1kh0: Difference between revisions

Line 1:

[[Image:1kh0.jpg|left|200px]]<br /><applet load="1kh0" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1kh0.jpg|left|200px]]<br /><applet load="1kh0" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1kh0, resolution 1.90Å" />

'''Accurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L'''<br />

==Overview==

The rational design of loops and turns is a key step towards creating, proteins with new functions. We used a computational design procedure to, create new backbone conformations in the second turn of protein L. The, Protein Data Bank was searched for alternative turn conformations, and, sequences optimal for these turns in the context of protein L were, identified using a Monte Carlo search procedure and an energy function, that favors close packing. Two variants containing 12 and 14 mutations, were found to be as stable as wild-type protein L. The crystal structure, of one of the variants has been solved at a resolution of 1.9 A, and the, backbone conformation in the second turn is remarkably close to that of, the in silico model (1.1 A RMSD) while it differs significantly from that, of wild-type protein L (the turn residues are displaced by an average of, 7.2 A). The folding rates of the redesigned proteins are greater than that, of the wild-type protein and in contrast to wild-type protein L the second, beta-turn appears to be formed at the rate limiting step in folding.

The rational design of loops and turns is a key step towards creating proteins with new functions. We used a computational design procedure to create new backbone conformations in the second turn of protein L. The Protein Data Bank was searched for alternative turn conformations, and sequences optimal for these turns in the context of protein L were identified using a Monte Carlo search procedure and an energy function that favors close packing. Two variants containing 12 and 14 mutations were found to be as stable as wild-type protein L. The crystal structure of one of the variants has been solved at a resolution of 1.9 A, and the backbone conformation in the second turn is remarkably close to that of the in silico model (1.1 A RMSD) while it differs significantly from that of wild-type protein L (the turn residues are displaced by an average of 7.2 A). The folding rates of the redesigned proteins are greater than that of the wild-type protein and in contrast to wild-type protein L the second beta-turn appears to be formed at the rate limiting step in folding.

==About this Structure==

1KH0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Finegoldia_magna Finegoldia magna]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1KH0 OCA].

1KH0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Finegoldia_magna Finegoldia magna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KH0 OCA].

==Reference==

Line 14:

[[Category: Single protein]]

[[Category: Baker, D.]]

[[Category: Kim, D.E.]]

[[Category: Kim, D E.]]

[[Category: Kuhlman, B.]]

[[Category: Neill, J.W.O.]]

[[Category: Neill, J W.O.]]

[[Category: Zhang, K.Y.]]

[[Category: Zhang, K Y.]]

[[Category: computational based protein design]]

[[Category: extensive amino acid mutations.]]

Line 23:

[[Category: type 1' beta turn]]

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@@ Line 1: / Line 1: @@
-[[Image:1kh0.jpg|left|200px]]<br /><applet load="1kh0" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kh0.jpg|left|200px]]<br /><applet load="1kh0" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1kh0, resolution 1.90&Aring;" />
 '''Accurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L'''<br />
 ==Overview==
-The rational design of loops and turns is a key step towards creating, proteins with new functions. We used a computational design procedure to, create new backbone conformations in the second turn of protein L. The, Protein Data Bank was searched for alternative turn conformations, and, sequences optimal for these turns in the context of protein L were, identified using a Monte Carlo search procedure and an energy function, that favors close packing. Two variants containing 12 and 14 mutations, were found to be as stable as wild-type protein L. The crystal structure, of one of the variants has been solved at a resolution of 1.9 A, and the, backbone conformation in the second turn is remarkably close to that of, the in silico model (1.1 A RMSD) while it differs significantly from that, of wild-type protein L (the turn residues are displaced by an average of, 7.2 A). The folding rates of the redesigned proteins are greater than that, of the wild-type protein and in contrast to wild-type protein L the second, beta-turn appears to be formed at the rate limiting step in folding.
+The rational design of loops and turns is a key step towards creating proteins with new functions. We used a computational design procedure to create new backbone conformations in the second turn of protein L. The Protein Data Bank was searched for alternative turn conformations, and sequences optimal for these turns in the context of protein L were identified using a Monte Carlo search procedure and an energy function that favors close packing. Two variants containing 12 and 14 mutations were found to be as stable as wild-type protein L. The crystal structure of one of the variants has been solved at a resolution of 1.9 A, and the backbone conformation in the second turn is remarkably close to that of the in silico model (1.1 A RMSD) while it differs significantly from that of wild-type protein L (the turn residues are displaced by an average of 7.2 A). The folding rates of the redesigned proteins are greater than that of the wild-type protein and in contrast to wild-type protein L the second beta-turn appears to be formed at the rate limiting step in folding.
 ==About this Structure==
-KH0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Finegoldia_magna Finegoldia magna]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KH0 OCA].
+KH0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Finegoldia_magna Finegoldia magna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KH0 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Baker, D.]]
-[[Category: Kim, D.E.]]
+[[Category: Kim, D E.]]
 [[Category: Kuhlman, B.]]
-[[Category: Neill, J.W.O.]]
+[[Category: Neill, J W.O.]]
-[[Category: Zhang, K.Y.]]
+[[Category: Zhang, K Y.]]
 [[Category: computational based protein design]]
 [[Category: extensive amino acid mutations.]]
@@ Line 23: / Line 23: @@
 [[Category: type 1' beta turn]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:21:15 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:02 2008''