The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

Concatenation of molecular docking and dynamics simulation of human papillomavirus type 16 E7 oncoprotein targeted ligands: In quest of cervical cancer's treatment

The Human papillomaviruses type 16 E7 oncoprotein is a 98-amino-acid, 11-kilodalton acidic oncoprotein with three conserved portions. Due to its interaction with the pRb-E2F complex, CKII, CKI (mostly p21), and even HDAC1, it possesses strong transformative and carcinogenic qualities that inhibit normal differentiation and cell cycle regulation. Here, we target the E7 oncoprotein using two prior research active compounds: asarinin and thiazolo[3,2-a]benzimidazole-3(2H)-one,2-(2-fluorobenzylideno)-7,8-dimethyl (thiazolo), and valproic acid as a control. We are performing molecular docking followed by molecular dynamic analysis. By acting as competitive inhibitors in the binding site, it was hypothesized that both drugs would inhibit E7-mediated pRb degradation and E7-mediated p21 degradation, resulting in decreased cell cycle progression, immortalization, and proliferation. In addition, we expect that the direct inhibitory action of valproic acid in E7 will target the CKII-mediated phosphorylation pathway necessary for destabilizing p130 and pRb. According to the results of the dynamic simulation, stable interactions exist between every compound. Despite the instability of E7 protein, stability results indicate that both natural chemicals are preferable, with thiazolo outperforming valproic acid.

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications

In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

The development process of plant-based meat alternatives: raw material formulations and processing strategies

With the rapid growth of the world's population, the demand for meat is gradually increasing. The emergence and development of plant-based meat alternatives (PBMs) offer a good alternative to solve the environmental problems and disease problems caused by the over-consumption of meat products. Soybean is now the primary material for the production of PBMs due to its excellent gelation properties, potential from fibrous structure, balanced nutritional value, and relatively low price. Extrusion is the most widely used process for producing PBMs, and it has a remarkable effect on simulating the fibrous structure of real meat products. However, interactions related to phase transitions in protein molecules or fibrous structures during extrusion remain a challenge. Currently, PBMs do not meet people's demand for realistic meat in terms of texture, taste, and flavor. Therefore, the objectives of this review are to explore how to improve fiber structure formation in terms of raw material formulation and processing technology. Factors to improve the taste and texture of PBMs are summarized in terms of optimizing process parameters, changing the composition of raw materials, and enriching taste and flavor. It will provide a theoretical basis for the future development of PBMs.

Structural and Dynamic Disturbances Revealed by Molecular Dynamics Simulations Predict the Impact on Function of CCT5 Chaperonin Mutations Associated with Rare Severe Distal Neuropathies

Mutations in genes encoding molecular chaperones, for instance the genes encoding the subunits of the chaperonin CCT (chaperonin containing TCP-1, also known as TRiC), are associated with rare neurodegenerative disorders. Using a classical molecular dynamics approach, we investigated the occurrence of conformational changes and differences in physicochemical properties of the CCT5 mutations His147Arg and Leu224Val associated with a sensory and a motor distal neuropathy, respectively. The apical domain of both variants was substantially but differently affected by the mutations, although these were in other domains. The distribution of hydrogen bonds and electrostatic potentials on the surface of the mutant subunits differed from the wild-type molecule. Structural and dynamic analyses, together with our previous experimental data, suggest that genetic mutations may cause different changes in the protein-binding capacity of CCT5 variants, presumably within both hetero- and/or homo-oligomeric complexes. Further investigations are necessary to elucidate the molecular pathogenic pathways of the two variants that produce the two distinct phenotypes. The data and clinical observations by us and others indicate that CCT chaperonopathies are more frequent than currently believed and should be investigated in patients with neuropathies.

Effects of the molecular weight of hyaluronan on the conformation and release kinetics of self-assembled 5-fluorouracil-loaded lysozyme-hyaluronan colloidal nanoparticles

Lysozyme (LYS) and hyaluronan with low (HA1: 3 kDa), medium (HA2: 120 kDa), and high (HA3: 1200 kDa) molecular weights were used to fabricate lysozyme-hyaluronan colloidal nanoparticles using a green self-assembly method. Fourier transform infrared spectroscopy indicated that hydrogen bonding, hydrophobic and electrostatic interactions promoted the formation of the colloidal nanoparticles. The hydrophobic area of prepared colloidal nanoparticles was quantified using a pyrene fluorescent probe, and the results showed that the LYS-HA3 nanoparticles had the strongest hydrophobic capacity. Furthermore, 5-fluorouracil (5-Fu) was used to evaluate encapsulation performance, demonstrating that the LYS-HA3 nanoparticles had the highest encapsulation ability (>90 %). All prepared 5-Fu-loaded lysozyme-hyaluronan (5-Fu@LYS-HA) colloidal nanoparticles exhibited excellent long-term storage stability at 4 °C for 60 days. Cellular uptake and in vitro release results indicated that the LYS-HA2 nanoparticles exhibited the highest cellular uptake efficiency, and the LYS-HA3 nanoparticles had the best slow-release effect, while the release process was mainly controlled by the combination of Fickian diffusion and structural relaxation, respectively. This study demonstrates the influence of molecular weight on the conformational and structural properties of colloidal nanoparticles, which has implications for the design of insoluble drug self-assembly systems.

Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.

High moisture extrusion cooking of meat analogs: A review of mechanisms of protein texturization

High-moisture extrusion cooking (HMEC) is an efficient method for converting proteins and polysaccharides into fibrous structure that is used in the industrial production of meat analogs. The purpose of this review is to systematically evaluate current knowledge regarding the modification of protein structure including denaturation and reassembly upon extrusion processing and to correlate this understanding to the structure of the final products. Although there is no consensus on the relative importance of a certain type of bond on extrudates' structure, literature suggests that, regardless of moisture level, these linkages and interactions give rise to distinctive hierarchical order. Both noncovalent and disulfide bonds contribute to the extrudates' fibrous structure. At high water levels, hydrogen and disulfide bonds play a dominant role in extrudates' texture. The process parameters including cooking temperature, screw speed, and moisture content have significant albeit different levels of impact on the texturization process. Their correlation with the ingredients' physiochemical properties provides a greater insight into the process-structure-function relationship of meat analogs. The tendency of protein and polysaccharide blends to phase separate rather than produce a homogeneous mix is a particularly important aspect that leads to the formation of fibrous layers when extruded. This review shows that systematic studies are required to measure and explain synergistic and competitive interactions between proteins and other ingredients such as carbohydrates with a focus on their incompatibility. The wide range of plant protein source can be utilized in the HMEC process to produce texturized products, including meat analogs.

Ionic Liquid-Based Strategy for Predicting Protein Aggregation Propensity and Thermodynamic Stability

Novel drug candidates are continuously being developed to combat the most life-threatening diseases; however, many promising protein therapeutics are dropped from the pipeline. During biological and industrial processes, protein therapeutics are exposed to various stresses such as fluctuations in temperature, solvent pH, and ionic strength. These can lead to enhanced protein aggregation propensity, one of the greatest challenges in drug development. Recently, ionic liquids (ILs), in particular, biocompatible choline chloride ([Cho]Cl)-based ILs, have been used to hinder stress-induced protein conformational changes. Herein, we develop an IL-based strategy to predict protein aggregation propensity and thermodynamic stability. We examine three key variables influencing protein misfolding: pH, ionic strength, and temperature. Using dynamic light scattering, zeta potential, and variable temperature circular dichroism measurements, we systematically evaluate the structural, thermal, and thermodynamic stability of fresh immunoglobin G4 (IgG4) antibody in water and 10, 30, and 50 wt % [Cho]Cl. Additionally, we conduct molecular dynamics simulations to examine IgG4 aggregation propensity in each system and the relative favorability of different [Cho]Cl-IgG4 packing interactions. We re-evaluate each system following 365 days of storage at 4 °C and demonstrate how to predict the thermodynamic properties and protein aggregation propensity over extended storage, even under stress conditions. We find that increasing [Cho]Cl concentration reduced IgG4 aggregation propensity both fresh and following 365 days of storage and demonstrate the potential of using our predictive IL-based strategy and formulations to radically increase protein stability and storage.

Freezing-induced denaturation of myofibrillar proteins in frozen meat

Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.

Combining a Genetically Engineered Oxidase with Hydrogen-Bonded Organic Frameworks (HOFs) for Highly Efficient Biocomposites

Enzymes incorporated into hydrogen‐bonded organic frameworks (HOFs) via bottom‐up synthesis are promising biocomposites for applications in catalysis and sensing. Here, we explored synthetic incorporation of d‐amino acid oxidase (DAAO) with the metal‐free tetraamidine/tetracarboxylate‐based BioHOF‐1 in water. N‐terminal enzyme fusion with the positively charged module Z_basic2 strongly boosted the loading (2.5‐fold; ≈500 mg enzyme g_material⁻¹) and the specific activity (6.5‐fold; 23 U mg⁻¹). The DAAO@BioHOF‐1 composites showed superior activity with respect to every reported carrier for the same enzyme and excellent stability during catalyst recycling. Further, extension to other enzymes, including cytochrome P450 BM3 (used in the production of high‐value oxyfunctionalized compounds), points to the versatility of genetic engineering as a strategy for the preparation of biohybrid systems with unprecedented properties.

Characterization of Antioxidant Peptides from Thai Traditional Semi-Dried Fermented Catfish

Herein, the antioxidant peptides from a Thai traditional semi-dried fermented farmed hybrid catfish (Clarias macrocephalus × Clarias gariepinus) catfish, Pla Duk Ra, were characterized. After extraction and deproteinization, Pla Duk Ra crude peptide extract (CPE) was fractioned using 2 connected Hitrap Sephadex-G25 columns, yielding two significant fractions, F1 with higher browning intensity (A420) and F2. CPE, F1, and F2 had different amino acid profiles, contents, and sequences evaluated by LC-MS/MS, which could be responsible for their antioxidant properties. F2 contained the highest numbers of hydrophobic amino acid (HBA) (47.45%) and aromatic amino acid (27.31%), followed by F1, and CPE. The peptides with 8–24 amino acid residues were detected in CPE and its fractions. In CPE, F1, and F2, there were 69, 68, and 85 peptides with varied HBA content, respectively. ARHSYGMLYCSCPPND (50% HBA), ALRKMGRK (37.5% HBA), and ANWMIPLM (87.5% HBA) were the most prevalent peptides found in CPE, F1, and F2. Overall, F2 was the most effective at inhibiting free radicals (DPPH● and ABTS●+) and reactive oxygen species (hydroxyl radical, singlet oxygen, and hydrogen peroxide), followed by F1 and CPE. The metal chelation of F1 was, however, superior to that of F2 and CPE. For the stability test, the effects of pH, heating temperature, and in vitro digestion on the DPPH● scavenging activity of F2 were investigated. The activity was boosted by lowering the pH and raising the heating temperature. In the gastrointestinal tract model system, however, roughly 50% of DPPH● scavenging activity reduced after digesting.

Zinc Binding to NAP-Type Neuroprotective Peptides: Nuclear Magnetic Resonance Studies and Molecular Modeling

Aggregation of amyloid-β peptides (Aβ) is a hallmark of Alzheimer’s disease (AD), which is affecting an increasing number of people. Hence, there is an urgent need to develop new pharmaceutical treatments which could be used to prevent the AD symptomatology. Activity-dependent neuroprotective protein (ADNP) was found to be deficient in AD, whereas NAP, an 8-amino-acid peptide (¹NAPVSIPQ⁸) derived from ADNP, was shown to enhance cognitive function. The higher tendency of zinc ion to induce Aβ aggregation and formation of amorphous aggregates is also well-known in the scientific literature. Although zinc binding to Aβ peptides was extensively investigated, there is a shortage of knowledge regarding the relationship between NAP peptide and zinc ions. Therefore, here, we investigated the binding of zinc ions to the native NAP peptide and its analog obtained by replacing the serine residue in the NAP sequence with tyrosine (¹NAPVYIPQ⁸) at various molar ratios and pH values by mass spectrometry (MS) and nuclear magnetic resonancespectroscopy (NMR). Matrix-assisted laser desorption/ionization time-of-flight (MALDI ToF) mass spectrometry confirmed the binding of zinc ions to NAP peptides, while the chemical shift of Asp¹, observed in ¹H-NMR spectra, provided direct evidence for the coordinating role of zinc in the N-terminal region. In addition, molecular modeling has also contributed largely to our understanding of Zn binding to NAP peptides.

From Critical Point to Critical Point: The Two-States Model Describes Liquid Water Self-Diffusion from 623 to 126 K

Liquid’s behaviour, when close to critical points, is of extreme importance both for fundamental research and industrial applications. A detailed knowledge of the structural–dynamical correlations in their proximity is still today a target to reach. Liquid water anomalies are ascribed to the presence of a second liquid–liquid critical point, which seems to be located in the very deep supercooled regime, even below 200 K and at pressure around 2 kbar. In this work, the thermal behaviour of the self-diffusion coefficient for liquid water is analyzed, in terms of a two-states model, for the first time in a very wide thermal region (126 K < T < 623 K), including those of the two critical points. Further, the corresponding configurational entropy and isobaric-specific heat have been evaluated within the same interval. The two liquid states correspond to high and low-density water local structures that play a primary role on water dynamical behavior over 500 K.

Sajedi R. Thermostability of Ctenophore and Coelenterate Ca2+-Regulated Apo-photoproteins: A Comparative Study

The stabilities of Ca²⁺-regulated ctenophore and coelenterate apo-photoproteins, apo-mnemiopsin (apo-Mne) and apo-aequorin (apo-Aeq), respectively, were compared biochemically, biophysically, and structurally. Despite high degrees of structural and functional conservation, drastic variations in stability and structural dynamics were found between the two proteins. Irreversible thermoinactivation experiments were performed upon incubation of apo-photoproteins at representative temperatures. The inactivation rate constants (k_inact) at 50 °C were determined to be 0.001 and 0.004 min^-1 for apo-Mne and apo-Aeq, respectively. Detailed analysis of the inactivation process suggests that the higher thermostability of apo-Mne is due to the higher activation energy (E_a) and subsequently higher values of ΔH* and ΔG* at a given temperature. According to molecular dynamics simulation studies, the higher hydrogen bond, electrostatic, and van der Waals energies in apo-Mne can validate the relationship between the thermal adaptation of apo-Mne and the energy barrier for the inactivation process. Our results show that favorable residues for protein thermostability such as hydrophobic, charged, and adopted α-helical structure residues are more frequent in the apo-Mne structure. Although the effect of acrylamide on fluorescence quenching suggests that the local flexibility in regions around Trp and Tyr residues of apo-Aeq is higher than that of apo-Mne, which results in it having a better ability to penetrate acrylamide molecules, the root-mean-square fluctuation of helix A in apo-Mne is higher than that in apo-Aeq. It seems that the greater flexibility of apo-Mne in these regions may be considered as a determining factor, affecting the thermal stability of apo-Mne through a balance between structural rigidity and flexibility.

Identification of transmissible proteotoxic oligomer-like fibrils that expand conformational diversity of amyloid assemblies

Protein misfolding and amyloid deposition are associated with numerous diseases. The detailed characterization of the proteospecies mediating cell death remains elusive owing to the (supra)structural polymorphism and transient nature of the assemblies populating the amyloid pathway. Here we describe the identification of toxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). While N21Q filaments share structural properties with cytocompatible fibrils, including the 4.7 Å inter-strand distance and β-sheet-rich conformation, they concurrently display characteristics of oligomers, such as low thioflavin-T binding, high surface hydrophobicity and recognition by the A11 antibody, leading to high potency to disrupt membranes and cause cellular dysfunction. The toxic oligomer-like conformation of N21Q fibrils, which is preserved upon elongation, is transmissible to naïve IAPP. These stable fibrils expanding the conformational diversity of amyloid assemblies represent an opportunity to elucidate the structural basis of amyloid disorders.

Nguyen et al identified cytotoxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). They presented evidence to show that these stable fibrils expand the conformational diversity of amyloid assemblies, which represents an opportunity to elucidate the structural basis of amyloid disorders.

Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study

Regarding the urgency of therapeutic measures for coronavirus disease 2019 (COVID-19) pandemic, the use of available drugs with FDA approval is preferred because of the less time and cost required for their development. In silico drug repurposing is an accurate way to speed up the screening of the existing FDA-approved drugs to find a therapeutic option for COVID-19. The similarity in SARS-CoV-2 and HIV-1 fusion mechanism to host cells can be a key point for Inhibit SARS-CoV-2 entry into host cells by HIV fusion inhibitors. Accordingly, in this study, an HIV-1 fusion inhibitor called Enfuvirtide (Enf) was selected. The affinity and essential residues involving in the Enf binding to the S2 protein of SARS-CoV-2, HIV-1 gp41 protein and angiotensin-converting enzyme 2 (ACE-2) as a negative control, was evaluated using molecular docking. Eventually, Enf-S2 and Enf-gp41 protein complexes were simulated by molecular dynamics (MD) in terms of binding affinity and stability. Based on the most important criteria such as docking score, cluster size, energy and dissociation constant, the strongest interaction was observed between Enf with the S2 protein. In addition, MD results confirmed that Enf-S2 protein interaction was remarkably stable and caused the S2 protein residues to undergo the fewest fluctuations. In conclusion, it can be stated that Enf can act as a strong SARS-CoV-2 fusion inhibitor and demonstrates the potential to enter the clinical trial phase of COVID-19.

Communicated by Ramaswamy H. Sarma

Nanocellulose-lysozyme colloidal gels via electrostatic complexation

Biohybrid colloids were fabricated based on electrostatic complexation between anionic TEMPO-oxidized cellulose nanofibrils (TO-CNF) and cationic hen egg white lysozyme (HEWL). By altering the loading of HEWL, physical colloidal complexes can be obtained at a relatively low concentration of TO-CNF (0.1 wt%). At neutral pH, increasing the HEWL loading induces an increase in charge screening, as probed by zeta-potential, resulting in enhanced TO-CNF aggregation and colloidal gel formation. Systematic rheological testing shows that mechanical reinforcement of the prepared biohybrid gels is easily achieved by increasing the loading of HEWL. However, due to the relatively weak nature of electrostatic complexation, the formed colloidal gels exhibit partial destruction when subjected to cyclic shear stresses. Still, they resist thermo-cycling up to 90 °C. Finally, the pH responsiveness of the colloidal complex gels was demonstrated by adjusting pH to above and below the isoelectric point of HEWL, representing a facile mechanism to tune the gelation of TO-CNF/HEWL complexes. This work highlights the potential of using electrostatic complexation between HEWL and TO-CNF to form hybrid colloids, and demonstrates the tunability of the colloidal morphology and rheology by adjusting the ratio between the two components and the pH.

Probing protein-induced membrane fouling with in-situ attenuated total reflectance fourier transform infrared spectroscopy and multivariate curve resolution-alternating least squares

Proteins are one of the major contributors to membrane fouling. The interaction between proteins and the polymer membrane at the molecular level is essential for the alleviation/prevention of membrane fouling, but remains unclear. In this work, time-dependent in-situ attenuated total reflectance Fourier transform infrared spectroscopy is applied to investigate the interaction process between two model proteins, bovine serum albumin and lysozyme, and the poly(vinylidene fluoride) (PVDF) membrane. Multivariate curve resolution-alternating least squares is integrated with two-dimensional correlation spectroscopy analysis to resolve the membrane-induced conformational changes of proteins. The multivariate curve resolution-alternating least squares analysis reveals a two-step process in the protein-membrane interaction and provides the kinetics of the conformational transition, which aids the segmentation of the spectral dataset. By applying two-dimensional correlation spectroscopy analysis to different groups of the time-dependent spectra, the sequential order of the secondary structural changes of proteins is determined. The proteins initially undergo unfolding transition to a more open, less structured state, which appears to be triggered by the hydrophobic membrane surface. Afterwards, the proteins become aggregated with the high anti-parallel β-sheet content, aggravating the membrane fouling. The conformational transition process of proteins was also confirmed by the atomic force microscopic images and quartz crystal microbalance measurement. Overall, this work provides an in-depth understanding of the interaction between proteins and the membrane surface, which is helpful for the development of membrane anti-fouling strategies.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.

Prediction of potential deleterious nonsynonymous single nucleotide polymorphisms of HIF1A gene: A computational approach

Hypoxia-inducible factor-1α (HIF-1α) is the oxygen sensitive subunit of HIF1 transcription factor. Its variations is associated with several diseases including different type of cancer, cardiovascular diseases, and liver and kidney failure. Despite all the investigations carried out on the single nucleotide polymorphisms (SNPs) of HIF1A gene and diseases, there are many uncharacterized nonsynonymous SNPs of this gene, which might have damaging effect on the protein function. Therefore, it is worthwhile to analyze these potential damaging nsSNPs, using different bioinformatics tools before launching large population studies. The objective of the present study was to predict the possible deleterious nsSNPs of HIF1A gene and their effects on the function and structure of HIF-1alpha protein, using different bioinformatics tools. Various prediction servers were used including SIFT, PROVEAN, PolyPhen-2, PANTHER, phD-SNP, SNP-GO, I-Mutant 2.0, Fathmm, SNPeffect 4.0, Mutation taster, CADD and RAMPAGE in a stepwise approach. After analyzing all 454 missense variants of the HIF1A gene using the abovementioned tools, we reported 11 variants with a significant impact on the function or structure of HIF-1α protein. Furthermore, among these variants only S274 P was predicted as stability enhancing variant with effect on protein function by increasing its stability. Although there are many advantages for computational analysis, the results has to be confirmed by experimental investigations.

Correlation between Tribological Properties and the Quantified Structural Changes of Lysozyme on Poly (2-hydroxyethyl methacrylate) Contact Lens

The ocular discomfort is the leading cause of contact lens wear discontinuation. Although the tear proteins as a lubricant might improve contact lens adaptation, some in vitro studies suggested that the amount of adsorbed proteins could not simply explain the lubricating performance of adsorbed proteins. The purpose of this study was to quantify the structural changes and corresponding ocular lubricating properties of adsorbed protein on a conventional contact lens material, poly (2-hydroxyethyl methacrylate) (pHEMA). The adsorption behaviors of lysozyme on pHEMA were determined by the combined effects of protein–surface and protein–protein interactions. Lysozyme, the most abundant protein in tear, was first adsorbed onto the pHEMA surface under widely varying protein solution concentrations to saturate the surface, with the areal density of the adsorbed protein presenting different protein–protein effects within the layer. These values were correlated with the measured secondary structures, and corresponding friction coefficient of the adsorbed and protein covered lens surface, respectively. The decreased friction coefficient value was an indicator of the lubricated surfaces with improved adaptation. Our results indicate that the protein–protein effects help stabilize the structure of adsorbed lysozyme on pHEMA with the raised friction coefficient measured critical for the innovation of contact lens material designs with improved adaptation.

Comparative modelling studies of fruit bromelain using molecular dynamics simulation

Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.

Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach

Calprotectin is a heterodimeric protein complex with two subunits called S100A8/A9. The protein has an essential role in inflammation process and various human diseases. It has the ability to bind to unsaturated fatty acids including Arachidonic acid, Oleic acid and etc., which could be considered as a major carrier for fatty acids. In this study we aimed to appraise the thermodynamics and structural changes of Calprotectin in presence of Arachidonic acid/Oleic acid) using docking and molecular dynami simulation method. To create the best conformation of Calprotectin-Oleic acid/Arachidonic acid complexes, the docking process was performed. The complexes with the best binding energy were selected as the models for molecular dynamics simulation process. Furthermore, the structural and thermodynamics properties of the complexes were evaluated too. The Root Mean Square Deviation and Root Mean Square Fluctuation results showed that the binding of Arachidonic acid/Oleic acid to Calprotectin can cause the protein structural changes which was confirmed by Define Secondary Structure of Proteins results. Accordingly, the binding free energy results verified that binding of Oleic acid to Calprotectin leads to instability of S100A8/A9 subunits in the protein. Moreover, the electrostatic energy contribution of the complexes (Calprotectin-Oleic acid/Arachidonic acid) was remarkably higher than van der Waals energy. Thus, the outcome of this study confirm that Oleic acid has a stronger interaction with Calprotectin in comparison with Arachidonic acid. Our findings indicated that binding of unsaturated fatty acids to Calprotectin leads to structural changes of the S100A8/A9 subunits which could be beneficial to play a biological role in inflammation process.

Strong proton-shared hydrogen bonding in a methyl imidazole⋯HCl complex: evidence from matrix isolation infrared spectroscopy and ab initio computations

Evidence for proton-shared hydrogen bonding is provided in a methyl imidazole⋯HCl complex using matrix isolation infrared spectroscopy and ab initio computations.

Importance of Combining Advanced Particle Size Analysis Techniques To Characterize Cell-Penetrating Peptide-Ferrocifen Self-Assemblies

The design of a simple platform to target the delivery of notably hydrophobic drugs into cancer cells is an ultimate goal. Here, three strategies were combined in the same nanovector, in limiting the use of excipients: cell-penetrating peptides, an amphiphilic prodrug, and self-assembly. Light scattering and cryogenic transmission electron microscopy revealed one size population of objects around 100 nm with a narrow size distribution. However, in-depth analysis of the suspension by nanoparticle tracking analysis, small-angle X-ray scattering, and nuclear magnetic resonance (NMR) diffusometry demonstrated the presence of another population of small objects (<2 nm). It has been shown that these small self-assemblies represented >99% of the matter! This presence was clearly and unambiguously demonstrated by NMR diffusometry experiments. The study highlights the importance and the complementary contribution of each characterization method to reflect the reality of the studied nanoassembly.

The Proton Density of States in Confined Water (H2O)

The hydrogen density of states (DOS) in confined water has been probed by inelastic neutron scattering spectra in a wide range of its P–T phase diagram. The liquid–liquid transition and the dynamical crossover from the fragile (super-Arrhenius) to strong (Arrhenius) glass forming behavior have been studied, by taking into account the system polymorphism in both the liquid and amorphous solid phases. The interest is focused in the low energy region of the DOS (E<10 meV) and the data are discussed in terms of the energy landscape (local minima of the potential energy) approach. In this latest research, we consider a unit scale energy (EC) linked to the water local order governed by the hydrogen bonding (HB). All the measured spectra, scaled according to such energy, evidence a universal power law behavior with different exponents (γ) in the strong and fragile glass forming regions, respectively. In the first case, the DOS data obey the Debye squared-frequency law, whereas, in the second one, we obtain a value predicted in terms of the mode-coupling theory (MCT) (γ≃1.6).

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.

Aggregation States of Aβ1-40, Aβ1-42 and Aβp3-42 Amyloid Beta Peptides: A SANS Study

Aggregation states of amyloid beta peptides for amyloid beta A β 1 - 40 to A β 1 - 42 and A β p 3 - 42 are investigated through small angle neutron scattering (SANS). The knowledge of these small peptides and their aggregation state are of key importance for the comprehension of neurodegenerative diseases (e.g., Alzheimer's disease). The SANS technique allows to study the size and fractal nature of the monomers, oligomers and fibrils of the three different peptides. Results show that all the investigated peptides have monomers with a radius of gyration of the order of 10 Å, while the oligomers and fibrils display differences in size and aggregation ability, with A β p 3 - 42 showing larger oligomers. These properties are strictly related to the toxicity of the corresponding amyloid peptide and indeed to the development of the associated disease.