The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

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{[CuSn5Sb3]2−}2: A Dimer of Inhomogeneous Superatoms

Reaction of the binary Zintl anion (Sn₂Sb₂)^2? with the β‐diketiminato complex [LCu(NCMe)] (L=nacnac=[(N(C₆H₃ⁱPr₂‐2,6)C(Me))₂CH]^?) in ethylenediamine or DMF affords the ternary cluster dimer {[CuSn₅Sb₃]^2?}₂ ( 1 ) as its [K(crypt‐222)]⁺ salt. The chemical formulation of 1 is supported by energy‐dispersive X‐ray spectroscopy (EDX) and quantum chemical calculations. Each monomeric part of the dimer represents a trimetallic “[CuSn₅Sb₃]^2?” cluster, with an architecture in between a tricapped trigonal prism and a capped square antiprism. As shown by quantum chemical investigations, the presence of Sb atoms and, in particular, of Cu atoms in the cluster skeleton makes the monomeric unit behave like an inhomogeneous superatom, which clearly prefers to dimerize, thereby producing a relatively short, yet virtually non‐bonding Cu???Cu distance.     

Exploring Regioselective Bond Cleavage and Cross‐Coupling Reactions using a Low‐Valent Nickel Complex

Recently, esters have received much attention as transmetalation partners for cross‐coupling reactions. Herein, we report a systematic study of the reactivity of a series of esters and thioesters with [{(dtbpe)Ni}₂(μ‐η²:η²‐C₆H₆)] (dtbpe=1,2‐bis(di‐tert‐butyl)phosphinoethane), which is a source of (dtbpe)nickel(0). Trifluoromethylthioesters were found to form η²‐carbonyl complexes. In contrast, acetylthioesters underwent rapid C_acyl?S bond cleavage followed by decarbonylation to generate methylnickel complexes. This decarbonylation could be pushed backwards by the addition of CO, allowing for regeneration of the thioester. Most of the thioester complexes were found to undergo stoichiometric cross‐coupling with phenylboronic acid to yield sulfides. While ethyl trifluoroacetate was also found to form an η²‐carbonyl complex, phenyl esters were found to predominantly undergo C_aryl?O bond cleavage to yield arylnickel complexes. These could also undergo transmetalation to yield biaryls. Attempts to render the reactions catalytic were hindered by ligand scrambling to yield nickel bis(acetate) complexes, the formation of which was supported by independent syntheses. Finally, 2‐naphthyl acetate was also found to undergo clean C_aryl?O bond cleavage, and although stoichiometric cross‐coupling with phenylboronic acid proceeded with good yield, catalytic turnover has so far proven elusive.     

Three‐Dimensional Metal–Fullerene Frameworks

Hexakis‐substituted [60]fullerene adducts with icosahedral symmetry provide an unprecedented scaffold for the spatial arrangement of twelve functional groups with high geometric precision. This unique molecular symmetry identifies such polyfunctional organic building blocks as potential highly connective linkers for coordination polymer and metal–organic framework synthesis. Hereby, the linker exhibits a higher connectivity than the metal ions and with the main connectivity based on the ligand, this can create a new type of inversely cross‐linked framework. Two hexakis adducts bearing either twelve glycolic acid or 3‐hydroxypropionic acid side chains attached to its malonate units were incorporated as organic connectivity centers in the first fullerene‐containing three‐dimensional frameworks by coordination with Zn²⁺.     

Microstructure and electrical properties of BaTiO<Subscript>3</Subscript> and (Ba,Sr)TiO<Subscript>3</Subscript> ferroelectric thin films on nickel electrodes

Nickel thin films have been sputtered on standard Si/SiO₂ substrates with TiO₂ as an adhesive layer. The thermal stability of these substrates was analyzed. SEM images show an increase in grain size with annealing temperature. They were found to be stable till 800°C, beyond which the nickel layer disintegrated. These substrates were used for deposition of BaTiO₃ and (Ba,Sr)TiO₃ dielectric thin films under a reducing atmosphere. The dielectric thin films were processed with various pyrolysis and annealing temperatures in order to optimize the dielectric properties. Increased pyrolysis temperatures showed an increase in the grain size. Results on these nickelised substrates were finally compared with dielectric films deposited on platinized silicon substrates under identical conditions but crystallized in an oxygen atmosphere.     

A practical synthesis of kifunensine analogues as inhibitors of endoplasmic reticulum alpha-mannosidase I

[reaction: see text] A practical synthesis of the potent class I alpha-mannosidase inhibitor kifunensine (1) beginning from the inexpensive and readily available starting material L-ascorbic acid (15) is described. The protected amino-alcohol ((2R,3R,4R,5R)-5-amino-2,3:4,6-diisopropylidenedioxyhexanol, 11) served as a key intermediate from which several N-1 substituted kifunensine analogues (including N-methyl, N-cyclohexyl, and N-bis(hydroxymethyl)methyl) and 2-desoxakifunensine analogues (including N-H and N-methyl) were prepared and screened for inhibition of human endoplasmic reticulum alpha-mannosidase I (ER Man I) and mouse Golgi alpha-mannosidase IA (Golgi Man IA). In addition, several pseudodisaccharide kifunensine analogues in which a mannose residue was tethered to N-1 of kifunensine via a two-, three-, or four-carbon linker and an affinity-bound kifunensine analogue were also prepared and evaluated for biological activity. While the synthesized N-1 kifunesine analogues were found to be less potent inhibitors of Class I alpha-mannosidases than kifuensine itself, the bis(hydroxymethyl)methylkifunensine analogue 6 was shown to selectively inhibit ER Man I over Golgi Man IA.     

Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics

The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction.