Exploring the Protein Funnel Energy Landscape for Folding and Function

1
Exploring the Protein Funnel Energy Landscape for
Folding and Function
José N. Onuchic Center for Theoretical
Biological Physics UCSD ctbp.ucsd.edu
Workshop III - Structural Proteomics IPAM -
UCLA Los Angeles, May 2004
2
Energy Landscape Idea

• Rough Landscape Random Heteropolymer

Frustration!!

• Proteins Try to minimize
  frustration!

Stability Gap
Tf
Stability
?
Tg
Roughness
Principle of Minimal Frustration
(Bryngelson/Wolynes, Go)
? Realization of Minimal Frustration in Funnels
3
(No Transcript)
4
(No Transcript)
5
Go-model
Tf/Tg1.6
Tf/Tg1.3
H. Nymeyer, N. Socci and J.Onuchic, PNAS 2000
6
C.Clementi, H.Nymeyer, J.Onuchic, JMB 2000
Go-like potential only native interactions
are taken into
account (named after a paper by Taketomi, Ueda,
Go 1975)
7
Analysis of two-state folders Transition State
structure for CI2 and SH3
Probability of contact formation at TS
SH3
distal loop
Diverging turn
CI2
These descriptions are in good agreement with
experimental results (Jackson Fersht 1991,
Grantcharova et al. 1998).
C.Clementi, H.Nymeyer, J.Onuchic, JMB 2000
8
Analysis of proteins which fold through the
formation of an intermediate results for
Barnase, RnaseH, CheY
Barnase
Rnase H
CheY
A local minimum in the free energy profile
between the unfolded and folded minima locates a
folding intermediate state.
C.Clementi, H.Nymeyer, J.Onuchic, JMB 2000
9
CheY
In agreement with experimental results
(Lopez-Hernandez Serrano, 1996) we found that
in the misfolded" structure, all the five
a-helices are rather structured, while in the
later occurring transition state ensemble, the
helices 4-5 are more unstructured.
10
How about water effects?
r
Desolvation models
Hummer, G., et al, PNAS 1997
M. Cheung, A. Garcia and J.Onuchic, PNAS 2002
11
Tf
M. Cheung, A. Garcia and J.Onuchic, PNAS 2002
12
What are the folding routes for SH3?
13
Why this kind of mutation?
Alanine
Q
Valine
Val ? Ala
Multiple ?-value analysis
Energy Landscape Theory
Pseudo Q
Val ? Thr
Threonine
with Luis Serrano
14
A kinetic analysis on SH3 mutants using LJ and
Desolvation potentials
Using a desolvation potential, V44T and V53T show
dramatic changes in folding time!
58
9
53
46
44
23
15
Although V44T and V53T show a dramatic decrease
in folding rates, the nature of their kinetic
traps are different.
By going through alternate rounds of theoretical
analysis and experimental development, we are
revealing the mechanism of protein folding
progressively!
16
RG
Q
J. Shea, J. Onuchic and C. Brooks III, 2002
17
Protein A - Distribution of F Values
N(F)
F
Turn/Helix I-II Turn II-III
Helix I-III
J. Shea, J. Onuchic and C. Brooks, PNAS 1999
18
Rmsd(A) vs. Native contacts T T
Folded state divided into two basins Folded
solvated Folded desolvated
with Angel Garcia
19
Replica Exchange Sample Trajectories
with Angel Garcia
20
The Nature of the landscape
Backbone Hydration
?G (minimal path)
Free energy
Helix formation
?H (minimal path)
Enthalpy
TTf
Energies in Kcal/mol
21
Collaborators

• Postdocs
• Osamu Miyashita
• Koby Levy
• Antitsa Stoycheva
• John Finke
• Yoko Suzuki
• Shachi Gosavi
• Cecilia Clementi Rice
• Joan-Emma Shea UCSB
• Steve Plotkin UBC
• Nick Socci Albert Einstein
• Chigusa Kobayashi - Kobe, Japan
• Eric Nelson Texas
• Students

• Other Research Groups
• Peter Wolynes UCSD
• Angel Garcia - LANL
• Pat Jennings UCSD
• Charles Brooks TSRI
• Zan Luthey-Schulten UIUC
• Vitor Leite and Jorge Chahine - Brazil
• Yoshitaka Tanimura - Kyoto, Japan
• Yuko Okamoto IMS, Japan
• Ulrich Hansmann Michigan Tech

Supported by the National Science Foundation and
the Burroughs Wellcome Fund