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Yagasaki T, Matubayasi N. High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:15046-15058. [PMID: 39004900 DOI: 10.1021/acs.langmuir.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The antifouling performance of polymer brushes usually improves with increasing hydrophilicity of the grafted polymer. However, in some cases, less hydrophilic polymers show comparable or better antifouling performance than do more hydrophilic polymers. We investigate the mechanism of this anomalous behavior using molecular dynamics (MD) simulations of coarse-grained (CG) models of weakly and strongly hydrophilic polymers. The antifouling performance is evaluated from the potential of mean force of a model protein. The strongly hydrophilic polymer exhibits a better antifouling performance than the weakly hydrophilic polymer when the substrate of the polymer brush is repulsive. However, when the substrate is sufficiently attractive, the weakly hydrophilic polymer brush becomes more effective than the strongly hydrophilic brush in a certain range of grafting density. This is because the weakly hydrophilic polymer chains form a tightly packed layer that prevents the adsorbate molecule from contacting the substrate. We also perform all-atom (AA) MD simulations for several standard polymers to examine the correspondence with the CG polymer models. The weakly hydrophilic CG polymer is found to be similar to poly[N-(2-hydroxypropyl)methacrylamide] and poly(2-hydroxyethyl methacrylate), both of which have a hydroxyl group in a monomer unit. The strongly hydrophilic CG polymer resembles zwitterionic poly(carboxybetaine methacrylate). A discussion referring to the adsorption free energies of proteins on surfaces calculated in previous AA MD studies suggests that the higher antifouling performance of less hydrophilic polymer brushes can be realized for various combinations of protein and surface.
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Affiliation(s)
- Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
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Lan J, Peng Y, Liang L, Duan X, Kong Z, Zhang L, Shen JW. Theoretical study of protein adsorption on graphene/h-BN heterostructures. Phys Chem Chem Phys 2023; 25:31206-31221. [PMID: 37955184 DOI: 10.1039/d3cp03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.
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Affiliation(s)
- Jun Lan
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Yiran Peng
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Xing Duan
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Zhe Kong
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia-Wei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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Khavani M, Mehranfar A, Mofrad MRK. On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. J Chem Inf Model 2023; 63:1276-1292. [PMID: 36735895 PMCID: PMC9924083 DOI: 10.1021/acs.jcim.2c01378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/05/2023]
Abstract
The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.
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Affiliation(s)
- Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
| | - Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
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Zhou H, Xie ZX, Liang L, Zhang P, Ma X, Kong Z, Shen JW, Hu W. Theoretical investigation on the adsorption orientation of DNA on two-dimensional MoSe2. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chatterjee S, Salimi A, Lee JY. Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective. ACS Chem Neurosci 2021; 12:3203-3213. [PMID: 34382391 DOI: 10.1021/acschemneuro.1c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The aggregation and structural conversion of normal prion peptide (PrPC) into the pathogenic scrapie form (PrPSc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [Nε2-H (ε) and Nδ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.
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Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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Sun N, Li M, Liu G, Jing M, He F, Cao Z, Zong W, Tang J, Gao C, Liu R. Toxic mechanism of pyrene to catalase and protective effects of vitamin C: Studies at the molecular and cell levels. Int J Biol Macromol 2021; 171:225-233. [PMID: 33418042 DOI: 10.1016/j.ijbiomac.2020.12.169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/10/2020] [Accepted: 12/22/2020] [Indexed: 11/17/2022]
Abstract
Polycyclic aromatic hydrocarbons, distributing extensively in the soil, would potentially threaten the soil organisms (Eisenia fetida) by triggering oxidative stress. As a ubiquitous antioxidant enzyme, catalase can protect organisms from oxidative damage. To reveal the potential impact of polycyclic aromatic hydrocarbon pyrene (Pyr) on catalase (CAT) and the possible protective effect of Ascorbic acid (vitamin C), multi-spectral and molecular docking techniques were used to investigate the influence of structure and function of catalase by pyrene. Fluorescence and circular dichroism analysis showed that pyrene would induce the microenvironmental changes of CAT amino acid residues and increase the α-helix in the secondary structure. Molecular simulation results indicated that the main binding force of pyrene around the active center of CAT is hydrogen bonding force. Furthermore, pyrene inhibited catalase activity to 69.9% compared with the blank group, but the degree of inhibition was significantly weakened after vitamin C added into the research group. Cell level experiments showed that pyrene can increase the level of ROS in the body cavity cell of earthworms, and put the cells under the threat of potential oxidative damage. Antioxidants-vitamin C has a protective effect on catalase and maintains the stability of intracellular ROS levels to a certain extent.
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Affiliation(s)
- Ning Sun
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Meifei Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Guiliang Liu
- Shandong Institute for Food and Drug Control, Jinan 250101, PR China
| | - Mingyang Jing
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Zhaozhen Cao
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, PR China
| | - Canzhu Gao
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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Emadi F, Emadi A, Gholami A. A Comprehensive Insight Towards Pharmaceutical Aspects of Graphene Nanosheets. Curr Pharm Biotechnol 2020; 21:1016-1027. [PMID: 32188383 DOI: 10.2174/1389201021666200318131422] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/12/2022]
Abstract
Graphene Derivatives (GDs) have captured the interest and imagination of pharmaceutical scientists. This review exclusively provides pharmacokinetics and pharmacodynamics information with a particular focus on biopharmaceuticals. GDs can be used as multipurpose pharmaceutical delivery systems due to their ultra-high surface area, flexibility, and fast mobility of charge carriers. Improved effects, targeted delivery to tissues, controlled release profiles, visualization of biodistribution and clearance, and overcoming drug resistance are examples of the benefits of GDs. This review focuses on the application of GDs for the delivery of biopharmaceuticals. Also, the pharmacokinetic properties and the advantage of using GDs in pharmaceutics will be reviewed to achieve a comprehensive understanding about the GDs in pharmaceutical sciences.
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Affiliation(s)
- Fatemeh Emadi
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA 5000, Iran
| | - Arash Emadi
- Faculty of Pharmacy and Pharmaceutical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ahmad Gholami
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, P.O. Box: 7146864685, Iran
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Xu M, Wan J, Niu Q, Liu R. PFOA and PFOS interact with superoxide dismutase and induce cytotoxicity in mouse primary hepatocytes: A combined cellular and molecular methods. ENVIRONMENTAL RESEARCH 2019; 175:63-70. [PMID: 31103794 DOI: 10.1016/j.envres.2019.05.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 05/08/2023]
Abstract
This study investigated the adverse effects of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) on mouse primary hepatocytes by conducting cell viability, apoptosis, intracellular oxidative stress level, superoxide dismutase (SOD), catalase (CAT) activity and glutathione level assays. It was shown that PFOA and PFOS altered antioxidant enzymes activities and triggered oxidative stress, and thus exhibited cytotoxicity to the hepatocytes. Molecular mechanisms of SOD activities were measured and structural changes were explored by isothermal titration calorimetry and multiple spectroscopy. PFOA and PFOS bind to SOD via electrostatic forces with 7.634 ± 0.06 and 9.7 ± 0.4 sites, respectively, leading to structural and conformational changes. The overall results demonstrated that PFOS and PFOA are able to interact with SOD directly, resulting in producing oxidative stress and induce apoptosis.
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Affiliation(s)
- Mengchen Xu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China
| | - Jingqiang Wan
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China.
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