Protein Conformational Stability Research Articles

Publisher’s note

The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools. In silico analysis was followed to predict the tertiary structure, putative binding site regions, and binding site residues. Also, the effects of this mutation on protein stability, aggregation propensity, and homodimerization were analyzed. Next, a molecular dynamic simulation was carried out to understand the dynamic behavior of wild-type, A69S, and phosphorylated A69S structures. The results showed alterations in the putative post-translational modification sites on the ARMS2 protein, due to the mutation. Furthermore, the stability of protein and putative homodimer conformations were affected by the mutation. Molecular dynamic simulation results revealed that the A69S mutation enhances the rigidity of the ARMS2 structure and residue serine at position 69 is buried and may not be phosphorylated; however, phosphorylated serine enhances the flexibility of the ARMS2 structure. In conclusion, our study provides new insights into the deleterious effects of the A69S mutation on the ARMS2 structure.

Nano-bio interactions between carbon nanomaterials and blood plasma proteins: why oxygen functionality matters

Carbon nanomaterials are some of the most versatile nanomaterials. Along with increasing explorations into their utilization in a plethora of biological and biomedical applications, there have been emerging interests and needs in understanding the molecular hemocompatibility of these engineered nanomaterials when coming into contact with blood. Here, we evaluate the nano-bio interactions of one-dimensional (1D) and two-dimensional (2D) carbon nanomaterials with blood plasma proteins. Different facets of the nanomaterial–protein interactions, specifically, the adsorption, equilibrium binding and conformational stability of proteins upon association with carbon nanomaterials are established, based on the quantification of various parameters, such as association constant, binding cooperativity and protein secondary structural change. In light of our data, we demonstrate that the carbon nanomaterial–plasma protein interactions may be significantly influenced by the density of the oxygenated functionalities of the nanomaterials and to a certain extent, their dimensionality and surface area. This work offers a broad insight into the nano-bio interactions between carbon nanomaterials and blood plasma proteins and provides a strong basis for the design and use of 1D and 2D carbon nanomaterials for a wide variety of bioapplications.

The transcriptional response of the Pacific oyster Crassostrea gigas against acute heat stress

The Pacific oyster, Crassostrea gigas, has evolved sophisticated mechanisms to adapt the changing ambient conditions, and protect themselves from stress-induced injuries. In the present study, the expression profiles of mRNA transcripts in the haemocytes of oysters under heat stress were examined to reveal the possible mechanism of heat stress response. There were 23,315, 23,904, 23,123 and 23,672 transcripts identified in the haemocytes of oysters cultured at 25 °C for 0, 6, 12, and 24 h (designed as B, H6, H12, H24), respectively. And 22,330 differentially expressed transcripts (DTs) were yielded in the pairwise comparisons between the above four samples, which corresponded to 8074 genes. There were 9, 12 and 22 Gene Ontology (GO) terms identified in the DT pairwise comparison groups of H6_B, H12_H6 and H24_H12, respectively, and the richest GO terms in biological process category were cellular catabolic process, translational initiation and apoptotic process, respectively. There were 108, 102 and 102 KEGG pathways successfully retrieved from DTs comparison groups DTH6_B, DTH12_H6 and DTH24_H12, respectively, among which 93 pathways were shared by all three comparison groups, and most of them were related to metabolism of protein, carbohydrate and fat. The expression patterns of 12 representative heat stress response-relevant genes detected by quantitative real-time PCR (qRT-PCR) were similar to those obtained from transcriptome analysis. By flow cytometric analysis, the apoptosis rate of haemocytes increased significantly after oysters were treated at 25 °C for 24 h and recovered at 4 °C for 12 h (p < 0.05) and 36 h (p < 0.01), and it also increased significantly when the heat treatment lasted to 60 h (p < 0.01). The present results indicated that, when oysters encountered short term heat stress, the expression of genes related to energy metabolism, as well as unfolded protein response (UPR) and anti-apoptotic system, were firstly regulated to maintain basic life activities, and then a large number of genes involved in stabilizing protein conformation and facilitating further protein refolding were activated to repair the stress injury. However, the stress injury gradually became irreparable with the stress persisting, and apoptosis was activated when the heat treatment prolonged to 24 h. The information was useful to better understand the molecular mechanism of heat stress response and develop strategies for the improvement of oyster survival rate during summer high-temperature period.

Effects on insulin adsorption due to zinc and strontium substitution in hydroxyapatite

Insulin-loaded calcium phosphate nanoparticles have been proposed as a potential drug delivery system for the oral treatment of diabetes and to stimulate bone cell proliferation and bone mineralization. The kinetics of insulin incorporation onto hydroxyapatite (HA) and Sr (SrHA)- and Zn (ZnHA)-substituted hydroxyapatite nanoparticles was investigated using X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR) spectroscopy, zeta potential measurements and circular dichroism (CD) spectroscopy. The increase in insulin concentration on HA, SrHA and ZnHA was a typical physical adsorption process controlled by electrostatic forces and followed a Freundlich isotherm model. Zn substitution enhanced the capacity of the apatite surface to adsorb insulin, whereas Sr substitution inhibited insulin uptake. The surface stoichiometry and mesopore specific area induced by Zn and Sr substitution are proposed as the main causes of the difference in insulin adsorption. Despite the weak interaction between insulin and the apatite surface, the CD spectra revealed a decrease in the insulin ellipticity when the protein was adsorbed on the HA, SrHA and ZnHA nanoparticles. A reduction in alpha-helical structures and an increase in beta sheets were observed when insulin interacted with the HA surface. A less pronounced effect was found for ZnHA, for which a subtle decrease in alpha-helical structures was followed by an increase in turn structures. Interaction with the SrHA surface did not change the native insulin conformation. In vitro cell culture experiments lasting 24h using F-OST stromal cells showed that the insulin loaded on HA and ZnHA did not affect cell proliferation but the insulin loaded on SrHA improved cell proliferation. These results suggest that the stability of the native protein conformation is an important factor to consider when cells interact with insulin adsorbed on metal-substituted HA surfaces.

Differential Scanning Calorimetry - A Method for Assessing the Thermal Stability and Conformation of Protein Antigen.

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural “fingerprint” that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

Differential Scanning Calorimetry &amp;#8212; A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural “fingerprint” that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation, dimerization and EGF hormone binding.

The epidermal growth factor receptor (EGFR) is an important transmembrane glycoprotein kinase involved the initiation or perpetuation of signal transduction cascades within cells. These processes occur after EGFR binds to a ligand [epidermal growth factor (EGF)], thus inducing its dimerization and tyrosine autophosphorylation. Previous publications have highlighted the importance of glycosylation and dimerization for promoting proper function of the receptor and conformation in membranes; however, the effects of these associations on the protein conformational stability have not yet been described. Molecular dynamics simulations were performed to characterize the conformational preferences of the monomeric and dimeric forms of the EGFR extracellular domain upon binding to EGF in the presence and absence of N-glycan moieties. Structural stability analyses revealed that EGF provides the most conformational stability to EGFR, followed by glycosylation and dimerization, respectively. The findings also support that EGF-EGFR binding takes place through a large-scale induced-fitting mechanism. Proteins 2017; 85:561-570. © 2016 Wiley Periodicals, Inc.

Amino Acid Properties of Trafficking Determinants in the Outer Pore-Forming Region of Kv1 Potassium Channels in Cell Lines

Different classes of Kv1 potassium channels have different trafficking patterns despite having very similar amino acid sequences. Two amino acids responsible for these differences have been identified in the outer pore turret region of Kv1.1 and Kv1.4. Here we tested a series of substitutions at these two determinants on Kv1.4. All P506 substitutions tested resulted in a significant decrease in surface protein, total protein, and protein half-life, indicating that proline is required at 506 to stabilize protein conformation and increase trafficking to the cell surface. All K533 substitutions tested had no effect on total protein, suggesting that the lysine at 533 is not important for maintaining Kv1.4 protein conformation. However, a basic or long polar amino acid, such as K, R, or Q, at this position favored high surface protein and efficient trafficking of Kv1.4, whereas an acidic or short amino acid, such as D, E, S, L, N, or H, at this position induced partial high endoplasmic reticulum-retention. This intracellular retention was not due to protein misfolding. We propose that these four prolines and four lysines in a Kv1.4 homotetramer might provide a binding site for a putative endoplasmic reticulum-export molecule to ensure high cell surface protein expression of the channel.

Kinetic characteristics of chimeric channelrhodopsins implicate the molecular identity involved in desensitization

Channelrhodopsin (ChR)-1 and ChR2 were the first-identified members of ChRs which are a growing subfamily of microbial-type rhodopsins. Light absorption drives the generation of a photocurrent in cell membranes expressing ChR2. However, the photocurrent amplitude attenuates and becomes steady-state during prolonged irradiation. This process, called desensitization or inactivation, has been attributed to the accumulation of intermediates less conductive to cations. Here we provided evidence that the dark-adapted (DA) photocurrent before desensitization is kinetically different from the light-adapted (LA) one after desensitization, that is, the deceleration of both basal-to-conductive and conductive-to-basal transitions. When the kinetics were compared between the DA and LA photocurrents for the ChR1/2 chimeras, the transmembrane helices, TM1 and TM2, were the determinants of both basal-to-conductive and conductive-to-basal transitions, whereas TM4 may contribute to the basal-to-conductive transitions and TM5 may contribute to the conductive-to-basal transitions, respectively. The fact that the desensitization-dependent decrease of the basal-to-conductive and conductive-to-basal transitions was facilitated by the TM1 exchange from ChR2 to ChR1 and reversed by the further TM2 exchange suggests that the conformation change for the channel gating is predominantly regulated by the interaction between TM1 and TM2. Although the exchange of TM1 from ChR2 to ChR1 showed no obvious influence on the spectral sensitivity, this exchange significantly induced the desensitization-dependent blue shift. Therefore, the TM1 and 2 are the main structures involved in two features of the desensitization, the stabilization of protein conformation and the charge distribution around the retinal-Schiff base (RSB+).

Computational investigation of the human SOD1 mutant, Cys146Arg, that directs familial amyotrophic lateral sclerosis.

The genetic substitution mutation of Cys146Arg in the SOD1 protein is predominantly found in the Japanese population suffering from familial amyotrophic lateral sclerosis (FALS). A complete study of the biophysical aspects of this particular missense mutation through conformational analysis and producing free energy landscapes could provide an insight into the pathogenic mechanism of ALS disease. In this study, we utilized general molecular dynamics simulations along with computational predictions to assess the structural characterization of the protein as well as the conformational preferences of monomeric wild type and mutant SOD1. Our static analysis, accomplished through multiple programs, predicted the deleterious and destabilizing effect of mutant SOD1. Subsequently, comparative molecular dynamic studies performed on the wild type and mutant SOD1 indicated a loss in the protein conformational stability and flexibility. We observed the mutational consequences not only in local but also in long-range variations in the structural properties of the SOD1 protein. Long-range intramolecular protein interactions decrease upon mutation, resulting in less compact structures in the mutant protein rather than in the wild type, suggesting that the mutant structures are less stable than the wild type SOD1. We also presented the free energy landscape to study the collective motion of protein conformations through principal component analysis for the wild type and mutant SOD1. Overall, the study assisted in revealing the cause of the structural destabilization and protein misfolding via structural characterization, secondary structure composition and free energy landscapes. Hence, the computational framework in our study provides a valuable direction for the search for the cure against fatal FALS.

Enhancing a long-range salt bridge with intermediate aromatic and nonpolar amino acids.

The interaction of a positively charged amino acid residue with a negatively charged residue (i.e. a salt bridge) can contribute substantially to protein conformational stability, especially when two ionic groups are in close proximity. At longer distances, this stabilizing effect tends to drop off precipitously. However, several lines of evidence suggest that salt-bridge interaction could persist at longer distances if an aromatic amino acid residue were positioned between the anion and cation. Here we explore this possibility in the context of a peptide in which a Lys residue occupies the i + 8 position relative to an i-position Glu on the solvent-exposed surface of a helix-bundle homotrimer. Variable temperature circular dichroism (CD) experiments indicate that an i + 4-position Trp enables a favorable long-range interaction between Glu and the i + 8 Lys. A substantial portion of this effect relies on the presence of a hydrogen-bond donor on the arene; however, non-polar arenes, a cyclic hydrocarbon, and an acyclic Leu side-chain can also enhance the long-range salt bridge, possibly by excluding water and ions from the space between Glu and Lys.

Loading of halloysite nanotubes with BSA, α-Lac and β-Lg: a Fourier transform infrared spectroscopic and thermogravimetric study

Halloysite nanotubes (HNTs) are considered as ideal materials for biotechnological and medical applications. An important feature of halloysite is that it has a different surface chemistry on the inner and outer sides of the tubes. This property means that negatively-charged molecules can be selectively loaded inside the halloysite nanoscale its lumen. Loaded HNTs can be used for the controlled or sustained release of proteins, drugs, bioactive molecules and other agents. We studied the interaction between HNTs and bovine serum albumin, α lactalbumin and β -lactoglobulin loaded into HTNs using Fourier transform infrared spectroscopy and thermogravimetry. These techniques enabled us to study the protein conformation and thermal stability, respectively, and to estimate the amount of protein loaded into the HNTs. TEM images confirmed the loading of proteins into HTNs.

Interpolyelectrolyte complexes of lysozyme with short poly[di(carboxylatophenoxy)phosphazene]. Binding energetics and protein conformational stability

Interaction of a biodegradable anionic polyphosphazene, poly[di(carboxylatophenoxy)phosphazene] (PCPP), with a model globular protein, hen egg white lysozyme, was investigated under near-physiological conditions by means of turbidimetry, high-sensitivity differential scanning and isothermal titration calorimetry (ITC). The formation of soluble (non-stoichiometric) and insoluble (stoichiometric) interpolyelectrolyte complexes was demonstrated upon changes in the reaction mixture composition. The denaturation parameters of the bound lysozyme in the stoichiometric and non-stoichiometric complexes were determined. They point to a substantial decrease in conformational stability of the bound protein in the stoichiometric complex. In the non-stoichiometric complexes corresponding to a loose protein loading on the PCPP matrix an additional decrease in conformational stability of lysozyme was observed. It indicates unfolding of the protein at room temperature. ITC experiments were carried out at different temperatures in two modes: direct and reversible titrations. The direct titration curves were well approximated by the McGhee-von Hippel model that resulted in determination of the binding constant (∼1 × 106 M−1), apparent ligand size (∼10), cooperativity parameter (∼11) as well as the enthalpies of binding and ligand-ligand interaction. The heat capacity increments associated with the binding of the protein ligands and contact interaction between the bound ligands were comparable by value but opposite in sign. We discuss this effect in terms of changes in polar and apolar accessible surface areas of the bound protein ligands caused by the ligand-matrix and ligand-ligand interactions.

Impact of additives on the formation of protein aggregates and viscosity in concentrated protein solutions

In concentrated protein solutions attractive protein interactions may not only cause the formation of undesired aggregates but also of gel-like networks with elevated viscosity. To guarantee stable biopharmaceutical processes and safe formulations, both phenomenons have to be avoided as these may hinder regular processing steps. This work screens the impact of additives on both phase behavior and viscosity of concentrated protein solutions. For this purpose, additives known for stabilizing proteins in solution or modulating the dynamic viscosity were selected. These additives were PEG 300, PEG 1000, glycerol, glycine, NaCl and ArgHCl. Concentrated lysozyme and glucose oxidase solutions at pH 3 and 9 served as model systems. Fourier-transformed-infrared spectroscopy was chosen to determine the conformational stability of selected protein samples. Influencing protein interactions, the impact of additives was strongly dependent on pH. Of all additives investigated, glycine was the only one that maintained protein conformational and colloidal stability while decreasing the dynamic viscosity. Low concentrations of NaCl showed the same effect, but increasing concentrations resulted in visible protein aggregation.

Modified Poisson equation for the electric field and electric field gradient

The dielectric polarization (P) is the key factor in calculating the solvation free energy to explore the stability of protein conformations, binding affinity of protein–protein/ligand interactions, and nonthermal effect of an external electric field on biomolecules. P can be decomposed into the product of the electric dipole per solvent (p), and the solvent molecular density (Nbulkg). p can be calculated from the electric field (E) and g can be calculated from the mean force (F) with the electric component of F calculated from ∇E. Here, the Poisson equation was modified for E and ∇E using a point dipole at the center of a hard sphere as the solvent model. Strategies to estimate the boundary conditions of E and ∇E were proposed. The dependence of p and g on Δh, and of the van der Waals component of F on Rcut were studied. The P and g values calculated from this strategy were similar to those derived from molecular dynamics simulations.

Conjugation Strategy Strongly Impacts the Conformational Stability of a PEG-Protein Conjugate

Site-specific PEGylation is an important strategy for enhancing the pharmacokinetic properties of protein drugs, and has been enabled by the recent development of many chemoselective reactions for protein side-chain modification. However, the impact of these different conjugation strategies on the properties of PEG-protein conjugates is poorly understood. Here we show that the ability of PEG to enhance protein conformational stability depends strongly on the identity of the PEG-protein linker, with the most stabilizing linkers involving conjugation of PEG to planar polar groups near the peptide backbone. We also find that branched PEGs provide superior stabilization relative to their linear counterparts, suggesting additional applications for branched PEGs in protein stabilization.

Dynamic Stabilization of Expressed Proteins in Engineered Diatom Biosilica Matrices.

Self-assembly of recombinant proteins within the biosilica of living diatoms represents a means to construct functional materials in a reproducible and scalable manner that will enable applications that harness the inherent specificities of proteins to sense and respond to environmental cues. Here we describe the use of a silaffin-derived lysine-rich 39-amino-acid targeting sequence (Sil3T8) that directs a single chain fragment variable (scFv) antibody or an enhanced green fluorescent protein (EGFP) to assemble within the biosilica frustule, resulting in abundance of >200 000 proteins per frustule. Using either a fluorescent ligand bound to the scFv or the intrinsic fluorescence of EGFP, we monitored protein conformational dynamics, accessibility to external quenchers, binding affinity, and conformational stability. Like proteins in solution, proteins within isolated frustules undergo isotropic rotational motion, but with 2-fold increases in rotational correlation times that are indicative of weak macromolecular associations within the biosilica. Solvent accessibilities and high-affinity (pM) binding are comparable to those in solution. In contrast to solution conditions, scFv antibodies within the biosilica matrix retain their binding affinity in the presence of chaotropic agents (i.e., 8 M urea). Together, these results argue that dramatic increases in protein conformational stability within the biosilica matrices arise through molecular crowding, acting to retain native protein folds and associated functionality with the potential to allow the utility of engineered proteins under a range of harsh environmental conditions associated with environmental sensing and industrial catalytic transformations.

Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein–protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss’s law of Maxwell’s equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

The contribution of electrostatic interactions to the collapse of oligoglycine in water.

Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in some cases without hydrogen bonds. The strongly repulsive solvent cavity formation is balanced by van der Waals attractions and electrostatic contributions. In order to investigate the competition between solvent exclusion and charge interactions we simulate the collapse of a long oligoglycine comprised of 15 residues while scaling the charges on the peptide from zero to fully charged. We examine the effect this has on the conformational properties of the peptide. We also describe the approximate thermodynamic changes that occur during the scaling both in terms of intrapeptide potentials and peptide-water potentials, and estimate the electrostatic solvation free energy of the system.

Disorders of Protein Conformation as a Typical Component of Various Human Disease Pathogenesis

The review is aimed to analyze the data of the recent studies and to describe all the disorders of protein conformation as a typical pathogenic process of protein structure and metabolism involved in various human disease pathogenesis. The existing group of the disorders of protein metabolism doesn’t clearly reflect the involvement of misfolding in the pathogenesis of many human diseases (as a significant factor) and the term disproteinosis is being broadly used only in the context of some «typical» protein misfolding diseases or conformational diseases (for example, amyloidosis and sickle cell anemia). However, protein conformational stability disorders are well-described as physico-chemical processes; there are diseases, in which the manifestations of protein disorders reach their maximum. The revealing of universal form of conformational stability pathology may eliminate the gaps in the understanding of many human diseases, including some diseases with high social significance.