IN THE TITLE COMPOUND [SYSTEMATIC NAME: (1R,3S,5R,6S)-8-methyl-3-(4-methyl-phenyl-sulfon-yloxy)-8-aza-bicyclo-[3.2.1]octan-6-yl acetate], C(17)H(23)NO(5)S, the fused piperidine ring exists in a chair conformation with the N atom and one C atom displaced by 0.876 (2) and -0.460 (3) Å, respectively, on opposite sides of the mean plane defined by the other four atoms. The fused pyrrolidine ring adopts an envelope conformation with the N atom deviating by 0.644 (3) Å from the mean plane of the other four atoms.
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http://dx.doi.org/10.1107/S1600536808035800 | DOI Listing |
Biophys J
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States. Electronic address:
Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems.
View Article and Find Full Text PDFNat Chem Biol
January 2025
Department of Gastroenterology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
In prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism underlying the oxygen-to-sulfur substitution remains enigmatic. In this study, we discovered a hypercompact DNA phosphorothioation system, TdpABC, in extreme thermophiles.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure-dynamics-function relationships of macromolecules to which they are attached, with the exception of nucleic acids. This is largely due to the inherent difficulties of not only studying the conformational dynamics of sugars using experimental methods but indeed also resolving their static structures.
View Article and Find Full Text PDFChemMedChem
January 2025
Shanghai University, Institute of Nanochemistry and Nanobiology, No.99 Shangda Rd. Rm201, Bldg. E, 200444, Shanghai, CHINA.
As a newly emerging technology, conformational engineering (CE) has been gradually displaying the power of producing protein-like nanoparticles (NPs) by tuning flexible protein fragments into their original native conformation on NPs. But apparently, not all types of NPs can serve as scaffolds for CE. To expedite the CE technology on a broader variety of NPs, the essential characteristic of NPs as scaffolds for CE needs to be identified.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
The soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein complex drives membrane fusion, and this process is further aided by accessory proteins, including complexin and α-synuclein. To understand the molecular mechanism underlying membrane fusion, we introduce an all-atom molecular dynamics (MD) simulation method. This method is used to understand and predict the conformations of protein and lipids, membrane geometry, and their interaction at femtosecond precision, by describing complex chemical systems with atomic models.
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