Family B heterotrimeric guanine nucleotide–binding protein (G protein)–coupled receptors (GPCRs) play important roles in carbohydrate metabolism. Recent structures of family B GPCR-Gs protein complexes reveal a disruption in the α-helix of transmembrane segment 6 (TM6) not observed in family A GPCRs. To investigate the functional impact of this structural difference, we compared the structure and function of the glucagon receptor (GCGR; family B) with the β2 adrenergic receptor (β2AR; family A). We determined the structure of the GCGR-Gs complex by means of cryo–electron microscopy at 3.1-angstrom resolution. This structure shows the distinct break in TM6. Guanosine triphosphate (GTP) turnover, guanosine diphosphate release, GTP binding, and G protein dissociation studies revealed much slower rates for G protein activation by the GCGR compared with the β2AR. Fluorescence and double electron-electron resonance studies suggest that this difference is due to the inability of agonist alone to induce a detectable outward movement of the cytoplasmic end of TM6.

No abstract

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements.

An optimized reverse micelle surfactant system has been developed for solution nuclear magnetic resonance studies of encapsulated proteins and nucleic acids dissolved in low viscosity fluids. Comprised of the nonionic 1-decanoyl-rac-glycerol and the zwitterionic lauryldimethylamine-N-oxide (10MAG/LDAO), this mixture is shown to efficiently encapsulate a diverse set of proteins and nucleic acids. Chemical shift analyses of these systems show that high structural fidelity is achieved upon encapsulation. The 10MAG/LDAO surfactant system reduces the molecular reorientation time for encapsulated macromolecules larger than ~20 kDa leading to improved overall NMR performance. The 10MAG/LDAO system can also be used for solution NMR studies of lipid-modified proteins. New and efficient strategies for optimization of encapsulation conditions are described. 10MAG/LDAO performs well in both the low viscosity pentane and ultra-low viscosity liquid ethane and therefore will serve as a general surfactant system for initiating solution NMR studies of proteins and nucleic acids.

In the search for rationally assembled functional materials, superatomic crystals (SACs) have recently emerged as a unique class of compounds that combine programmable nanoscale building blocks and atomic precision. As such, they bridge traditional semiconductors, molecular solids, and nanocrystal arrays by combining their most attractive features. Here, we report the first study of thermal transport in SACs, a critical step towards their deployment as electronic, thermoelectric, and phononic materials. Using frequency domain thermoreflectance (FDTR), we measure thermal conductivity in two series of SACs: the unary compounds CoE(PEt) (E = S, Se, Te) and the binary compounds [CoE(PEt)][C]. We find that phonons that emerge from the periodicity of the superstructures contribute to thermal transport. We also demonstrate a transformation from amorphous to crystalline thermal transport behaviour through manipulation of the vibrational landscape and orientational order of the superatoms. The structural control of orientational order enabled by the atomic precision of SACs expands the conceptual design space for thermal science.

The controlled introduction of impurities into the crystal lattice of solid-state compounds is a cornerstone of materials science. Intercalation, the insertion of guest atoms, ions or molecules between the atomic layers of a host structure, can produce novel electronic, magnetic and optical properties in many materials. Here we describe an intercalation compound in which the host [CoTe(PPr)][C], formed from the binary assembly of atomically precise molecular clusters, is a superatomic analogue of traditional layered atomic compounds. We find that tetracyanoethylene (TCNE) can be inserted into the superstructure through a single-crystal-to-single-crystal transformation. Using electronic absorption spectroscopy, electrical transport measurements and electronic structure calculations, we demonstrate that the intercalation is driven by the exchange of charge between the host [CoTe(PPr)][C] and the intercalant TCNE. These results show that intercalation is a powerful approach to manipulate the material properties of superatomic crystals.

No abstract

Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O 2 ) values of amide NAH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O 2 values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R 2 of 0.8.