We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

Sandbox Reserved 960

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:27, 23 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.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
Click the 3D button (when editing, above the wikitext box) to insert Jmol.
show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

Crystal structure of the Antennal Specific Protein-1 from Apis mellifera (AmelASP1) with a serendipitous ligand at pH 5.5

The protein AmelASP1 has been identified in the antennae from the honeybee A.mellifera. Its primary sequence is a 144 amino acids polypeptide with a molecular weight of 13.180 kDa. AmelASP1 is part of the Pheromone Binding Protein (PBP) family. The 3D representation shown below was obtained at pH 5.5 using the nano-drops technique.

^[1]

^[2] ^[3] ^[4]

Updated on 23-December-2014

1 Biological function
- 1.1 Social relevance
- 1.2 Location in the antenna and transport of pheromones
2 Structure
3 Ligands
- 3.1 Artificial ligands
- 3.2 Natural ligands
4 Related structures
5 Relevance
6 Structural highlights

Biological function

Social relevance

Location in the antenna and transport of pheromones

Structure

Image:3fe6 cartoon.jpg

Fig.1 Ribbon colored representation

Domains and family

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 the 25th residue. AmelASP1 binds its ligand at low pH and releases it at neutral pH.

Key residues

AmelASP1 is composed of ^[5]

- : residues 8–25
- : residues 27–36
- : residues 42–56
- : residues 66–74
- : residues 75–77 (rarely mentionned in publications because of its tiny size)
- : 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 (at residue Ala 14) induced by a disruption in the helical conformation, due to hydrogen bonds with water molecules.

Components implicated in the structure rigidity

AmelASP1 presents which are greatly enhancing its structure’s rigidity by linking four of the helices together. The six cysteines and their interval spacing are the most striking features shared by proteins belonging to the PBP family.

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, among the numerous other, two hydrogene bonds are particularly noticeable because of their importance in the formation of the loop stabilizing H4. is established by Asp 66 and Leu 58 whereas is formed between Asp 60 and Ala 63.

Cavity

The dynamic structure of the protein is responsible of the ligand’s binding by adjustment of position. The structure looses its flexibility when binds. The successful delivery of the effector to the receptor relies on this property. The ligand binding pocket consists in a cavity formed by the helices H2, H4 and H5(scene), arranged in a globular shape which leads to a clear separation of the ligand from the hydrophilic environment. The top of the cavity is not closed and can establish contacts with the solvent. The cavity is prone to accept ligand such as 9-ODA because of its specific composition. Indeed, cavity's components are mainly .They consequently interact with the ligand's hydrophobic carbon chain and are localized on the internal face of the helix.Thus, it implies that these residues respect a regular distance pattern in the primary structure of the AmelASP1.

pH influence

Ligands

Artificial ligands

Fig.2 CMJ Ligplot

Fig.3 GOL Ligplot

Fig.4 Cl Ligplot

Natural ligands

Related structures

These structures shown below representing the same protein with variable ligand and pH emphasize and illustrate the binding versatility of PBP.

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
↑ Lartigue A, Gruez A, Briand L, Blon F, Bezirard V, Walsh M, Pernollet JC, Tegoni M, Cambillau C. Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L. J Biol Chem. 2004 Feb 6;279(6):4459-64. Epub 2003 Oct 31. PMID:14594955 doi:10.1074/jbc.M311212200
↑ http://www.genome.jp/dbget-bin/www_bget?pdb:3FE6

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

@@ Line 25: / Line 25: @@
-<scene name='60/604479/Helixes/1'>7 helices</scene>
-<scene name='60/604479/H1/2'>H1</scene>
-<scene name='60/604479/H2/2'>H2</scene>
-<scene name='60/604479/H3/2'>H3</scene>
-<scene name='60/604479/H4/1'>H4</scene>
-<scene name='60/604479/H5/1'>H5</scene>
-<scene name='60/604479/H6/1'>H6</scene>
-<scene name='60/604479/H7/1'>H7</scene> (rarely mentionned in publications because of its tiny size)
@@ Line 57: / Line 41: @@
 ** <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/H5/1'>H5</scene>: residues 75–77 (rarely mentionned in publications because of its tiny size)
 ** <scene name='60/604479/H6/1'>H6</scene>: residues 78–90
-** <scene name='60/604479/H7/1'>H7</scene>: residues 96–112 (rarely mentionned in publications because of its tiny size)
+** <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 <scene name='60/604479/Kink/1'>kink</scene> (at residue Ala 14) induced by a disruption in the helical conformation, due to hydrogen bonds with water molecules.