of Debrecen , Egyetem tér 1 , H-4032 , Debrecen , Hungary .
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36
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Díaz N, Suárez D. Role of the Protonation State on the Structure and Dynamics of Albumin. J Chem Theory Comput 2016; 12:1972-88. [DOI: 10.1021/acs.jctc.5b01001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Natalia Díaz
- C/Julián
Clavería
8. Dpto. de Química Física y Analítica, Universidad de Oviedo, Oviedo, 33006 Asturias, Spain
| | - Dimas Suárez
- C/Julián
Clavería
8. Dpto. de Química Física y Analítica, Universidad de Oviedo, Oviedo, 33006 Asturias, Spain
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37
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Pongprayoon P, Gleeson MP. Probing the binding site characteristics of HSA: A combined molecular dynamics and cheminformatics investigation. J Mol Graph Model 2014; 54:164-73. [DOI: 10.1016/j.jmgm.2014.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/08/2014] [Accepted: 10/11/2014] [Indexed: 10/24/2022]
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38
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Yang D, Chen W, Hu J. Design of Controlled Drug Delivery System Based on Disulfide Cleavage Trigger. J Phys Chem B 2014; 118:12311-7. [DOI: 10.1021/jp507763a] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Dong Yang
- State Key Laboratory of Molecular
Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Wulian Chen
- State Key Laboratory of Molecular
Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Jianhua Hu
- State Key Laboratory of Molecular
Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
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39
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Phuangsawai O, Hannongbua S, Gleeson MP. Elucidating the Origin of the Esterase Activity of Human Serum Albumin Using QM/MM Calculations. J Phys Chem B 2014; 118:11886-94. [DOI: 10.1021/jp506629y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Oraphan Phuangsawai
- Department
of Chemistry,
Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Supa Hannongbua
- Department
of Chemistry,
Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - M. Paul Gleeson
- Department
of Chemistry,
Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
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40
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Del Giudice A, Leggio C, Balasco N, Galantini L, Pavel NV. Ibuprofen and Propofol Cobinding Effect on Human Serum Albumin Unfolding in Urea. J Phys Chem B 2014; 118:10043-51. [DOI: 10.1021/jp504280n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alessandra Del Giudice
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Claudia Leggio
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Nicole Balasco
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Luciano Galantini
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
| | - Nicolae V. Pavel
- Dipartimento
di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy
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41
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Anoop A, Ranganathan S, Das Dhaked B, Jha NN, Pratihar S, Ghosh S, Sahay S, Kumar S, Das S, Kombrabail M, Agarwal K, Jacob RS, Singru P, Bhaumik P, Padinhateeri R, Kumar A, Maji SK. Elucidating the role of disulfide bond on amyloid formation and fibril reversibility of somatostatin-14: relevance to its storage and secretion. J Biol Chem 2014; 289:16884-903. [PMID: 24782311 DOI: 10.1074/jbc.m114.548354] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The storage of protein/peptide hormones within subcellular compartments and subsequent release are crucial for their native function, and hence these processes are intricately regulated in mammalian systems. Several peptide hormones were recently suggested to be stored as amyloids within endocrine secretory granules. This leads to an apparent paradox where storage requires formation of aggregates, and their function requires a supply of non-aggregated peptides on demand. The precise mechanism behind amyloid formation by these hormones and their subsequent release remain an open question. To address this, we examined aggregation and fibril reversibility of a cyclic peptide hormone somatostatin (SST)-14 using various techniques. After proving that SST gets stored as amyloid in vivo, we investigated the role of native structure in modulating its conformational dynamics and self-association by disrupting the disulfide bridge (Cys(3)-Cys(14)) in SST. Using two-dimensional NMR, we resolved the initial structure of somatostatin-14 leading to aggregation and further probed its conformational dynamics in silico. The perturbation in native structure (S-S cleavage) led to a significant increase in conformational flexibility and resulted in rapid amyloid formation. The fibrils formed by disulfide-reduced noncyclic SST possess greater resistance to denaturing conditions with decreased monomer releasing potency. MD simulations reveal marked differences in the intermolecular interactions in SST and noncyclic SST providing plausible explanation for differential aggregation and fibril reversibility observed experimentally in these structural variants. Our findings thus emphasize that subtle changes in the native structure of peptide hormone(s) could alter its conformational dynamics and amyloid formation, which might have significant implications on their reversible storage and secretion.
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Affiliation(s)
- Arunagiri Anoop
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Srivastav Ranganathan
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Bhagwan Das Dhaked
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Narendra Nath Jha
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Supriya Pratihar
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Saikat Ghosh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Shruti Sahay
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Santosh Kumar
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Subhadeep Das
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, the IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | - Mamata Kombrabail
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Kumud Agarwal
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Reeba S Jacob
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Praful Singru
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ranjith Padinhateeri
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ashutosh Kumar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
| | - Samir K Maji
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
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