Molecular dynamics analysis of a buckyball–antibody complex
- William H. Noon*,
- Yifei Kong†, and
- Jianpeng Ma*,†,‡,§
- *Department of Bioengineering, Rice University, 6100 Main, MS-142, Houston, TX 77005; and †Graduate Program of Structural and Computational Biology and Molecular Biophysics, and ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030
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Edited by William N. Lipscomb, Harvard University, Cambridge, MA, and approved November 28, 2001 (received for review October 5, 2001)
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Figure 1Ribbon diagram of the crystal structure of the Fab fragment of the fullerene-specific antibody (ref. 23; PDB ID code, 1EMT). The two polypeptide chains, variable region heavy chain (VH) and light chain (VL), are marked. The suggested binding site of the buckyball substrate is indicated by the circle. The figure is made by using software MOLSCRIPT (39) and rendered by RASTER3D (40).
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Figure 2The molecular dynamics simulation system with the stochastic boundary condition. It contains 106 protein residues (ribbon), the buckyball (space-filling model in yellow), and 166 water molecules (ball-and-stick).
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Figure 3Solvent-exposed surface area as a function of time in a 5-ns simulation window. The average value is about 17%.
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Figure 4(a) Stereo pair snapshot of the buckyball inside the binding site of the antibody. Some key protein side chains are explicitly drawn and the rest of the protein matrix is given in a dotted surface representation. The view is from the top in Fig. 1. (b) Stereo pair of a triple π-stacking. A piece of the buckyball and the side chains of Trp-33 (VH) and Tyr-52 (VH) are shown. (c) Stereo pair of stacking interactions made by Trp-47 (VH) and Phe-96 (VL). The Hɛ atom of Trp-47 (VH) points directly toward the ball, which can induce a weak hydrogen bond with the π-electron of the ball. Phe-96 (VL) is in stacking with the ball as well. (d) Stereo pair of a different configuration of the interactions in c. The side chain motions bring the guanidinium group of Arg-50 (VH) to a triple π-stacking with Trp-47 (VH) and the ball. The side chain of Phe-96 (VL) moves aside, but remains in stacking with the ball.
Footnotes
- Copyright © 2002, The National Academy of Sciences
