Computational study of escherichia coli signal recognition particle gtpases
1 / 15

Computational Study of Escherichia coli Signal Recognition Particle GTPases - PowerPoint PPT Presentation

  • Uploaded on

Computational Study of Escherichia coli Signal Recognition Particle GTPases. BZH. Kelly Elkins. GPBM 2002: June 25, 2002. Why Modelling?. GTACTTACCCTAGTAC CATGAATGGGATCATG. ?. Gene Structure Function. Outline.

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

PowerPoint Slideshow about 'Computational Study of Escherichia coli Signal Recognition Particle GTPases' - stormy

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
Computational study of escherichia coli signal recognition particle gtpases
Computational Study of Escherichia coliSignal Recognition Particle GTPases


Kelly Elkins

GPBM 2002: June 25, 2002

Why modelling
Why Modelling?




Gene Structure Function


  • What is the signal recognition particle?

    …proteins necessary for the proper export/transport of secretory

    and membrane proteins.

A computational study of a protein-protein complex:

Build a model of Ffh

Evaluate proposed SRP:SR interaction model

Is model valid in an apo-form? with Mg2+ bound?

with GTP-Mg2+?

Other possible models?


Signal recognition particle
Signal Recognition Particle

  • Universally conserved system for protein trafficking

  • In humans, 6 proteins and 1 RNA

  • In E. coli:

    • 2 proteins: SRP and receptor; 1 RNA: 4.5S RNA

    • Both are GTPases

    • Ffh (SRP) 48 kDa GTPase protein

    • FtsY (receptor) GTPase protein

1FTS.pdb- G. Montoya, et al. (1997) Nature, 385, 365-368.

1DUL.pdb- R.T. Batey, et al. (2000) Science, 287, 1232-1239.

E coli ffh srp model
E. coli Ffh SRP model

Comparative Modelling

pdb structures:

Ffh model
Ffh Model

  • Swiss Model

  • 1) First Approach Mode- templates:

  • -1JPJ.pdb (T. aquaticus Ffh

  • NG fragment bound GMPPNP)

  • -1FTS.pdb (E. coli apo-

  • FtsY NG fragment)

  • -1NG1.pdb (T. aquaticus Ffh

  • NG fragment bound GDP-Mg2+)

  • -1J8M.pdb (A. ambivalens

  • apo-Ffh NG fragment)

  • Optimize Project Mode- adjusted

  • sequence alignment with Swiss PDB Viewer to retain secondary structure elements

  • -Same templates

  • Checked Model with Procheck

  • and Whatif

1FTS.pdb- G. Montoya, et al. (1997) Nature, 385, 365-368.

1NG1.pdb- D.M. Freymann, et al. (1999) Nature Struct. Biol., 6, 793-801.

1JPJ.pdb- S. Padmanabhan, & D.M. Freymann, (2001) Structure (Camb.), 9, 859-867.

1J8M.pdb- G. Montoya, et al. (2000) Structure, 8, 515-525.

Ffh model1
Ffh Model

Superimposition of the Ffh

model on the 4 templates


1NG1- 2.93 Angstroms

1J8M- 0.96 Angstroms

1JPJ- 3.04 Angstroms

1FTS- 2.94 Angstroms

Evaluation of a proposed protein protein interaction model
Evaluation of a Proposed Protein-Protein Interaction Model

Proposed Model: Ffh-FtsY complex superimposed on 1N2C.pdb

(nitrogenase iron protein) by structural similarity

(Montoya, G., te Kaat, K., Moll, R., Schaefer, G., & Sinning, I. (2000). Structure, 8, 515-525.)

Calculated the superimposed

proposed model- sup2pdbs

program (R.Gabdoulline)-

Ca superimposition

Gtp mg 2 docking
GTP-Mg2+ Docking

  • Superimposition

  • 42 GTP molecules- Protein Data Bank (23 Jan. 2002)

  • Superimposed GTPs with superimp program (G.M. Ullmann)-

    like atoms of 2 molecules are superimposed

  • Superimposed all GTPs into Ffh model and FtsY using

    1NG1.pdb GDP as template

  • Mg2+ placement according to 1NG1.pdb GDP-Mg2+ structure

  • Energy minimized apo, Mg2+, and GTP-Mg2+ docked forms

    using AMBER7

  • Visualize superimposed GTPs using Molsurfer

  • Electrostatics calculations of the complexes using UHBD with

    CHARMm forcefield parameters (unminimized forms)

J.D. Madura, et al. (1994) Biological applications of electrostatic calculations and brownian dynamics simulations. In: “Reviews in Computational Chemistry, Volume V“, Lipkowitz, K.B., & Boyd, D. (Eds.), VCH Publishers, Inc., New York.

R.R. Gabdoulline & R.C. Wade, (1997) Biophys. J., 72, 1917-1929.R.R. Gabdoulline & R.C. Wade, (2001) J. Mol. Biol., 306, 1139-1155.R.R. Gabdoulline& R.C. Wade, (1999) TIBS, 24, 285-287.

Gtp mg 2 docking1
GTP-Mg2+ Docking

GTP-Mg2+ docked to Ffh

Evaluation of a proposed protein protein interaction model1
Evaluation of a Proposed Protein-Protein Interaction Model

SDA (Simulated Diffusional Association)- ab initio models

unrestricted search

search restricted to GTP-binding region

UHBD calculations- compare electrostatic surfaces, charged regions

DALI- propose other homology models (

Energy minimization with AMBER7- relieve bad contacts

Future work
Future Work

  • Transform pdb coordinates and rotate according to DALI output to

    examine proposed alternate homology models with UHBD

    and Molsurfer

  • Evaluate ab initio models produced by SDA and by a

    hydrophobic patch pairing

  • Model the M domain of Ffh and the 4.5S RNA into the associated


  • Alternative GTP-Mg2+ placement using GRID20


  • We have made a homology model of E. coli Ffh

  • We have docked GTP-Mg2+ to both Ffh and FtsY

  • The energy-minimized Ffh:FtsY complex produced by homology with the nitrogenase iron protein homodimer is not viable, but may need only small adjustments to relieve bad side- chain contacts and to obtain better hydrophobic contacts

  • The electrostatics calculations indicate that the charge landscapes of Ffh and FtsY are very complex and that hydrophobic residues must also mediate complex formation


Rebecca Wade, European Media Laboratory

Irmi Sinning, University of Heidelberg

Timm Essigke

Razif Gabdoulline

Ting Wang

J. William Fulbright Foreign Scholarship Board and the German Fulbright Kommission

Klaus Tschira Stiftung (KTS)