Article
Chemistry, Medicinal
Ruirui Liu, Honglin Zhai, Yajie Meng, Min Zhu, Tao Wen, Nengzhi Jin
Summary: This study investigates the biological properties of three representative 2D nanomaterials using molecular dynamics simulations. The results suggest that C2N may have better biocompatibility compared to BP and GR. Additionally, the BBA protein exhibits biological behaviors consistent with the alpha-helix and beta-sheet motifs on BP and C2N surfaces.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Carlos A. H. Fernandes, Dania Zuniga, Charline Fagnen, Valerie Kugler, Rosa Scala, Gerard Pehau-Arnaudet, Renaud Wagner, David Perahia, Said Bendahhou, Catherine Venien-Bryan
Summary: This study revealed the unique structural features of human Kir2.1 channels, as well as the connection between the G-loop and gating, shedding light on the pathological mechanisms associated with this channel.
Article
Chemistry, Multidisciplinary
Janske Nel, David Siniscalco, Cecilia Hognon, Mathilde Bouche, Nadege Touche, Emilie Brunner, Philippe C. Gros, Antonio Monari, Stephanie Grandemange, Gregory Francius
Summary: This study characterized the effects of iron-based complexes on the structural and morphological properties of breast cell lines. The complexes caused cell softening, increased size, and subsequent re-stiffening. They also induced cytoskeletal and mitochondrial reorganization. Molecular dynamic simulation suggested direct internalization of the complexes and demonstrated that their effects were not solely due to physical interaction with the cell membrane.
Article
Biology
Wenxin Hu, Hongjin Zheng
Summary: Wenxin Hu et al. used cryo-EM and biochemical assays to describe the functional activity and structure of the ferrichrome importer, FhuCDB in E. coli. Their results reveal a new structural twist in the type II ABC importer subfamily and provide biological insights in the transport of iron-chelated siderophores.
COMMUNICATIONS BIOLOGY
(2021)
Article
Engineering, Chemical
Jiayang Lin, Yue Liu, Shen Hu, Yifan Zhang, Cheng Qian, Aimin Li, Shupeng Zhang
Summary: This study utilized organic covalent bonds, supramolecular self-assembly, and soft chemistry to construct a magnetically separable ethanolamine-functionalized graphene adsorption material for rapid removal of organic pollutants, demonstrating high adsorption efficiency.
SEPARATION AND PURIFICATION TECHNOLOGY
(2021)
Article
Chemistry, Physical
Kai Chen, Zhijun Xu, Xiaoning Yang
Summary: This study investigates the adsorption behavior of amphiphilic monolayer graphene oxides (GOs) at oil-water interfaces using molecular dynamics simulations, and reveals the correlation between the adsorption structures and chemical compositions of GOs. The results provide new insights into the molecular arrangement and packing of GOs at interfaces, which can guide the preparation of GO-related materials and micro-emulsification processes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Analytical
Hum Bahadur Lamichhane, Terence G. Henares, Mark J. Hackett, Damien W. M. Arrigan
Summary: Understanding protein interactions at interfaces, particularly using experimental methods such as ITIES, can provide insights into how protein structure is influenced by interactions at interfaces. In this study, the destabilization of native insulin secondary structure and the promotion of helix secondary structures at interfaces were found to be driven by protein-interface interactions, highlighting the potential of ITIES as a tool for studying protein structure and interactions.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Na Li, Shimeng Yu, Jiyuan Fang, Yanfei Yu, Ping Jiang, Shaoyun Pu, Wei Wang
Summary: In this study, the adsorption effect of illite as an adsorbent for graphene oxide (GO) was investigated using adsorption tests and various characterization methods. The results showed that illite had excellent adsorption properties for GO under specific conditions, and the adsorption process was a spontaneous endothermic reaction.
APPLIED CLAY SCIENCE
(2022)
Article
Engineering, Environmental
Binbin Sun, Yinqing Zhang, Xinwei Liu, Kunkun Wang, Yi Yang, Lingyan Zhu
Summary: This study systematically investigated the interactions between photoaged graphene oxide (GO) and proteins. The results showed that photoaged GO had stronger binding affinities with proteins, causing more significant changes in the conformational structure and stronger inhibition on fibrillation of proteins. This study provided new insights into the increased ecological risks of photoaged GO.
Review
Biochemistry & Molecular Biology
Janis Hoetzel, Beatrix Suess
Summary: Synthetic riboswitches, which consolidate sensing and execution functions in a single RNA molecule, are powerful tools in synthetic biology. However, there is a scarcity of in vitro selected aptamers suitable for engineering synthetic riboswitches. Studies have shown that the key characteristics of regulatory active RNAs, such as structural switching abilities and binding dynamics, are insufficiently represented in conventional SELEX approaches. This review proposes a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied in synthetic riboswitch engineering.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Engineering, Chemical
Wenting Zhou, Wenxiang Zhang, Yanpeng Cai
Summary: This study investigates the water purification performance of laccase immobilized graphene oxide (Lac-GO) and explores the mechanism of enzyme-enhanced adsorption. The results show that laccase immobilization does not affect the adsorption behavior of graphene oxide, but the enzyme-enhanced adsorption process exhibits higher adsorption capacity and rate due to the enzymatic degradation of adsorbed micro-pollutants. Furthermore, the study reveals a clear synergy mechanism between adsorption and enzymatic degradation, leading to improved micro-pollutant removal.
SEPARATION AND PURIFICATION TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Lili Guo, Jing Zhao, Zongfu An, Sieun Kim, Jaekwang Kim, Yeseul Yu, Anton Middelberg, Jingxiu Bi, Marijana Markovic, Jung Kyu Kim, Pil J. Yoo, Woo-Seok Choe
Summary: This study presents a novel protein refolding sensor that uses liquid crystals to analyze the structural changes of proteins during unfolding and refolding. The sensor can discriminate different protein structures by measuring the brightness of polarized optical microscope images. This LC-based sensor is compatible with various refolding conditions and enables real-time analysis of protein refolding, making it a valuable tool for studying protein refolding processes.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Marcos Nieves, Alejandro Buschiazzo, Felipe Trajtenberg
Summary: All living organisms possess signaling devices for perceiving and adapting to the changing environment. Two-component systems play a role in regulating genetic and biochemical programs in response to specific signals. Recent advances in our molecular understanding of these systems have opened up possibilities for developing synthetic networks and biocomputing systems. This review focuses on the structural perspective of utilizing sensor and effector protein modules in two-component systems to construct new synthetic circuits.
BIOCHEMICAL JOURNAL
(2023)
Article
Environmental Sciences
Xiaoxia Yang, Chao Yu, Butera Hassan, Lun Zhang, Changkai Wang, Huan He, Bin Huang, Xuejun Pan
Summary: This study investigates the pyrolytic mechanism of starch, protein, and lipid in the presence of CaO, finding that CaO catalytically lowers the pyrolysis temperature, promotes the conversion into small molecules, and increases syngas production. The combination of char with the carbonation and calcination cycle of CaO also significantly boosts syngas yield and selectivity. The findings provide valuable insights for predicting the pyrolysis behavior of sewage sludge and syngas production in industrial applications.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Xiangzhe Jiang, Wei Wang, Gang Yu, Shubo Deng
Summary: In this study, the contribution of nanobubbles for PFAS adsorption on pristine and functionalized graphene was investigated using density functional theory and molecular dynamics simulations. It was found that nanobubbles played a significant role in the adsorption mechanisms of PFAS on different graphene surfaces, with a greater impact on long-chain PFAS.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Pengyang Xin, Linqi Xu, Wenpei Dong, Linlin Mao, Jingjing Guo, Jingjing Bi, Shouwei Zhang, Yan Pei, Chang-Po Chen
Summary: In this study, novel artificial K+ channels were developed by rebuilding the core modules of natural K+ channels in artificial systems. These channels exhibited high selectivity for K+ over Na+ and showed a selectivity sequence of K+≈Rb+ during the transport process, which is consistent with the cation permeability characteristics of natural K+ channels. Moreover, these artificial channels could efficiently insert into cell membranes, mediate K+ transmembrane transport, disrupt cellular K+ homeostasis, and trigger cell apoptosis. These findings demonstrate that the structures, transport behaviors, and physiological functions of natural K+ channels can be mimicked in synthetic channels by rebuilding their core modules in artificial systems.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
Summary: This study evaluated the impact of structural dynamic information on binding affinity prediction and found that the optimized molecular dynamics protocol improved the predictive performance for the TAF1-BD2 target with high structural flexibility, but not for the less flexible JAK1 and DDR1 targets.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Mengrong Li, Yiqiong Bao, Miaomiao Li, Jingjing Guo
Summary: G protein-coupled receptors (GPCRs), as a large superfamily of cell-surface proteins, play crucial roles in cell signaling and regulate various physiological and pathological processes, making them an important source of drug targets. However, due to the challenging dynamic structures of GPCRs, only a few allosteric ligands have been approved as drugs. Fortunately, the development of computational biology provides insights into the mechanism of GPCR allosteric ligands, which is vital for the discovery of new therapeutic agents. This article provides a comprehensive overview of the resources and approaches in computational biology related to GPCR allostery and conformational dynamics, as well as the current limitations and challenges in the field.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Cell Biology
Mengrong Li, Yiqiong Bao, Ran Xu, Miaomiao Li, Lili Xi, Jingjing Guo
Summary: The identification and development of non-peptide allosteric modulators for PTH1R have gained attention. It has been found that a negative allosteric modulator (NAM) inhibits the activation of PTH1R, but the mechanism is unclear. Molecular dynamics simulations and analytical approaches reveal that NAM destabilizes the PTH1R-PTH-spep/qpep complexes, weakens PTH/peps-PTH1R binding, and reduces intra- and inter-molecular couplings in PTH1R. Compared with positive allosteric effects induced by extracellular Ca2+, the negative allosteric regulator significantly reduces the correlation between PTH and G-protein binding sites. These findings contribute to the development of new therapeutics for diseases caused by PTH1R abnormal activation.
Article
Chemistry, Physical
Wen Xi, Youfang Zhang, Rui Wang, Yansheng Gong, Beibei He, Huanwen Wang, Jingjing Guo, Fangfang Jiao, Jun Jin
Summary: 2D MXene sheets are considered promising capacitive deionization (CDI) electrodes due to their high conductivity, hydrophilic surface, excellent adsorption capacity, and reversible intercalation of metal cations. The CDI behavior of Ti3C2Tx MXene has been comprehensively investigated using a symmetrical device. The effect of electrode thickness and electrode/electrolyte on the CDI behavior of the Ti3C2Tx MXene electrodes is deeply explored. The optimized MXene||MXene CDI device with an electrode thickness of 18.41 μm exhibits a high salt removal capacity of 100.9 mg g-1 in NaCl solution at 1.2 V. (c) 2023 Published by Elsevier B.V.
JOURNAL OF ALLOYS AND COMPOUNDS
(2023)
Article
Biochemistry & Molecular Biology
Syed Jawad Ali Shah, Qianqian Zhang, Jingjing Guo, Hongli Liu, Huanxiang Liu, Jordi Villa-Freixa
Summary: The microtubule-associated protein tau plays a critical role in the development and protection of the nervous system. Dysfunction and accumulation of tau in the brain can lead to various neurodegenerative diseases. This study reveals the detailed mechanism of acetylation-driven tau aggregation.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Shuoyan Tan, Jun Wang, Peng Gao, Guotong Xie, Qianqian Zhang, Huanxiang Liu, Xiaojun Yao
Summary: Understanding the selectivity mechanisms of inhibitors for highly similar proteins is crucial in new drug discovery. Developing highly selective targeting of leucine-rich repeat kinase 2 (LRRK2) kinases for Parkinson's disease is challenging due to the similarity of the kinase ATP binding pocket. In this study, computational methods and comprehensive analyses were conducted to investigate the selectivity mechanisms of two representative LRRK2 inhibitors (DNL201 and GNE7915). The results suggest that structural and kinetic differences between the proteins may play a key role in determining the activity of selective small-molecule inhibitors. The proposed selectivity mechanisms could aid in the rational design of novel LRRK2 kinase inhibitors for Parkinson's disease.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
Yang Yue, Shu Li, Lingling Wang, Huanxiang Liu, Henry H. Y. Tong, Shan He
Summary: In this study, a novel framework called MpbPPI is proposed for accurate prediction of amino acid mutations on protein-protein interactions. Pre-training on a strictly screened dataset enables MpbPPI to generate high-quality representations and support flexible application on different mutant-type protein-protein complexes.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Yunhao Ma, Hongmei Zhu, Xinrong Jiang, Zhongkun Zhou, Yong Zhou, Yanan Tian, Hao Zhang, Mengze Sun, Lixue Tu, Juan Lu, Yuqing Niu, Huanxiang Liu, Yingqian Liu, Peng Chen
Summary: This study evaluated the cytotoxicity of 8-methoxy-2,5-dimethyl-5H-indolo[2,3-b]quinoline (MMNC) in colorectal cancer cells and found that MMNC exerted cytotoxicity by inhibiting the expression of PI3K/AKT/mTOR signaling pathway-related proteins, inhibiting cell proliferation, blocking the cell cycle, and inducing apoptosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Artificial Intelligence
Lei Wu, Erqi Chen, Qiang Guo, Dengpan Xu, Wensheng Xiao, Jingjing Guo, Mowen Zhang
Summary: The Whale Optimization Algorithm (WOA) has gained significant attention for its excellent exploitation ability. However, the exploration process of WOA requires improvement and specialized mechanisms to enhance exploration ability. To address this, a novel Smooth Exploration System (SES) called Smooth WOA (SWOA) is proposed, which includes three mechanisms: unordered dimension sampling, random crossover, and sequential mutation. Comparative analysis with other variants of WOA and advanced algorithms on benchmark functions demonstrates the remarkable performance of SWOA.
KNOWLEDGE-BASED SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Jiangtao Mei, Lei Wu, Erqi Chen, Wensheng Xiao, Liang Zhong, Jingjing Guo, Wentao Li
Summary: In this study, an improved differential evolution algorithm and back-propagation neural network (BPNN) are proposed to improve the development of structural damage detection. Based on the results of modal analysis, the proposed method effectively locates and quantifies the severity of structural damage. The numerical results show that the IDE-BP model outperforms other methods for single and multiple damage scenarios.
KNOWLEDGE-BASED SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Chao Liu, Lei Wu, Wensheng Xiao, Guangxin Li, Dengpan Xu, Jingjing Guo, Wentao Li
Summary: In this study, a novel variant of ant colony optimization algorithm called improved heuristic mechanism ACO (IHMACO) is proposed. It contains four improved mechanisms to enhance the efficiency and effectiveness of path planning. Experimental results show that IHMACO outperforms existing approaches in terms of path turn times.
KNOWLEDGE-BASED SYSTEMS
(2023)
Review
Chemistry, Multidisciplinary
Jingjing Guo, Yiqiong Bao, Mengrong Li, Shu Li, Lili Xi, Pengyang Xin, Lei Wu, Huanxiang Liu, Yuguang Mu
Summary: Biological membranes are complex structures vital for life. Experimental investigation of biomembranes is challenging, but computational approaches such as molecular dynamics (MD) simulations have provided insights into their atomic details and cellular functions. This review highlights the latest advancements in computational methods, from force fields to MD simulations and trajectory analysis. It also discusses current research topics, challenges, and future directions for applying computational technologies in biomembrane systems.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biology
Qianqian Wang, Mingyu Zhang, Aohan Li, Xiaojun Yao, Yingqing Chen
Summary: The development of PARP-1 inhibitors is crucial for the treatment of various cancers. This study investigates the structural regulation of PARP-1 by different allosteric inhibitors, revealing the basis of allosteric inhibition and providing guidance for the discovery of more innovative PARP-1 inhibitors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
