1
|
Kamboukos A, Williams-Noonan BJ, Charchar P, Yarovsky I, Todorova N. Graphitic nanoflakes modulate the structure and binding of human amylin. NANOSCALE 2024; 16:16870-16886. [PMID: 39219407 DOI: 10.1039/d4nr01315h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Human amylin is an inherently disordered protein whose ability to form amyloid fibrils is linked to the onset of type II diabetes. Graphitic nanomaterials have potential in managing amyloid diseases as they can disrupt protein aggregation processes in biological settings, but optimising these materials to prevent fibrillation is challenging. Here, we employ bias-exchange molecular dynamics simulations to systematically study the structure and adsorption preferences of amylin on graphitic nanoflakes that vary in their physical dimensions and surface functionalisation. Our findings reveal that nanoflake size and surface oxidation both influence the structure and adsorption preferences of amylin. The purely hydrophobic substrate of pristine graphene (PG) nanoflakes encourages non-specific protein adsorption, leading to unrestricted lateral mobility once amylin adheres to the surface. Particularly on larger PG nanoflakes, this induces structural changes in amylin that may promote fibril formation, such as the loss of native helical content and an increase in β-sheet character. In contrast, oxidised graphene nanoflakes form hydrogen bonds between surface oxygen sites and amylin, and as such restricting protein mobility. Reduced graphene oxide (rGO) flakes, featuring lower amounts of surface oxidation, are amphiphilic and exhibit substantial regions of bare carbon which promote protein binding and reduced conformational flexibility, leading to conservation of the native structure of amylin. In comparison, graphene oxide (GO) nanoflakes, which are predominantly hydrophilic and have a high degree of surface oxidation, facilitate considerable protein structural variability, resulting in substantial contact area between the protein and GO, and subsequent protein unfolding. Our results indicate that tailoring the size, oxygen concentration and surface patterning of graphitic nanoflakes can lead to specific and robust protein binding, ultimately influencing the likelihood of fibril formation. These atomistic insights provide key design considerations for the development of graphitic nanoflakes that can modulate protein aggregation by sequestering protein monomers in the biological environment and inhibit conformational changes linked to amyloid fibril formation.
Collapse
Affiliation(s)
- Alexa Kamboukos
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
- School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| |
Collapse
|
2
|
Li K, Tan H, Li J, Li Z, Qin F, Luo H, Qin D, Weng H, Zhang C. Unveiling the Effects of Carbon-Based Nanomaterials on Crop Growth: From Benefits to Detriments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11860-11874. [PMID: 37492956 DOI: 10.1021/acs.jafc.3c02768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
To systematically assess the impact of typical CNMs on the growth effects of cereal crops, we conducted a meta-analysis of 48 independent studies worldwide. The pooled results showed that shoot weight (13.39%) and antioxidant metabolite content (SOD: 106.32%, POD: 32.29%, CAT: 22.63%) of cereal crops exposed to the presence of CNMs were significantly increased, but phytohormones secretion (17.84%) was inhibited. The results of subgroup analysis showed that there were differences in the results of different CNM types with the same exposure concentration on growth effects. Short-term exposure adversely affected the root and photosynthetic capacity of the crop, but prolonged exposure instead showed a promoting effect. Multiple linear regression analysis showed that the concentration of CNMs and cereal variety variables were significantly associated with changes in multiple growth effect values. This work could offer references and fresh perspectives for investigating how nanoparticles and crops interact.
Collapse
Affiliation(s)
- Keteng Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| | - Hao Tan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Jialing Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
- School of Design, Hunan University, Changsha 410082, China
| | - Zetong Li
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, Sichuan Province, P. R. China
| | - Fanzhi Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| | - Hanzhuo Luo
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| | - Deyu Qin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| | - Hao Weng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| | - Chen Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, Hunan University, Changsha 410082, China
| |
Collapse
|
3
|
Atabay M, Sardroodi JJ, Ebrahimzadeh AR, Avestan MS. Modeling the Interaction of Anticancer Protein Azurin with the Nanosheets for Medical Applications. ChemistrySelect 2022. [DOI: 10.1002/slct.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Physics Azarbaijan Shahid Madani University Tabriz Iran
| | | |
Collapse
|
4
|
Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022; 13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023] Open
Abstract
Insulin is a peptide hormone known for chiefly regulating glucose level in blood among several other metabolic processes. Insulin remains the most effective drug for treating diabetes mellitus. Insulin is synthesized in the pancreatic β-cells where it exists in a compact hexameric architecture although its biologically active form is monomeric. Insulin exhibits a sequence of conformational variations during the transition from the hexamer state to its biologically-active monomer state. The structural transitions and the mechanism of action of insulin have been investigated using several experimental and computational methods. This review primarily highlights the contributions of molecular dynamics (MD) simulations in elucidating the atomic-level details of conformational dynamics in insulin, where the structure of the hormone has been probed as a monomer, dimer, and hexamer. The effect of solvent, pH, temperature, and pressure have been probed at the microscopic scale. Given the focus of this review on the structure of the hormone, simulation studies involving interactions between the hormone and its receptor are only briefly highlighted, and studies on other related peptides (e.g., insulin-like growth factors) are not discussed. However, the review highlights conformational dynamics underlying the activities of reported insulin analogs and mimetics. The future prospects for computational methods in developing promising synthetic insulin analogs are also briefly highlighted.
Collapse
Affiliation(s)
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, United States
| |
Collapse
|
5
|
Sadrjavadi K, Barzegari E, Khaledian S, Derakhshankhah H, Fattahi A. Interactions of insulin with tragacanthic acid biopolymer: Experimental and computational study. Int J Biol Macromol 2020; 164:321-330. [PMID: 32682034 DOI: 10.1016/j.ijbiomac.2020.07.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 02/07/2023]
Abstract
Alternative methods for insulin delivery instead of subcutaneous injection in diabetic patients is of great essential, and biocompatible polymers are one of the most efficient vehicles for this purpose. This research aims to investigate the capability of tragacanthic acid (TA) to bind insulin and release it under physiological conditions without alteration in the structure and conformation of insulin. Interactions between TA and insulin were studied using spectroscopic techniques and computational modeling by docking and molecular dynamics simulations. Our results demonstrate an entropy-driven spontaneous interaction between insulin and TA, where hydrogen bonds act as the main enthalpic contribution. According to our findings, the weak interaction between insulin and TA provides the basis for efficient capture and appropriate release of insulin by TA as a potential part of the insulin delivery system. In conclusion, tragacanth acid can be a proper candidate for insulin delivery.
Collapse
Affiliation(s)
- Komail Sadrjavadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran; Department of Biology, Faculty of Science, Razi University, Kermanshah 6714115111, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technologies Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran
| | - Salar Khaledian
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran
| | - Ali Fattahi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran; Medical Biology Research Center, Health Technologies Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran.
| |
Collapse
|
6
|
Mantecón-Oria M, Diban N, Berciano MT, Rivero MJ, David O, Lafarga M, Tapia O, Urtiaga A. Hollow Fiber Membranes of PCL and PCL/Graphene as Scaffolds with Potential to Develop In Vitro Blood-Brain Barrier Models. MEMBRANES 2020; 10:E161. [PMID: 32708027 PMCID: PMC7464335 DOI: 10.3390/membranes10080161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022]
Abstract
There is a huge interest in developing novel hollow fiber (HF) membranes able to modulate neural differentiation to produce in vitro blood-brain barrier (BBB) models for biomedical and pharmaceutical research, due to the low cell-inductive properties of the polymer HFs used in current BBB models. In this work, poly(ε-caprolactone) (PCL) and composite PCL/graphene (PCL/G) HF membranes were prepared by phase inversion and were characterized in terms of mechanical, electrical, morphological, chemical, and mass transport properties. The presence of graphene in PCL/G membranes enlarged the pore size and the water flux and presented significantly higher electrical conductivity than PCL HFs. A biocompatibility assay showed that PCL/G HFs significantly increased C6 cells adhesion and differentiation towards astrocytes, which may be attributed to their higher electrical conductivity in comparison to PCL HFs. On the other hand, PCL/G membranes produced a cytotoxic effect on the endothelial cell line HUVEC presumably related with a higher production of intracellular reactive oxygen species induced by the nanomaterial in this particular cell line. These results prove the potential of PCL HF membranes to grow endothelial cells and PCL/G HF membranes to differentiate astrocytes, the two characteristic cell types that could develop in vitro BBB models in future 3D co-culture systems.
Collapse
Affiliation(s)
- Marián Mantecón-Oria
- Department of Chemical and Biomolecular Engineering, ETSIIyT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain; (M.M.-O.); (M.J.R.); (A.U.)
| | - Nazely Diban
- Department of Chemical and Biomolecular Engineering, ETSIIyT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain; (M.M.-O.); (M.J.R.); (A.U.)
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Cardenal H. Oria s/n, 39011 Santander, Spain; (M.T.B.); (M.L.); (O.T.)
| | - Maria T. Berciano
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Cardenal H. Oria s/n, 39011 Santander, Spain; (M.T.B.); (M.L.); (O.T.)
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 528031 Madrid, Spain
- Department of Molecular Biology, University of Cantabria, Cardenal H. Oria s/n, 39011 Santander, Spain
| | - Maria J. Rivero
- Department of Chemical and Biomolecular Engineering, ETSIIyT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain; (M.M.-O.); (M.J.R.); (A.U.)
| | - Oana David
- TECNALIA, Basque Research and Technology Alliance (BRTA), Mikeletegi Pasealekua 2, 20009 San Sebastián, Spain;
| | - Miguel Lafarga
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Cardenal H. Oria s/n, 39011 Santander, Spain; (M.T.B.); (M.L.); (O.T.)
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 528031 Madrid, Spain
- Department of Anatomy and Cell Biology, University of Cantabria, Cardenal H. Oria s/n, 39011 Santander, Spain
| | - Olga Tapia
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Cardenal H. Oria s/n, 39011 Santander, Spain; (M.T.B.); (M.L.); (O.T.)
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 528031 Madrid, Spain
- Universidad Europea del Atlántico, Parque Científico y Tecnológico de Cantabria, Isabel Torres 21, 39011 Santander, Spain
| | - Ane Urtiaga
- Department of Chemical and Biomolecular Engineering, ETSIIyT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain; (M.M.-O.); (M.J.R.); (A.U.)
- Instituto de Investigación Marqués de Valdecilla (IDIVAL), Cardenal H. Oria s/n, 39011 Santander, Spain; (M.T.B.); (M.L.); (O.T.)
| |
Collapse
|
7
|
Kumar S, Parekh SH. Linking graphene-based material physicochemical properties with molecular adsorption, structure and cell fate. Commun Chem 2020; 3:8. [PMID: 36703309 PMCID: PMC9814659 DOI: 10.1038/s42004-019-0254-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/03/2019] [Indexed: 01/29/2023] Open
Abstract
Graphene, an allotrope of carbon, consists of a single layer of carbon atoms with uniquely tuneable properties. As such, graphene-based materials (GBMs) have gained interest for tissue engineering applications. GBMs are often discussed in the context of how different physicochemical properties affect cell physiology, without explicitly considering the impact of adsorbed proteins. Establishing a relationship between graphene properties, adsorbed proteins, and cell response is necessary as these proteins provide the surface upon which cells attach and grow. This review highlights the molecular adsorption of proteins on different GBMs, protein structural changes, and the connection to cellular function.
Collapse
Affiliation(s)
- Sachin Kumar
- Department of Biomedical Engineering, University of Texas at Austin, 107 W. Dean Keeton Rd., Austin, TX, 78712, USA
| | - Sapun H Parekh
- Department of Biomedical Engineering, University of Texas at Austin, 107 W. Dean Keeton Rd., Austin, TX, 78712, USA.
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, DE, USA.
| |
Collapse
|
8
|
Computational simulations and experimental validation of structure- physicochemical properties of pristine and functionalized graphene: Implications for adverse effects on p53 mediated DNA damage response. Int J Biol Macromol 2018; 110:540-549. [DOI: 10.1016/j.ijbiomac.2017.10.106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/07/2017] [Accepted: 10/16/2017] [Indexed: 01/11/2023]
|
9
|
Ke D, Sui LZ, Liu DL, Wang YS, Li SY, Jiang YF, Chen AM, Jin MX. Hidden Relaxation Channels in Aqueous Methylene Blue after Functionalization of Graphene Oxide Probed by Transient Absorption Spectroscopy. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1704070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
10
|
Hovancová J, Šišoláková I, Oriňaková R, Oriňak A. Nanomaterial-based electrochemical sensors for detection of glucose and insulin. J Solid State Electrochem 2017. [DOI: 10.1007/s10008-017-3544-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
11
|
Nejad MA, Mücksch C, Urbassek HM. Insulin adsorption on crystalline SiO2: Comparison between polar and nonpolar surfaces using accelerated molecular-dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
12
|
Atabay M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. Adsorption and immobilisation of human insulin on graphene monoxide, silicon carbide and boron nitride nanosheets investigated by molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1270452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Azarbaijan Shahid Madani University, Tabriz, Iran
| |
Collapse
|
13
|
Dwivedi AD, Dubey SP, Sillanpää M, Kwon YN, Lee C, Varma RS. Fate of engineered nanoparticles: Implications in the environment. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.12.014] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
14
|
Kong Z, Zheng W, Wang Q, Wang H, Xi F, Liang L, Shen JW. Charge-tunable absorption behavior of DNA on graphene. J Mater Chem B 2015; 3:4814-4820. [DOI: 10.1039/c5tb00635j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Charge-tunable absorption behavior of DNA on graphene: 0 is uncharged; − is negative charge; + is positive charge.
Collapse
Affiliation(s)
- Zhe Kong
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Wei Zheng
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People's Republic of China
| | - Qi Wang
- Soft Matter Research Center and Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Hongbo Wang
- College of Automation
- Hangzhou Dianzi University
- Hangzhou
- People's Republic of China
| | - Fengna Xi
- Department of Chemistry
- Zhejiang Sci-Tech University
- Hangzhou
- Zhejiang 310018
- China
| | - Lijun Liang
- Soft Matter Research Center and Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
- Department of Polymer Science and Engineering
| | - Jia-Wei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People's Republic of China
| |
Collapse
|
15
|
Mu Q, Jiang G, Chen L, Zhou H, Fourches D, Tropsha A, Yan B. Chemical basis of interactions between engineered nanoparticles and biological systems. Chem Rev 2014; 114:7740-81. [PMID: 24927254 PMCID: PMC4578874 DOI: 10.1021/cr400295a] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Qingxin Mu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
- Present address: Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas, 66047
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lingxin Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Hongyu Zhou
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, 30322, U.S.A
| | | | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Bing Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
| |
Collapse
|
16
|
Liang L, Zhang Z, Shen J, Zhe K, Wang Q, Wu T, Ågren H, Tu Y. Theoretical studies on the dynamics of DNA fragment translocation through multilayer graphene nanopores. RSC Adv 2014. [DOI: 10.1039/c4ra05909c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA translocation through multilayer graphene nanopore with a change of current.
Collapse
Affiliation(s)
- Lijun Liang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
- Division of Theoretical Chemistry and Biology
| | - Zhisen Zhang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Jiawei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016, People's Republic of China
| | - Kong Zhe
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Tao Wu
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- KTH Royal Institute of Technology
- SE-10691 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- KTH Royal Institute of Technology
- SE-10691 Stockholm, Sweden
| |
Collapse
|
17
|
Ding Z, Ma H, Chen Y. Interaction of graphene oxide with human serum albumin and its mechanism. RSC Adv 2014. [DOI: 10.1039/c4ra09613d] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We show that GONS inhibit HSA function via two routes: blocking protein active sites, or destroying protein structure.
Collapse
Affiliation(s)
- Zhijia Ding
- Key Laboratory for Nano-Bio Interface Research
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, P. R. China
| | - Hongwei Ma
- Key Laboratory for Nano-Bio Interface Research
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, P. R. China
| | - Yanyan Chen
- Key Laboratory for Nano-Bio Interface Research
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, P. R. China
| |
Collapse
|
18
|
Todorova N, Makarucha AJ, Hine NDM, Mostofi AA, Yarovsky I. Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations. PLoS Comput Biol 2013; 9:e1003360. [PMID: 24339760 PMCID: PMC3854483 DOI: 10.1371/journal.pcbi.1003360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/09/2013] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.
Collapse
Affiliation(s)
| | | | - Nicholas D. M. Hine
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Arash A. Mostofi
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Irene Yarovsky
- Health Innovations Research Institute, Melbourne, Australia
| |
Collapse
|
19
|
Liang LJ, Wang Q, Wu T, Sun TY, Kang Y. Contribution of Water Molecules in the Spontaneous Release of Protein by Graphene Sheets. Chemphyschem 2013; 14:2902-9. [DOI: 10.1002/cphc.201300414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Indexed: 11/07/2022]
|
20
|
Liang LJ, Wu T, Kang Y, Wang Q. Dispersion of graphene sheets in aqueous solution by oligodeoxynucleotides. Chemphyschem 2013; 14:1626-32. [PMID: 23554343 DOI: 10.1002/cphc.201201084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 11/09/2022]
Abstract
Applications of graphene sheets in the fields of biosensors and biomedical devices are limited by their insolubility in water. Consequently, understanding the dispersion mechanism of graphene in water and exploring an effective way to prepare stable dispersions of graphene sheets in water is of vital importance for their application in biomaterials, biosensors, biomedical devices, and drug delivery. Herein, a method for stable dispersion of graphene sheets in water by single-stranded oligodeoxynucleotides (ssODNs) is studied. Owing to van der Waals interactions between graphene sheets, they undergo layer-to-layer (LtL) aggregation in water. Molecular dynamics simulations show that, by disrupting van der Waals interaction of graphene sheets with ssODNs, LtL aggregation of graphene sheets is prevented, and water molecules can be distributed stably between graphene sheets. Thus, graphene sheets are dispersed stably in water in the presence of ssODNs. The effects of size and molarity of ssODNs and noncovalent modification of graphene sheets are also discussed.
Collapse
Affiliation(s)
- Li-Jun Liang
- Soft Matter Research Center and Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
| | | | | | | |
Collapse
|
21
|
Mücksch C, Urbassek HM. Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12938-12943. [PMID: 21877733 DOI: 10.1021/la201972f] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.
Collapse
Affiliation(s)
- Christian Mücksch
- Fachbereich Physik und Forschungszentrum OPTIMAS, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | | |
Collapse
|
22
|
Mücksch C, Urbassek HM. Adsorption of BMP-2 on a hydrophobic graphite surface: A molecular dynamics study. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.05.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
23
|
Nanomaterials in biological environment: a review of computer modelling studies. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:103-15. [DOI: 10.1007/s00249-010-0651-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/18/2010] [Accepted: 11/23/2010] [Indexed: 01/13/2023]
|