Article
Biochemical Research Methods
Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang, Ziding Zhang
Summary: The study introduces a database called HVIDB that provides comprehensive annotated data on human-virus protein-protein interactions and integrates online PPI prediction tools. Users can easily access reliable information on various human virus PPIs and conduct in-depth analysis through this database.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marin-Lopez, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva
Summary: The study introduces SPServer, a web server that utilizes Split-Statistical Potentials to analyze protein folds and interfaces. SPServer provides global scores and residue/residue pair profiles for users to identify problematic regions, disruptive amino acid pairs, and compare structural quality.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Davyd R. Bohdan, Valeria V. Voronina, Janusz M. Bujnicki, Eugene F. Baulin
Summary: Understanding the 3D structure of RNA is crucial for understanding its function. Current research has focused more on local motifs, while long-range motifs formed by distant loops and helical regions have been largely understudied. This study surveyed long-range RNA tertiary motifs using a new dataset called LORA and developed an algorithm called ARTEM for annotating and superposing RNA 3D modules. The most common long-range motifs were observed to be planar staples, tilted staples, and helical packing motifs, including many previously undescribed interactions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Daniel E. Mattox, Chris Bailey-Kellogg
Summary: The study comprehensively investigates specificity-conferring features of lectin-glycan interactions and provides a novel approach for predicting the identity of bound glycans and understanding lectin specificity through systematic characterization and analysis.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Food Science & Technology
Pingping Shen, Yan Peng, Xiaoyang Zhou, Xuewa Jiang, Richa Raj, Haixia Ge, Weiwei Wang, Boyang Yu, Jian Zhang
Summary: This study used surface plasmon resonance, fluorescence spectroscopy, and molecular simulations to investigate the interaction mechanisms between quercetin, isoquercitrin, rutin and HMGB1 protein, providing important insights into the molecular mechanisms of flavonoids in HMGB1-related inflammatory diseases.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maral Afshinpour, Logan A. Smith, Suvobrata Chakravarty
Summary: AQcalc is a computational tool that can identify weak molecular interactions, specifically anion-quadrupole (AQ) interactions, which play an important role in protein structure and function. By analyzing weak interactions in protein models, even in the absence of experimental structures, AQcalc helps us understand the contributions of these interactions to deleterious structural changes associated with diseases. Additionally, the tool has revealed that amyloid fibrils utilize AQ interactions at a higher frequency compared to globular proteins. Overall, AQcalc enriches our understanding of residue interaction networks and facilitates hypothesis testing of these important but weak interactions.
Article
Engineering, Multidisciplinary
Shahriar Dastjerdi, Amin Alibakhshi, Bekir Akgoz, Omer Civalek
Summary: This paper applies a semi-analytical polynomial method (SAPM) to solve the mechanical governing equations of nano-sized spherical functionally graded structures. The SAPM is based on polynomial functions and assumes the spherical coordinate system. The results obtained are compared with those in other articles to examine the accuracy of the solution method.
INTERNATIONAL JOURNAL OF ENGINEERING SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Aleksei Golubev, Alexey S. Kubasov, Alexander Yu Bykov, Andrey P. Zhdanov, Grigorii A. Buzanov, Alexander A. Korlyukov, Konstantin Yu Zhizhin, Nikolay T. Kuznetsov
Summary: A series of compounds based on perbrominated disubstituted sulfonium derivatives of the closo-decaborate anion were synthesized and characterized. The study revealed the effect of different alkyl groups on the intermolecular interactions, and provided valuable insights into the molecular structure and properties of these compounds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Anuja Jain, Shikha Mittal, Lokesh P. Tripathi, Ruth Nussinov, Shandar Ahmad
Summary: Recognition of pathogen-derived nucleic acids by host cells is crucial for detecting pathogenic invasion and triggering immune responses. Understanding the interactions between pathogen nucleic acids and host factors is essential for therapeutic intervention.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Chemistry, Multidisciplinary
Iqra Bano, Anum Sumera Soomro, Syed Qamar Abbas, Amirhossein Ahmadi, Syed Shams ul Hassan, Tapan Behl, Simona Bungau
Summary: Ubiquitination is a protein modification process regulated by enzymes like Cul5. Cul5 regulates cellular development, proliferation, and is involved in specific cancer cells and tumor progression.
Article
Biochemistry & Molecular Biology
Christophe J. Moreau, Guillaume Audic, Laura Lemel, Katarzyna Niescierowicz, M. Dolores Garcia-Fernandez
Summary: GPCRs are a large family of transmembrane proteins that play crucial roles in various physiological functions. Cholesterol can affect the activity of certain GPCRs either indirectly through changes in the membrane properties or directly by binding to the receptor. Recent advancements in structural biology have provided insights into the structures of many GPCRs, revealing the presence of cholesterol molecules or substitutes in 240 structures. This review summarizes the locations of these molecules and provides a comparative analysis of the structural changes based on the receptor state.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Chemistry, Inorganic & Nuclear
Zheng Zhou, Okten Ungor, Zheng Wei, Michael Shatruk, Alexandra Tsybizova, Renana Gershoni-Poranne, Marina A. Petrukhina
Summary: The monoanion of triphenylene was generated using alkali metals as reducing agents and crystallized with corresponding cations in the presence of crown ethers. Different metals led to different coordination environments of the monoanion-radicals, as confirmed by UV-vis spectroscopy and X-ray diffraction. The magnetic behavior and phase transitions of the compounds were found to be correlated with the arrangement of triphenylene radicals in the crystal structures, with antiferromagnetic interactions and varying strengths of exchange coupling.
INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Tobias Muehlethaler, Dario Gioia, Andrea E. Prota, May E. Sharpe, Andrea Cavalli, Michel O. Steinmetz
Summary: Using a combined computational and crystallographic approach, researchers identified 27 distinct binding sites in tubulin, including 11 previously unknown sites. They also observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. These results provide a structural basis for developing novel small molecules as tubulin modulators and lay down a framework that may aid in discovering new pockets in other pharmaceutically important targets.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Jamin L. B. Martin, Michael F. Reid, Jon-Paul R. Wells
Summary: In this study, we investigated the synthesis, spectroscopy, and energy transfer mechanisms of trivalent samarium-doped KY3F10 nanocrystals. Our measured fluorescence transients, which are concentration-dependent, suggest a dipole-quadrupole energy transfer mechanism. The inferred energy transfer rate is faster than what has been reported in similar hosts. We also observed the formation of α-KYF4:Sm3+ at high dopant concentrations, indicating a potential limit for doping larger lanthanide ions. Unlike the bulk crystal, no divalent samarium was detected in the nanocrystals.
JOURNAL OF ALLOYS AND COMPOUNDS
(2023)
Article
Biochemistry & Molecular Biology
Li Guo, Yihao Kang, Yiqi Xiong, Lin Jia, Xiaoqiang Yan, Daoliang Xia, Jiafeng Yu, Jun Wang, Tingming Liang
Summary: This study identified key genes and RNAs associated with prostate adenocarcinoma (PRAD) and constructed a risk model that could potentially serve as a biomarker for cancer prognosis. The study also revealed potential interactions among different RNAs and surveyed the landscape of isomiRs in homologous miRNA loci. Furthermore, the study characterized TK1, miR-222-3p, and SNHG3 as crucial RNAs with correlations to poor survival outcomes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)