Understanding structural excursions of proteins under folding conditions is crucial to map energy landscapes of proteins. In the present study, OneG computational tool has been used for analyzing possible existence of cryptic intermediates and metastable states of 26 proteins for which three prerequisite inputs of the OneG such as atomic coordinates of proteins, free energy of unfolding (ΔG) and free energy of exchange (ΔG) determined in the absence of denaturant were available during the course of the study. The veraciousness of the tool on predicting the partially folded states of the proteins has been comprehensively described using experimental data available for 15 of the 26 proteins. Meanwhile, possible existence of partially structured states in the folding pathways of 11 other proteins has also been delineated as predicted by the OneG. In addition to mapping the folding pathways of proteins, the salient merits of the tool on systematically addressing the discrepancy between the ΔG and the ΔG of the proteins have also been dealt.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1904288 | DOI Listing |
J Cheminform
January 2025
School of Systems Biomedical Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, 06978, Seoul, Republic of Korea.
G protein-coupled receptors (GPCRs) play vital roles in various physiological processes, making them attractive drug discovery targets. Meanwhile, deep learning techniques have revolutionized drug discovery by facilitating efficient tools for expediting the identification and optimization of ligands. However, existing models for the GPCRs often focus on single-target or a small subset of GPCRs or employ binary classification, constraining their applicability for high throughput virtual screening.
View Article and Find Full Text PDFDiabetol Metab Syndr
January 2025
The Centre for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Badachu Road, Shijingshan District, Beijing, 100144, People's Republic of China.
Background: Adipose tissue plays a critical role in the development of metabolically unhealthy obesity (MUO), with distinct adipose depots demonstrating functional differences. This study aimed to investigate the unique characteristics of subcutaneous (SA) and visceral adipose tissue (VA) in MUO.
Methods: Paired omental VA and abdominal SA samples were obtained from four male patients with MUO and subjected to Four-Dimensional Data Independent Acquisition (4D-DIA) proteomic and lysine acetylation (Kac) analyses.
BMC Pharmacol Toxicol
January 2025
Department of Anatomy, College of Health Sciences, University of Ilorin, Ilorin, 240003, Nigeria.
Background: Glia mediated neuroinflammation and degeneration of inhibitory GABAergic interneurons are some of the hall marks of pyrethroid neurotoxicity. Here we investigated the sex specific responses of inflammatory cytokines, microglia, astrocyte and parvalbumin positive inhibitory GABAergic interneurons to λ-cyhalothrin (LCT) exposures in rats.
Methods: Equal numbers of male and female rats were given oral corn oil, 2 mg/kg.
BMC Microbiol
January 2025
Center for Public Health Research, Medical School of Nanjing University, Nanjing, China.
Background: Enterovirus 71 (EV71) is one of the major causative agents of hand, foot, and mouth disease (HFMD), and can cause severe cerebral complications and even fatality in children younger than 5 years old. However, there is no specific medication for EV71 infection in clinical practice. Our previous studies had identified the 6-thioguanine (6-TG), an FDA-approved anticancer drug, as a potential antiviral agent, but its anti-EV71 activity is largely unknown, therefore, we aim to explore the antiviral effect of 6-TG on EV71.
View Article and Find Full Text PDFJ Biomol NMR
January 2025
Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
The NMR signals from protein sidechains are rich in information about intra- and inter-molecular interactions, but their detection can be complicated due to spectral overlap as well as conformational and hydrogen exchange. In this work, we demonstrate a protocol for multi-dimensional solid-state NMR spectral editing of signals from basic sidechains based on Hadamard matrix encoding. The Hadamard method acquires multi-dimensional experiments in such a way that both the backbone and under-sampled sidechain signals can be decoded for unambiguous editing in the N spectral frequency dimension.
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