7V0V

GFP Nanobody NMR Structure

Summary for 7V0V

• Entry DOI: 10.2210/pdb7v0v/pdb
• Related: 3OGO
• NMR Information: BMRB: 31020
• Descriptor: Anti-GFP Nanobody (1 entity in total)
• Functional Keywords: nanobody gfp, immune system
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 13759.22

Authors

Mueller, G.A. (deposition date: 2022-05-11, release date: 2022-06-08, Last modification date: 2024-05-15)

Primary citation

Fernandez-Quintero, M.L.,DeRose, E.F.,Gabel, S.A.,Mueller, G.A.,Liedl, K.R.
Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR.
Int J Mol Sci, 23:-, 2022

PubMed Abstract: Variable domains of camelid antibodies (so-called nanobodies or VH) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding nanobody by using molecular dynamics simulations in combination with experimentally derived data from nuclear magnetic resonance (NMR) spectroscopy. The NMR data contain both structural and dynamic information resolved at various timescales, which allows an assessment of the quality of protein MD simulations. Thus, in this study, we compared the ensembles for the anti-GFP-binding nanobody obtained from MD simulations with results from NMR. We find excellent agreement of the NOE-derived distance maps obtained from NMR and MD simulations and observe similar conformational spaces for the simulations with and without NOE time-averaged restraints. We also compare the measured and calculated order parameters and find generally good agreement for the motions observed in the ps-ns timescale, in particular for the CDR3 loop. Understanding of the CDR3 loop dynamics is especially critical for nanobodies, as this loop is typically critical for antigen recognition.

PubMed: 35628231
DOI: 10.3390/ijms23105419

Experimental method

SOLUTION NMR