24 March 2003

Biol 6312

Protein Folding

Pathways of Protein Folding

Daggett V, Fersht AR.
Is there a unifying mechanism for protein folding?
Trends Biochem Sci. 2003 Jan;28(1):18-25. Review.

Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SM, Alonso DO, Daggett V, Fersht AR.
The complete folding pathway of a protein from nanoseconds to microseconds.
Nature. 2003 Feb 20;421(6925):863-7.

Honig B
Protein folding: from the levinthal paradox to structure prediction
J Mol Biol 1999 Oct 22;293(2):283-93

Rumbley J, Hoang L, Mayne L, Englander SW
An amino acid code for protein folding.
Proc Natl Acad Sci U S A 2001 Jan 2;98(1):105-12

Tsai CJ, Maizel JV, Nussinov R
Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape.
Proc Natl Acad Sci U S A 2000 Oct 24;97(22):12038-43

Knots in Proteins

Taylor WR.
A deeply knotted protein structure and how it might fold.
Nature. 2000 Aug 24;406(6798):916-9.

Link to my Chime view of the knotted protein

Protein folding Energy landscapes:

Plotkin SS, Onuchic JN.
Understanding protein folding with energy landscape theory. Part I: Basic concepts.
Q Rev Biophys. 2002 May;35(2):111-67.

Understanding protein folding with energy landscape theory. Part II: Quantitative aspects.
Q Rev Biophys. 2002 Aug;35(3):205-86.

Intra-cellular Protein Folding

Formation of Disulfide bonds.

Proline isomerization

Hsp60 (GroEL/ES) Chime

Hsp70

Hsp90

Walter S, Buchner J
Molecular chaperones--cellular machines for protein folding.
Angew Chem Int Ed Engl. 2002 Apr 2;41(7):1098-113.

Prions

Short review:

Weissmann C
Molecular genetics of transmissible spongiform encephalopathies.
J Biol Chem 1999 Jan 1;274(1):3-6 Full text

Structures:

Riek R, Hornemann S, Wider G, Billeter M, Glockshuber R, Wuthrich K
NMR structure of the mouse prion protein domain PrP(121-321).
Nature 1996 Jul 11;382(6587):180-2

Donne DG, Viles JH, Groth D, Mehlhorn I, James TL, Cohen FE, Prusiner SB, Wright PE, Dyson HJ
Structure of the recombinant full-length hamster prion protein PrP(29-231): the N terminus is highly flexible.
Proc Natl Acad Sci U S A 1997 Dec 9;94(25):13452-7 Full text

Zahn R, Liu A, Luhrs T, Riek R, von Schroetter C, Lopez Garcia F, Billeter M, Calzolai L, Wider G, Wuthrich K
NMR solution structure of the human prion protein.
Proc Natl Acad Sci U S A 2000 Jan 4;97(1):145-50 Full text

Lopez Garcia F, Zahn R, Riek R, Wuthrich K
NMR structure of the bovine prion protein.
Proc Natl Acad Sci U S A 2000 Jul 18;97(15):8334-9 Full text

Calzolai L, Lysek DA, Guntert P, von Schroetter C, Riek R, Zahn R, Wuthrich K
NMR structures of three single-residue variants of the human prion protein.
Proc Natl Acad Sci U S A 2000 Jul 18;97(15):8340-5 Full text

Links to my chime views of prions

Korth C, Stierli B, Streit P, Moser M, Schaller O, Fischer R, Schulz-Schaeffer W, Kretzschmar H, Raeber A, Braun U, Ehrensperger F, Hornemann S, Glockshuber R, Riek R, Billeter M, Wuthrich K, Oesch B
Prion (PrPSc)-specific epitope defined by a monoclonal antibody.
Nature 1997 Nov 6;390(6655):74-7

Alonso DO, DeArmond SJ, Cohen FE, Daggett V
Mapping the early steps in the pH-induced conformational conversion of the prion protein.
Proc Natl Acad Sci U S A 2001 Mar 13;98(6):2985-9 Full text

Knaus KJ, Morillas M, Swietnicki W, Malone M, Surewicz WK, Yee VC.
Crystal structure of the human prion protein reveals a mechanism for oligomerization.
Nat Struct Biol. 2001 Sep;8(9):770-4.

Copper binding

Viles JH, Cohen FE, Prusiner SB, Goodin DB, Wright PE, Dyson HJ
Copper binding to the prion protein: structural implications of four identical cooperative binding sites.
Proc Natl Acad Sci U S A 1999 Mar 2;96(5):2042-7 Full text

Whittal RM, Ball HL, Cohen FE, Burlingame AL, Prusiner SB, Baldwin MA
Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry.Medline
Protein Sci 2000 Feb;9(2):332-43

Yeast prions

True HL, Lindquist SL
A yeast prion provides a mechanism for genetic variation and phenotypic diversity.
Nature 2000 Sep 28;407(6803):477-83

Balbirnie M, Grothe R, Eisenberg DS
An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid
Proc Natl Acad Sci U S A 2001 Feb 27;98(5):2375-2380