1. NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide
- Author
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Justyna Samaszko-Fiertek, Barbara Dmochowska, Krzysztof Brzozowski, Janusz Madaj, and Rafal Slusarz
- Subjects
Models, Molecular ,Magnetic Resonance Spectroscopy ,QH301-705.5 ,vancomycin ,muramyl pentapeptide ,NMR ,NOESY ,HSQC ,MD ,hydrogen bond ,trajectory analysis ,Peptidoglycan ,Molecular Dynamics Simulation ,Catalysis ,Inorganic Chemistry ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Biology (General) ,Molecular Biology ,QD1-999 ,Spectroscopy ,Organic Chemistry ,Hydrogen Bonding ,General Medicine ,Anti-Bacterial Agents ,Computer Science Applications ,Chemistry ,Carbohydrate Sequence ,Muramic Acids - Abstract
The article describes an NMR spectroscopy study of interactions between vancomycin and a muramyl pentapeptide in two complexes: vancomycin and a native muramyl pentapeptide ended with D-alanine (MPP-D-Ala), and vancomycin and a modified muramyl pentapeptide ended with D-serine (MPP-D-Ser). The measurements were made in a 9:1 mixture of H2O and D2O. The obtained results confirmed the presence of hydrogen bonds previously described in the literature. At the same time, thanks to the pentapeptide model used, we were able to prove the presence of two more hydrogen bonds formed by the side chain amino group of L-lysine and oxygen atoms from the vancomycin carboxyl and amide groups. This type of interaction has not been described before. The existence of these hydrogen bonds was confirmed by the 1H NMR and molecular modeling. The formation of these bonds incurs additional through-space interactions, visible in the NOESY spectrum, between the protons of the L-lysine amino group and a vancomycin-facing hydrogen atom in the benzylic position. The presence of such interactions was also confirmed by molecular dynamics trajectory analysis.
- Published
- 2022