Category Archives: Crystallography

Crystallography Techniques: Application to Lithium Mining

The Crystallographic study suggests a blending model of chemical solutions over a network of interconnected pipes and pumps.  The master goal of this current study is to rationalize a number of quality requirements in the network´s output.    It is well known that the traditional methodology and strategy used to tackle this kind of technical problem has been to consider a modeling methodology based upon flow and quality.  In this study, we suggest a new model and the overall method has been focused on the actual feasibility and throughout the course of the current study it is shown that, the whole process is reduced to a non-convex problem.

A rather complete and informative analysis of the intermolecular and intermolecular potentials is put forward with reference to the lanthanide type systems, such as in the, space group.  A particular situation occurs in both extreme of the series, say for   and respectively.  The thirteen trivalent lanthanide ions, moving along the series from  to , for these ions the shell is not fully occupied and therefore the physical and chemical properties are indeed, somehow challenging and interesting to examine using structural, spectroscopic and theoretical methods and model calculations.

Using these methods of mining and mineralogy there has been development and many implementation in the new model by employing a numerical analysis method and the results obtained show up to be quite sensible and consistent so as to provide sound and realistic solutions. This area of research is quite relevant since new mobile technology; digital cameras, laptops and electro mobility and so forth have become essential to humankind. It is, well known that the operational availability is limited by the quality of the batteries employed. Prolonged operative life per load requirements has motivated research aimed to develop a new technology of energy storage. There are several options, nevertheless in this specific study we have chosen batteries based in Lithium since they have become attractive and highly efficient, due to the characteristic of this chemical element (Z=3). In this research a feasibility problem is modeling using a least square objective function over a convex polyhedral, where the only variables are the ones related to flow and the quality variables are “transferred” to the objective function, reducing the complexity of the constraints which makes the problem amenable to traditional techniques which are easy to implement. The Frank-Wolf´s method was used to solve the complex problem with a quite satisfactory performance. From a model viewpoint, this is a new approach and we believe that this methodology and strategy could seduce researchers to make improvements for the whole model presented in this article.

In this current research work, we have elaborated some physical models and carried out a substantial amount of calculations, so as to estimate the reticular energy and also, employing a thermodynamic Born-Haber cycle, we have been able to make some sound predictions and numerical estimate of heat of formations for the above series of lanthanide type crystals. The calculated energy values associated with these observables seems to be most reasonable, and these follow the expected trends, as may be anticipated from theoretical and experimental grounds. Both, the advantages and disadvantages of the current model calculations, have been tested against other previous calculations performed.

Nanotechnology Strategy by developing Nanocrystalline Materials

cryDevelopment of nanocrystalline tungsten-25%Rhenium alloy reinforced with hafnium carbide is a challenging task as these alloys are difficult to synthesize by conventional methods. The problem of these difficult to alloy elements can be addressed by using a unique combination of mechanical alloying and Spark Plasma Sintering SPS techniques via powder metallurgy route.  Rhenium was added to lower ductile-to-brittle transition temperature and to increase recrystallization temperature of tungsten. SPS is rapid consolidating technique which prevents grain growth.

Basically, glycan beautifies all mammalian cell surfaces through glycosylation. Glycan is one of the most important post-modifications of proteins. Glycans on cell surfaces facilitate a wide variety of biological processes, including cell growth and differentiation, cell-cell communication, immune response, intracellular signalling events and host-pathogen interactions. High-performance optical sensors are very important for rapid, sensitive and precise detection of chemical and biological species for various fields, including biomedical diagnosis, drug screening, food safety, environmental protection etc.

To explore the novel kinds of sensors with low cost, portability, sufficient sensitivity, high specificity, excellent reproducibility, and multiplexing detection capability still remain in high demand. Therefore, a significant advancement of silicon nanotechnology, functional silicon nanomaterial/Nano hybrids (e.g., fluorescent silicon nanoparticles, gold/silver nanoparticles-decorated silicon nanowires or silicon wafer, etc) featuring unique optical properties have been intensively employed for the design of high-quality fluorescent and surface-enhanced Raman scattering (SERS) biosensors. Therefore, currently exists increasing concerns on the development of a kind of high-performance SERS platform, which is suitable for glycan expression of different cell lines and as well as used for the sensitive detection of glycans on live cells. Herein, we introduce the possibility of silicon-based probe for biomolecules of interest in the vicinity of cells using SERS.

These tool materials can withstand high temperatures and harsh conditions in joining application such as Friction Stir Welding FSW of steel and titanium alloys. FSW is a green process which does not emit fume and toxic fumes during the process.  Sintering was carried between 1500-1800oC. Mechanically alloyed and Spark Plasma Sintered alloy and composite were characterized by optical microscopy. Spark plasma sintered samples were further electrochemically etched in one molar concentrated solution of NaOH. The results of the FESEM images confirm microstructural revelation of these difficult to etch alloy and composites. Field Emission Scanning Electron Microscopy FESEM and X-ray Diffraction.  Microstructural investigation of consolidated specimens was initially carried out by conventional etching and metallography techniques. Optical micrographs showed no visible signs of grain boundary etching.

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.

Synthesis, Structural Analysis and Antibacterial Effect of a Novel Hetero-nuclear-Coordination Polymer

CryThe crystal complex was crystallised the triclinic space group. The smallest repeating unit of the complex contains an [Fe(TPT)Ag2(H2O)2](ClO4)3 unit. The Fe atom is coordinated by three nitrogen of terpyridine moiety from one TPT ligand and by three nitrogen of terpyridine moiety from another TPT ligand in an octahedral geometry fashion. While one Ag atom is coordinated by two nitrogen atoms of one pyrazolyl moiety from a TPT ligand and two nitrogen atoms of adjacent pyrazolyl moiety from another TPT ligand to generate a linear coordination polymer in a tetragedral geometry. The third nitrogen atom of the last pyrazolyl part is also coordinated to a silver ion which was itself coordinated to two water molecules through their oxygen atoms in a trigonal planar geometry. In vitro study of the complex against some bacterial pathogens were also investigated.

The synthesis and crystal structure of a novel polymeric silver(I)-Iron(II) complex containing bridging ligand 4’-(4-(2,2,2-tris(1H-pyrazol-1-ido)ethoxymethyl)phenyl-2,2’:6’,2”-terpyridine (TPT) are described. The reaction of TPT with FeCl2.6H2O afforded a complex [Fe(TPT)2]Cl2 which in turn reacted with a range of silver salts such as AgNO3, AgClO4 resulted in the formation of heterometal complexes which were characterised using 1H NMR and ES-MS techniques. The reaction solution of the [Fe(TPT)2]Cl2 complex with molar eqiuvalnet of AgClO4 resulted in a solution with gace needdle-like crystals suitable for single X-ray crystallography.

There has been extensive studies of binding of chiral Ru(II) complexes to DNA backbone structures. J. K. Barton has studies the cationic coordination of a variety of chiral poly-pyridine Ru(II) complexes to demonstrate chiral discrimination in binding to different forms of DNA. Many experimental techniques have been applied to study the interaction of tris(phenanthroline)ruthenium(II) with DNA, but despite this, its binding mode and its effect on the DNA structure are uncertain and have been the subject of much controversy. In this study, bis[4'-(4-methylphenyl)-2,2':6',2"-terpyridine]Co(III) tris(nitrate) complex was synthesized and characterized using conventional method such as 1H NMR, ES-MS, UV-vis spectrophotometry. The Co ion was six coordinated, but the geometry was significantly distorted from that of an ideal octahedral. In this study, the terpyridine type ligand fragment appealed because the ligand structure ensures a meridional arrangement of the donor atoms, which reduces the number of possible isomers. Co(III) ion was attracted because of its higher positive charge compared to Ru(II) which will have more affinity towards the negatively charged DNA structure.

Absorbance and fluorescence methods, and circular dichroism, were used to study the interaction of the Co(III) complex solution in water with DNA.

Advanced Materials for Protein Crystallization

The crystallization of proteins, nucleic acids, biological complexes, will depend on the creation of a solution that is supersaturated in the macromolecule. Since 60 years, X-ray crystallography provides structural details of protein molecules, information that is crucial to unravel biological mechanisms at molecular level. Crystallography requires that sample is in crystal form. Getting such crystals at an acceptable quality for crystallographic analysis is not trivial and strategies to make this process less expensive and time-consuming are not available, still now.

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Technologies that assist with Protein crystallization

  • High throughput crystallization screening
  • Protein engineering

Advanced materials represent a turning point in this field because they can be exploited to control nucleation and growth step making more effective the crystallization process. Researchers are developing membrane-based materials able to trigger protein crystallization also in conditions that are not fruitful by standard methods.  Such materials have a great impact both in the industry and academic studies because significantly reduce cost and time of the protein purification and crystallization process. Then they developed membrane-materials functionalized by hydrogel that proved ability in getting very stress-resistant crystals, which are suitable for structure-based drug design studies that require very harsh soaking conditions. This material, similarly to our metal oxide nanoparticle-functionalized membrane, significantly widens the crystallization window and produce crystals having good diffraction quality.

Methods of protein crystallization

  • Vapor diffusion
  • Microbatch
  • Microdialysis
  • Free-interface diffusion

Membrane-based materials are showing very effective in protein crystallization and to produce crystals having specific features. Our efforts are focusing now in functionalizing such materials by Nano template to crystallize very challenging proteins such as intact antibodies, and to develop membrane able to promote bio mineralization and to enable polymorphs selection.

Graphene nanoribbons- Quantum chains

Scientists have discovered a leap forward that could be utilized for exact Nano transistors-perhaps even quantum PCs. A material that comprises of atom of a solitary component however has totally unique properties relying upon the nuclear plan – this may sound odd, yet is really reality with graphene nano-strips. The strips, which are just a couple of carbon iotas wide and precisely one particle thick, have altogether different electronic properties relying upon their shape and width: conductor, semiconductor.

These days analysts have now prevailing in definitely changing the properties of the strips by particularly change their shape. The specific component of this innovation is that not electronic properties of atom said above to be changed – it can likewise be utilized to produce particular neighbourhood quantum states. On the off chance that the width of a restricted graphene nanoribbon changes, for this situation from seven to nine molecules, an uncommon zone is made at the progress: in light of the fact that the electronic properties of the two different contrast in an extraordinary, alleged topological way, an ensured and consequently exceptionally vigorous new quantum state is made in the change zone.

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In light of these novel quantum chains, exact nano-transistors could be fabricated later on for the best approach to Nano gadgets. This isn’t exactly as basic: for the fast and development of the electronic properties, every one of the few hundred or even a large number of iotas must be in the perfect place.

While in transit to nanoelectronics Based on these novel quantum chains, exact nano-transistors could be produced later on an outing into the quantum domain: Ultrasmall transistors – and in this way the subsequent stage in the further scaling down of electronic circuits – are the conspicuous application potential outcomes here: despite the fact that they are in fact testing, hardware in light of nano-transistors really work essentially as microelectronics. Regardless of whether this potential can really be misused for future quantum PCs stays to be seen, be that as it may. It isn’t sufficient to make limited topological states in the nanoribbons.

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.

Conclusions
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.

Crystallization: Protein and X-Ray crystallisation

Protein crystallization is the procedure of development of a protein crystal. While some protein crystal have been seen in nature, protein crystallization is mostly utilized for logical or modern purposes, most prominently for consider by X-beam crystallography. Proteins are the natural macromolecules that are made out of long chain of amino acids. It is the procedure for the development of tiny protein crystal. This procedure is generally utilized by mechanical and logical purposes.

A protein regularly works in liquid conditions in this way protein crystallization process is for the most part completed in water. The primary objective behind protein crystallization and crystallography is to grow very much arranged protein precious stones that conquer the intrinsic delicacy of protein particles. The exploration consider inspects the protein crystallography item advertise with help of various criteria, for example, the item compose, application, and its land extension. Numerous elements, for example, immaculateness of proteins, grouping of proteins, pH, temperature of medium, may impact the procedure of protein crystallization and crystallography.

Different methods of Protein Crystallisation:

  • Vapor diffusion
  • Microbatch
  • Microdialysis
  • High throughput crystallization screening
  • Free-interface diffusion
  • x-ray diffraction

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Protein and X-ray crystallography is basically a type of terribly high resolution research. It allows us to examine super molecule structures at the atomic level and enhances our understanding of supermolecule perform. Specifically we are able to study however proteins move with alternative molecules; however they endure conformational changes, and the way they perform chemical process within the case of enzymes. Armed with this info we are able to design novel drugs that concentrate on a specific super molecule, or rationally engineer associate protein for a selected process. The crystallization of biological macromolecules has been represented in great detail. every crystallographer approached the matter in an individual way; the procedures are mostly standardized, particularly as a results of the supply of crystallization kits, in addition as robots for the preparation of solutions, setting up crystallizations

Fabrication of Nanostructured Arrays on Polymer Films

 The development of Fabrication of Nanostructured Arrays on Polymer Films is a creation procedure for varieties of nanostructures (e.g., nanocones) on adaptable polymer films. The manufacture procedure takes into consideration the nanocone clusters to be made on an expansive scale (e.g., 10-100 sq. inches) on an adaptable polymer film by means of a two-advance process. The initial step comprises of self-gathering a layer of polymer microspheres or nano spheres on an alternate polymer film. The second step comprises of the concurrent differential carving of the polymer circles and film to make the nanostructured surface. The resultant nanocone exhibits would then be able to be covered by an ultrathin metal, polymer, oxide, or semiconductor film or nanoparticles. The subsequent nanostructured surfaces have exceptional optical and wetting properties, and the thin movies are sufficiently adaptable to coat bended or convoluted surfaces.

Varieties of nanostructures composed on surfaces are exceedingly fascinating because they can display one of a kind surface property, for example, basic radiance, hostile to reflectivity, superhydrophobicity, improved synergist action and coupled plasmonic optical resonances. These nanostructured surfaces can be possibly actualized as fundamental parts in an assortment of essential application gadgets including biosensors, against intelligent coatings, sun powered boards, self-cleaning surfaces, and bactericidal surfaces. There is a neglected requirement for an economical, basic, fast, and versatile innovation to functionalize extensive surface territories with nanostructures in the zones of therapeutic diagnostics, vitality enterprises and military businesses – even possibly for regular articles (e.g., auto, garments).

Schematic-illustration-of-the-PS-surface-nano-patterning-Different-surface

Techniques that use “top-down” manufacture, for example, centered particle shaft scratching and e-pillar lithography can be utilized to make metallic, semiconductor and oxide nanostructures with exact control, however are exorbitant, moderately moderate and constrained altogether realistic organized region. Moreover, objects with bended surfaces or complex shapes can’t be utilized. The UCI scientists have built up another two-advance manufacture process for making nanostructure clusters on thin polymer films that is anything but difficult to actualize, reasonable, flexible, and quick.

 

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

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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.