1ezp: Difference between revisions

Revision as of 13:33, 21 February 2008

GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN USING PEPTIDE ORIENTATIONS FROM DIPOLAR COUPLINGS

OverviewOverview

The global fold of maltose-binding protein in complex with the substrate beta-cyclodextrin was determined by solution NMR methods. The two-domain protein is comprised of a single polypeptide chain of 370 residues, with a molecular mass of 42 kDa. Distance information in the form of H(N)-H(N), H(N)-CH(3) and CH(3)-CH(3) NOEs was recorded on (15)N, (2)H and (15)N, (13)C, (2)H-labeled proteins with methyl protonation in Val, Leu, and Ile (C(delta1) only) residues. Distances to methyl protons, critical for the structure determination, comprised 77 % of the long-range restraints. Initial structures were calculated on the basis of 1943 NOEs, 48 hydrogen bond and 555 dihedral angle restraints. A global pair-wise backbone rmsd of 5.5 A was obtained for these initial structures with rmsd values for the N and C domains of 2.4 and 3.8 A, respectively. Direct refinement against one-bond (1)H(N)-(15)N, (13)C(alpha)-(13)CO, (15)N-(13)CO, two-bond (1)H(N)-(13)CO and three-bond (1)H(N)-(13)C(alpha) dipolar couplings resulted in structures with large numbers of dipolar restraint violations. As an alternative to direct refinement against measured dipolar couplings we have developed an approach where discrete orientations are calculated for each peptide plane on the basis of the dipolar couplings described above. The orientation which best matches that in initial NMR structures calculated from NOE and dihedral angle restraints exclusively is used to refine further the structures using a new module written for CNS. Modeling studies from four different proteins with diverse structural motifs establishes the utility of the methodology. When applied to experimental data recorded on MBP the precision of the family of structures generated improves from 5.5 to 2.2 A, while the rmsd with respect to the X-ray structure (1dmb) is reduced from 5.1 to 3.3 A.

About this StructureAbout this Structure

1EZP is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein., Mueller GA, Choy WY, Yang D, Forman-Kay JD, Venters RA, Kay LE, J Mol Biol. 2000 Jun 30;300(1):197-212. PMID:10864509

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OCA

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-[[Image:1ezp.jpg|left|200px]]<br /><applet load="1ezp" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ezp.jpg|left|200px]]<br /><applet load="1ezp" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ezp" />
 '''GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN USING PEPTIDE ORIENTATIONS FROM DIPOLAR COUPLINGS'''<br />
 ==Overview==
-The global fold of maltose-binding protein in complex with the substrate, beta-cyclodextrin was determined by solution NMR methods. The two-domain, protein is comprised of a single polypeptide chain of 370 residues, with a, molecular mass of 42 kDa. Distance information in the form of H(N)-H(N), H(N)-CH(3) and CH(3)-CH(3) NOEs was recorded on (15)N, (2)H and (15)N, (13)C, (2)H-labeled proteins with methyl protonation in Val, Leu, and Ile, (C(delta1) only) residues. Distances to methyl protons, critical for the, structure determination, comprised 77 % of the long-range restraints., Initial structures were calculated on the basis of 1943 NOEs, 48 hydrogen, bond and 555 dihedral angle restraints. A global pair-wise backbone rmsd, of 5.5 A was obtained for these initial structures with rmsd values for, the N and C domains of 2.4 and 3.8 A, respectively. Direct refinement, against one-bond (1)H(N)-(15)N, (13)C(alpha)-(13)CO, (15)N-(13)CO, two-bond (1)H(N)-(13)CO and three-bond (1)H(N)-(13)C(alpha) dipolar, couplings resulted in structures with large numbers of dipolar restraint, violations. As an alternative to direct refinement against measured, dipolar couplings we have developed an approach where discrete, orientations are calculated for each peptide plane on the basis of the, dipolar couplings described above. The orientation which best matches that, in initial NMR structures calculated from NOE and dihedral angle, restraints exclusively is used to refine further the structures using a, new module written for CNS. Modeling studies from four different proteins, with diverse structural motifs establishes the utility of the methodology., When applied to experimental data recorded on MBP the precision of the, family of structures generated improves from 5.5 to 2.2 A, while the rmsd, with respect to the X-ray structure (1dmb) is reduced from 5.1 to 3.3 A.
+The global fold of maltose-binding protein in complex with the substrate beta-cyclodextrin was determined by solution NMR methods. The two-domain protein is comprised of a single polypeptide chain of 370 residues, with a molecular mass of 42 kDa. Distance information in the form of H(N)-H(N), H(N)-CH(3) and CH(3)-CH(3) NOEs was recorded on (15)N, (2)H and (15)N, (13)C, (2)H-labeled proteins with methyl protonation in Val, Leu, and Ile (C(delta1) only) residues. Distances to methyl protons, critical for the structure determination, comprised 77 % of the long-range restraints. Initial structures were calculated on the basis of 1943 NOEs, 48 hydrogen bond and 555 dihedral angle restraints. A global pair-wise backbone rmsd of 5.5 A was obtained for these initial structures with rmsd values for the N and C domains of 2.4 and 3.8 A, respectively. Direct refinement against one-bond (1)H(N)-(15)N, (13)C(alpha)-(13)CO, (15)N-(13)CO, two-bond (1)H(N)-(13)CO and three-bond (1)H(N)-(13)C(alpha) dipolar couplings resulted in structures with large numbers of dipolar restraint violations. As an alternative to direct refinement against measured dipolar couplings we have developed an approach where discrete orientations are calculated for each peptide plane on the basis of the dipolar couplings described above. The orientation which best matches that in initial NMR structures calculated from NOE and dihedral angle restraints exclusively is used to refine further the structures using a new module written for CNS. Modeling studies from four different proteins with diverse structural motifs establishes the utility of the methodology. When applied to experimental data recorded on MBP the precision of the family of structures generated improves from 5.5 to 2.2 A, while the rmsd with respect to the X-ray structure (1dmb) is reduced from 5.1 to 3.3 A.
 ==About this Structure==
-EZP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EZP OCA].
+EZP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EZP OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
-[[Category: Choy, W.Y.]]
+[[Category: Choy, W Y.]]
-[[Category: Forman-Kay, J.D.]]
+[[Category: Forman-Kay, J D.]]
-[[Category: Kay, L.E.]]
+[[Category: Kay, L E.]]
-[[Category: Mueller, G.A.]]
+[[Category: Mueller, G A.]]
-[[Category: Venters, R.A.]]
+[[Category: Venters, R A.]]
 [[Category: Yang, D.]]
 [[Category: deuteration]]
@@ Line 23: / Line 23: @@
 [[Category: residual diplar couplings]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:28:21 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:33:24 2008''