To What Extent is FAIMS Beneficial in the Analysis of Proteins?

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.

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What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs?

The understanding of noncovalent interactions in protein–ligand complexes is essential in modern biochemistry and should contribute toward the discovery of new drugs. In the present review, we summarize recent work aimed at a better understanding of the physical nature of molecular recognition in protein–ligand complexes and also at the development and application of new computational tools that exploit our current knowledge on structural and energetic aspects of protein–ligand interactions in the design of novel ligands. These approaches are based on the exponentially growing amount of information about the geometry of protein structures and the properties of small organic molecules exposed to a structured molecular environment. The various contributions that determine the binding affinity of ligands toward a particular receptor are discussed. Their putative binding site conformations are analyzed, and some predictions are attempted. The similarity of ligands is examined with respect to their recognition properties. This information is used to understand and propose binding modes. In addition, an overview of the existing methods for the design and selection of novel protein ligands is given.     

How Much Can We Coarse‐Grain while Retaining the Chemical Specificity? A Study of Sulfonated Poly(ether ether ketone)

For mesoscale structural studies of polymers, obtaining maximum level of coarse‐graining that maintains the chemical specificity is highly desirable. Here we present a systematic coarse‐graining study of sulfonated poly(ether ether ketone), sPEEK, and show that a 71:3 coarse‐grained (CG) mapping is the maximum possible map within a CG bead‐spring model. We perform single chain atomistic simulation on the system to collect various structural distributions, against which the CG potentials are optimized using iterative Boltzmann inversion technique. The potentials thus extracted are shown to reproduce the target distributions for larger single chains as well as for multiple chains. The structure at the atomistic level is shown to be preserved when we back‐map the CG system to re‐introduce the atomistic details. By using the same CG mapping for another repeat unit sequence of sPEEK, we show that the nature of the effective interaction at the CG level depends strongly on the polymer sequence and cannot be assumed based on the nature of the corresponding atomistic unit. These CG potentials will be the key to future mesoscopic simulations to study the structure of sPEEK based polymer electrolyte membranes.

     

Scalar Coupling between the 15N Centres in Methylated 1,8‐Diaminonaphthalenes and 1,6‐Diazacyclodecane: To What Extent is 2HJNN a Reliable Indicator of N?N Distance?

The scalar couplings between hydrogen bonded nitrogen centres ((2H)J(NN)) in the free-base and protonated forms of the complete series of [(15)N(2)]-N-methylated 1,8-diamino naphthalenes in [D(7)]DMF solution have been determined, either directly (15N[1H] NMR), or, indirectly (13C[1H] NMR and simulation of the X part of the ABX spectrum (X=13C, A,B=15N)). Additionally, the (2H)J(NN) value in the HBF(4) salt of [(15)N(2)]-1,6-dimethyl-1,6-diazacyclodecane was determined, indirectly by 13C[(1H] NMR spectroscopy. As confirmed by DFT calculations and by reference to CSD, the rigid nature of the naphthalene scaffold results in rather low deviations in N,N distance or H-N,N angle within each series, apart from the free base of the permethylated compound (proton sponge) where the naphthalene ring is severely distorted to relieve strain. Despite such restrictions, the (2H)J(NN) values increase smoothly from 1.5 to 8.5 Hz in the protonated series as the degree of methylation increases. The effect in the free-base forms is much less pronounced (2.9 to 3.7 Hz) with no scalar N,N coupling detected in the permethylated compound (proton sponge) due to the lack of hydrogen bond between the N,N centres. Neither the pK(a) nor the N-N distance in the protonated forms correlates with (2H)J(NN). However, the sum of the (13)C NMR shifts of the naphthalene ring C(1,8) carbons which are attached directly to the nitrogen centres correlates linearly with (2H)J(NN) and with the degree of methylation. The gas-phase computed (2H)J(NN) is almost constant throughout the homologous series, and close to the experimental value for the tetramethylated ion. However, the computed coupling constant is attenuated in structures involving microsolvation of each N-H unit, and the trend then matches experiment. These experimental and computational observations suggest that Fermi contact between the two N centres is decreased upon formation of strong charge-dispersing intermolecular hydrogen bonds of the free N-H groups with the solvent.     

Can Crude Oil Exploration Influence the Phytochemicals and Bioactivity of Medicinal Plants? A Case of Nigerian Vernonia amygdalina and Ocimum gratissimum

The Nigerian Niger-Delta crude oil exploration often results in spills that affect indigenous medicinal plant biodiversity, likely changing the phytochemical profile of surviving species, their bioactivity or toxicity. In crude oil-rich Kokori and crude oil-free Abraka, classic examples of indigenous plants occupying the medicine-food interface include Vernonia amygdalina (VAL) and Ocimum gratissimum leaves (OGL). These plants are frequently utilised during pregnancy and in anaemia. To date, no scientific investigation has been reported on the potential changes to the phytochemical or bioactivity of the study plants. To discuss the similarities and dissimilarities in antisickling bioactivity and phytochemicals in VAL and OGL collected from Kokori (VAL-KK and OGL-KK) and Abraka (VAL-AB and OGL-AB), in silico, in vitro and comparative UPLC-QTOF-MS analysis was performed. Nine unique compounds were identified in OGL-KK, which have never been reported in the literature, while differences in antisickling potentials were observed in VAL-KK, OGL-KK and, VAL-AB, OGL-AB. Our findings show that VAL-AB and OGL-AB are richer and more diverse in phytochemicals and displayed a slightly higher antisickling activity than VAL-KK and OGL-KK. Ligand-based pharmacophore modelling was performed to understand the potential compounds better; this study may provide a basis for explaining the effect of crude oil spills on secondary metabolites and a reference for further research.     

Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions

Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.     

What Is the Mechanism Driving the Reduction of Cardiovascular Events from Glucagon-like Peptide-1 Receptor Agonists?—A Mini Review

Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are considered the standard of care for type 2 diabetes in many countries worldwide. These molecules have profound anti-hyperglycaemic actions with a favourable safety profile. They are now being considered for their robust cardiovascular (CV) protective qualities in diabetic patients. Most recent CV outcome trials have reported that GLP-1 RAs reduce major adverse cardiovascular events (MACE). Furthermore, the GLP-1 RAs seem to target the atherosclerotic CV disease processes preferentially. GLP-1 RAs also improve a wide range of routinely measured surrogate markers associated with CV risk. However, mediation analysis suggests these modest improvements may contribute indirectly to the overall anti-atherogenic profile of the molecules but fall short in accounting for the significant reduction in MACE. This review explores the body of literature to understand the possible mechanisms that contribute to the CV protective profile of GLP-1 RAs.     

Can we understand the different coordinations and structures of closed‐shell metal cation‐water clusters?

We present a model potential for studying M(q+)(H(2)O)(n=1,9) clusters where M stands for either Na(+), Cs(+), Ca(2+), Ba(2+), or La(3+). The potential energy surfaces (PES) are explored by the Monte Carlo growth method. The results for the most significant equilibrium structures of the PES as well as for energetics are favorably compared to the best ab initio calculations found in the literature and to experimental results. Most of these complexes have a different coordination number in cluster compared to experimental results in solution or solid phase. An interpretation of the coordination number in clusters is given. In order to well describe the transition between the first hydration sphere and the second one we show that an autocoherent treatment of the electric field is necessary to correctly deal with polarization effects. We also explore the influence of the cation properties (charge, size, and polarizability) on both structures and coordination number in clusters, as well as the meaning of the second hydration sphere. Such an approach shows that the leading term in the interaction energy for a molecule in the second hydration sphere is an electrostatic attraction to the cation and not a hydrogen bond with the water molecules in the first hydration sphere.     

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.     

Can Serendipity Still Hold Any Surprises in the Coordination Chemistry of Mixed-Donor Macrocyclic ligands? The Case Study of Pyridine-Containing 12-Membered Macrocycles and Platinum Group Metal ions PdII,PtII, and RhIII

This study investigates the coordination chemistry of the tetradentate pyridine-containing 12-membered macrocycles L¹-L³ towards Platinum Group metal ions Pd^II, Pt^II, and Rh^III. The reactions between the chloride salts of these metal ions and the three ligands in MeCN/H₂O or MeOH/H₂O (1:1 v/v) are shown, and the isolated solid compounds are characterized, where possible, by mass spectroscopy and ¹H- and ¹³C-NMR spectroscopic measurements. Structural characterization of the 1:1 metal-to-ligand complexes [Pd(L¹)Cl]₂[Pd₂Cl₆], [Pt(L¹)Cl](BF₄), [Rh(L¹)Cl₂](PF₆), and [Rh(L³)Cl₂](BF₄)·MeCN shows the coordinated macrocyclic ligands adopting a folded conformation, and occupying four coordination sites of a distorted square-based pyramidal and octahedral coordination environment for the Pd^II/Pt^II, and Rh^III complexes, respectively. The remaining coordination site(s) are occupied by chlorido ligands. The reaction of L₃ with PtCl₂ in MeCN/H₂O gave by serendipity the complex [Pt(L³)(μ-1,3-MeCONH)PtCl(MeCN)](BF₄)₂·H₂O, in which two metal centers are bridged by an amidate ligand at a Pt1-Pt2 distance of 2.5798(3) Å and feature one square-planar and one octahedral coordination environment. Density Functional Theory (DFT) calculations, which utilize the broken symmetry approach (DFT-BS), indicate a singlet d⁸-d⁸ Pt^II-Pt^II ground-state nature for this compound, rather than the alleged d⁹-d⁷ Pt^I-Pt^III mixed-valence character reported for related dinuclear Pt-complexes.     

Should We ‘Eat a Rainbow’? An Umbrella Review of the Health Effects of Colorful Bioactive Pigments in Fruits and Vegetables

Health promotion campaigns have advocated for individuals to ‘eat a rainbow’ of fruits and vegetables (FV). However, the literature has only focused on individual color pigments or individual health outcomes. This umbrella review synthesized the evidence on the health effects of a variety of color-associated bioactive pigments found in FV (carotenoids, flavonoids, betalains and chlorophylls), compared to placebo or low intakes. A systematic search of PubMed, EMBASE, CINAHL and CENTRAL was conducted on 20 October 2021, without date limits. Meta-analyzed outcomes were evaluated for certainty via the GRADE system. Risk of bias was assessed using the Centre for Evidence-Based Medicine critical appraisal tools. A total of 86 studies were included, 449 meta-analyzed health outcomes, and data from over 37 million participants were identified. A total of 42% of health outcomes were improved by color-associated pigments (91% GRADE rating very low to low). Unique health effects were identified: n = 6 red, n = 10 orange, n = 3 yellow, n = 6 pale yellow, n = 3 white, n = 8 purple/blue and n = 1 green. Health outcomes associated with multiple color pigments were body weight, lipid profile, inflammation, cardiovascular disease, mortality, type 2 diabetes and cancer. Findings show that color-associated FV variety may confer additional benefits to population health beyond total FV intake.     

What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C−H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.     

Can we predict the structure and stability of molecular crystals under increased pressure? First‐principles study of glycine phase transitions

The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goal a series of geometry optimization and thermodynamic parameters calculations were performed for γ‐glycine and δ‐glycine structures at different pressure values using CASTEP program. In order to perform most accurate geometry optimization various exchange‐correlation functionals defined within generalized gradient approximation (GGA): PBE, PW91, RPBE, WC, PBESOL as well as defined within local density approximation (LDA), i.e. CAPZ, were tested. Geometry optimization was carried out using different dispersion correction methods (i.e. Grimme, TS, OBS) or without them. The linear response density functional perturbation theory (DFPT) was used to obtain the phonon dispersion curves and phonon density of states from which thermodynamic parameters, such as: free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) were evaluated. The results of the geometry optimization depend strongly on the choice of the DFT functional. Calculated differences between the free energy of the studied polymorphic forms at the studied pressure values were consistent with experimental observations on their stability. The computations of thermodynamic properties not only confirmed the order of stability of two studied forms, but also enabled to predict the pressure at which this order is reversed. The results obtained in this study have proven that the plane‐wave basis set first principles calculations under periodic conditions is suitable for accurate prediction of crystal structure and stability. © 2018 Wiley Periodicals, Inc.     

Vibrational Study on the Local Structure of Post‐Synthesis and Hybrid Mesoporous Materials: Are There Fundamental Distinctions?

Organic-inorganic mesoporous materials of the MCM-41 type are important materials that can be prepared by either post-synthesis or one-pot synthesis procedures. A complete control of the characteristics at a local level is of the utmost importance in view of the applications of such materials. However, there are not many studies relating such features with synthetic approaches. In this work, we prepared samples by post-synthesis derivatization of materials from Si-based MCM-41, with bidentate nitrogen ligands bearing one or two silylated arms, and by one-pot synthesis of organic-inorganic hybrid materials. The bulk properties of the two kinds of materials were comparable. Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy and Raman spectroscopy were used to investigate the local environment, namely, the number of OH groups and distribution of SiO(4) units (large and small ring units). Hydrophilicity correlates with both the type of organic moiety used (mono- or disilylated), as well as with the synthetic procedure. The same vibrational studies showed how the structure in the channels changes as a function of pressure, reflecting the low mechanical stability of the mesoporous materials.     

Health-Promoting Properties of Medicinal Mushrooms and Their Bioactive Compounds for the COVID-19 Era—An Appraisal: Do the Pro-Health Claims Measure Up?

Many mushroom species are consumed as food, while significant numbers are also utilised medicinally. Mushrooms are rich in nutrients and bioactive compounds. A growing body of in vitro, in vivo, and human research has revealed their therapeutic potentials, which include such properties as anti-pathogenic, antioxidant, anti-inflammatory, immunomodulatory, gut microbiota enhancement, and angiotensin-converting enzyme 2 specificity. The uses of medicinal mushrooms (MMs) as extracts in nutraceuticals and other functional food and health products are burgeoning. COVID-19 presents an opportunity to consider how, and if, specific MM compounds might be utilised therapeutically to mitigate associated risk factors, reduce disease severity, and support recovery. As vaccines become a mainstay, MMs may have the potential as an adjunct therapy to enhance immunity. In the context of COVID-19, this review explores current research about MMs to identify the key properties claimed to confer health benefits. Considered also are barriers or limitations that may impact general recommendations on MMs as therapy. It is contended that the extraction method used to isolate bioactive compounds must be a primary consideration for efficacious targeting of physiological endpoints. Mushrooms commonly available for culinary use and obtainable as a dietary supplement for medicinal purposes are included in this review. Specific properties related to these mushrooms have been considered due to their potential protective and mediating effects on human exposure to the SARS CoV-2 virus and the ensuing COVID-19 disease processes.     

Oligomers of β2- and of β3-Homoproline: What are the Secondary Structures of β-Peptides Lacking H-Bonds?

To study the role of H-bonds in stabilizing β-peptidic secondary structures, we have synthesized β-oligopeptides (up to the octadecamer 12 ) consisting of β²- and β³-homoproline, i.e., β-peptides lacking amide protons. The enantiomer purity of the building block β²-homoproline (nipecotic acid, 4 ) was determined by HPLC analysis of the N-(2,4-dinitrophenyl) derivative 5 on a Chiralcel-OD column (cf. Fig. 2). The CD spectra of the all-(S)-β²- and all-(S)-β³-HPro-containing β-peptides display novel and intensive CD patterns which may be indicative of a secondary structure (cf. Fig. 3). It is noteworthy that a distinct CD pattern was observed with the β³-HPro derivatives containing as few as three residues ( 7a ). The crystal structure of a N-deprotected β³-HPro-tripeptide 7c is presented (cf. Figs. 4 and 5), and a model for the structure of β-peptides consisting of β³-HPro is discussed (cf. Figs. 6 and 7).     

Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry?

Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high‐performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).     

Can Anisotropic Exchange Be Reliably Calculated Using Density Functional Methods? A Case Study on Trinuclear MnIII‐MIII‐MnIII (M=Fe,Ru, and Os) Cyanometalate Single‐Molecule Magnets

Density functional studies have been performed on a set of trinuclear single‐molecule magnets (SMMs) of general formula [{Mn₂(5‐Br salen)₂(MeOH)₂}M(CN)₆](NEt₄) (M=Fe^III ( 1 ), Ru^III ( 2 ) and Os^III ( 3 ); 5‐Brsalen=N,N′‐ethylenebis(5‐bromosalicylidene)iminato anion). We have computed the orbital‐dependent exchange interaction for all three complexes for the first time using DFT and complete active space self‐consistent field (CASSCF) methods. DFT calculations yield the anisotropic exchange as J_ξξ=3.5 cm^?1 for 1 ; J_ξξ=12.1 cm^?1, J_ζζ=?6.9 cm^?1 and J_ηη=?14 cm^?1 for 2 ; and J_ξξ=23.7 cm^?1 and J_ζζ=?11.1 cm^?1 for 3 . The computed values are in agreement with the experimental report, and this suggests that the established methodology can be used to compute the anisotropic exchange in larger clusters. Our calculations reiterate the fact that the exchange is described by a three‐axis anisotropic exchange for complexes 2 and 3 as evidenced by the experiments. A stronger exchange coupling as we move down the periodic table from 3d to 5d is reproduced by our calculations, and the origin of this enhancement in the exchange interaction has been probed by using molecular orbital analysis. The electronic origin of different types of exchange observed in this series is found to be related to the energy difference between possible degenerate pairs and the nature of orbital interactions. By computing the exchange interaction, the single‐ion anisotropy of Mn^III and zero‐field splitting of the S=9/2 ground state of complexes 1 – 3 using CASSCF and/or DFT methods, we have attempted to shed light on the issue of anisotropic exchange and the barrier height for the magnetisation reversal in SMMs. Comprehensive magneto–structural correlations have been developed to offer clues on how to further enhance the barrier height in this class of SMMs.