Dissociation of Multisubunit Protein–Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB₅) with the pentasaccharide (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1)) and corresponding glycosphingolipid (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S₄) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB₅ + 5GM1)ⁿ⁺ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB₅ + 5GM1)^n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S₄ + 4B)^n+/– ions, as well as for deprotonated (S₄ + 4Btl)^n– ions, was loss of the ligand. However, subunit loss from the (S₄ + 4B)ⁿ⁺ ions was observed as a minor pathway. The (S₄ + 4Btl)ⁿ⁺ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB₅ + 5GM1)¹⁵⁺ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein–ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.

Cross‐Linking/Mass Spectrometry for Studying Protein Structures and Protein–Protein Interactions: Where Are We Now and Where Should We Go from Here?

Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable three‐dimensional structural information on proteins and protein complexes, and it complements existing techniques, such as NMR spectroscopy and X‐ray crystallography. Structural MS unites different MS‐based techniques, such as hydrogen/deuterium exchange, native MS, ion‐mobility MS, protein footprinting, and chemical cross‐linking/MS, and it allows fundamental questions in structural biology to be addressed. In this Minireview, I will focus on the cross‐linking/MS strategy. This method not only delivers tertiary structural information on proteins, but is also increasingly being used to decipher protein interaction networks, both in vitro and in vivo. Cross‐linking/MS is currently one of the most promising MS‐based approaches to derive structural information on very large and transient protein assemblies and intrinsically disordered proteins.     

Ligand Design for Site-Selective Metal Coordination: Synthesis of Transition-Metal Complexes with η6-Coordination of the Central Ring of Anthracene

A polycyclic aromatic ligand for site-selective metal coordination was designed by using DFT calculations. The computational prediction was confirmed by experiments: 2,3,6,7-tetramethoxy-9,10-dimethylanthracene initially reacts with [(C₅H₅)Ru(MeCN)₃]BF₄ to give the kinetic product with a [(C₅H₅)Ru]⁺ fragment coordinated at the terminal ring, which is then transformed into the thermodynamic product with coordination through the central ring. These isomeric complexes have markedly different UV/Vis spectra, which was explained by analysis of the frontier orbitals. At the same time, the calculations suggest that electrostatic interactions are mainly responsible for the site selectivity of the coordination.     

Small‐Molecule Stabilization of Protein–Protein Interactions: An Underestimated Concept in Drug Discovery?

The modulation of protein-protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI-stabilizing natural products have already found application as important drugs. Moreover, directed small-molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs.     

On the Quantitative Click Conjugation of Molecular Weight Distributions: What Can Theoretically Be Expected?

The assessment of the success of a click conjugation for block copolymer formation often occurs via ill‐defined criteria based on the qualitative shape of the size exclusion chromatography (SEC) distribution as well as unsuitable characteristics of these molecular weight distribution such as the peak molecular weight, M_p. The data presented herein illustrate that from the shape of the SEC distribution, w(log M) versus log M, of the click product—under the assumption of a 100% efficient conjugation reaction—a conclusion about the effectiveness of the click conjugation cannot be derived. It is demonstrated that under certain conditions multi‐modal molecular weight distributions are obtained from two well‐defined monomodal initial distributions. Similarly, the comparison of peak maxima between the conjugate and the initial SEC distributions is a poorly defined criterion to assess the success of a conjugation. The only reliable assessment for the success of the click coupling reaction is the true number average molecular weight, , of the SEC distribution of the click product, as well as a plot of the concentration or number distributions, c versus M, of the precursors and product polymer.

     

Labile Interactions and Inert Entities in Supramolecular Chemistry—the Identification of Recognition Mechanisms for Macrobicyclic Amine Complexes

Consideration of crystallographic data concerning metal complexes of hexa-azabicyclo[6.6.6]icosane, “sarcophagine”, and various derivatives provides evidence for the importance of hydrogen-bonding, labile metal ion coordination, aliphatic- and aromatic-group interactions in determining the lattice structures. These “cage amine” complexes not only involve different metal ions, almost all rendered kinetically inert towards substitution by their complexation, but they can be obtained in conformationally locked forms and with a wide variety of substituents, so that they have considerable potential as supramolecular tectons.     

The GABAergic System and Endocannabinoids in Epilepsy and Seizures: What Can We Expect from Plant Oils?

Seizures and epilepsy are some of the most common serious neurological disorders, with approximately 80% of patients living in developing/underdeveloped countries. However, about one in three patients do not respond to currently available pharmacological treatments, indicating the need for research into new anticonvulsant drugs (ACDs). The GABAergic system is the main inhibitory system of the brain and has a central role in seizures and the screening of new ACD candidates. It has been demonstrated that the action of agents on endocannabinoid receptors modulates the balance between excitatory and inhibitory neurotransmitters; however, studies on the anticonvulsant properties of endocannabinoids from plant oils are relatively scarce. The Amazon region is an important source of plant oils that can be used for the synthesis of new fatty acid amides, which are compounds analogous to endocannabinoids. The synthesis of such compounds represents an important approach for the development of new anticonvulsant therapies.     

Nickelatetrazoles as Intermediates in the Course of the Photolysis of Nickel(II) Azido Complexes? – A Theoretical Study

The primary photoreactions due to charge transfer excitation of d⁸ transition metal complexes of [MP₂(N₃)₂] constitution (P₂: mono‐ or diphosphane ligands) are strongly influenced by the central ion. While [MP₂(N₃)₂] complexes of both palladium(II) and platinum(II) yield primarily the corresponding metal(I) species and azidyl radicals, nickel(II) complexes of the same constitution lead to intermediate generation of nitrenes as has been indirectly shown by various scavenging reactions. During the course of the succeeding reactions, the intermediate generation of nickelatetrazoles is assumed. Both nitrene and metallatetrazole intermediates could not be identified directly so far. Therefore, the proposed reaction pathway has been modeled theoretically to get indications regarding the probability of the formation of such intermediates. Based on density functional theory (DFT) calculations, the energetics of the proposed pathway is compared with those of possible other pathways. The calculations support the proposed reaction pathway and point to possible reasons for the different behaviour of nickel(II) compared to palladium(II) and platinum(II).     

New evidence from stable isotope for the uplift of mountains in northern edge of the Qinghai-Tibetan Plateau

New data of oxygen and carbonate isotope in calcite cements from Cenozoic rocks inthe Jianggelesayi area to reconstruct the uplift history of mountains in northern edge of the Qing-hai-Tibetan Plateau are presented. Analyses results show that rapid changes of δ~(18)O and δ~(13)C inthe calcite cement occurred in both the Early Oligocene and Early Miocene. Studies on sedimen-tary features indicate that a rapid up-coarsing of the sediments size occurred in the Early Miocene,and sedimentary velocity increased rapidly during the Pliocene and Early Quaternary. Thus, it issuggested that the uplift of mountains in the northern edge of the Qinghai-Tibetan Plateau initiatedfrom the Early Oligocene, and a rapid uplift occurred in the early stage of the Miocene, while thesharp difference in topography between the northern plateau and the Tarim Basin predominatelyformed later than the Miocene.     

Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems

Herein, various molecular balances used for comparing the strengths of intramolecular noncovalent interactions are reviewed. Our overview indicates that considerable quantitative insight into the strength of noncovalent interactions can be gained through the careful design of molecular balances. Many exciting opportunities certainly exist for the design of further new balances to quantify and dissect the relative strengths of noncovalent interactions as a function of solvation and the importance of the many factors that contribute to overall molecular recognition. However, even simple model molecules can show a multiplicity of intramolecular noncovalent interactions acting in a combined fashion. It is therefore essential to undertake a detailed computational analysis to identify all possible noncovalent interactions present in a selected molecular balance prior to a quantitative experimental assessment of the strength of a particular noncovalent interaction. It is also argued that the words “torsion” and “molecular balance” seem to have become inextricably linked and, in consequence, even top pan and seesaw balances have been mistakenly referred to in these terms.     

Can the progress in quality management tools for POC tame the fiends from Pandora's box?

POCT provides the opportunity to significantly improve the overall quality of blood testing in an organization. The design of the product, the redesign of the testing process and the tools used to manage a completely distributed testing process, are key to the quality implementation of POCT. Both theoretical considerations and practical outcomes are discussed in this paper, using the i-STAT^® System as an example of a POCT system.     

What are the spectroscopic properties of HFC‐32? Answers from DFT

Although coupled cluster theory coupled to large basis sets can reach impressive accuracies for thermochemical and spectroscopic properties, it is still limited to small/medium sized molecules. Density functional theory (DFT) represents the working option for systems composed of hundreds to thousands heavy atoms. In this context, investigations are required aimed at characterizing the performances of the different density functionals (DF). This work focuses on the study of DFT performances in the prediction of spectroscopic properties, with particular attention to the vibrational problem, by focusing on the CH₂F₂ molecule as a test case. An extensive and systematic investigation is performed on several DFT model chemistries by testing their predictions of molecular constants and vibrational frequencies and intensities against CCSD(T)/aug‐cc‐pCVQZ data. B3LYP, B3PW91, B97‐1, PBE0, TPSSh, M05, M05‐2X, and B2PLYP DFs are used in conjunction with a variety of basis sets. Anharmonic frequencies are derived from the VPT2 treatment of anharmonic‐ and hybrid CCSD(T)/DFT‐force fields. A software for VPT2 computations is also presented. © 2014 Wiley Periodicals, Inc.