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

Generally flat hexagonal crystals 

Ice also forms rounded and concentrically zoned spheres as hail stones.  It can be stalactitic, and massive granular.

COLOR AND OTHER OPTICAL PROPERTIES

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

http://www.lsbu.ac.uk/water/phase.html

http://www.its.caltech.edu/~atomic/snowcrystals/primer/primer.htm

Water Phase Diagram and Morphology Diagram

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.

- 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.

Ice II (rhombohedral) Ice III (tetragonal) Ice V (monoclinic)

Ice VI (tetragonal) Ice VIII (tetragonal) Ice X (cubic)

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).

Prism face

http://www.lsbu.ac.uk/water/ice1h.html

a1

a2

c(a3)

a1= a2

a = 4.51Å, c =7.35Å

γ =120°

Hexagonal Ice Structure (Ice Ih)

•Hexagonal ice plate formed from vapor deposition in air at 0 to -3 or -10 to -35 ºC. LT-SEM image with inset light microscope image.

•Classic snowflake formed from vapor-rich air between -10 to -22 ºC . LT-SEM image with inset light

© Eric Erbe / Beltsville Agricultural Research Center

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

Other isolated clusters of ice molecules trimer, tetramer,

pentamer, hexamer hexamer is the most

energetically likely

Isolated groups only somewhat useful in bulk study

Hydrogen bonding and the hexagonal structure of ice

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

Applications:

1. Drug design and structural biology

2. Bio-separation

3. Controlled drug delivery

Protein Crystallography

X-ray crystallography :

1. Protein structures at the atomic level

2. How proteins interact with other molecules

3. 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

After repeated seeding a nice crystal obtained

0.21X 0.12X 0.02 mm

Leinala et al.,2002: Grather,SP et al.,1999

Leinala et al.,2002

Crystals of recombinant Spruce budworm antifreeze proteins

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/

spring2003/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