Thursday, 19 November 2015

Bernal Lecture 2015: Terminating Protein Synthesis

Professor J.D. Bernal, known to his colleagues and contemporaries as ‘Sage’, spent much of his career as a professor of Physics at Birkbeck and became the first chair of the Department of Crystallography in 1963. When he retired in 1968 the college founded a series of lectures in his honour. The first of the Bernal Lectures, in 1969, was given by Dorothy Hodgkin, winner of the 1964 Nobel Prize for Chemistry for solving the structures of ‘important biological substances’, mainly penicillin and vitamin B12. In 2015 we were honoured to welcome another Chemistry Nobel Laureate to give this annual lecture. Professor Sir Venki Ramakrishnan of the MRC Laboratory of Molecular Biology in Cambridge was awarded the prize in 2009 with Thomas Steitz of Yale University, USA and Ada Yonath of the Weizmann Institute of Science, Israel, for studies of the structure and function of the ribosome: the ‘molecular machine’ that catalyses the synthesis of proteins from their messenger RNA (mRNA) templates.

The lecture, held on 19 October 2015, was introduced by David Latchman, Master of Birkbeck College and Professor of Genetics. He welcomed three generations of Bernal’s descendants to Birkbeck, highlighted the success of the lecture series in attracting some of the most distinguished researchers in structural biology and allied disciplines, and explained that the topic of the lecture overlapped with some of his own research interests in the regulation of gene expression.

Prof. Ramakrishnan began his lecture by explaining that protein synthesis was a complex process, involving many proteins as well as the ribosome itself, and that he would be talking about a particular point in this process: namely, how it ends (formally, the termination of protein translation). He showed an image of a ribosome in the process of protein synthesis that, he explained, represented the culmination of 40 years’ work on its structure, and explained how the linear mRNA molecule wound through a cleft between the two subunits of the ribosome. As the mRNA passes through the ribosome each of its three-base ‘codons’ comes into contact with three sub-parts of the ribosome’s active site – the A-site, P-site and E-site – in turn. When a codon enters the A-site it binds to the anti-codon of the transfer RNA (tRNA) carrying the next amino acid; the amino acid is bonded to the previous amino acid in the growing protein chain in the P-site, and the now empty tRNA released from the ribosome in the E-site. This continues until the new protein chain is complete. This is signalled by one of the so-called ‘stop codons’ UGA, UAG and UAA, which have no corresponding tRNAs, entering the ribosome’s A-site. The new protein is released from the ribosome to fold into its native structure, and the ribosome subunits dissociate.

Diagram of a ribosome showing the three tRNA binding sites during protein elongation
Taken from the PDB ‘Structural View of Biology: The Ribosome
© David Goodsell, 2010

Although the process of adding amino acids to a protein chain is extremely similar in all organisms, there are significant differences between bacteria (prokaryotes) and eukaryotes in the process of termination – as, indeed, there are in the initiation of protein synthesis. We are beginning to understand these mechanisms only now that we can obtain high resolution structures of ‘snapshots’ of the ribosome at different points during the protein synthesis cycle and follow the sequence of conformational changes that occur then.

All stop codons are recognised and decoded by proteins known as a release factors. Bacteria have two of these: RF1 recognises UAG, RF2 recognises UGA and they both recognise UAA. Eukaryotes have only one RF, which can recognise all these codons. These three proteins all have a common sequence motif, GGQ, which is known to be involved in the release of the protein from the ribosome. The structures of the eukaryotic and prokaryotic release factors are different, but all bind to the ribosome in such a way that the GGQ motif and the part of the structure that recognises the stop codon are exactly the same distance apart as the length of a tRNA molecule. These parts of the protein will therefore interact with the peptide and the stop codon at the same time.

Prof. Ramakrishnan and his group spent years trying to obtain near atomic resolution structures of functional ribosome-release factor complexes; this problem was solved initially for the smaller prokaryotic ribosomes but now for eukaryotic ones as well. In all cases, the release factors bind to the ribosome in a different way to the tRNA molecules, inducing a different conformational change in the complex. Using the bacterial structures, the group was able to understand why the factors RF1 and RF2 only recognise the codons that they do.

In the case of eukaryotes, not only were the structures harder to obtain, but the basic question to be asked was more complex: how can a single protein recognise the stop codons UGA, UAG and UAA, but not UGG (which codes for the amino acid tryptophan)? Ramakrishnan reasoned that mutating the GGQ motif in the release factor would make it inactive, and that binding this mutant protein to the ribosome with an ATPase might ‘trap’ the complex in the structure that it takes up before protein is released and allow the structure to be determined. Electron micrographs of these structures have shown that the three anti-codons and no others are recognised through a combination of base stacking and hydrogen bonding. Ramakrishnan ended his talk by comparing anti-codon binding to a NAND gate in electronics, with G representing ‘1’ and A ‘0’: any combination except GG (‘11’) in the second and third anti-codon positions leads to termination of translation and protein release.

This work was published in Nature in August 2015 and the (very large!) structures of the complexes – one snapshot with the release factor bound in each of the ribosome subsites – are available in the PDB as entries 3JAG,3JAH and 3JAI. These are some of the most recent of the 103 PDB structures on which Prof Ramakrishnan has so far been named as an author; you can view them all on a timeline on the PDB site.

Note: If you are reading this blog post as a current PPS student, don’t be surprised if you find it difficult to understand. We will cover the structure and mechanism of the ribosome later in the course (in Section 8: The Protein Lifecycle). If you bookmark this blog post and come back to it after you have studied that section you should find that you can make much more out of it.

Tuesday, 29 September 2015

Welcome to PPS students 2015-16!

This post is extremely like those I have written at this time of year for the past few years. This is because what I have to say now is very, very similar...

I would like to offer a warm welcome to the Principles of Protein Structure blog to all students who have just started studying Birkbeck's Principles of Protein Structure (PPS) course, and a welcome back to any who have taken a break in studies and intend to complete the course this year.

I run this blog to link the material that you will be studying in the course to new research developments in the areas of protein structure and function and related aspects of biotechnology and medicine. I might, example, report on talks given in the ISMB seminar series run jointly by the Department of Biological Sciences at Birkbeck and research departments in neighbouring University College London. The programme for Autumn 2015 focuses on transcription, which is the process through which DNA is copied into RNA; this will be covered in some detail in one of the later sections of the course, the Protein Lifecycle. Other posts may be reports from conferences or summaries of recently published papers in protein structure, protein bioinformatics and allied areas. Look out for an account of a lecture to be given at Birkbeck in October by Venki Ramakrishnan, who was awarded a share of the Nobel Prize for Chemistry in 2009 for structural studies of ribosomes and will shortly take over as President of the Royal Society.

Some posts on this blog are written by "guest blogger" Jill Faircloth, who took the MSc in Structural Molecular Biology a few years ago and is now working as a freelance science communicator. She introduces herself in this post written in March 2012, in which she also describes how she found the later part of the PPS course and her thoughts on the two choices available for the second year of the MSc.

Do, if you get a chance, look through some blog posts from earlier years to see the kind of topics that we will be discussing. However, don't be discouraged if at this stage of the course you find the science presented there difficult to understand. I can assure you that it will get easier!

I particularly recommend that you look at a couple of posts from December 2013 and July 2014 about the history of structural science, particularly X-ray crystallography. Crystallography was the first method to be developed for solving the structure of biological macromolecules, and it is still the most important. The year 2014 was designated by the United Nations as the International Year of Crystallography, marking the year between the centenaries of the publication of the first papers on X-ray diffraction and the award of the 1915 Nobel Prize for Physics to the father-and-son team of William and Lawrence Bragg who made the principal discoveries.

So - the best of luck for the 2015-16 PPS course and for your studies at Birkbeck! We hope that many of you will go on to complete our MSc in Structural Molecular Biology.

Best wishes,

Dr Clare Sansom Senior Associate Lecturer, Biological Sciences, Birkbeck and Tutor, Principles of Protein Structure

Wednesday, 8 July 2015

Microtubules and Microscopes: Exploring the Cytoskeleton

Electron microscopist Carolyn Moores, the most recently appointed professor in the Department of Biological Sciences at Birkbeck, gave her inaugural lecture at the college on June 1.

Moores arrived at Birkbeck in 2004 to start her research group and has risen rapidly and steadily up the academic ladder ever since. Introducing the lecture, the Master of Birkbeck, David Latchman, explained that Moores’ CV stood out in every way; she was clearly as gifted a teacher and administrator as she was a researcher. Furthermore, as she has won several awards for science communication, he predicted that the audience would be in for a treat. We were not disappointed.

Moores began her lecture by saying that she would talk about three different things: her own career development; her group’s research into the structure and function of microtubules; and the advancement of women in science, a cause that is close to her heart.

She remembered that she had wanted to work as a scientist as soon as she knew what a laboratory was, and she started young, as an intern in a research lab at Middlesex Hospital while still in the sixth form. School was followed by a BSc in Biochemistry at Oxford and a PhD in John Kendrick-Jones’ lab at the world-famous Laboratory for Molecular Biology (LMB) in Cambridge. She then moved to work as a post-doc with Ron Milligan at the Scripps Research Institute in La Jolla, California, USA, and it was there that she began her studies on microtubules.

The award of a David Phillips research fellowship in 2004 gave her the opportunity to return to the UK as an independent researcher. She explained that there were three reasons – or more accurately three people – that led her to choose to come to Birkbeck. Working in electron microscopy, she was inspired by the work of Helen Saibil, one of the UK’s principal exponents of that technique; she had known Nicholas Keep, then a lecturer in Biological Sciences, as a friend since her time at the LMB; and she knew that she would value the interdisciplinary working environment of the Institute for Structural Molecular Biology under the ‘inspired’ leadership of Gabriel Waksman.

Moores then moved on to discuss the main topic of her group’s research: the three-dimensional structure, function and role in disease of tiny cylindrical structures known as microtubules. These are one of the building blocks of the cytoskeleton, which forms a framework for our cells in the same way that our skeletons form a framework for our bodies. They are about 25nm in diameter, which puts them firmly into the ‘nano-scale’ of biology that is easily studied using electron microscopy.

There is a cytoskeleton in every living cell, and it, and the microtubules that form it, are involved in many important cellular processes including shape definition, movement and cell division. Diseases as diverse as cancer, epilepsy, neurodegeneration and kidney disease have been linked to microtubule defects. Understanding their fundamental structure and function, as Moores’ group aims to, should help in understanding these disease processes and perhaps also in developing effective treatments.

Microtubules are built up from many copies of a small protein called tubulin, which, in turn, is a dimer of two similar proteins called alpha and beta tubulin. These tubulin dimers make contacts with each other both head-to-tail and side-to-side to create the cylindrical microtubule wall, fuelled by energy derived from the molecule GTP. Each tubulin unit has a definite “top” and a “bottom” and, as the units are oriented in parallel, so has the complete microtubule.

Microtubules are dynamic structures; they continue to grow by the addition of tubulin units to one end as long as GTP is available, and then begin to unravel and shrink. This dynamism, which allows them to respond to the changing needs of the cell, is essential for their function in healthy cells. In particular, microtubules organise chromosome structures during cell division and are therefore necessary for cell proliferation. As cancer is a disease of uncontrolled cell proliferation, it is possible to imagine that a molecule that could specifically block microtubule growth and assembly in the nucleus might be useful as an anti-cancer drug.

Moores and her group are aiming to understand the process of microtubule growth at as high resolution as possible, using electron microscopy. Unfortunately, however, the most detailed images can only be obtained if the specimen is at very low temperatures (in so-called cryo-elecron microscopy) and using this means that the dynamics of the specimens must be “frozen” into a still image. While it is now possible to see the individual tubulin subunits in the static microtubule images, many details of their structure can only be inferred from computational analysis.

Moores went on to describe one project in her lab in a little more detail. This was an investigation of the structure and role of proteins that bind only to growing microtubule ends, falling off when the growth stops. It is possible to obtain low-resolution images of microtubules in which these molecules have been made to fluoresce, so only growing microtubules are tracked.

In order to understand the growth process in detail, the group developed an analogue of the GTP “fuel” molecule which can bind to the tip of a microtubule that is extending but not break down to release its energy, so the microtubule does not in fact grow. This forms a static analogue of a growing microtubule that retains all the characteristics of the dynamic structure but that can be studied at low temperatures.

The binding site for End Binding protein 1 (highlighted in green) on the microtubule lattice at the corner of four tubulin dimers, visualised using cryo-electron microscopy
Image from Maurer et al. 2012, Cell 149(2):371-82. Full text here.

Images of this structure have shown that the end binding proteins bind at the corner of four of the tubulin units. They have explained a lot of the properties of growing microtubules, but there is still more to learn. A full understanding will need structures that are at even higher resolution, where the positions of individual atoms can be made out. Following many years of technical development, today’s most powerful electron microscopes are now making this possible.

In the last section of the lecture, Moores left the topic of research to talk briefly about another of her passions: the promotion of women in science. She explained that although 65% of under-graduates in the biological sciences are now women, the proportion of women drops to 40% at any academic grade and 25% for full professors.

A study cited by the European Molecular Biology Organisation has suggested that the barriers for women scientists to progress are set so high that at the current rate of progress full equality would never be achieved. Birkbeck has signed up to the Athena SWAN Charter, set up to encourage higher education institutions to transform their culture and promote gender equality. She described her work with the Athena SWAN team that has so far resulted in the college gaining a bronze award as being as exciting as, but also as challenging as, her studies of microtubules.

There is more information about the structure and function of microtubules on this page in section 7 of the PPS course. The technique of cryo-electron microscopy is covered in some detail in the second-year MSc module Techniques in Structural Molecular Biology.

Tuesday, 28 April 2015

Protein Machines in the Molecular Arms Race

Birkbeck’s Science Week 2015 was held from Monday 23 to Thursday 26 March and included three evenings of public talks by senior researchers. The first two lectures, on the Tuesday, were given by two of the college’s most distinguished women scientists: Helen Saibil from the Department of Biological Sciences and Karen Hudson-Edwards from Earth and Planetary Sciences; they were billed together as a ‘Women in Science Evening’.

The lectures were all introduced by the Dean of the Faculty of Science, Nicholas Keep who described Saibil, a close colleague, as “our most eminent female scientist”. She came to Birkbeck from Canada via a PhD at King’s College London under the supervision of Nobel laureate Maurice Wilkins and post-doctoral work at Oxford.

Since arriving here in the 1980s she has built up an internationally renowned structural biology lab, focusing in particular on the technique of electron microscopy. She has been a Fellow of the Royal Society since 2006 and of the Academy of Medical Sciences since 2009.

Saibil began her lecture by explaining that proteins can act as little machines, performing mechanical tasks that are essential for the maintenance of life. Her group has been interested for some time in proteins that can punch holes in the walls of cells. This allows the cell contents to leak out in a damaging process known as lysis, and it also allows toxins to enter the cells. These proteins can therefore be thought of as powerful weapons, and they are deployed on both sides of a ‘molecular arms race’: by pathogens and by the immune systems of humans and other animals.

Most soluble proteins fold into a single stable structure that tries, as far as possible, to keep their hydrophobic (“water-hating”) parts – the side chains of certain amino acids – in the interior of the protein, with the hydrophilic (“water-loving”) side chains on the outside, in contact with the watery environment inside or outside cells.

Pore-forming proteins, however, have a ‘Jekyll and Hyde’ like identity: they can form two distinctly different shapes, one as individual, soluble molecules and the other when they associate with each other into membrane-bound rings to form cylindrical pores. These structures, and the conformational change between them, are remarkably similar in proteins from bacteria and from the immune system.

Pore-forming toxins have been found in types of bacteria that are responsible for some deadly human diseases, including meningitis and pneumonia. The structure of a monomeric form of one of these proteins in solution was first solved in 1998, using X-ray crystallography. However, large complexes of many protein molecules are more readily solved by electron microscopy, particularly when those complexes are embedded in membranes.

In 2005 Saibil and her group described structures of the pore-forming toxin pneumolysin from Streptococcus pneumoniae, in complex with a model cell membrane. They found that the proteins formed two distinctly different ring-shaped structures. Initially, they formed into a ring sitting on top of the membrane, which was termed the pre-pore; then they changed shape to burrow part of each protein deep into the membrane and form the pore itself. Each monomer in the pre-pore had a structure that was similar to that of the molecule in solution, but they underwent large structural changes to form the pore.

Schematic illustration of how suilysin, a bacterial cholesterol-dependent cytolysin, drills holes in cell membranes. Image © Adrian Hodel, London Centre for Nanotechnology

Most structures solved by electron microscopy are at lower resolution than those solved by X-ray crystallography, and it is not possible to trace the positions of individual atoms at lower resolutions (e.g. worse than 3 A). Saibil and her colleagues were able to interpret the structure of the proteins making up the pore by fitting pieces of the X-ray structure of the isolated molecule into their electron density.

They found a dramatic change in structure, with the tall, thin protein structure collapsing into an arch and a helical region stretching out to form a long, extended beta hairpin. It is these hairpins that join together to form the walls of the pore. The process of pore forming therefore has three stages: firstly the toxin molecules bind to the surface of their target cells, then they associate into the circular pre-pores and finally they change shape in a concerted manner, punching holes in the cell membranes by ejecting a disc of membrane, letting other toxins in and cell contents out.

Saibil then turned the focus of her talk from attack by bacteria to the human immune system’s defence. Natural killer (NK) cells are specialised lymphocytes (white blood cells) that kill virally-infected and cancerous cells in the bloodstream. They kill on contact with their target cells by releasing a toxic protein into those cells that stimulates those target cells to commit suicide in a process known as programmed cell death or apoptosis. We have only recently learned that the mechanism through which the NK cells work is very similar to the mechanism of the bacterial pore-forming toxins.

Natural killer cells express a protein called perforin that has a similar structure in solution to the bacterial pneumolysin. Although there is very little sequence similarity between these proteins – there is only one amino acid conserved throughout all the known bacterial and vertebrate proteins of this family, a glycine at a critical position for the conformational change – the structures are similar enough to suggest that the proteins all once had a common ancestor.

Saibil and her colleagues used electron microscopy to discover that this protein forms a pore through a similar mechanism to pneumolysin: the helical region that unfolds into the beta hairpin to form the pore forms the core of the molecular machine and is largely unchanged between the structures. There are some differences between the structures, however; in particular, there is no need for the perforin structure to ‘collapse’ as the molecule has ‘arms’ that are long enough to form the hairpin and punch the hole without bending into an arch.

The mechanism through which the NK cells kill their target cells is now quite well understood. When the two cells come into contact they form a temporary structure called an immune synapse that allows the pore to form and proteases called granzymes, which induce apoptosis, to enter the target cells. This YouTube video illustrates the natural killer cells’ mechanism of action, and this one shows a detailed view of the immune synapse. Other, similar proteins have been identified in oyster mushrooms; these form more rigid structures that are easier to work with. Saibil’s group and their collaborators have been able to solve the structure of this protein in intermediate stages of pore formation and are beginning to gain an understanding of exactly how it unfolds.

The pore of the oyster mushroom protein pleurotolysin, a member of the pneumolysin family. Image © Natalya Lukoyanova and Helen Saibil, from Lukoyanova et al., PLoS Biology 13:e1002049

Mutations in perforin that prevent it from functioning cause a rare disease called haemophagocytic lymphohistiocytosis, which is almost invariably fatal in childhood. Understanding the mechanism of action of this important family of protein ‘weapons’ in both attack and defence may help find a cure for this devastating condition, as well as for some commoner disorders of the immune system and important infectious diseases.

This post is cross-posted from the Birkbeck Events blog.

PPS students can learn much more about electron microscopy by taking the second-year module Techniques in Structural Molecular Biology to complete the MSc.

Wednesday, 25 March 2015

Claudins, allowing flow in a tight situation

Suzuki, H., Tani, K., Tamura, A., Tsukita, S. (2015) Model for the Architecture of Claudin-Based Paracellular Ion Channels through Tight Junctions. J Mol Biol. 2015 Jan 30; 427(2):291-297

Epithelial cells form a border between the inside and outside of the body.  They cover both the external surface of the body (skin) and the lining of internal cavities such as the lungs or the gastrointestinal tract.  These cells are sealed together by tight junctions, which are just beneath the external surface.

The tight junctions form a cell to cell adhesion network that simultaneously blocks the passage of some substances across the epithelia and allows the highly regulated movement of specific ions and solutes across the barrier and between cells.

The primary components of tight junctions are claudins and recently there have been great advances in explaining their structure and function. 

The first crystal structure of a single claudin monomer, solved in 2014, is shown below. 

Image adapted from (Suzuki, H. et al., (2014)).  Crystal structure of mouse claudin-15  (PDB 4P79)

The claudin protomer (monomer) has two distinct sections:  a tight bundle of four α helices, which are embedded in the membrane of an epithelial cell, and five β strands, which form a curved sheet on the extracellular side.  These extracellular β sheets contain several negatively charged residues which have previously been shown to be necessary for both the formation of a tight barrier between cells and its selectivity for positive ions (cations).  They are also thought to form the paracellular channels that traverse the epithelium. 

Two of these functions have been demonstrated by elegant experiments that substituted the acidic residues on the β sheet with positively charged ones, resulting in paracellular channels that were selective for anions.

The monomer structure alone, however, could not provide explanations for either the structure of tight junction strands, which form the mesh that creates cell adhesion, or the transcellular channels that allow interaction between cells.

A recent study by the same team that solved the first claudin structure, (Suzuki, H. et al., (2015)), uses cysteine crosslinking experiments to suggest an arrangement of the claudin monomers which would produce paracellular channels which run across the epithelium, transcellular channels which are perpendicular to the paracellular channels, and linear tight junction strands.

The proposed model uses a basic building block of two claudin monomers lying alongside each other but antiparallel so that the outer edges of the β sheets connect via hydrogen bonds to form half of a β barrel structure.  These dimers then associate to form long polymers of the double row of claudins (see figure).

Image adapted from (Suzuki, H. et al., (2015)).  The first image shows the association of claudin monomers and their polymerization.  The second image shows the same structure rotated through 90˚ so that we are looking down the half β barrel .

This model was tested by substituting Cys residues for key Asn positions at the proposed interface between the outer β strands.  The mutant claudins were found to form dimers that reverted to ther usual monomeric structure in reducing conditions.  This illustrates that the molecules normally associate face to face, along the proposed  β strands, so that once the substitutions were made disulphide bridges could be formed.

More corroboration was obtained using electron microscopy (EM), which is studied in the second-year TSMB course.  A form of EM known as  freeze fracture electron microscopy, which is often used to examine proteins embedded in lipid membranes, was used to provide images of tight junction strands, which appear as a network of linear strands whose width is consistent with the model.

In the epithelial sheet, a claudin double row would be anchored in the cell membrane with its half β barrel projecting out.  By lining itself up against a similarly projecting double row in the adjacent cell we can see how tight junction strands with paracellular channels could be formed.  The diameter of this channel would be less than 10 Å, enough to allow the passage of hydrated ions but to restrict their flow.

Image adapted from (Suzuki, H. et al., (2015)).  The image shows the joining of a row of half β barrels from adjacent cells, forming a row of paracellular channels.

Epithelial cells maintain the separation of several internal spaces within the body and each of the interfaces has its own requirements for substances that are allowed to cross the border.  This means that the paracellular channels need different ion specificity depending on which boundary they maintain.  This could be provided by the charges and orientation of the residues in the channel lining and may also be influenced by flexible loops that link the β strands.  It is also possible that these loops, which are not well conserved among the 27 members of the claudin family in the mouse (or human) proteome, could function as recognition regions so that only claudins of the same type can associate.

Possibly the most remarkable aspect of this model, however, can be seen by rotating it through 90˚.

Image adapted from (Suzuki, H. et al., (2015)).  In this image the paracellular channels are seen in magenta whilst the α helices are aligned perpendicular to the page. 

Further gaps can now be seen; these could provide transcellular channels allowing the flow of ions and solutes between epithelial cells.

In short this model appears to provide solutions to all of the functions required by claudins in tight junctions between epithelial cells and it will be very interesting to see if it proves to be correct as further crystal  structures are solved.

Do look at the original paper if you have the chance as it includes an excellent short animation that shows the association of single claudin monomers into tight junction strands and then rotates the structure to show the different channels. (Follow the web link to the Supplementary Data.) 

Wednesday, 7 January 2015

From Crystallography to Light (according to the United Nations)

Those of you who started the PPS course in 2014 may not have realised that they began their studies of structural biology at an auspicious time for this subject. Last year was designated the International Year of Crystallography to mark the centenaries of both the discovery of X-ray diffraction by crystals (first published in 2013) and the award, in 2015, of the Nobel Prize to the father-and-son team of William and Lawrence Bragg who made the discovery. I have blogged about this in much more detail over the previous year, with a post in December 2013 on "a very short history of crystallography" and one in July reporting on lectures by two of our distinguished emeritus professors, Paul Barnes and David Moss. Professor Moss took the subject up to date with a race through the history of structural biology, from the publication of the first protein structures - myoglobin and haemoglobin - in 1958 to the 100,000th structure that entered the Protein Data Bank in 2014. If you want to read more about the numerous events and publications around the world that honoured and publicised crystallographers during 2014, the best place to start is probably the official website of IYCr2014. And if you have access to Chemistry World, the membership magazine of the Royal Society of Chemistry, you can read two more pieces by me: "Crystal Clear" in the January 2014 issue and "Life in the Freeze Frame", featuring structural biology, in September. (Unfortunately, it is not available in the Birkbeck e-library.)

2014 was designated as the International Year of Crystallography by the United Nations, as part of its programme of using anniversaries to highlight topics and issues that it sees as important. There have been many international years on science-based topics, some broader than others: 2005, for example, was the International Year of Physics. And in this new year the focus moves on to another physical science topic. 2015 is the International Year of Light: or more precisely that "... of Light and Light-based Technologies".

And optics, the science of light, is very closely related to crystallography. Both light and X-rays are parts of the electro-magnetic spectrum and as such are both particles and waves; the differences in their frequencies and wavelengths lead to their very different properties. The first X-ray diffraction experiments were conducted mainly to find out whether the hypothesis that X-rays were electromagnetic waves with a wavelength of about 1 Angstrom was correct. The utility of this technique as a probe for molecular structure was initially a side effect of the similarity between this wavelength and the length of a covalent bond. (So-called "copper K-alpha" radiation, which is often used in crystallography, has a wavelength of 1.54Å, which is exactly equivalent to the length of a single C-C bond.) And the basic equation that defines X-ray diffraction - Bragg's Law, or nλ = 2d sin θ - applies to all electromagnetic radiation, not just to X-rays.

Advances in optical technology have been responsible for some important advances in crystallography. The discovery, in the mid- twentieth century, that charged particles emit electromagnetic radiation in the form of X-rays when accelerated radially was initially viewed as a problem of energy loss. This "lost" radiation, which is orders of magnitude more intense than the X-rays used in the first diffractometers, was soon exploited in synchrotron radiation sources and most non-routine protein structures are now solved using synchrotron radiation. The UK's synchrotron source, a doughnut-shaped structure half a kilometre across located at Harwell in Oxfordshire, is even known officially as "Diamond Light Source". And recent advances in optics are gradually reducing the size of intense X-ray sources so that it will become possible to do complex structural biology that now needs a synchrotron using a lab-based machine.

The next big technical advance to influence X-ray crystallography is the free electron laser, which can generate pulses of X-rays that are much more intense than those produced by even the largest synchrotrons. This is a beam of electrons that is accelerated to almost the speed of light through a side-to-side magnetic field to produce pulses of extremely intense electromagnetic radiation. These pulses are exceptionally short, each lasting only a few femtoseconds (1 fs = 10-15s). This is a feature of the technology that leads to two advantages: the crystals remain intact, even though they are exposed to extremely intense radiation, and it becomes possible to take "snapshot" structures very close together in time study the dynamic behaviour of molecules. Free electron laser radiation also enables precise structures to be obtained from much smaller crystals, which makes large complexes and membrane-bound proteins more tractable to crystallography. And it may one day be possible, using this technique, to determine a structure from the smallest "crystal" of all - a single molecule - and thus liberate protein crystallography from one of its most important bottlenecks: the need to grow protein crystals.

Acknowledgement:This post owes much to this one on the "Crystallography 365" blog (author unknown)