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Peptoid-based macrodiscs of variable lipid composition for structural studies of membrane proteins by oriented-sample solid-state NMR.
J Struct Biol X
June 2024
Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
Solid-state Nuclear Magnetic Resonance (NMR) in combination with magnetically aligned discoidal lipid mimics allows for studying the conformations of membrane proteins in planar, lipid-rich bilayer environments and at the physiological temperature. We have recently demonstrated the general applicability of macrodiscs composed of DMPC lipids and peptoid belts, which yield magnetic alignment and NMR spectroscopic resolution comparable or superior to detergent-containing bicelles. Here we report on a considerable improvement in the magnetic alignment and NMR resolution of peptoid-based macrodiscs consisting of a mixture of the zwitterionic and negatively charged lipids (DMPC/DMPG at the 85% to 15% molar ratio).
View Article and Find Full Text PDFSolution structure ensemble of human obesity-associated protein FTO reveals druggable surface pockets at the interface between the N- and C-terminal domain.
J Biol Chem
May 2022
Department of Chemistry, Iowa State University, Ames, Iowa, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA. Electronic address:
The fat mass and obesity-associated FTO protein catalyzes demethylation of the N-methyladenosine, an epigenetic mark that controls several metabolic pathways by modulating the transcription, translation, and cellular localization of RNA molecules. Since the discovery that its overexpression links to the development of obesity and cancer, FTO was the target of screening campaigns and structure-based drug design efforts. Although several FTO inhibitors were generated, these often lack potency or selectivity.
View Article and Find Full Text PDFH/C/N triple-resonance experiments for structure determinaton of membrane proteins by oriented-sample NMR.
Solid State Nucl Magn Reson
February 2021
Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA. Electronic address:
The benefits of triple-resonance experiments for structure determination of macroscopically oriented membrane proteins by solid-state NMR are discussed. While double-resonance H/N experiments are effective for structure elucidation of alpha-helical domains, extension of the method of oriented samples to more complex topologies and assessing side-chain conformations necessitates further development of triple-resonance (H/C/N) NMR pulse sequences. Incorporating additional spectroscopic dimensions involving C spin-bearing nuclei, however, introduces essential complications arising from the wide frequency range of the H-C dipolar couplings and C CSA (>20 kHz), and the presence of the C-C homonuclear dipole-dipole interactions.
View Article and Find Full Text PDFActive Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics.
Biophys J
November 2018
Department of Chemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa. Electronic address:
AlkB homolog 5 (Alkbh5) is one of nine members of the AlkB family, which are nonheme Fe/α-ketoglutarate-dependent dioxygenases that catalyze the oxidative demethylation of modified nucleotides and amino acids. Alkbh5 is highly selective for the N-methyladenosine modification, an epigenetic mark that has spawned significant biological and pharmacological interest because of its involvement in important physiological processes, such as carcinogenesis and stem cell differentiation. Herein, we investigate the structure and dynamics of human Alkbh5 in solution.
View Article and Find Full Text PDFAutomated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing.
J Magn Reson
August 2018
Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States. Electronic address:
An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on N-N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks.
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