Amino Acid Residues Research Articles

Virtual screening and molecular dynamics simulation of natural compounds as potential inhibitors of serine/threonine kinase 16 for anticancer drug discovery.

Serine/threonine kinase 16 (STK 16) is involved in many facets of cellular regulation; activation of STK 16 plays a crucial role in the migration of cancer cells. Therefore, it is a novel target for the discovery of anticancer agents. Herein, virtual screening and dynamics simulation were used to screen a large library of natural compounds against STK 16 using Schrodinger suit 2021-2 and GROMACS 2021.6. The results predicted five molecules with high binding affinity against the target, with NPC132329 (Arcyriaflavin C) and NPC160898 having higher binding affinity and molecular mechanics generalized born surface area (MM/GBSA), suggesting that it is better than the standard inhibitor. The molecular dymanics (MD) simulation studies showed that the STK 16-NPC132329 complex has the lowest root mean square deviation, and STK 16-NPC160898 was the most stable compared with the standard drug and selective STK 16 inhibitor. The minimal fluctuation was observed in the STK 16-NPC132329 and STK 16-NPC160898 complexes based on the root mean square fluctuation trajectory with NPC132329 and NPC160898 forming 2 and 3 hydrogen bonds respectively with the amino acid residue of the target's binding site. Overall, NPC132329 and NPC160898 are better STK 16 inhibitors than the standard drug and selective inhibitor, which can be further studied to discover novel anticancer drugs.

Study of bromelain and carboxymethyl cellulose surface interaction features in the process of their adsorption immobilisation

Adsorption immobilisation is a common approach to stabilise the catalytic activity of enzymes. It involves the attachment of their macromolecules to the surface of a carrier due to weak physical interactions and hydrogen bonds. According to modern concepts, this process is the ‘gentlest’ immobilisation technique in terms of the structure of the enzyme globule. Despite this fact, the activity of the immobilised preparation is often lower compared to the native enzyme. To understand the reasons, it is necessary to study the specific features of interactions within the enzyme-carrier system and to identify the types of interactions occurring between its components. When studying the structure of enzymes, it is critical to determine the nature and qualitative composition of amino acid residues on the surface of the enzyme macromolecule that interact with the carrier. If catalytically important residues are involved in the process, there may be a significant decrease in the enzyme activity. In this regard, the aim of the work was to study the features of interaction between bromelain, which is a cysteine protease, and carboxymethyl cellulose by desorption of the enzyme from the formed complex under different conditions (in the presence of ammonium sulphate or surfactant Triton X-100, including at different temperatures), as well as by flexible molecular docking. The studied substances are promising components for the production of biocatalysts for food or biomedical applications, so the study of their interaction features will expand the applications of bromelain. We determined that incubation of bromelain immobilised on carboxymethyl cellulose in solutions of ammonium sulphate with a concentration of 32 mM or higher and Triton X-100 with a concentration of 100 mM or higher resulted in the destruction of the complex and the desorption of the enzyme. It confirms that non-covalent interactions contribute to the formation of immobilised preparation. When we increased the incubation temperature of the complex above 60 °C, we also observed the release of the enzyme from the preparation, indicating the formation of hydrogen bonds between the enzyme and the carrier. In silico study confirmed the formation of these types of bonds and interactions. It was determined that the amino acid residues forming the active site of bromelain also formed bonds with the carrier.

Crucial Structural Understanding for Selective HDAC8 Inhibition: Common Pharmacophores, Molecular Docking, Molecular Dynamics, and Zinc Binder Analysis of selective HDAC8 inhibitors.

Overexpression of HDAC8 was observed in various cancers and inhibition of HDAC8 has emerged as a promising therapeutic approach in recent decades. This review aims to facilitate the discovery of novel selective HDAC8 inhibitors by analyzing the structural scaffolds of 66 known selective HDAC8 inhibitors, along with their IC50 values against HDAC8 and other HDACs. The inhibitors were clustered based on structural symmetry, and common pharmacophores for each cluster were identified using Phase. Molecular docking with all HDACs was performed to determine binding affinity and crucial interacting residues for HDAC8 inhibition. Representative inhibitors from each cluster were subjected to molecular dynamics simulation to analyze RMSD, RMSF, active site amino acid residues, and crucial interacting residues responsible for HDAC8 inhibition. The study reviewed the active site amino acid information, active site cavities of all HDACs, and the basic structure of Zn2+ binding groups. Common pharmacophores identified included AADHR_1, AADDR_1, ADDR_1, ADHHR_1, and AADRR_1. Molecular docking analysis revealed crucial interacting residues: HIS- 142, GLY-151, HIS-143, PHE-152, PHE-20 in the main pocket, and ARG-37, TYR-100, TYR-111, TYR-306 in the secondary pocket. The RMSD of protein and RMSF of active site amino acid residues for stable protein-ligand complexes were less than 2.4 Å and 1.0 Å, respectively, as identified from MD trajectories. The range of Molecular Mechanics Generalized Born Surface Area (MMGBSA) ΔG predicted from MD trajectories was between -15.8379 Å and -61.5017 Å kcal/mol. These findings may expedite the rapid discovery of selective HDAC8 inhibitors subject to experimental evaluation.

Crystal structure and characterization of monascin from the extracts of Monascus purpureus-fermented rice.

We present a novel solid form of monascin, an azaphilonoid derivative extracted from Monascus purpureus-fermented rice. The crystal structure, C21H26O5, was characterized by single-crystal X-ray diffraction and belongs to the orthorhombic space group P212121. To gain insight into the electronic properties of the short contacts in the crystalline state of monascin, we utilized the Experimental Library of Multipolar Atom Model 2 (ELMAM2) database to transfer the electron density of monascin in its crystalline state. Hirshfeld surface analysis, fingerprint analysis, electronic properties and energetic characterization reveal that intermolecular C-H...O hydrogen bonds play a crucial role in the noncovalent bonding interactions by connecting molecules into two- and three-dimensional networks. The molecular electrostatic potential (MEP) map of the monascin molecule demonstrates that negatively charged regions located at four O atoms are favoured binding sites for more positively charged amino acid residues during molecular recognition. In addition, powder X-ray diffraction confirms that no transformation occurs during the crystallization of monascin.

Biodegradable chitosan-based biofilms incorporated with Camellia oleifera residue protein for food packaging

Biodegradable films have attracted considerable eco-friendly applications in food packaging, preservation, and separation. This research used a protein mixture containing polyphenols, flavonoids, and tea saponins extracted from Camellia oleifera residues through alkaline dissolution and acid precipitation to prepare biodegradable films. By blending the protein with chitosan, the obtained biopolymer films exhibited improved properties such as hydration, permeability, strength and flexibility, while also showing reduced water solubility. In addition, chitosan-based C. oleifera residue protein biofilms also possessed a significant enhancement in the biofilm's antioxidant, antimicrobial and biodegradable capabilities. Scanning electron microscopy revealed slight irregularities on the film surface when augmented with C. oleifera residue protein, leading to increased cross-sectional roughness and porosity compared to pure chitosan films. These enhancements notably prolonged the shelf life of perishable fruits such as strawberries. Overall, this research used a protein mixture strength, and flexibility while showing reduced also significantly enhanced the biofilm's antioxidant, creating eco-friendly and effective biodegradable food packaging biofilms, contributing to the advancement of sustainable packaging materials.

Kinase-catalyzed biotinylation for discovery and validation of substrates to multispecificity kinases NME1 and NME2

Protein phosphorylation by kinases regulates mammalian cell functions, such as growth, division, and signal transduction. Among human kinases, NME1 and NME2 are associated with metastatic tumor suppression, but remain understudied due to the lack of tools to monitor their cellular substrates. In particular, NME1 and NME2 are multi-specificity kinases phosphorylating serine, threonine, histidine, and aspartic acid residues of substrate proteins, and the heat and acid sensitivity of phosphohistidine and phosphoaspartate complicates substrate discovery and validation. To provide new substrate monitoring tools, we established the γ-phosphate modified ATP analog, ATP-biotin, as a cosubstrate for phosphorylbiotinylation of NME1 and NME2 cellular substrates. Building upon this ATP-biotin compatibility, the Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS) method enabled validation of a known substrate and the discovery of seven NME1 and three NME2 substrates. Given the paucity of methods to study kinase substrates, ATP-biotin and the K-BILDS method are valuable tools to characterize the roles of NME1 and NME2 in human cell biology.

Development of a Crystallographic Screening to Identify Sudan Virus VP40 Ligands.

The matrix protein VP40 of the highly pathogenic Sudan virus (genus Orthoebolavirus) is a multifunctional protein responsible for the recruitment of viral nucleocapsids to the plasma membrane and the budding of infectious virions. In addition to its role in assembly, VP40 also downregulates viral genome replication and transcription. VP40's existence in various homo-oligomeric states is presumed to underpin its diverse functional capabilities during the viral life cycle. Given the absence of licensed therapeutics targeting the Sudan virus, our study focused on inhibiting VP40 dimers, the structural precursors to critical higher-order oligomers, as a novel antiviral strategy. We have established a crystallographic screening pipeline for the identification of small-molecule fragments capable of binding to VP40. Dimeric VP40 of the Sudan virus was recombinantly expressed in bacteria, purified, crystallized, and soaked in a solution of 96 different preselected fragments. Salicylic acid was identified as a crystallographic hit with clear electron density in the pocket between the N- and the C-termini of the VP40 dimer. The binding interaction is predominantly coordinated by amino acid residues leucine 158 (L158) and arginine 214 (R214), which are key in stabilizing salicylic acid within the binding pocket. While salicylic acid displayed minimal impact on the functional aspects of VP40, we delved deeper into characterizing the druggability of the identified binding pocket. We analyzed the influence of residues L158 and R214 on the formation of virus-like particles and viral RNA synthesis. Site-directed mutagenesis of these residues to alanine markedly affected both VP40's budding activity and its effect on viral RNA synthesis, underscoring the potential of the salicylic acid binding pocket as a drug target. In summary, our findings lay the foundation for structure-guided drug design to provide lead compounds against Sudan virus VP40.

Novel ACE inhibitory peptides from enzymatic hydrolysate of Channa punctata protein: In vitro and In silico assay of structure-activity relationship

Channa punctata flesh meat is well known for its ethnomedicinal values. The objective of this study was to isolate and identify peptides having Angiotensin-Converting Enzyme (ACE) inhibitory potential from the Channa punctata fish protein hydrolysates (FPH) and to investigate the inhibitory mechanism by docking study. ACE inhibitory potential of the ultrafiltrate of C. punctata 240 min protein hydrolysates was analysed. The PrAHyd240 (<3 kDa) had the strongest ACE inhibitory potential as it has the lowest IC50 value i.e., 66.08 μg/ml. To identify the ACE inhibitory peptides, PrAHyd240 (<3 kDa) was evaluated by LC ESI mass spectrometer. The amino acid residues of 3 peptides within the intensity count 100–250 were determined by de novo sequencing.The docking analysis reveals that the peptides were deeply buried in the active site of ACE. Thr 5 of ISISTSGGSFR, Val 3 of SLVNLGGSK, and Val 6, Ala 7 of SISISVAR form highly stable metal coordination bonds with the Zn cofactor present in the binding site of ACE. Similar to captopril, the peptide SISISVAR interacted with the amino acids His 353 and His 513 of the binding sites of ACE via H-bond interactions. The MD simulation study reveals that the peptides ISISTSGGSFR, SLVNLGGSK, and SISISVAR interacted with the Zn+ ion via H-bond with 100% occupancy respectively. The above study reveals that Channa punctata protein hydrolysate is a rich source of ACE inhibitory peptides and the isolated peptides ISISTSGGSFR, SLVNLGGSK, and SISISVAR are potential ingredients in the preparation of functional foods.

Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening.

ADCK3 is a member of the UbiB family of atypical protein kinases in humans, with homologues in archaea, bacteria, and eukaryotes. In lieu of protein kinase activity, ADCK3 plays a role in the biosynthesis of coenzyme Q10 (CoQ10), and inactivating mutations can cause a CoQ10 deficiency and ataxia. However, the exact functions of ADCK3 are still unclear, and small-molecule inhibitors could be useful as chemical probes to elucidate its molecular mechanisms. In this study, we applied structure-based virtual screening (VS) to discover a novel chemical series of ADCK3 inhibitors. Through extensive structural analysis of the active-site residues, we developed a pharmacophore model and applied it to a large-scale VS. Out of ∼170,000 compounds virtually screened, 800 top-ranking candidate compounds were selected and tested in both ADCK3 and p38 biochemical assays for hit validation. In total, 129 compounds were confirmed as ADCK3 inhibitors, and among them, 114 compounds are selective against p38, which was used as a counter-target. Molecular dynamics (MD) simulations were then conducted to predict the binding modes of the most potent compounds within the ADCK3 active site. Through metadynamics analysis, we successfully detected the key amino acid residues that govern intermolecular interactions. The findings provided in this study can serve as a promising starting point for drug development.

Enzymes in Synergy: Bacteria Specific Molecular Probe for Locoregional Imaging of Urinary Tract Infection in vivo

AbstractUropathogenic Escherichia coli (UPECs) is a leading cause for urinary tract infections (UTI), accounting for 70–90 % of community or hospital‐acquired bacterial infections owing to high recurrence, imprecision in diagnosis and management, and increasing prevalence of antibiotic resistance. Current methods for clinical UPECs detection still rely on labor‐intensive urine cultures that impede rapid and accurate diagnosis for timely UTI therapeutic management. Herein, we developed a first‐in‐class near‐infrared (NIR) UPECs fluorescent probe (NO−AH) capable of specifically targeting UPECs through its collaborative response to bacterial enzymes, enabling locoregional imaging of UTIs both in vitro and in vivo. Our NO−AH probe incorporates a dual protease activatable moiety, which first reacts with OmpT, an endopeptidase abundantly present on the outer membrane of UPECs, releasing an intermediate amino acid residue conjugated with a NIR hemicyanine fluorophore. Such liberated fragment would be subsequently recognized by aminopeptidase (APN) within the periplasm of UPECs, activating localized fluorescence for precise imaging of UTIs in complex living environments. The peculiar specificity and selectivity of NO−AH, facilitated by the collaborative action of bacterial enzymes, features a timely and accurate identification of UPECs‐infected UTIs, which could overcome misdiagnosis in conventional urine tests, thus opening new avenues towards reliable UTI diagnosis and personalized antimicrobial therapy management.

Genome-Wide Identification and Characterization of CCT Gene Family from Microalgae to Legumes.

The CCT (CO, COL and TOC1) gene family has been elucidated to be involved in the functional differentiation of the products in various plant species, but their specific mechanisms are poorly understood. In the present investigation, we conducted a genome-wide identification and phylogenetic analysis of CCT genes from microalgae to legumes. A total of 700 non-redundant members of the CCT gene family from 30 species were identified through a homology search. Phylogenetic clustering with Arabidopsis and domain conservation analysis categorized the CCT genes into three families. Multiple sequence alignment showed that the CCT domain contains important amino acid residues, and each CCT protein contains 24 conserved motifs, as demonstrated by the motif analysis. Whole-genome/segment duplication, as well as tandem duplication, are considered to be the driving forces in the evolutionary trajectory of plant species. This comprehensive investigation into the proliferation of the CCT gene family unveils the evolutionary dynamics whereby WGD/segment duplication is the predominant mechanism contributing to the expansion of the CCT genes. Meanwhile, the examination of the gene expression patterns revealed that the expression patterns of CCT genes vary in different tissues and at different developmental stages of plants, with high expression in leaves, which is consistent with the molecular regulation of flowering in photosynthesis by CCT. Based on the protein-protein interaction analysis of CCT genes in model plants, we propose that the CCT gene family synergistically regulates plant development and flowering with light-signaling factors (PHYs and PIFs) and MYB family transcription factors. Understanding the CCT gene family's molecular evolution enables targeted gene manipulation for enhanced plant traits, including optimized flowering and stress resistance.

Design of Novel TRPA1 Agonists Based on Structure of Natural Vasodilator Carvacrol-In Vitro and In Silico Studies.

Considering the escalating global prevalence and the huge therapeutic demand for the treatment of hypertension, there is a persistent need to identify novel target sites for vasodilator action. This study aimed to investigate the role of TRPA1 channels in carvacrol-induced vasodilation and to design novel compounds based on carvacrol structure with improved activities. In an isolated tissue bath experiment, it was shown that 1 µM of the selective TRPA1 antagonist A967079 significantly (p < 0.001) reduced vasodilation induced by 3 mM of carvacrol. A reliable 3D-QSAR model with good statistical parameters was created (R2 = 0.83; Q2 = 0.59 and Rpred2 = 0.84) using 29 TRPA1 agonists. Obtained results from this model were used for the design of novel TRPA1 activators, and to predict their activity against TRPA1. Predicted pEC50 activities of these molecules range between 4.996 to 5.235 compared to experimental pEC50 of 4.77 for carvacrol. Molecular docking studies showed that designed molecules interact with similar amino acid residues of the TRPA1 channel as carvacrol, with eight compounds showing lower binding energies. In conclusion, carvacrol-induced vasodilation is partly mediated by the activation of TRPA1 channels. Combining different in silico approaches pointed out that the molecule D27 (2-[2-(hydroxymethyl)-4-methylphenyl]acetamide) is the best candidate for further synthesis and experimental evaluation in in vitro conditions.

Combined clinical, structural, and cellular studies discriminate pathogenic and benign TRPV4 variants.

Dominant mutations in the calcium-permeable ion channel TRPV4 (transient receptor potential vanilloid 4) cause diverse and largely distinct channelopathies, including inherited forms of neuromuscular disease, skeletal dysplasias, and arthropathy. Pathogenic TRPV4 mutations cause gain of ion channel function and toxicity that can be rescued by small molecule TRPV4 antagonists in cellular and animal models, suggesting that TRPV4 antagonism could be therapeutic for patients. Numerous variants in TRPV4 have been detected with targeted and whole exome/genome sequencing, but for the vast majority, their pathogenicity remains unclear. Here, we used a combination of clinical information and experimental structure-function analyses to evaluate 30 TRPV4 variants across various functional protein domains. We report clinical features of seven patients with TRPV4 variants of unknown significance and provide extensive functional characterization of these and an additional 17 variants, including structural position, ion channel function, subcellular localization, expression level, cytotoxicity, and protein-protein interactions. We find that gain-of-function mutations within the TRPV4 intracellular ankyrin repeat domain target charged amino acid residues important for RhoA interaction, whereas ankyrin repeat domain residues outside of the RhoA interface have normal or reduced ion channel activity. We further identify a cluster of gain-of-function variants within the intracellular intrinsically disordered region that may cause toxicity via altered interactions with membrane lipids. In contrast, assessed variants in the transmembrane domain and other regions of the intrinsically disordered region do not cause gain of function and are likely benign. Clinical features associated with gain of function and cytotoxicity include congenital onset of disease, vocal cord weakness, and motor predominant disease, whereas patients with likely benign variants often demonstrated late-onset and sensory-predominant disease. These results provide a framework for assessing additional TRPV4 variants with respect to likely pathogenicity, which will yield critical information to inform patient selection for future clinical trials for TRPV4 channelopathies.

Enzymes in Synergy: Bacteria Specific Molecular Probe for Locoregional Imaging of Urinary Tract Infection in vivo.

Uropathogenic Escherichia coli (UPECs) is a leading cause for urinary tract infections (UTI), accounting for 70-90 % of community or hospital-acquired bacterial infections owing to high recurrence, imprecision in diagnosis and management, and increasing prevalence of antibiotic resistance. Current methods for clinical UPECs detection still rely on labor-intensive urine cultures that impede rapid and accurate diagnosis for timely UTI therapeutic management. Herein, we developed a first-in-class near-infrared (NIR) UPECs fluorescent probe (NO-AH) capable of specifically targeting UPECs through its collaborative response to bacterial enzymes, enabling locoregional imaging of UTIs both in vitro and in vivo. Our NO-AH probe incorporates a dual protease activatable moiety, which first reacts with OmpT, an endopeptidase abundantly present on the outer membrane of UPECs, releasing an intermediate amino acid residue conjugated with a NIR hemicyanine fluorophore. Such liberated fragment would be subsequently recognized by aminopeptidase (APN) within the periplasm of UPECs, activating localized fluorescence for precise imaging of UTIs in complex living environments. The peculiar specificity and selectivity of NO-AH, facilitated by the collaborative action of bacterial enzymes, features a timely and accurate identification of UPECs-infected UTIs, which could overcome misdiagnosis in conventional urine tests, thus opening new avenues towards reliable UTI diagnosis and personalized antimicrobial therapy management.

Iodine deficiency in Russia: Current state of the problem, global practice and new approaches to therapy

Iodine performs a number of important functions in the body, participating in the synthesis of thyroid hormones, which creates the need for constant replenishment of the element in adequate amounts. Continuous monitoring of micronutrient deficiency in the Russian Federation reveals low average daily iodine intake and an increase in the number of cases of thyroid diseases in the period from 2010 to 2020. This actualizes the need to develop new therapeutic and preventive approaches to replenish iodine deficiency. The aim of the review is to analyze the problem of iodine deficiency in Russia and existing practices of its leveling in order to develop a new approach to the prevention and treatment of iodine deficiency conditions. The sample includes publications in Russian and English in the period from 2002 to 2023, using the resources of scientific metric databases Elibrary, Google Scholar, CyberLeninka, PubMed and ScienceDirect. The research work showed that the common practice of eliminating iodine deficiency is to increase the level of consumption of the trace element in the diet, the consequence of which is the availability of a wide range of iodized food supplements and products on the market. However, the analysis of the current functional nutrition sector has revealed a number of drawbacks associated with low bioavailability of the element and its resistance to technological factors in the production of food products. The article presents the key factors influencing the effectiveness of nutritional supplements being developed for nutritional correction of iodine deficiency. They are based on the evaluation of existing means of prevention. The study proposes the development of the technology of whey hydrolysates enriched with iodine and zinc. Application in food production of a food additive based on protein components of milk whey opens new opportunities for processing of secondary dairy raw materials and for full utilization of all milk components. The rich amino acid composition of the additive helps to increase the concentration of essential trace elements in products, as amino acid residues are able to bind iodine and chelate zinc.

Mechanism of action of plasma-activated water on biomacromolecules in Salmonella Enteritidis: Biological effect, computer simulation, and transcriptomics-based analysis

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most important causes of foodborne illness in the food industry. In this work, plasma-activated water (PAW) generated from the plasma jet was employed to reduce S. Enteritidis contamination. The antibacterial mechanism of PAW was revealed from biological changes, molecular docking, and transcriptomics. Results revealed that the addition of lactic acid could improve the antibacterial activity and efficiency of PAW, and confirmed the existence and antibacterial activity of free radicals (OH, 1O2, and NO) in PAW. Meanwhile, PAW treatment caused damage to characteristic functional groups of biomolecules, and led to the oxidation of lipids and degradation of DNA. Molecular docking results further suggested that the reactive species could interact with amino acid residues around key binding sites through hydrogen bonding, affecting the stability of structures. Furthermore, the transcriptomics results indicated that PAW is primarily active on bacterial proteins and to a lesser extent on membrane lipids and DNA. Overall, the action mechanism of PAW on biomacromolecules is comprehensively analyzed in this work, and it provides a theoretical basis for the broad application of plasma technology.

Exploiting Hydrophobic Amino Acid Scanning to Develop Cyclic Peptide Inhibitors of the SARS-CoV-2 Main Protease with Antiviral Activity.

The development of novel antivirals is crucial not only for managing current COVID-19 infections but for addressing potential future zoonotic outbreaks. SARS-CoV-2 main protease (Mpro) is vital for viral replication and viability and therefore serves as an attractive target for antiviral intervention. Herein, we report the optimization of a cyclic peptide inhibitor that emerged from an mRNA display selection against the SARS-CoV-2 Mpro to enhance its cell permeability and in vitro antiviral activity. By identifying mutation-tolerant amino acid residues within the peptide sequence, we describe the development of a second-generation Mpro inhibitor bearing five cyclohexylalanine residues. This cyclic peptide analogue exhibited significantly improved cell permeability and antiviral activity compared to the parent peptide. This approach highlights the importance of optimizing cyclic peptide hits for activity against intracellular targets such as the SARS-CoV-2 Mpro.

Multiscale Materials Engineering via Self-Assembly of Pentapeptide Derivatives from SARS CoV E Protein.

Short peptide-based supramolecular hydrogels hold enormous potential for a wide range of applications. However, the gelation of these systems is very challenging to control. Minor changes in the peptide sequence can significantly influence the self-assembly mechanism and thereby the gelation propensity. The involvement of SARS CoV E protein in the assembly and release of the virus suggests that it may have inherent self-assembling properties that can contribute to the development of hydrogels. Here, three pentapeptide sequences derived from C-terminal of SARS CoV E protein are explored with same amino acid residues but different sequence distributions and discovered a drastic difference in the gelation propensity. By combining spectroscopic and microscopic techniques, the relationship between peptide sequence arrangement and molecular assembly structure are demonstrated, and how these influence the mechanical properties of the hydrogel. The present study expands the variety of secondary structures for generating supramolecular hydrogels by introducing the 310-helix as the primary building block for gelation, facilitated by a water-mediated structural transition into β-sheet conformation. Moreover, these Fmoc-modified pentapeptide hydrogels/supramolecular assemblies with tunable morphology and mechanical properties are suitable for tissue engineering, injectable delivery, and 3D bio-printing applications.

Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers.

The structure and mechanism of the water-oxidation chemistry that occurs in photosystem II have been subjects of great interest. The advent of X-ray free electron lasers allowed the determination of structures of the stable intermediate states and of steps in the transitions between these intermediate states, bringing a new perspective to this field. The room-temperature structures collected as the photosynthetic water oxidation reaction proceeds in real time have provided important novel insights into the structural changes and the mechanism of the water oxidation reaction. The time-resolved measurements have also given us a view of how this reaction-which involves multielectron, multiproton processes-is facilitated by the interaction of the ligands and the protein residues in the oxygen-evolving complex. These structures have also provided a picture of the dynamics occurring in the channels within photosystem II that are involved in the transport of the substrate water to the catalytic center and protons to the bulk.

2'-O-Alkyl-N 3-Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability.

Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m3U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m3U and 2'-OEt-m3U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m3U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein.