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| | ==Crystal structure of the computationally designed NNOS-Syntrophin complex== | | ==Crystal structure of the computationally designed NNOS-Syntrophin complex== |
| - | <StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution|resolution]] 2.29Å' scene=''> | + | <StructureSection load='4hop' size='340' side='right'caption='[[4hop]], [[Resolution|resolution]] 2.29Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HOP FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qav|1qav]]</td></tr> | + | </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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [https://pdbe.org/4hop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [https://www.ebi.ac.uk/pdbsum/4hop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://pdbe.org/4hop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE]] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate. [[http://www.uniprot.org/uniprot/NOS1_RAT NOS1_RAT]] Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum. Probably has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such SRR. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum. | + | [https://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Nitric Oxide Synthase|Nitric Oxide Synthase]] | + | *[[Nitric Oxide Synthase 3D structures|Nitric Oxide Synthase 3D structures]] |
| | + | *[[Syntrophin|Syntrophin]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Buffalo rat]] | + | [[Category: Large Structures]] |
| - | [[Category: Lk3 transgenic mice]] | + | [[Category: Mus musculus]] |
| - | [[Category: Harwood, I M]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Kortemme, T]] | + | [[Category: Harwood IM]] |
| - | [[Category: Melero, C]] | + | [[Category: Kortemme T]] |
| - | [[Category: Ollikainen, N]] | + | [[Category: Melero C]] |
| - | [[Category: Dimerization]]
| + | [[Category: Ollikainen N]] |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Membrane protein-oxidoreductase complex]]
| + | |
| - | [[Category: Mutation]]
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| - | [[Category: Pdz]]
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| - | [[Category: Protein binding]]
| + | |
| Structural highlights
Function
SNTA1_MOUSE Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate.
Publication Abstract from PubMed
Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.
Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.,Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T Proc Natl Acad Sci U S A. 2014 Oct 13. pii: 201410624. PMID:25313039[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci U S A. 2014 Oct 13. pii: 201410624. PMID:25313039 doi:http://dx.doi.org/10.1073/pnas.1410624111
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