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New page: left|200px<br /> <applet load="1fsd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fsd" /> '''FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA...
 
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[[Image:1fsd.gif|left|200px]]<br />
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'''FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES'''<br />


==Overview==
==FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES==
The first fully automated design and experimental validation of a novel, sequence for an entire protein is described. A computational design, algorithm based on physical chemical potential functions and, stereochemical constraints was used to screen a combinatorial library of, 1.9 x 10(27) possible amino acid sequences for compatibility with the, design target, a betabetaalpha protein motif based on the polypeptide, backbone structure of a zinc finger domain. A BLAST search shows that the, designed sequence, full sequence design 1 (FSD-1), has very low identity, to any known protein sequence. The solution structure of FSD-1 was solved, by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms, a compact well-ordered structure, which is in excellent agreement with the, design target structure. This result demonstrates that computational, methods can perform the immense combinatorial search required for protein, design, and it suggests that an unbiased and quantitative algorithm can be, used in various structural contexts.
<StructureSection load='1fsd' size='340' side='right'caption='[[1fsd]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1fsd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. The October 2005 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Designer Proteins''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2005_10 10.2210/rcsb_pdb/mom_2005_10]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FSD FirstGlance]. <br>
</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=1fsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fsd OCA], [https://pdbe.org/1fsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fsd RCSB], [https://www.ebi.ac.uk/pdbsum/1fsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fsd ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.


==About this Structure==
De novo protein design: fully automated sequence selection.,Dahiyat BI, Mayo SL Science. 1997 Oct 3;278(5335):82-7. PMID:9311930<ref>PMID:9311930</ref>
1FSD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. The following page contains interesting information on the relation of 1FSD with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb70_1.html Designer Proteins]]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FSD OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
De novo protein design: fully automated sequence selection., Dahiyat BI, Mayo SL, Science. 1997 Oct 3;278(5335):82-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9311930 9311930]
</div>
<div class="pdbe-citations 1fsd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Designer Proteins]]
[[Category: Designer Proteins]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Synthetic construct]]
[[Category: Synthetic construct]]
[[Category: Dahiyat, B.I.]]
[[Category: Dahiyat BI]]
[[Category: Mayo, S.L.]]
[[Category: Mayo SL]]
[[Category: computational design]]
[[Category: novel sequence]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:00:27 2007''

Latest revision as of 21:36, 29 November 2023

FULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURESFULL SEQUENCE DESIGN 1 (FSD-1) OF BETA BETA ALPHA MOTIF, NMR, 41 STRUCTURES

Structural highlights

1fsd is a 1 chain structure with sequence from Synthetic construct. The October 2005 RCSB PDB Molecule of the Month feature on Designer Proteins by David S. Goodsell is 10.2210/rcsb_pdb/mom_2005_10. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.

De novo protein design: fully automated sequence selection.,Dahiyat BI, Mayo SL Science. 1997 Oct 3;278(5335):82-7. PMID:9311930[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science. 1997 Oct 3;278(5335):82-7. PMID:9311930
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