slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Structural Bioinformatics: Comparative Modeling PowerPoint Presentation
Download Presentation
Structural Bioinformatics: Comparative Modeling

Loading in 2 Seconds...

play fullscreen
1 / 35

Structural Bioinformatics: Comparative Modeling - PowerPoint PPT Presentation


  • 114 Views
  • Uploaded on

Structural Bioinformatics: Comparative Modeling. Target T0205 5 th Best in world-wide CASP5 experiment. sb.nrbsc.org. Towards a High-Resolution Understanding of Biology.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Structural Bioinformatics: Comparative Modeling' - ghita


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
slide1

Structural Bioinformatics:

Comparative Modeling

Target T0205

5th Best in world-wide

CASP5 experiment

sb.nrbsc.org

slide2

Towards a High-Resolution Understanding of Biology

Structural Biological Analyses can provide the ultimate insight into the mechanism behind a biological function, understand how biological function follows structure.

slide6

Hydrogen bond donors and acceptors

Can lose a proton to act as nucleophiles

slide7

Hydrogen bond donors and acceptors

Assist in catalyzing reactions

slide8

Positively charged amino acids, Can donate a proton as part of enzymatic reactions, general acids, electrophilic

slide9

Negatively charged, hydrogen bond acceptors, can abstract a proton as part of enzyme mechanism, general bases, nucleophiles

slide10

Can participate in cation-pi interactions, hydrogen bonding, hydrophobic interactions. Tyrosine can donate or accept protons.

slide11

Rotation around Ca-C = psi

Rotation around C-N = phi

Ramachandran plot

Tertiary structure of MsrA

helix 3 6 amino acids per turn with h bonds between every 4th residue
 helix: 3.6 amino acids per turn, with H-bonds between every 4th residue

Secondary Structure Elements

Secondary structure refers to the interactions that occur between the C=O and NH groups on amino acids in a polypeptide chain, and form helices, sheets, turns and loops.

 sheet: Formed by H-bonds between 5-10 consecutive amino acids in one section of the chain with another 5-10 in another section

slide13

Tyrosine 7

Glutathione S-Transferase backbone structures from 100 picosecond MD simulation.

Lys121

slide14

Structure Determination by x-ray crystallography or NMR is still relatively difficult and expensive

Synchrotron in Grenoble, France.

At present there are only 57 synchrotrons in the world

750MHz NMR

cryo electron microscopy
Cryo-Electron Microscopy
  • Allows visualization of structure and dynamics of biological assemblies at resolutions spanning from molecular (20-30 Ǻ) to near atomic (3 Ǻ).
  • Near atomic models can be built by combining information from high resolution structures of individual components in the complex with low resolution structure of entire assembly.
slide16

Sequence-Structure Disparity

More than 2.5 million proteins have been sequenced (Maroon).

Only 45,000 structures have been experimentally solved (Turquoise).

Structure prediction methods can provide a method to address this disparity

slide17

Basis of Comparative Protein Modeling

  • Predicts the three-dimensional structure of a given protein sequence (TARGET) based on an alignment to one or more known protein structures (TEMPLATES)
  • If similarity between the TARGET sequence and the TEMPLATE sequence is detected, structural similarity can be assumed.

Structural superposition of ALDH Family members

Comparative Protein Models will be increasingly utilized to help solve biological problems

slide18

Basic Comparative Protein Modeling Procedures

Start

End

Yes

Model ok?

Identify templates

No

Select templates

Evaluate the model

Align target with template

Build the model

slide19

Identifying Templates by Sequence-based methods

  • BLAST, PSI-BLAST
  • Use MEME program to identify motifs
  • Increase the signal-to-noise ratio by using patterns called “motifs” as the query. Motifs describe only a small portion of the query sequences which reduce chance similarities.
  • MAST (Motif Alignment and Search Tool)
    • http://meme.sdsc.edu/meme/website/mast.html
slide20

Basic Comparative Protein Modeling Procedures

Start

End

Yes

Model ok?

Identify templates

No

Select templates

Evaluate the model

Align target with template

Build the model

slide21

Factors to Consider in Selecting Templates

  • Phylogenetic tree construction can help find the subfamily closest to the target sequence
  • Consider Multiple Templates if possible.

Other concerns:

Ligands present?

Environmental conditions? pH

  • Some structures have been solved at multiple resolutions.
slide22

ALDH2(blue)/ALDH1(yellow) overlay

ALDH2/ALDH3(red) overlay

  • Sequence Identity w/ ALDH2RMSCD over domains
  • ALDH1 67% < 1.0 Ǻ
  • ALDH3 27% > 2.0 Ǻ
  • RMSCD (root mean square coordinate difference) over Cα atoms.
slide23

Selection of the Correct Template

Critical Assessment of Structure Prediction (CASP6) Results

Target T0282:

Rank and Name: GDT (% correct):

1. Ginalski 70.6

2. Skolnick 70.4

3. Venclovas 68.2

93. Wymore (1PQ3) 57.09

(3 ) Wymore (1GQ6) 70.1

Would have been 3rd best

slide24

Basic Comparative Protein Modeling Procedures

Start

End

Yes

Model ok?

Identify templates

No

Select templates

Evaluate the model

Align target with template

Build the model

slide25

Initial 3D-Model Construction

  • Essentially copy coordinates of equivalent atoms from the template to the target structure.
  • Internal coordinates are used for remaining unknown coordinates
  • Generate stereochemical and homology derived restraints

Template: -GGMG-

Target: -GGKG-

Template: -GGSG-

Target: -GGTG-

slide26

Errors in Homology Modeling

a) Side chain packing b)Distortions and shifts c) no template

---template

Actual

Model

slide27

Errors in Homology Modeling

d) Misalignments e) incorrect template

Marti-Renom et al., Ann. Rev. Biophys. Biomol. Struct., 2000, 29:291-325.

slide28

Comparative Modeling Tutorial

Determining the Basis for Stereoselectivity in R- and S-HPCDHs

?

R-HPCDH

S-HPCDH

slide29

Tutorial Philosophy

  • Tutorial is currently appropriate for students that have completed either an organic chemistry or biochemistry undergraduate class. (??)
  • Goal is to integrate it into a sequence-based bioinformatics course
  • Attempting to teach bio-molecular structure through the web without having to learn “any” technical details about visualization or modeling software. Can choose to be more intimate with programs.
  • Tutorial progresses in a logical manner from learning about the properties of the substrate to the binding interactions between enzyme and substrate and finally to understanding the enzyme mechanism.
  • Comparative modeling is the tool by which to construct a structure-function relationship. We are striving to weave structure-function relationships throughout all the tutorials.
slide30

C

C

O

C

S

C

C

O

S

O

R-Hydroxypropylthioethanesulfonate {R-HPC}

slide32

The enzymatic oxidation of HPC is accomplished through a proton transfer from the substrate to Tyr155 and a hydride transfer from the substrate to NAD.

slide35

Enhancing the tutorial in the future

  • Students could read the journal article that reports on the kinetic characterization of wild-type and site-directed mutants before the tutorial to see what was thought about the enzyme prior to the structure being solved. Biochemistry, 2004, 43:6763-6771
  • What did the authors correctly predict? What details were probably surprising to the authors upon solving the structure?
  • Start off examining the deposited PDB id: 2CFC. The deposited structure contains a co-crystallized product molecule. How would the structure differ if we could examine the enzyme bound to the reactant? Compare between x-ray model and computational model.
  • Examine the NAD binding residues. Are they conserved?
  • Docking of the substrate into the S-HPCDH binding site.
  • Would this tutorial work in reverse? (i.e. If the structure of S-HPCDH had been solved and we were asked to model R-HPCDH)