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Rotameric preferences of a protein spin label at edge-strand ?-sheet sites.

ABSTRACT: 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 ?-helical environment have been developed to partially account for flexibility, similar work in ?-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge ?-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 ?-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 ?-sheet environment. These results show that interpretation of R1 behavior in ?-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge ?-strand sites.

SUBMITTER: Cunningham TF

PROVIDER: S-EPMC4838652 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Rotameric preferences of a protein spin label at edge-strand β-sheet sites.

Cunningham Timothy F TF Pornsuwan Soraya S Horne W Seth WS Saxena Sunil S

Protein science : a publication of the Protein Society 20160321 5

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 pr ...[more]

PMID: 26948069

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Project description:The fact that natural beta-sheet proteins are usually soluble but that fragments or designs of beta structure usually aggregate suggests that natural beta proteins must somehow be designed to avoid this problem. Regular beta-sheet edges are dangerous, because they are already in the right conformation to interact with any other beta strand they encounter. We surveyed edge strands in a large sample of all-beta proteins to tabulate features that could protect against further beta-sheet interactions. beta-barrels, of course, avoid edges altogether by continuous H-bonding around the barrel cylinder. Parallel beta-helix proteins protect their beta-sheet ends by covering them with loops of other structure. beta-propeller and single-sheet proteins use a combination of beta-bulges, prolines, strategically placed charges, very short edge strands, and loop coverage. beta-sandwich proteins favor placing an inward-pointing charged side chain on one of the edge strands where it would be buried by dimerization; they also use bulges, prolines, and other mechanisms. One recent beta-hairpin design has a constrained twist too great for accommodation into a larger beta-sheet, whereas some beta-sheet edges are protected by the bend and reverse twist produced by an Lbeta glycine. All free edge strands were seen to be protected, usually by several redundant mechanisms. In contrast, edge strands that natively form beta H-bonded dimers or rings have long, regular stretches without such protection. These results are relevant to understanding how proteins may assemble into beta-sheet amyloid fibers, and they are especially applicable to the de novo design of beta structure. Many edge-protection strategies used by natural proteins are beyond our current abilities to constrain by design, but one possibility stands out as especially useful: a single charged side chain near the middle of what would ordinarily be the hydrophobic side of the edge beta strand. This minimal negative-design strategy changes only one residue, requires no backbone distortion, and is easy to design. The accompanying paper [Wang, W. & Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760-2765] makes use of the inward-pointing charge strategy with great success, turning highly aggregated beta-sandwich designs into soluble monomers.

Dataset Information

Rotameric preferences of a protein spin label at edge-strand ?-sheet sites.

Publications

Rotameric preferences of a protein spin label at edge-strand β-sheet sites.

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