2sga: Difference between revisions
New page: left|200px<br /> <applet load="2sga" size="450" color="white" frame="true" align="right" spinBox="true" caption="2sga, resolution 1.5Å" /> '''ELECTRON DENSITY CAL... |
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[[Image:2sga.gif|left|200px]]<br /> | [[Image:2sga.gif|left|200px]]<br /><applet load="2sga" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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'''ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION'''<br /> | '''ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
Ab initio quantum mechanical calculations have been used to obtain details | Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it. | ||
==About this Structure== | ==About this Structure== | ||
2SGA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_chryseus Streptomyces chryseus]. This structure | 2SGA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_chryseus Streptomyces chryseus]. This structure supersedes the now removed PDB entry 1SGA. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SGA OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptomyces chryseus]] | [[Category: Streptomyces chryseus]] | ||
[[Category: James, M | [[Category: James, M N.G.]] | ||
[[Category: Sielecki, A | [[Category: Sielecki, A R.]] | ||
[[Category: hydrolase (serine proteinase)]] | [[Category: hydrolase (serine proteinase)]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:49:05 2008'' | ||
Revision as of 19:49, 21 February 2008
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ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION
OverviewOverview
Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.
About this StructureAbout this Structure
2SGA is a Single protein structure of sequence from Streptomyces chryseus. This structure supersedes the now removed PDB entry 1SGA. Full crystallographic information is available from OCA.
ReferenceReference
Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution., Moult J, Sussman F, James MN, J Mol Biol. 1985 Apr 20;182(4):555-66. PMID:3892015
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