6MY2

Solution structure of gomesin at 298 K

Summary for 6MY2

• Entry DOI: 10.2210/pdb6my2/pdb
• Related: 1KFP 6MY3 6MYI
• NMR Information: BMRB: 30535
• Descriptor: gomesin (1 entity in total)
• Functional Keywords: spider venom peptides; beta hairpin motif, toxin
• Biological source: Acanthoscurria gomesiana
• Total number of polymer chains: 1
• Total formula weight: 2279.76

Authors

Chin, Y.K.-Y.,Deplazes, E. (deposition date: 2018-10-31, release date: 2019-11-06, Last modification date: 2024-10-16)

Primary citation

Deplazes, E.,Chin, Y.K.,King, G.F.,Mancera, R.L.
The unusual conformation of cross-strand disulfide bonds is critical to the stability of beta-hairpin peptides.
Proteins, 88:485-502, 2020

PubMed Abstract: The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.

PubMed: 31589791
DOI: 10.1002/prot.25828

Experimental method

SOLUTION NMR