2M54

Refined NMR solution structure of metal-modified DNA

Summary for 2M54

• Entry DOI: 10.2210/pdb2m54/pdb
• Related: 2K68 2KE8
• NMR Information: BMRB: 16138
• Descriptor: DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3'), SILVER ION (2 entities in total)
• Functional Keywords: dna, artificial nucleobase, imidazole nucleoside
• Total number of polymer chains: 2
• Total formula weight: 10354.23

Authors

Kumbhar, S.,Johannsen, S.,Sigel, R.K.,Waller, M.P.,Mueller, J. (deposition date: 2013-02-13, release date: 2013-05-15, Last modification date: 2024-05-15)

Primary citation

Kumbhar, S.,Johannsen, S.,Sigel, R.K.,Waller, M.P.,Muller, J.
A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.
J.Inorg.Biochem., 127:203-210, 2013

PubMed Abstract: A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures.

PubMed: 23622950
DOI: 10.1016/j.jinorgbio.2013.03.009

Experimental method

SOLUTION NMR