3cti
From Proteopedia
(New page: 200px<br /><applet load="3cti" size="450" color="white" frame="true" align="right" spinBox="true" caption="3cti" /> '''RELAXATION MATRIX REFINEMENT OF THE SOLUTION...) |
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| - | [[Image:3cti.jpg|left|200px]]<br /><applet load="3cti" size=" | + | [[Image:3cti.jpg|left|200px]]<br /><applet load="3cti" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3cti" /> | caption="3cti" /> | ||
'''RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF SQUASH TRYPSIN INHIBITOR'''<br /> | '''RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF SQUASH TRYPSIN INHIBITOR'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the small squash trypsin inhibitor CMTI-I is refined by | + | The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A. |
==About this Structure== | ==About this Structure== | ||
| - | 3CTI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Cucurbita_maxima Cucurbita maxima]. Full crystallographic information is available from [http:// | + | 3CTI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Cucurbita_maxima Cucurbita maxima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTI OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Cucurbita maxima]] | [[Category: Cucurbita maxima]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Bruenger, A | + | [[Category: Bruenger, A T.]] |
[[Category: Habazettl, J.]] | [[Category: Habazettl, J.]] | ||
| - | [[Category: Holak, T | + | [[Category: Holak, T A.]] |
[[Category: Nilges, M.]] | [[Category: Nilges, M.]] | ||
[[Category: proteinase inhibitor (trypsin)]] | [[Category: proteinase inhibitor (trypsin)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:08:58 2008'' |
Revision as of 17:09, 21 February 2008
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RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF SQUASH TRYPSIN INHIBITOR
Overview
The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.
About this Structure
3CTI is a Single protein structure of sequence from Cucurbita maxima. Full crystallographic information is available from OCA.
Reference
Relaxation matrix refinement of the solution structure of squash trypsin inhibitor., Nilges M, Habazettl J, Brunger AT, Holak TA, J Mol Biol. 1991 Jun 5;219(3):499-510. PMID:2051485
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