2b2x
From Proteopedia
(New page: 200px<br /> <applet load="2b2x" size="450" color="white" frame="true" align="right" spinBox="true" caption="2b2x, resolution 2.200Å" /> '''VLA1 RdeltaH I-dom...) |
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| - | [[Image:2b2x.gif|left|200px]]<br /> | + | [[Image:2b2x.gif|left|200px]]<br /><applet load="2b2x" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="2b2x" size=" | + | |
caption="2b2x, resolution 2.200Å" /> | caption="2b2x, resolution 2.200Å" /> | ||
'''VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab'''<br /> | '''VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Improving the affinity of a high-affinity protein-protein interaction is a | + | Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies. |
==About this Structure== | ==About this Structure== | ||
| - | 2B2X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 2B2X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B2X OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Rattus norvegicus]] | [[Category: Rattus norvegicus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Boriack-Sjodin, P | + | [[Category: Boriack-Sjodin, P A.]] |
| - | [[Category: Clark, L | + | [[Category: Clark, L A.]] |
[[Category: Eldredge, J.]] | [[Category: Eldredge, J.]] | ||
[[Category: Fitch, C.]] | [[Category: Fitch, C.]] | ||
[[Category: Friedman, B.]] | [[Category: Friedman, B.]] | ||
| - | [[Category: Hanf, K | + | [[Category: Hanf, K J.]] |
[[Category: Jarpe, M.]] | [[Category: Jarpe, M.]] | ||
[[Category: Li, Y.]] | [[Category: Li, Y.]] | ||
| - | [[Category: Liparoto, S | + | [[Category: Liparoto, S F.]] |
[[Category: Lugovskoy, A.]] | [[Category: Lugovskoy, A.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: computational design]] | [[Category: computational design]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:33:35 2008'' |
Revision as of 14:33, 21 February 2008
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VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab
Overview
Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.
About this Structure
2B2X is a Single protein structure of sequence from Mus musculus and Rattus norvegicus with as ligand. Full crystallographic information is available from OCA.
Reference
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design., Clark LA, Boriack-Sjodin PA, Eldredge J, Fitch C, Friedman B, Hanf KJ, Jarpe M, Liparoto SF, Li Y, Lugovskoy A, Miller S, Rushe M, Sherman W, Simon K, Van Vlijmen H, Protein Sci. 2006 May;15(5):949-60. Epub 2006 Apr 5. PMID:16597831
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