Here we provide a guide for adapting the tools developed for protein X-ray crystallography to study the structures and supramolecular assembly of peptides. Peptide crystallography involves selecting a suitable peptide, crystallizing the peptide, collecting X-ray diffraction data, processing the diffraction data, determining the crystallographic phases and generating an electron density map, building and refining models, and depositing the crystallographic structure in the Protein Data Bank (PDB). Advances in technology make this process easy for a newcomer to adopt. This paper describes techniques for determining the X-ray crystallographic structures of peptides: incorporation of amino acids containing heavy atoms for crystallographic phase determination, commercially available kits to crystallize peptides, modern techniques for X-ray crystallographic data collection, and free user-friendly software for data processing and producing a crystallographic structure.
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http://dx.doi.org/10.1002/ijch.201400179 | DOI Listing |
Int J Mol Sci
January 2025
Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Nagano, Japan.
Osteocalcin is a useful biomarker for bone formation and bone-related diseases. KTM219 is an anti-osteocalcin C-terminal peptide antibody. The single-chain variable region (scFv) and antigen-binding fragment (Fab) of KTM219 are applicable to the Quenchbody (Q-body) immunoassay.
View Article and Find Full Text PDFNat Commun
January 2025
University of St Andrews, School of Biology, North Haugh, Biomolecular Sciences Building, St Andrews, UK.
Cyclic dipeptides are produced by organisms across all domains of life, with many exhibiting anticancer and antimicrobial properties. Oxidations are often key to their biological activities, particularly C-C bond oxidation catalysed by tailoring enzymes including cyclodipeptide oxidases. These flavin-dependent enzymes are underexplored due to their intricate three-dimensional arrangement involving multiple copies of two distinct small subunits, and mechanistic details underlying substrate selection and catalysis are lacking.
View Article and Find Full Text PDFChin J Nat Med
January 2025
Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China. Electronic address:
Amoenucles A-F (1-6), six previously undescribed nucleoside derivatives, and two known analogs (7 and 8) were isolated from the culture of Aspergillus amoenus TJ507. Their structures were elucidated through spectroscopic analysis, single-crystal X-ray crystallography, and chemical reactions. Notably, 3 and 4 represent the first reported instances of nucleosides with an attached pyrrole moiety.
View Article and Find Full Text PDFEur J Pharmacol
January 2025
Department of Drug and Health Sciences, Pharmacology and Toxicology Section, University of Catania, Italy; Oasi Research Institute-IRCCS, 94018 Troina, Italy. Electronic address:
Background: Adamantane derivatives, such as memantine (Mem) and amantadine (Ada), have distinct mechanisms and therapeutic applications. Ada is primarily utilized as an antiviral and anti-Parkinson drug without significant pro-cognitive effects, Mem is effective in various clinical conditions characterized by cognitive deficits, including Alzheimer's disease. Recent evidence highlights a neuroprotective role for Aβ monomers, suggesting that preventing their aggregation into toxic oligomers could be a promising therapeutic strategy.
View Article and Find Full Text PDFProtein Sci
February 2025
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, St. Paul, Minnesota, USA.
N-Methylation of the peptide backbone confers pharmacologically beneficial characteristics to peptides that include greater membrane permeability and resistance to proteolytic degradation. The borosin family of ribosomally synthesized and post-translationally modified peptides offer a post-translational route to install amide backbone α-N-methylations. Previous work has elucidated the substrate scope and engineering potential of two examples of type I borosins, which feature autocatalytic precursors that encode N-methyltransferases that methylate their own C-termini in trans.
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