Review
Biochemistry & Molecular Biology
Rossana Galassi, Lorenzo Luciani, Junbiao Wang, Silvia Vincenzetti, Lishan Cui, Augusto Amici, Stefania Pucciarelli, Cristina Marchini
Summary: This article reviews recent scientific findings on two classes of gold compounds containing phosphane or carbene ligands, as well as the recent developments in the application of Auranofin for breast cancers.
Article
Chemistry, Medicinal
Dorina Cibotaru, Marie N. Celestin, Michael P. Kane, Florin M. Musteata
Summary: The study aimed to develop new methods for measuring the free concentration, total concentration, and plasma binding capacity of compounds in samples, which were validated by analyzing clinical and known concentration samples. The methods using labeled compound addition were found to be the fastest and most reproducible. Microextraction-based methods showed higher sensitivity and accuracy for clinical samples compared to ultrafiltration-based methods. Overall, the new approach provides more information from samples and has great potential for personalized drug dosage and therapy for individual patients.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Review
Biochemical Research Methods
Meng Wang, Lukasz Kurgan, Min Li
Summary: HLA-I molecules bind intracellular peptides and present them to T cells for immune recognition. Predicting peptides that bind HLA-I molecules is crucial for immunotherapy. We survey 27 tools, evaluating their input/output characteristics, predictive models, and performance. Results show accuracy and meaningful binding motifs in all methods, but no universal superiority. Our comprehensive analysis provides information to identify suitable tools and design future methods.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Chemistry, Analytical
Behrouz Seyfinejad, Sibel A. Ozkan, Abolghasem Jouyban
Summary: The article discusses the presence of drugs in the bloodstream in both free and bound forms, and how protein binding affects the free concentration of the drug. It highlights the importance of measuring the free concentration of drugs, their protein binding, and the benefits for personalized medicine and therapeutic drug monitoring.
Article
Multidisciplinary Sciences
Bingyi Chen, Siting Luo, Songxuan Zhang, Yingchen Ju, Qiong Gu, Jun Xu, Xiang-Lei Yang, Huihao Zhou
Summary: Reveromycin A (RM-A) selectively inhibits eukaryotic cytoplasmic isoleucyltRNA synthetase (IleRS). The co-crystal structure suggests that RM-A molecule occupies the tRNA(Ile) binding site of Saccharomyces cerevisiae IleRS, and that RM-A cooperates with isoleucine or isoleucyl-adenylate for IleRS binding.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Phorutai Pearngam, Sira Sriswasdi, Trairak Pisitkun, Andrew R. Jones
Summary: MHC-peptide binding prediction is crucial for understanding immune responses and developing immunotherapeutics. Introducing global FDR and PEP estimation provides a more reliable evaluation of predicted results. MHCVision offers a better balance between sensitivity and precision in comparison to using traditional threshold values.
Article
Biochemistry & Molecular Biology
Nathania Puspitasari, Cheng-Kang Lee
Summary: Hydrophobins are highly surface-active proteins that can reverse surface hydrophobicity through self-assembly at interfaces, with potential applications in surface functional modifications. By fusing cellulose-binding domain with hydrophobins, soluble expression in E. coli can be enhanced for rapid isolation and purification. This strategy also retains the interfacial activity of hydrophobins and accelerates PETase hydrolysis against PET fiber.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Peter M. Bruno, Richard T. Timms, Nouran S. Abdelfattah, Yumei Leng, Felipe J. N. Lelis, Duane R. Wesemann, Xu G. Yu, Stephen J. Elledge
Summary: Identification of CD8(+) T cell epitopes is crucial for immunotherapy development. The EpiScan method, using surface MHC class I levels as a readout for ligand discovery, can screen large-scale MHC class I peptides and predict binding affinities. The EpiScan Predictor performs comparably to other algorithms and overcomes the underrepresentation of cysteine-containing peptides. This targeted immunopeptidomics approach will accelerate individual-specific immunotherapy.
NATURE BIOTECHNOLOGY
(2023)
Correction
Multidisciplinary Sciences
Bingyi Chen, Siting Luo, Songxuan Zhang, Yingchen Ju, Qiong Gu, Jun Xu, Xiang-Lei Yang, Huihao Zhou
Summary: A correction to this paper has been published.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Yue Shen, Jerry M. Parks, Jeremy C. Smith
Summary: This study presents a method for classifying HLA class I molecules using three-dimensional structures, which improves the breadth, accuracy, stability, and flexibility of classification. The findings show that structural similarity is highly correlated with peptide binding specificity. This new classification is useful in peptide-based vaccine development and HLA-disease association studies.
JOURNAL OF IMMUNOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Benjamin Alexander Albert, Yunxiao Yang, Xiaoshan M. M. Shao, Dipika Singh, Kellie N. N. Smith, Valsamo Anagnostou, Rachel Karchin
Summary: Researchers propose a method based on long short-term memory ensembles and transfer learning to predict effective neoepitopes that elicit an immune response. This method can help address the challenge of predicting immunogenicity of neoepitopes in developing personalized cancer vaccines. Compared to other state-of-the-art classifiers, this method significantly improves the prediction of epitope presentation.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Plant Sciences
Cecilia M. Lara-Mondragon, Alexandria Dorchak, Cora A. MacAlister
Summary: In Arabidopsis pollen tubes, class I formins play a crucial role in organizing actin arrays during tube elongation, with their localization and mobility being dependent on O-glycosylation of their extracellular domain. The extracellular domain is necessary for the function of two pollen-expressed class I formins, AtFH3 and AtFH5, and specific O-glycans are attached to these sequences. Loss of O-glycosylation alters membrane localization and disrupts actin organization. The different O-glycans also affect lateral mobility in the plasma membrane. This study highlights the importance of protein sub-functionalization in pollen tube elongation.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Biochemistry & Molecular Biology
Kwangwoon Lee, Samuel D. Whedon, Zhipeng A. Wang, Philip A. Cole
Summary: This article summarizes the research progress of classical histone deacetylases (HDACs), discussing the structure, enzymatic properties, and functional roles of these enzymes in gene expression regulation.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Haruhito Hiiro, Tatsuki Hashimoto, Makoto Mizoguchi, Mika Kaneko, Nanoka Deguchi, Yuna Takahashi, Shogo Hamaguchi, Iyuki Namekata, Hikaru Tanaka
Summary: This study examined the negative inotropic effects of nine Vaughan Williams class I antiarrhythmic drugs on guinea pig ventricular tissue. The potency of the drugs to decrease contractile force correlated with their reported IC50 values to block the L-type Ca2+ channel rather than the Na+ channel. The effects of the drugs were similar under a high extracellular K+ solution, indicating that the negative inotropic effects can be largely explained by the blockade of the L-type Ca2+ channel.
BIOLOGICAL & PHARMACEUTICAL BULLETIN
(2023)
Article
Multidisciplinary Sciences
Lenong Li, Xubiao Peng, Mansoor Batliwala, Marlene Bouvier
Summary: This study presents X-ray crystal structures of MHC I molecules interacting with peptides, revealing conformational fluctuations and providing a better understanding of peptide selection dynamics. The unusual crystal structures of the MHC I-peptide complexes explain how MHC I molecules edit peptides in antigen presentation.
NATURE COMMUNICATIONS
(2023)