Analysis of Protein Interactions by Surface Plasmon Resonance

Development of faba protein-tannic acid conjugate via free radical grafting: Evaluation of interaction mechanisms and antioxidative properties

A soluble fraction of faba bean protein was conjugated with tannic acid via the free-radical grafting method using a mixture of ascorbic acid and hydrogen peroxide. Surface plasmon resonance showed a strong bonding between them, while the free amino and thiol group measurements indicated tannic acid's bonding with the amino groups and cysteine residues on the proteins. Structural analysis using intrinsic fluorescence and surface hydrophobicity demonstrated tannic acid's interaction with the aromatic and hydrophobic amino acids of the protein. The conjugate showed about 77 % DPPH, 89 % ABTS, and 83 % hydroxyl radical scavenging activities and superior ferric-reducing ability compared to the protein alone and the mixture of protein and tannic acid. Electron paramagnetic resonance (EPR) spectroscopy revealed 97.8 % radical scavenging ability of the conjugate, comparable to the pure tannic acid. The exceptional antioxidative properties of conjugate can be utilized to delay lipid oxidation in protein-stabilized oil-in-water emulsions.

Monoclonal antibodies against jellyfish collagen

Collagens are abundant structural proteins found in both mammalian and marine species, and attractive biomaterials used in various fields. Jellyfish collagen-based products have become increasingly popular because of their clinically proven health benefits such as the effects of skin wound healing and immune stimulation. To develop detection tools for jellyfish collagen, we generated four monoclonal antibodies, MCOL1, 2, 3, and 4, by immunizing mice with moon jellyfish collagen. The nucleotide and amino acid sequences of the variable regions of the monoclonal antibodies were determined. The antibody-binding kinetics toward collagens from moon jellyfish were evaluated using a surface plasmon resonance (SPR) biosensor, and the binding specificity was evaluated in comparison with binding to collagens from edible jellyfish, fish scales, and pig and cow skins. MCOL1, 3, and 4 specifically bound to moon jellyfish collagen, whereas MCOL2 bound to both moon and edible jellyfish collagens. Considering the results showing that the SPR responses of MCOL2 binding were greater than those seen with the other antibodies, MCOL2 could recognize the common and repetitive sequences of the two jellyfish collagens. Therefore, this monoclonal antibody will be most applicable for detecting jellyfish collagen.

ClsC protein encoded by a stress-responsive operon in Escherichia coli functions as a trans-acting activator of RNase III

RNase III, an endoribonuclease that cleaves double-stranded RNAs (dsRNAs), significantly impacts Escherichia coli (E. coli) adaptation by regulating global RNA gene expression. YmdB from E. coli was characterized as a trans-acting regulator of RNase III. However, no protein encoded in E. coli has been characterized as an activator of RNase III. This study reports the discovery of ClsC protein, a phospholipase D (PLD) superfamily enzyme previously known as the third cardiolipin synthase (Cls) and a biofilm inhibitor in E. coli, as a novel RNase III activator. Overexpression of clsC in vivo stimulated the cleavage of RNase III-targeted lacZ fusions and antagonized the inhibition of RNase III by YmdB. Additional in vitro cleavage assays of RNase III-targeted RNAs using RNase III and ClsC confirmed this activity. Moreover, we identified multiple RNAs targeted by RNase III that are regulated dependently on cellular ClsC levels. Mechanistic investigations revealed that ClsC interacts with RNase III. Moreover, the isoleucine residue at the 466th position from the N-terminus of ClsC was identified as crucial for ClsC function. This study is the first to demonstrate that the ymdAB-clsC operon serves as an unexpected source for RNase III regulation in E. coli.

Subtractive Inhibition Assay Based on PagN-Specific Monoclonal Antibody for the Detection of Salmonella Using Surface Plasmon Resonance

Salmonella is a common foodborne zoonotic pathogen that poses a great threat to human health and breeding industry. The rapid detection of Salmonella is necessary for early prevention and control. In this study, a subtractive inhibition assay (SIA) based on surface plasmon resonance (SPR) for the rapid detection of Salmonella was developed. Mouse-specific monoclonal antibody 3B3 against Salmonella membrane protein PagN was first incubated with Salmonella. The unbound free antibody was separated using a sequential process of centrifugation and then detected using an immobilized goat anti-mouse immunoglobulin G polyclonal antibody on the SPR sensor chip. This SIA-SPR method showed excellent sensitivity for Salmonella with a limit of detection of about 300 CFU mL-1. This method is sensitive to different serotypes of Salmonella strains but not for non-Salmonella strains. It was able to detect Salmonella in the contaminated water and milk powder at less than 102 and 103 CFU mL-1, respectively, which was consistent with the bacterial plate count results. In addition, this method could be used to evaluate the lysis effect of phages on bacteria. Since the culturing detection method needs more than 48 h, this method has the potential for the rapid and sensitive clinical detection of Salmonella. For our knowledge, this is the first report for Salmonella detection using SIA-SPR method.

Heritability and Genome-Wide Association Study of Dog Behavioral Phenotypes in a Commercial Breeding Cohort

Background: Canine behavior plays an important role in the success of the human-dog relationship and the dog's overall welfare, making selection for behavior a vital part of any breeding program. While behaviors are complex traits determined by gene × environment interactions, genetic selection for desirable behavioral phenotypes remains possible. Methods: No genomic association studies of dog behavior to date have been reported on a commercial breeding (CB) cohort; therefore, we utilized dogs from these facilities (n = 615 dogs). Behavioral testing followed previously validated protocols, resulting in three phenotypes/variables [social fear (SF), non-social fear (NSF), and startle response (SR)]. Dogs were genotyped on the 710 K Affymetrix Axiom CanineHD SNP array. Results: Inbreeding coefficients indicated that dogs from CB facilities are statistically less inbred than dogs originating from other breeding sources. Heritability estimates for behavioral phenotypes ranged from 0.042 ± 0.045 to 0.354 ± 0.111. A genome-wide association analysis identified genetic loci associated with SF, NSF, and SR; genes near many of these loci have been previously associated with behavioral phenotypes in other populations of dogs. Finally, genetic risk scores demonstrated differences between dogs that were more or less fearful in response to test stimuli, suggesting that these behaviors could be subjected to genetic improvement. Conclusions: This study confirms several canine genetic behavioral loci identified in previous studies. It also demonstrates that inbreeding coefficients of dogs in CB facilities are typically lower than those in dogs originating from other breeding sources. SF and NSF were more heritable than SR. Risk allele and weighted risk scores suggest that fearful behaviors could be subjected to genetic improvement.

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

High throughput methods to study protein-protein interactions during host-pathogen interactions

The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host and pathogen proteins. Such interactions can be both intra- and extracellular and may define the outcome of an infection. There are a range of innovative biochemical, biophysical and bioinformatic techniques currently available to identify protein-protein interactions (PPI) between the host and the pathogen. However, the complexity and the diversity of host-pathogen PPIs has led to the development of several high throughput (HT) techniques that enable the study of multiple interactions at once and/or screen multiple samples at the same time, in an unbiased manner. We review here the major HT laboratory-based technologies employed for host-bacterial interaction studies.

Evaluating the biomolecular interaction between delamanid/formulations and human serum albumin by fluorescence, CD spectroscopy and SPR: Effects on protein conformation, kinetic and thermodynamic parameters

Delamanid is an anti-tuberculosis drug used for the treatment of drug-resistant tuberculosis. Since delamanid has a high protein bound potential, even patients with low albumin levels should experience high and rapid delamanid clearance. However, the interaction between delamanid and albumin should be better controlled to optimize drug efficacy. This study was designed to evaluate the binding characteristics of delamanid to human serum albumin (HSA) using various methods: fluorescence spectroscopy, circular dichroism (CD), surface plasmon resonance (SPR), and molecular docking simulation. The fluorescence emission band without any shift indicated the interaction was not affected by the polarity of the fluorophore microenvironment. The reduction of fluorescence intensity at 344 nm was proportional to the increment of delamanid concentration as a fluorescence quencher. UV-absorbance measurement at the maximum wavelength (λmax, 280 nm) was evaluated using inner filter effect correction. The HSA conformation change was explained by the intermolecular energy transfer between delamanid and HSA during complex formation. The study, which was conducted at temperatures of 298 K, 303 K, and 310 K, revealed a static quenching mechanism that correlated with a decreased of bimolecular quenching rate constant (kq) and binding constant (Ka) at increased temperatures. The Ka was 1.75-3.16 × 104 M-1 with a specific binding site with stoichiometry 1:1. The negative enthalpy change, negative entropy change, and negative Gibbs free energy change demonstrated an exothermic-spontaneous reaction while van der Waals forces and hydrogen bonds played a vital role in the binding. The molecular displacement approach and molecular docking confirmed that the binding occurred mainly in subdomain IIA, which is a hydrophobic pocket of HSA, with a theoretical binding free energy of -9.33 kcal/mol. SPR exhibited a real time negative sensorgram that resulted from deviation of the reflex angle due to ligand delamanid-HSA complex forming. The binding occurred spontaneously after delamanid was presented to the HSA surface. The SPR mathematical fitting model revealed that the association rate constant (kon) was 2.62 × 108 s-1M-1 and the dissociation rate constant (koff) was 5.65 × 10-3 s-1. The complexes were performed with an association constant (KA) of 4.64 × 1010 M-1 and the dissociation constant (KD) of 2.15 × 10-11 M. The binding constant indicated high binding affinity and high stability of the complex in an equilibrium. Modified CD spectra revealed that conformation of the HSA structure was altered by the presence of delamanid during preparation of the proliposomes that led to the reduction of secondary structure stabilization. This was indicated by the percentage decrease of α-helix. These findings are beneficial to understanding delamanid-HSA binding characteristics as well as the drug administration regimen.

Screening, separation and identification of metal-chelating peptides for nutritional, cosmetics and pharmaceutical applications

Metal-chelating peptides, which form metal-peptide coordination complexes with various metal ions, can be used as biofunctional ingredients notably to enhance human health and prevent diseases. This review aims to discuss recent insights into food-derived metal-chelating peptides, the strategies set up for their discovery, their study, and identification. After understanding the overall properties of metal-chelating peptides, their production from food-derived protein sources and their potential applications will be discussed, particularly in nutritional, cosmetics and pharmaceutical fields. In addition, the review provides an overview of the last decades of progress in discovering food-derived metal-chelating peptides, addressing several screening, separation and identification methodologies. Furthermore, it emphasizes the methods used to assess peptide-metal interaction, allowing for better understanding of chemical and thermodynamic parameters associated with the formation of peptide-metal coordination complexes, as well as the specific amino acid residues that play important roles in the metal ion coordination.

Factors affecting product association as a mechanism of host-cell protein persistence in bioprocessing

Product association of host-cell proteins (HCPs) to monoclonal antibodies (mAbs) is widely regarded as a mechanism that can enable HCP persistence through multiple purification steps and even into the final drug substance. Discussion of this mechanism often implies that the existence or extent of persistence is directly related to the strength of binding but actual measurements of the binding affinity of such interactions remain sparse. Two separate avenues of investigation of HCP-mAb binding are reported here. One is the measurement of the affinity of binding of individual, commonly persistent Chinese hamster ovary (CHO) HCPs to each of a set of mAbs, and the other uses quantitative proteomic measurements to assess binding of HCPs in a null CHO harvested cell culture fluid (HCCF) to mAbs produced in the same cell line. The individual HCP measurements show that the binding affinities of individual HCPs to different mAbs can vary appreciably but are rarely very high, with only weak pH dependence. The measurements on the null HCCF allow estimation of individual HCP-mAb affinities; these are typically weaker than those seen in affinity measurements on isolated HCPs. Instead, the extent of binding appears correlated with the initial abundance of individual HCPs in the HCCF and the forms of the HCPs in the solution, i.e., whether HCPs are present as free molecules or as parts of large aggregates. Separate protein A chromatography experiments performed by feeding different fractions of a mAb-containing HCCF obtained by size-exclusion chromatography (SEC) showed clear differences in the number and identity of HCPs found in the protein A eluate. These results indicate a significant role for HCP-mAb association in determining HCP persistence through protein A chromatography, presumably through binding of HCP-mAb complexes to the resin. Overall, the results illustrate the importance of considering more fully the biophysical context of HCP-product association in assessing the factors that may affect the phenomenon and determine its implications. Knowledge of the abundances and the forms of individual or aggregated HCPs in HCCF are particularly significant, emphasizing the integration of upstream and downstream bioprocessing and the importance of understanding the collective properties of HCPs in addition to just the biophysical properties of individual HCPs.

Insights into spirotetramat-induced thyroid disruption during zebrafish (Danio rerio) larval development: An integrated approach with in vivo, in vitro, and in silico analyses

Spirotetramat (SPT), a tetronic acid-derived insecticide, is implicated in reproductive and lipid metabolism disorders, as well as developmental toxicity in fish. While these effects are documented, the precise mechanisms underlying its developmental toxicity are not fully elucidated. In this study, zebrafish embryos (2 h post-fertilization, hpf) were exposed to four concentrations of SPT (0, 60, 120, and 240 μg/L) until 21 dpf (days post-fertilization). We delved into the mechanisms by examining its potential disruption of the thyroid endocrine system, employing in vivo, in vitro, and in silico assays. The findings showed notable developmental disturbances, including reduced hatching rates, shortened body lengths, and decelerated heart rates. Additionally, there was an increase in malformations and a decline in locomotor activity. Detailed analyses revealed that SPT exposure led to elevated thyroid hormone levels, perturbed the hypothalamic-pituitary-thyroid (HPT) axis transcript levels, amplified deiodinase type I (Dio1) and deiodinase type II (Dio2) activities, and both transcriptionally and proteomically upregulated thyroid receptor beta (TRβ) in larvae. Techniques like molecular docking and surface plasmon resonance (SPR) confirmed SPT's affinity for TRβ, consistent with in vitro findings suggesting its antagonistic effect on the T3-TR complex. These insights emphasize the need for caution in using tetronic acid-derived insecticides.

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).

Identification of chemical compounds of Schizonepeta tenuifolia Briq. and screening of neuraminidase inhibitors based on AUF-MS and SPR technology

Schizonepeta tenuifolia Briq., as a traditional Chinese medicine, has the effect of treating influenza. There have been few comprehensive studies on the holistic chemical composition of Schizonepeta tenuifolia and the active substances acting on neuraminidase (NA) to treat influenza. In present study, a synthetic identification method including GC-MS and UPLC-Q-Orbitrap-MS combined with GNPS (Global Natural Product Social Molecular Network) technology was established and applied to identify the chemical constituents of Schizonepeta tenuifolia Briq. A total of 134 compounds were identified, including 42 volatile components and 92 non-volatile components. The potential NA inhibitors of Schizonepeta tenuifolia were explored by an affinity ultrafiltration - mass spectrometry - surface plasmon resonance (AUF-MS-SPR) strategy. Eleven compounds were screened out by AUF-MS and their binding forces to NA were detected by SPR. Among them, 5 compounds with excellent binding ability were further tested the KD value. Meanwhile, the NA inhibitory activities of the 11 compounds were verified in vitro. In conclusion, a holistic material base was established to provide a reference for further development of Schizonepeta tenuifolia and an AUF-MS-SPR strategy based on binding ability was selected to screen substances of interest from complex systems.

Use of Open Surface Plasmon Resonance (OpenSPR) to Characterize the Binding Affinity of Protein-Protein Interactions

Surface Plasmon Resonance(SPR) is a label-free optical technique to assess protein-protein interaction kinetics and affinities in a real-time setting. Traditionally, Biacore SPR employs a continuous film of gold to detect any change in the angle of re-emitted light when the refractive index of a ligand conjugated to the flat gold surface is altered by its interaction with a local analyte. In contrast, the Nicoya Lifesciences' OpenSPR technology uses gold nanoparticles to detect small changes in the absorbance peak wavelength of a conjugated ligand after its engagement by an analyte. Specifically, when broadband white light is shone onto the gold nanoparticles, it produces a strong resonance absorbance peak corresponding to the refractive index of a ligand conjugated to the surface of gold nanoparticles. Upon its interaction with an analyte, however, the absorbance wavelength peak of the conjugated ligand will be changed and timely recorded as sensorgrams of dynamic ligand-analyte interactions. Thus, the improvement in the detection method (from traditional detection of changes in the angle of re-emitted light to the contemporary detection of changes in the wavelength of the absorbance peak) features OpenSPR as a cost-effective and user-friendly technique for in-depth characterization of protein-protein interactions. Here, we describe the detailed method that we used to characterize procathepsin L (pCTS-L) interactions with two putative pattern recognition receptors (TLR4 and RAGE) using the 1st generation of Nicoya Lifesciences' OpenSPR instrument with a 1-channel detection. Key features • Nicoya OpenSPR is a benchtop small-size equipment that provides in-depth label-free binding kinetics and affinity measurement for protein-protein interactions in real-time fashion. • This technology is relatively intuitive and user-friendly for scientists at any skill level. • OpenSPR sensors employ nanotechnology to reduce the cost of manufacturing complex optical hardware and Sensor Chips, and similarly reduce the consumption of precious analyte samples. • The manufacturer provides online training for OpenSPR (Catalog: TRAIN-REMOTE) and TraceDrawer (Catalog: TRAIN-TD) to customer scientists.

Soluble endoglin reduces thrombus formation and platelet aggregation via interaction with αIIbβ3 integrin

BACKGROUND

The circulating form of human endoglin (sEng) is a cleavage product of membrane-bound endoglin present on endothelial cells. Because sEng encompasses an RGD motif involved in integrin binding, we hypothesized that sEng would be able to bind integrin αIIbβ3, thereby compromising platelet binding to fibrinogen and thrombus stability.

METHODS

In vitro human platelet aggregation, thrombus retraction, and secretion-competition assays were performed in the presence of sEng. Surface plasmon resonance (SPR) binding and computational (docking) analyses were carried out to evaluate protein-protein interactions. A transgenic mouse overexpressing human sEng (hsEng+) was used to measure bleeding/rebleeding, prothrombin time (PT), blood stream, and embolus formation after FeCl3-induced injury of the carotid artery.

RESULTS

Under flow conditions, supplementation of human whole blood with sEng led to a smaller thrombus size. sEng inhibited platelet aggregation and thrombus retraction, interfering with fibrinogen binding, but did not affect platelet activation. SPR binding studies demonstrated that the specific interaction between αIIbβ3 and sEng and molecular modeling showed a good fitting between αIIbβ3 and sEng structures involving the endoglin RGD motif, suggesting the possible formation of a highly stable αIIbβ3/sEng. hsEng+ mice showed increased bleeding time and number of rebleedings compared to wild-type mice. No differences in PT were denoted between genotypes. After FeCl3 injury, the number of released emboli in hsEng+ mice was higher and the occlusion was slower compared to controls.

CONCLUSIONS

Our results demonstrate that sEng interferes with thrombus formation and stabilization, likely via its binding to platelet αIIbβ3, suggesting its involvement in primary hemostasis control.

A split GAL4 RUBY assay for visual in planta detection of protein-protein interactions

Protein-protein interactions (PPIs) are a fundamental process in cellular biogenesis. Here we have developed a split GAL4 RUBY assay that enables macroscopically visual PPI detection in plant leaves in real time. Candidate interacting protein partners are fused to specific domains of the yeast GAL4 and herpes simplex virus VP16 transcription factors and transiently expressed in Nicotiana benthamina leaves by Agrobacterium infiltration. PPI, that may be either direct or indirect, results in transcriptional activation of a RUBY reporter gene leading to the production of the highly visual metabolite, betalain, in leaf tissue of living plants. Samples require no processing for in planta visual qualitative assessment, but with very simple processing steps the assay is quantitative. Its accuracy is demonstrated using a series of known interacting protein partners and mutant derivatives including transcription factors, signalling molecules and plant resistance proteins with cognate pathogen effectors. Using this assay, association between the wheat Sr27 stem rust disease resistance protein and corresponding AvrSr27 avirulence effector family produced by the rust pathogen is detected. Interaction is also observed between this resistance protein and the effector encoded by the corresponding avrSr27-3 virulence allele. However, this association appears weaker in the split GAL4 RUBY assay, which coupled with lower avrSr27-3 expression during stem rust infection, likely enables virulent races of the rust pathogen to avoid Sr27-mediated detection.

Sensing Mechanisms of Rough Plasmonic Surfaces for Protein Binding of Surface Plasmon Resonance Detection

Surface plasmon resonance (SPR) has been utilized in various optical applications, including biosensors. The SPR-based sensor is a gold standard for protein kinetic measurement due to its ultrasensitivity on the plasmonic metal surface. However, a slight change in the surface morphology, such as roughness or pattern, can significantly impact its performance. This study proposes a theoretical framework to explain sensing mechanisms and quantify sensing performance parameters of angular surface plasmon resonance detection for binding kinetic sensing at different levels of surface roughness. The theoretical investigation utilized two models, a protein layer coating on a rough plasmonic surface with and without sidewall coatings. The two models enable us to separate and quantify the enhancement factors due to the localized surface plasmon polaritons at sharp edges of the rough surfaces and the increased surface area for protein binding due to roughness. The Gaussian random surface technique was employed to create rough metal surfaces. Reflectance spectra and quantitative performance parameters were simulated and quantified using rigorous coupled-wave analysis and Monte Carlo simulation. These parameters include sensitivity, plasmonic dip position, intensity contrast, full width at half maximum, plasmonic angle, and figure of merit. Roughness can significantly impact the intensity measurement of binding kinetics, positively or negatively, depending on the roughness levels. Due to the increased scattering loss, a tradeoff between sensitivity and increased roughness leads to a widened plasmonic reflectance dip. Some roughness profiles can give a negative and enhanced sensitivity without broadening the SPR spectra. We also discuss how the improved sensitivity of rough surfaces is predominantly due to the localized surface wave, not the increased density of the binding domain.

Protein Interaction Analysis by Surface Plasmon Resonance

Surface plasmon resonance (SPR) is an optical technique that is utilized for detecting molecular interactions that occur in direct protein-protein interactions. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light that is completely reflected, after polarized light impinges upon the surface, is altered and monitored as a change in detector position for a dip in reflected intensity (the surface plasmon resonance phenomenon). Because the method strictly detects mass, there is no need to label the interacting components, thus eliminating possible changes of their molecular properties. One of the advantages in SPR is its high sensitivity, compatible with the need for purification of small amounts of protein for analysis. This chapter concentrates on practical methodologies for performing surface plasmon resonance analysis.

Analytical Method for Experimental Validation of Computer-Designed Antibody

In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (K_D) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate K_D value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.

The role of KiSS1 gene on the growth and migration of prostate cancer and the underlying molecular mechanisms

Metastatic prostate cancers have a high mortality rate. KiSS1 was originally identified as a metastasis suppressor gene in metastatic melanoma and breast cancer, but its role in prostate cancer has been contradictory. This study was therefore undertaken to investigate the effects of KiSS1 overexpression on the growth and migration of human metastatic prostate cancer cells. We first tested the effect of KiSS1 overexpression on the growth and migration of DU145 human metastatic prostate cancer cells in vitro. DU145 cells were infected with the culture medium of 293T cells, which produce lentivirus particles containing KiSS1. A 2.5-fold increase in proliferation of KiSS1-overexpressing cancer cells was observed, and these cells formed tumor spheroids about 3 times larger than the vector control group. qPCR and immunoblotting revealed the association between increased cell growth and regulation of the PI3K/Akt and cell cycle genes, and also that increases in β-catenin and CD133 contribute to tumor aggregation. KiSS1 overexpression resulted in upregulation of the β-arrestin1/2 and Raf-MEK-ERK-NF-κB pathways via KiSS1R. Moreover, the migration and invasion of KiSS1-overexpressing cells were determined to be faster than the control group, along with 1.6-fold increased metastatic colonization of the KiSS1-overexpressing cancer cells. These were associated to the regulation of EMT gene expressions, such as E-cadherin and N-cadherin, and the upregulation of MMP9. In a xenograft mouse model inoculated with DU145 cells infected GFP or KiSS1 via a lentiviral vector, KiSS1 statistically significantly increased the tumor growth, with upregulation of PCNA and Ki-67 in the tumor tissues. In addition, KiSS1 increased the angiogenic capacity by upregulating VEGF-A and CD31, both in vitro and in vivo. Taken together, our results indicate that KiSS1 not only induces prostate cancer proliferation, but also promotes metastasis by increasing the migration, invasion, and angiogenesis of malignant cells.

Lipid Metabolic Disorder Induced by Pyrethroids in Nonalcoholic Fatty Liver Disease of Xenopus laevis

Pyrethroids, an effective and widely used class of pesticides, have attracted considerable concerns considering their frequent detection in environmental matrices. However, their potential health risks to amphibians remain unclear. In our study, female Xenopus laevis were exposed to 0, 0.06, and 0.3 μg/L typical pyrethroid, cis-bifenthrin (cis-BF), for 3 months. Elevated activities of both aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were observed, indicating an ongoing liver injury. Furthermore, exposure to cis-BF led to hyperlipidemia and lipid accumulation in the liver of Xenopus. The targeted lipidomic analysis further revealed that treatment with cis-BF perturbed liver steroid homeostasis, as evidenced by the enriched lipids in the steroid biosynthesis pathway. Consistent with the targeted lipidomic result, treatment with cis-BF changed the liver transcriptome profile with induction of 808 and 1230 differentially expressed genes. Kyoto Encyclopedia of Genes and Genomes analysis underlined the adverse effects of cis-BF exposure on steroid biosynthesis, primary bile acid biosynthesis, and the PPAR signaling pathway in the Xenopus liver. Taken together, our study revealed that exposure to cis-BF at environmentally relevant concentrations resulted in lipid metabolic disorder associated with nonalcoholic fatty liver disease of X. laevis, and our results provided new insight into the potential long-term hazards of pyrethroids.

Membrane Progesterone Receptors (mPRs, PAQRs): Review of Structural and Signaling Characteristics

The role of membrane progesterone receptors (mPRs), which belong to the progestin and adipoQ receptor (PAQR) family, in mediating rapid, nongenomic (non-classical) progestogen actions has been extensively studied since their identification 20 years ago. Although the mPRs have been implicated in progestogen regulation of numerous reproductive and non-reproductive functions in vertebrates, several critical aspects of their structure and signaling functions have been unresolved until recently and remain the subject of considerable debate. This paper briefly reviews recent developments in our understanding of the structure and functional characteristics of mPRs. The proposed membrane topology of mPRα, the structure of its ligand-binding site, and the binding affinities of steroids were predicted from homology modeling based on the structures of other PAQRs, adiponectin receptors, and confirmed by mutational analysis and ligand-binding assays. Extensive data demonstrating that mPR-dependent progestogen regulation of intracellular signaling through mPRs is mediated by activation of G proteins are reviewed. Close association of mPRα with progesterone membrane receptor component 1 (PGRMC1), its role as an adaptor protein to mediate cell-surface expression of mPRα and mPRα-dependent progestogen signaling has been demonstrated in several vertebrate models. In addition, evidence is presented that mPRs can regulate the activity of other hormone receptors.

Designer DNA nanostructures for viral inhibition

Emerging viral diseases can substantially threaten national and global public health. Central to our ability to successfully tackle these diseases is the need to quickly detect the causative virus and neutralize it efficiently. Here we present the rational design of DNA nanostructures to inhibit dengue virus infection. The designer DNA nanostructure (DDN) can bind to complementary epitopes on antigens dispersed across the surface of a viral particle. Since these antigens are arranged in a defined geometric pattern that is unique to each virus, the structure of the DDN is designed to mirror the spatial arrangement of antigens on the viral particle, providing very high viral binding avidity. We describe how available structural data can be used to identify unique spatial patterns of antigens on the surface of a viral particle. We then present a procedure for synthesizing DDNs using a combination of in silico design principles, self-assembly, and characterization using gel electrophoresis, atomic force microscopy and surface plasmon resonance spectroscopy. Finally, we evaluate the efficacy of a DDN in inhibiting dengue virus infection via plaque-forming assays. We expect this protocol to take 2-3 d to complete virus antigen pattern identification from existing cryogenic electron microscopy data, ~2 weeks for DDN design, synthesis, and virus binding characterization, and ~2 weeks for DDN cytotoxicity and antiviral efficacy assays.

Probing GPCR Dimerization Using Peptides

G protein-coupled receptors (GPCRs) are the largest class of membrane proteins and the most common and extensively studied pharmacological target. Numerous studies over the last decade have confirmed that GPCRs do not only exist and function in their monomeric form but in fact, have the ability to form dimers or higher order oligomers with other GPCRs, as well as other classes of receptors. GPCR oligomers have become increasingly attractive to investigate as they have the ability to modulate the pharmacological responses of the receptors which in turn, could have important functional roles in diseases, such as cancer and several neurological & neuropsychiatric disorders. Despite the growing evidence in the field of GPCR oligomerisation, the lack of structural information, as well as targeting the 'undruggable' protein-protein interactions (PPIs) involved in these complexes, has presented difficulties. Outside the field of GPCRs, targeting PPIs has been widely studied, with a variety of techniques being investigated; from small-molecule inhibitors to disrupting peptides. In this review, we will demonstrate several physiologically relevant GPCR dimers and discuss an array of strategies and techniques that can be employed when targeting these complexes, as well as provide ideas for future development.

A Fiber-Optic Surface Plasmon Resonance Sensor for Bio-Detection in Visible to Near-Infrared Images

In this paper, we demonstrate a fiber-optic surface plasmon resonance (FO-SPR) biosensor based on image processing and back propagation (BP) neural network. The transmitted light of the FO-SPR sensor was captured by using visible (VIS) and near-infrared (NIR) CMOS sensors. The optical information related to the SPR effect was extracted from images based on grayscale conversion and an edge detection algorithm. To achieve accurate monitoring of refractive index (RI) changes, the grayscale means of the VIS and NIR images and the RGB summation of the edge-detected images were used as training and test inputs for the BP neural network. We verified the effectiveness and superiority of this sensing system by experiments on sodium chloride solution identification and protein binding detection. This work is promising for practical applications in standardized biochemical sensing.

Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection

Ligand-dependent changes in protein conformation are foundational to biology. Historical mechanistic models for substrate-specific proteins are induced fit (IF) and conformational selection (CS), which invoke a change in protein conformation after ligand binds or before ligand binds, respectively. These mechanisms have important, but rarely discussed, functional relevance because IF vs. CS can differentially affect a protein's substrate specificity or promiscuity, and its regulatory properties. The modern view of proteins as conformational ensembles in both ligand free and bound states, together with the realization that most proteins exhibit some substrate promiscuity, demands a deeper interpretation of the historical models and provides an opportunity to improve mechanistic analyses. Here we describe alternative analytical strategies for distinguishing the historical models, including the more complex expanded versions of IF and CS. Functional implications of the different models are described. We provide an alternative perspective based on protein ensembles interacting with ligand ensembles that clarifies how a single protein can 'apparently' exploit different mechanisms for different ligands. Mechanistic information about protein ensembles can be optimized when they are probed with multiple ligands.

A strategy of screening and binding analysis of bioactive components from traditional Chinese medicine based on surface plasmon resonance biosensor

Elucidating the active components of traditional Chinese medicine (TCM) is essential for understanding the mechanisms of TCM and promote its rational use as well as TCM-derived drug development. Recent studies have shown that surface plasmon resonance (SPR) technology is promising in this field. In the present study, we propose an SPR-based integrated strategy to screen and analyze the major active components of TCM. We used Radix Paeoniae Alba (RPA) as an example to identify the compounds that can account for its anti-inflammatory mechanism via tumor necrosis factor receptor type 1 (TNF-R1). First, RPA extraction was analyzed using an SPR-based screening system, and the potential active ingredients were collected, enriched, and identified as paeoniflorin and paeonol. Next, the affinity constants of paeoniflorin and paeonol were determined as 4.9 and 11.8 μM, respectively. Then, SPR-based competition assays and molecular docking were performed to show that the two compounds could compete with tumor necrosis factor-α (TNF-α) while binding to the subdomain 1 site of TNF-R1. Finally, in biological assays, the two compounds suppressed cytotoxicity and apoptosis induced by TNF-α in the L929 cell line. These findings prove that SPR technology is a useful tool for determining the active ingredients of TCM at the molecular level and can be used in various aspects of drug development. The SPR-based integrated strategy is reliable and feasible in TCM studies and will shed light on the elucidation of the pharmacological mechanism of TCM and facilitate its modernization.

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A surface plasmon resonance-based integrated strategy was established to analyze traditional Chinese medicine.

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Surface plasmon resonance technology can be used for ligand screening, affinity detection, and binding site confirmation.

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Paeoniflorin and paeonol were identified as TNF-R1-bound ingredients in RPA.

Thrombopoietin receptor-based protein-protein interaction screening (THROPPIS)

As protein-protein interactions (PPIs) are involved in many cellular events, development of mammalian cytosolic PPI detection systems is important for drug discovery as well as understanding biological phenomena. We have previously reported a c-kit-based PPI screening (KIPPIS) system, in which proteins of interest were fused with a receptor tyrosine kinase c-kit, leading to intracellular PPI-dependent cell growth. However, it has not been investigated whether PPI can be detected using other receptors. In this study, we employed a thrombopoietin receptor, which belongs to the Type I cytokine receptor family, to develop a thrombopoietin receptor-based PPI screening (THROPPIS) system. To improve the sensitivity of THROPPIS, we examined two strategies of (i) localization of the chimeric receptors on the cell membrane, and (ii) addition of a helper module to the chimeric receptors. Intriguingly, the nonlocalized chimeric receptor showed the best performance of THROPPIS. Furthermore, the addition of the helper module dramatically improved the detection sensitivity. In total, 5 peptide-domain interactions were detected successfully, demonstrating the versatility of THROPPIS. In addition, a peptide-domain interaction was detected even when insulin receptor or epidermal growth factor receptor was used as a signaling domain, demonstrating that this PPI detection system can be extended to other receptors.

Analysis of Effects of Surface Roughness on Sensing Performance of Surface Plasmon Resonance Detection for Refractive Index Sensing Application

This paper provides a theoretical framework to analyze and quantify roughness effects on sensing performance parameters of surface plasmon resonance measurements. Rigorous coupled-wave analysis and the Monte Carlo method were applied to compute plasmonic reflectance spectra for different surface roughness profiles. The rough surfaces were generated using the low pass frequency filtering method. Different coating and surface treatments and their reported root-mean-square roughness in the literature were extracted and investigated in this study to calculate the refractive index sensing performance parameters, including sensitivity, full width at half maximum, plasmonic dip intensity, plasmonic dip position, and figure of merit. Here, we propose a figure-of-merit equation considering optical intensity contrast and signal-to-noise ratio. The proposed figure-of-merit equation could predict a similar refractive index sensing performance compared to experimental results reported in the literature. The surface roughness height strongly affected all the performance parameters, resulting in a degraded figure of merit for surface plasmon resonance measurement.

Quantification of chromogranin A using a surface plasmon resonance-based biosensor

The chromogranin A (CgA) level in the blood is an important biomarker for neuroendocrine tumors and other diseases. Traditional methods for detecting CgA are expensive and time-consuming with low reproducibility. In this study, surface plasmon resonance (SPR), a simple and label-free technique, was validated for quantifying CgA. CgA antibody (CgA-Ab) was immobilized on the CM5 sensor chip (CgA-Ab-CM5) at optimal conditions (pH 5.0, 10 μg mL^-1). Next, different concentrations of CgA were measured by CgA-Ab-CM5. The binding and regeneration conditions were optimized and used in each measurement. A binding time of 240 s, and flow rate of 30 μL min^-1 were chosen as the optimal binding conditions. A pH of 1.75 was the optimal regeneration condition. Compared to the detection range of 23.4-187 ng mL^-1 for enzyme-linked immunosorbent assay (ELISA), a linear range of 0.2-187 ng mL^-1 was detected based on the response unit (RU), showing high sensitivity and reliability of SPR. Finally, the reproducibility of the CgA-Ab-CM5 chip was accessed by consecutive binding-regeneration cycles for 300 times. In conclusion, the SPR-based CgA-Ab-CM5 chip is a sensitive and reproducible method for quantifying CgA levels in a real-time manner.

Structure - Functionality of lentil protein-polyphenol conjugates

Lentil protein isolate (LPI) was conjugated with plant polyphenols (quercetin, rutin, ellagic acid), and the structural and functional characteristics of the conjugates were determined in comparison with the proteins and pure polyphenols. The interaction between polyphenols and protein was achieved by a grafting method at pH 9.0 in the presence of atmospheric oxygen. Surface plasmon resonance measurements showed polyphenols' direct interaction with LPI, with the order of binding strength quercetin > ellagic acid > rutin. The degree of conjugation also followed the same order. Structural analysis of the conjugates was performed using FTIR, intrinsic fluorescence, and surface hydrophobicity. A significant improvement in DPPḢ radical scavenging and ferric reducing antioxidant power of the conjugates was observed compared to the polyphenols. However, there was a decrease in the surface activity of the conjugates compared to LPI. Such conjugation provides a novel way to combine the advantages of using plant protein and polyphenols in developing a novel food ingredient.

Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions

Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.

Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication

Characteristically, cells must sense and respond to environmental cues. Despite the importance of cell-cell communication, our understanding remains limited and often lacks glycans. Glycans decorate proteins and cell membranes at the cell-environment interface, and modulate intercellular communication, from development to pathogenesis. Providing further challenges, glycan biosynthesis and cellular behavior are co-regulating systems. Here, we discuss how glycosylation contributes to extracellular responses and signaling. We further organize approaches for disentangling the roles of glycans in multicellular interactions using newly available datasets and tools, including glycan biosynthesis models, omics datasets, and systems-level analyses. Thus, emerging tools in big data analytics and systems biology are facilitating novel insights on glycans and their relationship with multicellular behavior.

Elucidating the protein substrate recognition of O-GlcNAc transferase (OGT) toward O-GlcNAcase (OGA) using a GlcNAc electrophilic probe

The essential human O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is the sole enzyme responsible for modifying thousands of intracellular proteins with the monosaccharide O-GlcNAc. This unique modification plays crucial roles in human health and disease, but the substrate recognition of OGT remains poorly understood. Intriguingly, the only human enzyme reported to remove this modification, O-GlcNAcase (OGA), is O-GlcNAc modified. Here, we exploited a GlcNAc electrophilic probe (GEP1A) to rapidly screen OGT mutants in a fluorescence assay that can discriminate between altered OGT-sugar and -protein substrate binding to help elucidate the binding mode of OGT toward OGA protein substrate. Since OGT tetratricopeptide repeat (TPR) domain plays a key role in OGT-OGA binding, we screened 30 OGT TPR mutants, which revealed 15 "ladder like" asparagine or aspartate residues spanning TPRs 3-7 and 10-13.5 that affect OGA O-GlcNAcylation. By applying a truncated OGA construct, we found that OGA's N-terminal region or pseudo histone acetyltransferase domain is not required for its O-GlcNAcylation, suggesting OGT functionally interacts with OGA through its catalytic and/or stalk domains. This work represents the first effort to systemically investigate each OGT TPR and our findings will facilitate the development of new strategies to investigate the role of substrate-specific O-GlcNAcylation.

Nanomolar Protein-Protein Interaction Monitoring with a Label-Free Protein-Probe Technique

Protein-protein interactions (PPIs) are an essential part of correct cellular functionality, making them increasingly interesting drug targets. While Förster resonance energy transfer-based methods have traditionally been widely used for PPI studies, label-free techniques have recently drawn significant attention. These methods are ideal for studying PPIs, most importantly as there is no need for labeling of either interaction partner, reducing potential interferences and overall costs. Already, several different label-free methods are available, such as differential scanning calorimetry and surface plasmon resonance, but these biophysical methods suffer from low to medium throughput, which reduces suitability for high-throughput screening (HTS) of PPI inhibitors. Differential scanning fluorimetry, utilizing external fluorescent probes, is an HTS compatible technique, but high protein concentration is needed for experiments. To improve the current concepts, we have developed a method based on time-resolved luminescence, enabling PPI monitoring even at low nanomolar protein concentrations. This method, called the protein probe technique, is based on a peptide conjugated with Eu3+ chelate, and it has already been applied to monitor protein structural changes and small molecule interactions at elevated temperatures. Here, the applicability of the protein probe technique was demonstrated by monitoring single-protein pairing and multiprotein complexes at room and elevated temperatures. The concept functionality was proven by using both artificial and multiple natural protein pairs, such as KRAS and eIF4A together with their binding partners, and C-reactive protein in a complex with its antibody.

Proteomics of host-bacterial interactions: new insights from dual perspectives

Mass-spectrometry (MS)-based proteomics is a powerful and robust platform for studying the interactions between biological systems during health and disease. Bacterial infections represent a significant threat to global health and drive the pursuit of novel therapeutic strategies to combat emerging and resistant pathogens. During infection, the interplay between a host and pathogen determines the ability of the microbe to survive in a hostile environment and promotes an immune response by the host as a protective measure. It is the protein-level changes from either biological system that define the outcome of infection, and MS-based proteomics provides a rapid and effective platform to identify such changes. In particular, proteomics detects alterations in protein abundance, quantifies protein secretion and (or) release, measures an array of post-translational modifications that influence signaling cascades, and profiles protein-protein interactions through protein complex and (or) network formation. Such information provides new insight into the role of known and novel bacterial effectors, as well as the outcome of host cell activation. In this Review, we highlight the diverse applications of MS-based proteomics in profiling the relationship between bacterial pathogens and the host. Our work identifies a plethora of strategies for exploring mechanisms of infection from dual perspectives (i.e., host and pathogen), and we suggest opportunities to extrapolate the current knowledgebase to other biological systems for applications in therapeutic discovery.

Unraveling the Effect of a Potentiating Anti-Factor H Antibody on Atypical Hemolytic Uremic Syndrome-Associated Factor H Variants

The complement system plays an important role in our innate immune system. Complement activation results in clearance of pathogens, immune complex, and apoptotic cells. The host is protected from complement-mediated damage by several complement regulators. Factor H (FH) is the most important fluid-phase regulator of the alternative pathway of the complement system. Heterozygous mutations in FH are associated with complement-related diseases such as atypical hemolytic uremic syndrome (aHUS) and age-related macular degeneration. We recently described an agonistic anti-FH mAb that can potentiate the regulatory function of FH. This Ab could serve as a potential new drug for aHUS patients and alternative to C5 blockade by eculizumab. However, it is unclear whether this Ab can potentiate FH mutant variants in addition to wild-type (WT) FH. In this study, the functionality and potential of the agonistic Ab in the context of pathogenic aHUS-related FH mutant proteins was investigated. The binding affinity of recombinant WT FH and the FH variants, W1183L, V1197A, R1210C, and G1194D to C3b was increased upon addition of the potentiating Ab and similarly, the decay-accelerating activity of all mutants is increased. The potentiating anti-FH Ab is able to restore the surface regulatory function of most of the tested FH mutants to WT FH levels on a human HAP-1 cell line and on sheep erythrocytes. In conclusion, our potentiating anti-FH is broadly active and able to enhance both WT FH function as well as most aHUS-associated FH variants tested in this study.

Development of a Microscale Thermophoresis-Based Method for Screening and Characterizing Inhibitors of the Methyl-Lysine Reader Protein MRG15

MRG15 is a transcription factor containing the methyl-lysine reader chromodomain. Despite its involvement in different physiological and pathological states, to date the role of this protein has not been fully elucidated due to the lack of a specific and potent chemical probe.In this work, we report the development of a microscale thermophoresis (MST)-based assay for the study of MRG15-ligand binding interactions. After the development, the assay was validated using a small focused library and UNC1215 as the reference compound, to yield the identification of 10 MRG15 ligands with affinities ranging from 37.8 nM to 59.1 µM.Hence, our method is robust, convenient, and fast and could be applied to other methylation reader domain-containing proteins for the identification of new chemical probes.

Low-Fouling Substrates for Plasmonic Sensing of Circulating Biomarkers in Biological Fluids

The monitoring of biomarkers in body fluids provides valuable prognostic information regarding disease onset and progression. Most biosensing approaches use noninvasive screening tools and are conducted in order to improve early clinical diagnosis. However, biofouling of the sensing surface may disturb the quantification of circulating biomarkers in complex biological fluids. Thus, there is a great need for antifouling interfaces to be designed in order to reduce nonspecific adsorption and prevent inactivation of biological receptors and loss of sensitivity. To address these limitations and enable their application in clinical practice, a variety of plasmonic platforms have been recently developed for biomarker analysis in easily accessible biological fluids. This review presents an overview of the latest advances in the design of antifouling strategies for the detection of clinically relevant biomarkers on the basis of the characteristics of biological samples. The impact of nanoplasmonic biosensors as point-of-care devices has been examined for a wide range of biomarkers associated with cancer, inflammatory, infectious and neurodegenerative diseases. Clinical applications in readily obtainable biofluids such as blood, saliva, urine, tears and cerebrospinal and synovial fluids, covering almost the whole range of plasmonic applications, from surface plasmon resonance (SPR) to surface-enhanced Raman scattering (SERS), are also discussed.

Evaluation of the binding properties of drugs to albumin from DSC thermograms

There is a demand in rapid and robust methods to determine the affinity of drugs to receptors, enzymes, and transport proteins. Differential scanning calorimetry (DSC) is a common method to prove the existence of ligand-protein binding from the shift of denaturation peak, but it is rarely used to obtain the binding constant values. The work is aimed to prove that the DSC experiments can be a source of reliable values of the binding constants and information on the stoichiometry of drug-albumin binding. DSC thermograms of bovine serum albumin denaturation in the presence of several drugs with different affinity and stoichiometry of binding to albumin: naproxen, warfarin, ibuprofen, and isoniazid were recorded. The dependences of the denaturation peak maximum temperature and area on the molar drug/protein ratio, which varied from 0 to 100, were considered. With the help of numerical modeling of the DSC curves, these dependences were predicted using the binding parameters determined in independent experiments and a simple two-state model of denaturation. The DSC data at relatively small concentrations of ligands are in good agreement with the calculation results. The deviations from the model predictions at high ligand concentrations in the cases of naproxen and ibuprofen indicate that albumin is able to bind several additional molecules of these drugs with its low-affinity sites. The fit was improved by using a sequential binding model with two binding constants K₁ = 1.0 × 10⁷ and K₂ = 1.0 × 10⁴ for naproxen and a cooperative binding model for ibuprofen. The stoichiometry of drug-albumin complexes fully saturated with drug ligand was calculated from the dependence of the denaturation temperature on the drug concentration. In the case of isoniazid, DSC thermograms indicated very weak binding to albumin.

Morphological analysis of Apolipoprotein E binding to Aβ Amyloid using a combination of Surface Plasmon Resonance, Immunogold Labeling and Scanning Electron Microscopy

Background

Immunogold labeling in combination with transmission electron microscopy analysis is a technique frequently used to correlate high-resolution morphology studies with detailed information regarding localization of specific antigens. Although powerful, the methodology has limitations and it is frequently difficult to acquire a stringent system where unspecific low-affinity interactions are removed prior to analysis.

Results

We here describe a combinatorial strategy where surface plasmon resonance and immunogold labeling are used followed by a direct analysis of the sensor-chip surface by scanning electron microscopy. Using this approach, we have probed the interaction between amyloid-β fibrils, associated to Alzheimer’s disease, and apolipoprotein E, a well-known ligand frequently found co-deposited to the fibrillar form of Aβ in vivo. The results display a lateral binding of ApoE along the amyloid fibrils and illustrates how the gold-beads represent a good reporter of the binding.

Conclusions

This approach exposes a technique with generic features which enables both a quantitative and a morphological evaluation of a ligand-receptor based system. The methodology mediates an advantage compared to traditional immunogold labeling since all washing steps can be monitored and where a high stringency can be maintained throughout the experiment.

Calcium-Induced Protein Folding in Calumenin and Calmodulin

Binding of calcium - and small molecules in general - often induce conformational changes in large molecules and complexes. The degree and type of change varies, but the resulting shift in specific affinities ultimately induces a physiological response. It is therefore important for our understanding of responses at the cellular level to define coupled changes at the molecular level.Calumenin, a six-EF-hand calcium-binding protein localized in the endoplasmic reticulum, undergoes substantial calcium-induced rearrangement. We have demonstrated how calumenin changes from being unfolded in the absence of calcium to a compact trilobal fold in the presence of calcium (Mazzorana et al., PLoS One 11:e0151547, 2016).Here, we describe protocols for the expression and purification of calumenin and calmodulin, another EF-hand protein modulated by calcium, along with protocols for biophysical techniques used to characterize calcium-induced changes to protein conformation. Analytical size-exclusion chromatography in the presence and absence of calcium provides an informed indication of any larger conformational movements. Circular dichroism spectroscopy reveals alterations to the secondary or tertiary structure, while small-angle X-ray scattering explores changes further providing low-resolution conformational details.Surface plasmon resonance estimates binding kinetics and affinities completing the biophysical description of these events.

The human complement receptor type 2 (CR2)/CR1 fusion protein TT32, a novel targeted inhibitor of the classical and alternative pathway C3 convertases, prevents arthritis in active immunization and passive transfer mouse models

Complement activation in human diseases is characterized by the local covalent deposition of the long-lived C3 fragments iC3b/C3dg/C3d. Previously, TT30, a complement alternative pathway (AP)-selective inhibitor, was designed as a fusion protein linking the first four short consensus repeats (SCRs) of human complement receptor type 2 (CR2) with the first five SCRs of human factor H (fH). TT30 acts by utilizing CR2 SCR1-4 to bind the initially formed iC3b/C3dg/C3d fragments and delivering surface-targeted inhibition of AP C3 and C5 convertases through fH SCR 1-5. In order to combine classical (CP) and lectin (LP) pathway inhibitory abilities employing CR2-mediated targeting, TT32 was developed. TT32 is a CR2-CR1 fusion protein using the first ten SCRs of CR1, chosen because they contain both C3 and C5 convertase inhibitory activity through utilization of decay-acceleration and cofactor activity for both AP and CP. In Wieslab assays, TT32 showed potent inhibition of the CP and AP with IC₅₀ of 11 and 46 nM, respectively. The TT32 inhibitory activity is partially blocked with a molar excess of a competing anti-CR2 mAb, thus demonstrating the importance of the CR2 targeting. TT32 was studied in the type II (CII) collagen-induced arthritis (CIA), an active immunization model, and the CII antibody-induced arthritis (CAIA) passive transfer model. In CIA, injection of 2.0 mg TT32 at day 21 and 28 post disease induction, but not untargeted CR1 alone, resulted in a 51.5% decrease in clinical disease activity (CDA). In CAIA, treatment with TT32 resulted in a 47.4% decrease in CDA. Therefore, a complement inhibitor that targets both the AP and CP/LP C3/C5 convertases was shown to limit complement-mediated tissue damage and inflammation in disease models in which all three complement activation pathways are implicated.

Anti-Drug Antibodies: Emerging Approaches to Predict, Reduce or Reverse Biotherapeutic Immunogenicity

The development of anti-drug antibodies (ADAs) following administration of biotherapeutics to patients is a vexing problem that is attracting increasing attention from pharmaceutical and biotechnology companies. This serious clinical problem is also spawning creative research into novel approaches to predict, avoid, and in some cases even reverse such deleterious immune responses. CD4⁺ T cells are essential players in the development of most ADAs, while memory B-cell and long-lived plasma cells amplify and maintain these responses. This review summarizes methods to predict and experimentally identify T-cell and B-cell epitopes in therapeutic proteins, with a particular focus on blood coagulation factor VIII (FVIII), whose immunogenicity is clinically significant and is the subject of intensive current research. Methods to phenotype ADA responses in humans are described, including T-cell stimulation assays, and both established and novel approaches to determine the titers, epitopes and isotypes of the ADAs themselves. Although rational protein engineering can reduce the immunogenicity of many biotherapeutics, complementary, novel approaches to induce specific tolerance, especially during initial exposures, are expected to play significant roles in future efforts to reduce or reverse these unwanted immune responses.