Académique Documents
Professionnel Documents
Culture Documents
interactions
Nanomaterials: proteins and water, cell membranes
L. Ridgway Scott
The Institute for Biophysical Dynamics, the Computation Institute, and the
Departments of Computer Science and Mathematics, The University of Chicago.
Last year at the IMA, Univ. of Minnesota (thanks to NSF).
This talk is based on joint work with Wah Chiu (Baylor College of Medicine),
Ariel Ferndandez (Rice Univ.), Andy McCammon (UCSD), Kristina Rogale
Plazonic (Princeton), Harold Scheraga (Cornell), and and at U. Chicago: Steve
Berry, Peter Brune, Chris Fraser, and Matt Knepley.
1
1 Ligand binding removes water: dehydrons
CHn CHn
CHn CHn CHn
CHn
C N C O H N
O H
H O
O H H
L IG A N D
H
Binding of ligand changes underprotected hydrogen
bond (high dielectric) to strong bond (low dielectric)
No intermolecular bonds needed!
2
1.1 Intermolecular versus intramolecular
CHn CHn
CHn CHn CHn
CHn
N C O H N
H
C O
L IG A N D
3
Dehydrons
in human hemoglobin, From PNAS
100: 6446-6451 (2003) Ariel Fernandez,
Jozsef Kardos, L. Ridgway Scott, Yuji Goto,
and R. Stephen Berry. Structural defects and
the diagnosis of amyloidogenic propensity.
Well-wrapped
hydrogen bonds are
grey, and dehydrons are green.
The standard ribbon model
of “structure” lacks indicators
of electronic environment.
4
1.2 Stickiness of dehydrons
5
Digital Biology: aligned backbones for two paralog kinases;
dehydrons for Chk1 are marked in green, those for Pdk1 are in red.
6
2 Conclusions, extensions and limitations
7
3 Other math modeling examples
•
8
4 Sustainable research
9
5 Thanks
This talk was based on joint work with Wah Chiu (Baylor College of Medicine),
Ariel Ferndandez (Rice Univ.), Andy McCammon (UCSD), Kristina Rogale
Plazonic (Princeton), Harold Scheraga (Cornell), and and at U. Chicago: Steve
Berry, Peter Brune, Chris Fraser, and Matt Knepley.
We are grateful to the