Three vignettes exemplify the potential of combining EM and X-ray crystallographic data with molecular dynamics (MD) simulation to explore the architecture, dynamics and functional properties of multicomponent, macromolecular complexes. The first two describe how EM and X-ray crystallography were used to solve structures of the ribosome and the Arp2/3-actin complex, which enabled MD simulations that elucidated functional dynamics. The third describes how EM, X-ray crystallography, and microsecond MD simulations of a GPCR:G protein complex were used to explore transmembrane signaling by the β-adrenergic receptor. Recent technical advancements in EM, X-ray crystallography and computational simulation create unprecedented synergies for integrative structural biology to reveal new insights into heretofore intractable biological systems.
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http://dx.doi.org/10.1016/j.sbi.2014.08.006 | DOI Listing |
Int J Biol Macromol
December 2024
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
Cyclin-dependent kinases (CDKs) regulate cell cycle progression and transcription. CDK7 plays a pivotal role in cell division and proliferation, and the CDK7 gene often exhibits mutations or copy number loss in cancer. Pharmacological targeting of CDK7 has been proposed as a cancer treatment strategy and several inhibitors are currently in clinical trials.
View Article and Find Full Text PDFSci Rep
December 2024
Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Kyungbook, Republic of Korea.
Alanine racemase (Alr) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization between L- and D-alanine in bacteria. Owing to the potential interest in targeting Alr for antibacterial drug development, several studies have determined the structures of Alr from different species, proposing models for the reaction mechanism. Insights into its reaction dynamics may be conducive to a better understanding of the Alr reaction mechanism.
View Article and Find Full Text PDFJ Mol Graph Model
December 2024
Post Graduate Department of Chemistry, Mehr Chand Mahajan DAV College for Women, Chandigarh, 160036, India.
A large population in the world lives in tropical and subtropical regions, showing a high risk of Zika viral infection which leads to a situation of global health emergency and demands extensive research to create effective antiviral medicines. Herein, we introduce the design of a new derivatized trans-stilbene molecule to investigate the inhibition of Zika virus entry into the host cell by molecular docking approach. The synthesized compound has been characterized by different analytical techniques such as FTIR, H NMR,C NMR and UV-visible spectroscopy as well as Mass spectrometry (MS).
View Article and Find Full Text PDFNat Commun
December 2024
Experimental Medicine & Immunotherapeutics, University of Cambridge, Cambridge, UK.
We describe a structural and functional study of the G protein-coupled apelin receptor, which binds two endogenous peptide ligands, apelin and Elabela/Toddler (ELA), to regulate cardiovascular development and function. Characterisation of naturally occurring apelin receptor variants from the UK Genomics England 100,000 Genomes Project, and AlphaFold2 modelling, identifies T89 as important in the ELA binding site, and R168 as forming extensive interactions with the C-termini of both peptides. Base editing to introduce an R/H168 variant into human stem cell-derived cardiomyocytes demonstrates that this residue is critical for receptor binding and function.
View Article and Find Full Text PDFMar Drugs
December 2024
CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.
Six new sesquiterpenes, including four eremophilane derivatives fureremophilanes A-D (-) and two acorane analogues furacoranes A and B ( and ), were characterized from the culture extract of the cold-seep derived fungus CS-280 co-cultured with autoclaved QDIO-4. All the six compounds were highly oxygenated especially and with infrequent epoxyethane and tetrahydrofuran ring systems. The structures of - were established on the basis of detailed interpretation of 1D and 2D NMR and MS data.
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