Review
Chemistry, Multidisciplinary
Miguel Paez-Perez, Marina K. Kuimova
Summary: This review discusses the principles and advances in the use of fluorescent molecular probes known as molecular rotors for exploring viscosity, crowding, and molecular interactions in biological environments. These probes have been employed as sensors for lipid order, protein crowding, temperature, and non-canonical nucleic acid structures in live cells and other relevant settings.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Emanuele Petretto, Quy K. Ong, Francesca Olgiati, Ting Mao, Pablo Campomanes, Francesco Stellacci, Stefano Vanni
Summary: Monolayer-protected metal nanoparticles have potential applications in industry and biology, and can be used to study the behavior of matter at nanoscopic scales. This study reveals that electrostatic interactions can lead to the formation of NP dimers at physiological ion concentrations.
Article
Biochemical Research Methods
Martin Kern, Sabrina Jaeger-Honz, Falk Schreiber, Bjorn Sommer
Summary: Molecular dynamics simulations provide insights into complex processes in cell membranes, and APL@Voro is a software that allows for interactive visualization and analysis of these simulations. It offers newly implemented algorithms and features to explore cell membrane compositions and dynamics.
Article
Chemistry, Physical
Majid Jafari, Faramarz Mehrnejad, Reza Talandashti, Farahnoosh Doustdar, Mohammad Reza Vakili, Afsaneh Lavasanifar
Summary: This study simulated 15 molecular systems to characterize the interactions between PAMAM dendrimers and membranes with different cholesterol ratios, explaining the structural features and geometry of their activity against cancer cells. The results demonstrated that cholesterol content in the membranes influenced the local membrane order parameters, and the dendrimers were able to create holes in cholesterol-containing membranes through hydrogen bonds and electrostatic interactions. Additionally, negatively charged phospholipids in cancer cell membranes played a crucial role in binding with the dendrimers, providing mechanistic insight into their activity against cancer cells.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Medicinal
Barbara Mavroidi, Archontia Kaminari, Elias Sakellis, Zili Sideratou, Dimitris Tsiourvas
Summary: This study investigated the effect of carbon dots on a model cell membrane. The results showed that carbon dots interact with liposomes, affecting the structure and thermodynamic properties of the bilayer. Furthermore, carbon dots increased the membrane's permeability to the anticancer drug doxorubicin.
Article
Biochemistry & Molecular Biology
Loretta Akakpo, Edward Ntim Gasu, Jehoshaphat Oppong Mensah, Lawrence Sheringham Borquaye
Summary: This study used molecular docking and molecular dynamics simulations to explore the inhibitory activity of some natural products against Plasmodium falciparum dihydrofolate reductase (PfDHFR). Two compounds were found to have stable binding and could be considered as potential antifolate agents.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Medicine, Research & Experimental
Jia Gu, Ya-Ning Shi, Neng Zhu, Hong-Fang Li, Chan-Juan Zhang, Li Qin
Summary: Lipid metabolism disorders play a crucial role in the development of various lipid-related diseases. Celastrol, extracted from the Chinese herb Tripterygium wilfordii Hook F, has shown promising therapeutic effects for these diseases. It can ameliorate lipid metabolism disorders by regulating lipid profiles and related processes. This review provides an overview of celastrol's lipid-regulating properties and its underlying molecular mechanisms, as well as suggesting potential strategies for enhancing its effects and overcoming limitations in clinical applications.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Chemistry, Physical
Fikret Aydin, Aleksander E. P. Durumeric, Gabriel C. A. da Hora, John D. M. Nguyen, Myong In Oh, Jessica M. J. Swanson
Summary: This study investigates the permeation mechanism of a drug molecule through a multicomponent membrane using molecular dynamics simulations and transition-tempered metadynamics. The use of collective variables obtained from an unsupervised machine learning algorithm improves performance and accelerates convergence of permeation potential calculations. The addition of cholesterol to the lipid bilayer increases the width and height of the free energy barrier, while also affecting the resistance to permeation in the lipid head group region.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Ji Min Baek, Woo Hyuk Jung, Eui-Sang Yu, Dong June Ahn, Yong -Sang Ryu
Summary: Passive water penetration across the cell membrane is essential for cell volume homeostasis. By studying cholesterol-enriched lipid rafts, we confirmed the suppressed water permeation and the biological role of lipid composition in water translocation. Molecular dynamics simulations also demonstrated improved membrane stability under hypertonic conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Le Luo, Swathi Manda, Yunjeong Park, Busra Demir, Jesse Sanchez, M. P. Anantram, Ersin Emre Oren, Ashwin Gopinath, Marco Rolandi
Summary: This study presents the integration of DNA nanopores with bioprotonic contacts to create programmable and efficient artificial ion-channel interfaces. This robust interface allows for electronic recognition and quantification of biomolecular signals.
NATURE COMMUNICATIONS
(2023)
Review
Nutrition & Dietetics
Yoshimi Nakagawa, Masaya Araki, Song-iee Han, Yuhei Mizunoe, Hitoshi Shimano
Summary: CREBH is a membrane-bound transcriptional factor expressed in the liver and small intestine, regulating triglyceride metabolism and controlled by circadian rhythm. Deficiency leads to hypertriglyceridemia and fatty liver, while knock out mice exhibit severe atherosclerosis, indicating the crucial role of CREBH in systemic lipid homeostasis.
Review
Physiology
Richa Aishwarya, Chowdhury S. Abdullah, Mahboob Morshed, Naznin Sultana Remex, Md Shenuarin Bhuiyan
Summary: The Sigma 1 receptor is a multifunctional inter-organelle signaling protein with a diverse role in cellular survival, and mutations in Sigmar1 have been linked to various diseases. Changes in Sigmar1's subcellular localization, expression, and signaling are associated with the progression of diseases such as neurodegenerative diseases and cardiovascular diseases.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Chemistry, Physical
Itay Schachter, Riku O. Paananen, Balazs Fabian, Piotr Jurkiewicz, Matti Javanainen
Summary: Through atomistic molecular dynamics simulations, differential scanning calorimetry, and fluorescence spectroscopy on L-o phase membranes, it was found that a stiff, hexagonally packed lipid structure in the L-o phase at room temperature excludes raft-associated proteins, but upon heating, this structure melts, leading to preferential solvation of proteins by order-preferring lipids.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Suchanda Dey, Madhusmita Rout, Sanghamitra Pati, Mahender Kumar Singh, Budheswar Dehury, Enketeswara Subudhi
Summary: In this study, the structure-function mechanism of the Small Multidrug Resistance efflux pump protein KpnE was elucidated, and potential inhibitors were identified through molecular dynamics simulations. The study identified semi-open and open conformations of KpnE, and highlighted the similarity between KpnE and EmrE in the binding cleft. Key amino acids Glu14, Trp63, and Tyr44 were found to be important for ligand recognition, and potential inhibitors like acarbose, rutin, and labetalol were recognized through molecular docking and binding free energy calculations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Food Science & Technology
Natalia Kuzmina, Pavel Volynsky, Ivan Boldyrev, Anna Alekseeva
Summary: Bee venom PLA2 exhibits two additional interface binding modes and enzyme activity through constant switching between different orientations. This switching has biological significance in terms of enzyme movement along the membrane, product release in a biological milieu, and enzyme desorption from the bilayer surface.
Article
Chemistry, Physical
Jingxin Shao, Caixia Wen, Mingjun Xuan, Hongyue Zhang, Johannes Frueh, Mingwei Wan, Lianghui Gao, Qiang He
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Multidisciplinary Sciences
Mingwei Wan, Lianghui Gao, Weihai Fang
Article
Biophysics
Yu Shi, Mingwei Wan, Lei Fu, Shan Zhang, Shiyuan Wang, Lianghui Gao, Weihai Fang
BIOPHYSICAL JOURNAL
(2018)
Article
Chemistry, Multidisciplinary
Shan Zhang, Lei Fu, Mingwei Wan, Junjie Song, Lianghui Gao, Weihai Fang
Article
Biophysics
Lei Fu, Mingwei Wan, Shan Zhang, Lianghui Gao, Weihai Fang
BIOPHYSICAL JOURNAL
(2020)
Article
Chemistry, Multidisciplinary
Mingwei Wan, Junjie Song, Wenli Li, Lianghui Gao, Weihai Fang
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Shan Zhang, Ming Ma, Zhuang Shao, Jincheng Zhang, Lei Fu, Xiangyuan Li, Weihai Fang, Lianghui Gao
Summary: Temporins are a family of antimicrobial peptides isolated from frog skin, which are very short, weakly charged, and highly hydrophobic. They execute bactericidal activities by folding into α-helices at the membrane surface, extracting lipids, and forming protrusions at high peptide concentrations. These unique antimicrobial mechanisms include lipid extraction and tubule-like protrusion formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biophysics
Lei Fu, Xiangyuan Li, Shan Zhang, Yi Dong, Weihai Fang, Lianghui Gao
Summary: By using molecular dynamics simulations, this study reveals that polymyxin B disrupts lipid homeostasis in bacterial membranes, proposing a lipid Scramble, membrane phase Separation, and peptide Translocation model. This novel mechanism sheds light on developing potent therapeutic agents targeting bacteria.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Yi Dong, Lei Fu, Junjie Song, Shan Zhang, Xiangyuan Li, Weihai Fang, Qiang Cui, Lianghui Gao
Summary: The study revealed that calcium ions have the highest binding affinity to a zwitterionic phospholipid bilayer, while magnesium and zinc ions' binding processes are exothermic and less preferred. Calcium ions release coordinated water upon binding, with less influence; while magnesium and zinc ions remain fully hydrated when interacting with lipids, making binding less favorable.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Junjie Song, Ming Ma, Yi Dong, Mingwei Wan, Weihai Fang, Lianghui Gao
Summary: A new coarse-grained force field for PEO and PEG aqueous solutions is developed based on a polarizable CG water model. The force field parameters are optimized to match multiple thermodynamic properties using a meta-multilinear interpolation parameterization algorithm. The accuracy and transferability of the force field are tested by predicting various thermodynamic and structural properties of longer PEO and PEG polymer aqueous solutions. The presented optimization algorithm and strategy can be extended to more complex polyelectrolytes and surfactants based on the CG water model.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Xiangyuan Li, Lei Fu, Shan Zhang, Yipeng Wang, Lianghui Gao
Summary: This study used molecular dynamics simulations to evaluate the damaging effects of sequence-truncated and residue-substituted variants of Alligator sinensis cathelicidins on the membranes of Gram-negative bacteria. The simulations predicted that these variants can disrupt the structures of the inner membrane of Gram-negative bacteria, but not the outer membrane. AS4-9, in particular, showed the highest antibacterial activity and was able to extract lipids from the membrane. These findings have the potential to inspire the development of potent therapeutic agents targeting bacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Ming Ma, Junjie Song, Yi Dong, Weihai Fang, Lianghui Gao
Summary: In this study, a novel coarse-grained force field was developed to reproduce the structural and thermodynamic properties of triglycerides in bulk phase, as well as at air and water interfaces. The force field accurately reproduced the self-assembled network and diverse molecular conformations of triglycerides in water, and correctly predicted experimental macroscopic thermodynamic properties. This work paves the way for studying complex systems involving triglycerides on a larger scale.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Mingwei Wan, Junjie Song, Ying Yang, Lianghui Gao, Weihai Fang
Summary: This study proposes a combined strategy to parameterize the self- and cross-termed interactions of zwitterionic phospholipids in water solution through a piecewise Morse potential. The self-interacting force parameters were optimized by matching experimental data, while the cross-termed interactions were optimized by fitting pseudo properties obtained from atomistic simulations. The proposed coarse-grained force field shows good accuracy and transferability in predicting the structural and thermodynamic properties of lipid membranes, as well as the vesicle self-assembly and fusion processes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Junjie Song, Mingwei Wan, Ying Yang, Lianghui Gao, Weihai Fang
Summary: This study introduces an indirect parametrization strategy for weakly polar groups by mapping them into CG beads connected to alkyl beads, avoiding freezing issue. The method shows satisfactory accuracy in predicting various properties of homologs of polar molecules and indicates transferability for fatty acid methyl esters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Mingwei Wan, Junjie Song, Ying Yang, Lianghui Gao, Weihai Fang
Summary: The Meta-MIP algorithm developed in this work significantly improves the parameterization efficiency of CG force fields for alcohols, predicting properties with less than 7% deviation from experimental values. By mapping alcohol molecules to a heterologous model, the algorithm successfully addresses the issues of low parameterization efficiency and poor accuracy.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
