1s4r
From Proteopedia
(New page: 200px<br /><applet load="1s4r" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s4r, resolution 1.9Å" /> '''Structure of a reacti...) |
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| - | [[Image:1s4r.jpg|left|200px]]<br /><applet load="1s4r" size=" | + | [[Image:1s4r.jpg|left|200px]]<br /><applet load="1s4r" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1s4r, resolution 1.9Å" /> | caption="1s4r, resolution 1.9Å" /> | ||
'''Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis'''<br /> | '''Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We determine the number of authentic reaction intermediates in the later | + | We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms. |
==About this Structure== | ==About this Structure== | ||
| - | 1S4R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila] with HC4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1S4R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila] with <scene name='pdbligand=HC4:'>HC4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4R OCA]. |
==Reference== | ==Reference== | ||
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[[Category: reaction intermediate]] | [[Category: reaction intermediate]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:58:07 2008'' |
Revision as of 12:58, 21 February 2008
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Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis
Overview
We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.
About this Structure
1S4R is a Single protein structure of sequence from Halorhodospira halophila with as ligand. Full crystallographic information is available from OCA.
Reference
Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data., Schmidt M, Pahl R, Srajer V, Anderson S, Ren Z, Ihee H, Rajagopal S, Moffat K, Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4799-804. Epub 2004 Mar 23. PMID:15041745
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