Quinary Structure Research Articles

Evolution of Oxygen Vacancy Sites in Ceria-Based High-Entropy Oxides and Their Role in N2 Activation.

In this work, a relatively new class of materials, rare earth (RE) based high entropy oxides (HEO) are discussed in terms of the evolution of the oxygen vacant sites (Ov) content in their structure as the composition changes from binary to HEO using both experimental and computational tools; the composition of HEO under focus is the CeLaPrSmGdO due to the importance of ceria-related (fluorite) materials to catalysis. To unveil key features of quinary HEO structure, ceria-based binary CePrO and CeLaO compositions as well as SiO2, the latter as representative nonreducible oxide, were used and compared as supports for Ru (6 wt % loading). The role of the Ov in the HEO is highlighted for the ammonia production with particular emphasis on the N2 dissociation step (N2(ads) → Nads) over a HEO; the latter step is considered the rate controlling one in the ammonia production. Density functional theory (DFT) calculations and 18O2 transient isotopic experiments were used to probe the energy of formation, the population, and the easiness of formation for the Ov at 650 and 800 °C, whereas Synchrotron EXAFS, Raman, EPR, and XPS probed the Ce-O chemical environment at different length scales. In particular, it was found that the particular HEO composition eases the Ov formation in bulk, in medium (Raman), and in short (localized) order (EPR); more Ov population was found on the surface of the HEO compared to the binary reference oxide (CePrO). Additionally, HEO gives rise to smaller and less sharp faceted Ru particles, yet in stronger interaction with the HEO support and abundance of Ru-O-Ce entities (Raman and XPS). Ammonia production reaction at 400 °C and in the 10-50 bar range was performed over Ru/HEO, Ru/CePrO, Ru/CeLaO, and Ru/SiO2 catalysts; the Ru/HEO had superior performance at 10 bar compared to the rest of catalysts. The best performing Ru/HEO catalyst was activated under different temperatures (650 vs 800 °C) so to adjust the Ov population with the lower temperature maintaining better performance for the catalyst. DFT calculations showed that the HEO active site for N adsorption involves the Ov site adjacent to the adsorption event.

Exploring the dynamics and structure of PpiB in living Escherichiacoli cells using electron paramagnetic resonance spectroscopy.

The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.

In-Cell Association of a Bioorthogonal Tubulin.

Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.

Chaperone-protein interactions in live zebrafish larvae.

Functional protein-protein interaction, in particular transient “quinary structure,” is sensitive to small changes in the local environment, occurring in the form of pH, crowding, electrostatic and other interactions with neighboring molecules. One reason for this sensitivity is reflected in their energy landscape, characterized by a shallow local minima in the neighborhood of the functional configurations. This motivates our study of a functional protein-protein interaction in its native environment - different cell types in a living organism. We study the binding of the metabolic enzyme phosphoglycerate kinase (PGK) to the chaperone Hsp70 of which it is a client, to quantify binding in individual cells of larval zebrafish. Using a customized temperature-control setup, we subject the organism expressing fluorescently labelled PGK and Hsp70 in selected cell types to a range of temperatures to induce a controlled heat shock. Using fluorescence resonance energy transfer (FRET), we detect the Hsp70 chaperone response via an increase in the affinity between the two proteins near the melting point of PGK

X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure.

Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.

Protein folding and surface interaction phase diagrams in vitro and in cells.

Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, interact, and function on the scale from a few molecules to macroscopic ensembles. This review discusses three aspects of protein phase diagrams: first, the relevance of phase diagrams to protein folding and function in vitro and in cells; next, how the evolution of protein surfaces impacts on interaction phase diagrams; and finally, how phase separation plays a role on much larger length-scales than individual proteins or oligomers, when liquid phase-separated regions form to assist protein function and cell homeostasis.

TE Transmittance properties of one-dimensional symmetric quinary photonic crystals

In this work, a symmetric one dimensional quinary photonic crystal structure is proposed. The unit cell of the proposed structure is composed of materials chosen in such a way that the refractive index of the central layer is the highest among the two neighbouring layers from both sides. Basically, the transmittance of the S-polarized transverse electric () mode is obtained numerically using the transfer matrix method. The effect of several parameters such as the number of periods, the layer thickness and the angle of incidence of radiation on transmittance of the structure is investigated. The effect of changing thickness and refractive index of the central layer on the transmittance is found to play the major rule in tuning the photonic bandgap. The proposed structure is expected to be a good candidate for applications such as antireflection coatings used in solar cells, wide-angle reflectors and pressure or temperature sensors.

Intact ribosomes drive the formation of protein quinary structure.

Transient, site-specific, or so-called quinary, interactions are omnipresent in live cells and modulate protein stability and activity. Quinary intreactions are readily detected by in-cell NMR spectroscopy as severe broadening of the NMR signals. Intact ribosome particles were shown to be necessary for the interactions that give rise to the NMR protein signal broadening observed in cell lysates and sufficient to mimic quinary interactions present in the crowded cytosol. Recovery of target protein NMR spectra that were broadened in lysates, in vitro and in the presence of purified ribosomes was achieved by RNase A digestion only after the structure of the ribosome was destabilized by removing magnesium ions from the system. Identifying intact ribosomal particles as the major protein-binding component of quinary interactions and consequent spectral peak broadening will facilitate quantitative characterization of macromolecular crowding effects in live cells and streamline models of metabolic activity.

Quinary Structure Modulates Consensus Protein Sequence Stability in Cells

Relying on evolutionary history within thousands of homologous sequences to map important residues, consensus sequence design has emerged as an effective approach for designing biologically functional proteins with high stability. Intriguingly, sequence differences between consensus and extant homologs are predominantly located at weakly conserved surface residues. Surface mutations can have large effects on protein quinary structure, interactions that organize protein interactions inside cells, which are largely dependent on surface charges.

Using fluorescence lifetime dequenching to estimate the average quinary stoichiometry of proteins in living cells

Biological proteins are understood in terms of five structural levels–primary, secondary, tertiary, quaternary and quinary. The quinary structure is defined as the set of macromolecular interactions that are transient in vivo. This includes non-covalent protein-protein interactions occurring within the crowded intracellular environment. For much of twentieth century science, the canonical approach to studying biological proteins involved test tube environments. These uncrowded in vitro studies inadvertently failed to replicate and observe the quinary structures present within the original cells. Consequently, contemporary literature surrounding the fifth level of protein organisation is lacking. In particular, there is a lack of literature on the size of transient clusters within living cells. In an attempt to reconcile this gap in knowledge, we propose a quantitative method for estimating the average quinary stoichiometry in living cells. The method is based on lifetime self-quenching of fluorescently-labelled proteins in living cells. Close approach of two or more proteins in a quinary complex will result in self-quenching of the fluorescence lifetime from the fluorescent labels. Our method utilises the random mixing of proteins during cell division to mix fluorescently labelled with unlabelled proteins. Such mixing reduces the probability of adjacency between labelled proteins and, hence, decreases the probability of fluorescence lifetime quenching from labels. By monitoring fluorescence lifetime dequenching during multiple cell divisions, we can determine the average quinary structure in living proliferating cells. We demonstrate this method with a case study on cultured HeLa cells. The average quinary stoichiometry was found to be between five and six. That is, at any given point in time, there are five or six weakly interacting partners in the immediate neighbourhood of any given protein.

In-Cell Protein–Protein Contacts: Transient Interactions in the Crowd

Proteins in vivo are immersed in a crowded environment of water, ions, metabolites, and macromolecules. In-cell experiments highlight how transient weak protein-protein interactions promote (via functional "quinary structure") or hinder (via competitive binding or "sticking") complex formation. Computational models of the cytoplasm are expensive. We tackle this challenge with an all-atom model of a small volume of the E. coli cytoplasm to simulate protein-protein contacts up to the 5 μs time scale on the special-purpose supercomputer Anton 2. We use three CHARMM-derived force fields: C22*, C36m, and C36mCU (with CUFIX corrections). We find that both C36m and C36mCU form smaller contact surfaces than C22*. Although CUFIX was developed to reduce protein-protein sticking, larger contacts are observed with C36mCU than C36m. We show that the lifespan Δt of protein-protein contacts obeys a power law distribution between 0.03 and 3 μs, with ∼90% of all contacts lasting <1 μs (similar to the time scale for downhill folding).

Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function

In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.

Quo Vadis Biomolecular NMR Spectroscopy?

In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.

The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity.

The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled target proteins and RNA broaden in-cell NMR spectra yielding apparent megadalton molecular weights in-cell. The in-cell spectra can be resolved by using cross relaxation-induced polarization transfer (CRINEPT), heteronuclear multiple quantum coherence (HMQC), transverse relaxation-optimized, NMR spectroscopy (TROSY). The effect is reproduced in vitro by using reconstituted total cellular RNA and purified ribosome preparations. Furthermore, ribosomal binding antibiotics alter protein quinary structure through protein-ribosome and protein-mRNA-ribosome interactions. The quinary interactions of Adenylate kinase, Thymidylate synthase and Dihydrofolate reductase alter kinetic properties of the enzymes. The results demonstrate that ribosomes may specifically contribute to the regulation of biological activity.

Harnessing Bottom‐Up Self‐Assembly To Position Five Distinct Components in an Ordered Porous Framework

AbstractPositioning a diverse set of building blocks in a well‐defined array enables cooperativity amongst them and the systematic programming of functional properties. The extension of this concept to porous metal–organic frameworks (MOFs) is challenging since the installation of multiple components in a well‐ordered framework requires careful design of the lattice topology, judicious selection of building blocks, and precise control of the crystallization parameters. Herein, we report how we met these challenges to prepare the first quinary MOF structure, FDM‐8, by bottom‐up self‐assembly from two metals, ZnII and CuI, and three distinct carboxylate‐ and pyrazolate‐based linkers. With a surface area of 3643 m2 g−1, FDM‐8 contains hierarchical pores and shows outstanding methane‐storage capacity at high pressure. Furthermore, functional groups introduced on the linkers became compartmentalized in predetermined arrays in the pores of the FDM‐8 framework.

Harnessing Bottom-Up Self-Assembly To Position Five Distinct Components in an Ordered Porous Framework.

Positioning a diverse set of building blocks in a well-defined array enables cooperativity amongst them and the systematic programming of functional properties. The extension of this concept to porous metal-organic frameworks (MOFs) is challenging since the installation of multiple components in a well-ordered framework requires careful design of the lattice topology, judicious selection of building blocks, and precise control of the crystallization parameters. Herein, we report how we met these challenges to prepare the first quinary MOF structure, FDM-8, by bottom-up self-assembly from two metals, ZnII and CuI , and three distinct carboxylate- and pyrazolate-based linkers. With a surface area of 3643 m2 g-1 , FDM-8 contains hierarchical pores and shows outstanding methane-storage capacity at high pressure. Furthermore, functional groups introduced on the linkers became compartmentalized in predetermined arrays in the pores of the FDM-8 framework.

Cluster Size and Quinary Structure Determine the Rheological Effects of Antibody Self-Association at High Concentrations.

The question of how nonspecific reversible intermolecular protein interactions affect solution rheology at high concentrations is fundamentally rooted in the translation of nanometer-scale interactions into macroscopic properties. Well-defined solutions of purified monoclonal antibodies (mAbs) provide a useful system with which to investigate the manifold intricacies of weak protein interactions at high concentrations. Recently, characterization of self-associating IgG1 antibody (mAb2) solutions has established the direct role of protein clusters on concentrated mAb rheology. Expanding on our earlier work with three additional mAbs (mAb1, mAb3, and mAb4), the observed concentration-dependent static light scattering and rheological data present a substantially more complex relationship between protein interactions and solution viscosity at high concentrations. The four mAb systems exhibited divergent correlations between cluster formation (size) and concentrated solution viscosities dependent on mAb primary sequence and solution conditions. To address this challenge, well-established features of colloidal cluster phenomena could be applied as a framework for interpreting our observations. The initial stages of mAb cluster formation were investigated with small-angle X-ray scattering (SAXS) and ensemble-optimized fit methods, to uncover shifts in the dimer structure populations which are produced by changes in mAb interaction modes and association valence under the different solution conditions. Analysis of mAb average cluster number and effective hydrodynamic radii at high concentrations revealed cluster architectures can have a wide range of fractal dimensions. Collectively, the static light scattering, SAXS, and rheological characterization demonstrate that nonspecific and anisotropic attractive intermolecular interactions produce antibody clusters with different quinary structures to regulate the rheological properties of concentrated mAb solutions.

Real-Time In-Cell Nuclear Magnetic Resonance: Ribosome-Targeted Antibiotics Modulate Quinary Protein Interactions.

How ribosome antibiotics affect a wide range of biochemical pathways is not well understood; changes in RNA-mediated protein quinary interactions and consequent activity inside the crowded cytosol may provide one possible mechanism. We developed real-time (RT) in-cell nuclear magnetic resonance (NMR) spectroscopy to monitor temporal changes in protein quinary structure, for ≥24 h, in response to external and internal stimuli. RT in-cell NMR consists of a bioreactor containing gel-encapsulated cells inside a 5 mm NMR tube, a gravity siphon for continuous exchange of medium, and a horizontal drip irrigation system to supply nutrients to the cells during the experiment. We showed that adding antibiotics that bind to the small ribosomal subunit results in more extensive quinary interactions between thioredoxin and mRNA. The results substantiate the idea that RNA-mediated modulation of quinary protein interactions may provide the physical basis for ribosome inhibition and other regulatory pathways.

Some geometrical aspects of binary, ternary, quaternary, quinary and senary structures in physics

It is observed that quinary and senary structures like in pentacene and several other polymers may be composed from binary and ternary structures in the sense of differentialequational and geometrical description. In the case of pentacene its leaves are attached to the silicon background and have the form of five connected carbon-hydrogen hexagons; in total they do not form the precisely planar structure but a slightly wavy structure which minimizes total energy. In the case of a quinary structure the leaves form solitary, nearly periodical zigzags and meanders.

Quantitative Determination of Interacting Protein Surfaces in Prokaryotes and Eukaryotes by Using In-Cell NMR Spectroscopy.

This paper describes three protocols for identifying interacting surfaces on 15N-labeled target proteins of known structure by using in-cell NMR spectroscopy. The first protocol describes how to identify protein quinary structure interaction surfaces in prokaryotes by using cross-relaxation-induced polarization transfer, CRIPT, based in-cell NMR. The second protocol describes how to introduce labeled protein into eukaryotic (HeLa) cells via electroporation for CRIPT-based in-cell studies. The third protocol describes how to quantitatively map protein interacting surfaces by utilizing singular value decomposition, SVD, analysis of STructural INTeractions by in-cell NMR, STINT-NMR, data.