NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization.
Molecular dynamics simulations based on the standard nonpolarizable AMBER force field and on quantum-derived polarized protein-specific charge (PPC) are performed to compute NMR scalar coupling constants across hydrogen bonds for three benchmark protein systems: ubiquitin, the GB1 domain of protein G, and the SMN Tudor domain. Direct comparison of the simulation result with experimental data gives strong evidence that intraprotein hydrogen bonds are significantly stabilized by electronic polarization, both in terms of NMR scalar coupling constants and X-ray determined geometries of hydrogen bonds. Without the polarization effect in the force field, hydrogen bonds are found to be "too loose", which leads to less stable or even unstable local structures of proteins.
Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
Chang G
CG
Ji
John Z H
JZ
Zhang
D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009419:Nerve Tissue Proteins / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D055533:Survival of Motor Neuron 1 Protein / Q000737:chemistry; D025801:Ubiquitin / Q000737:chemistry
C029152:G-substrate; D009419:Nerve Tissue Proteins; D011506:Proteins; D055533:Survival of Motor Neuron 1 Protein; D025801:Ubiquitin