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| - | [[Image:1w5i.gif|left|200px]]<br /><applet load="1w5i" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1w5i, resolution 2.30Å" /> | |
| - | '''ABA DOES NOT AFFECT TOPOLOGY OF PLI.'''<br /> | |
| | | | |
| - | ==Overview== | + | ==ABA does not affect topology of pLI.== |
| - | A detailed understanding of the mechanisms by which particular amino acid, sequences can give rise to more than one folded structure, such as for, proteins that undergo large conformational changes or misfolding, is a, long-standing objective of protein chemistry. Here, we describe the, crystal structures of a single coiled-coil peptide in distinct parallel, and antiparallel tetrameric configurations and further describe the, parallel or antiparallel crystal structures of several related peptide, sequences; the antiparallel tetrameric assemblies represent the first, crystal structures of GCN4-derived peptides exhibiting such a, configuration. Intriguingly, substitution of a single solvent-exposed, residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the, antiparallel configuration, suggesting that the two configurations are, close enough in energy for subtle sequence changes to have important, structural consequences. We present a structural analysis of the small, changes to the helix register and side-chain conformations that, accommodate the two configurations and have supplemented these results, using solution studies and a molecular dynamics energetic analysis using a, replica exchange methodology. Considering the previous examples of, structural nonspecificity in coiled-coil peptides, the findings reported, here not only emphasize the predisposition of the coiled-coil motif to, adopt multiple configurations but also call attention to the associated, risk that observed crytstal structures may not represent the only (or even, the major) species present in solution.
| + | <StructureSection load='1w5i' size='340' side='right'caption='[[1w5i]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1w5i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W5I FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</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=1w5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w5i OCA], [https://pdbe.org/1w5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w5i RCSB], [https://www.ebi.ac.uk/pdbsum/1w5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w5i ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GCN4_YEAST GCN4_YEAST] Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'. |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins. |
| | | | |
| - | ==About this Structure==
| + | Structure-based engineering of internal cavities in coiled-coil peptides.,Yadav MK, Redman JE, Leman LJ, Alvarez-Gutierrez JM, Zhang Y, Stout CD, Ghadiri MR Biochemistry. 2005 Jul 19;44(28):9723-32. PMID:16008357<ref>PMID:16008357</ref> |
| - | 1W5I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W5I OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution., Yadav MK, Leman LJ, Price DJ, Brooks CL 3rd, Stout CD, Ghadiri MR, Biochemistry. 2006 Apr 11;45(14):4463-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16584182 16584182]
| + | </div> |
| - | [[Category: Single protein]]
| + | <div class="pdbe-citations 1w5i" style="background-color:#fffaf0;"></div> |
| - | [[Category: Ghadiri, M.R.]]
| + | |
| - | [[Category: Leman, L.]]
| + | |
| - | [[Category: Stout, C.D.]]
| + | |
| - | [[Category: Yadav, M.K.]]
| + | |
| - | [[Category: aba]]
| + | |
| - | [[Category: four helix bundle]]
| + | |
| | | | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:14:08 2007''
| + | ==See Also== |
| | + | *[[Gcn4 3D Structures|Gcn4 3D Structures]] |
| | + | *[[Gnc4 3D Structures|Gnc4 3D Structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Saccharomyces cerevisiae]] |
| | + | [[Category: Ghadiri MR]] |
| | + | [[Category: Leman LJ]] |
| | + | [[Category: Stout CD]] |
| | + | [[Category: Yadav MK]] |
| Structural highlights
Function
GCN4_YEAST Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'.
Publication Abstract from PubMed
Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.
Structure-based engineering of internal cavities in coiled-coil peptides.,Yadav MK, Redman JE, Leman LJ, Alvarez-Gutierrez JM, Zhang Y, Stout CD, Ghadiri MR Biochemistry. 2005 Jul 19;44(28):9723-32. PMID:16008357[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yadav MK, Redman JE, Leman LJ, Alvarez-Gutierrez JM, Zhang Y, Stout CD, Ghadiri MR. Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry. 2005 Jul 19;44(28):9723-32. PMID:16008357 doi:10.1021/bi050742a
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