210l: Difference between revisions

Revision as of 17:20, 21 February 2008

PROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETION MUTANTS IN T4 LYSOZYME

OverviewOverview

To further investigate the ways in which proteins respond to changes in the length of the polypeptide chain, a series of 32 insertions and five deletions were made within nine different alpha-helices of T4 lysozyme. In most cases, the inserted amino acid was a single alanine, although in some instances up to four residues, not necessarily alanine, were used. Different insertions destabilized the protein by different amounts, ranging from approximately 1 to 6 kcal/mol. In one case, no protein could be obtained. An "extension" mutant in which the carboxy terminus of the molecule was extended by four alanines increased stability by 0.3 kcal/mol. For the deletions, the loss in stability ranged from approximately 3 to 5 kcal/mol. The structures of six insertion mutants, as well as one deletion mutant and the extension mutant, were determined, three in crystal forms nonisomorphous with wild type. In all cases, including previously described insertion mutants within a single alpha-helix, there appears to be a strong tendency to preserve the helix by translocating residues so that the effects of the insertion are propagated into a bend or loop at one end or the other of the helix. In three mutants, even the hydrophobic core was disrupted so as to permit the preservation of the alpha-helix containing the insertion. Translocation (or "register shift") was also observed for the deletion mutant, in this case a loop at the end of the helix being shortened. In general, when translocation occurs, the reduction in stability is only moderate, averaging 2.5 kcal/mol. Only in the most extreme cases does "bulging" or "looping-out" occur within the body of an alpha-helix, in which case the destabilization is substantial, averaging 4.9 kcal/mol. Looping-out can occur for insertions close to the end of a helix, in which case the destabilization is less severe, averaging 2.6 kcal/mol. Mutant A73-[AAA] as well as mutants R119-[A] and V131-[A], include shifts in the backbone of 3-6 A, extending over 20 residues or more. As a result, residues 114-142, which form a "cap" on the carboxy-terminal domain, undergo substantial reorganizations such that the interface between this "cap" and the rest of the protein is altered substantially. In the case of mutant A73-[AAA], two nearby alpha-helices, which form a bend of approximately 105 degrees in the wild-type structure, reorganize in the mutant structure to form a single, essentially straight helix. These structural responses to mutation demonstrate the plasticity of protein structures and illustrate ways in which their three-dimensional structures might changes during evolution.

About this StructureAbout this Structure

210L is a Single protein structure of sequence from Bacteriophage t4 with as ligand. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.

ReferenceReference

Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme., Vetter IR, Baase WA, Heinz DW, Xiong JP, Snow S, Matthews BW, Protein Sci. 1996 Dec;5(12):2399-415. PMID:8976549

Page seeded by OCA on Thu Feb 21 16:20:55 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:210l.jpg|left|200px]]<br /><applet load="210l" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:210l.jpg|left|200px]]<br /><applet load="210l" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="210l, resolution 1.89&Aring;" />
 '''PROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETION MUTANTS IN T4 LYSOZYME'''<br />
 ==Overview==
-To further investigate the ways in which proteins respond to changes in, the length of the polypeptide chain, a series of 32 insertions and five, deletions were made within nine different alpha-helices of T4 lysozyme. In, most cases, the inserted amino acid was a single alanine, although in some, instances up to four residues, not necessarily alanine, were used., Different insertions destabilized the protein by different amounts, ranging from approximately 1 to 6 kcal/mol. In one case, no protein could, be obtained. An "extension" mutant in which the carboxy terminus of the, molecule was extended by four alanines increased stability by 0.3, kcal/mol. For the deletions, the loss in stability ranged from, approximately 3 to 5 kcal/mol. The structures of six insertion mutants, as, well as one deletion mutant and the extension mutant, were determined, three in crystal forms nonisomorphous with wild type. In all cases, including previously described insertion mutants within a single, alpha-helix, there appears to be a strong tendency to preserve the helix, by translocating residues so that the effects of the insertion are, propagated into a bend or loop at one end or the other of the helix. In, three mutants, even the hydrophobic core was disrupted so as to permit the, preservation of the alpha-helix containing the insertion. Translocation, (or "register shift") was also observed for the deletion mutant, in this, case a loop at the end of the helix being shortened. In general, when, translocation occurs, the reduction in stability is only moderate, averaging 2.5 kcal/mol. Only in the most extreme cases does "bulging" or, "looping-out" occur within the body of an alpha-helix, in which case the, destabilization is substantial, averaging 4.9 kcal/mol. Looping-out can, occur for insertions close to the end of a helix, in which case the, destabilization is less severe, averaging 2.6 kcal/mol. Mutant A73-[AAA], as well as mutants R119-[A] and V131-[A], include shifts in the backbone, of 3-6 A, extending over 20 residues or more. As a result, residues, 114-142, which form a "cap" on the carboxy-terminal domain, undergo, substantial reorganizations such that the interface between this "cap" and, the rest of the protein is altered substantially. In the case of mutant, A73-[AAA], two nearby alpha-helices, which form a bend of approximately, 105 degrees in the wild-type structure, reorganize in the mutant structure, to form a single, essentially straight helix. These structural responses, to mutation demonstrate the plasticity of protein structures and, illustrate ways in which their three-dimensional structures might changes, during evolution.
+To further investigate the ways in which proteins respond to changes in the length of the polypeptide chain, a series of 32 insertions and five deletions were made within nine different alpha-helices of T4 lysozyme. In most cases, the inserted amino acid was a single alanine, although in some instances up to four residues, not necessarily alanine, were used. Different insertions destabilized the protein by different amounts, ranging from approximately 1 to 6 kcal/mol. In one case, no protein could be obtained. An "extension" mutant in which the carboxy terminus of the molecule was extended by four alanines increased stability by 0.3 kcal/mol. For the deletions, the loss in stability ranged from approximately 3 to 5 kcal/mol. The structures of six insertion mutants, as well as one deletion mutant and the extension mutant, were determined, three in crystal forms nonisomorphous with wild type. In all cases, including previously described insertion mutants within a single alpha-helix, there appears to be a strong tendency to preserve the helix by translocating residues so that the effects of the insertion are propagated into a bend or loop at one end or the other of the helix. In three mutants, even the hydrophobic core was disrupted so as to permit the preservation of the alpha-helix containing the insertion. Translocation (or "register shift") was also observed for the deletion mutant, in this case a loop at the end of the helix being shortened. In general, when translocation occurs, the reduction in stability is only moderate, averaging 2.5 kcal/mol. Only in the most extreme cases does "bulging" or "looping-out" occur within the body of an alpha-helix, in which case the destabilization is substantial, averaging 4.9 kcal/mol. Looping-out can occur for insertions close to the end of a helix, in which case the destabilization is less severe, averaging 2.6 kcal/mol. Mutant A73-[AAA] as well as mutants R119-[A] and V131-[A], include shifts in the backbone of 3-6 A, extending over 20 residues or more. As a result, residues 114-142, which form a "cap" on the carboxy-terminal domain, undergo substantial reorganizations such that the interface between this "cap" and the rest of the protein is altered substantially. In the case of mutant A73-[AAA], two nearby alpha-helices, which form a bend of approximately 105 degrees in the wild-type structure, reorganize in the mutant structure to form a single, essentially straight helix. These structural responses to mutation demonstrate the plasticity of protein structures and illustrate ways in which their three-dimensional structures might changes during evolution.
 ==About this Structure==
-L 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 HED as [http://en.wikipedia.org/wiki/ligand ligand]. 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=210L OCA].
+L 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=HED:'>HED</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=210L OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Lysozyme]]
 [[Category: Single protein]]
-[[Category: Baase, W.A.]]
+[[Category: Baase, W A.]]
-[[Category: Heinz, D.W.]]
+[[Category: Heinz, D W.]]
-[[Category: Matthews, B.W.]]
+[[Category: Matthews, B W.]]
 [[Category: Snow, S.]]
-[[Category: Vetter, I.R.]]
+[[Category: Vetter, I R.]]
-[[Category: Xiong, J.P.]]
+[[Category: Xiong, J P.]]
 [[Category: HED]]
 [[Category: bacteriolytic enzyme]]
@@ Line 25: / Line 25: @@
 [[Category: m13 plasmid]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:46:32 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:20:55 2008''