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Garduño-Juárez R, Tovar-Anaya DO, Perez-Aguilar JM, Lozano-Aguirre Beltran LF, Zubillaga RA, Alvarez-Perez MA, Villarreal-Ramirez E. Molecular Dynamic Simulations for Biopolymers with Biomedical Applications. Polymers (Basel) 2024; 16:1864. [PMID: 39000719 PMCID: PMC11244511 DOI: 10.3390/polym16131864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 07/17/2024] Open
Abstract
Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.
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Affiliation(s)
- Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - David O Tovar-Anaya
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | | | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Marco Antonio Alvarez-Perez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Eduardo Villarreal-Ramirez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
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Zou F, Gu Z, Perez-Aguilar JM, Luo Y. Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure. Sci Rep 2024; 14:9168. [PMID: 38649777 PMCID: PMC11035638 DOI: 10.1038/s41598-024-59780-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Fluorinated graphene, a two-dimensional nanomaterial composed of three atomic layers, a central carbon layer sandwiched between two layers of fluorine atoms, has attracted considerable attention across various fields, particularly for its potential use in biomedical applications. Nonetheless, scant effort has been devoted to assessing the potential toxicological implications of this nanomaterial. In this study, we scrutinize the potential impact of fluorinated graphene on a protein model, HP35 by utilizing extensive molecular dynamics (MD) simulation methods. Our MD results elucidate that upon adsorption to the nanomaterial, HP35 undergoes a denaturation process initiated by the unraveling of the second helix of the protein and the loss of the proteins hydrophobic core. In detail, substantial alterations in various structural features of HP35 ensue, including alterations in hydrogen bonding, Q value, and RMSD. Subsequent analyses underscore that hydrophobic and van der Waals interactions (predominant), alongside electrostatic energy (subordinate), exert influence over the adsorption of HP35 on the fluorinated graphene surface. Mechanistic scrutiny attests that the unrestrained lateral mobility of HP35 on the fluorinated graphene nanomaterial primarily causes the exposure of HP35's hydrophobic core, resulting in the eventual structural denaturation of HP35. A trend in the features of 2D nanostructures is proposed that may facilitate the denaturation process. Our findings not only substantiate the potential toxicity of fluorinated graphene but also unveil the underlying molecular mechanism, which thereby holds significance for the prospective utilization of such nanomaterials in the field of biomedicine.
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Affiliation(s)
- Fangrong Zou
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), 72570, University City, Puebla, Mexico
| | - Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China.
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Luo Y, Gu Z, Perez-Aguilar JM, Liao W, Huang Y, Luo Y. Moderate binding of villin headpiece protein to C 3N 3 nanosheet reveals the suitable biocompatibility of this nanomaterial. Sci Rep 2023; 13:13783. [PMID: 37612444 PMCID: PMC10447452 DOI: 10.1038/s41598-023-41125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023] Open
Abstract
Since its recent successful synthesis and due to its promising physical and chemical properties, the carbon nitrite nanomaterial, C3N3, has attracted considerable attention in various scientific areas. However, thus far, little effort has been devoted to investigating the structural influence of the direct interaction of this 2D nanomaterial and biomolecules, including proteins and biomembranes so as to understand the physical origin of its bio-effect, particularly from the molecular landscape. Such information is fundamental to correlate to the potential nanotoxicology of the C3N3 nanomaterial. In this work, we explored the potential structural influence of a C3N3 nanosheet on the prototypical globular protein, villin headpiece (HP35) using all-atom molecular dynamics (MD) simulations. We found that HP35 could maintain its native conformations upon adsorption onto the C3N3 nanosheet regardless of the diversity in the binding sites, implying the potential advantage of C3N3 in protecting the biomolecular structure. The adsorption was mediated primarily by vdW interactions. Moreover, once adsorbed on the C3N3 surface, HP35 remains relatively fixed on the nanostructure without a distinct lateral translation, which may aid in keeping the structural integrity of the protein. In addition, the porous topological structure of C3N3 and the special water layer present on the C3N3 holes conjointly contributed to the restricted motion of HP35 via the formation of a high free energy barrier and a steric hindrance to prevent the surface displacement. This work revealed for the first time the potential influence of the 2D C3N3 nanomaterial in the protein structure and provided the corresponding in-depth molecular-level mechanism, which is valuable for future applications of C3N3 in bionanomedicine.
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Affiliation(s)
- Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong, China.
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), 72570, University City, Puebla, Mexico
| | - Weihua Liao
- Department of Radiology, Guangzhou Nansha District Maternal and Child Health Hospital, No. 103, Haibang Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Yiwen Huang
- Department of Emergency, Nansha Hospital, Guangzhou First People's Hospital, Guangzhou, Guangdong, China
| | - Yanbo Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong, China
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Feng Y, Lao J, Zou J, Zhu Z, Li D, Liu G, Mao L. Interaction of Graphitic Carbon Nitride with Cell Membranes: Probing Phospholipid Extraction and Lipid Bilayer Destruction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17663-17673. [PMID: 36456188 DOI: 10.1021/acs.est.2c05560] [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] [Indexed: 06/17/2023]
Abstract
Understanding how nanomaterials interact with cell membranes has important implications for ecotoxicology and human health. Here, we investigated the interactions between graphitic carbon nitride (g-C3N4, CN) and red blood cells, a plausible contact target for nanoparticles when they enter the bloodstream. Through a hemolysis assay, the cytotoxicity of CN derived from different precursors was quantitatively assessed, which is highly related to the surface area of CN. Reactive oxygen species (ROS) generation and lipid peroxidation detection confirmed that CN causes rapid cell membrane rupture by a physical interaction mechanism rather than ROS-related chemical oxidation. Dye leakage assay and theoretical simulation indicated that the less-layered CN is prone to folding inward to wrap and extract lipid molecules from cell membranes. The electron-rich inherent pores of CN play a dominant role in capturing the headgroups of phospholipids, whereas the hydrophobic interaction is critical for the anchoring of lipid tails. Our further experimental evidence demonstrated that the destructive extraction of phospholipids from cell membranes by CN occurs primarily in the outer leaflet, and phosphatidylcholine is the most easily extracted lipid. Moreover, the formation of protein corona on CN was found to decrease the nonspecific interactions but increase steric repulsion, thus mitigating CN cytotoxicity. Overall, our data provide a molecular basis for CN's cytotoxicity.
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Affiliation(s)
- Yiping Feng
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou510006, China
| | - Jiayong Lao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou510006, China
| | - Jiale Zou
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou510006, China
| | - Zhiyu Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing210023, China
| | - Daguang Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou510006, China
| | - Guoguang Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou510006, China
| | - Liang Mao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing210023, China
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Padervand M, Nasiri F, Hajiahmadi S, Bargahi A, Esmaeili S, Amini M, Karimi Nami R, Shahsavari Z, Karima S. Ag@Ag2MoO4 decorated polyoxomolybdate/C3N4 nanostructures as highly efficient photocatalysts for the wastewater treatment and cancer cells killing under visible light. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Mild adsorption of carbon nitride (C 3N 3) nanosheet on a cellular membrane reveals its suitable biocompatibility. Colloids Surf B Biointerfaces 2021; 205:111896. [PMID: 34098364 DOI: 10.1016/j.colsurfb.2021.111896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 11/22/2022]
Abstract
Recently, the novel hole-containing carbon nitride C3N3 nanomaterial was successfully synthesized, featuring outstanding and unique mechanical and electrical properties. However, to fully exploit this nanomaterial in biomedical applications, information regarding its biocompatibility is necessary. Herein, by using all-atom molecular dynamics simulations, we evaluate the interactions between a C3N3 nanosheet and a critical cellular component, that is, a lipid membrane bilayer. Our results indicate that the C3N3 nanosheet is able to interact with the lipid bilayer surface without affecting the membrane's structural integrity. Moreover, our results showed that the C3N3 nanosheet is adsorbed on the surface of the lipid bilayer without inflicting any structural damage to the membrane, regardless of the conditions of the system (that is, with and without restrains in the C3N3 nanosheet). Also, we found that both energy contributions, namely vdW and Coulomb energies, conjointly mediated the C3N3 adsorption process. In comparison and as expected, pristine graphene significantly disturbed the membrane structure. Perpendicularly-oriented-sheet simulations described the significance of the surface charges of the C3N3 nanosheet in prohibiting its insertion into the membrane. Detailed analysis indicated that the electrostatic attraction between the pores in the C3N3 structure and the lipid head amino groups stabilized the interaction restricting the insertion of the C3N3 structure deeper into the membrane. Our results suggested the importance of the negatively charged C3N3 pores when interacting with lipid membranes. Our findings shed light on the potential compatibility of C3N3 with biomembranes and its underlying molecular mechanism, which might provide a useful foundation for the future exploration of this 2D nanomaterial in biomedical applications.
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