Post on 03-Jul-2015
description
transcript
Structural Understanding of
Intrinsically Disordered Proteins
Joe Passman
April 26, 2013
6/24/20131
While I Have Your Attention…
6/24/20132
Overview
6/24/20133
Rise, Prevalence, and
Possible Roles of Disorder in
Proteins
Background
6/24/20134
Structure / Function Paradigm
Transcription
mRNA
mRNA
Translation
Peptide
3D Protein
Folding
Output
Nucleus
DNA
Splicing
Export
RNA
???
6/24/20135
Disorder Becomes Apparent
Early discovery
Bovine serum albumin binding sites (Karush,1950)
Later…
Rapid rise of genomic data (~1990)
Predictors of natural disordered regions (PONDRs)
Early proton NMR experiments (Daniels et al, 1978)
0
200
400
600
800
2013
2010
2007
2004
2001
1998
1995
1992
1989
1986
1983
1978
Nu
mb
er
of
Pu
bli
cati
on
s
Year
6/24/20136
Disorder, Disorder, (most)Everywhere!
Hosoda et al, 2011
6/24/20137
Why Did We Miss It?
Unobserved
Bias of experiment
Access to genomic data
limited before ~1990
Crystal structure
relatively uninformative
Ignored
Crystal structure artifacts
dismissed
Disorder thought to be an
artifact
Dyson & Wright, 2005
6/24/20138
What is Disorder in Proteins?
Definition:
A protein that does not adopt a well-defined native
structure when isolated in solution under near-
physiological conditions (Eliezer, 2009)
2 types
Denatured state ensembles (DSEs)
Intrinsically disordered proteins (IDPs)
Vast and malleable configurational ensembles (CEs)
Charged
What can impact disorder?
6/24/20139
Why are IDPs Interesting?
Diverse Roles!
Regulatory
Homeostasis of signaling pathways
Translation/Transcription
Structural
Flexible Linkers
AND….. They can kill you.
Disease states
Cancer (lack of cell cycle regulation)
Brain (amyloid plaque formation)Lee et al, 2003
6/24/201310
Proposed Mechanisms
6/24/201311
Regulation
Folding upon binding
Highly specific / low affinity binding
Multiple interaction sites
Aggregation
Dyson & Wright, 2005Schärpf et al, 2001
Background
6/24/201312
Structure
6/24/201313
107 residues (1799 atoms)
Positively charged side chains
Proportion of arginine to lysine: 22%
Structure Position Length
(residues)
Visual
Helix 4-10 7
Helix 12-20 9
Helix 23-25 3
Beta Strand 26-29 4
Beta Sheet
Alpha Helix
Function
6/24/201314
Transient complex
Interacts with
RNA
RNA polymerase
End Result
Prevent termination of
transcription
Goldenberg, 2012
More on Interaction with RNA
6/24/201315
Schärpf et al, 2001
6/24/201316
Regulatory function
Multiple interaction partners
Extensively unfolded in isolation
Flexible structure
Background
6/24/201317
Questions, hypothesis, and
goals
What Are We Trying to Address?
6/24/201318
Goldenberg, 2011
Hypothesis/Expected Outcomes
6/24/201319
Goals
6/24/201320
Provide a set of atomistic properties
Quantify correspondence with macroscopic ensemble-
averaged experimental data
Develop reference point for crowding studies
Context: Alzheimer’s Disease
NIH / National Institute on Aging
6/24/201321