Seminarium z fizyki biologicznej i bioinformatyki
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2022-05-11 (15:15) 
Dr hab. Piotr Setny (Centrum Nowych Technologii UW, Warszawa)
Granger causality analysis of protein beta-hairpin folding
https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
Meeting ID: 919 7615 3012
Passcode: 747922
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Bogdan Lesyng (UW)
Anna Niedźwiecka (IF PAN)
Piotr Zielenkiewicz (IBB)
ABSTRACT
Computer simulations allow capturing increasingly long fragments of molecular dynamics. Still, revealing functional relations or allosteric communication pathways that usually involve cascades of transient events is often difficult and calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. An approach towards the analysis of complex temporal signals is Granger causality analysis. It has found applications in the fields of neuroscience or econometrics and provides means to assess which components of multidimensional time series are most influential for the evolution of the entire system. Here, we apply Granger analysis to a long molecular dynamics trajectory depicting reversible folding of a mini beta-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for its folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together these findings clearly favour the concept of zipper-like folding, which is one of two postulated beta-hairpin folding mechanisms. On a broader perspective, the results demonstrate the possibility of conclusive application of Granger causality analysis to a biomolecular system.
Meeting ID: 919 7615 3012
Passcode: 747922
One tap mobile
+48223073488,,91976153012#,,,,*747922# Poland
+48223987356,,91976153012#,,,,*747922# Poland
Dial by your location
+48 22 307 3488 Poland
+48 22 398 7356 Poland
+48 22 306 5342 Poland
Join by Skype for Business
https://zoom.us/skype/91976153012
Bogdan Lesyng (UW)
Anna Niedźwiecka (IF PAN)
Piotr Zielenkiewicz (IBB)
ABSTRACT
Computer simulations allow capturing increasingly long fragments of molecular dynamics. Still, revealing functional relations or allosteric communication pathways that usually involve cascades of transient events is often difficult and calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. An approach towards the analysis of complex temporal signals is Granger causality analysis. It has found applications in the fields of neuroscience or econometrics and provides means to assess which components of multidimensional time series are most influential for the evolution of the entire system. Here, we apply Granger analysis to a long molecular dynamics trajectory depicting reversible folding of a mini beta-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for its folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together these findings clearly favour the concept of zipper-like folding, which is one of two postulated beta-hairpin folding mechanisms. On a broader perspective, the results demonstrate the possibility of conclusive application of Granger causality analysis to a biomolecular system.