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SUMMARY:The Computational Key to Unlocking the Conformational Landscape of 
 Biological Processes
LOCATION:Chemistry A101
TZID:America/Denver
DTSTART:20230302T160000
UID:2026-04-21-12-30-52@natsci.colostate.edu
DTSTAMP:20260421T123052
Description:About the Seminar\n\nThe conformational landscape of biological
  processes such as protein folding\, and allosteric   regulation is esse
 ntial for understanding their underlying mechanisms. However\, its complex
 ity poses a challenge to theoretical modeling. In this talk\, I will discu
 ss structural clustering of molecular dynamics (MD) simulation data and pr
 esent a new algorithm based on particle positions that requires only a few
  intuitive parameters. The advantages of Shape-GMM are demonstrated on a �
 ��known-truth” model representing a structural transition between a righ
 t- and left-handed helix. The method is then applied to an extensive MD da
 ta set of a fast-folding protein\, HP35\, to capture subtle structural flu
 ctuations that occur during the folding process. In the second half of my 
 talk\, I will introduce the exemplar allosteric enzyme\, Imidazole Glycero
 l Phosphate Synthase (IGPS). This enzyme exhibits long range communication
  between distinct active sites in its dimeric form\, giving rise to a 4500
 -fold increase in glutamine hydrolysis activity. I will present a Density 
 Functional Theory (DFT) study on large (237 atoms) active site cluster mod
 els of IGPS in the presumed “active” and “inactive” states to inve
 stigate the relationship between conformation and catalysis. Future direct
 ions for qualitative understanding and quantitative modeling in enzyme cat
 alysis are proposed\, addressing current challenges regarding conformation
 al interconversion at timescales inaccessible to conventional QM treatment
 s. 4:00 pm
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