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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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Saeki Y, Kayanuma M, Nitta A, Shigeta Y, Kawamura I, Nakagawa T, Ubukata T, Yokoyama Y. On-Demand Chirality Transfer of Human Serum Albumin to Bis(thiophen-2-yl)hexafluorocyclopentenes through Their Photochromic Ring Closure. J Org Chem 2021; 86:12549-12558. [PMID: 34324316 DOI: 10.1021/acs.joc.1c00849] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photochromic 1,2-bis(5-carboxy-3-methyl-2-thienyl)hexafluorocyclopentene and its dimethyl ester incorporated in human serum albumin (HSA) showed highly enantioselective photochromic ring-closing reactions upon 366 nm light irradiation. The absolute stereochemistry of the major ring-closed form of the dicarboxylic acid at the newly formed sp3 carbon atoms was determined to be (S,S) by the process of docking simulation of the diarylethene molecule and HSA followed by molecular dynamics calculations and comparison of the measured and calculated CD spectra. Esterification of the major closed form of the diacid gave the minor closed form of the diester. The absolute stereochemistry of the major diester was thus determined to be (R,R).
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Affiliation(s)
- Yuri Saeki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Aki Nitta
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Izuru Kawamura
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Tetsuya Nakagawa
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Takashi Ubukata
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Yasushi Yokoyama
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5, Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
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Gorman SD, D'Amico RN, Winston DS, Boehr DD. Engineering Allostery into Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:359-384. [PMID: 31707711 PMCID: PMC7508002 DOI: 10.1007/978-981-13-8719-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Our ability to engineer protein structure and function has grown dramatically over recent years. Perhaps the next level in protein design is to develop proteins whose function can be regulated in response to various stimuli, including ligand binding, pH changes, and light. Endeavors toward these goals have tested and expanded on our understanding of protein function and allosteric regulation. In this chapter, we provide examples from different methods for developing new allosterically regulated proteins. These methods range from whole insertion of regulatory domains into new host proteins, to covalent attachment of photoswitches to generate light-responsive proteins, and to targeted changes to specific amino acid residues, especially to residues identified to be important for relaying allosteric information across the protein framework. Many of the examples we discuss have already found practical use in medical and biotechnology applications.
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Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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