This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

Sandbox Reserved 433

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:15, 2 April 2015

This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439.

1 Introduction
2 Overall Structure
3 Binding Interactions
4 Additional Features
5 Quiz Question 1
6 Quiz Question 2
7 See Also
8 Credits
9 References

Introduction

This is a sample scene created with SAT to by Group, and another to make of the protein.

Introduction guide line: Glycogen Synthase Kinase-3 (GSK-3)

1. Begin with "GSK-3 is serine/threonine protein kinase..." explain what that is (structure and general function) 2. Speak about GSK-3 alpha and GSK-3 beta. 3. Begin to describe green screen in relation to the general structure of serine/threonine protein kinase --> specific differences in GSK-3 4.Talk about which species contain GSK-3

 i. Speak about where in which species bodies GSK-3 is present versus humans 
 ii. Explain function in different species structures versus humans

5. Talk about interactions with other molecules and effects of these interactions.

 i. Effects of changing concentrations of GSK-3 and effects of changing the concentrations of molecules it interacts with 
 ii. Talk about potential effects of mutations

6. Lead previous section (effects of varying amounts and interactions) into diseases caused by GSK-3. Talk about potential therapeutic uses of it and new treatments under research.

Green Screen Caption: Show GSK-3 alpha and GSK-3 beta (if possible?)

Overall Structure

-GSK-3beta has the typical two-domain kinase fold with a beta strand domain at the N-terminal end and an alpha-helical domain at the C-terminal end

-The ATP-binding site is at the interface of the alpha-helical and beta-strand domain and is bordered by the glycine-rich loop and the hinge

-The activation loop runs along the surface of the substrate binding groove

-The C-terminal residues are outside the core kinase fold and form a small domain that packs against the alpha-helical domain

-The beta-strand domain consists of seven antiparallel beta-strands

-Two phosphorylation sites that influence the catalytic activity of the protein

Haar, Ernst ter., Coll, Joyce T., Austen, Douglas A., Hsiao, Hsun-Mei., Swenson, Lora., Jain, Jugnu. Structure of GSK3B reveals a primed phosphorylation mechanism. Vertex Pharmaceuticals Incoprporated, Cambridge MA. Nature Publishing Group, Vol 8 No 7. July 2001.

-Monomer

-Overall structures of the enzyme are similar to that of the apoenzyme

-The crystals contain two molecules of GSK-3beta in the asymmetric unit and the two molecules are treated as identical

-Glycogen Synthase Kinase-3 (GSK-3) is a serine/threonine protein kinase

-Both isoforms have a conserved N-terminal serine reside (S21 for alpha and S9 for beta)

-Phosphorylation of the N-terminal serine residue plays an important role for further activity

Mishra, Nibha et al. Structure based virtual screening of GSK-3beta: Importance of protein flexibility and induced fit, 2009. Bioorganic & Medicinal Chemistry Letters, 2009, Vol. 19 Iss. 19, pp. 5582-5585. Retreived from http://www.sciencedirect.com/science/article/pii/S0960894X09011780

Binding Interactions

1)Folding of protein

  a) location and description of position of alpha and beta sheets (Show in separate color on green screen)
  b) crystal structure data (Table 1, Structural Characterizaiton of the GSK-3B Active Site Using Selective and Non-selective ATP-mimetic Inhibitors)

2)Substrate binding

  a)  “phosphate-binding” pocket: describe three crucial basic residues (Show in different color on green screen)
  b)  GSK-3 substrates and binding specifics- S/TxxxS/T (S=Serine, T=threonine, X= any amino acid)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217193/ http://www.rcsb.org/pdb/explore/explore.do?pdbId=1Q3D

Additional Features

1. Difference that can be observed from complexes of Staurosporine with GSK-3 beta and other protein kinases such as CDK2, Chk1, Lck and PKA

+ In GSK-3 beta complex with Staurosporine, water is a part of a hydrogen-bonding network

+ Only direct hydrogen bonds are observed between GSK-3 beta and Staurosporine

2. Comparison of GSK-3 beta complexes with Staurosporine and other inhibitors (AMP-PNP, indirubin-3'-monoxime)

+ Between GSK-3 beta complex with Stauroporine and AMP-PNP, the position of N-terminal domain varies.

+ The angle of binding in the active site are different

+ Water is also used as intermediate in hydrogen bonding in GSK-3 beta complex with Indirubin-3'-monoxime (same with complex in Staurosporine )

http://www.sciencedirect.com.silk.library.umass.edu/science/article/pii/S0022283603010593

Quiz Question 1

Which isoform of GSK-3 would work best for ___ function in ___ pathway?

What type of bonding would GSK-3B exhibit with Staurosporine? A picture of the Staurosporine molecule is found below.

The green screen above may help you as well.

Answer: hydrogen bonding

Quiz Question 2

What are the locations of the active sites with respect to the beta strand domain and the alpha helical domain on each isophorm?

These green screens may help you. Both scenes are interactive; be sure to change perspective and zoom to fully explore the structure. Use the provided color key to interpret the second scene.

Amino Terminus

Carboxy Terminus

Answer: At the interface of the N-terminus beta strand domain and the C-terminus alpha helical domain

J.A. Bertrand, S. Thieffine, A. Vulpetti, C. Cristiani, B. Valsasina, S. Knapp, H.M. Kalisz, M. Flocco, Structural Characterization of the GSK-3β Active Site Using Selective and Non-selective ATP-mimetic Inhibitors, Journal of Molecular Biology, Volume 333, Issue 2, 17 October 2003, Pages 393-407, ISSN 0022-2836, http://dx.doi.org/10.1016/j.jmb.2003.08.031.

(http://www.sciencedirect.com/science/article/pii/S0022283603010593)

Credits

Introduction - Zachary Plourde

Overall Structure - Sarah Johnson

Binding Interactions - Christina Lincoln

Additional Features - Bach Pham & Elvan Cevac

Quiz Question 1 - Nerses Haroutunian

Quiz Question 2 - Nick H-K

References

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_433"

Sandbox Reserved 433

From Proteopedia

Revision as of 18:15, 2 April 2015

Contents

Introduction

Overall Structure

Binding Interactions

Additional Features

Quiz Question 1

Quiz Question 2

See Also

Credits

References

Views

Personal tools

Navigation

Search

Toolbox

@@ Line 28: / Line 28: @@
 ==Overall Structure==
-The overall structure of the Glycogen Synthase Kinase-3β (GSK-β) enzyme is a monomer, and is similar to that of the apoenzyme. GSK-3β has a two-domain kinase fold with a β-strand domain (blue, residues 25-138) at the N-terminus, and an α-helical domain (red, residues 139-343) at the C-terminus. Bordering the ATP-binding site is a hinge and glycine-rich loop, found at the boundary of the α-helical and β-strand domain. The activation loop, found along the surface of the substrate-binding groove, can be seen in the (green, residues 200-226). The C-terminal resides form a domain that packs against the α -helical domain, which are outside the main kinase fold. The β-strand domain consists of seven β-strands that run in an antiparallel formation. These seven strands include a β -barrel that is interrupted in the middle by a short helix (orange, residue 96-102) that packs against the β-barrel. Two of the helixes residues, which are conserved in all kinases, play key roles in the catalytic action of the enzyme. Ser9 is one phosphorylation site that is responsible for the inactivation of GSK-3 β, and the phosphorylation of site Tyr210 is responsible for increasing the catalytic activity. Tyr201 is found on the activation loop, in (green).
+-GSK-3beta has the typical two-domain kinase fold with a beta strand domain at the N-terminal end and an alpha-helical domain at the C-terminal end
+-The ATP-binding site is at the interface of the alpha-helical and beta-strand domain and is bordered by the glycine-rich loop and the hinge
+-The activation loop runs along the surface of the substrate binding groove
+-The C-terminal residues are outside the core kinase fold and form a small domain that packs against the alpha-helical domain
+-The beta-strand domain consists of seven antiparallel beta-strands
+-Two phosphorylation sites that influence the catalytic activity of the protein
 Haar, Ernst ter., Coll, Joyce T., Austen, Douglas A., Hsiao, Hsun-Mei., Swenson, Lora., Jain, Jugnu. Structure of GSK3B reveals a primed phosphorylation mechanism. Vertex Pharmaceuticals Incoprporated, Cambridge MA. Nature Publishing Group, Vol 8 No 7. July 2001.
+-Monomer
+-Overall structures of the enzyme are similar to that of the apoenzyme
+-The crystals contain two molecules of GSK-3beta in the asymmetric unit and the two molecules are treated as identical
+-Glycogen Synthase Kinase-3 (GSK-3) is a serine/threonine protein kinase
+-Both isoforms have a conserved N-terminal serine reside (S21 for alpha and S9 for beta)
+-Phosphorylation of the N-terminal serine residue plays an important role for further activity
+Mishra, Nibha et al. Structure based virtual screening of GSK-3beta: Importance of protein flexibility and induced fit, 2009. Bioorganic & Medicinal Chemistry Letters, 2009, Vol. 19 Iss. 19, pp. 5582-5585. Retreived from http://www.sciencedirect.com/science/article/pii/S0960894X09011780
 <scene name='48/483890/Sarahs_scene/2'>GSK_3beta Overall Structure</scene>
@@ Line 83: / Line 105: @@
 ==Quiz Question 2==
-What are the locations of the active sites with respect to the two isoforms?
+What are the locations of the active sites with respect to the beta strand domain and the alpha helical domain on each isophorm?
-These green screens may help you. Both scenes are interactive; be sure change perspective and zoom to fully explore the structure. Use the provided color key to interpret the second scene.
+These green screens may help you. Both scenes are interactive; be sure to change perspective and zoom to fully explore the structure. Use the provided color key to interpret the second scene.
 <scene name='48/483890/Isophorms/2'> Green and blue color representations of the two isophorms complexed with the staurosporine ligands</scene>
@@ Line 93: / Line 115: @@
 {{Template:ColorKey_Amino2CarboxyRainbow}}
-Answer: At the interface of the N-terminus beta strand domain and the C-terminus alpha helix domain
+Answer: At the interface of the N-terminus beta strand domain and the C-terminus alpha helical domain
 J.A. Bertrand, S. Thieffine, A. Vulpetti, C. Cristiani, B. Valsasina, S. Knapp, H.M. Kalisz, M. Flocco, Structural Characterization of the GSK-3β Active Site Using Selective and Non-selective ATP-mimetic Inhibitors, Journal of Molecular Biology, Volume 333, Issue 2, 17 October 2003, Pages 393-407, ISSN 0022-2836, http://dx.doi.org/10.1016/j.jmb.2003.08.031.