1acp
From Proteopedia
(New page: 200px<br /><applet load="1acp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1acp" /> '''REFINEMENT OF THE NMR STRUCTURES FOR ACYL CA...) |
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| - | [[Image:1acp.gif|left|200px]]<br /><applet load="1acp" size=" | + | [[Image:1acp.gif|left|200px]]<br /><applet load="1acp" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1acp" /> | caption="1acp" /> | ||
'''REFINEMENT OF THE NMR STRUCTURES FOR ACYL CARRIER PROTEIN WITH SCALAR COUPLING DATA'''<br /> | '''REFINEMENT OF THE NMR STRUCTURES FOR ACYL CARRIER PROTEIN WITH SCALAR COUPLING DATA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Structure determination of small proteins using NMR data is most commonly | + | Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly. |
==About this Structure== | ==About this Structure== | ||
| - | 1ACP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_b Escherichia coli b]. Full crystallographic information is available from [http:// | + | 1ACP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_b Escherichia coli b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ACP OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Kim, Y.]] | [[Category: Kim, Y.]] | ||
| - | [[Category: Prestegard, J | + | [[Category: Prestegard, J H.]] |
[[Category: fatty acid synthesis protein]] | [[Category: fatty acid synthesis protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:43:08 2008'' |
Revision as of 09:43, 21 February 2008
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REFINEMENT OF THE NMR STRUCTURES FOR ACYL CARRIER PROTEIN WITH SCALAR COUPLING DATA
Overview
Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
About this Structure
1ACP is a Single protein structure of sequence from Escherichia coli b. Full crystallographic information is available from OCA.
Reference
Refinement of the NMR structures for acyl carrier protein with scalar coupling data., Kim Y, Prestegard JH, Proteins. 1990;8(4):377-85. PMID:2091027
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