Economou Lab-Teaching BIO1502/BIO1403


BIO502 Proteins in the cell Protein Biotechnology graduate program  

Lecture Downloads
Α. Introduction to structure and function of the Cell  
The bacterial model cell E.coli
PDF
Β. Proteins: structure, folding, modification, function  

Protein structure/folding/function 1

PDF
Protein structure/folding/function 2
PDF
Chaperones
PDF

Protein structure browser (Lab Practical)

link
C. Protein targeting and transport   
ER/bacterial Sec system and bacterial pathogens
PDF

Recommended Textbooks:

1. Branden and Tooze, 1999 Introduction to Protein structure 2nd edition (home)

2. Petsko and Ringe, 2004 Protein structure and function (home)

3. Alberts et al, 2002 Molecular Biology of the Cell 4th edition (home)

4. Stryer, 2003 Biochemistry 5th edition (home); Greek translation 2004; Crete University Press (home)

5. Pollack, 2001 Cells and gels and the engines of life (home)

Movies

   

 

Movies from The Theoretical and Computational Biophysics Group (TCBG)- NIH  Resource for Macromolecular Modeling and Bioinformatics

Links
LifeExplorer: a 3D navigation tool for cells
Animations show how you work at the molecular scale (video) | Cutting Edge - CNET News

NEWS
     
Date Title Source
14 Sep 2012 Behind the Movement Cell
07 Nov 2011 Scientists pleasantly 'shocked' by skills of Foldit gamers Health Tech - CNET News
16 Sep 2011 F.-Ulrich Hartl and Arthur Horwich share the Lasker Basic Medical Science Award for 2011 Cell
19 May 2011 Protein flaws responsible for complex life? BBC News

 

Further Reading:

(** essential)

Visualizing Proteins In the Cell
The Machineries of Life of Escherichia coli
 Abstract PDF


(** essential)

From single moleculues to ensembles
Central dogma at the single-molecule level in living cells
 Abstract PDF


Protein Import Mitochondrial/Chloroplast
Pfanner and Geissler Rev Mol Cel Biol

** A highly readable and very complete review for import into mitos

 Abstract PDF

Sickmann et al

The most complete proteome of a cellular organelle (yeast mitochondrial proteome)

Abstract PDF

Wiedemann et al

* A short review. Good first glimpse of the molecules and mechanisms involved in mito protein import

Abstract PDF 

 

Alder and Theg

** Energetics of protein import at its best!   Not just for mitos and chloros, but for other membrane protein import systems as well

Abstract PDF 

 

Soll and Schleiff

* All you need to know about Tocs and Tics(but no thylakoids)

Abstract PDF 

 

Kessler and Schleiff

Why on earth use GTPases for chloro import?

Abstract PDF

 

Robinson et al

The third chloro membrane (thylakoids)

Abstract PDF

Protein export: Sec and bacterial pathogens

**Pugsley AP, Francetic O, Driessen AJ, de Lorenzo V. (2004) Getting out: protein traffic in prokaryotes. Mol Microbiol. 52, 3-11.

Abstract PDF

Dalbey RE, Kuhn A. (2004) YidC family members are involved in the membrane insertion, lateral
integration, folding, and assembly of membrane proteins. J Cell Biol. 166, 769-774.

Abstract PDF

Randall LL, Hardy SJ. (2002) SecB, one small chaperone in the complex milieu of the cell. Cell Mol Life Sci. 59, 1617-1623.

Abstract PDF

Keenan RJ, Freymann DM, Stroud RM, Walter P. (2001) The signal recognition particle. Annu Rev Biochem.70:755-775

Abstract PDF

**Clemons WM Jr, Menetret JF, Akey CW, Rapoport TA. (2004) Structural insight into the protein translocation channel.
Curr Opin Struct Biol. 14, 390-396.

Abstract PDF

**Vrontou and Economou, A. (2004) Structure and function of SecA, the preprotein translocase nanomotor.BBA Mol Cell Reviews (in press)

Abstract PDF

*Gauthier A, Thomas NA, Finlay BB. (2003) Bacterial injection machines. J Biol Chem. 278, 25273-25276.

Abstract PDF

Protein folding in the cell: chaperones

Bukau B, Horwich AL.  (1998) The Hsp70 and Hsp60 chaperone machines.
Cell. 1998 Feb 6;92(3):351-66.

Abstract PDF

**Hartl FU, Hayer-Hartl M. (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein.
Science. 295, 1852-1858.

Abstract PDF

Jason C. Young, Joseã M. Barral and F. Ulrich Hartl (2003) More than folding: localized functions
of cytosolic chaperones.TIBS 28, 541-547

Abstract PDF

 

Molecular motors/machines: linear/rotary/ribosome

General machines:

Alberts Cell 1998

** If you only read one paper on mol machines read this one.

Abstract PDF

Taylor EB Wilson Lecture

* A highly readable review, broad overview

Abstract PDF

General motors:

Vale Cell 2003

* Good review, mainly linear motors

Abstract PDF

Vale and Milligan Science 2000

* Similar to above, highly illustrative

Abstract PDF

 

Ribosome:

Yusupov Science

* An outstanding effort. The Xray structure of the ribosome.

Abstract PDF

Spahn   Cell 2001

EM structure of ribosome

Abstract PDF

Beckmann Cell 2001

EM structure of ribosome peptide channel

Abstract PDF

Frank Chem Biol

** The ribosome as a machine

Abstract PDF

 

Moore PB Biochem 2001

Historical and focused on the ribosome mechanism – useful comment on the Xray structure determination

Abstract PDF

Myosin:

Okten NSMB 2004

The myosin hand over hand mechanism

Abstract PDF

 

ATPase:

Cross Nature 2004

**Short Comment on the rotary mechanism (Itoh paper see below)

Abstract PDF

 

Itoh et al Nature 2004

* Fantastic work, insightful and technically outstanding

Abstract PDF

 

Sambongi Science 2001

* similar to above. ATPase mechanism, now textbook material!

Abstract PDF

Stock et al Science 1999

Tour de force of Xray crystallography! A classic!

Abstract PDF

Ion channels

Doyle et al Science 1998

** A Nobel Prize worth of information!

Abstract PDF

Agre Nobel Lecture

Read for historic perspective and fun

Abstract PDF

 

MacKinnon

A medical doctor saw the light and turned into a scientist turned into a Nobel Prize winner

Abstract PDF

 

Facciotti TIBS 2004

A more general membrane   signal transduction review

Abstract PDF

 

Toyoshima

* the Ca –pump Xray structure

Abstract PDF

Disease/Biotechnology

Choi JH, Lee SY. (2004) Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol. 64, :625-635.

Abstract PDF

Steidler L, Hans W, Schotte L, Neirynck S, Obermeier F, Falk W, Fiers W, Remaut E. (2000) Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science. 289, 1352-1355.

Abstract PDF

Dobson CM. (2002) Getting out of shape. Nature. 418, 729-730.

Abstract PDF