Category Archives: Biochemistry

Using Fluorescence Microscopy to Study Proteins

The approach of fluorescence microscopy has made it feasible to visualize proteins inside live cells. This is especially useful when studying the location of signaling pathways and binding partners.

Studying protein localization

The function of a protein can be assumed by its localization, particularly when a signaling pathway is known. The location of the protein is determined through the use of recombinant proteins fused with a reporter molecule, fluorescent dyes, or protein-specific fluorescent antibodies.

Fluorescent proteins recombined with either target protein or regulatory regions can be overexpressed inside cells to know fundamental cellular processes. An advantage of using genetic systems to express proteins is that the fluorescent proteins can be selectively activated in specific regions of tissues or cells. This makes the process of visualizing proteins easy.

Studying protein structure

The techniques earlier applied to analyze protein structure include cryo-electron microscopy, protein NMR, and X-ray crystallography. In cryo-electron microscopy, high energy electrons are focused at the sample to form a 2D projection. After capturing the 2D orientation of molecules from all angles, a 3D image is developed. However, this process cannot be performed in live samples and it requires large sample preparation.

Alternatively, nuclear magnetic resonance (NMR) captures the magnetic and chemical properties of the atoms but requires a pure solution of the sample which is again not optimal for studying cells. X-ray crystallography needs the sample to be crystallized before it can be imaged. In this case, the process of crystallization can modify the native conformation of proteins.

Contradictory, super-resolution methods, such as photoactivated localization microscopy (PALM) or stimulated emission depletion microscopy (STED) have a high resolution of 20-30 nanometers. This is below the diffraction limit of conventional microscopes which is 250 nanometers. Using these techniques, protein and membrane structure can be visualized to a great detail in their in vivo surroundings.

Studying protein dynamics

Using fluorescent recovery after photobleaching or FRAP, it can be measured how a protein moves or diffuses inside a cell. The diffusion of a protein is associated with its folded or misfolded status, its stability, and binding to other molecules. Thus, understanding its movement or diffusion can tell us its structure and function inside cells.

In this process, the fluorescent molecules in a specific region of a cell are completely bleached by shining an intense and constant beam of light. It results in the recovery of the fluorescence in the bleached region is measured as a function of time to map its diffusion parameters.

Studying protein signaling and interaction

This is defined using a fluorescence method called Forster resonance energy transfer or FRET. This technique is based on the transfer of energy between two closely placed molecules conveniently called donor and acceptor molecules.

The donor chromophore is originally in an excited state and as it is close in proximity to another molecule, it transfers its energy to a donor chromophore. This transfer is proportional to the sixth power of the distance between donor and acceptor.

Hence, based on the efficiency of the transfer of energy, the distance between two molecules or protein domains can be concluded. Thus, allowing scientists to determine which protein domains are interacting during a signaling event.

Studying protein levels

Apart from signaling, structure, and function, the fluorescence of a protein can also be utilized to determine the levels of a protein expressed inside a cell or a tissue. It is mostly used in cases where the fluorescent probe is recombined with the gene or reporter of a gene. The expression of the reporter reflects the levels of protein it is recombined with.

Tracking Pesticides Through An Insect’s Body

download (14)By combining laser-scanning with mass spectroscopy, researchers have managed to track the distribution of pesticides in the bodies of fruit flies.

A method has been developed to visualize how pesticides are distributed inside the bodies of insects.

Pesticides have been linked with declining honey bee numbers, raising questions about the use of these chemicals in agriculture. By gaining a better understanding of the interactions between pesticides and insects, researchers could help develop new and safer pesticides, as well as offer better guidance on the way pesticides are used.

A team of scientists developed a method that allows researchers to identify where pesticides accumulate in insects’ bodies. They examined a type of fruit fly belonging to the Drosophila family by scanning a laser across thin sections of the insect’s

When the laser hits the tissue section, it ejects material from the surface of the tissue, which can then be analysed using a mass spectrometer. By looking out for the chemical signature of the pesticide and its breakdown products, the researchers could trace the distribution and metabolism of the pesticide in different parts of the insect body.

This is a timely contribution, given the mounting evidence of negative effects of certain pesticides on ecosystems. The technique will help to gain new insights into pesticide metabolism that might help limit the effects of pesticides to their targets, without harming beneficial pollinating insects.

Optimizing Factors to Reduce Quantitative Evaluation Errors in NMR

1bThe integration of NMR spectra is capable of being carried out with high accuracy, but this is only feasible if several error sources are appropriately handled. Accuracy of ±5% can be achieved easily on a modern spectrometer, given that relaxation issues are adequately handled. Several factors need to be kept in mind and optimized to achieve errors of less than 1%.

Signal to Noise

The spectrum needs to have sufficient signal to noise ratio to support the degree of accuracy required for the experiment. This means using more scans, if required.

Saturation Effects

NMR spectroscopy is thought of as unique among spectroscopic methods because the relaxation processes are relatively slow (on the order of seconds or tenths of seconds), in comparison to mass spectroscopy. In other words, as soon as the spectrometer has disturbed the equilibrium population of nuclei via pulsing at the resonance frequency, they come back to their original populations in 0.1 to 10s of seconds.

Typically, the T1 (spin-lattice relaxation time1) is measured to calculate a suitable relaxation delay. The spectra can become saturated if the pulse angle and repetition rates are very high. Integrations become less accurate because the relaxation rates of different protons in the sample are not the same. The effects of saturation are primarily severe for small molecules in mobile solvents because these typically have the longest T1 relaxation times.

To attain trustworthy integrations, the NMR spectrum has to be achieved in a way that avoids saturation. It is impossible to decide if a spectrum was operated correctly just by inspection, as it relies on the operator to take suitable precautions, such as putting in a 5-10 second relaxation delay between scans, if optimal integrations are required.

It is vital to recognize that integration errors as a result of saturation effects will depend on the relative relaxation rates of several protons in a molecule. Errors will be bigger when distinct kinds of protons are being evaluated, for instance aromatic CH to a methyl group, than when the protons are the same or similar (such as two methyl groups).1A

Line Shape Considerations

NMR signals in a perfectly tuned instrument are Lorenzian in shape, so the concentration covers some distance on both sides of the center of the peak. Integrations have to be carried out over an appropriately broad frequency range to catch enough of the peak for the favored level of accuracy.

Therefore, if the width of the peak at half height is 1 Hz, then an integration of ±2.3 Hz from the center of the peak is required to catch 90% of the area, ±5 Hz for 95%, ±11 Hz for 98%, and ±18 Hz for more than 99% of the area.

This means that carefully spaced peaks cannot be accurately combined via the standard method, but might need line-shape stimulations with a program like NUTS in order to measure relative peak areas accurately.

Digital Resolution

A peak has to be decided by an adequate number of points to attain an accurate integration. The errors produced are very small and can achieve 1% if a resonance with a width at half height of 0.5 Hz is sampled every 0.25 Hz.

Isotopic Satellites

All C-H signals have 13C satellites2 situated ±JC-H/2(usually 115-135 Hz, however, numbers above 250 Hz are known) from the center of the peak. Combined, these satellites constitute 1.1% of the area of the central peak (0.55% each). They need to be kept in mind if integration at the >99% level of accuracy is desired.

Bigger errors are presented if the satellites from an adjacent very strong peak fall under the signal being incorporated. The easiest technique to right this problem is by decoupling of 13C, which condenses the satellites into the central peak. A number of other elements have critical fractions of spin ½ nuclei at natural abundance, and these will also create satellites big enough to impede integrations. Most noteworthy are 117/119Sn, 29Si, and 77Se.

13C satellites have a positive side: they can be employed as internal standards to quantify small amounts of contaminants or isomers, because their size relative to the central peak is accurately identified.

Spinning Sidebands

Spinning sidebands can be seen at ± the spinning speed in Hz in spectra conducted on weakly tuned spectrometers and/or with samples in low-quality tubes. They absorb intensity coming from the central peak. SSBs are not often significant on modern spectrometers.

Baseline Slant and Curvature

Under particular circumstances, spectra can show substantial distortions of the baseline, which can obstruct the procurement of high-quality integrations. Conventional NMR work-up programs, like NUTS, have procedures for baseline adjustments.

Scientists Reveal Structure of Amino Acid Transporter Involved in Cancer

A team of scientists have used cryo-electron microscopy to elucidate the structure of the protein, which may generate leads for drug (12)

The human glutamine transporter ASCT2 is increased in several forms of cancer. It is the docking platform for a wide range of pathogenic retroviruses. The ASCT2 protein imports the amino acid glutamine in the human cells and maintains the amino acid balance in many tissues. The amount of ASCT2 is increased in several types of cancer usually because of an increased demand for glutamine. Moreover, several types of retrovirus infect human cells by first docking on this protein.


ASCT2 belongs to a larger family of similar transporters. To understand the working of this family of amino acid transporters and to help in designing the drugs that block glutamine transport by ASCT2 or its role as a viral docking station the scientists have resolved the 3D structure of the protein. They resorted to the technique of single particle cryo-electron microscopy, as they did not succeed in growing crystals from the protein, which are required for X-ray diffraction studies. The human gene for ASCT2 was expressed in yeast cells and the human protein was purified for (11)

The structure was determined at a resolution of 3.85 Å revealing the striking new insights. It was a challenging target for scientist as it is rather small for cryo-EM. But it also has a good symmetric trimeric structure, which helps.


The cryo-EM images reveal a familiar type of ‘lift-structure’, where a part of the protein travels up and down through the cell membrane. The substrate enters the lift in the upper position and then moves down to release the substrate inside the cell. The structure of ASCT2 depicts the lift in the lower position. It had been thought that the substrate enters and leaves the lift through different openings, but the results suggest it might well use the same opening.

This information could help design molecules that stop glutamine transport by ASCT2. Some tests in mice with small molecules that block transport have been published. Blocking glutamine transport would be a way to kill cancer cells. This new structure allows for a more rational design of transport inhibitors.


Another observation was the surprise for the scientists as they observed the spikes that protrude on the outside of each of the three monomers. These are the places where retroviruses dock. This proved to be consistent with mutagenic studies performed by others. By knowing the shape of the spikes could help design molecules which block the viruses from docking. The protein structure was resolved in some time duration, which is remarkably fast for cryo-EM.

Future studies will be done to capture ASCT2 in different configurations, like inside a lipid bilayer rather than the detergent micelles used in the present study and with the lift in different positions. Thus, it was concluded that studying different states will help them understand how this protein functions.

Human skin hindrance structure and capacity examined by cryo-EM and sub-atomic progression re-enactment

In vitro experimentation on biomolecular buildings has today achieved an abnormal state of complexity, exemplified by ongoing advancement in cryo-electron microscopy (cryo-EM) single molecule examination. Be that as it may, a more entire comprehension of biomolecular capacity may just be accomplished by additionally considering biomolecular edifices straightforwardly in their regular habitat inside the living cell or tissue. Natural cells, or tissues, are commonly swarmed multicomponent conditions lacking long-run arrange. This makes it hard to acquire unmistakable diffraction designs from inside cells. By and by, access to cell close local high-goals information is today conceivable through the cryo-EM of vitreous segments innovation.Microsoft Word - Graphical Abstract

Molecular structure and function of the skin’s permeability barrier

In the present examination the atomic structure and capacity of the human skin’s boundary structure were dissected. The skin was produced 360 million years back to enable the primary vertebrates to leave the seas and adjust to an existence ashore, by filling in as a hindrance shielding from lack of hydration.

The skin’s boundary limit is situated to an intercellular lipid structure implanting the cells of the shallow most layer of skin—the stratum corneum. The lipid structure comprises of stacked lipid layers made from ceramides (CER), cholesterol (CHOL) and free unsaturated fats (FFA) in a generally molar 1:1:1 proportion.md_ckant_overview

Analysis of cellular cryo-EM data using MD simulation and EM simulation
Atomistic MD recreation joined with EM re-enactment might be utilized to examine cell high goals cryo-EM information. Picture examination is then considering an iterative procedure where the MD demonstrate is changed in a stepwise manner until the point that ideal correspondence is accomplished between the first cryo-EM information got from the natural example and the mimicked EM information got from the MD display.

Molecular dynamics simulations
Through atomistic MD reenactments thermodynamically stable sub-atomic models might be built and equilibrated, ideally at long time scales. The connections between the particles of the model are depicted by biomolecular constrain fields partitioned into a fortified (communications portrayed utilizing securities, edges and torsion edges) and a non-reinforced part. MD recreations might be utilized to contemplate the atomic properties of a framework at a level difficult to reach by certifiable analyses. In any case, with a specific end goal to create significant data the recreated information must be approved against unique exploratory information. One method for doing this is by looking at reproduced EM pictures got from atomistic MD models with unique cryo-EM pictures gathered from organic cells or tissues.

Optimization of the skin barrier model
Beginning from the lipid hindrance show framework portrayed by the spread bilayer demonstrate, the framework was improved in an iterative way concerning I) the relative lipid piece (counting sphingosine-and phytosphingosine based ceramides, CHOL, FFA, acyl ceramides, cholesterol sulfate, and charged FFA), ii) the appropriation of CHOL over the layered structure, iii) the dispersion of lipid chain lengths and, iv) the quantity of water particles related with the lipid headgroups.

MD demonstrating joined with cryo-EM to break down the atomic structure and capacity of the human skin’s porousness boundary.

EM designs coordinating unique cryo-EM designs from skin amazingly nearly. Strikingly, the closer the individual MD model’s lipid structure was to that announced in human stratum corneum, the better was the match between the MD model’s EM recreation designs and the first cryo-EM designs. In addition, the nearest coordinating MD model’s figured water penetrability and thermotropic conduct were observed to be good with that of human skin.

The new information on the point by point structure and arrangement of the skin’s porousness hindrance, alongside the accessibility of MD recreation, will encourage thorough material science-based skin penetrability counts utilizing more practical models than have already been accessible. This may help anticipating properties of medications cooperating with the skin and upgrading them for percutaneous medication conveyance. Also, it might be utilized for skin danger appraisal. The impacts and components of skin porousness improving plans may likewise be explored and streamlined in silico.

Scientists define key binding characteristics of protein associated with heart disease and breast cancer

Galectins can attach itself to the other proteins via the carbohydrates on their surfaces i.e. sugar-binding proteins. This impacts on a range of processes in the cell associated with several diseases, including heart disease and breast cancer.

Understanding the binding of galectins and differentiating between various sugars can help in guiding the design of new molecules that act as inhibitors, blocking the process and therefore limiting the development of certain diseases. However, researchers are trying to get the full picture and exact knowledge of the binding patterns involved in the interactions between different sugars. A knowledge of the hydrogen bond networks in the protein-sugar complexes plays an important part as it presents a better foundation in the efforts for designing a new efficient galectin inhibitor.image

The specialists in neutron and X-ray crystallography had discovered the hydrogen bonding networks in detail for the C-terminal carbohydrate recognition domain of galectin-3.

Till now, most of our understanding of these binding processes has been guesswork as determining the positions of hydrogen atoms is extremely difficult using X-rays due to the weak scattering of hydrogen with X-rays. Even with extremely high-resolution X-ray crystallography experiments, only about half of the most ordered hydrogen atoms can be observed. Neutron crystallography is one the ideal technique that reveal the positions of hydrogen atoms and the geometry of hydrogen bonds, as hydrogen atoms scatter neutrons with approximately the same magnitude as the other elements of a protein (i.e. carbon, nitrogen, oxygen and sulfur). Hence the positions of hydrogen atoms can be directly detected with neutrons rather than X-ray crystallography where it is being inferred from the positions of heavier atoms.

The recent study demonstrates that by using neutron crystallography the positions of the hydrogen atoms and the hydrogen bonding networks can be revealed which provides a better understanding of the binding interactions involved. In addition, by determining the neutron structure of the sugar-free form of galectin-3C (apo galectin-3C) the positions and orientations of water molecules in the binding site before binding is also revealed. Hence the comparison of the apo- and sugar-bound structures enables us to observe how the interactions changes upon binding and help us to improve our understanding of the role water played in the binding process.

Scientists are combining advanced and traditional techniques to understand protein shapes and functions.


A protein’s shape plays a fundamental role in its function. Structural biology strives to construct models, ultimately at atomic resolution that represent snapshots of biological macromolecules and to describe the ways in which these molecules move.

The current dearth of protein structural information reflects the complexity of this challenge. Of the approximately 15,000 protein families, there are still about 5,200 with unknown structure outside the range of comparative modeling. Moreover, the behavior of the vast variety of proteins and their rapidly changing conformations depends on the experimental conditions, making it difficult to study them with a single technique. Over the last few decades, biologists analyzed protein structures using X-ray crystallography, nuclear magnetic resonance (NMR), or electron microscopy (cryo-EM) on samples at cryogenic temperatures. These are vital techniques, because the resolution achieved can be down to the nanometer, angstra, or atomic level. They provide essential information, but they capture the structure in a frozen state. To unravel protein function, scientists must explore protein dynamics, and that can be done with mass spectrometry (MS).

MS captures a sample’s mass-to-charge ratio, which can be used to identify and quantify proteins. By integrating results from different types of MS, scientists can determine protein structures and the mechanisms behind specific functions. This process often requires computational tools. The combination of data and models from different experiments reveals how a protein or protein complex works, including the role of binding factors, post-translational modifications, and interactions with other molecules such as drugs.Science Magazine

Such integrative approaches unveil the basic biology of proteins, and how they can be used. By combining MS with the right set of more conventional techniques, such as EM, researchers can make the most of a method’s strong points and offset its weaknesses. Despite advances in using and combining these techniques, scientists and engineers keep searching for improvements.

MS options

Even though MS can be combined with traditional techniques used in structural biology, one kind of MS is often not enough. Unfortunately, no MS technique does everything the best. For example, a protein or complex of proteins can be kept in the native state i.e. its typical shape under ordinary biological environmental conditions and analyzed with MS. The intact weighing of the mass of the protein complex lets us to find out which proteins and cofactors are part of it. This method keeps proteins in natural assemblies when delivering them to the detector. Another kind of MS technique, crosslinking MS (XL-MS), can be used to determine which parts of a protein or complex are in contact. A chemical glue is used to connect two lysine groups in close proximity. They might be in a single protein or proteins close to each other. Applying this technique to many lysine groups reveals structural constraints because we can see which parts of a protein or which proteins in a group are in proximity.

XL-MS can also be combined with cryo-EM. The combination of cryo-EM and crosslinking was used to study a molecular complex involved in transcribing DNA to RNA. The cryo-EM and XL-MS was also combined to explore the structures involved in splicing RNA.

Scientists can also study the structure of macromolecules with hydrogen-deuterium exchange MS (HDX-MS). Here, the sample is dissolved in heavy water, D2O. All the amide hydrogen on the protein’s surface starts to get exchanged for deuterium. Hydrogens that are less accessible, buried somewhere inside the protein structure are exchanged substantially slower, and this can tell which parts of the protein are outside, and which are inside.

Although scientists developed HDX-MS several decades ago, it could only be used on one small protein at a time. Now, scientists can apply HDX-MS to whole viruses, because of several advances in MS and data processing.

Ups and downs of MS

Although today’s scientists can select from a range of MS techniques, that doesn’t make structural analysis easy. For one thing, exploring protein structure with MS requires upstream processing, including sample preparation and some form of separation, like liquid chromatography (LC) or capillary electrophoresis. The MS platform also needs to provide high sensitivity. In some samples, scientists search for extremely rare components, such as crosslinked peptides. There we need Nano-LC to separate all the peptides, followed by fast and sensitive MS.

Despite some of the challenges of applying MS to protein structure determination, this technology comes with many strengths, such as identifying small binding proteins and protein post-translational modifications; quantifying the heterogeneity of a sample; determining the ratio of the subunits in a protein complex and how the ratio changes over time or under different conditions; and tracking changes in protein conformations.

Advances in MS technology, both in hardware and software have turned it into a tool for probing structural biology. Today’s mass spectrometry is so much faster and more sensitive and the software to analyze the data is faster, more flexible, and provides smarter algorithms for looking at different sets of large data.

Tag-team technologies

The conventional techniques used to analyze the structure of biological molecules, like X-ray crystallography, can reveal the locations of components down to the atom. To use this technique, however, the recombinant protein must be crystallized, which is extremely challenging with some proteins, particularly if they are membrane-bound. In those cases, researchers can use cryo-EM to prepare very high-resolution images. But cryo-EM gives us one image of one specific moment in time.

To study the dynamics of protein structures, today’s scientists turn to MS. Although the resolution is lower with MS, the ability to examine temporal changes increases substantially with this technology and combining the various forms of MS can tease out different aspects of a molecular structure. So, X-ray crystallography, NMR, or cryo-EM can be combined with one or more forms of MS such that each collects information on some aspect of a protein’s structure.

Further on down the road

Currently, scientists must cobble together various methods and techniques, often manually integrating the results to generate the best data. As those steps turn into a more cohesive workflow, integrative structural biology will be applied to an even wider range of questions, including novel functions of structures, protein–protein interactions, therapeutic targets, and more. Along the way, this field will uncover new knowledge about how biological systems work, and how they fail. The latter will help clinical researchers understand, diagnose, and treat diseases. However, doing that depends on combining areas of expertise from protein biophysics to drug discovery and beyond with the right collection of tools for probing and analyzing complicated biological structures, all on a very fine scale. Only then will we have a complete understanding of the very specific ways that a protein’s shape determines its function.

Potential Advance in turning around impacts of Alzheimers:

The Possibility that anticipating and regarding Alzheimer’s ailment could be as simple as wearing specific eye wear that conveys quick gleams of light. Since the main instance of Alzheimer’s illness was recognized more than 100 years prior, the quantity of individuals with the infection in the United States has developed to more than 5 million and is relied upon to increment. Analysts have gained significant ground in describing the atomic and protein brokenness that happens in Alzheimer’s ailment, yet none of the present FDA-endorsed medicines can turn around, stop, or even back off its movement

Potential -lg

Its trademark pathology are beta-amyloid proteins that bunch together and shape lethal plaques outside of cells, and unusual tau proteins that cluster together and frame poisonous tangles inside cells. The most longstanding hypothesis of Alzheimer’s infection places that beta-amyloid protein variations from the norm drive the tau protein anomalies. Thus, these drive different markers of cerebrum brokenness of Alzheimer’s ailment, for example, neuroinflammation and cell passing. Generally, the demise of cells and neurotransmitters (parts of cells that permit correspondence with each other) are likely in charge of dementia, an essential piece of the ailment. Indeed, even before beta-amyloid groups into plaques, in any case, certain parts of beta-amyloid are delivered at too high a level and bother mind work.

A few analysts have discovered proof that amyloid levels might be raised in individuals for a long time, maybe even decades, previously manifestations end up clear. The moderate movement of the sickness may imply that cerebrum brokenness has just advanced too far when indications are distinguished for medications to be viable. This is one reason a noteworthy focal point of research is to discover organic markers — ideally noninvasive — that could enable clinicians to identify the most punctual phases of Alzheimer’s sickness before across the board and irreversible harm happens.


The adequacy of the light flicker treatment in the mice proposes that, if these discoveries can be effectively meant people. Maybe somebody with an expanded hazard for Alzheimer’s ailment could consider doing this treatment preventively.

A New Drug Puts Cancer Cells Permanently to ‘SLEEP’

Scientist discovered anti-cancer drug without the usual side effects of conventional cancer treatments.2
Research up to now has proven progress in delaying cancer relapse in addition to treating some forms of cancer.

The technique of preventing the growth of tumours occurs without damaging any cell’s DNA, which takes place in traditional treatments including chemotherapy and radiotherapy.

The future of cancer therapy might be is to have directed and focused treatments so as to work on specific patient groups. A new kind of approach to cancer therapy that is preventing cancer cells from growing, however, leaving the normal cells especially unaffected and that’s by harnessing the body’s normal defences against unrestricted growth.

The development of the drug is at a pre-clinical stage. The research indicates that by targeting certain proteins recognized to play the primary function in the development of cancer, doctors can essentially prevent the disease.

These proteins are known as KAT6A and KAT6B and they’re proteins that affect certain genes most commonly observed in cancers. The disease-causing protein that has been targeted has actually not been able to be targeted before with a small-molecule potential drug. Researchers developed a small molecule that inhibits these proteins.

The way that those epigenetic drugs work especially this drug is that it freezes the cell, however, does not kill it off. In case you are at a late stage disease and have lots of tumours in your body, we obviously need to get rid of that first before seeking to prevent the cells from growing. This drug could be definitely beneficial after the usage of initial therapy that gets rid of the original tumour mass and we might use that new type of epigenetic drug to prevent any tumours from developing back, that’s a truly beneficial concept and idea.

Five reasons we’re excited by how structural biology is advancing cancer research

protein-structure-screenshot-1-33-ratioThe researchers are most excited to know about the potential that structural biology has, enabling the discovery of brand new cancer drugs. Several research teams are devoted to structural biology which is a crucial discipline in cancer research shedding light on some of life’s most fundamental processes. There are five key reasons why structural biology research excites us:

  • looking at proteins in atomic detail.
  • X-ray crystallography and electron microscopy is used to visualize proteins.
  • The techniques can be used to make maps.
  • Usage of state-of-the-art technology.
  • Our knowledge of proteins is used to discover new drugs.407052584
  1. looking at proteins in atomic detail.

The structural biologists explore the shapes of proteins in detail, down to the individual atom, and work out how they interlock with other proteins and potential drugs. Proteins are the drivers of all our biological processes, which are hijacked in cancer to drive cell growth and spread.

Researchers are interested in finding out what a protein looks like in three dimensions, to better understand its function and how, in cancer cells, it can go wrong. If we can determine which parts of the protein are important for its role in normal cells and cancer cells, then the drug discovery teams might be able to design drugs that turn the protein on or off.

  1. 2. X-ray crystallography and electron microscopy is used to visualize proteins.

X-ray crystallography is a technique that offers a fascinating way by which we can look at proteins to understand how they work. Scientist has used this technique to help understand which parts of certain proteins might be targets for cancer drugs.

For protein X-ray crystallography, we make a crystal containing millions of copies of our protein of interest, all slotting together in a highly ordered way. Then we irradiate the crystal with X-rays to create a map of the atoms’ positions.

Another technique is called electron microscopy. This means the proteins are imaged at around 50,000 times magnification using a beam of electrons, rather than light.

  1. The techniques can be used to make maps.

Several research programmers are using the techniques mentioned above to improve the knowledge of key cancer-causing proteins. One focus is cell division – normally a highly regulated process but hijacked by cancer to drive its continued growth. Recent studies have produced detailed maps of two major players in this process: the proteasome and the anaphase promoting complex.

These maps have advanced the understanding of how the various parts of both complexes weave together and pull apart during cell division – not only in humans, but in all animals and plants.

  1. Usage of state-of-the-art technology

Some of the researchers are using a developing technology that is sparking much excitement in the field, called cryo-electron microscopy. This involves freezing and imaging samples at -180°C to preserve the finest details of the protein shapes. This type of microscopy is an emerging and tremendously exciting approach in cancer drug design.

As well as offering much greater detail than it did even a few years ago, it provides the opportunity to study protein complexes in conditions closer to those in the human body which should make it much easier to design entirely new cancer drugs.

  1. Our knowledge of proteins is used to discover new drugs.

The structural biologists work closely with the drug discoverers, exploring how prototype drugs interact with proteins to block signaling pathways. We are particularly keen to focus on hard to treat cancer targets, that no current drugs are effective against.

 According to a recent study that explored how tiny fragment molecules could be used to block a protein called Hsp70 – a ‘master controller’ that oversees several cancer driving signals. Because of its shape, Hsp70 is a challenging target – but the research has shown how it might be possible to make drugs that block its action.