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Conformational Ensembles from Experimental Data
and Computer Simulations
Poster Abstracts
84
49-POS
Board 9
Dramatic Shape Changes Occur as Cytochrome c Folds
Serdal Kirmizialtin
1
, Felicia Pitici
2
, Alfredo Cardenas
3
, Ron Elber
2,3
, Devarajan Thirumalai
2
.
1
New York University Abu Dhabi, Abu Dhabi, United Arab Emirates,
2
The University of Texas
Austin, Austin, TX, USA,
3
The University Of Texas Austin, Austin, TX, USA.
The protein folding has been the focus of intense study. Cytochrome c (cyt c) has been a model
protein for folding studies and extensive experimental work has been done on the folding of cyt c
demanding computations to characterize the structural transitions and the corresponding times
during the folding process. Here, we use simulation methods to create a conformational
ensemble that describe the folding of cyt c. Atomically detailed folding trajectories generated by
the Stochastic Difference Equation in Length fitted to time resolved Small Angle X-ray
experiments. We were able to find a linear relationship between average trajectory length and
real time of the folding process that allowed us to monitor the changes in the folding process
from microseconds to seconds in unprecedented atomic detail that is otherwise impossible. We
identify folding intermediates and characterize the stages of folding both in the form of global
shape and size changes and in the form of secondary and tertiary fold formation kinetics.