Atomic structures of excited state Aâ??T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations
Atomic structures of excited state Aâ??T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations
NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watsonâ??Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1Aâ??T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3â?² and C4â?² spin relaxation in the rotating frame (R1Ï?) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1Aâ??T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state Aâ??T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.
[NMR paper] Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.
Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.
Biopolymers. 2014 Jan;101(1):13-20
Authors: ...
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[NMR paper] Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.
Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.
Chem Commun (Camb). 2013 Jul 28;49(59):6680-2
Authors: Holland GP, Mou Q, Yarger JL
Abstract
Two-dimensional (2D) (1)H-(13)C...
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01-18-2014 11:31 AM
Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R1Ï?: an application to αB-crystallin
Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R1Ï?: an application to αB-crystallin
Abstract Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible â??excitedâ?? conformational states. Recently it has also become possible to determine atomic resolution...
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04-09-2012 01:19 AM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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02-11-2012 10:31 AM
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Proteins. 2011 Feb 16;
Authors: Xu X, Ishima R, Ames JB
Recoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, serves as a calcium sensor in retinal rod cells. Ca(2+) -induced conformational changes in recoverin promote extrusion of its...
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04-06-2011 10:54 AM
Measurement of signs of chemical shift differences between ground and excited protein
Abstract Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond exchange processes between a major, populated ground state and one or more minor, low populated and often invisible â??excitedâ?? conformers. Analysis of CPMG data-sets also provides the magnitudes of the chemical shift difference(s) between exchanging states (|Î?Ï?|), that inform on the structural properties of the excited state(s). The sign of Î?Ï? is, however, not available from CPMG data. Here we present...
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08-14-2010 04:19 AM
Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively 13C labeled samples
Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively 13C labeled samples
Patrik Lundström, D. Flemming Hansen and Lewis E. Kay
Journal of Biomolecular NMR; 2008; 42(1); pp 35 - 47
Abstract: Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy has emerged as a powerful method for quantifying chemical shifts of excited protein states. For many applications of the technique that involve the measurement of relaxation rates of carbon...
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09-21-2008 11:36 PM
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
D. Flemming Hansen, Pramodh Vallurupalli and Lewis E. Kay
Journal of Biomolecular NMR; 2008; 41(3); pp 113 - 120
Abstract:
Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers...