How far can we go with structural mass spectrometry of protein complexes?

Physical interactions between proteins and the formation of stable complexes form the basis of most biological functions. Therefore, a critical step toward understanding the integrated workings of the cell is to determine the structure of protein complexes, and reveal how their structural organization dictates function. Studying the three-dimensional organization of protein assemblies, however, represents a major challenge for structural biologists, due to the large size of the complexes, their heterogeneous composition, their flexibility, and their asymmetric structure. In the last decade, mass spectrometry has proven to be a valuable tool for analyzing such noncovalent complexes. Here, I illustrate the breadth of structural information that can be obtained from this approach, and the steps taken to elucidate the stoichiometry, topology, packing, dynamics, and shape of protein complexes. In addition, I illustrate the challenges that lie ahead, and the future directions toward which the field might be heading.     

Mass spectrometry and the amyloid problem—How far can we go in the gas phase?

A number of proteins are capable of converting from their soluble, monomeric form into highly-ordered, insoluble aggregates known as amyloid fibrils. In vivo, these fibrils, which accumulate in organs and tissues, are associated with a wide range of amyloid diseases for which there are currently no therapeutic solutions. The molecular details of the pathway from native monomer through oligomeric intermediates to the final amyloid fibril remain a challenging enigma. Over the past few years, mass spectrometry has been applied to investigate the various stages of amyloid fibril formation, and this report summarizes the key steps achieved to date.     

Pushing the detectability of voltammetry: how low can we go?

The coupling of adsorptive accumulation with catalytic reactions results in remarkably low (sub-picomolar) detection limits. This review assesses various strategies for attaining such dual-amplification effects, that lead to the most sensitive voltammetric technique, adsorptive-catalytic stripping voltammetry (AdCtSV).     

Optical immunosensors for environmental monitoring: How far have we come?

Immunosensing has proved to be a very interesting research area. This review discusses what has actually been achieved in the field of optical immunosensing for environmental screening, and what still needs to be done. The review is presented from a practical point of view. In terms of the basic design of the immunosensor, there is a trend towards decreasing assay time; indeed, this has been reduced from 15–20 minutes to less than 5 minutes. Another goal is to simplify the manifold, and label-free approaches combining indirect assay formats and the detection of antibody binding are popular. Rapid displacement assays have also been investigated thoroughly. In terms of some important features of immunosensing devices, the reusability of the sensing element has been studied in great depth, and working lifetimes of more than five hundred assays can now be found for all assay formats. Multianalyte assays are now being investigated, and current systems are able to monitor 2–3 target compounds, although this number is set to increase greatly (to >30) in the near future. In this sense, an increasing number of publications can be found on microarrays intended for multianalyte determinations. The application of immunosensing to real situations is the main challenge. Immunosensors are barely commercialized and are yet to be established as research or routine tools, due to a lack of validated protocols for a wide range of sample matrices. Regarding compounds considered as analytes, some significant pollutants such as dioxins or pharmaceuticals are rarely chosen as targets, although the current tendency is towards a broader spectrum of analytes. New immunoreagents should be raised for these compounds, for use in immunosensors that can be used as screening tools.     

The way to AI-controlled synthesis: how far do we need to go?

Chemical synthesis always plays an irreplaceable role in chemical, materials, and pharmacological fields. Meanwhile, artificial intelligence (AI) is causing a rapid technological revolution in many fields by replacing manual chemical synthesis and has exhibited a much more economical and time-efficient manner. However, the rate-determining step of AI-controlled synthesis systems is rarely mentioned, which makes it difficult to apply them in general laboratories. Here, the history of developing AI-aided synthesis has been overviewed and summarized. We propose that the hardware of AI-controlled synthesis systems should be more adaptive to execute reactions with different phase reagents and under different reaction conditions, and the software of AI-controlled synthesis systems should have richer kinds of reaction prediction modules. An updated system will better address more different kinds of syntheses. Our viewpoint could help scientists advance the revolution that combines AI and synthesis to achieve more progress in complicated systems.

It is still a long march for AI-controlled synthesis to enter into general laboratories. Flaws in the architecture of AI-controlled synthesis systems must be overcome.     

Improving the intrinsic activity of electrocatalysts for sustainable energy conversion: where are we and where can we go?

As we are in the midst of a climate crisis, there is an urgent need to transition to the sustainable production of fuels and chemicals. A promising strategy towards this transition is to use renewable energy for the electrochemical conversion of abundant molecules present in the earth''s atmosphere such as H₂O, O₂, N₂ and CO₂, to synthetic fuels and chemicals. A cornerstone to this strategy is the development of earth abundant electrocatalysts with high intrinsic activity towards the desired products. In this perspective, we discuss the importance and challenges involved in the estimation of intrinsic activity both from the experimental and theoretical front. Through a thorough analysis of published data, we find that only modest improvements in intrinsic activity of electrocatalysts have been achieved in the past two decades which necessitates the need for a paradigm shift in electrocatalyst design. To this end, we highlight opportunities offered by tuning three components of the electrochemical environment: cations, buffering anions and the electrolyte pH. These components can significantly alter catalytic activity as demonstrated using several examples, and bring us a step closer towards complete system level optimization of electrochemical routes to sustainable energy conversion.

We evaluate the improvements over the past two decades in intrinsic activity of electrocatalysts for sustainable energy conversion, and highlight opportunities from tuning the electrolyte.     

Solid-phase microextraction. How far are we from clinical practice?

The current review briefly discusses the future development of solid-phase microextraction (SPME) and its potential application in the field of clinical medicine, including pharmacokinetic studies, therapeutic drug monitoring, biomarker discovery, and targeted and untargeted metabolomics. We also discuss aspects of automation and high-throughput analysis as major requirements of daily clinical practice. We give examples of clinically-validated applications of SPME and point out the regulatory restrictions limiting some in-vivo SPME studies. We briefly review the current state of progress in this extraction technique in the context of its future application in medical research and laboratory testing, including new directions (i.e. personalized medicine).     

AFM of biological complexes: What can we learn?

The term “biological complexes” broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected non-membrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications.     

How far can a sodium ion travel within a lipid bilayer?

Analogues of a synthetic ion channel made from a helical peptide were used to study the mechanism of cation translocation within bilayer membranes. Derivatives bearing two, three, four, and six crown ethers used as ion relays were synthesized, and their transport abilities across lipid bilayers were measured. The results showed that the maximum distance a sodium ion is permitted to travel between two binding sites within a lipid bilayer environment is 11 ?.     

Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?

Carr-Purcell-Meiboom-Gill relaxation dispersion NMR spectroscopy has evolved into a powerful approach for the study of low populated, invisible conformations of biological molecules. One of the powerful features of the experiment is that chemical shift differences between the exchanging conformers can be obtained, providing structural information about invisible excited states. Through the development of new labeling approaches and NMR experiments it is now possible to measure backbone 13C(alpha) and 13CO relaxation dispersion profiles in proteins without complications from 13C-13C couplings. Such measurements are presented here, along with those that probe exchange using 15N and 1HN nuclei. A key experimental design has been the choice of an exchanging system where excited-state chemical shifts were known from independent measurement. Thus it is possible to evaluate quantitatively the accuracy of chemical shift differences obtained in dispersion experiments and to establish that in general very accurate values can be obtained. The experimental work is supplemented by computations that suggest that similarly accurate shifts can be measured in many cases for systems with exchange rates and populations that fall within the range of those that can be quantified by relaxation dispersion. The accuracy of the extracted chemical shifts opens up the possibility of obtaining quantitative structural information of invisible states of the sort that is now available from chemical shifts recorded on ground states of proteins.     

Topology prediction of helical transmembrane proteins: how far have we reached?

Transmembrane protein topology prediction methods play important roles in structural biology, because the structure determination of these types of proteins is extremely difficult by the common biophysical, biochemical and molecular biological methods. The need for accurate prediction methods is high, as the number of known membrane protein structures fall far behind the estimated number of these proteins in various genomes. The accuracy of these prediction methods appears to be higher than most prediction methods applied on globular proteins, however it decreases slightly with the increasing number of structures. Unfortunately, most prediction algorithms use common machine learning techniques, and they do not reveal why topologies are predicted with such a high success rate and which biophysical or biochemical properties are important to achieve this level of accuracy. Incorporating topology data determined so far into the prediction methods as constraints helps us to reach even higher prediction accuracy, therefore collection of such topology data is also an important issue.     

How far can ion trap miniaturization go? Parameter scaling and space‐charge limits for very small cylindrical ion traps

A broad effort is underway to make radiofrequency (RF) ion trap mass spectrometers small enough for portable chemical analysis. A variety of trap geometries and fabrication approaches are under development from several research groups. A common issue is the reduced trapping capacity in smaller traps, with the associated reduction in sensitivity. This article explores the key variables that scale with trap size including RF voltage, frequency, electrical capacitance, power and pseudopotential well depth. High‐field electric breakdown constrains the maximum RF voltages used in smaller ion traps. Simulations show the effects of space charge and the limits of trapping capacity as a function of trap dimensions for cylindrical ion traps down to the micrometer level. RF amplitudes that scale as the1/3, 1/2 and 2/3 power of trap radius, r₀, were studied. At a fixed level of performance, the number of analyzable ions scales as r₀ⁿ, with n ranging from 1.55 to 1.75 depending on the choice of voltage scaling. The implications for miniaturized ion trap mass spectrometry are discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

35 years of palladium-catalyzed cross-coupling with Grignard reagents: how far have we come?

This tutorial review is intended to provide the reader with a timely review of major developments and the current state-of-the-art of palladium-catalyzed cross-coupling reactions with Grignard reagents. Organomagnesium reagents, the most reactive and most easily accessible nucleophiles for carbon-carbon bond forming cross-coupling reactions, were the first nucleophiles ever employed in cross-coupling reactions, but have only recently been re-discovered for highly efficient and (stereo)selective coupling reactions. This is mostly a consequence of improved catalyst systems with bulky phosphine, phosphonate or carbene ligands and new metal-halogen exchange procedures for the generation of functionalized Grignard reagents.     

Is the 31P chemical shift anisotropy of aluminophosphates a useful parameter for NMR crystallography?

The ³¹P chemical shift anisotropy (CSA) offers a potential source of new information to help determine the structures of aluminophosphate (AlPO) framework materials. We investigate how to measure the CSAs, which are small (span of ~20–30 ppm) for AlPOs, demonstrating the need for CSA-amplification experiments (often in conjunction with ²⁷Al and/or ¹H decoupling) at high magnetic field (20.0 T) to obtain accurate values. We show that the most shielded component of the chemical shift tensor, δ₃₃, is related to the length of the shortest P─O bond, whereas the more deshielded components, δ₁₁ and δ₂₂ can be related more readily to the mean P─O bond lengths and P─O─Al angles. Using the case of Mg-doped STA-2 as an example, the CSA is shown to be much larger for P(OAl)_4–n(OMg)_n environments, primarily owing to a much shorter P─O(Mg) bond affecting δ₃₃, however, because the mean P─O bond lengths and P─O─T (T = Al, Mg) bond angles do not change significantly between P(OAl)₄ and P(OAl)_4–n(OMg)_n sites, the isotropic chemical shifts for these species are similar, leading to overlapped spectral lines. When the CSA information is included, spectral assignment becomes unambiguous, therefore, although the specialist conditions required might preclude the routine measurement of ³¹P CSAs in AlPOs, in some cases (particularly doped materials), the experiments can still provide valuable additional information for spectral assignment.     

Photochemical properties of carotenoids: what can we get from the VB model?

Photo-isomerization and anti-oxidation of carotenoids have been studied for many years be-cause of their diverse roles in photobiology, photochemistry and photomedicine[1—6]. The experi-mental works revealed that the changes in the geometry between S0 (the ground state) and T1 (the first triplet state) states are very important for the two processes. Meanwhile, theoretical studies have also been carried out to investigate these processes. The polyenes have usually been used as the models for…     

Resonance raman spectroscopy of conjugated polymers what can we learn?

This paper gives a review on the use of resonance Raman spectroscopy to analyse electronic and molecular structures of π-conjugated and σ-conjugated polymers. It starts with a short introduction into the present state of research in the field of conducting polymers and with a very short introduction into the principles of resonance Raman spectroscopy. Then the potentialities of the technique are demonstrated for the examples of the analysis of conjugation length in polyacetylene, for studying the thermochromic phase transition in polysilanes and in polyalkylthiophenes, for a sudy of the doping processes in polyaniline and finally for an analysis of the ground state in the narrow gap system polyisothianaphthene. Advantages and pitfalls for such analyses are outlined.     

Analogy of silicon clusters with deltahedral boranes: how far can it go? Reexamining the structure of Sin and Sin 2-, n=5-13 clusters

Silicon clusters of 5 up to 13 atoms, Si(n), n=5-13, and their dianions are studied in the light of an anticipated analogy with the corresponding isoelectronic boranes suggested recently by Zdetsis [J. Chem. Phys. 127, 014314 (2007)]. It is demonstrated that this analogy is a fruitful and powerful concept which allows the straightforward determination of the structures of silicon clusters, based on the structure of corresponding closo-boranes, meeting the requirements of well known structural rules. All lowest-lying structures of Si(n), n=5-13 clusters, have been obtained through a systematic way on the basis of this analogy. For magic clusters, such as Si(6) and Si(10), characterized by special stability, the analogy to boranes seems to be much stronger.     

How far can hydroxyl radicals travel? An electrochemical study based on a DNA mediated electron transfer process

Using photocatalytic reactive nanoparticles and DNA composite modified gold electrodes, exploiting the sensitivity of DNA-mediated electron transfer to base pair stacking, we examined the effects of DNA oxidation damage by photocatalytically generated hydroxyl radicals (˙OH) on charge transfer efficiency and proposed an electrochemical technique to read the effective diffusing distance of ˙OH.