1re3: Difference between revisions
New page: left|200px<br /> <applet load="1re3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1re3, resolution 2.45Å" /> '''Crystal Structure o... |
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[[Image:1re3.gif|left|200px]]<br /> | [[Image:1re3.gif|left|200px]]<br /><applet load="1re3" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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caption="1re3, resolution 2.45Å" /> | caption="1re3, resolution 2.45Å" /> | ||
'''Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide'''<br /> | '''Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide'''<br /> | ||
==Overview== | ==Overview== | ||
We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and | We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerization site. We examined thrombin- and batroxobin-catalyzed polymerization by turbidity measurements and found that BbetaE397A and BbetaD398A were impaired while BbetaD432A was normal. Changes in polymerization as a function of calcium were similar for variant and normal fibrinogens. We determined crystal structures of fragment D from the variant BbetaD398A in the absence and presence of GHRPam. In the absence of peptide, the structure showed that the alanine substitution altered only specific local interactions, as alignment of the variant structure with the analogous normal structure resulted in an RMSD of 0.53 A over all atoms. The structure also showed reduced occupancy of the beta2 calcium-binding site that includes the side chain carbonyl of BbetaD398, suggesting that calcium was not bound at this site in our polymerization studies. In the presence of peptide, the structure showed that GHRPam was not bound in the "b" site and the conformational changes associated with peptide binding to normal fragment D did not occur. This structure also showed GHRPam bound in the "a" polymerization site, although in two different conformations. Calcium binding was associated with only one of these conformations, suggesting that calcium binding to the gamma2-site and an alternative peptide conformation were induced by crystal packing. We conclude that BbetaE397 and BbetaD398 are essential for the "B:b" interaction, while BbetaD432 is not. | ||
==Disease== | ==Disease== | ||
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==About this Structure== | ==About this Structure== | ||
1RE3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1RE3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RE3 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Betts, L.]] | [[Category: Betts, L.]] | ||
[[Category: Gorkun, O | [[Category: Gorkun, O V.]] | ||
[[Category: Kostelansky, M | [[Category: Kostelansky, M S.]] | ||
[[Category: Lord, S | [[Category: Lord, S T.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
[[Category: bbetad398a fibrinogen]] | [[Category: bbetad398a fibrinogen]] | ||
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[[Category: variant fibrinogen]] | [[Category: variant fibrinogen]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:53 2008'' | ||
Revision as of 15:49, 21 February 2008
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Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide
OverviewOverview
We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerization site. We examined thrombin- and batroxobin-catalyzed polymerization by turbidity measurements and found that BbetaE397A and BbetaD398A were impaired while BbetaD432A was normal. Changes in polymerization as a function of calcium were similar for variant and normal fibrinogens. We determined crystal structures of fragment D from the variant BbetaD398A in the absence and presence of GHRPam. In the absence of peptide, the structure showed that the alanine substitution altered only specific local interactions, as alignment of the variant structure with the analogous normal structure resulted in an RMSD of 0.53 A over all atoms. The structure also showed reduced occupancy of the beta2 calcium-binding site that includes the side chain carbonyl of BbetaD398, suggesting that calcium was not bound at this site in our polymerization studies. In the presence of peptide, the structure showed that GHRPam was not bound in the "b" site and the conformational changes associated with peptide binding to normal fragment D did not occur. This structure also showed GHRPam bound in the "a" polymerization site, although in two different conformations. Calcium binding was associated with only one of these conformations, suggesting that calcium binding to the gamma2-site and an alternative peptide conformation were induced by crystal packing. We conclude that BbetaE397 and BbetaD398 are essential for the "B:b" interaction, while BbetaD432 is not.
DiseaseDisease
Known diseases associated with this structure: Afibrinogenemia, congenital OMIM:[134820], Afibrinogenemia, congenital OMIM:[134830], Amyloidosis, hereditary renal OMIM:[134820], Dysfibrinogenemia, alpha type, causing bleeding diathesis OMIM:[134820], Dysfibrinogenemia, alpha type, causing recurrent thrombosis OMIM:[134820], Dysfibrinogenemia, beta type OMIM:[134830], Dysfibrinogenemia, gamma type OMIM:[134850], Hypofibrinogenemia, gamma type OMIM:[134850], Thrombophilia, dysfibrinogenemic OMIM:[134830], Thrombophilia, dysfibrinogenemic OMIM:[134850]
About this StructureAbout this Structure
1RE3 is a Protein complex structure of sequences from Homo sapiens with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
B beta Glu397 and B beta Asp398 but not B beta Asp432 are required for "B:b" interactions., Kostelansky MS, Bolliger-Stucki B, Betts L, Gorkun OV, Lord ST, Biochemistry. 2004 Mar 9;43(9):2465-74. PMID:14992584
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