Small Globular Proteins Research Articles

Dynamic Protein Corona of Gold Nanoparticles with an Evolving Morphology.

Much has been learned about the protein coronae and their biological implications within the context of nanomedicine and nanotoxicology. However, no data is available about the protein coronae associated with nanoparticles undergoing spontaneous surface-energy minimization, a common phenomenon during the synthesis and shelf life of nanomaterials. Accordingly, here we employed gold nanoparticles (AuNPs) possessing the three initial states of spiky, midspiky, and spherical shapes and determined their acquisition of human plasma protein coronae with label-free mass spectrometry. The AuNPs collected coronal proteins that were different in abundance, physicochemical parameters, and interactive biological network. The size and structure of the coronal proteins matched the morphology of the AuNPs, where small globular proteins and large fibrillar proteins were enriched on spiky AuNPs, while large proteins were abundant on spherical AuNPs. Furthermore, the AuNPs induced endothelial leakiness to different degrees, which was partially negated by their protein coronae as revealed by confocal fluorescence microscopy, in vitro and ex vivo transwell assays, and signaling pathway assays. This study has filled a knowledge void concerning the dynamic protein corona of nanoparticles possessing an evolving morphology and shed light on their implication for future nanomedicine harnessing the paracellular pathway.

Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations.

Metallothionein (MT) is a small globular protein that binds to trace metals. However, it was still unclear how the existence of metal ions affects the structure of MT. Therefore, we performed all-atom molecular dynamics (MD) simulations under several surrounding conditions with or without Zn2+ ions. As a result of 10 μs MD simulation, MT without Zn2+ ions tended to adopt an extended β-hairpin structure, while MT with Zn2+ ions became a globular structure like the NMR structure. Furthermore, we also found that the capture of Zn2+ ions by the second and third cysteines played a crucial role in the formation of the native structure. The finding of the Zn2+ binding for the specific cysteines and the unknown β-hairpin structure will provide new insights into the structural mechanism of metal signaling.

An Interim Report on a Phase 1/2 Study of HPN217, a Half-Life Extended Tri-Specific T Cell Activating Construct (TriTAC ®) Targeting B Cell Maturation Antigen for the Treatment of Relapsed/Refractory Multiple Myeloma

An Interim Report on a Phase 1/2 Study of HPN217, a Half-Life Extended Tri-Specific T Cell Activating Construct (TriTAC ®) Targeting B Cell Maturation Antigen for the Treatment of Relapsed/Refractory Multiple Myeloma

Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel

After translation, nascent proteins must escape the ribosomal exit tunnel to attain complete folding to their native states. This escape process also frees up the ribosome tunnel for a new translation job. In this study, we investigate the impacts of energetic interactions between the ribosomal exit tunnel and nascent proteins on the protein escape process by molecular dynamics simulations using partially coarse-grained models that incorporate hydrophobic and electrostatic interactions of the ribosome tunnel of Haloarcula marismortui with nascent proteins. We find that, in general, attractive interactions slow down the protein escape process, whereas repulsive interactions speed it up. For the small globular proteins considered, the median escape time correlates with both the number of hydrophobic residues, Nh, and the net charge, Q, of a nascent protein. A correlation coefficient exceeding 0.96 is found for the relation between the median escape time and a combined quantity of Nh + 5.9Q, suggesting that it is ∼6 times more efficient to modulate the escape time by changing the total charge than the number of hydrophobic residues. The estimated median escape times are found in the submillisecond-to-millisecond range, indicating that the escape does not delay the ribosome recycling. For various types of the tunnel model, with and without hydrophobic and electrostatic interactions, the escape time distribution always follows a simple diffusion model that describes the escape process as a downhill drift of a Brownian particle, suggesting that nascent proteins escape along barrier-less pathways at the ribosome tunnel.

How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing.

Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.

Highly Efficient Trityl-Nitroxide Biradicals for Biomolecular High-Field Dynamic Nuclear Polarization.

Dynamic nuclear polarization (DNP) is a powerful method to enhance the sensitivity of solid-state magnetic nuclear resonance (ssNMR) spectroscopy. However, its biomolecular applications at high magnetic fields (preferably>14 T) have so far been limited by the intrinsically low efficiency of polarizing agents and sample preparation aspects. Herein, we report a new class of trityl-nitroxide biradicals, dubbed SNAPols that combine high DNP efficiency with greatly enhanced hydrophilicity. SNAPol-1, the best compound in the series, shows DNP enhancement factors at 18.8 T of more than 100 in small molecules and globular proteins and also exhibits strong DNP enhancements in membrane proteins and cellular preparations. By integrating optimal sensitivity and high resolution, we expect widespread applications of this new polarizing agent in high-field DNP/ssNMR spectroscopy, especially for complex biomolecules.

Relation between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Droplets.

Charged droplets have been associated with distinct chemical reactivity. It is assumed that the composition of the surface layer plays a critical role in enhancing the reaction rates in the droplets relative to their bulk solution counterparts. We use atomistic modeling to relate the localization of ions in the surface layer to their ejection propensity. We find that ion ejection takes place via a two-stage process. First, a conical protrusion emerges as a result of a global droplet deformation that is insensitive to the locations of the single ions. The ions are subsequently ejected as they enter the conical regions. The study provides mechanistic insight into the ion-evaporation mechanism, which can be used to revise the commonly used ion-evaporation models. We argue that atomistic molecular dynamics simulations of minute nanodrops do not sufficiently distinguish the ion-evaporation mechanism from a Rayleigh fission. We explain mass spectrometry data on the charge state of small globular proteins and the existence of supercharged droplet states that have been detected in experiments.

Stability of the Retinoid X Receptor-α Homodimer in the Presence and Absence of Rexinoid and Coactivator Peptide.

Differential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-α ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. The apo-RXRα LBD homodimer displayed a single thermal unfolding transition with a Tm of 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to the apo-homodimer increased Tm by 5 to 9 °C and increased the ΔG of the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. GRIP-1 binding to holo-homodimers containing rexinoid resulted in additional increases in ΔG of 14 kJ/mol, a value that was the same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. The complexes of UAB110 and UAB111 are each more stable than the UAB30 complex by 8 kJ/mol due to enhanced hydrophobic interactions in the binding pocket because of their larger end groups. This increase in thermodynamic stability positively correlates with their improved RXR activation potency. Thermodynamic measurements are thus valuable in predicting agonist potency.

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation.

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R1) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain 15N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.

Improving Reproducibility of Automatically Generated Markov Models from Molecular Dynamics Trajectories

Generating Markov models is a broadly used method to capture dominant processes in protein dynamics from molecular dynamics(MD) trajectories. In such models, dynamics are represented as a graph of transition rates (edges) between essential states (nodes) such that transitions are independent of previously visited states. Generating Markov models from MD trajectories is a challenging task: It not only requires a large amount of sampling but often special knowledge about the analyzed system to handpick suitable reaction coordinates. However, if many different systems need to be analyzed or suitable reaction coordinates are not at hand, an automated approach for Markov model generation is required. Against that background, here we asked to which extent the construction of Markov models from MD trajectories is reproducible, and -- related -- how much of the protein dynamics these models actually capture. We used standard protocols (e.g. tICA, k-Means clustering, maximum likelihood transition matrix estimation) and neural network approaches (e.g. VAMPnet) to analyze three independent 1μs MD trajectories of 200 small globular proteins, selected to cover known folds and functions, and compared the resulting timescales. Their reproducibility depends on the method used to generate Markov models. Neural network approaches yield better reproducibility compared to standard protocols. We identified the high dimensionality of configuration space as a major factor that limits reproducibility. To address the well-known curse of dimensionality, we use a minimally-coupled subspace approach (MCSA) that decomposes configuration space into lower-dimensional independent subspaces. In summary, our results demonstrate that the reproducibility of Markov models generated using currently available methods in an automated way can be improved significantly.

Computational Probing of Temperature-Dependent Unfolding of a Small Globular Protein: From Cold to Heat Denaturation

Fully atomistic replica exchange molecular dynamics simulations are performed to compute the stability curve of a small globular protein as accurately as possible. To investigate the individual roles of the protein and water parts, we compute the conformational entropy change of this protein directly from the simulation ensembles. This entropy calculation enables complete separations of the unfolding changes of enthalpy and the entropy into their own protein and hydration components. From this decomposition, we are able to determine the main thermodynamic factors governing the cold and heat unfolding events: the cold and heat unfolding events are largely driven by the hydration enthalpy gain and the protein conformational entropy gain, respectively. This computational study discloses several temperature-dependent unfolding thermodynamic behaviors of the protein and water compartments and establishes their unique relationship. Upon unfolding, the changes of enthalpy and entropy in the protein part are all positive convex functions of temperature, whereas the equivalent changes in the water part are all negative concave functions of temperature. Hence, these two mutually opposing effects from the protein and water parts dictate the thermodynamics of unfolding. Furthermore, consistent with the temperature-dependent behaviors of the protein part, the changes of the solvent-accessible surface area and the radius of gyration of the protein upon unfolding are also convex functions of temperature. Hence, all these new temperature dependences, combined together, pave the way to unveiling the thermodynamic and structural features of protein denaturation events at various temperature conditions.

Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding

Protein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.

Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond.

Autophagy is a common name for a number of catabolic processes, which keep the cellular homeostasis by removing damaged and dysfunctional intracellular components. Impairment or misbalance of autophagy can lead to various diseases, such as neurodegeneration, infection diseases, and cancer. A central axis of autophagy is formed along the interactions of autophagy modifiers (Atg8-family proteins) with a variety of their cellular counter partners. Besides autophagy, Atg8-proteins participate in many other pathways, among which membrane trafficking and neuronal signaling are the most known. Despite the fact that autophagy modifiers are well-studied, as the small globular proteins show similarity to ubiquitin on a structural level, the mechanism of their interactions are still not completely understood. A thorough analysis and classification of all known mechanisms of Atg8-protein interactions could shed light on their functioning and connect the pathways involving Atg8-proteins. In this review, we present our views of the key features of the Atg8-proteins and describe the basic principles of their recognition and binding by interaction partners. We discuss affinity and selectivity of their interactions as well as provide perspectives for discovery of new Atg8-interacting proteins and therapeutic approaches to tackle major human diseases.

Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ3

Differential scanning calorimetry (DSC) indicated that PDZ3 undergoes a peculiar thermal denaturation, exhibiting two endothermic peaks because of the formation of reversible oligomers at high temperature (N↔I6↔D). This contrasts sharply with the standard two-state denaturation model observed for small, globular proteins. We performed an alanine scanning analysis by individually mutating three hydrophobic residues at the crystallographic oligomeric interface (Phe340, Leu342, and Ile389) and one away from the interface (Leu349, as a control). DSC analysis indicated that PDZ3-F340A and PDZ3-L342A exhibited a single endothermic peak. Furthermore, PDZ3-L342A underwent a perfect two-state denaturation, as evidenced by the single endothermic peak and confirmed by detailed DSC analysis, including global fitting of data measured at different protein concentrations. Reversible oligomerization (RO) at high temperatures by small globular proteins is a rare event. Furthermore, our present study showing that a point mutation, L342A, designed based on the crystal structure inhibited RO is surprising because RO occurs at a high-temperature. Future studies will determine how and why mutations designed using crystal structures determined at ambient temperatures influence the formation of RO at high temperatures, and whether high-temperature ROs are related to the propensity of proteins to aggregate or precipitate at lower temperatures, which would provide a novel and unique way of controlling protein solubility and aggregation.

NMR Relaxation of Nuclei of Buffer as a Probe for Monitoring Protein Solutions Including Aggregation Processes

Characterization of protein solutions is of great importance for biophysical research, pharmaceutical industry, and medicine. Particularly, the monitoring of the protein aggregation is crucial at all stages of biotechnological production and in the diagnosis of dangerous diseases. The present work is focused on a study of prospects and possibilities of NMR relaxation of solvent nuclei for monitoring the state of proteins in solutions. The spin–lattice and spin–spin relaxation rates (R1 and R2) of solvent nuclei were measured in the solutions of a small globular protein, RRM2 domain of TDP-43 protein. The solvent was either H2O- or D2O-based buffer with pH 6.5 and contained 20 mM sodium phosphate and 150 mM NaCl. The relaxation rates of the solvent 1H, 2H, 23Na, and 35Cl nuclei in solutions of soluble and aggregated RRM2 domain of TDP-43 protein were studied. The aggregation was induced by mild oxidative stress, using treatment by hydrogen peroxide. It was found that aggregation of protein could be detected using NMR relaxation of 1H nuclei. The observed CPMG dispersion for R2 rates confirms the millisecond timescale for the hydrogen exchange between water and protein sites. The correlation times and binding constants for sodium and chlorine ions were estimated using concentration dependences for relaxation rates (23Na, 35Cl). The relaxation rates of solvent nuclei are sensitive to the presence of protein in solution even at low protein concentrations, and the relaxation rates of different nuclei reflect various aspects of the state of the protein.

In silico study of osmolytic effects of choline-O-sulfate on urea induced unfolding of Trp-cage mini-protein: An atomistic view from replica exchange molecular dynamics simulation

The event of protein folding is associated with essential biological functionalities and unfolding of protein native state can cause intra-cellular toxicity leading to biological dysfunctions and even cell death. The present study discusses the folding-unfolding equilibrium of the small globular protein Trp-cage in presence of denaturing and protecting osmolytes urea and choline-O-sulfate (COS), respectively, employing Replica Exchange Molecular Dynamics (REMD), extensive free energy calculations and temperature scanned free energy landscapes. It is shown that, while 6 M urea quite easily denatures the protein, 0.5 M and 1 M COS is able to protect the protein from urea induced denaturation at room temperature. However, REMD simulations reveal that while the protein in pure water can withstand a simulation temperature as high as 420 K without melting, the protecting effect of 0.5 M and 1 M COS is operative up to 300 and 340 K respectively. This study furnishes evidences to shed light into the protecting mechanism of COS regarding urea induced protein unfolding, thereby putting forward the use of COS as a proper protecting osmolyte towards different types of proteins.

Formulation and Functional Properties of Whey Protein-Based Tissue Adhesive Using Totarol as an Antimicrobial Agent

Tissue adhesives have been widely used in surgical procedures. Compared to traditional surgical sutures, tissue adhesives provide fast bonding experiences and full closure of wounds. However, current tissue adhesives are mostly fossil-based synthetic products. Therefore, it is of great significance to explore the use of natural materials in tissue adhesives. Whey is a low-end byproduct of cheese manufacturing. Whey protein, a group of small globular proteins, can exhibit adhesive properties if their structures are modified by physical or chemical means. The objectives of this study were to investigate the functional and structural properties of whey protein-based tissue adhesive, along with the antibacterial effect of totarol, a natural antimicrobial agent. Whey protein isolate (WPI) solutions (25%–33% protein) were mixed with different levels (0.1%–0.3% w/w) of totarol. The mixtures were analyzed for total plate count and yeast and mold count. The lap-shear bonding strength was tested after the WPI-totarol solutions were mixed with a crosslinking agent, glutaraldehyde (GTA). The lap-shear bonding strength of the tissue adhesive was about 20 kPa, which is comparable to that of a commercial BioGlue®. The microstructures of the mixtures were analyzed by scanning electron microscopy (SEM).

Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions.

In this review we present the developmental, histological, evolutionary and functional properties of insect chemosensory proteins (CSPs) in insect species. CSPs are small globular proteins folded like a prism and notoriously known for their complex and arguably obscure function(s), particularly in pheromone olfaction. Here, we focus on direct functional consequences on protein function depending on duplication, expression and RNA editing. The result of our analysis is important for understanding the significance of RNA-editing on functionality of CSP genes, particularly in the brain tissue.

In Situ Phase Transition of Elastin-Like Polypeptide Chains Regulates Thermoresponsive Properties of Elastomeric Protein-Based Hydrogels.

Engineering protein-based hydrogels that can change their physical and mechanical properties in response to environmental stimuli have attracted considerable interest due to their promising applications in biomedical engineering. Among environmental stimuli, temperature is of particular interest. Most thermally responsive protein hydrogels are constructed from thermally responsive elastin-like polypeptides (ELPs), which exhibit a lower critical solution temperature (LCST) transition, or nonstructured elastomeric proteins fused with ELPs. Here we report the engineering of thermally responsive elastomeric protein-based hydrogels by fusing ELPs to elastomeric proteins made of tandemly arranged folded globular proteins. By fusing ELP sequence (VPGVG)n to an elastomeric protein (GR)4, which is made of small globular protein GB1 (G) and random coil sequence resilin (R), we engineered a series of protein block copolymers, Vn-(GR)4. The fusion proteins Vn-(GR)4 exhibit temperature-responsive behaviors in aqueous solution that are different from that of Vn-ELPs, as they did not exhibit the macroscopic phase transitions in the turbidity test. Instead, V48-(GR)4 and V72-(GR)4 form micelles at temperatures higher than the transition temperature of V48 and V72 at the same concentration. Using the well-developed ruthenium-mediated photochemical cross-linking method, Vn-(GR)4 polymers can be cross-linked into hydrogels, in which Vn-ELP serve as side chains of the hydrogel network. These hydrogels exhibited thermoresponsive properties due to the temperature dependent phase transition behaviors of the incorporated Vn-ELPs blocks. At elevated temperatures, the Vn-ELPs side chains in the hydrogel network underwent aggregation, leading to secondary physical cross-linking. The aggregation of the Vn-ELPs resulted in higher Young's modulus and reduced swelling ratio. Furthermore, the amplitude of such property changes can be tuned by side chain length and composition. These results demonstrate that in situ phase behaviors of ELP side chains can regulate thermoresponsiveness of protein-based hydrogels. We anticipate that this method can be applied to other elastomeric proteins for potential biomedical applications.

SDS-induced multi-stage unfolding of a small globular protein through different denatured states revealed by single-molecule fluorescence.

Ionic surfactants such as sodium dodecyl sulfate (SDS) unfold proteins in a much more diverse yet effective way than chemical denaturants such as guanidium chloride (GdmCl). But how these unfolding processes compare on a molecular level is poorly understood. Here, we address this question by scrutinising the unfolding pathway of the globular protein S6 in SDS and GdmCl with single-molecule Förster resonance energy transfer (smFRET) spectroscopy. We show that the unfolding mechanism in SDS is strikingly different and convoluted in comparison to denaturation in GdmCl. In contrast to the reversible two-state unfolding behaviour in GdmCl characterised by kinetics on the timescale of seconds, SDS demonstrated not one, but four distinct regimes of interactions with S6, dependent on the surfactant concentration. At ≤1 mM SDS, S6 and surfactant molecules form quasi-micelles on a minute timescale; at millimolar [SDS], the protein denatures through an unfolded/denatured ensemble of highly heterogeneous states on a multi-second timescale; at tens of millimolar of SDS, the protein unfolds into a micelle-packed conformation on the second timescale; and >50 mM SDS, the protein unfolds with millisecond timescale dynamics. We propose a detailed model for multi-stage unfolding of S6 in SDS, which involves at least three different types of denatured states with different level of compactness and dynamics and a continually changing landscape of interactions between protein and surfactant. Our results highlight the great potential of single-molecule fluorescence as a direct probe of nanoscale protein structure and dynamics in chemically complex surfactant environments.