The year 2014 has been declared by the
UNESCO -
the United Nations Educational, Scientific and Cultural
Organization the as the
International Year of
Crystallography (IYCr), starting January 2014
with an
Opening Ceremony at the UNESCO headquarters and world-wide
activities in science education. The IYCr therefore ranks
prominently in importance amongst other globally relevant themes of
UN
Observances such as Sustainable Energy, Water Conservation,
or Biodiversity. The question is, why should we care about a
field of science few of us may ever have heard about?
Let us preface the substantial reasons why in fact a celebration
of
crystallography is a worthy occasion with two quotes:
"Crystallography borders, naturally, on pure
physics, chemistry, biology,
mineralogy, technology and also on
mathematics,
but is distinguished by being concerned with the methods and
results of investigating the
arrangement of atoms in matter, particularly
when that arrangement has regular features." Paul
Ewald (1948) Acta Crystallogr. 1, 2
"Almost all aspects of life
are engineered at the molecular level, and without understanding
molecules we can only have a sketchy understanding of life
itself." Francis Crick, Nobel
Laureate and co-discoverer of the DNA structure,
(1988), What Mad Pursuit: A Personal View of Scientific
Discovery, p. 61
Molecular structure defines function
The molecular structure of matter
defines its properties and
function. This simple but far-reaching statement is true for all
matter. The properties of gasses, liquids, rocks, minerals,
semiconductors, or small organic molecules are defined
by their molecular structure, as are the functions of
proteins and their complex macromolecular assemblies,
the molecular machines of
life. The science that allows us to examine matter at the
most detailed, atomic or molecular level is crystallography. In
all techniques of crystallography the fact is used that atoms or even complex molecules,
once arranged in an ordered,
periodic pattern - also known as a crystal - diffract X-rays,
neutrons, or electrons, which allows to reconstruct the
molecular structure in atomic detail. A fundamental requirement
for
crystallography therefore is the presence of a natural or
laboratory-grown crystal of the matter of interest.
Although crystallography is in its
fundamental principle straightforward (Figure 1), it utilizes
some of the most sophisticated machinery at
synchrotron facilities, and requires an elaborate
reconstruction of the diffraction data into an atomic model of
the diffracting matter. It is not just a simple microscopic imaging or
viewing technique.
|
Figure 1: The principle of X-ray crystallography.
A crystal - here consisting of ordered protein molecules
- is mounted on a goniostat with at least one rotatable
axis. It is exposed to a finely collimated, intense X-ray
beam, and diffraction images are recorded on an area
detector and combined into a diffraction data set.
Diffraction data are transforms of the molecular shape
into reciprocal space, equivalent to being transformed
into “secret code.” This secret reciprocal space code
must be deciphered for each structure by the
crystallographer. The basic mathematical tool of
back-transformation from reciprocal diffraction space
into direct molecular space is the Fourier transform
(FT), which together with separately acquired phases for
each diffraction spot allows reconstructing the electron
density (blue grid) of the molecules self-assembled into
the diffracting crystal. An atomic model of the
structure, represented in the figure by a ribbon model,
is then built into the 3-dimensional electron density.
The absence of phases in the diffraction data is the
origin of the phase problem in crystallography and a
suitable phasing strategy needs to be developed for each
structure determination. |
The beginnings of X-ray crystallography
Analysis of the first X-ray diffraction patterns, obtained
in 1912 by Walther Friedrich and Paul Knipping
in Max von Laue’s laboratory (Sidebar 1) from crystals of simple
compounds consisting of only one or few different elements such
as diamond
(figures below), rock
salt, or
zinc sulfide, confirmed in a fundamental way the atomic
constitution of matter and the interactions and bonding of the
atoms. Given that the atom theory and particularly quantum
mechanics were then in their infancy, these early diffraction
experiments provided the much needed crucial evidence and
support for the development of the atomic theory of
matter (nobody had ever really 'seen' atoms until this
point). Interestingly, shortly after X-rays were discovered by
Wilhelm Conrad Röntgen in 1895 and even before the first
diffraction patterns of simple compounds were recorded, it was
already known that also proteins - very complex and large
molecules - could form crystals. It would take more than three
decades of technical developments until the first diffraction
patterns of protein crystals could be recorded and another two
decades until the successful determination of the first
macromolecular structure,
myoglobin, in 1957 (Sidebar 10-1).
Sidebar 1: Early history of
Crystallography and its first Nobel prizes. The
mathematical formulation of the reflection conditions in
a 3-dimensional crystal was formulated first by
Max von Laue, who received the
Nobel Prize in Physics in 1914 for the
discovery of diffraction of X-rays by crystals.
His theoretical derivations were tested in 1912 (when he
was Privatdozent in Munich) by Arnold Sommerfeld’s
assistants W. Friedrich and P. Knipping, who conducted
the first diffraction experiments with X-rays. These
experiments nearly did not happen, because Sommerfeld
was occupied at this time with the study of the
directional dependence of the Bremsstrahlung, and
thought little of testing von Laue’s
“Raumgitterhypothese.” While the experiments
unambiguously established both the
electromagnetic wave nature of X-rays and that
matter consists of discrete atoms, the
three separate diffraction conditions expressed as Laue
equations for each direction in the crystal lattice are
not overly convenient and not easy to visualize in
practical use. Laue’s diffraction pictures were actually
obtained using “white” (polychromatic) X-ray
radiation, and were finally interpreted by
Sir William Lawrence Bragg. Born in Australia, W.
Lawrence Bragg was exposed to X-rays at the early age of
5 years, when he crashed his tricycle and broke his arm.
His father
W. Henry had recently read about Röntgen’s first
X-ray imaging experiments and used the newly discovered
X-rays to examine his own son’s broken arm. The affinity
to X-rays appears to have stuck with W. Lawrence, and he
continued to work in Cambridge on X-ray diffraction
in collaboration with his father, who ran an X-ray
laboratory in Leeds. Sir W. Henry built the first “X-ray
spectrometer,” a prototype of the modern diffractometer
that used monochromatic X-rays, which greatly simplifies
the interpretation of the diffraction patterns. W.
Lawrence Bragg finally came up with the brilliant idea
to interpret X-ray diffraction as reflection on
discrete lattice planes (hkl), leading to the
famous and indispensable Bragg equation that relates
the diffraction angle to the lattice spacing dhkl:
When the Braggs received the Nobel Prize in
Physics jointly in 1915, W. Lawrence was the
youngest Nobel recipient ever, at an age of 25
years. An interesting reminiscence of his early work
with W. L. Bragg in Cambridge was compiled by
Austrian-born Nobel laureate
Max Perutz, who worked for over three
decades in England on the structure of
hemoglobin and received the 1962 Nobel Prize
in Chemistry together with John Kendrew for
their studies of the structures of globular proteins.
Click here for a full account of all
Nobel Prizes in or associated with
Crystallography. |
Crystals - from
minerals to therapeutic drugs

A beautiful specimen of a
Quartz Scepter Crystal - great beauty but no
magic. |
Already the
simple visual inspection of crystals leads one
to suspect that the regularity of faces and
dihedral angles between the crystal faces in
some form represents the internal order
of that crystal. Such ideas have been
developed very early on, and the fascinating
regularity of crystals strongly influenced the
concept of platonic bodies and atomicity during
the Greek antique (ca. 400 BC). Even today,
in rather enlightened times (at least in secular
aspects), the regularity and beauty of crystals
has in some circles given rise to the erroneous
superstition that crystals harbor special and
magic powers. Crystals are certainly
special in their properties, but they
do not possess any magic powers. |
Early attempts of a rational
explanation of crystal properties in the 17th century by
Huygens and other scientists followed, and a
well-developed descriptive crystallography based on
careful measurements of mineral crystals emerged. At the
end of the 19th century the idea that the macroscopic
appearance of crystals is a manifestation of their
microscopic regularity was well established, but the
final proof had to wait for the actual X-ray diffraction
experiments of
Max
von Laue and Coworkers and by
Sir William Henry and his son
Sir William Lawrence Bragg (Sidebar 1). From that
point on, the tremendous impact of
crystallography on the understanding of the physics and
chemistry of material properties has led to
a quantum leap in our capability to design and
engineer the advanced materials we now use on a daily
basis. Since the early 1950’s, when protein structure
determination became feasible, a similar
revolution in our understanding of biological structure
and function has taken place, and
crystallography plays an indispensable role in modern
structure guided drug discovery.
 |
While not all solid
matter forms beautiful and well-shaped crystals (some
growing to a size of 30 meters in length in
subterranean caves, left), much of
the solid world is microcrystalline, such as
various rocks, composed of
billions of tiny microscopic crystals. Some solid
materials such as glass are amorphous, that is, they
have no precisely ordered internal atomic arrangement.
|
Why is diamond so
hard?
One of the first
crystal structures determined by X-ray crystallography
was the structure of diamond, a hard crystal created
under high pressure and temperature from carbon. The
crystal structure immediately explained why diamond is so
hard, and why a different crystalline form of carbon,
graphite, is soft and can be used as the core of
pencils.

The diamond structure (bottom left side of Figure 3) shows
that each carbon atom is covalently bound to 4 other
atoms in a tetrahedral coordination, meaning that
very
strong atomic binding forces between the atoms extend in
4 directions across the entire crystal - which makes
diamond crystals very hard. Compare this to the crystal
structure of graphite (right side of Figure 3) - here
the carbon atoms are hexagonally arranged in stacked
layers. The covalent bonding between the atoms
within each layer is still very strong, while
the non-bonded interactions between the layers
are much weaker. The crystals therefore are
soft in one direction with little resistance to sheer -
that is why graphite is useful as a pencil core or
lubricant. X-ray
crystallography has also revealed that for example the
color of some gem stone quality diamonds (some are
bluish, pink or yellow) originates from substitution of
some carbon atoms with nitrogen atoms. Many refractory
(hard) materials used in machine cutting tools have also
been refined based on the knowledge of atomic
substitutions in their material structure.
 |
Carbon can also form
very complex structures such as
carbon nanotubes or
buckyballs. The structure of those exciting
multi-carbon atom nanomaterials useful in
applications ranging from electronics to material strengthening
and drug delivery was also determined from their
crystals by X-ray crystallography. Carbon
nanotubes are the strongest and stiffest
materials yet discovered in terms of
tensile strength and
elastic modulus. The
Nobel prizes in Chemistry 1996 and in
Physics 2010 were awarded for work on
complex carbon nanostructures. |
|
Crystals of the molecules of life
Even the huge
protein
molecules in the tissues of animals and plants, where
they perform a wide variety of functions, are able to
self-organize into ordered crystals. Their crystals are
at least as beautiful as those of minerals, but there is
a crucial difference: They grow only very small,
and they are very sensitive and fragile.
This can be immediately understood from their crystal
structures: there are only few nonbonded contacts
connecting huge molecules, with the remaining
intermolecular space - on average 50% - filled with the
solvent those crystals grew in. One of the biggest
surprises from the determination of the first protein
crystal structures was the total absence of any
symmetry in the protein molecules themselves
which made up the beautiful and symmetric protein
crystals. You can watch movies of protein
crystals growing
(courtesy George Sheldrick and students),
crystals absorbing a colored ligand,
and get some idea about the process of
structure guided drug discovery.
|
The
tetragonal crystals to the right are only 0.3 mm in size (which is
actually quite large for protein crystals) and they are viewed
through a microscope. They appear blue because they have
taken up a colored ligand through their intermolecular
solvent channels visible in the packing
diagram (far right). Soaking small pharmaceutical molecules
in to protein crystals is important for structure-guided
therapeutic drug development. |
  |
|
|
How do pharmaceutical drugs work?
X-ray crystal
structures can reveal
how a small molecule ligand binds to a protein target.
As an example, bacterial proteins necessary for the
pathogen's function, or protein receptors necessary for
the uncontrolled proliferation of a cancer cell can be
inhibited by a small molecule therapeutic drug. By
examining the binding patterns of the drug or its
precursor molecule, we are often able to design a
better
binding and more specific drug with
less side effects.
The active form of the antitubercular drug isoniazid
Isoniazid (isonicotinic
acid hydrazide) is converted by the mycobacterial
enzyme KatG into the active drug isonicotinic acyl-NADH,
shown on top as a stick model (yellow: carbon atoms;
blue: nitrogen; red: oxygen; purple: phosphorous;
hydrogen atoms are usually not seen in X-ray structures
and omitted) in its electron density (blue grid, which
is what the crystallographer actually sees and
interprets) and below the model of the molecule in the binding pocket of the target InhA, an
enoyl-acyl-carrier-protein reductase, essential for the
biosynthesis of mycolic fatty acids in the bacterium's
cell wall. The
clear electron density obtained in the
1.75 Å structure of its complex with InhA by Jim
Sacchettini confirmed
beyond doubt the chemical composition and the inhibiting
mode of the modified drug. PDB
entry 2nv6. |
Human cells do not
possess the same fatty-acid rich cell walls as the
tuberculosis causing mycobacteria, and therefore the
human body does not need an enzyme for the synthesis of
this special cell wall component. Humans can safely take
this inhibitor and are not affected, while the bacteria
die. Sometimes the bacteria can develop
resistance to a drug, and a new one must be
found, often by modifying the known drugs by analyzing
the structures in complex with their protein target.
|
Keeping your DNA neatly organized.
The human genome is encoded in molecular
material called DNA,
deoxyribonucleic acid. Four different nucleotides, are
connected into long,2-stranded helical DNA macromolecules, consisting in
total of approximately 3 billion nucleotide pairs organized into
23 chromosomes. Uncoiled and extended end to end, the DNA would
extend about 3 meters, which obviously needs
some clever packing to fit into the
nucleus of a human cell of about 6 micrometer
in diameter. In humans, the genetic material is thus neatly
organized in complexes of DNA with core protein histones
and other chromosomal proteins that together form nuclear
chromatin. The nucleosome core chromatin repeating unit includes
two copies each of four core histones H2A, H2B, H3 and H4
(collective molecular mass 206 kDa) wrapped by 146-147 residues
of contiguous DNA. The question was, how these nucleosome core
particles assemble and how exactly the DNA wraps around the core
histone proteins.
|
The crystal structure of the
nucleosome core particle was the culmination of
more than 15 years of work by Timothy Richmond
and coworkers involving laborious
protein preparation, persistent protein-DNA complex
crystallization and solid protein crystallography. The
four core histone proteins were individually expressed
in milligram quantities in E. coli bacteria,
purified under denaturing conditions, then refolded into
histone octamers and assembled into nucleosome core
particles using 147 base pair defined-sequence DNA fragment
derived from human -satellite
DNA. The final result was the depicted model
containing the entire DNA and histone octamer
The nucleosome core particle. The nucleosome
core particle consists of two copies each of the four core
histone proteins, H2A, H2B, H3 and H4, wrapped by 146
base pairs of DNA. The tails of the histone proteins,
some of which are seen protruding from between the base
pairs, form strong or weak nucleosomal interactions,
depending on their state of acetylation: When
hyperacetylated, nucleosomal interactions are weakened,
the DNA is not constrained on the surface of the
nucleosome and becomes accessible to
transcription
factors.
PDB entry 1aoi.
|
Crystallography
rocks!
The few selected examples should have demonstrated that
crystallography has contributed significantly to much of the
progress in all fields of science and engineering which concern
themselves with crystallizable matter. The materials with
properties understood, improved, and designed based on detailed
molecular structure revealed by crystallography range from
semiconductors in your cell phone, alloys and advanced materials
in aerospace, to the therapeutic drugs you take to maintain your
health or to fight disease. All brought to you by
crystallography.
|