[Colloquium] Orlova/MS Presentation/Nov 25, 2013

[Margaret Jaffey]

This is an announcement of Tatiana Orlova's MS Presentation.

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Date:  Monday, November 25, 2013

Time:  3:00 AM

Place:  Ryerson 251

M.S. Candidate:  Tatiana Orlova

M.S. Paper Title: Hydrogen Bond Geometry in Protein Helices

Abstract:
Protein backbone helical structures have the same values of dihedral
angles phi and psi from unit to unit and thus, can be uniquely
determined by a pair (phi, psi). We focus our attention on two types
of protein secondary structure alpha- and 3_10-helices stabilized by
1-5 and 1-4 hydrogen bonding pattern respectively. Even though both
alpha and 3_10 helices each represent a group of helices, various
studies show that dihedral angle pairs (-63,-43) and (-60,-25)
characterize the most stable helices within each group respectively.
Hydrogen bond has geometrical constraints with respect to linearity,
length and various associated angles, that must influence the
formation of most stable helices. The relationship between hydrogen
bond geometrical requirements and stability of various protein
secondary structures has been extensively studied by applying
statistical analysis to protein experimental data. Here, we study this
relationship via mathematical optimization. Previously, mathematical
optimization was only applied to alpha helix and considered just the
linearity of a hydrogen bond. We express other various geometrical
parameters of a hydrogen bond as functions of dihedral angles and
study their influence on helical stability. In particular, we take two
major hydrogen bond requirements: linearity and length constraints and
ask whether the most stable alpha- and 3_10-helix result from
optimization with respect to a linear combination of these two
criteria. We show that these criteria are not sufficient to explain
the peaks. Moreover, we show that another hydrogen bond parameters
play an important role in helical stability.

Tatiana's advisor is Prof. L. Ridgway Scott

Login to the Computer Science Department website for details:
 https://www.cs.uchicago.edu/phd/ms_announcements#orlova

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Margaret P. Jaffey            margaret at cs.uchicago.edu
Department of Computer Science
Student Support Rep (Ry 156)               (773) 702-6011
The University of Chicago      http://www.cs.uchicago.edu
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