Unlabelled: We describe here the ncIDP-assign extension for the popular NMR assignment program SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of connected resonances to the correct position in the sequence by making use of IDP random coil chemical shifts.
Availability: The ncIDP-assign extension is available at http://www.protein-nmr.org/.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065690 | PMC |
http://dx.doi.org/10.1093/bioinformatics/btr054 | DOI Listing |
Exp Eye Res
January 2025
Institute of Biomedical Engineering, University of Montréal, Montréal, Canada; Research Center, CHU Sainte-Justine University Hospital Centre, Montréal, Canada; Department of Radiology, Radio-oncology and Nuclear Medicine, University of Montréal, Montréal, Canada. Electronic address:
The morphology and thickness of the retinal layers are valuable biomarkers for retinal health and development. The retinal layers in mice are similar to those in humans; thus, a mouse is appropriate for studying the retina. The objectives of this systematic review were: (1) to describe normal retinal morphology quantitatively using retinal layer thickness measured from birth to age 6 months in healthy mice; and (2) to describe morphological changes in physiological retinal development over time using the longitudinal (in vivo) and cross-sectional (ex vivo) data from the included studies.
View Article and Find Full Text PDFBiomol NMR Assign
January 2025
Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
Cyclic GMP-AMP synthase (cGAS) is a DNA-sensing enzyme that is a member of the nucleotidyltransferase (NTase) family and functions as a DNA sensor. The protein is comprised of a catalytic NTase core domain and an unstructured hypervariable N-terminal domain (NTD) that was reported to increase protein activity by providing an additional DNA-binding surface. We report nearly complete H, N, and C backbone chemical-shift assignments of mouse cGAS NTD (residues 5-146), obtained with a set of 3D and 4D solution NMR experiments.
View Article and Find Full Text PDFNeuroradiology
January 2025
Department of Neurology, Second Affiliated Hospital of Xuzhou Medical University, No. 32, Meijian Road, Quanshan District, Xuzhou, 221006, Jiangsu, China.
Introduction: Residual dizziness (RD) is common in patients with benign paroxysmal positional vertigo (BPPV) after successful canalith repositioning procedures. This study aimed to investigate the therapeutic effects of vestibular rehabilitation (VR) on BPPV patients experiencing RD, and to explore the impact of VR on functional connectivity (FC), specifically focusing on the bilateral parietal operculum (OP) cortex.
Methods: Seventy patients with RD were randomly assigned to either a four-week VR group or a control group that received no treatment.
J Magn Reson
December 2024
Department of Medicine, University of Alberta, Canada; Department of Biochemistry, University of Alberta, Canada. Electronic address:
Solution NMR studies of large systems are hampered by rapid signal decay. We hereby introduce ROCSY (relaxation-optimized total correlation spectroscopy), which maximizes transfer efficiency across J-coupling-connected spin networks by minimizing the amount of time magnetization spends in the transverse plane. Hard pulses are substituted into the Clean-CITY TOCSY pulse element first developed by Ernst and co-workers, allowing for longer delays in which magnetization is aligned along the z-axis.
View Article and Find Full Text PDFFront Chem Biol
August 2024
Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University Wisconsin, Mequon, WI, United States.
Introduction: Dual specific phosphatases (DUSPs) are mitogen-activated protein kinase (MAPK) regulators, which also serve as drug targets for treating various vascular diseases. Previously, we have presented mechanistic characterizations of DUSP5 and its interaction with pERK, proposing a dual active site.
Methods: Herein, we characterize the interactions between the DUSP5 phosphatase domain and the pT-E-pY activation loop of ERK2, with specific active site assignments.
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