Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion

Antimalarial Delivery with a Ferritin-Based Protein Cage: A Step toward Developing Smart Therapeutics against Malaria

Over the past two decades, the utilization of protein cages has witnessed exponential growth driven by their extensive applications in biotechnology and therapeutics. In the context of the recent Covid-19 pandemic, protein-cage-based scaffolds played a pivotal role in vaccine development. Beyond vaccines, these protein cages have proven valuable in diverse drug delivery applications thanks to their distinctive architecture and structural stability. Among the various types of protein cages, ferritin-based cages have taken the lead in drug delivery applications. This is primarily attributed to their ease of production, exceptional thermal stability, and nontoxic nature. While ferritin-based cages are commonly employed in anticancer drug delivery and contrast agent delivery, their efficacy in malarial drug delivery had not been explored until this study. In this investigation, several antimalarial drugs were encapsulated within horse spleen ferritin, and the binding and loading processes were validated through both experimental and computational techniques. The data unequivocally demonstrate the facile incorporation of antimalarial drugs into ferritin without disrupting its three-dimensional structure. Computational docking and molecular dynamics simulations were employed to pinpoint the precise location of the drug binding site within ferritin. Subsequent efficacy testing on Plasmodium revealed that the developed nanoconjugate, comprising the drug-ferritin conjugate, exhibited significant effectiveness in eradicating the parasite. In conclusion, the findings strongly indicate that ferritin-based carrier systems hold tremendous promise for the future of antimalarial drug delivery, offering high selectivity and limited side effects.

Mung bean protein isolate: Extraction, structure, physicochemical properties, modifications, and food applications

The intake of plant-based proteins is rapidly growing around the world due to their nutritional and functional properties, as well as growing demand for vegetarian and vegan diets. Mung bean seeds have been traditionally consumed in Asian countries due to their unique botanical and health-promoting characteristics. In recent years, mung bean protein isolate (MBPI) has attracted much attention due to its ideal techno-functional features, such as water and oil absorption capacity, solubility, emulsifying, foaming, and thermal properties. Therefore, it can be utilized in a native or modified form in different food sectors, such as biodegradable/edible films, colloidal systems, and plant-based alternative products. This study provides a comprehensive review on the extraction methods, amino acid profile, structure, physicochemical properties, modifications, and food applications of MBPI.

Unraveling the binding behavior of the antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one with human serum albumin: Multi-spectroscopic, atomic force microscope, computational simulation, and esterase activity

As a marine antifouling biocide, 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) exhibited high toxicity to marine organisms. This study investigated the interaction between DCOIT and human serum albumin (HSA) using several spectroscopic techniques combined with computer prediction methods. The UV-vis absorption spectra, Stern-Volmer constant (KSV) and fluorescence resonance energy transfer (FRET) results indicated that DCOIT caused static quenching of HSA fluorescence. The ΔG°, ΔH° and ΔS° values were - 31.03 ± 0.17 kJ·mol-1, -133.54 ± 0.88 kJ·mol-1 and - 348.46 ± 2.86 J.mol-1·K-1, respectively, suggesting that van der Waals forces and hydrogen bonds governed the spontaneous formation of the complex. Synchronous fluorescence and circular dichroism (CD) spectroscopy observed the burial of Trp residues within HSA and the unfolding of HSA secondary structure induced by DCOIT. Three-dimensional (3D) fluorescence and Atomic Force Microscopy (AFM) further detected DCOIT-induced loosening of HSA peptide chain structure. Site displacement experiments indicated that DCOIT binding at site I of HSA. Computational predictions indicated that hydrophobic interactions were also essential in the complex. The increased RMSD, Rg, SASA, and RMSF confirmed that DCOIT weakened the stability and compactness of HSA, rendering residues more flexible. Lastly, esterase activity assays demonstrated that DCOIT inhibited esterase activity and interfered with the human detoxification process.

Interaction of the lysozyme with anticoagulant drug warfarin: Spectroscopic and computational analyses

Warfarin is a cardiovascular drug, used to treat or inhibit the coagulation of the blood. In this paper, we have studied the interaction of lysozyme with warfarin using several experimental (fluorescence, UV-visible and circular dichroism spectroscopies) and computational (molecular docking, molecular dynamics and DFT) approaches. Experimental studies have suggested that there was a strong interaction between lysozyme and warfarin. Inner filter effect played important role in fluorescence experimental data which show that the emission intensity of lysozyme decreased on the addition of warfarin, however, after inner filter effect correction the actual outcome turned out be the fluorescence enhancement. The extent of binding, increased with temperature rise. The interaction was primarily taken place via the dominance of hydrophobic forces. Small amount of warfarin didn't influence the secondary structure of lysozyme; however, the higher concentration of warfarin caused a decrease in the helicity of the protein and a consequent partial unfolding. Molecular docking studies were also performed which revealed that warfarin binds with lysozyme mainly with hydrophobic forces along with a significant contribution of hydrogen bonding. The flexibility of warfarin played important role in fitting the molecule into the binding pocket of lysozyme. Frontier molecular orbitals of warfarin, using DFT, in free as well as complexed form have also been calculated and discussed. Molecular dynamics simulations of unbound and warfarin bound lysozyme reveal a stable complex with slightly higher RMSD values in the presence of warfarin. Despite slightly increased RMSF values, the overall compactness and folding properties remain consistent, emphasizing strong binding towards lysozyme through the results obtained from intermolecular hydrogen bonding analysis. Essential dynamics analysis suggests warfarin induces slight structural changes without significantly altering the conformation, additionally supported by SASA patterns. Aside from the examination of global and essential motion, the MM/PBSA-based analysis of binding free energy elucidates the significant binding of warfarin to lysozyme, indicating a binding free energy of -13.3471 kcal/mol.

Lysine-homologue substitution: Impact on antimicrobial activity and proteolytic stability of cationic stapled heptapeptides

Numerous natural antimicrobial peptides (AMPs) exhibit a cationic amphipathic helical conformation, wherein cationic amino acids, such as lysine and arginine, play pivotal roles in antimicrobial activity by aiding initial attraction to negatively charged bacterial membranes. Expanding on our previous work, which introduced a de novo design of amphipathic helices within cationic heptapeptides using an 'all-hydrocarbon peptide stapling' approach, we investigated the impact of lysine-homologue substitution on helix formation, antimicrobial activity, hemolytic activity, and proteolytic stability of these novel AMPs. Our results demonstrate that substituting lysine with ornithine enhances both the antimicrobial activity and proteolytic stability of the stapled heptapeptide AMP series, while maintaining low hemolytic activity. This finding underscores lysine-homologue substitution as a valuable strategy for optimizing the therapeutic potential of diverse cationic AMPs.

Poly(A)-binding protein promotes VPg-dependent translation of potyvirus through enhanced binding of phosphorylated eIFiso4F and eIFiso4F∙eIF4B

The phosphorylation of eukaryotic translational initiation factors has been shown to play a significant role in controlling the synthesis of protein. Viral infection, environmental stress, and growth circumstances cause phosphorylation or dephosphorylation of plant initiation factors. Our findings indicate that casein kinase 2 can phosphorylate recombinant wheat eIFiso4E and eIFiso4G generated from E. coli in vitro. For wheat eIFiso4E, Ser-207 was found to be the in vitro phosphorylation site. eIFiso4E lacks an amino acid that can be phosphorylated at the position corresponding to Ser-209, the phosphorylation site in mammalian eIF4E, yet phosphorylation of eIFiso4E has effects on VPg binding affinity that are similar to those of phosphorylation of mammalian eIF4E. The addition of VPg and phosphorylated eIFiso4F to depleted wheat germ extract (WGE) leads to enhancement of translation of both uncapped and capped viral mRNA. The addition of PABP together with eIFiso4Fp and eIF4B to depleted WGE increases both uncapped and capped mRNA translation. However, it exhibits a translational advantage specifically for uncapped mRNA, implying that the phosphorylation of eIFiso4F hinders cap binding while promoting VPg binding, thereby facilitating uncapped translation. These findings indicate TEV virus mediates VPg-dependent translation by engaging a mechanism entailing phosphorylated eIFiso4Fp and PABP. To elucidate the molecular mechanisms underlying these observed effects, we studied the impact of PABP and/or eIF4B on the binding of VPg with eIFiso4Fp. The inclusion of PABP and eIF4B with eIFiso4Fp resulted in about 2-fold increase in affinity for VPg (Kd = 24 ± 1.7 nM), as compared to the affinity of eIFiso4Fp alone (Kd = 41.0 ± 3.1 nM). The interactions between VPg and eIFiso4Fp were determined to be both enthalpically and entropically favorable, with the enthalpic contribution accounting for 76-97% of the ΔG at 25°C, indicating a substantial role of hydrogen bonding in enhancing the stability of the complex. The binding of PABP to eIFiso4Fp·4B resulted in a conformational alteration, leading to a significant enhancement in the binding affinity to VPg. These observations suggest PABP enhances the affinity between eIFiso4Fp and VPg, leading to an overall conformational change that provides a stable platform for efficient viral translation.

Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity

Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.

The Development of CDC25A-Derived Phosphoseryl Peptides That Bind 14-3-3ε with High Affinities

Overexpression of the 14-3-3ε protein is associated with suppression of apoptosis in cutaneous squamous cell carcinoma (cSCC). This antiapoptotic activity of 14-3-3ε is dependent on its binding to CDC25A; thus, inhibiting 14-3-3ε - CDC25A interaction is an attractive therapeutic approach to promote apoptosis in cSCC. In this regard, designing peptide inhibitors of 14-3-3ε - CDC25A interactions is of great interest. This work reports the rational design of peptide analogs of pS, a CDC25A-derived peptide that has been shown to inhibit 14-3-3ε-CDC25A interaction and promote apoptosis in cSCC with micromolar IC50. We designed new peptide analogs in silico by shortening the parent pS peptide from 14 to 9 amino acid residues; then, based on binding motifs of 14-3-3 proteins, we introduced modifications in the pS(174-182) peptide. We studied the binding of the peptides using conventional molecular dynamics (MD) and steered MD simulations, as well as biophysical methods. Our results showed that shortening the pS peptide from 14 to 9 amino acids reduced the affinity of the peptide. However, substituting Gln176 with either Phe or Tyr amino acids rescued the binding of the peptide. The optimized peptides obtained in this work can be candidates for inhibition of 14-3-3ε - CDC25A interactions in cSCC.

Understanding the complex formation of falstatin; an endogenous macromolecular inhibitor of falcipains

Proteolytic activity constitutes a fundamental process essential for the survival of the malaria parasite and is thus highly regulated. Falstatin, a protease inhibitor of Plasmodium falciparum, tightly regulates the activity of cysteine hemoglobinases, falcipain-2 and 3 (FP2, FP3), by inhibiting FP2 through a single surface exposed loop. However, the multimeric nature of falstatin and its interaction with FP2 remained unexplored. Here we report that the N-terminal falstatin region is highly disordered, and needs chaperone activity (heat-shock protein 70, HSP70) for its folding. Protein-protein interaction assays showed a significant interaction between falstatin and HSP70. Further, characterization of the falstatin multimer through a series of biophysical techniques identified the formation of a falstatin decamer, which was extremely thermostable. Computational analysis of the falstatin decamer showed the presence of five falstatin dimers, with each dimer aligned in a head-to-tail orientation. Further, the falstatin C-terminal region was revealed to be primarily involved in the oligomerization process. Stoichiometric analysis of the FP2-falstatin multimer showed the formation of a heterooligomeric complex in a 1:1 ratio, with the participation of ten subunits of each protein. Taken together, our results report a novel protease-inhibitor complex and strengthens our understanding of the regulatory mechanisms of major plasmodium hemoglobinases.

Preorganized cyclic modules facilitate the self-assembly of protein nanostructures

The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.

Deciphering the binding mode and structural perturbations in floxuridine-human serum albumin complexation with spectroscopic, microscopic, and computational techniques

The binding mode of antineoplastic antimetabolite, floxuridine (FUDR), with human serum albumin (HSA), the leading carrier in blood circulation, was ascertained using multi-spectroscopic, microscopic, and computational techniques. A static fluorescence quenching was established due to decreased Ksv values with rising temperatures, suggesting FUDR-HSA complexation. UV-vis absorption spectral results also supported this conclusion. The binding constant, Ka values, were found within 9.7-7.9 × 103 M-1 at 290, 300, and 310 K, demonstrating a moderate binding affinity for the FUDR-HSA system. Thermodynamic data (ΔS = +46.35 J.mol-1.K-1 and ΔH = -8.77 kJ.mol-1) predicted the nature of stabilizing forces (hydrogen-bonds, hydrophobic, and van der Waals interactions) for the FUDR-HSA complex. Circular dichroism spectra displayed a minor disruption in the protein's 2° and 3° structures. At the same time, atomic force microscopy images proved variations in the FUDR-HSA surface morphology, confirming its complex formation. The protein's microenvironment around Trp/Tyr residues was also modified, as judged by 3-D fluorescence spectra. FUDR-bound HSA showed better resistance against thermal stress. As disclosed from ligand displacement studies, the FUDR binding site was placed in subdomain IIA (Site I). Further, the molecular docking analysis corroborated the competing displacement studies. Molecular dynamics evaluations revealed that the complex achieved equilibrium during simulations, confirming the FUDR-HSA complex's stability.

Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin

Eis (Enhanced intracellular survival) protein is an aminoglycoside acetyltransferase enzyme classified under the family - GNAT (GCN5-related family of N-acetyltransferases) secreted by Mycobacterium tuberculosis (Mtb). The enzymatic activity of Eis results in the acetylation of kanamycin, thereby impairing the drug's action. In this study, we expressed and purified recombinant Eis (rEis) to determine the enzymatic activity of Eis and its potential inhibitor. Glide-enhanced precision docking was used to perform molecular docking with chosen ligands. Quercetin was found to interact Eis with a maximum binding affinity of -8.379 kcal/mol as compared to other ligands. Quercetin shows a specific interaction between the positively charged amino acid arginine in Eis and the aromatic ring of quercetin through π-cation interaction. Further, the effect of rEis was studied on the antibiotic activity of kanamycin A in the presence and absence of quercetin. It was observed that the activity of rEis aminoglycoside acetyltransferase decreased with increasing quercetin concentration. The results from the disk diffusion assay confirmed that increasing the concentration of quercetin inhibits the rEis protein activity. In conclusion, quercetin may act as a potential Eis inhibitor.

Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma

14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion, or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is overexpressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence, inhibition of the 14-3-3ε-CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of the 14-3-3ε-CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptide binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε-CDC25A interactions in cSCC cells and thus inducing their apoptosis.

Sugar osmolyte inhibits and attenuates the fibrillogenesis in RNase A: An in vitro and in silico characterizations

Mechanisms of protein aggregation are of immense interest in therapeutic biology and neurodegenerative medicine. Biochemical processes within the living cell occur in a highly crowded environment. The phenomenon of macromolecular crowding affects the diffusional and conformational dynamics of proteins and modulates their folding. Macromolecular crowding is reported to cause protein aggregation in some cases, so it is a cause of concern as it leads to a plethora of neurodegenerative disorders and systemic amyloidosis. To divulge the mechanism of aggregation, it is imperative to study aggregation in well-characterized model proteins in the presence of macromolecular crowder. One such protein is ribonuclease A (RNase A), which deciphers neurotoxic function in humans; therefore we decided to explore the amyloid fibrillogenesis of this thermodynamically stable protein. To elucidate the impact of crowder, dextran-70 and its monomer glucose on the aggregation profile of RNase-A various techniques such as Absorbance, Fluorescence, Fourier Transforms Infrared, Dynamic Light Scattering and circular Dichroism spectroscopies along with imaging techniques like Atomic Force Microscopy and Transmission Electron Microscopy were employed. Thermal aggregation and fibrillation were further promoted by dextran-70 while glucose counteracted the effect of the crowding agent in a concentration-dependent manner. This study shows that glucose provides stability to the protein and prevents fibrillation. Intending to combat aggregation, which is the hallmark of numerous late-onset neurological disorders and systemic amyloidosis, this investigation unveils that naturally occurring osmolytes or other co-solutes can be further exploited in novel drug design strategies.

The Saccharomyces cerevisiae SR protein Npl3 interacts with hyperphosphorylated CTD of RNA Polymerase II

The catalytic subunit of RNA Polymerase II contains a highly conserved carboxy terminal domain (CTD) composed of multiple tandem heptad sequence Tyr1Ser2Pro3Thr4Ser5Pro6Ser7. The non-proline residues in CTD undergo posttranslational modifications, with Ser5 phosphorylation (Ser5P) predominating at the start of the transcription cycle and Ser2P at the end, while other phosphorylation levels are high all throughout. The differentially phosphorylated CTD is recognized by regulatory proteins, helpful during mRNA transcription and export. One such protein Npl3 is composed of two RNA binding domains and a C-terminus RGG/SR domain. The Ser411 of Npl3 is reported to make direct contact with Ser2P of CTD for its recruitment and function, while the Npl3 lacking of C-terminal 25 amino acids (Npl3Δ389-414) showed no apparent defects in mRNA synthesis. Here, we report that the RNA binding domains of Npl3 are separate folding units and interact also with the CTD. The interaction between Npl3 and CTD appears to involve not just Ser2P, but also the Ser5P and Ser7P. The Arg126 of the first RNA binding domain interacts with Ser2P whereas the Arg235 of the second RNA binding domain interacts with either Ser7P or Ser5P of another heptad. The finding provides new insight of Npl3 function for mRNA transcription.

Structural and Functional Insights into the Biomineralized Zeolite Imidazole Frameworks

Biomineralization is a natural process of mineral formation mediated by biomacromolecules, allowing access to hierarchical structures integrating biological, chemical, and material properties. In this contribution, we comprehensively investigate the biomineralization of zeolite imidazole frameworks (ZIFs) for one-step synthesis of an enzyme-MOF biocomposite, in terms of differential crystallization behaviors, fine microstructure of resultant ZIF biominerals, the enzyme's conformation evolution, and protective effect of ZIF mineral. We discover that the biomineralization ability is ZIF organic linker dependent and the biocatalytic function is highly related to the ZIF mineral species and their distinguishable topologies and defect structures. Importantly, a side-by-side analysis suggests that the protective effect of ZIF mineral toward the hosted enzyme is highly associated with the synergistic effect of size dimension and chemical microenvironment of the ZIF pores. This work provides important insight into the ZIF-dependent biomineralization behaviors and highlights the important role of the ZIF microstructure in its biocatalytic activity and durability, which has been underestimated previously.

Phytochemical profiling, human insulin stability and alpha glucosidase inhibition of Gymnema latifolium leaves aqueous extract: Exploring through experimental and in silico approach

Diabetes mellitus Type 2 (DM2T) is a rapidly expanding metabolic endocrine disorder worldwide. It is caused due to inadequate insulin secretion by pancreatic beta cells as well as development of insulin resistance. This study aimed to investigate the anti-α-glucosidase, insulin stabilization effect, and non-cytotoxic nature of Gymnema latifolium leaf aqueous extract (GLAE). FTIR analysis revealed the functional groups of compounds present in GLAE. Through LC/ESI-MS/MS analysis, about 12 compounds which belongs to different classes, triterpene glycosides, flavonoids, phenolics, stilbene glycosides and chlorophenolic glycosides were identified. GLAE showed in vitro antioxidant activity. GLAE stabilized insulin by increasing its α-helical content. GLAE inhibited the mammalian α-glucosidase (IC50 = 144 μg/mL) activity through competitive mode (Ki = 61.30 µg/mL). GLAE did not affect the viability of normal cell line (Vero cell line) which shows its non-toxic nature. Molecular docking of phytocompounds identified in GLAE was done with human α-glucosidase and insulin. The top 2 compounds [Gymnema saponin V (GSV) and quercetin 3-(2-galloylglucoside) (QGG) with α-glucosidase; GSV and Z)-resveratrol 3,4'-diglucoside (RDG) with human insulin] with low binding free energy were subjected to 100 ns molecular dynamics simulation to ascertain the stable binding of ligand with protein. The MM/GBSA analysis revealed binding free energy of GSV/α-glucosidase and QGG /α-glucosidase to be - 20.9935 and, - 30.9461 kcal/mol, respectively. Altogether GLAE is valuable source of anti-α-glucosidase inhibitors and insulin stabilizing compounds, suggesting potential lead for further exploration as complementary medicine against DM2T.

Elucidating the structure-function attributes of a trypanosomal arginyl-tRNA synthetase

Aminoacyl-tRNA synthetases (aaRSs) are fundamental components of the protein translation machinery. In light of their pivotal role in protein synthesis and structural divergence among species, they have always been considered potential targets for the development of antimicrobial compounds. Arginyl-tRNA synthetase from Trypanosoma cruzi (TcArgRS), the parasite responsible for causing Chagas Disease, contains a 100-amino acid insertion that was found to be completely absent in the human counterpart of similar length, as ascertained from multiple sequence alignment results. Thus, we were prompted to perform a preliminary characterization of TcArgRS using biophysical, biochemical, and bioinformatics tools. We expressed the protein in E. coli and validated its in-vitro enzymatic activity. Additionally, analysis of DTNB kinetics, Circular dichroism (CD) spectra, and ligand-binding studies using intrinsic tryptophan fluorescence measurements aided us to understand some structural features in the absence of available crystal structures. Our study indicates that TcArgRS can discriminate between L-arginine and its analogues. Among the many tested substrates, only L-canavanine and L-thioarginine, a synthetic arginine analogue exhibited notable activation. The binding of various substrates was also determined using in silico methods. This study may provide a viable foundation for studying small compounds that can be targeted against TcArgRS.

Gonadotropic activity of a second relaxin-type peptide in starfish

In starfish, a relaxin-like gonad-stimulating peptide (RGP) acts as a gonadotropin that triggers gamete maturation and spawning. In common with other relaxin/insulin superfamily peptides, RGP consists of an A- and a B-chain, with cross-linkages mediated by one intra- and two inter-chain disulfide bonds. In this study, a second relaxin-like peptide (RLP2) was identified in starfish species belonging to the orders Valvatida, Paxillosida, and Forcipulatida. Like RGP, RLP2 precursors comprise a signal peptide and a C-peptide in addition to the A- and B-chains. However, a unique cysteine motif [CC-(3X)-C-(10X)-C] is present in the A-chain of RLP2, which contrasts with the cysteine motif in other members of the relaxin/insulin superfamily [CC-(3X)-C-(8X)-C]. Importantly, in vitro pharmacological tests revealed that Patiria pectinifera RLP2 (Ppe-RLP2) and Asterias rubens RLP2 (Aru-RLP2) trigger shedding of mature eggs from ovaries of P. pectinifera and A. rubens, respectively. Furthermore, the potencies of Ppe-RLP2 and Aru-RLP2 as gonadotropic peptides were similar to those of Ppe-RGP and Aru-RGP, respectively, and the effect of RLP2 exhibited partial species-specificity. These findings indicate that two relaxin-type peptides regulate spawning in starfish and therefore we propose that RGP and RLP2 are renamed RGP1 and RGP2, respectively.

Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma

14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is over expressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence inhibition of the 14-3-3ε - CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of 14-3-3ε - CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide, and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptides binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε -CDC25A interactions in cSCC cells; thus, inducing their apoptosis.

Structure-Based Design and Synthesis of Stapled 10Panx1 Analogues for Use in Cardiovascular Inflammatory Diseases

Following a rational design, a series of macrocyclic ("stapled") peptidomimetics of 10Panx1, the most established peptide inhibitor of Pannexin1 (Panx1) channels, were developed and synthesized. Two macrocyclic analogues SBL-PX1-42 and SBL-PX1-44 outperformed the linear native peptide. During in vitro adenosine triphosphate (ATP) release and Yo-Pro-1 uptake assays in a Panx1-expressing tumor cell line, both compounds were revealed to be promising bidirectional inhibitors of Panx1 channel function, able to induce a two-fold inhibition, as compared to the native 10Panx1 sequence. The introduction of triazole-based cross-links within the peptide backbones increased helical content and enhanced in vitro proteolytic stability in human plasma (>30-fold longer half-lives, compared to 10Panx1). In adhesion assays, a "double-stapled" peptide, SBL-PX1-206 inhibited ATP release from endothelial cells, thereby efficiently reducing THP-1 monocyte adhesion to a TNF-α-activated endothelial monolayer and making it a promising candidate for future in vivo investigations in animal models of cardiovascular inflammatory disease.

Chirality in Light-Matter Interaction

The scientific effort to control the interaction between light and matter has grown exponentially in the last 2 decades. This growth has been aided by the development of scientific and technological tools enabling the manipulation of light at deeply sub-wavelength scales, unlocking a large variety of novel phenomena spanning traditionally distant research areas. Here, the role of chirality in light-matter interactions is reviewed by providing a broad overview of its properties, materials, and applications. A perspective on future developments is highlighted, including the growing role of machine learning in designing advanced chiroptical materials to enhance and control light-matter interactions across several scales.

Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study

Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.

Oligomerization and Adjuvant Activity of Peptides Derived from the VirB4-like ATPase of Clostridioides difficile

In a previous study, we demonstrated that the Clostridioides difficile VirB4-like ATPase forms oligomers in vitro. In the current investigation, to study the observed phenomenon in more detail, we prepared a library of VirB4-derived peptides (delVirB4s) fused to a carrier maltose-binding protein (MBP). Using gel chromatography and polyacrylamide gel electrophoresis, we found a set of overlapping fragments that contribute most significantly to protein aggregation, which were represented as water-soluble oligomers with molecular masses ranging from ~300 kD to several megadaltons. Membrane filtration experiments, sucrose gradient ultracentrifugation, and dynamic light scattering measurements indicated the size of the soluble complex to be 15-100 nm. It was sufficiently stable to withstand treatment with 1 M urea; however, it dissociated in a 6 M urea solution. As shown by the changes in GFP fluorescence and the circular dichroism spectra, the attachment of the delVirB4 peptide significantly altered the structure of the partner MBP. The immunization of mice with the hybrid consisting of the selected VirB4-derived peptide and MBP, GST, or GFP resulted in increased production of specific antibodies compared to the peptide-free carrier proteins, suggesting significant adjuvant activity of the VirB4 fragment. This feature could be useful for the development of new vaccines, especially in the case of "weak" antigens that are unable to elicit a strong immune response by themselves.

The role of native cysteine residues in the oligomerization of KCNQ1 channels

KCNQ1, the major component of the slow-delayed rectifier potassium channel, is responsible for repolarization of cardiac action potential. Mutations in this channel can lead to a variety of diseases, most notably long QT syndrome. It is currently unknown how many of these mutations change channel function and structure on a molecular level. Since tetramerization is key to proper function and structure of the channel, it is likely that mutations modify the stability of KCNQ1 oligomers. Presently, the C-terminal domain of KCNQ1 has been noted as the driving force for oligomer formation. However, truncated versions of this protein lacking the C-terminal domain still tetramerize. Therefore, we explored the role of native cysteine residues in a truncated construct of human KCNQ1, amino acids 100-370, by blocking potential interactions of cysteines with a nitroxide based spin label. Mobility of the spin labels was investigated with continuous wave electron paramagnetic resonance (CW-EPR) spectroscopy. The oligomerization state was examined by gel electrophoresis. The data provide information on tetramerization of human KCNQ1 without the C-terminal domain. Specifically, how blocking the side chains of native cysteines residues reduces oligomerization. A better understanding of tetramer formation could provide improved understanding of the molecular etiology of long QT syndrome and other diseases related to KCNQ1.

Conserved acidic second shell residue modulates the structure, stability and activity of non-seleno human peroxiredoxin 6

1-Cys peroxiredoxin6 (Prdx6) is unique and inducible bifunctional enzyme in the mammalian lungs and plays a role in the progression and inhibition of cancerous cells at different stages. The enzyme possesses two distinct active sites for phospholipase A2 and peroxidase activity. The conserved residues surrounding the peroxidase active site, also called as second shell residues are Glu50, Leu71, Ser72, His79 and Arg155. Since there is no study done about the active site stabilization of the transition state of Prdx6, there are a lot of questions unanswered regarding the Prdx6 peroxidase activity. In order to evaluate the role of second shell conserved residue Glu50, present in close vicinity to peroxidatic active site, we substituted this negatively charged residue with Alanine and Lysine. To explore the effect of mutation on the biophysical parameters, the mutant proteins were compared with Wild-Type by using biochemical, biophysical, and in silico methods. Comparative spectroscopic methods and enzyme activity demonstrate that the Glu50 plays a significant role in maintaining the structure, stability, and function of protein. From the results we conclude that Glu50 significantly controls the structure; stability and may be involved in the active site stabilization of transition state for proper position of diverse peroxides.

A novel single sensor hemoglobin domain from the thermophilic cyanobacteria Thermosynechococcus elongatus BP-1 exhibits higher pH but lower thermal stability compared to globins from mesophilic organisms

Thermosynechococcus elongatus-BP1 belongs to the class of photoautotrophic cyanobacterial organisms. The presence of chlorophyll a, carotenoids, and phycocyanobilin are the characteristics that categorize T. elongatus as a photosynthetic organism. Here, we report the structural and spectroscopic characteristics of novel hemoglobin (Hb) Synel Hb from T.elongatus, synonymous with Thermosynechococcus vestitus BP-1. The X-ray crystal structure (2.15 Å) of Synel Hb suggests the presence of a globin domain with a pre-A helix similar to the sensor domain (S) family of Hbs. The rich hydrophobic core accommodates heme in a penta-coordinated state and readily binds an extraneous ligand(imidazole). The absorption and circular dichroic spectral analysis of Synel Hb reiteratedthat the heme is in Fe^III+ state with a predominantly α-helical structure similar to myoglobin. Synel Hb displays higher resistance to structural perturbations induced via external stresses like pH and guanidium hydrochloride, which is comparable to Synechocystis Hb. However, Synel Hb exhibited lower thermal stability compared to mesophilic hemoglobins. Overall, the data is suggestive of the structural sturdiness of Synel Hb, which probably corroborates its origin in extreme thermophilic conditions. The stable globin provides scope for further investigation and may lead to new insights with scope for engineering stability in hemoglobin-based oxygen carriers.

The C-terminally amidated relaxin-like gonad-stimulating peptide in the starfish Astropecten scoparius

A relaxin-like gonad-stimulating peptide (RGP) in starfish was the first identified invertebrate gonadotropin, consisting of A- and B-chain. Recently, an RGP ortholog (Asc-RGP) from Astropecten scoparius in the order Paxillosida was found to harbor an amidation signal (Gly-Arg) at the C-terminus of the B-chain (Mita et al., 2020a). Two cleavage sites were also predicted within the signal peptide of the Asc-RGP precursor. Thus, four kinds of analogs (Asc-RGP-NH₂(S), Asc-RGP-GR(S), Asc-RGP- NH₂(L), Asc-RGP-GR(L) were hypothesized as natural Asc-RGPs. To identify the natural Asc-RGP, an extract of radial nerve cords from A. scoparius was analyzed using reverse-phase high-performance liquid chromatography and MALDI-TOF-mass spectrometry. The molecular weight of Asc-RGP was 4585.3, and those of A- and B-chains were 2511.8 and 2079.8, respectively. This strongly suggests that natural RGP in A. scoparius is Asc-RGP-NH₂(S). Asc-RGP-NH₂(S) stimulated 1-methyladenine and cyclic AMP production in isolated ovarian follicle cells of A. scoparius. On the other hand, the concentrations of four synthetic Asc-RGP analogs required for the induction of spawning in 50% of ovarian fragments were almost the same. The size and C-terminal amidation of the B-chain might not be important for spawning-inducing activity. C-terminally amidated RGPs in the B-chain were also observed in other species of starfish belonging to the order Paxillosida, particularly the family Astropectinidae, but not the family Luidiidae.

Iron response elements (IREs)-mRNA of Alzheimer's amyloid precursor protein binding to iron regulatory protein (IRP1): a combined molecular docking and spectroscopic approach

The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP IRE mRNA∙IRP1 reveals that 11 residues are involved in hydrogen bonding as the main driving force for the interaction. Fluorescence binding results revealed a strong interaction between APP IRE mRNA and IRP1 with a binding affinity and an average binding sites of 31.3 × 10⁶ M^-1 and 1.0, respectively. Addition of Fe²⁺(anaerobic) showed a decreased (3.3-fold) binding affinity of APP mRNA∙IRP1. Further, thermodynamic parameters of APP mRNA∙IRP1 interactions were an enthalpy-driven and entropy-favored event, with a large negative ΔH (-25.7 ± 2.5 kJ/mol) and a positive ΔS (65.0 ± 3.7 J/mol·K). A negative ΔH value for the complex formation suggested the contribution of hydrogen bonds and van der Waals forces. The addition of iron increased the enthalpic contribution by 38% and decreased the entropic influence by 97%. Furthermore, the stopped-flow kinetics of APP IRE mRNA∙IRP1 also confirmed the complex formation, having the rate of association (k_on) and the rate of dissociation (k_off) as 341 μM^-1 s^-1, and 11 s^-1, respectively. The addition of Fe²⁺ has decreased the rate of association (k_on) by ~ three-fold, whereas the rate of dissociation (k_off) has increased by ~ two-fold. The activation energy for APP mRNA∙IRP1 complex was 52.5 ± 2.1 kJ/mol. The addition of Fe²⁺ changed appreciably the activation energy for the binding of APP mRNA with IRP1. Moreover, circular dichroism spectroscopy has confirmed further the APP mRNA∙IRP1 complex formation and IRP1 secondary structure change with the addition of APP mRNA. In the interaction between APP mRNA and IRP1, iron promotes structural changes in the APP IRE mRNA∙IRP1 complexes by changing the number of hydrogen bonds and promoting a conformational change in the IRP1 structure when it is bound to the APP IRE mRNA. It further illustrates how IRE stem-loop structure influences selectively the thermodynamics and kinetics of these protein-RNA interactions.

Probing the interaction between niobium pentoxide nanoparticles and serum albumin proteins by Spectroscopic approaches

Nanoparticles (NPs) can directly or indirectly enter into the body because of their small size; then they tend to alter the conformation and function of proteins upon interaction with them. Thus, it is crucial to understand the impact of NPs in a biological medium. Recently, niobium pentoxide nanoparticles (Nb2O5 NPs) are finding increasing applications in the biological system, for example, bone tissue and dental material, matrix for biosensing of proteins, etc. In all such applications, the Nb2O5 NP interacts with proteins and other biomolecules. Hence, the study of such interactions is of considerable importance. Here in this work, we present the impact of Nb2O5 NP on the structure, stability and activity of blood proteins, bovine serum albumin (BSA) and human serum albumin (HSA) by means of various spectroscopic approaches. Steady-state fluorescence studies indicated that intrinsic fluorescence intensities of both serum albumin proteins got quenched upon their interaction with NP. The nature of the quenching was elucidated by time-resolved fluorescence and absorption measurements. Using circular dichroism (CD) and synchronous fluorescence spectroscopy (SFS), the structural perturbations of the protein molecules after interaction with NP were investigated. Moreover, the role of temperature on protein stability upon complexation with NP was also explored. In addition, the effect of NP on protein functionality was probed by esterase-like activity assays.Communicated by Ramaswamy H. Sarma.

Urea induced unfolding of rai seed cystatin: Influence of glycerol as a chemical chaperone

Cystatin superfamily members, by virtue of their thiol protease regulatory properties, show involvement in myriad physiological processes important for survival and well-being. The current study involves urea-induced denaturation of a novel variant of the cystatin superfamily, rai seed cystatin (RSC), employing a variety of biophysical assays in order to characterize different folding intermediates generated on unfolding. Urea as a denaturant presented the passage of RSC through a series of events resulting in the loss of RSC functional capability, accompanied by changes in the archetype at secondary and tertiary structural levels, as evident from protease inhibitory, UV absorption, and intrinsic fluorescence assays, respectively. ANS fluorescence also revealed routing of RSC through discrete multiple sub-states thus presenting the generation of intermediate states somewhat close to the pre-molten globule and/or molten globule forms of RSC. Furthermore, far-UV circular dichroism analysis revealed a concentration-dependent gradual loss in typical -helical RSC peaks, indicating a nearly 50 % loss in secondary structural elements around 5 M urea treatment. The study also reports the possible role of glycerol in the refolding and/or reactivation of the urea unfolded RSC form. Glycerol presented itself as a potent structural stabilizer as it assisted in the refolding and reactivation of the unfolded RSC in a dosage-dependent manner, concomitantly paving the way for unravelling the mechanistic approach involved in the phenomenon, which can facilitate future studies.

Understanding Conformational Changes in Human Serum Albumin and Its Interactions with Gold Nanorods: Do Flexible Regions Play a Role in Corona Formation?

The importance of protein-nanoparticle (NP) conjugates for biomedical applications has seen an exponential growth in the past few years. The protein corona formation on NPs with human serum albumin (HSA), being the most abundant protein in blood serum, has become one of the most studied protein analyses under NP-protein interactions as HSA is readily adsorbed on the surface of the NPs. Understanding the fate of the NPs in physiological media along with the change in biological responses due to the formation of the protein corona thus becomes important. We analyzed the HSA protein corona formation on gold nanorods (AuNRs) through different spectroscopic studies in addition to the effects of change in the protein concentration on the protein-NP interactions. Different imaging techniques such as high-resolution transmission electron microscopy, field emission scanning electron microscopy, and atomic force microscopy were used to determine the morphology and the dimensions of the nanorods and the protein-nanorod conjugates. Fourier-transform infrared data showed a reduction in the α-helix content and an increase in β-sheet content for the HSA-AuNR conjugate compared to the native protein. A decrease in steady-state fluorescence intensity occurred with instant addition of AuNR to HSA showing better and efficient quenching of Trp fluorescence for the lower concentration of protein. Time-correlated single photon counting results showed greater energy transfer efficiency and faster decay rate for higher concentrations of proteins. The circular dichroism study gives insight into the secondary structural changes due to unfolding, and a greater change was observed for lower concentrations of protein due to a thermodynamically stable protein corona formation. Surface-enhanced Raman spectroscopy (SERS) indicated the presence of aromatic residues such as Phe, Tyr, and Cys that appear to be close to the surface of the AuNRs in addition to hydrophobic interactions between AuNR and the protein. The disordered and flexible regions mapped onto HSA (PDB: 1AO6), predicted by the intrinsically disordered region predictors, point toward the interactions of similar residues with the nanorods observed from SERS and fluorescence studies. These studies could provide a clearer understanding of the interactions between HSA and AuNRs for possible biological applications.

Discovery of structural and functional transition sites for membrane-penetrating activity of sheep myeloid antimicrobial peptide-18

Cathelicidin antimicrobial peptides have an extended and/or unstructured conformation in aqueous solutions but fold into ordered conformations, such as the α-helical structure, when interacting with cellular membranes. These structural transitions can be directly correlated to their antimicrobial activity and its underlying mechanisms. SMAP-18, the N-terminal segment (residues 1-18) of sheep cathelicidin (SMAP-29), is known to kill microorganisms by translocating across membranes and interacting with their nucleic acids. The amino acid sequence of SMAP-18 contains three Gly residues (at positions 2, 7, and 13) that significantly affect the flexibility of its peptide structure. This study investigated the role of Gly residues in the structure, membrane interaction, membrane translocation, and antimicrobial mechanisms of SMAP-18. Five analogs were designed and synthesized through Gly → Ala substitution (i.e., G2A, G7A, G13A, G7,13A, and G2,7,13A); these substitutions altered the helical content of SMAP-18 peptides. We found that G7,13A and G2,7,13A changed their mode of action, with circular dichroism and nuclear magnetic resonance studies revealing that these analogs changed the structure of SMAP-18 from a random coil to an α-helical structure. The results of this experiment suggest that the Gly residues at positions 7 and 13 in SMAP-18 are the structural and functional determinants that control its three-dimensional structure, strain-specific activity, and antimicrobial mechanism of action. These results provide valuable information for the design of novel peptide-based antibiotics.

Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods

Cuminol (4-Isopropylbenzyl alcohol), found in the essential oils of several plant sources, is an important constituent of several cosmetics formulations. The interaction of cuminol with model plasma protein bovine serum albumin was studied in this paper. The experimental studies were mainly carried out using fluorescence spectrophotometry aided with UV visible and CD spectroscopies. Intrinsic fluorescence measurements showed that there was a weak binding between cuminol and BSA. The mechanism of binding involved static quenching with around 1:1 binding. The binding was chiefly supported by hydrophobic forces although a little contribution of hydrogen bonding was also found in the interaction and the values of enthalpy change were negative with positive entropy change. The secondary structure of BSA didn't change significantly in presence of low concentrations of cuminol, however, partial unfolding of the former taken place when the concentration of the latter increased. Molecular docking analyses showed cuminol binds at the intersection of subdomains IIA and IIIA, i.e. its binding site is in between Sudlow sites I and II. Molecular dynamics simulations results have shown that BSA forms a stable complex with cuminol and the structure of the former didn't change much in presence of later. Communicated by Ramaswamy H. Sarma.

Development of Antimicrobial Peptide-Antibiotic Conjugates to Improve the Outer Membrane Permeability of Antibiotics Against Gram-Negative Bacteria

Antibiotics have been widely used in the medical field as a treatment for infectious diseases, but they are not effective against all Gram-negative bacteria because of their low permeability to the outer membrane. One of the strategies to improve the antibacterial activity of antibiotics is the coadministration of antibiotics and membrane-perturbing antimicrobial peptides for their synergistic effects. However, because of their different pharmacokinetics, their coadministration may not exert expected effects in the clinical stage. Here, we designed various antimicrobial peptide-antibiotic conjugates as a novel approach to improve the antimicrobial activity of antibiotics. Ampicillin was chosen as a model antibiotic with poor outer membrane permeability, and the effects of the chemistry and position of conjugation and the choice of antimicrobial peptides were examined. One of the ampicillin conjugates exhibited significantly improved antimicrobial activity against ampicillin-resistant Gram-negative bacteria without exerting cytotoxicity against human cultured cells, demonstrating that our novel approach is an effective strategy to improve the antimicrobial activity of antibiotics with low outer membrane permeability.

Interaction of mancozeb with human hemoglobin: Spectroscopic, molecular docking and molecular dynamic simulation studies

Mancozeb is a broad-spectrum fungicide used extensively in agriculture to protect plants from numerous diseases. Hemolysis of human erythrocytes on exposure to mancozeb has been reported. In the present study, we investigated the interaction of mancozeb with human hemoglobin (Hb) using multi-spectroscopic techniques, molecular docking and molecular dynamic simulation. UV-visible spectroscopy studies suggested intimate binding of mancozeb to Hb. Mancozeb quenched the intrinsic fluorescence of Hb and Stern-Volmer plots revealed that the quenching mechanism was of static type. Evaluation of thermodynamic parameters indicated that the binding of Hb to mancozeb was spontaneous, with van der Waals forces and hydrogen bonding being the key contributors in the binding reaction. Synchronous fluorescence experiments demonstrated that mancozeb altered the microenvironment around tryptophan residues, whereas polarity around tyrosine residues was not changed. Circular dichroism studies showed a decrease in the α helical content of Hb upon interaction with mancozeb. The inhibition of esterase activity showed that mancozeb can impair the enzymatic functions of Hb. Molecular docking study revealed that strong binding affinity existed between mancozeb and Hb, with hydrophobic forces playing a crucial role in the interaction. Molecular dynamic simulation showed that mancozeb formed a stable complex with Hb resulting in slight unfolding of the protein. To sum up, the results of this study show that mancozeb binds strongly to Hb, induces conformational changes in Hb and adversely affects its function.

A Novel Hyperthermostable Recombinant Protein Nanocage

Background

Background: Ferritin has an important role in iron storage in the cells, and due to its nanocage structure and self-assembly properties, it has wide application prospects in nanobiotechnology.

Methods

Methods: The maize (Zea mays) ferritin gene ZmFer1 was cloned and expressed in Escherichia coli BL21 (DE3) for the first time. Change in macromolecular structure of ZmFer1 ferritin due to heat treatment was investigated using native PAGE electrophoresis, dynamic light scattering (DLS), and transmission electron microscopy (TEM). Change in the secondary structures of the protein was evaluated using circular dichroism spectroscopy. Moreover, alteration in the conformation of the protein was evaluated using UV-absorption spectra and intrinsic fluorescence spectra. The melting temperature (Tm) of ZmFer1 was obtained using differential scanning calorimetry (DSC). Finally, the effect of heat on the function of ZmFer1 was assessed by iron loading ability.

Results

Results: The purified ZmFer1 protein showed a homopolymer nanocage structure. The results of native PAGE electrophoresis, DLS, and TEM techniques showed that ZmFer1 protein nanocage is stable to heat treatment up to 90 °C, and some of the protein nanocages retain their macromolecular structures even at 100 °C in liquid aqueous solution. Based on the DSC results, ZmFer1 protein nanocage had a Tm of 81.9 °C. After treatment at 100 °C, stable ZmFer1 protein nanocages were able to store iron atoms.

Conclusion

Conclusion: Recombinant ZmFer1 ferritin with a Tm > 80°C is a hyperthermostable protein nanocage. The results of this study are beneficial for the development of protein nanocages that are stable under extreme temperature conditions, as well as application of ZmFer1 in nanobiotechnology, biomaterials, and biomedical fields.

Characterization and localization of relaxin-like gonad-stimulating peptide in the crown-of-thorns starfish, Acanthaster cf. solaris

In starfish, a relaxin-like gonad-stimulating peptide (RGP) is the gonadotropin responsible for final gamete maturation. RGP comprises two different peptides, A- and B-chains with two interchain and one intrachain disulfide bonds. The existence of two isomers of RGP in the crown-of-thorns starfish, Acanthaster planci, has been reported previously, but it was recently shown that A. planci represents a species complex with four different species. Here we elucidated the authentic sequence of the Pacific species, Acanthaster cf. solaris, RGP (Aso-RGP). The Aso-RGP precursor encoded by a 354 base pair open reading frame was composed of 117 amino acids (aa). The amino acid identity of Aso-RGP to Patiria pectinifera RGP (Ppe-RGP) and Asterias amurensis RGP (Aam-RGP) was 74% and 60%, respectively. Synthetic Aso-RGP induced spawning of ovarian fragments from A. cf. solaris. Ppe-RGP and Aam-RGP also induced spawning by A. cf. solaris ovaries. In contrast, Ppe-RGP and Aso-RGP induced spawning by P. pectinifera ovaries, but Aam-RGP was inactive. Notably, anti-Ppe-RGP antibodies recognized Aso-RGP as well as Ppe-RGP. Localization of Aso-RGP was observed immunohistochemically using anti-Ppe-RGP antibodies, showing that Aso-RGP was mainly present in the radial nerve cords of A. cf. solaris. Aso-RGP was distributed not only in the epithelium of the ectoneural region but also in the neuropile of the ectoneural region. These results suggest that Aso-RGP is synthesized in the epithelium of the ectoneural region, then transferred to fibers in the neuropile of the ectoneural region in radial nerve cords.

Interaction of the insecticide bioallethrin with human hemoglobin: biophysical, in silico and enzymatic studies

Bioallethrin is an insecticide that is widely used in households resulting in human exposure. Bioallethrin is cytotoxic to human erythrocytes. Here we have studied the interaction of bioallethrin with human hemoglobin (Hb) using in silico and biophysical approaches. Incubation of Hb (5 μM) with bioallethrin (1-50 µM) led to increase in absorbance at 280 nm while the Soret band at 406 nm was slightly reduced. The intrinsic fluorescence of Hb was enhanced with the appearance of a new peak around 305 nm. Synchronous fluorescence showed that the binding of bioallethrin to Hb mainly affects the tyrosine microenvironment. The structural changes in Hb were confirmed with a significant shift in CD spectra and about 25% loss of α-helix. Molecular docking and visualisation through Discovery studio confirmed the formation of Hb-bioallethrin complex with a binding energy of -7.3 kcal/mol. Molecular simulation showed the stability and energy dynamics of the binding reaction between bioallethrin and Hb. The structural changes induced by bioallethrin led to inhibition of the esterase activity of Hb. In conclusion, this study shows that bioallethrin forms a stable complex with human Hb which may lead to loss of Hb function in the body.Communicated by Ramaswamy H. Sarma.

Mineralization Profile of Annexin A6-Harbouring Proteoliposomes: Shedding Light on the Role of Annexin A6 on Matrix Vesicle-Mediated Mineralization

The biochemical machinery involved in matrix vesicles-mediated bone mineralization involves a specific set of lipids, enzymes, and proteins. Annexins, among their many functions, have been described as responsible for the formation and stabilization of the matrix vesicles′ nucleational core. However, the specific role of each member of the annexin family, especially in the presence of type-I collagen, remains to be clarified. To address this issue, in vitro mineralization was carried out using AnxA6 (in solution or associated to the proteoliposomes) in the presence or in the absence of type-I collagen, incubated with either amorphous calcium phosphate (ACP) or a phosphatidylserine-calcium phosphate complex (PS–CPLX) as nucleators. Proteoliposomes were composed of 1,2-dipalmitoylphosphatidylcholine (DPPC), 1,2-dipalmitoylphosphatidylcholine: 1,2-dipalmitoylphosphatidylserine (DPPC:DPPS), and DPPC:Cholesterol:DPPS to mimic the outer and the inner leaflet of the matrix vesicles membrane as well as to investigate the effect of the membrane fluidity. Kinetic parameters of mineralization were calculated from time-dependent turbidity curves of free Annexin A6 (AnxA6) and AnxA6-containing proteoliposomes dispersed in synthetic cartilage lymph. The chemical composition of the minerals formed was investigated by Fourier transform infrared spectroscopy (FTIR). Free AnxA6 and AnxA6-proteoliposomes in the presence of ACP were not able to propagate mineralization; however, poorly crystalline calcium phosphates were formed in the presence of PS–CPLX, supporting the role of annexin-calcium-phosphatidylserine complex in the formation and stabilization of the matrix vesicles’ nucleational core. We found that AnxA6 lacks nucleation propagation capacity when incorporated into liposomes in the presence of PS–CPLX and type-I collagen. This suggests that AnxA6 may interact either with phospholipids, forming a nucleational core, or with type-I collagen, albeit less efficiently, to induce the nucleation process.

A Computational–Experimental Investigation of the Molecular Mechanism of Interleukin-6-Piperine Interaction

Herein, we elucidate the biophysical aspects of the interaction of an important protein, Interleukin-6 (IL6), which is involved in cytokine storm syndrome, with a natural product with anti-inflammatory activity, piperine. Despite the role of piperine in the inhibition of the transcriptional protein NF-κB pathway responsible for activation of IL6 gene expression, there are no studies to the best of our knowledge regarding the characterisation of the molecular interaction of the IL6-piperine complex. In this context, the characterisation was performed with spectroscopic experiments aided by molecular modelling. Fluorescence spectroscopy alongside van’t Hoff analyses showed that the complexation event is a spontaneous process driven by non-specific interactions. Circular dichroism aided by molecular dynamics revealed that piperine caused local α-helix reduction. Molecular docking and molecular dynamics disclosed the microenvironment of interaction as non-polar amino acid residues. Although piperine has three available hydrogen bond acceptors, only one hydrogen-bond was formed during our simulation experiments, reinforcing the major role of non-specific interactions that we observed experimentally. Root mean square deviation (RMSD) and hydrodynamic radii revealed that the IL6-piperine complex was stable during 800 ns of simulation. Taken together, these results can support ongoing IL6 drug discovery efforts.

Human Serum Amyloid a Impaired Structural Stability of High-Density Lipoproteins (HDL) and Apolipoprotein (Apo) A-I and Exacerbated Glycation Susceptibility of ApoA-I and HDL

Human serum amyloid A (SAA) is an exchangeable apolipoprotein (apo) in high-density lipoprotein (HDL) that influences HDL quality and functionality, particularly in the acute phase of inflammation. On the other hand, the structural and functional correlations of HDL containing SAA and apoA-I have not been reported. The current study was designed to compare the change in HDL quality with increasing SAA content in the lipid-free and lipid-bound states in reconstituted HDL (rHDL). The expressed recombinant human SAA1 (13 kDa) was purified to at least 98% and characterized in the lipid-free and lipid-bound states with apoA-I. The dimyristoyl phosphatidylcholine (DMPC) binding ability of apoA-I was impaired severely by the addition of SAA, while SAA alone could not bind with DMPC. The recombinant human SAA1 was incorporated into the rHDL (molar ratio 95:5:1, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC): cholesterol: apoA-I) with various apoA-I:SAA molar ratios from 1:0 to 1:0.5, 1:1 and 1:2. With increasing SAA1 content, the rHDL particle size was reduced from 98 Å to 93 Å, and the α-helicity of apoA-I:SAA was decreased from 73% to 40% for (1:0) and (1:2), respectively. The wavelength maximum fluorescence (WMF) of tryptophan in rHDL was red-shifted from 339 nm to 345 nm for (1:0) and (1:2) of apoA-I:SAA, respectively, indicating that the addition of SAA to rHDL destabilized the secondary structure of apoA-I. Upon denaturation by urea treatment from 0 M to 8 M, SAA showed only a 3 nm red-shift in WMF, while apoA-I showed a 16 nm red-shift in WMF, indicating that SAA is resistant to denaturation and apoA-I had higher conformational flexibility than SAA. The glycation reaction of apoA-I in the presence of fructose was accelerated up to 1.8-fold by adding SAA in a dose-dependent manner than that of apoA-I alone. In conclusion, the incorporation of SAA in rHDL impaired the structural stability of apoA-I and exacerbated glycation of HDL and apoA-I.

A circular dichroism study of the protective role of polyphosphoesters polymer chains in polyphosphoester-myoglobin conjugates

Protein‐polymer conjugates are a blooming class of hybrid systems with high biomedical potential. Despite a plethora of papers on their biomedical properties, the physical–chemical characterization of many protein‐polymer conjugates is missing. Here, we evaluated the thermal stability of a set of fully‐degradable polyphosphoester‐protein conjugates by variable temperature circular dichroism, a common but powerful technique. We extensively describe their thermodynamic stability in different environments (in physiological buffer or in presence of chemical denaturants, e.g., acid or urea), highlighting the protective role of the polymer in preserving the protein from denaturation. For the first time, we propose a simple but effective protocol to achieve useful information on these systems in vitro, useful to screen new samples in their early stages.

Intron-Encoded Domain of Herstatin, An Autoinhibitor of Human Epidermal Growth Factor Receptors, Is Intrinsically Disordered

Human epidermal growth factor receptors (HER/ERBB) form dimers that promote cell proliferation, migration, and differentiation, but overexpression of HER proteins results in cancer. Consequently, inhibitors of HER dimerization may function as effective antitumor drugs. An alternatively spliced variant of HER2, called herstatin, is an autoinhibitor of HER proteins, and the intron 8-encoded 79-residue domain of herstatin, called Int8, binds HER family receptors even in isolation. However, the structure of Int8 remains poorly understood. Here, we revealed by circular dichroism, NMR, small-angle X-ray scattering, and structure prediction that isolated Int8 is largely disordered but has a residual helical structure. The radius of gyration of Int8 was almost the same as that of fully unfolded states, although the conformational ensemble of Int8 was less flexible than random coils. These results demonstrate that Int8 is intrinsically disordered. Thus, Int8 is an interesting example of an intrinsically disordered region with tumor-suppressive activity encoded by an intron. Furthermore, we show that the R371I mutant of Int8, which is defective in binding to HER2, is prone to aggregation, providing a rationale for the loss of function.

Quantification and Improvement of the Dynamics of Human Serum Albumin and Glycated Human Serum Albumin with Astaxanthin/Astaxanthin-Metal Ion Complexes: Physico-Chemical and Computational Approaches

Glycated human serum albumin (gHSA) undergoes conformational changes and unfolding events caused by free radicals. The glycation process results in a reduced ability of albumin to act as an endogenous scavenger and transporter protein in diabetes mellitus type 2 (T2DM) patients. Astaxanthin (ASX) in native form and complexed with metal ions (Cu²⁺ and Zn²⁺) has been shown to prevent gHSA from experiencing unfolding events. Furthermore, it improves protein stability of gHSA and human serum albumin (HSA) as it is shown through molecular dynamics studies. In this study, the ASX/ASX-metal ion complexes were reacted with both HSA/gHSA and analyzed with electronic paramagnetic resonance (EPR) spectroscopy, rheology and zeta sizer (particle size and zeta potential) analysis, circular dichroism (CD) spectroscopy and UV-Vis spectrophotometer measurements, as well as molecular electrostatic potential (MEP) and molecular docking calculations. The addition of metal ions to ASX improves its ability to act as an antioxidant and both ASX or ASX-metal ion complexes maintain HSA and gHSA stability while performing their functions.

Spectroscopic and Molecular Docking Investigation on the Interaction of Cumin Components with Plasma Protein: Assessment of the Comparative Interactions of Aldehyde and Alcohol with Human Serum Albumin

The interaction of the important plasma protein, human serum albumin (HSA), with two monoterpenes found in cumin oil, i.e., cuminaldehyde (4-isopropylbenzaldehyde) and cuminol (4-isopropylbenzyl alcohol), was studied in this paper. Both experimental and computational methods were utilized to understand the mechanism of binding. The UV absorption profile of HSA changes in the presence of both cuminaldehyde and cuminol, due to the interaction between HSA with both monoterpenes. The intrinsic fluorescence intensity of HSA was also quenched on the sequential addition of both ligands, due to change in the microenvironment of the fluorophore present in the former. Quenching of HSA by cuminaldehyde was much higher in comparison to that in the presence of cuminol. Fluorescence quenching data were analyzed using modified Stern-Volmer and Lineweaver-Burk methods, which suggested that the binding mechanism was of a static type for both ligands. In both cases, the binding was favored by the domination of hydrophobic as well as hydrogen bonding/Van der Waals forces. Both ligands partially unfolded the secondary structure of HSA, although the effect of cuminaldehyde was more pronounced, as compared to cuminol. The preferred binding site of cuminaldehyde and cuminol inside HSA was also the same; namely, drug binding site 1, located in subdomain IIA. The study showed that cuminaldehyde binds strongly with albumin as compared to its alcohol counterpart, which is due to the more hydrophobic nature of the former.

Complexation of ellagic acid with α-lactalbumin and its antioxidant property

Ellagic acid possesses numerous bioactivities such as antioxidant activity and anti-inflammatory effect. In this work, the binding interaction between ellagic acid and α-lactalbumin was investigated by multi-spectroscopy and the results suggested that ellagic acid could change the conformation of α-lactalbumin. Chromatographic analysis proved the interaction of α-lactalbumin with ellagic acid taken place in less than 30 min and this interaction was stable. Computer simulations showed that both aromatic clusters Ⅰ and Ⅱ of α-lactalbumin were active sites for ellagic acid. Interestingly, both the results of molecular docking and molecular dynamics simulations suggested that ellagic acid tended to bind to aromatic cluster Ⅱ rather than aromatic cluster Ⅰ. Moreover, α-lactalbumin could enhance the antioxidant property of ellagic acid, indicating that the solubility of ellagic acid might be improved by combining α-lactalbumin. Overall, this work suggested that α-lactalbumin exhibited binding affinity for ellagic acid and enhanced its antioxidant property.