1acp: Difference between revisions

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[[Image:1acp.gif|left|200px]]


<!--
==REFINEMENT OF THE NMR STRUCTURES FOR ACYL CARRIER PROTEIN WITH SCALAR COUPLING DATA==
The line below this paragraph, containing "STRUCTURE_1acp", creates the "Structure Box" on the page.
<StructureSection load='1acp' size='340' side='right'caption='[[1acp]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1acp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ACP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ACP FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-->
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1acp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1acp OCA], [https://pdbe.org/1acp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1acp RCSB], [https://www.ebi.ac.uk/pdbsum/1acp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1acp ProSAT]</span></td></tr>
{{STRUCTURE_1acp|  PDB=1acp |  SCENE= }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/ACP_ECOLI ACP_ECOLI] Carrier of the growing fatty acid chain in fatty acid biosynthesis.[HAMAP-Rule:MF_01217]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ac/1acp_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1acp ConSurf].
<div style="clear:both"></div>


'''REFINEMENT OF THE NMR STRUCTURES FOR ACYL CARRIER PROTEIN WITH SCALAR COUPLING DATA'''
==See Also==
 
*[[Acyl carrier protein 3D structures|Acyl carrier protein 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Escherichia coli B]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Kim Y]]
1ACP is a [[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].
[[Category: Prestegard JH]]
 
==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:[http://www.ncbi.nlm.nih.gov/pubmed/2091027 2091027]
[[Category: Escherichia coli b]]
[[Category: Single protein]]
[[Category: Kim, Y.]]
[[Category: Prestegard, J H.]]
[[Category: Fatty acid synthesis protein]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:06:30 2008''
Retrieved from "https://proteopedia.org/1acp"