Crystal structure of
Ice and Protein
PHYS 571
Yeliz Celik
Young Eun Choi
Andrew DiLullo
Outline

Ice


Physical Properties
Types of Ice
Hexagonal Ice Structure (Ice Ih)
Hydrogen bonding and the hexagonal structure of ice
The hexamer and the hexagonal crystal structure

Protein Crystallization

Examples of Protein structures



Ice

Physical Properties
CHEMISTRY
H2O , Hydrogen dioxide
CRYSTALLOGRAPHYH
Hexagonal (Ih)
CRYSTAL GROWTH
AND
HABITS
COLOR AND OTHER
OPTICAL PROPERTIES
Generally flat hexagonal crystals
Ice also forms rounded and concentrically
zoned spheres as hail stones. It can be
stalactitic, and massive granular.
Clear to white, Pale blue, Greenish blue,
transparent to translucent
HARDNESS
1.5
DENSITY
0.9167 g/cm3
BREAKABILITY
Very brittle fracture producing small,
conchoidal fragments

Water Phase Diagram and Morphology Diagram
http://www.lsbu.ac.uk/water/phase.html
http://www.its.caltech.edu/~atomic/snowcrystals/primer/primer.htm

Types of Ice
-
With both cooling and pressure different types exist : Ice II,III, V, VI, VII,VIII,
IX, and X. The types are differentiated by their crystalline structure, ordering
and density.
Ice II (rhombohedral)
Ice III (tetragonal)
Ice VI (tetragonal)
Ice VIII (tetragonal)
Ice V (monoclinic)
Ice X (cubic)
- There are also two metastable phases of ice under pressure, both fully
hydrogen disordered: IV and XII.
Ices XI, XIII, and XIV are hydrogen-ordered forms of ices Ih, V, and XII
respectively.

Types of Ice
- Everyday
ice and snow has a hexagonal crystal structure (ice Ih).
- Only a little less stable (metastable) than Ih is the cubic structure (Ic).
Hexagonal Ice Structure (Ice Ih)
c(a3)
γ =120°
a2
a1
a a
,c=
•Classic snowflake
from vapor-rich
1= formed
2
air between -10 to -22 ºC . LT-SEM image
7.35Å
with inset4.51Å
light
a=
© Eric Erbe / Beltsville Agricultural Research
Center
Prism face
•Hexagonal ice plate formed from vapor
deposition
in air at 0 to -3 or -10 to -35 ºC.
http://www.lsbu.ac.uk/water/ice1h.html
LT-SEM image with inset light microscope
image.
Hydrogen Bonding in Ice

Hydrogen bonding in general:
 shared
bonding of H between two highly
electronegative atoms such as F, O, or N

Hydrogen bonding in water and ice:
 isolated
two molecule (dimer) system
Hydrogen bonding and the
hexagonal structure of ice

Other isolated clusters
of ice molecules
 trimer,
tetramer,
pentamer, hexamer
 hexamer is the most
energetically likely

Isolated groups only
somewhat useful in
bulk study
The hexamer and the hexagonal
crystal structure of ice




2.8Å O-O distance
Reason for decreased
density of ice
Expect 4 hydrogen
bonds per molecule
Measured 3.69
hydrogen bonds per
molecule
Protein Crystallization

1.
2.
3.
Applications:
Drug design and structural biology
Bio-separation
Controlled drug delivery
Protein Crystallography

1.
2.
3.
X-ray crystallography :
Protein structures at the atomic level
How proteins interact with other
molecules
How they undergo conformational
changes
Spruce Budworm Antifreeze
Protein
Insect antifreeze protein
 Molecular weight is ~9 kDa
 Protects from freezing at T below 0
degrees

Protein Crystallography
Pure protein (an insect antifreeze protein)
 Sample needs to be concentrated
 Dilute buffer
 Hanging drop vapor diffusion method

Hanging Drop Vapor Diffusion Method
http://www.bio.davidson.edu/COURSES/Molbio/MolStudents/spring2003/Kogoy/protein.html
Crystals of Spruce budworm antifreeze proteins
0.21X 0.12X 0.02 mm
After repeated seeding a nice crystal obtained
Leinala et al.,2002: Grather,SP et al.,1999
Crystals of recombinant Spruce budworm antifreeze
proteins
Leinala et al.,2002
Result of x-ray crystallography is a three dimensional map that shows the
distribution of electrons in the structure.
http://www.jic.ac.uk/staff/david-lawson/xtallog/summary.htm
Crystal structure of the protein: Single Anomalous Scattering,
NMR


Left-handed Beta helical structure
15 amino-acid loops
Leinala, EK et al., 2002
How shape morphology changes when ice crystal is grown
in a solution of the insect antifreeze protein
References









Petrenko,VF, et al.,Physics of Ice,1999, Oxford University Press,
New York
Grather,SP et al.,1999, Journal of Structural Biology,126,72-75.
Leinala, EK, 2002, Structure,10,619-627.
http://www.bio.davidson.edu/COURSES/Molbio/MolStudents/spring
2003/Kogoy/protein.html
http://www.its.caltech.edu/~atomic/snowcrystals/primer/primer.htm
http://www.lsbu.ac.uk/water/phase.html
http://www.jic.ac.uk/staff/david-lawson/xtallog/summary.htm
http://www.lsbu.ac.uk/water/phase.html
http://www.its.caltech.edu/~atomic/snowcrystals/primer/primer.htm