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Design of a light and Ca switchable organic-peptide hybrid.
Proc Natl Acad Sci U S A
February 2025
SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea.
The design of organic-peptide hybrids has the potential to combine our vast knowledge of protein design with small molecule engineering to create hybrid structures with complex functions. Here, we describe the computational design of a photoswitchable Ca-binding organic-peptide hybrid. The designed molecule, designated Ca-binding switch (CaBS), combines an EF-hand motif from classical Ca-binding proteins such as calmodulin with a photoswitchable group that can be reversibly isomerized between a spiropyran (SP) and merocyanine (MC) state in response to different wavelengths of light.
View Article and Find Full Text PDFIn-Cell Mass Spectrometry and Ultraviolet Photodissociation Navigates the Intracellular Protein Heterogeneity.
J Am Chem Soc
January 2025
State Key Laboratory of Molecular Reaction Dynamics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Directly probing the heterogeneous conformations of intracellular proteins within their native cellular environment remains a significant challenge in mass spectrometry (MS). Here, we establish an in-cell MS and ultraviolet photodissociation (UVPD) strategy that directly ejects proteins from living cells into a mass spectrometer, followed by 193 nm UVPD for structural analysis. Applying this approach to calmodulin (CaM), we reveal that it adopts more extended conformations within living cells compared with purified samples , highlighting the unique influence of intracellular environments on protein folding.
View Article and Find Full Text PDFG-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes.
Nucleic Acids Res
January 2025
Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, United States.
G-quadruplex (G4) structure is a nucleic acid secondary structure formed by guanine-rich sequences, playing essential roles in various biological processes such as gene regulation and environmental stress adaptation. Although prokaryotes growing at high temperatures have higher GC contents, the pattern of G4 structure associated with GC content variation in thermal adaptation remains elusive. This study analyzed 681 bacterial genomes to explore the role of G4 structures in thermal adaptation.
View Article and Find Full Text PDFCryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting.
Nucleic Acids Res
January 2025
Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, United States.
The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states.
View Article and Find Full Text PDFSelf-Assembly of Mycolic Acid in Water: Monolayer or Bilayer.
Langmuir
January 2025
Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science (IISc), Bangalore 560012, India.
The enduring pathogenicity of can be attributed to its lipid-rich cell wall, with mycolic acids (MAs) being a significant constituent. Different MAs' fluidity and structural adaptability within the bacterial cell envelope significantly influence their physicochemical properties, operational capabilities, and pathogenic potential. Therefore, an accurate conformational representation of various MAs in aqueous media can provide insights into their potential role within the intricate structure of the bacterial cell wall.
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