BIOPHYSICAL THEORY AND MODELING |
Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths and bond angles of the GTP ligand induced by the Ras-protein
Marco Klähn 1, Jürgen Schlitter 1 and Klaus Gerwert 1*
1 University of Bochum
* To whom correspondence should be addressed. E-mail: juergen{at}bph.rub.de.
Submitted on December 29, 2004
Revised on February 2, 2005
Accepted on 21 March 2005
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Abstract |
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The GTPase Ras p21 is a crucial switch in cellular signal transduction. FTIR spectra of the substrate guanosine triphosphate (GTP) show remarkable changes when it binds to the enzyme. The reduced band widths indicate that the flexible GTP molecule is guided by the protein into a preferred conformation. The delocalized phosphate vibrations of unbound GTP become localized. The frequency shifts show an electron movement towards beta-phosphate, which probably contributes to catalysis by reducing the free activation energy. To quantify these qualitative observations we performed QM/MM molecular dynamics (MD) simulations of Ras•GTP in solution and GTP in water. The triphosphate part of GTP was treated quantum mechanically using DFT. Vibrational spectra were calculated in harmonic approximation with an average deviation of 3% from the experimental frequencies. This provides a high confidence in the computational results as vibrational spectra are highly sensitive to conformation and charge distribution. As compared to GTP in water, Ras-bound GTP shows a shift of negative charge of about 0.2 e towards the beta-phosphate from gamma-phosphate and from alpha-phosphate due to the positive charge of the magnesium ion, to a lesser extent of Lysine 16, and surprisingly without any effect of the P-loop backbone. Magnesium and Gly13 twist and bend the gamma-O beta bonds such that the crucial bond is stretched before cleaving.
Key Words:
FTIR Spectroscopy, G-Protein, QM/MM, Ras, enzyme catalysis, simulation
