Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid- β

Journal Article · Fri Sep 01 00:00:00 EDT 2017 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2017.06.067· OSTI ID:1462505

Sasmal, Sukanya ^[1]; Lincoff, James ^[1]; Head-Gordon, Teresa ^[2]

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1. University of California, Berkeley, Berkeley, CA (United States). Department of Chemical and Biomolecular Engineering
2. University of California, Berkeley, Berkeley, CA (United States). Department of Chemical and Biomolecular Engineering, Department of Chemistry, Department of Bioengineering, Pitzer Center for Theoretical Chemistry

Paramagnetic relaxation enhancement is an NMR technique that has yielded important insight into the structureof folded proteins, although the perturbation introduced by the large spin probe might be thought to diminish its usefulness whenapplied to characterizing the structural ensembles of intrinsically disordered proteins (IDPs). We compare the computationallygenerated structural ensembles of the IDP amyloid-b42 (Ab42) to an alternative sequence in which a nitroxide spin labelattached to cysteine has been introduced at its N-terminus. Based on this internally consistent computational comparison,we find that the spin label does not perturb the signature population of the b-hairpin formed by residues 16–21 and 29–36that is dominant in the Ab42 reference ensemble. However, the presence of the tag induces a strong population shift in a subsetof the original Ab42 structural sub-populations, including a sevenfold enhancement of the b-hairpin formed by residues 27–31and 33–38. Through back-calculation of NMR observables from the computational structural ensembles, we show that the struc-tural differences between the labeled and unlabeled peptide would be evident in local residual dipolar couplings, and possiblydifferences in homonuclear ¹H-¹H nuclear Overhauser effects (NOEs) and heteronuclear ¹H-¹⁵N NOEs if the paramagneticcontribution to the longitudinal relaxation does not suppress the NOE intensities in the real experiment. This work shows thatmolecular simulation provides a complementary approach to resolving the potential structural perturbations introduced by re-porter tags that can aid in the interpretation of paramagnetic relaxation enhancement, double electron-electron resonance,and fluorescence resonance energy transfer experiments applied to IDPs.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
• Sponsoring Organization: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1462505
• Journal Information: Biophysical Journal, Vol. 113, Issue 5; ISSN 0006-3495
• Publisher: Elsevier
• Country of Publication: United States
• Language: English