Article
Biochemical Research Methods
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
Summary: Cancer is a major cause of death globally, and there is a need for innovative methods to stratify patients and identify biomarkers using molecular data. spongEffects is a novel method that infers subnetworks from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.
Article
Biochemistry & Molecular Biology
Baoxing Song, Edward S. Buckler, Hai Wang, Yaoyao Wu, Evan Rees, Elizabeth A. Kellogg, Daniel J. Gates, Merritt Khaipho-Burch, Peter J. Bradbury, Jeffrey Ross-Ibarra, Matthew B. Hufford, M. Cinta Romay
Summary: Thousands of species are set to be sequenced in the coming years, and understanding the functionality of their genomes requires molecular and evolutionary approaches. A study focusing on the Andropogoneae tribe, which includes multiple crop species, revealed highly conserved noncoding sequences rich in functional elements. These findings shed light on the evolution and functional significance of CNSs in maize.
Review
Biochemistry & Molecular Biology
Seyedeh Tayebeh Ahmadpour, Charlotte Orre, Priscila Silvana Bertevello, Delphine Mirebeau-Prunier, Jean-Francois Dumas, Valerie Desquiret-Dumas
Summary: This review highlights the importance of long noncoding RNAs (lncRNAs) in breast cancer chemoresistance. LncRNAs regulate multiple pathways involved in breast cancer development and treatment response. Understanding these mechanisms in detail may improve the clinical outcomes for breast cancer patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ilya N. Bindeman, Dmitri A. Ionov, Peter M. E. Tollan, Alexander V. Golovin
Summary: The study focuses on the oxygen isotopic ratios in the mantle, revealing a subtle but significant decrease in δ O-18 in the shallow continental lithospheric mantle, which may be related to plate tectonics and subduction.
NATURE COMMUNICATIONS
(2022)
Review
Medicine, Research & Experimental
Shengrong Long, Yu Yan, Hongyu Xu, Lesheng Wang, Jiazhi Jiang, Ziyue Xu, Runming Liu, Qiangqiang Zhou, Xiaopeng Huang, Jincao Chen, Zhiqiang Li, Wei Wei, Xiang Li
Summary: Epitranscriptomic abnormalities play a crucial role in the development of gliomas, especially RNA methylation modifications. These modifications are associated with various cancer types and are mediated by proteins such as writers, erasers, and readers. This review focuses on the role of RNA methylation modifications in gliomas and proposes new approaches and prognostic indicators for patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Chemistry, Organic
Jean-Marico Speldrich, Jens Christoffers
Summary: Delta-valerolactone derivatives are formed through the cerium-catalyzed aerobic coupling of beta-oxoesters with enol acetates and dioxygen. The reaction bears similarities to Baeyer-Villiger oxidation but exhibits unique migration patterns, with retention of configuration through 1,2-alkyl shift. Additionally, evidence of a radical chain mechanism in the coupling reaction has been demonstrated.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Review
Immunology
Avik Dutta, Bin Zhao, Paul E. Love
Summary: This review discusses the importance of T cell receptor (TCR) beta-selection in mammalian T cell development and recent mechanistic findings that have helped decode the molecular dynamics of the beta-selection checkpoint.
TRENDS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Yunyun Wang, Zhenni Li, Xinyu Wang, Ziyuan Zhao, Li Jiao, Ruming Liu, Keying Wang, Rui Ma, Yang Yang, Guo Chen, Yong Wang, Xin Bian
Summary: This study investigates the molecular basis of membrane association by the SMP domain of extended synaptotagmin (E-Syt) through in vitro DNA brick-assisted lipid transfer assays and molecular dynamics simulations. The results show that the SMP domain recognizes the highly curved subdomain of the tubular ER and the acidic-lipid-enriched plasma membrane for efficient lipid transfer. These findings support a model for the action of the SMP domain at membrane contact sites (MCSs).
NATURE COMMUNICATIONS
(2023)
Review
Medicine, General & Internal
Maria Sanchez-Villalobos, Miguel Blanquer, Jose M. Moraleda, Eduardo J. Salido, Ana B. Perez-Oliva
Summary: In this article, the main pathophysiological pathways involved in beta-thalassemia are reviewed, with a focus on the development of new therapies directed at new therapeutic targets.
FRONTIERS IN MEDICINE
(2022)
Article
Chemistry, Physical
Andrea Felli, Silvia Mauri, Marcello Marelli, Piero Torelli, Alessandro Trovarelli, Marta Boaro
Summary: In this study, in situ temperature-programmed (TP) analyses and multiple analytical methods were used to investigate the redox properties and structural changes of PBM-based materials. The transformation process from m-PBM to r-PBM and o-PBM, as well as the redox behavior of Mn, were revealed. This has significant implications for the application of PBM-based materials as oxygen carriers and catalytic promoters in CO2 enhancement technologies.
ACS APPLIED ENERGY MATERIALS
(2022)
Article
Chemistry, Inorganic & Nuclear
E. H. Driscoll, A. Orera, P. A. Anderson, M. L. Sanjuan, P. R. Slater
Summary: Solar perovskites have attracted attention for their high PCE, with FAPbI(3) showing higher PCE due to optimal band gap and doping strategies. Raman spectroscopy was used to study phase change and the impact of water on transformation.
DALTON TRANSACTIONS
(2021)
Article
Materials Science, Multidisciplinary
Raquel Cortes-Gil, Antonio Hernando, Jose M. Alonso, Kevin M. Sigcho-Villacis, Alberto Azor-Lafarga, Jose L. Martinez, M. Luisa Ruiz-Gonzalez, Jose M. Gonzalez-Calbet
Summary: LaMnO3+delta nanoparticles are able to modify their behavior by adjusting their non-stoichiometry, microstructure, and magnetotransport properties as a function of cationic vacancy concentration. The accommodation of compositional variations triggers Mn3+ -> Mn4+ oxidation, leading to the emergence of magnetoresistance.
JOURNAL OF MATERIALS CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Yuying Liu, Ying Wang, Chaohui Tong, Guanghong Wei, Feng Ding, Yunxiang Sun
Summary: The self-assembly dynamics of two repeating modules in suckerin of squid sucker ring teeth were investigated using simulations. It was found that the glycine-rich module has a strong self-association ability and enables the formation of nanoconfined beta-sheets in the matrix through microphase separation. These molecular insights are important for understanding the structure and function of suckerin and can aid in the design of functional block-copolymer peptides for nanotechnology and biomedicine applications.
Article
Chemistry, Physical
Minhua Zhang, Xinyue Guan, Jianyu Zhuang, Yingzhe Yu
Summary: In this study, the structural properties of open and closed sites on Zr-beta zeolite and the mechanism of ETB reaction were investigated using density functional theory (DFT) calculations. The results showed that Zr-OH participation in the proton transfer step at open site reduced the energy barrier, making the Meerwein-Ponndorf-Verley (MPV) reaction the rate-limiting step at open site. The number of Zr-beta open sites was positively correlated with catalytic performance.
APPLIED SURFACE SCIENCE
(2022)
Article
Biology
Amit Kumar, Oscar Vadas, Nicolas Dos Santos Pacheco, Xu Zhang, Kin Chao, Nicolas Darvill, Helena O. Rasmussen, Yingqi Xu, Gloria Meng-Hsuan Lin, Fisentzos A. Stylianou, Jan Skov Pedersen, Sarah L. Rouse, Marc L. Morgan, Dominique Soldati-Favre, Stephen Matthews
Summary: The intracellular parasites belonging to the phylum of Apicomplexa employ substrate-dependent gliding motility to invade host cells. The glideosome-associated connector (GAC), a conserved protein, plays a crucial role in this process. The crystal structure of Toxoplasma gondii GAC reveals a unique armadillo repeat region that adopts a closed ring conformation. The properties of GAC suggest that it can adopt multiple conformations from closed to open and extended, and a multi-conformational model is proposed for its assembly and regulation within the glideosome.
Article
Chemistry, Physical
Emiliano Brini, Dima Kozakov, Ken A. Dill
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Biochemistry & Molecular Biology
Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos Coutsias, Ken A. Dill, Dima Kozakov
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2020)
Article
Biochemistry & Molecular Biology
Alisa Khramushin, Orly Marcu, Nawsad Alam, Orly Shimony, Dzmitry Padhorny, Emiliano Brini, Ken A. Dill, Sandor Vajda, Dima Kozakov, Ora Schueler-Furman
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Assen Marintchev, Takuhiro Ito
Article
Biochemistry & Molecular Biology
Israel T. Desta, Kathryn A. Porter, Bing Xia, Dima Kozakov, Sandor Vajda
Article
Chemistry, Medicinal
Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo S. Castilho, Dima Kozakov, Gyorgy M. Keseru, Adrian Whitty, Sandor Vajda
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biochemistry & Molecular Biology
Megan Egbert, Usman Ghani, Ryota Ashizawa, Sergei Kotelnikov, Thu Nguyen, Israel Desta, Nasser Hashemi, Dzmitry Padhorny, Dima Kozakov, Sandor Vajda
Summary: The study investigates binding properties in models submitted to CASP and finds that maintaining surface binding characteristics depends not only on overall accuracy but also on specific binding details. It also explores the potential of models in predicting binding sites and protein-protein interactions, showcasing their ability to approach the quality of X-ray crystallography.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Eleanor Elise Paul, Kay Ying Lin, Nathan Gamble, Amy Wei-Lun Tsai, Simon H. K. Swan, Yu Yang, Matthew Doran, Assen Marintchev
Summary: Translation initiation in eukaryotes involves complex interactions between eIFs and ribosomal preinitiation complex. This study reveals the importance of intramolecular contact rearrangement in PIC remodeling, mediated by specific regions of eIF5. Phosphorylation of eIF5 by CK2 enhances its affinity for eIF2 and may contribute to translation and cell proliferation.
BIOPHYSICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Daniel Friedrich, Assen Marintchev, Haribabu Arthanari
Summary: In this review, the authors examine the versatility and functionality of HEAT domains in the regulation of mRNA translation initiation. They describe the basic structural architecture of HEAT domains and their involvement in various cellular processes. The focus is on proteins in the translation initiation system that feature HEAT domains, highlighting their remarkably flexible interactions and the functional importance of these domains.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Medicinal
Amanda E. Wakefield, David Bajusz, Dima Kozakov, Gyoergy M. Keseru, Sandor Vajda
Summary: Despite the limited number of GPCR structures cocrystallized with allosteric inhibitors, protein mapping has revealed the presence of druggable sites at the same locations in a large variety of GPCRs. These sites cluster at nine distinct locations and can be specifically targeted for allosteric modulation across GPCRs. The FTMap server facilitates protein mapping and is freely available for academic and governmental use.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Multidisciplinary Sciences
Eleanor Elise Paul, Assen Marintchev
Summary: The HEAT and PCI domains are two related domain families, but the PCI domains may be a subset of the HEAT domain family. The PCI domains have structural similarity with the HEAT domains due to the acquisition of the WH subdomain.
Article
Biochemistry & Molecular Biology
Israel T. Desta, Sergei Kotelnikov, George Jones, Usman Ghani, Mikhail Abyzov, Yaroslav Kholodov, Daron M. Standley, Maria Sabitova, Dmitri Beglov, Sandor Vajda, Dima Kozakov
Summary: In this study, a computational protocol utilizing template-based modeling and docking was proposed to predict epitope residues of antibodies. The results show that this method improves upon existing epitope prediction methods and interestingly, prediction accuracy starting from antibody sequence alone is comparable to that starting from unbound antibody structures.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Editorial Material
Multidisciplinary Sciences
Shi-Jie Chen, Mubashir Hassan, Robert L. Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C. Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin R. Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D. Rose
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Mathematical & Computational Biology
Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov
Summary: MHC-I molecules play a crucial role in presenting antigen-derived peptides on cell surfaces for immune detection. Predicting peptide-MHC binding is an important step in this process, and computational approaches have been developed. This study explores the application of pretrained deep learning models on large protein sequence datasets for predicting MHC Class I-peptide binding, showing superior performance compared to the current state-of-the-art method.
FRONTIERS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Nathan Gamble, Eleanor Elise Paul, Bibin Anand, Assen Marintchev
Summary: Translation initiation in eukaryotes is dependent on a complex network of interactions, with eIF5 playing a central role in PIC assembly and remodeling. Phosphorylation by CK2 increases eIF5's affinity for eIF1A, shedding light on the mechanisms underlying CK2 stimulation of protein synthesis and cell proliferation. This study also reveals a new contact interface between eIF5-CTD and the OB domain of eIF1A, contributing to the overall affinity between the two proteins.
CURRENT RESEARCH IN STRUCTURAL BIOLOGY
(2022)