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PDBsum entry 5bmh
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Immune system
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PDB id
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5bmh
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References listed in PDB file
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Key reference
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Title
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Rotameric preferences of a protein spin label at edge-Strand β-Sheet sites.
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Authors
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T.F.Cunningham,
S.Pornsuwan,
W.S.Horne,
S.Saxena.
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Ref.
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Protein Sci, 2016,
25,
1049-1060.
[DOI no: ]
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PubMed id
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Abstract
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Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful
method to measure protein dynamics and structure by electron spin resonance.
However, R1 measurements are complicated by the flexibility of the side chain.
While analysis approaches for solvent-exposed α-helical environment have been
developed to partially account for flexibility, similar work in β-sheets is
lacking. The goal of this study is to provide the first essential steps for
understanding the conformational preferences of R1 within edge β-strands using
X-ray crystallography and double electron electron resonance (DEER) distance
measurements. Crystal structures yielded seven rotamers for a
non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The
observed rotamers indicate contextual differences in R1 conformational
preferences compared to other solvent-exposed environments. For the DEER
measurements, each strand site was paired with the same α-helical site
elsewhere on the protein. The most probable distance observed by DEER is
rationalized based on the rotamers observed in the crystal structure.
Additionally, the appropriateness of common molecular modeling methods that
account for R1 conformational preferences are assessed for the β-sheet
environment. These results show that interpretation of R1 behavior in β-sheets
is difficult and indicate further development is needed for these computational
methods to correctly relate DEER distances to protein structure at edge
β-strand sites.
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