6MY2 image
Entry Detail
PDB ID:
6MY2
Keywords:
Title:
Solution structure of gomesin at 298 K
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2018-10-31
Release Date:
2019-11-06
Method Details:
Experimental Method:
Conformers Calculated:
200
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy and best stereochemical properties as judged by Molprobity
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:gomesin
Chain IDs:A
Chain Length:19
Number of Molecules:1
Biological Source:Acanthoscurria gomesiana
Ligand Molecules
Primary Citation
The unusual conformation of cross-strand disulfide bonds is critical to the stability of beta-hairpin peptides.
Proteins 88 485 502 (2020)
PMID: 31589791 DOI: 10.1002/prot.25828

Abstact

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.

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