132d
From Proteopedia
(New page: 200px<br /><applet load="132d" size="450" color="white" frame="true" align="right" spinBox="true" caption="132d" /> '''SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX G...) |
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caption="132d" /> | caption="132d" /> | ||
'''SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE'''<br /> | '''SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The solution structure of the self-complementary DNA duplex | + | The solution structure of the self-complementary DNA duplex [d(GCCGTTAACGGC)]2, which contains the HpaI restriction site GTTAAC, has been elucidated by two-dimensional NMR, distance geometry (DG), and NOE back-calculation methods. Initial distance constraints were determined by polynomial fitting the two-spin initial NOE rates; backbone constraints from NOE and J-coupling observations (Kim et al., 1992) were included. RMSDs between initial-distance-refined structures derived from random-embedded DG, A-DNA, and B-DNA starting structures were all in the range 0.5-1.0 A, indicating good convergence properties of the algorithm, regardless of the starting structure. A semiautomatic back-calculation refinement procedure was developed and used to generate more refined structures for which the BKCALC-simulated NOE volumes matched the experimental data. The six final structures refined from various starting structures exhibit very good agreement with the experimental data (R values = 0.18) and converge well to within 0.8-A RMSD differences for the central 8 base pairs. The torsion and pseudorotation phase angles were found to be well determined by the data, and the local helical parameters for each base step converged quite well. The final structures show that the central T6-A7 step is somewhat underwound (twist angle ca. 29 degrees), with a large negative cup and a normal (wide) minor groove width, while the T5-T6 and A7-A8 steps have a partially narrowed minor groove. |
==About this Structure== | ==About this Structure== | ||
| - | 132D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 132D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=132D OCA]. |
==Reference== | ==Reference== | ||
Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site., Kim SG, Reid BR, Biochemistry. 1992 Dec 8;31(48):12103-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1457407 1457407] | Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site., Kim SG, Reid BR, Biochemistry. 1992 Dec 8;31(48):12103-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1457407 1457407] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Kim, S | + | [[Category: Kim, S G.]] |
| - | [[Category: Reid, B | + | [[Category: Reid, B R.]] |
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: hpa 1 restriction site]] | [[Category: hpa 1 restriction site]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:59 2008'' |
Revision as of 09:38, 21 February 2008
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SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE
Overview
The solution structure of the self-complementary DNA duplex [d(GCCGTTAACGGC)]2, which contains the HpaI restriction site GTTAAC, has been elucidated by two-dimensional NMR, distance geometry (DG), and NOE back-calculation methods. Initial distance constraints were determined by polynomial fitting the two-spin initial NOE rates; backbone constraints from NOE and J-coupling observations (Kim et al., 1992) were included. RMSDs between initial-distance-refined structures derived from random-embedded DG, A-DNA, and B-DNA starting structures were all in the range 0.5-1.0 A, indicating good convergence properties of the algorithm, regardless of the starting structure. A semiautomatic back-calculation refinement procedure was developed and used to generate more refined structures for which the BKCALC-simulated NOE volumes matched the experimental data. The six final structures refined from various starting structures exhibit very good agreement with the experimental data (R values = 0.18) and converge well to within 0.8-A RMSD differences for the central 8 base pairs. The torsion and pseudorotation phase angles were found to be well determined by the data, and the local helical parameters for each base step converged quite well. The final structures show that the central T6-A7 step is somewhat underwound (twist angle ca. 29 degrees), with a large negative cup and a normal (wide) minor groove width, while the T5-T6 and A7-A8 steps have a partially narrowed minor groove.
About this Structure
132D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site., Kim SG, Reid BR, Biochemistry. 1992 Dec 8;31(48):12103-16. PMID:1457407
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