Review
Biotechnology & Applied Microbiology
Liping Zhao, Xu Zhang, Xiaoxia Wang, Xiuwen Guan, Weifeng Zhang, Jinlong Ma
Summary: Photothermal therapy (PTT) is a promising approach in cancer treatment, but challenges such as accurate laser exposure and potential side effects need to be addressed. Enhancing the selectivity of PTT involves increasing the accumulation of photothermal agents at tumor sites and giving them self-regulating photothermal conversion functions.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Review
Medicine, Research & Experimental
Wen Li, Pengcheng He, Yuge Huang, Yi-Fang Li, Jiahong Lu, Min Li, Hiroshi Kurihara, Zhuo Luo, Tian Meng, Mashun Onishi, Changle Ma, Lei Jiang, Yongquan Hu, Qing Gong, Dongxing Zhu, Yiming Xu, Rong Liu, Lei Liu, Cong Yi, Yushan Zhu, Ningfang Ma, Koji Okamoto, Zhiping Xie, Jinbao Liu, Rong-Rong He, Du Feng
Summary: Autophagy is a physiological process that degrades over-abundant or damaged organelles via the lysosomal system, induced by stress and occurring in both non-selective and selective manners. Selective autophagy plays a crucial role in maintaining cellular homeostasis and its dysfunction is implicated in various diseases.
Review
Chemistry, Multidisciplinary
Duan Ni, Zongtao Chai, Ying Wang, Mingyu Li, Zhengtian Yu, Yaqin Liu, Shaoyong Lu, Jian Zhang
Summary: Allostery is a biological phenomenon where orthosteric sites are regulated by distal allosteric sites, triggering responses to perturbations such as ligand binding or mutations. Recent advances in biophysics, particularly in structural bioinformatics, have improved understanding of allosteric effects, leading to more rational structure-based drug discovery methods.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Review
Chemistry, Inorganic & Nuclear
Shenglun Xiong, M. V. Nanda Kishore, Wei Zhou, Qing He
Summary: This review summarizes recent advances in macrocyclic receptors for selective recognition of fluoride, including design principles, structural features, working mechanism, and recognition efficacy. The focus is on the applications of macrocyclic receptors in fluoride sensing, extraction, transmembrane transport, nanodevices, and logic gate construction.
COORDINATION CHEMISTRY REVIEWS
(2022)
Review
Materials Science, Multidisciplinary
Hanlin Cao, Shanshan Chai, Zifang Tan, Hong Wu, Xue Mao, Liang Wei, Fenglei Zhou, Runjun Sun, Chengkun Liu
Summary: In recent decades, the rapid development of IoT and AI technologies has driven the research boom in physical sensors. Researchers in the field of advanced manufacturing have paid extensive attention to the material selection, structure design, and performance research of physical sensors. Significant technological progress has been made in physical sensors for applications in various fields such as electronic skin, biomedicine, and tissue engineering. Among various methods for preparing physical sensors, electrospun nanofibers or nanofiber membranes have shown advantages over other materials, such as nanosize effect, high specific surface area, and high porosity. This review introduces the working principles of various physical sensors and summarizes recent research progress in electrospun nanofiber-based physical sensors. Future research trends and challenges for the large-scale adoption of electrospun physical sensors are also proposed.
ACS MATERIALS LETTERS
(2023)
Review
Chemistry, Applied
Yongzhen Peng, Zhichun Chen, Jian Xu, Qi Wu
Summary: This review provides an overview of recent progress in photobiocatalysis, including the regeneration of cofactors, generation of H2O2 in situ, cascades involving a photobiocatalytic transformation, and the photoinduced enzymatic reactions inspired by the photoactive cofactor within the enzyme.
ORGANIC PROCESS RESEARCH & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Farindra Kumar Mahto, Akash Bhattacharya, Swati Bhattacharya
Summary: The Hsp70 chaperone protein system is crucial for protein folding and homeostasis. Molecular dynamics simulations reveal that the Lid domain has greater conformational flexibility than previously expected.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Chemistry, Physical
Qiqi Lu, Jianguo Liu, Longlong Ma
Summary: This review discusses the significance of hydrogenation of nitriles into primary amines, focusing on the control of selectivity and the impact of different catalyst systems. It also examines the effects of substrate structures on selectivity and substrate scope, especially highlighting functional groups and aliphatic nitriles. Additionally, the review compiles and evaluates the best results for various chemoselectivity issues, aiming to provide new perspectives on catalyst design and application.
JOURNAL OF CATALYSIS
(2021)
Review
Engineering, Environmental
Ziying Chen, Zhan Li, Jia Chen, Parashuram Kallem, Fawzi Banat, Hongdeng Qiu
Summary: With the rapid development of the rare earth industry, the demand for rare earth elements continues to rise, making high-purity separation of rare earth elements particularly important. The article summarizes the latest developments and advantages and disadvantages of rare earth element separation technologies, and looks ahead to future prospects.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Review
Chemistry, Multidisciplinary
Tianxue Zhu, Yimeng Ni, Gill M. Biesold, Yan Cheng, Mingzheng Ge, Huaqiong Li, Jianying Huang, Zhiqun Lin, Yuekun Lai
Summary: This review explores the recent advances in multifunctional conductive hydrogels for electronic devices, including their different components and functionalities. The applications of hydrogels in flexible devices are illustrated, and the current challenges and future development prospects are discussed.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Analytical
Rajni Sharma, Marzieh Geranpayehvaghei, Fatemeh Ejeian, Amir Razmjou, Mohsen Asadnia
Summary: Nanostructured ion-selective membranes (ISMs) have extensive applications in biomedical engineering, enabling health monitoring, precise biosensing, controlled drug delivery, and disease diagnosis. Recent technological advancements have miniaturized ion-selective electrodes, allowing for more innovative and intelligent designs for clinical applications.
Review
Chemistry, Inorganic & Nuclear
Guilong Lu, Feng Chu, Xiubing Huang, Yaqiong Li, Kaiyan Liang, Ge Wang
Summary: The review summarizes strategies for constructing efficient photocatalyst systems and advanced techniques for investigating reaction mechanisms; discusses the application of MOFs in photocatalytic selective oxidation reactions and summarizes the role of reactive oxygen species (ROS) and corresponding regulation strategies; anticipates challenges and future developments of MOFs-based photocatalysts in this research area.
COORDINATION CHEMISTRY REVIEWS
(2022)
Review
Chemistry, Multidisciplinary
Changlin Yao, Shufang Zhang, Lei Wang, Xutang Tao
Summary: Polymorphism is a common phenomenon in organic crystals, with the ability to influence the physicochemical properties of solid materials in various fields. The use of different polymorph discovery methods can increase the chances of finding polymorphs with desired properties and optimize the performance of the final product. This paper reviews recent advances in polymorph screening methods, including solution crystallization, melt crystallization, and crystal structure prediction. It also discusses nucleation theory and mechanisms of polymorph discovery, while addressing the challenges and aims of making the process more efficient.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Pharmacology & Pharmacy
Qin Shi, Haibiao Chen, Yanan Wang, Jia Xu, Ziying Liu, Chen Zhang
Summary: This paper provides an overview of recent advances in the research on polymorphic drug systems including understandings on nucleation, crystal growth, dissolution, mechanical properties, polymorphic transformation. It also highlights new strategies and mechanisms in the control of polymorphic forms, and briefly discusses challenges and trends in the development of polymorphic drugs, aiming at developing effective and efficient pharmaceutical formulations containing the polymorphic drugs.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2022)
Review
Polymer Science
Wen-Tao Guo, Xin-Gui Tang, Zhenhua Tang, Qi-Jun Sun
Summary: This paper reviews recent progress on polymer composite-based flexible pressure sensors, introduces the parameters and working principles of pressure sensors, and discusses in detail their applications in human physiology monitoring, health monitoring, artificial skin, and self-powered smart systems. The remaining challenges and outlook of these sensors are summarized at the end.
Article
Biochemistry & Molecular Biology
Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Jimin Pei, Nick Grishin
Summary: The Rossmann-like fold is a prevalent and diversified double-helical superstructure of ancient evolutionary origin, present in various metabolic enzymes; RLM-containing proteins constitute approximately 15% of the human proteome, with disease-causing mutations more frequent within RLM domains, highlighting their importance for human health.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lisa N. Kinch, R. Dustin Schaeffer, Andriy Kryshtafovych, Nick V. Grishin
Summary: An evolutionary-based definition and classification of target evaluation units (EUs) were presented for CASP14, with targets split into categories based on existing templates and server performance. Analysis of sequence and structure similarity, as well as server performance, highlighted trends in target difficulty for the 84 experimental models submitted. The study assigned EUs to tertiary structure assessment categories based on their evolutionary relationship to existing ECOD fold space, showing overlapping clusters and the complexity of server performance in predicting target structures.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Lisa N. Kinch, Jimin Pei, Andriy Kryshtafovych, R. Dustin Schaeffer, Nick Grishin
Summary: This report summarizes the tertiary structure prediction assessment of difficult modeling targets in CASP14, with the top-performing AlphaFold2 group providing high quality models. Despite significant progress in protein structure prediction, challenges remain with flexible regions and obligate oligomeric assemblies. Performance-based PCA and heatmap clusters offer insight into target difficulties and successful structure prediction methodologies.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
R. Dustin Schaeffer, Lisa Kinch, Andriy Kryshtafovych, Nick Grishin
Summary: This study evaluated the accuracy of CASP14 models in structure predictions, focusing on the difficulty of structure assembly in multidomain targets, with AlphaFold2 performing exceptionally well.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N. Kinch, R. Dustin Schaeffer, Claudia Millan, Hahnbeom Park, Carson Adams, Caleb R. Glassman, Andy DeGiovanni, Jose H. Pereira, Andria V. Rodrigues, Alberdina A. van Dijk, Ana C. Ebrecht, Diederik J. Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K. Rathinaswamy, Udit Dalwadi, Calvin K. Yip, John E. Burke, K. Christopher Garcia, Nick V. Grishin, Paul D. Adams, Randy J. Read, David Baker
Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.
Article
Chemistry, Multidisciplinary
R. Dustin Schaeffer, Lisa N. Kinch, Jimin Pei, Kirill E. Medvedev, Nick Grishin
Summary: Domain classifications are useful for computational analysis of protein structure, but their composition can be difficult for potential users to understand. Comparing ECOD with SCOPe, SCOP2, and CATH, it was found that ECOD and CATH provide the most extensive structural coverage of the PDB, with ECOD and SCOPe having the most consistent domain boundaries, while CATH and SCOP2 show significant differences.
Article
Biochemical Research Methods
Kirill E. Medvedev, Jimin Pei, Nick Grishin
Summary: This study developed a database of human proteome IDRs that are significantly enriched in particular amino acids, providing information on function terms, disorder prediction, enriched IDR composition, and ranks of human proteins with similar enriched IDRs. The distribution analysis revealed significant overrepresentation of R- and Y-enriched IDRs in metabolic and enzymatic activities, and F-enriched IDRs in transport. Approximately 75% of functional categories contain IDPs with IDRs significantly enriched in hydrophobic residues important for protein-protein interactions.
Meeting Abstract
Oncology
Anna Savelyeva, Feng Wang, Lei Guo, John T. Lafin, Liwei Jia, Kirill Medvedev, Cheryl Lewis, Payal Kapur, Vitaly Margulis, Solomon L. Woldu, Xiaosong Meng, Nick Grishin, James F. Amatruda, Lin Xu, Aditya Bagrodia
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Anna V. Savelyeva, Kirill E. Medvedev
Summary: Seminoma is the most common type of testicular germ cell tumors (TGCTs) among young men. The current treatments have severe side effects, and immunotherapy could be an alternative, but its efficacy is still uncertain. Recent research identified two distinct subtypes of seminoma, with subtype 1 having a poor immune microenvironment and subtype 2 having a higher immune score.
Article
Biochemistry & Molecular Biology
Kirill E. Medvedev, R. Dustin Schaeffer, Jimin Pei, Nick V. Grishin
Summary: The dysregulation of protein kinase signaling pathways is frequently associated with various human diseases, including cancer. In this study, pathogenic mutations in human protein kinase domains were mapped and categorized based on their relevance to disease type. It was found that cancer-associated mutations primarily occurred within the catalytic and activation loops of the kinase domain, while non-cancer-related mutations were mainly located outside of these regions. Additionally, a previously unexplored hotspot at residue R371 of the AURKA structure was identified, which harbored a high number of exclusively non-cancer-related pathogenic mutations (21).
Article
Multidisciplinary Sciences
Kirill E. Medvedev, R. Dustin Schaeffer, Kenneth S. Chen, Nick V. Grishin
Summary: The recent progress in protein structure prediction achieved a historic milestone with AlphaFold predicting 200 million protein models comparable to experimental methods. These predicted structures have the potential to provide previously unavailable information about cancer biology, which is crucial for understanding evolution and identifying drug targets. Our team evaluated the pan-cancer structurome by classifying domains from human protein models released by AlphaFold, revealing significant differences in the representation of beta sandwich and alpha helical domains in different cancer types. This suggests a potential correlation between the prevalence of these domains and tumor development-related inflammation as well as the promotion of successful oncogenesis.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Kirill E. Medvedev, R. Dustin Schaeffer, Jimin Pei, Nick V. Grishin
Summary: This study mapped pathogenic mutations in 497 human protein kinase domains to the reference structure of Aurora kinase A (AURKA) and categorized them based on disease type. The majority of cancer-related mutation hotspots were found within the catalytic and activation loops of the kinase domain, while non-cancer-related hotspots were located outside of these regions. A hotspot at residue R371 of the AURKA structure with the highest number of exclusively non-cancer-related pathogenic mutations (21) was also identified.
Article
Oncology
Kirill E. Medvedev, Anna Savelyeva, Kenneth S. Chen, Aditya Bagrodia, Liwei Jia, Nick Grishin
Summary: This computational study identified two clinically relevant subtypes of pure seminoma based on transcriptomic data. Significant molecular differences were observed between the subtypes, including pluripotency stage, activity of DNA repair mechanisms, rates of loss of heterozygosity, and expression of lncRNA responsible for cisplatin resistance. The identification of these subtypes may improve treatment approaches for seminoma.
CANCER INFORMATICS
(2022)
Meeting Abstract
Biophysics
Kirill E. Medvedev, Lisa N. Kinch, Nick V. Grishin
BIOPHYSICAL JOURNAL
(2020)
