Protein Chain Research Articles

HEPARAN SULFATE: LANDING SITE FOR THE DENGUE VIRAL STRAINS TO GAIN ENTRY TO THE HOST CELLS

Humans usually contract dengue by being bitten by arthropods, and more than 3.6 billion people are at risk per year. Although studies are conducted to screen and trace out the possible pathophysiology of the virus, an adequate receptor-based study has not been completed. Understanding how the dengue virus (DV) engraves its landing sites requires identification of such cellular receptors. In many model studies, heparan sulfate (HS) has been reported to act as a DV receptor under various conditions. However, the physiological relevance of these findings remains uncertain. Therefore, it is still unclear whether HS is used by viral strains or not, and if at all used by clinical or non-cell culture-adapted strains of DV. The present review aims to identify relevant experimental evidences that confirm the possible interaction between envelope protein and HS chains. We collected data from a series of studies to conclude the interactive role.

Distance-based reconstruction of protein quaternary structures from inter-chain contacts.

Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.

On the deformation and frequency analyses of SARS-CoV-2 at nanoscale

The SARS-CoV-2 virus, which has emerged as a Covid-19 pandemic, has had the most significant impact on people's health, economy, and lifestyle around the world today. In the present study, the SARS-CoV-2 virus is mechanically simulated to obtain its deformation and natural frequencies. The virus under analysis is modeled on a viscoelastic spherical structure. The theory of shell structures in mechanics is used to derive the governing equations. Whereas the virus has nanometric size, using classical theories may give incorrect results.Consequently, the nonlocal elasticity theory is used to consider the effect of interatomic forces on the results. From the mechanical point of view, if a structure vibrates with a natural frequency specific to it, the resonance phenomenon will occur in that structure, leading to its destruction. Therefore, it is possible that the protein chains of SARS-CoV-2 would be destroyed by vibrating it at natural frequencies. Since the mechanical properties of SARS-CoV-2 are not clearly known due to the new emergence of this virus, deformation and natural frequencies are obtained in a specific interval. Researchers could also use this investigation as a pioneering study to find a non-vaccine treatment solution for the SARS-CoV-2 virus and various viruses, including HIV.

An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel

The influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.

Structure, Activity, and Function of PRMT1.

PRMT1, the major protein arginine methyltransferase in mammals, catalyzes monomethylation and asymmetric dimethylation of arginine side chains in proteins. Initially described as a regulator of chromatin dynamics through the methylation of histone H4 at arginine 3 (H4R3), numerous non-histone substrates have since been identified. The variety of these substrates underlines the essential role played by PRMT1 in a large number of biological processes such as transcriptional regulation, signal transduction or DNA repair. This review will provide an overview of the structural, biochemical and cellular features of PRMT1. After a description of the genomic organization and protein structure of PRMT1, special consideration was given to the regulation of PRMT1 enzymatic activity. Finally, we discuss the involvement of PRMT1 in embryonic development, DNA damage repair, as well as its participation in the initiation and progression of several types of cancers.

Selective activation of cannabinoid receptor-2 reduces white matter injury via PERK signaling in a rat model of traumatic brain injury

Background and purposeTraumatic brain injury (TBI) destroys white matter, and this destruction is aggravated by secondary neuroinflammatory reactions. Although white matter injury (WMI) is strongly correlated with poor neurological function, understanding of white matter integrity maintenance is limited, and no available therapies can effectively protect white matter. One candidate approach that may fulfill this goal is cannabinoid receptor 2 (CB2) agonist treatment. Here, we confirmed that a selective CB2 agonist, JWH133, protected white matter after TBI. MethodsThe motor evoked potentials (MEPs), open field test, and Morris water maze test were used to assess neurobehavioral outcomes. Brain tissue loss, WM damage, Endoplasmic reticulum stress (ER stress), microglia responses were evaluated after TBI. The functional integrity of WM was measured by diffusion tensor imaging (DTI) and transmission electron microscopy (TEM). Primary microglia and oligodendrocyte cocultures were used for additional mechanistic studies. ResultsJWH133 increased myelin basic protein (MBP) and neurofilament heavy chain (NF200) levels and anatomic preservation of myelinated axons revealed by DTI and TEM. JWH133 also increased the numbers of oligodendrocyte precursor cells and mature oligodendrocytes. Furthermore, JWH133 drove microglial polarization toward the protective M2 phenotype and modulated the redistribution of microglia in the striatum. Further investigation of the underlying mechanism revealed that JWH133 downregulated phosphorylation of the protein kinase R (PKR)-like endoplasmic reticulum (ER) kinase (PERK) signaling pathway and its downstream signals eukaryotic translation initiation factor 2 α (eIF2α), activating transcription factor 4 (ATF4) and Growth arrest and DNA damage-inducible protein (GADD34); this downregulation was followed by p-Protein kinase B(p-Akt) upregulation. In primary cocultures of microglia and oligodendrocytes, JWH133 decreased phosphorylated PERK expression in microglia stimulated with tunicamycin and facilitated oligodendrocyte survival. These data reveal that JWH133 ultimately alleviates WMI and improves neurological behavior following TBI. However, these effects were prevented by SR144528, a selective CB2 antagonist. ConclusionsThis work illustrates the PERK-mediated interaction between microglia and oligodendrocytes. In addition, the results are consistent with recent findings that microglial polarization switching accelerates WMI, highlighting a previously unexplored role for CB2 agonists. Thus, CB2 agonists are potential therapeutic agents for TBI and other neurological conditions involving white matter destruction.

Breeding Canola (Brassica napus L.) for Protein in Feed and Food.

Interest in canola (Brassica napus L.). In response to this interest, scientists have been tasked with altering and optimizing the protein production chain to ensure canola proteins are safe for consumption and economical to produce. Specifically, the role of plant breeders in developing suitable varieties with the necessary protein profiles is crucial to this interdisciplinary endeavour. In this article, we aim to provide an overarching review of the canola protein chain from the perspective of a plant breeder, spanning from the genetic regulation of seed storage proteins in the crop to advancements of novel breeding technologies and their application in improving protein quality in canola. A review on the current uses of canola meal in animal husbandry is presented to underscore potential limitations for the consumption of canola meal in mammals. General discussions on the allergenic potential of canola proteins and the regulation of novel food products are provided to highlight some of the challenges that will be encountered on the road to commercialization and general acceptance of canola protein as a dietary protein source.

Autogenous Cross-Linking of Recycled Keratin from Poultry-Feather Waste to Hydrogels for Plant-Growth Media.

The global rise in atmospheric temperature is leading to an increasing spread of semi-arid and arid regions and is accompanied by a deterioration of arable land. Polymers can help in a number of ways, but they must not be a burden to the environment. In this context, we present herein a method by which goose feathers, representative of keratin waste in general, can be transformed into hydrogels for use as a plant growth medium. The treatment of shredded feathers in Na2S solution at ambient conditions dissolves approx. 80% of the keratin within 30 min. During evaporation, the thiol groups of cysteine reoxidise to disulphide bridges. Additionally, the protein chains form β-sheets. Both act as cross-links that enables the formation of gels. The drying conditions were found to be crucial as slower evaporation affords gels with higher degrees of swelling at the cost of reduced gel yields. The cress germination test indicated the absence of toxic substances in the gel, which strongly adheres to the roots. Thereby, the plants are protected from drought stress as long as the gel still contains moisture.

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.

The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.

Modulating Surface Properties of the Linothele fallax Spider Web by Solvent Treatment.

Linothele fallax (Mello-Leitão) (L. fallax) spider web, a potentially attractive tissue engineering material, was investigated using quantitative peak force measurement atomic force microscopy and scanning electron microscopy with energy dispersive spectroscopy both in its natural state and after treatment with solvents of different protein affinities, namely, water, ethanol, and dimethyl sulfoxide (DMSO). Native L. fallax silk threads are densely covered by globular objects, which constitute their inseparable parts. Depending on the solvent, treating L. fallax modifies its appearance. In the case of water and ethanol, the changes are minor. In contrast, DMSO practically removes the globules and fuses the threads into dense bands. Moreover, the solvent treatment influences the chemistry of the threads’ surface, changing their adhesive and, therefore, biocompatibility and cell adhesion properties. On the other hand, the solvent-treated web materials’ contact effect on different types of biological matter differs considerably. Protein-rich matter controls humidity better when wrapped in spider silk treated with more hydrophobic solvents. However, carbohydrate plant materials retain more moisture when wrapped in native spider silk. The extracts produced with the solvents were analyzed using nuclear magnetic resonance (NMR) and liquid chromatography–mass spectrometry techniques, revealing unsaturated fatty acids as representative adsorbed species, which may explain the mild antibacterial effect of the spider silk. The extracted metabolites were similar for the different solvents, meaning that the globules were not “dissolved” but “fused into” the threads themselves, being supposedly rolled-in knots of the protein chain.

Peptidases production by fungi obtained from Manihot esculenta Crantz waste and its application in gluten hydrolysis

The growing number of people who develop food intolerance has worried researchers around the world. In this context, studies have been developed to find alternatives that minimize the side effects of these disorders. Positive results have been obtained through the enrichment of foods which contain gluten with specific enzymes able to hydrolyze their protein chains. Therefore, this study investigated fungi associated with stems and leaves of Manihot esculenta Crantz waste which produce peptidases capable of hydrolyzing gluten. The peptidase production capacity of the fungi was tested, and the best results were observed for the ST5 fungus (Alternaria sp.) with specific activity of 1.28 ± 0.004 U/mg. For this fungus, tests were carried out and it was verified that pH 3.0 was the best for its growth using sucrose as a carbon source (2.06 ± 0.001 mg/mg of protein). The pre-purification of the enzyme by saline precipitation with ammonium sulphate showed the best activity (81.69 mg/mg of protein) was achieved in the supernatant obtained after saturation of 75.0%. In the gluten hydrolysis reaction, the ideal reaction time was 24 h and the pH approximately equal to 4. In addition, it was demonstrated that the enzymatic activity involved in gluten hydrolysis was blocked by the inhibitor of aspartyl-peptidase-pepstatin.

Sequence-specific response of collagen-mimetic peptides to osmotic pressure

Native collagen molecules usually contract upon dehydration, but the details of their interaction with water are poorly understood. Previous molecular modeling studies indicated a spatially inhomogeneous response, with a combination of local axial expansion and contraction. Such sequence-dependent effects are difficult to study with native collagen. In this article, we use collagen-mimetic peptides (CMPs) to investigate the effect of osmotic pressure on several collagen-mimetic sequences. Synchrotron x-ray diffraction combined with molecular dynamics simulations shows that CMPs pack differently depending on osmotic pressure and exhibit changes in the helical rise per residue of individual molecules. Infrared spectroscopy reveals that osmotic pressure affects the stability of the triple helix through changes in triple helix-stabilizing hydrogen bonds. Surprisingly, CMPs with the canonical collagen sequence glycine–proline–hydroxyproline are found to elongate upon dehydration, while sequence modifications are able to reverse this tendency. This strongly suggests that the overall contraction of native collagen molecules is not programmed into the canonical sequence but is specific to local amino acids that substitute for proline or hydroxyproline along the protein chain. Collagen is an essential protein in mammalian extracellular tissues and a better understanding of its mechanical function is important both from a materials science and from a biomedical viewpoint. Recently, collagen has been shown to contract along the fibre direction when subjected to osmotic stress, a process that could play important roles in strengthening bone and in developing tissue tension during extracellular matrix development. The present work uses collagen-like short peptides to show that the canonical collagen sequence is not responsible for this contraction. The conclusion is that the collagen amino acid sequence must have evolved to include guest sequences within the canonical glycine-proline-hydroxyproline repeat that provide the observed contractility.Impact statementCollagen is an essential protein in mammalian extracellular tissues and a better understanding of its mechanical function is important both from a materials science and from a biomedical viewpoint. Recently, collagen has been shown to contract along the fibre direction when subjected to osmotic stress, a process that could play important roles in strengthening bone and in developing tissue tension during extracellular matrix development. The present work uses collagen-like short peptides to show that the canonical collagen sequence is not responsible for this contraction. The conclusion is that the collagen amino acid sequence must have evolved to include guest sequences within the canonical glycine-proline-hydroxyproline that provide the observed contractility.Graphic

Serum GFAP and NfL levels in benign relapsing-remitting multiple sclerosis

ObjectiveWe aimed to investigate serum glial fibrillary acidic protein (GFAP) and serum neurofilament light chain (NfL) levels as potential discriminative biomarkers between benign relapsing-remitting multiple sclerosis (BRRMS) and aggressive relapsing-remitting MS (ARRMS). MethodsSerum GFAP and NfL levels were analyzed in patients with BRRMS (n = 34), ARRMS (n = 29), and healthy controls (n = 14) by using Single Molecule Array (Simoa). Patients with ARRMS had been treated with highly effective disease-modifying treatments (DMT) (fingolimod or natalizumab). ResultsSerum GFAP levels in both BRRMS (median 210.19 pg/ml, IQR 163.69–287.19) and in ARRMS (median 188.60 pg/ml, IQR39.23–244.93) were significantly higher (p = 0.035 and p = 0.034, respectively) compared to healthy controls (median 117.93 pg/ml, IQR 60.28–183.83). Serum GFAP levels did not differ between BRRMS and ARRMS. There were no statistical differences in NfL levels between BRRMS, ARRMS and healthy controls. GFAP level was significantly higher (p = 0.04) in BRRMS without DMT (median 216.04 pg/ml, IQR 188.60–274.79) than in those BRRMS patients who had used DMT (median 196.26 pg/ml, IQR 133.33–325.54). ConclusionsWe found elevated levels of serum GFAP in both BRRMS and ARRMS compared to healthy controls, reflecting astrocytic activation. Serum NfL did not differ between BRRMS and ARRMS, probably due to the stable inflammatory phase of the disease and effective DMT use in ARRMS. Single serum NfL and GFAP measurements cannot separate a patient with BRRMS from effectively treated ARRMS after a long history of the disease, thus consecutive samples are needed in the follow-up.

A Mathematical Graph-Theoretic Model of Single Point Mutations Associated with Sickle Cell Anemia Disease

Many diseases like cystic fibrosis and sickle cell anemia disease (SCD), among others, arise from single point mutations in the respective proteins. How a single point mutation might lead to a global devastating consequence on a protein remains an intellectual mystery. SCD is a genetic blood-related disorder resulting from mutations in the beta chain of the human hemoglobin protein (simply, β-globin), subsequently affecting the entire human body. Higher mortality and morbidity rates have been reported for patients with SCD, especially in sub-Saharan Africa. Clinical management of SCD often requires specialized interdisciplinary clinicians. SCD presents a major global burden, hence an improved understanding of how single point mutations in β-globin results in different phenotypes of SCD might offer insight into protein engineering, with potential therapeutic intervention in view. By use of mathematical modeling, we built a hierarchical (nested) graph-theoretic model for the β-globin. Subsequently, we quantified the network of interacting amino acid residues, representing them as molecular system of three distinct stages (levels) of interactions. Using our nested graph model, we studied the effect of virtual single point mutations in β-globin that results in varying phenotypes of SCD, visualized by unsupervised machine learning algorithm, the dendrogram.

Structural Characterization of the Cooperativity of Unfolding of a Heterodimeric Protein using Hydrogen Exchange-Mass Spectrometry

Little is known about how the sequence of structural changes in one chain of a heterodimeric protein is coupled to those in the other chain during protein folding and unfolding reactions, and whether individual secondary structural changes in the two chains occur in one or many coordinated steps. Here, the unfolding mechanism of a small heterodimeric protein, double chain monellin, has been characterized using hydrogen exchange-mass spectrometry. Transient structure opening, which enables HX, was found to be describable by a five state N ↔ I1 ↔ I2 ↔ I3 ↔ U mechanism. Structural changes occur gradually in the first three steps, and cooperatively in the last step. β strands 2, 4 and 5, as well as the α-helix undergo transient unfolding during all three non-cooperative steps, while β1 and the two loops on both sides of the helix undergo transient unfolding during the first two steps. In the absence of GdnHCl, only β3 in chain A of the protein unfolds during the last cooperative step, while in the presence of 1 M GdnHCl, not only β3, but also β2 in chain B unfolds cooperatively. Hence, the extent of cooperative structural change and size of the cooperative unfolding unit increase when the protein is destabilized by denaturant. The naturally evolved two-chain variant of monellin folds and unfolds in a more cooperative manner than does a single chain variant created artificially, suggesting that increasing folding cooperativity, even at the cost of decreasing stability, may be a driving force in the evolution of proteins.

Synthesis and Evaluation of Ubiquitin-Dioxetane Conjugate as a Chemiluminescent Probe for Monitoring Deubiquitinase Activity.

The removal of ubiquitin (Ub) from a modified protein or Ub chain is a process that occurs regularly by the ubiquitin–proteasome system. This process is known to be mediated by various deubiquitinating enzymes (DUBs) in order to control the protein’s half-life and its expression levels among many other signaling processes. Since the function of DUBs is also involved in numerous human diseases, such as cancer, there is an obvious need for an effective diagnostic probe that can monitor the activity of these enzymes. We have developed the first chemiluminescence probe for detection of DUBs activity. The probe was prepared by conjugation of the chemically synthesized C-terminally activated Ub(1-75) with a Gly-enolether precursor. Subsequent oxidation, under aqueous conditions, of the enolether conjuagate with singlet-oxygen furnished the dioxetane probe Ub-CL. This synthesis provides the first example of a dioxetane–luminophore protein conjugate. The probe’s ability to detect deubiquitinating activity was successfully validated with three different DUBs. In order to demonstrate the advantage of our new probe, comparison measurements for detection of DUB UCH-L3 activity were performed between the chemiluminescent probe Ub-CL and the well-known Ub-AMC probe. The obtained data showed significantly higher S/N, for probe Ub-CL (>93-fold) in comparison to that observed for Ub-AMC (1.5-fold). We anticipate that the successful design and synthesis of the turn-ON protein–dioxetane conjugate probe, demonstrated in this work, will provide the insight and motivation for preparation of other relevant protein–dioxetane conjugates.

Development of soybeans starch based tough, water resistant and mildew-proof adhesives through multiple cross linking cooperation strategy

The exploitation of the environment-friendly and renewable biomass adhesive is a promising alternative compared to petroleum-based ones in the wood industry. In this study, soybean flour (SF) was chosen as a renewable starting material for the preparation of the biomass adhesive. The soy protein structure was unfolded by the calcium hydroxide and multiple reactive groups (-COOH, –NH2, –OH, –SH) of the protein chain were exposed. Inspired by the marine mussel protein, tannic acid (TA) with many poly-catechol/pyrogallol groups was capable of interacting with protein molecules under the alkaline conditions and the strong metal coordination between Ca2+ and TA enable to reinforce the network structure of adhesive. Furthermore, the incorporation of 1,6-Hexanediol diglycidyl ether (HDE) into the pristine protein adhesive had reacted with protein molecules via chemical covalent bonds to form the stable and toughness cross-linking network. The as-obtained adhesive showed improved bonding strength and comparable water resistance. Notably, the enhanced adhesive showed an outstanding wet shear strength of 1.12 MPa, meeting China's interior furnishing requirements (≥0.7 MPa). Additionally, in contrast to unmodified adhesive, the mildew resistance of the cooperation modified adhesive was improved and the storage life extended. This research provides a novel and green way to develop a formaldehyde-free adhesive for the wood industry.

Chemical approaches for the preparation of ubiquitinated proteins via natural linkages.

Ubiquitination is an important posttranslation modification (PTM) that regulates a variety of cellular processes, including protein degradation, DNA repair, and viral infections. In this process, the C-terminal carboxyl group of ubiquitin (Ub) or poly-Ub is attached to the ε-amine of lysine (Lys) side chain of an acceptor protein through an isopeptide bond. Studying a molecular mechanism of ubiquitination and deubiquitination is fundamental for unraveling its precise role in health and disease and hence crucial for drug development. Enzymatic approaches for protein ubiquitination possess limited ability to selectivity install Ub or Ub chain on the desired position of an acceptor protein and often lead to heterogeneous mixtures. In the past decades, chemical protein (semi)synthesis has been proved to be an efficient tool to facilitate site-specific protein ubiquitination, which significantly contributes to decode the Ub signal at molecular and structural levels. In this review, we summarize the synthetic strategies developed for protein ubiquitination, and the achievements to generate monoubiquitinated, di-ubiquitinated, and tetraubiquitinated proteins with native isopeptide and ester bonds.

Entropy-Enthalpy Compensations Fold Proteins in Precise Ways.

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

Anticancer Effect of Cardamom Extract on Hep-2 Cell Line

To investigate the anticancer effect of Cardamom extract on Hep-2 cell line which may aid in development of a novel treatment modality to Head and Neck Squamous Cell Carcinoma. Hep-2 cell line was divided into five groups: one control group, two groups treated with Cardamom extract, and another two treated with Doxorubicin, each of the two treatments was applied for 24 and 48 hours, respectively. Then, cellular viability was measured using microculture tetrazolium assay, cell cycle analysis was done using Flow Cytometry and eventually, apoptotic activity was evaluated using enzyme-linked immunosorbent assay to measure the concentration of BAX protein and real time polymerase chain reaction to measure the fold change for caspase-3 enzyme. Cardamom extract succeeded to decrease the percentage of viable and proliferating cells with increasing dose. On the other hand, it increased the percentage of apoptotic cells and levels of caspase-3 and BAX protein. Cardamom extract has a potential cytotoxic effect on Head and Neck Squamous Cell Carcinoma cell line in a dose and time dependent manner, and exerts this action through induction of apoptosis, and its action is comparable to Doxorubicin action.