1sy8
From Proteopedia
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| - | [[Image:1sy8.gif|left|200px]] | + | [[Image:1sy8.gif|left|200px]] |
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| - | '''Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics''' | + | {{Structure |
| + | |PDB= 1sy8 |SIZE=350|CAPTION= <scene name='initialview01'>1sy8</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1SY8 is a [ | + | 1SY8 is a [[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=1SY8 OCA]. |
==Reference== | ==Reference== | ||
| - | Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics., Barthwal R, Awasthi P, Monica, Kaur M, Sharma U, Srivastava N, Barthwal SK, Govil G, J Struct Biol. 2004 Oct;148(1):34-50. PMID:[http:// | + | Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics., Barthwal R, Awasthi P, Monica, Kaur M, Sharma U, Srivastava N, Barthwal SK, Govil G, J Struct Biol. 2004 Oct;148(1):34-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15363786 15363786] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Awasthi, P.]] | [[Category: Awasthi, P.]] | ||
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[[Category: 2d-nmr of d-tgatca]] | [[Category: 2d-nmr of d-tgatca]] | ||
[[Category: dna flexibility]] | [[Category: dna flexibility]] | ||
| - | [[Category: restrained molecular | + | [[Category: restrained molecular dynamic]] |
[[Category: sequence related conformation]] | [[Category: sequence related conformation]] | ||
[[Category: tpg/cpa basepair step]] | [[Category: tpg/cpa basepair step]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:11:11 2008'' |
Revision as of 12:11, 20 March 2008
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Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics
Overview
The 5' d-TpG 3' element is a part of DNA sequences involved in regulation of gene expression and is also a site for intercalation of several anticancer drugs. Solution conformation of DNA duplex d-TGATCA containing this element has been investigated by two-dimensional NMR spectroscopy. Using a total of 12 torsional angles and 121 distance constraints, structural refinement has been carried out by restrained molecular dynamics (rMDs) in vacuum up to 100 ps. The structure is characterized by a large positive roll at TpG/CpA base pair step and large negative propeller twist for AT and TA base pairs. The backbone torsional angle, gamma(O5'-C5'-C4'-C3'), of T1 residue adopts a trans-conformation which is corroborated by short intra nucleotide T1H6-T1H5' (3.7A) distance in nuclear overhauser effect spectroscopy (NOESY) spectra while the backbone torsional angle, beta(P-O5'-C5'-C4'), exists in trans as well as gauche state for T1 and C5 residues. There is evidence of significant flexibility of the sugar-phosphate backbone with rapid inter-conversion between two different conformers at TpG/CpA base pair step. The base sequence dependent variations and local structural heterogeneity have important implications in specific recognition of DNA by ligands.
About this Structure
1SY8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics., Barthwal R, Awasthi P, Monica, Kaur M, Sharma U, Srivastava N, Barthwal SK, Govil G, J Struct Biol. 2004 Oct;148(1):34-50. PMID:15363786
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