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Sandbox Reserved 960

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Revision as of 21:08, 22 December 2014

This Sandbox is Reserved from 15/11/2014, through 15/05/2015 for use in the course "Biomolecule" taught by Bruno Kieffer at the Strasbourg University. This reservation includes Sandbox Reserved 951 through Sandbox Reserved 975.

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Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand at pH 5.5

^[1] ^[2] ^[3]

Updated on 22-December-2014

1 Function
2 Structure
3 Related Forms
4 Relevance
5 Structural highlights

Function

Structure

Image:3fe6 cartoon.jpg

Fig.1 Ribbon colored representation

ASP1 is composed of [ http://www.genome.jp/dbget-bin/www_bget?pdb:3FE6]

- : residues 8–25
- : residues 27–36
- : residues 42–56
- : residues 66–74
- : residues 75–77
- : residues 78–90
- : residues 96–112

has a break in the hydrogen-bonding pattern of its structure, forming tight substitute hydrogen bonds with water molecules. Thus, it results in a kink (at residue Ala 14)(scene) induced by a disruption in the helical conformation, due to hydrogen bonds with water molecules.

The C terminal(scene) domain of this molecule presents a characteristic PBP-GOP domain. While this protein is composed of 144 residues the domain PBP begin at 25 residue. ASP1 binds its ligand at low pH and releases it at neutral pH.

Components implicated in the structure rigidity:

ASP1 presents which are greatly enhancing its structure’s rigidity by linking four of the helixes together.

The is established between and through Cysteins 20 and 51. links and through Cys 47 and 98, and the connects and thanks to Cys 89 and Cys 107.

Furthermore, non covalent bonds also play an important role.

Indeed, at pH 5.5, Asp 66 and Leu 58 establish an hydrogene bond which is able to fix a key component structure such as H4. (scene) With their hydrogene bond Val 118 and Ile 119 stabilize alpha helix 2 and C terminal’s position. (scene)

Cavity

The dynamic structure of the protein is responsible of the ligand’s binding by adjustement of position. The structure looses its flexibility when binds. The successful delivery of the effector to the receptor relies on this property. The ligand accepting entry of the cavity is formed by H2, H4 and H5 (scene). However, the inside of the cavity is formed by the loop between helixes H3 and H4, and the region from H4 to H5(scene). The cavity is prone to accept such ligand because of its specific composition. Indeed, cavity components are mainly and are localized in the same faces of the helix.Thus, it implies that this residues are regularly distant in the primary structure.

Ligands

Fig.2 CMJ Ligplot

Fig.3 GOL Ligplot

Fig.4 Cl Ligplot

(A REFAIRE)

Related Forms

Autres versions de la protéine à pH variable

- 3fe8 The same protein in complex with a serendipitous ligand soaked at pH 4.0
- 3fe9 The same protein in complex with a serendipitous ligand soaked at pH 7.0

- 3cdn The same protein in apo form soaked at pH 4.0
- 2h8v The same protein in apo form at pH 5.5
- 3cz2 The same protein in apo form at pH 7.0

- 3bfa The same protein in complex with the QMP at pH 5.5
- 3bfb The same protein in complex with the 9-ODA at pH 5.5
- 3bfh The same protein in complex with the HDOA at pH 5.5
- 3bjh The same protein in complex with the nBBSA at pH 5.5

- 3cyz The same protein in complex with the 9-ODA at pH 7.0
- 3cz0 The same protein in complex with the QMP at pH 7.0
- 3cz1 The same protein in complex with the nBBSA at pH 7.0
- 3cab The same protein in complex with the nBBSA soaked at pH 7.0

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References for further information on the pheromone binding protein from Apis mellifera

↑ Pesenti ME, Spinelli S, Bezirard V, Briand L, Pernollet JC, Tegoni M, Cambillau C. Structural basis of the honey bee PBP pheromone and pH-induced conformational change. J Mol Biol. 2008 Jun 27;380(1):158-69. Epub 2008 Apr 27. PMID:18508083 doi:10.1016/j.jmb.2008.04.048
↑ Pesenti ME, Spinelli S, Bezirard V, Briand L, Pernollet JC, Campanacci V, Tegoni M, Cambillau C. Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release. J Mol Biol. 2009 Jul 31;390(5):981-90. Epub 2009 May 28. PMID:19481550 doi:10.1016/j.jmb.2009.05.067
↑ Han L, Zhang YJ, Zhang L, Cui X, Yu J, Zhang Z, Liu MS. Operating mechanism and molecular dynamics of pheromone-binding protein ASP1 as influenced by pH. PLoS One. 2014 Oct 22;9(10):e110565. doi: 10.1371/journal.pone.0110565., eCollection 2014. PMID:25337796 doi:http://dx.doi.org/10.1371/journal.pone.0110565

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_960"

@@ Line 37: / Line 37: @@
 [[Image: 3fe6_cartoon.jpg|250px|left|thumb|'''Fig.1''' Ribbon colored representation]]
-ASP1 is composed of <scene name='60/604479/Helixes/1'>7 right-handed alpha helixes</scene>  (<scene name='60/604479/H1/2'>H1</scene>, residues 8–25; <scene name='60/604479/H2/2'>H2</scene>, residues 27–36; <scene name='60/604479/H3/2'>H3</scene>, residues 42–56; <scene name='60/604479/H4/1'>H4</scene>, residues 66–74 ; <scene name='60/604479/H5/1'>H5</scene>, residues 75–77 ; <scene name='60/604479/H6/1'>H6</scene>,residues 78–90 ;<scene name='60/604479/H7/1'>H7</scene>, residues 96–112)
+ASP1 is composed of <scene name='60/604479/Helixes/1'>7 right-handed alpha helixes</scene>[ http://www.genome.jp/dbget-bin/www_bget?pdb:3FE6]
+** <scene name='60/604479/H1/2'>H1</scene>: residues 8–25
+** <scene name='60/604479/H2/2'>H2</scene>: residues 27–36
+** <scene name='60/604479/H3/2'>H3</scene>: residues 42–56
+** <scene name='60/604479/H4/1'>H4</scene>: residues 66–74
+** <scene name='60/604479/H5/1'>H5</scene>: residues 75–77
+** <scene name='60/604479/H6/1'>H6</scene>: residues 78–90
+** <scene name='60/604479/H7/1'>H7</scene>: residues 96–112
 <scene name='60/604479/H1/2'>H1</scene> has a break in the hydrogen-bonding pattern of its structure, forming tight substitute hydrogen bonds with water molecules. Thus, it results in a kink (at residue Ala 14)(scene) induced by a disruption in the helical conformation, due to hydrogen bonds with water molecules.

Sandbox Reserved 960

From Proteopedia

Revision as of 21:08, 22 December 2014

Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand at pH 5.5

Contents

Function

Structure

Components implicated in the structure rigidity:

Cavity

Ligands

Related Forms

Relevance

Structural highlights

References for further information on the pheromone binding protein from Apis mellifera

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