Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 6, Issue 2, Pages 467-476Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct9005695
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Funding
- Swiss National Science Foundation [200021-117810]
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Hydrogen bonds (H bonds) are fundamental for the stability, structure, and dynamics of chemically and biologically relevant systems. One of the direct means to detect H bonds in proteins is NMR spectroscopy. As H bonds are dynamic in nature, atomistic simulations offer a meaningful way to characterize and analyze properties of hydrogen bonds, provided a sufficiently accurate interaction potential is available. Here, we use explicit H-bond potentials to investigate scalar coupling constants (h3)J(NC') and characterize the conformational ensemble for increasingly accurate intermolecular potentials. By considering a range of proteins with different overall topology a general procedure to improve the hydrogen-bonding potential (morphing potentials) based on experimental information is derived. The robustness of this approach is established through explicit simulations in full solvation and comparison with experimental results. The H-bond potentials used here lead to more directional H bonds than conventional electrostatic representations employed in molecular mechanics potentials. It is found that the optimized potentials lead to H-bond geometries in remarkable agreement with previous ab initio and knowledge-based approaches to H bonds in model systems and in proteins. This suggests that, by combining theory, computation, and experimental data, H-bonding potentials can be improved and are potentially useful to better study coupling, energy transfer, and allosteric communication in proteins.
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