8F11

T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label

Summary for 8F11

• Entry DOI: 10.2210/pdb8f11/pdb
• Descriptor: Endolysin, BETA-MERCAPTOETHANOL, 1-[(1r,3r,5r,7r)-6-hydroxy-2,6-diazatricyclo[3.3.1.1~3,7~]decan-2-yl]ethan-1-one, ... (6 entities in total)
• Functional Keywords: spin label, glycan hydrolase, hydrolase
• Biological source: Escherichia phage T4
• Total number of polymer chains: 1
• Total formula weight: 19139.39

Authors

Wilson, M.A.,Madzelan, P.,Rajca, A.,Stein, R.,Yang, Z. (deposition date: 2022-11-04, release date: 2023-02-15, Last modification date: 2023-12-13)

Primary citation

Yang, Z.,Stein, R.A.,Pink, M.,Madzelan, P.,Ngendahimana, T.,Rajca, S.,Wilson, M.A.,Eaton, S.S.,Eaton, G.R.,Mchaourab, H.S.,Rajca, A.
Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins.
J.Am.Chem.Soc., 145:25726-25736, 2023

PubMed Abstract: We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, = 1.9 × 10 M, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τ, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τ and electron spin coherence time, , along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.

PubMed: 37963181
DOI: 10.1021/jacs.3c09184

Experimental method

X-RAY DIFFRACTION (1.12 Å)