Article
Biochemistry & Molecular Biology
Amina Djurabekova, Etienne Galemou Yoga, Aino Nyman, Antti Pirttikoski, Volker Zickermann, Outi Haapanen, Vivek Sharma
Summary: In this study, various methods were used to investigate respiratory complex I in Yarrowia lipolytica. A quinone binding site near the horizontal amphipathic helices of ND1 and NDUFS7 subunits was identified and the binding and dynamics of a quinone molecule at this site were studied. These findings are important for understanding the mechanism of complex I.
Article
Biochemistry & Molecular Biology
Prateek Kumar, Taniya Bhardwaj, Ankur Kumar, Neha Garg, Rajanish Giri
Summary: The study seeks to understand the molecular interactions between hydroxychloroquine and the main protease (Mpro) of SARS-CoV-2 through one-microsecond long molecular dynamics simulations. The analysis shows that hydroxychloroquine binds to the catalytic pocket of Mpro and remains stable for approximately one-third of the simulation time but causes increased fluctuations thereafter. The lack of pre-formed hydrogen bonds or other noncovalent interactions with Mpro suggests instability in binding at the catalytic pocket, indicating that hydroxychloroquine may not inhibit Mpro.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Qin Li, Yongchang Zhu, Xiaoxiao Meng, Henry H. Y. Tong, Huanxiang Liu
Summary: PB2 and PB3 have been found to inhibit PrP aggregation and may serve as potential therapeutic agents for prion diseases. PB2 stabilizes the protein through salt bridges, while PB3 prevents dimerization of PrP. These findings provide valuable insights for drug development against prion diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Min-Kang Hsieh, Yalun Yu, Jeffery B. Klauda
Summary: This article discusses the modeling of complex cellular membranes using all-atom force fields, focusing on the CHARMM36 lipid force field and its update. By incorporating long-range dispersion, the models can better reflect the structural, mechanical, and dynamic properties of realistic membranes, allowing for the study of biological processes involving other molecules.
Article
Engineering, Chemical
Rui Cui, Shanlong Li, Chunyang Yu, Yuling Wang, Yongfeng Zhou
Summary: This study used molecular dynamics simulations to investigate the effect of water content and equivalent weight on the diffusion of nitrogen molecules in PFSA hydrated membranes, revealing different behaviors of nitrogen molecules under different conditions, providing a fundamental understanding of nitrogen transport in PFSA hydrated membranes.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xueting Cao, Xiao Yang, Min Xiao, Xukai Jiang
Summary: By conducting all-atom molecular dynamics simulations, we observed significant conformational transitions in several sialidases in the Glycoside Hydrolase family 33 (GH33). These sialidases formed a new cleft adjacent to the active site, which plays a crucial role in accommodating the glycosyl acceptor. Additionally, the residues involved in substrate-specific interactions were conserved in the whole GH33 family, highlighting their importance in catalysis. Our findings contribute to a better understanding of the catalytic mechanism of GH33 sialidases and have potential implications in the rational design of sialidases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Bin Ma, Chen Chen, Zi-Xian Du, Li Zhang
Summary: In this study, PIM-1 membranes were prepared using a 21-step method via molecular dynamics simulations. The structure and separation performance of these membranes for CO2/N2 mixture were explored. The results revealed that the permeation behavior of CO2/N2 mixture through PIM-1 membrane is dominated by solubility, and the cyano group and terminal hydroxyl groups in the PIM1 chain play important roles in gas adsorption and permeation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Zhiyi Wu, Philip C. Biggin
Summary: Absolute binding free-energy calculations play a crucial role in drug design, but accuracy is of utmost importance. This study explores the most suitable approach for simulation boxes containing lipid bilayers, and introduces the Rocklin correction method for lipid bilayer systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Engineering, Chemical
Jianjun Jiang, Lei Fang, Zhijing Huang, Liang Chen, Yusong Tu, Zonglin Gu
Summary: The interlayer spacing of graphene oxide (GO) membranes can be controlled by cations, but the specific role of anions in treating GO membranes has not been reported. This study reveals that anions can also stabilize the interlayer spacing of GO membranes through the formation of ion bridges. The ion bridges greatly enhance the interaction between neighboring GO sheets, providing a new approach for the design of membrane materials.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Dong Fan, Aydin Ozcan, Naseem A. Ramsahye, Dan Zhao, Guillaume Maurin, Rocio Semino
Summary: The study challenges the assumption that avoiding interfacial porosity is always necessary for high gas-separation performance in MOF/polymer mixed matrix membranes. By investigating the NUS-8/PIM-1 MMM, researchers found that microvoids at the interface can actually enhance CO2 interactions and improve selectivity, leading to a new solubility-driven separation mechanism. This discovery has the potential to change current paradigms and pave the way for more efficient gas separation membranes.
ACS MATERIALS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Tingting Xu, Bin Wu, Linxiao Hou, Yanran Zhu, Fangmeng Sheng, Zhang Zhao, Yun Dong, Jiandang Liu, Bangjiao Ye, Xingya Li, Liang Ge, Huanting Wang, Tongwen Xu
Summary: This study reports porous organic cage membranes with hierarchical channels, which can selectively separate monovalent ions from divalent ions. The dual nanometer-sized cavities provide pathways for fast ion transport with high ion permselectivity. Molecular dynamics simulations illustrate the ion transport trajectory and offer guidelines for developing efficient ion separation membranes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Polymer Science
Vladimir Yu V. Rudyak, Artem S. Sergeev, Elena Yu E. Kozhunova, Vyacheslav V. Molchanov, Olga Philippova, Alexander Chertovich
Summary: In this work, the viscosities of randomly cross-linked microgels were studied using computer simulations methods. It was found that the cross-linking density and particle shape play crucial roles in the shear viscosity of microgels. Additionally, microgel dispersions in good solvent show less shear thinning compared to simpler polymer systems.
Article
Biophysics
Martin Girard, Tristan Bereau
Summary: The plasma membrane of eukaryotes exhibits lipid asymmetry, with different lipids primarily located in different leaflets. Using computational simulations, it has been found that saturation asymmetry arises as a result of phospholipid number asymmetry and sphingomyelin contents. This suggests that some asymmetries in lipid composition may naturally result from others and do not require external factors. The asymmetry of cholesterol, on the other hand, is fairly mild and influenced by all the other asymmetries.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Wanhao Cai, Miriam Jaeger, Jakob T. Bullerjahn, Thorsten Hugel, Steffen Wolf, Bizan N. Balzer
Summary: In this study, the rupture force and friction of the biotin-streptavidin complex under a externally applied force were investigated using AFM-based single molecule force spectroscopy and molecular dynamics simulations. Anisotropic friction, arising from an experimentally uncontrolled orientation parameter, was identified. The study suggests that anisotropic friction should be taken into account for a complete understanding of friction in biomolecular dynamics and anisotropic mechanical environments.
Article
Biochemistry & Molecular Biology
Alexandre Blanco-Gonzalez, Angel Pineiro, Rebeca Garcia-Fandino
Summary: This article discusses the hierarchical structure of membrane models and defines different levels of structure. By analyzing lipid composition, interaction between layers, the existence and interaction of domains caused by lipid behavior, and the perturbation of lipid organization around macromolecules embedded in the membrane, primary, secondary, tertiary, and quaternary structures are defined respectively. Molecular Dynamics simulations are used to support this proposal.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)