Application of computational approaches in biomembranes: From structure to function

被引:7
作者
Guo, Jingjing [1 ,2 ,8 ]
Bao, Yiqiong [3 ]
Li, Mengrong [4 ]
Li, Shu [1 ]
Xi, Lili [4 ]
Xin, Pengyang [5 ]
Wu, Lei [6 ]
Liu, Huanxiang [1 ]
Mu, Yuguang [7 ]
机构
[1] Macao Polytech Univ, Fac Appl Sci, Ctr Artificial Intelligence Driven Drug Discovery, Macau, Peoples R China
[2] Macao Polytech Univ, Engn Res Ctr Appl Technol Machine Translat & Artif, Macau, Peoples R China
[3] Nanjing Agr Univ, Coll Life Sci, Nanjing, Peoples R China
[4] Lanzhou Univ, Hosp 1, Off Inst Drug Clin Trial, Lanzhou, Peoples R China
[5] Henan Normal Univ, Sch Chem & Chem Engn, Pingyuan Lab, NMPA Nat Med Prod Adm,Key Lab Res & Evaluat Innova, Xinxiang, Peoples R China
[6] China Univ Petr East China, Sch Petr Engn, Qingdao, Peoples R China
[7] Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore
[8] Macao Polytech Univ, Fac Appl Sci, Ctr Artificial Intelligence Driven Drug Discovery, Macau 999078, Peoples R China
基金
中国国家自然科学基金;
关键词
biological membranes; lipids; membrane proteins; molecular dynamics simulation; molecular modeling; MOLECULAR-DYNAMICS SIMULATIONS; BIOMOLECULAR FORCE-FIELD; GUI MEMBRANE-BUILDER; COARSE-GRAINED MODEL; FLUID-MOSAIC MODEL; LIPID-MEMBRANE; UNITED-ATOM; PHOSPHATIDYLCHOLINE MEMBRANES; GOLD NANOPARTICLES; ENERGY FUNCTION;
D O I
10.1002/wcms.1679
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Biological membranes (biomembranes) are one of the most complicated structures that allow life to exist. Investigating their structure, dynamics, and function is crucial for advancing our knowledge of cellular mechanisms and developing novel therapeutic strategies. However, experimental investigation of many biomembrane phenomena is challenging due to their compositional and structural complexity, as well as the inherently multi-scalar features. Computational approaches, particularly molecular dynamics (MD) simulations, have emerged as powerful tools for addressing the atomic details of biomembrane systems, driving breakthroughs in our understanding of biomembranes and their roles in cellular function. This review presents an overview of the latest advancements in related computational approaches, from force fields and model construction to MD simulations and trajectory analysis. We also discussed current hot research topics and challenges. Finally, we outline future directions, emphasizing the integration of force field development, enhanced sampling techniques, and data-driven approaches to accelerate the growth of this field in the years to come. We aim to equip readers with an understanding of the promise and limitations of emerging computational technologies in biomembrane systems and offer valuable recommendations for future research endeavors.This article is categorized under:Structure and Mechanism > Computational Biochemistry and BiophysicsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
引用
收藏
页数:34
相关论文
共 50 条
[31]   Insights into hERG K+ channel structure and function from NMR studies [J].
Ng, Chai Ann ;
Torres, Allan M. ;
Pages, Guilhem ;
Kuchel, Philip W. ;
Vandenberg, Jamie I. .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2013, 42 (01) :71-79
[32]   From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity [J].
Rossetti, Paolo ;
Trollmann, Marius F. W. ;
Wichmann, Christina ;
Gutsmann, Thomas ;
Eggeling, Christian ;
Bockmann, Rainer A. .
SMALL, 2025,
[33]   From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis [J].
Ghosh, Pooja ;
Kundu, Agnibin ;
Ganguly, Debabani .
JOURNAL OF MATERIALS CHEMISTRY B, 2025, 13 (03) :858-881
[34]   Targeting Chikungunya virus by computational approaches: from viral biology to the development of therapeutic strategies [J].
Rabelo, Vitor Won-Held ;
Nunes de Palmer Paixao, Izabel Christina ;
Abreu, Paula Alvarez .
EXPERT OPINION ON THERAPEUTIC TARGETS, 2020, 24 (01) :63-78
[35]   Biochemical and biophysical approaches to study the structure and function of the chloride channel (ClC) family of proteins [J].
Abeyrathne, Priyanka D. ;
Chami, Mohamed ;
Stahlberg, Henning .
BIOCHIMIE, 2016, 128 :154-162
[36]   Theoretical and computational approaches to predicting the viscosity of liquids [J].
Kondratyuk, N. D. ;
Pisarev, V. V. .
PHYSICS-USPEKHI, 2023, 66 (04) :410-432
[37]   Computational approaches in modeling spectra of biological chromophores [J].
Nemukhin, Alexander V. ;
Grigorenko, Bella L. ;
Bochenkova, Anastasia V. ;
Bravaya, Ksenia B. ;
Savitsky, Alexander P. .
SMALL ANIMAL WHOLE-BODY OPTICAL IMAGING BASED ON GENETICALLY ENGINEERED PROBES, 2008, 6868
[38]   Computational approaches to understanding protein aggregation in neurodegeneration [J].
Redler, Rachel L. ;
Shirvanyants, David ;
Dagliyan, Onur ;
Ding, Feng ;
Kim, Doo Nam ;
Kota, Pradeep ;
Proctor, Elizabeth A. ;
Ramachandran, Srinivas ;
Tandon, Arpit ;
Dokholyan, Nikolay V. .
JOURNAL OF MOLECULAR CELL BIOLOGY, 2014, 6 (02) :104-115
[39]   From sequence to structure to function: a case study [J].
Douguet, D ;
Bolla, JM ;
Munier-Lehmann, H ;
Labesse, G .
ENZYME AND MICROBIAL TECHNOLOGY, 2002, 30 (03) :289-294
[40]   Neuroglobin: From structure to function in health and disease [J].
Ascenzi, Paolo ;
di Masi, Alessandra ;
Leboffe, Loris ;
Fiocchetti, Marco ;
Nuzzo, Maria Teresa ;
Brunori, Maurizio ;
Marino, Maria .
MOLECULAR ASPECTS OF MEDICINE, 2016, 52 :1-48