Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 113, Issue 42, Pages 13898-13900Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp908002n
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Funding
- National Basic Research Program of China [2004CB719901]
- National Natural Science Foundation of China [20773060, 20933002]
- Shanghai PuJiang program [09PJ1404000]
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Molecular dynamics simulations based oil 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 or proteins.
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