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Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins

Huang, Jing and Meuwly, Markus. (2010) Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins. Journal of Chemical Theory and Computation, 6 (2). pp. 467-476.

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Official URL: http://edoc.unibas.ch/dok/A5842410

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Abstract

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 h3JNC′ 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.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Publisher:American Chemical Society
ISSN:1549-9626
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:07 Dec 2016 13:49
Deposited On:14 Sep 2012 06:59

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