{"id":24452,"date":"2021-11-27T10:32:32","date_gmt":"2021-11-27T10:32:32","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=24452"},"modified":"2021-11-27T10:32:32","modified_gmt":"2021-11-27T10:32:32","slug":"biotins-biggest-lesson-is-the-importance-of-nonclassical-h-bonds-in-protein%e2%88%92ligand-complexes","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=24452","title":{"rendered":"Biotin\u2019s biggest lesson is the importance of nonclassical H-bonds in protein\u2212ligand complexes."},"content":{"rendered":"
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The title comes from the abstract of an article[1]<\/a><\/span> analysing why Biotin (vitamin B7) is such a strong and effective binder to proteins, with a free energy of (non-covalent) binding approaching 21 kcal\/mol. The author argues that an accumulation of both CH-\u03c0 and CH-O together with more classical hydrogen bonds and augmented by a sulfur centered hydrogen bond, oxyanion holes and water solvation, accounts for this large binding energy. \"\"<\/p>\n

Here, I thought I would present a visualisation of the surroundings of biotin using the method of NCI (non-covalent-interaction) analysis, which looks at the behaviour of the electron density in the “weak” (i.e.<\/i> non-covalent) regions of the biotin. This provides a more objective measure of the important interactions, independent of what we might consider important by virtue of having labels attached (such as e.g.<\/i> “hydrogen bond”).<\/p>\n

    \n
  1. I started by getting the coordinates of streptavidin (DOI: 10.2210\/pdb3RY2\/pdb<\/a>) a protein where biotin has been co-crystallised.[2]<\/a><\/span><\/li>\n
  2. Loaded into the CCDC Mercury program, I selected the molecule biotin itself and then added to the selection its close contacts with various groups in the streptavidin protein. These additions were truncated and capped with a methyl group to allow a wavefunction for the assembly to be calculated.<\/li>\n
  3. Hydrogens were then added to this structure to complete atom valencies, using “idealised” positions and ensuring that when rotamers were possible, they were set up to form hydrogen bonds.\t<\/li>\n
  4. A calculation (DOI: 10.14469\/hpc\/9982<\/a>\u00a0at the \u03c9B97XD\/Def2-TZVPP\/SCRF=water level)\u00a0was performed.\n<\/li>\n
  5. The heavy atom coordinates (i.e.<\/i> not hydrogens) are unaltered from the X-ray structure. Since atom positions as measured by X-ray diffraction and as computed using a DFT procedure are slightly different, the original coordinates were also subjected to three cycles of DFT-based geometry optimisation (DOI: 10.14469\/hpc\/9983<\/a>) to better reflect the electron density in the molecule.<\/li>\n
  6. The resulting wavefunctions in the form of an .fchk<\/b> file (for both unoptimised and partially optimised geometries) were then used to compute a grid of total electron density points<\/li>\n
  7. The density, in the form of a cube of points, was fed to Jmol using the commands
    \nload biotin_den.cub; isosurface parameters [0.5 1 0.0005 0.05 0.95 1.00] NCI \"\"; color isosurface \"bgyor\" range -0.04 0.04;<\/tt>
    \nand the resulting NCI surface was written out using the command write biotin.jvxl<\/tt> for inclusion here.<\/li>\n
  8. This is the NCI plot obtained from the raw coordinates from the PDB file.
    \n\"\"<\/li>\n
  9. This is the NCI plot obtained from the coordinates from the PDB file after three geometry optimisation cycles. Can you spot any differences?
    \n
    \n\"\"<\/li>\n
  10. These models are now available for you to explore by clicking on the images above.\n