Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

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.

84