1zyt: Difference between revisions

Revision as of 17:20, 21 February 2008

Crystal structure of spin labeled T4 Lysozyme (A82R1)

OverviewOverview

High resolution (1.43-1.8 A) crystal structures and the corresponding electron paramagnetic resonance (EPR) spectra were determined for T4 lysozyme derivatives with a disulfide-linked nitroxide side chain [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density is clearly resolved for the disulfide group, revealing distinct rotamers of the side chain, defined by the dihedral angles X(1) and X(2). The electron density associated with the nitroxide ring in the different mutants is inversely correlated with its mobility determined from the EPR spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1) = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter state is apparently stabilized by interaction of the disulfide with a Gln at i + 4, a situation also observed at 65R1. R1 residues at helix surface site 65 and tertiary contact site 75 make intra- as well as intermolecular contacts in the crystal and serve to identify the kind of molecular interactions possible for the R1 side chain. A single conformation of the entire 75R1 side chain is stabilized by a variety of interactions with the nitroxide ring, including hydrophobic contacts and two unconventional C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with tyrosine) and the other in which it acts as an acceptor (with phenylalanine). The interactions revealed in these structures provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure. A library of such interactions will provide a basis for the quantitative interpretation of EPR spectra in terms of protein structure and dynamics.

About this StructureAbout this Structure

1ZYT is a Single protein structure of sequence from Bacteriophage t4 with , and as ligands. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure., Langen R, Oh KJ, Cascio D, Hubbell WL, Biochemistry. 2000 Jul 25;39(29):8396-405. PMID:10913245

Page seeded by OCA on Thu Feb 21 16:20:23 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1zyt.gif|left|200px]]<br /><applet load="1zyt" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1zyt.gif|left|200px]]<br /><applet load="1zyt" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1zyt, resolution 1.70&Aring;" />
 '''Crystal structure of spin labeled T4 Lysozyme (A82R1)'''<br />
 ==Overview==
-High resolution (1.43-1.8 A) crystal structures and the corresponding, electron paramagnetic resonance (EPR) spectra were determined for T4, lysozyme derivatives with a disulfide-linked nitroxide side chain, [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical, with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density, is clearly resolved for the disulfide group, revealing distinct rotamers, of the side chain, defined by the dihedral angles X(1) and X(2). The, electron density associated with the nitroxide ring in the different, mutants is inversely correlated with its mobility determined from the EPR, spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1), = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and, the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter, state is apparently stabilized by interaction of the disulfide with a Gln, at i + 4, a situation also observed at 65R1. R1 residues at helix surface, site 65 and tertiary contact site 75 make intra- as well as intermolecular, contacts in the crystal and serve to identify the kind of molecular, interactions possible for the R1 side chain. A single conformation of the, entire 75R1 side chain is stabilized by a variety of interactions with the, nitroxide ring, including hydrophobic contacts and two unconventional, C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with, tyrosine) and the other in which it acts as an acceptor (with, phenylalanine). The interactions revealed in these structures provide an, important link between the dynamics of the R1 side chain, reflected in the, EPR spectrum, and local protein structure. A library of such interactions, will provide a basis for the quantitative interpretation of EPR spectra in, terms of protein structure and dynamics.
+High resolution (1.43-1.8 A) crystal structures and the corresponding electron paramagnetic resonance (EPR) spectra were determined for T4 lysozyme derivatives with a disulfide-linked nitroxide side chain [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density is clearly resolved for the disulfide group, revealing distinct rotamers of the side chain, defined by the dihedral angles X(1) and X(2). The electron density associated with the nitroxide ring in the different mutants is inversely correlated with its mobility determined from the EPR spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1) = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter state is apparently stabilized by interaction of the disulfide with a Gln at i + 4, a situation also observed at 65R1. R1 residues at helix surface site 65 and tertiary contact site 75 make intra- as well as intermolecular contacts in the crystal and serve to identify the kind of molecular interactions possible for the R1 side chain. A single conformation of the entire 75R1 side chain is stabilized by a variety of interactions with the nitroxide ring, including hydrophobic contacts and two unconventional C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with tyrosine) and the other in which it acts as an acceptor (with phenylalanine). The interactions revealed in these structures provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure. A library of such interactions will provide a basis for the quantitative interpretation of EPR spectra in terms of protein structure and dynamics.
 ==About this Structure==
-ZYT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with AZI, CL and HED as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZYT OCA].
+ZYT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=AZI:'>AZI</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=HED:'>HED</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZYT OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Cascio, D.]]
-[[Category: Fleissner, M.R.]]
+[[Category: Fleissner, M R.]]
 [[Category: Hideg, K.]]
-[[Category: Hubbell, W.L.]]
+[[Category: Hubbell, W L.]]
-[[Category: Sawaya, M.R.]]
+[[Category: Sawaya, M R.]]
 [[Category: AZI]]
 [[Category: CL]]
@@ Line 26: / Line 26: @@
 [[Category: nitroxide spin label]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:44:45 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:20:23 2008''