1nkf: Difference between revisions
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|PDB= 1nkf |SIZE=350|CAPTION= <scene name='initialview01'>1nkf</scene> | |PDB= 1nkf |SIZE=350|CAPTION= <scene name='initialview01'>1nkf</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=LA:LANTHANUM+(III)+ION'>LA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkf OCA], [http://www.ebi.ac.uk/pdbsum/1nkf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nkf RCSB]</span> | |||
}} | }} | ||
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==Overview== | ==Overview== | ||
A 12-residue peptide AcDKDGDGYISAAENH2 analogous to the third calcium-binding loop of calmodulin strongly coordinates lanthanide ions (K = 10(5) M-1). When metal saturated, the peptide adopts a very rigid structure, the same as in the native protein, with three last residues AAE fixed in the alpha-helical conformation. Therefore, the peptide provides an ideal helix nucleation site for peptide segments attached to its C terminus. NMR and CD investigations of peptide AcDKDGDGYISAAEAAAQNH2 presented in this paper show that residues A13-Q16 form an alpha-helix of very high stability when the La3+ ion is bound to the D1-E12 loop. In fact, the lowest estimates of the helix content in this segment give values of at least 80% at 1 degreesC and 70% at 25 degreesC. This finding is not compatible with existing helix-coil transition theories and helix propagation parameters, s, reported in the literature. We conclude, therefore, that the initial steps of helix propagation are characterized by much larger s values, whereas helix nucleation is even more unfavorable than is believed. In light of our findings, thermodynamics of the nascent alpha-helices is discussed. The problem of CD spectra of very short alpha-helices is also addressed. | A 12-residue peptide AcDKDGDGYISAAENH2 analogous to the third calcium-binding loop of calmodulin strongly coordinates lanthanide ions (K = 10(5) M-1). When metal saturated, the peptide adopts a very rigid structure, the same as in the native protein, with three last residues AAE fixed in the alpha-helical conformation. Therefore, the peptide provides an ideal helix nucleation site for peptide segments attached to its C terminus. NMR and CD investigations of peptide AcDKDGDGYISAAEAAAQNH2 presented in this paper show that residues A13-Q16 form an alpha-helix of very high stability when the La3+ ion is bound to the D1-E12 loop. In fact, the lowest estimates of the helix content in this segment give values of at least 80% at 1 degreesC and 70% at 25 degreesC. This finding is not compatible with existing helix-coil transition theories and helix propagation parameters, s, reported in the literature. We conclude, therefore, that the initial steps of helix propagation are characterized by much larger s values, whereas helix nucleation is even more unfavorable than is believed. In light of our findings, thermodynamics of the nascent alpha-helices is discussed. The problem of CD spectra of very short alpha-helices is also addressed. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Ejchart, A.]] | [[Category: Ejchart, A.]] | ||
[[Category: Sticht, H.]] | [[Category: Sticht, H.]] | ||
[[Category: alpha-helix]] | [[Category: alpha-helix]] | ||
[[Category: calcium-binding]] | [[Category: calcium-binding]] | ||
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[[Category: nmr structure]] | [[Category: nmr structure]] | ||
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