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Fibroblast growth factors (FGFs) are expressed in both developing and adult tissues and play important roles in embryogenesis, tissue homeostasis, angiogenesis, and neoplastic transformation. Here we report the elevated expression of FGF16 in human breast tumor and investigate its potential involvement in breast cancer progression. The onset of epithelial-mesenchymal transition (EMT), a prerequisite for cancer metastasis, was observed in human mammary epithelial cell-line MCF10A by FGF16. Further study unveiled that FGF16 alters mRNA expression of a set of extracellular matrix genes to promote cellular invasion. Cancer cells undergoing EMT often show metabolic alteration to sustain their continuous proliferation and energy-intensive migration. Similarly, FGF16 induced a significant metabolic shift towards aerobic glycolysis. At the molecular level, FGF16 enhanced GLUT3 expression to facilitate glucose transport into cells, which through aerobic glycolysis generates lactate. The bi-functional protein, 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 4 (PFKFB4) was found to be a mediator in FGF16-driven glycolysis and subsequent invasion. Furthermore, PFKFB4 was found to play a critical role in promoting lactate-induced cell invasion since silencing PFKFB4 decreased lactate level and rendered the cells less invasive. These findings support potential clinical intervention of any of the members of FGF16-GLUT3-PFKFB4 axis to control the invasion of breast cancer cells.

Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.

The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.

Effect of pore size and its distribution on the noise reduction coefficient of jute felt were studied through capillary flow porometer and impedance tube. The inter-criteria correlation method was ...

The present work aimed at efficient utilization of resources viz., water, dyes and chemicals (without using any supportive chemical) for colouration of polyester. Disperse dye microcapsules were prepared using the method of complex coacervation. Bio-shell coated microcapsules of disperse dyes were analyzed for their resource efficient auxiliary chemicals free colouration on polyester (PET) over conventionally dyed one. The remnant liquor recovered from colouration of polyester was recycled for subsequent four colouration cycles (without treatment) showing acceptable shade difference. The remnant liquor obtained from fourth colouration cycles treated with basic primary water treatments and was found to be translucent, neutral in pH and low effluent load (TDS > 231 ppm, BOD > 114 mg/l, and COD > 469 mg/l). The solids recovered from bath were analyzed and found to be nontoxic (LD50,> 8000) as well. Cost involved in microencapsulated colouration (USD $ 6.48) is lower than that of conventional process of colouration (USD $ 8.40). Thus, microencapsulated colouration is easily adoptable in existing process line of polyester colouration, which leads to small liquid discharge of low.

The present study is an attempt to evaluate the potentiality of a specified variety of banana fiber (Musa domestica var. balbisiana) for textile use. Retting period for extraction of the newer vari...

The challenges that instructors of critical theory face today, particularly in global contexts, range from a public-health crisis, to a continued struggle for racial and economic justice, to the changing landscape of higher education. The solution we propose is twofold and involves decolonizing theory and making the classroom increasingly student centered.

An eco-friendly sustainable thermal insulator has been developed as a replacement of some commercially available manmade materials to control heat transfer in case of buildings, and semi-permanent/...

Transfer RNAs (tRNAs) are fundamental molecules in cellular translation. In this study we have highlighted a fluorescence-based perceptive approach for tRNAs by using a quinoxaline small molecule. We have synthesised a water-soluble fluorescent pyrimido-quinoxaline-fused heterocycle containing a mandatory piperazine tail (DS1) with a large Stokes shift (∼160 nm). The interaction between DS1 and tRNA results in significant fluorescence enhancement of the molecule with Kd ∼5 μM and multiple binding sites. Our work reveals that the DS1 binding site overlaps with the specific Mg2+ ion binding site in the D loop of tRNA. As a proof-of-concept, the molecule inhibited Pb2+ -induced cleavage of yeast tRNAPhe in the D loop. In competitive binding assays, the fluorescence of DS1-tRNA complex is quenched by a known tRNA-binder, tobramycin. This indicates the displacement of DS1 and, indeed, a substantiation of specific binding at the site of tertiary interaction in the central region of tRNA. The ability of compound DS1 to bind tRNA with a higher affinity compared to DNA and single-stranded RNA offers a promising approach to developing tRNA-based biomarker diagnostics in the future.

An attempt has been made to study the effect of thickness and compactness of natural fibre assembly in the reduction of noise. Fourteen available natural fibres i.e. banana, bhimal, roselle, coconu...

The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria—one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12551-020-00621-8) contains supplementary material, which is available to authorized users.

Tiara is the only fiber variety flax recently been introduced in India. The water retted flax fibers were mechanically extracted and subjected to degum and bleach using various chemicals and enzyme...

Interaction between human positive coactivator 4 (PC4), an abundant nuclear protein, and the tumor suppressor protein p53 plays a crucial role in initiating apoptosis. In certain neurodegenerative diseases PC4 assisted-p53-dependent apoptosis may play a central role. Thus, disruption of p53-PC4 interaction may be a good drug target for certain disease pathologies. A p53-derived short peptide (AcPep) that binds the C-terminal domain of PC4 (C-PC4) is known to disrupt PC4-p53 interaction. To fully characterize its binding mode and binding site on PC4, we co-crystallized C-PC4 with the peptide and determined its structure. The crystal, despite exhibiting mass spectrometric signature of the peptide, lacked peptide electron density and showed a novel crystal lattice, when compared to C-PC4 crystals without the peptide. Using peptide-docked models of crystal lattices, corresponding to our structure and the peptide-devoid structure we show the origin of the novel crystal lattice to be dynamically bound peptide at the previously identified putative binding site. The weak binding is proposed to be due to the lack of the N-terminal domain of PC4 (N-PC4), which we experimentally show to be disordered with no effect on PC4 stability. Taking cue from the structure, virtual screening of ∼18.6 million small molecules from the ZINC15 database was performed, followed by toxicity and binding free energy filtering. The novel crystal lattice of C-PC4 in presence of the peptide, the role of the disordered N-PC4 and the high throughput identification of potent small molecules will allow a better understanding and control of p53-PC4 interaction.

Replacement of a single residue in a β-hairpin by Gly-Pro, a 'united-residue' known to be overrepresented in protein β-sheets as Gly-cisPro without causing much structural distortion, and comparison of the resulting β-hairpin with those of other single/double residue substitutions show that Gly-Pro but not Pro-Gly is well accommodated in the isolated β-hairpin.

The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of

A novel low alkali-based chemical recipe was formulated for controlled degumming of ramie (Boehmeria Nivea L.) fiber to maintain residual gum 7–8% aiming at to improve yarn tensile performa...

Hepatitis C virus (HCV) requires an essential host factor, human La protein, for its translation and replication activity. Earlier, it was demonstrated that a 24-mer synthetic peptide (LaR2C) encompassing residues 112 to 184 of the natural human La protein interacts with the HCV internal ribosome entry site (IRES) and inhibits translation. Interestingly, a shorter version of the same LaR2C peptide, LaR2C-N7, containing residues 174 to 180 (KYKETDL), with a unique β-turn secondary structure, is sufficient to inhibit IRES mediated translation of HCV. Hence, it is imperative to understand the role of each amino acid of this heptapeptide towards β-turn formation which will then help in designing potential drugs against HCV infection. Here, we use Nanoscale Molecular Dynamics (NAMD) simulation to investigate the factors modulating its β-turn formation and stability. Using 100 ns simulation paradigms, we find that the peptide populated the type 1 β-turn conformation in its free form in solution. However, simulation of the single-site mutants of the heptapeptide revealed that none of the 7 mutants retained the β-turn conformation with sufficient stability. We observed that the β-turn was stabilized mainly by the side chain interaction, salt-bridge and weak hydrogen bonds between K3 and D6 residues. Y2, K1 and K3 sites upon mutation heavily destabilized the β-turn when compared to alteration at the E4 and T5 sites which would then drastically reduce its HCV RNA IRES binding capabilities. Taken together, our results provide a basis for designing peptidomimetics as potential anti-HCV drug candidates.

Remnant obtained from chemical retting of coconut fibre was found to have an exorbitant COD, BOD, TDS, sulphide content having blackish brown colour. Traditional (physico-chemical) treatment could not reduce its COD, TDS, colour substantially. Further, the traditional method was lengthy, consumed huge chemicals and time. Present paper reports a quicker, simpler, economic i.e., an industrially viable method to separate the chemicals and biomass by employing electrocoagulation (EC). The performance of EC was analyzed by keeping temperature, and pH of remnant constant, while varying current flow (100–2000 mA), time (15–90 min) and number of iron electrodes (2,4,6). Efficacy of EC was evaluated in terms of reduction in conductivity, pH, TDS, COD, TOC, colour and quantity of sludge generated from the wastewater. Six electrodes with 2000 mA current flow for 90 min were found to give noticeable reduction on COD (92.8%), TOC (56%), TDS (99%), and colour. To reduce pH, and TDS to an acceptable level, filtration with activated charcoal was attempted on recovered water from EC. Resultant water was also found to have acceptable LC50 value for safe disposal. Carbon content (53%) in the sludge was high, contained lignin and cellulose whiskers also, as revealed from the EDX and FTIR, SEM respectively. Cost of EC ($ 0.087 USD/L) was found to be much less as compared to traditional method ($ 0.384 USD/L).

Plants use a diverse set of proteins to mitigate various abiotic stresses. The intrinsically disordered protein dehydrin is an important member of this repertoire of proteins, characterized by a canonical amphipathic K-segment. It can also contain other stress-mitigating noncanonical segments—a likely reflection of the extremely diverse nature of abiotic stress encountered by plants. Among plants, the poikilohydric mosses have no inbuilt mechanism to prevent desiccation and therefore are likely to contain unique noncanonical stress-responsive motifs in their dehydrins. Here we report the recurring occurrence of a novel amphipathic helix-forming segment (D-segment: EGφφD(R/K)AKDAφ, where φ represents a hydrophobic residue) in Physcomitrella patens dehydrin (PpDHNA), a poikilohydric moss. NMR and CD spectroscopic experiments demonstrated the helix-forming tendency of the D-segment, with the shuffled D-segment as control. PpDHNA activity was shown to be size as well as D-segment dependent from in vitro, in vivo, and in planta studies using PpDHNA and various deletion mutants. Bimolecular fluorescence complementation studies showed that D-segment-mediated PpDHNA self-association is a requirement for stress abatement. The D-segment was also found to occur in two rehydrin proteins from Syntrichia ruralis, another poikilohydric plant like P. patens. Multiple occurrences of the D-segment in poikilohydric plant dehydrins/rehydrins, along with the experimental demonstration of the role of D-segment in stress abatement, implies that the D-segment mediates unique resurrection strategies, which may be employed by plant dehydrins that are capable of mitigating extreme stress.

Replacement of a single residue in a β-hairpin by Gly-Pro, a 'united-residue' known to be overrepresented in protein β-sheets as Gly-cisPro without causing much structural distortion, and comparison of the resulting β-hairpin with those of other single/double residue substitutions show that Gly-Pro but not Pro-Gly is well accommodated in the isolated β-hairpin.