1b6h
From Proteopedia
(New page: 200px<br /><applet load="1b6h" size="450" color="white" frame="true" align="right" spinBox="true" caption="1b6h, resolution 1.8Å" /> '''OLIGO-PEPTIDE BINDING...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1b6h.jpg|left|200px]]<br /><applet load="1b6h" size=" | + | [[Image:1b6h.jpg|left|200px]]<br /><applet load="1b6h" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1b6h, resolution 1.8Å" /> | caption="1b6h, resolution 1.8Å" /> | ||
'''OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE'''<br /> | '''OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The oligopeptide-binding protein OppA provides a useful model system for | + | The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted. |
==About this Structure== | ==About this Structure== | ||
| - | 1B6H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with U1 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1B6H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=U1:'>U1</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6H OCA]. |
==Reference== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Salmonella typhimurium]] | [[Category: Salmonella typhimurium]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Davies, T | + | [[Category: Davies, T G.]] |
| - | [[Category: Tame, J | + | [[Category: Tame, J R.H.]] |
[[Category: U1]] | [[Category: U1]] | ||
[[Category: periplasmic peptide binding protein]] | [[Category: periplasmic peptide binding protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:52:03 2008'' |
Revision as of 09:52, 21 February 2008
|
OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE
Overview
The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.
About this Structure
1B6H is a Single protein structure of sequence from Salmonella typhimurium with as ligand. Full crystallographic information is available from OCA.
Reference
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes., Davies TG, Hubbard RE, Tame JR, Protein Sci. 1999 Jul;8(7):1432-44. PMID:10422831
Page seeded by OCA on Thu Feb 21 11:52:03 2008
