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Biophysical Chemistry

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https://www.readbyqxmd.com/read/30014891/antagonistic-role-of-klotho-derived-peptides-dynamics-in-the-pancreatic-cancer-treatment-through-obstructing-wnt-1-and-frizzled-binding
#1
Muhammad Fakhar, Najumuddin, Mehreen Gul, Sajid Rashid
Klotho is an anti-aging protein that is engaged in the suppression of canonical WNT signaling. In this study, we investigated the expression pattern of human WNTs and Klotho in the pancreatic cancer. In the cancerous cells, WNT-1 exhibited much higher expression as compared to other WNTs, while no WNT expression was detected in the normal tissue. In contrast, Klotho expression was significantly low in the cancerous tissue. Based on these observations, we intended to explore Klotho binding to WNT-1 and cystein-rich domains (CRDs) of Frizzled (FZD) homologs through molecular docking and dynamics simulation assays...
July 7, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29957358/effects-of-lyotropic-anions-on-thermodynamic-stability-and-dynamics-of-horse-cytochrome-c
#2
Rishu Jain, Mukesh Chand Agarwal, Rakesh Kumar, Deepak Sharma, Rajesh Kumar
This paper evaluates the effect of various lyotropic anions (chloride, sulfate, perchlorate, iodide, nitrate, bromide) on the thermodynamic stability and dynamics of native cytochrome c (Cyt c) at pH 7.0. The results of equilibrium and kinetic studies revealed that: (i) at low to intermediate concentrations (≤ 0.5 M), both chaotropic and kosmotropic anions restrict the dynamics of native protein, (ii) at relatively higher concentrations (≥ 1.0 M), the denaturing effect of chaotropic anions dominates, which increases the level of structural-fluctuations responsible to unfold the protein according to Hofmeister series (perchlorate > iodide > nitrate > bromide), and (iii) the lyotropic anions affect the thermal and global stability of Cyt c according to Hofmeister series...
June 19, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29945014/a-theoretical-study-on-the-cross-talk-of-stress-regulatory-pathways-in-root-cells
#3
Wei Cao, Liang Luo, Ming Yi, Ya Jia
The plants developed more dedicated regulatory pathways than the animals did to response various environment stresses, since they could not run away. The cross-talk among the pathways generally introduce non-trivial regulatory behaviors, from which the plants may benefit. For better understanding the regulatory mechanism due to cross-talk, we study in this work two entangled stress regulatory pathways in root cells. A quantitative model of the regulatory network is constructed in the simplest fashion. An analytic parameter-free approach is then employed to analyse the response tendencies...
June 19, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29913331/unraveling-the-binding-interaction-of-a-bioactive-pyrazole-based-probe-with-serum-proteins-relative-concentration-dependent-1-1-and-2-1-probe-protein-stoichiometries
#4
Pronab Kundu, Nitin Chattopadhyay
Molecular interactions and binding of probes/drugs with biomacromolecular systems are of fundamental importance in understanding the mechanism of action and hence designing of proactive drugs. In the present study, binding interactions of a biologically potent fluorophore, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with two serum transport proteins, human serum albumin and bovine serum albumin, have been investigated exploiting multi-spectroscopic techniques. The spectrophotometric and fluorometric studies together with fluorescence quenching, fluorescence anisotropy, urea induced denaturation studies and fluorescence lifetime measurements reveal strong binding of DSDP with both the plasma proteins...
June 15, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/30014892/the-hydrolysis-of-6-phosphogluconolactone-in-the-second-step-of-pentose-phosphate-pathway-occurs-via-a-two-water-mechanism
#5
Tabeer Fatima, Sadaf Rani, Stefan Fischer, Thomas Efferth, Farooq Ahmad Kiani
Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown...
June 12, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29906639/development-of-a-machine-learning-model-to-predict-gibbs-free-energy-of-binding-for-protein-ligand-complexes
#6
Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions is still an open problem in the simulation of biological systems, and the development of a new generation machine-learning model is an active research field. In this work, we propose a novel scoring function to predict Gibbs free energy of binding (ΔG) based on the crystallographic structure of complexes involving a protein and an active ligand...
June 7, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29885563/constrained-dynamics-of-the-sole-tryptophan-in-the-third-intracellular-loop-of-the-serotonin-1-a-receptor
#7
Sreetama Pal, Ramdas Aute, Parijat Sarkar, Shroddha Bose, Mandar V Deshmukh, Amitabha Chattopadhyay
G protein-coupled receptors (GPCRs) are major signaling proteins in eukaryotic cells and are important drug targets. In spite of their role in GPCR function, the extramembranous regions of GPCRs are relatively less appreciated. The third intracellular loop (ICL3), which connects transmembrane helices V and VI, is important in this context since its crucial role in signaling has been documented for a number of GPCRs. Unfortunately, the structure of this loop is generally not visualized in x-ray crystallographic studies since this flexible loop is either stabilized using a monoclonal antibody or replaced with lysozyme...
June 1, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29883882/small-phospho-donors-phosphorylate-morr-without-inducing-protein-conformational-changes
#8
Nathália S S Castro, César A T Laia, Biplab K Maiti, Nuno M F S A Cerqueira, Isabel Moura, Marta S P Carepo
Phosphorylation is an essential mechanism of protein control and plays an important role in biology. The two-component system (TCS) is a bacterial regulation mechanism mediated by a response regulator (RR) protein and a kinase protein, which synchronize the regulatory circuit according to the environment. Phosphorylation is a key element in TCS function as it controls RR activity. In the present study, we characterize the behavior of MorR, an RR associated with Mo homeostasis, upon acetylphosphate and phosphoramidate treatment in vitro...
May 31, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29890403/correlating-interfacial-water-dynamics-with-protein-protein-interaction-in-complex-of-gdf-5-and-bmpri-receptors
#9
Tasneem Kausar, Shahid M Nayeem
GDF-5 mediated signal transduction regulating chondrogenesis and skeletogenesis involves three different type-I receptors viz. Act-RI, BMPRIA and BMPRIB. BMPRIA and BMPRIB generally shows temporal and spatial co-expression but some spatially different expression pattern has also been observed. BMPRIA receptor is the key receptor implicated in BMP signalling during osteogenesis and is expressed in osteoblasts during the course of bone formation. However, BMPRIB appears to be primarily expressed in mesenchymal pre-cartilage condensations and also found in differentiated osteoblast and chondrocytes...
May 26, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29885564/cooperative-unfolding-of-apolipoprotein-a-1-induced-by-chemical-denaturation
#10
D Eckhardt, X Li-Blatter, H-J Schönfeld, H Heerklotz, J Seelig
Apolipoprotein A-1 (Apo A-1) plays an important role in lipid transfer and obesity. Chemical unfolding of α-helical Apo A-1 is induced with guanidineHCl and monitored with differential scanning calorimetry (DSC) and CD spectroscopy. The unfolding enthalpy and the midpoint temperature of unfolding decrease linearly with increasing guanidineHCl concentration, caused by the weak binding of denaturant. At room temperature, binding of 50-60 molecules guanidineHCl leads to a complete Apo A-1 unfolding. The entropy of unfolding decreases to a lesser extent than the unfolding enthalpy...
May 25, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29857171/crystal-structure-of-the-ferric-homotetrameric-%C3%AE-4-human-hemoglobin
#11
Lelio Mazzarella, Antonello Merlino, Nicole Balasco, Anna Balsamo, Alessandro Vergara
Spectroscopic studies carried out in the early seventies have shown that the β-homotetramer of human hemoglobin (β4 -HbA) in the ferric state is a mixture of aquomet and bis-histidyl forms. Here we present the first crystal structure, solved at 2.10 Å resolution, of the oxidized form of β4 -HbA. The overall quaternary structure of the protein in the ferric state is virtually indistinguishable from that of the ferrous deoxygenated and carbomonoxy forms. The structure reveals that the four hemes are exclusively in an aquomet coordination, without any trace of bis-histidyl coordination...
May 23, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29857170/elastic-compliance-of-fibrillar-assemblies-in-type-i-collagen
#12
Vaidyanathan Vaidyanathan Ganesan, Madhumitha Dhanasekaran, Nandhini Thangavel, Aruna Dhathathreyan
Fibrillary assemblies of Type I collagen find important applications in tissue engineering and as matrices for biophysical studies. The mechanical and structural properties of these structures are governed by factors such as protein concentration, temperature, pH and ionic strength. This study reports on an impedance based analysis of the elastic compliance of fibrillary assemblies of Type I collagen using quartz crystal microbalance with dissipation (QCM-D) at a fundamental frequency of 5 MHz and overtones (n = 3,5,7,9,11)...
May 23, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29857169/estimation-of-the-bacteriochlorophyll-c-oligomerisation-extent-in-chloroflexus-aurantiacus-chlorosomes-by-very-low-frequency-vibrations-of-the-pigment-molecules-a-new-approach
#13
A G Yakovlev, A S Taisova, V A Shuvalov, Z G Fetisova
In green photosynthetic bacteria, the chlorosomal bacteriochlorophyll molecules are organized via self-assembly and do not require proteins to provide a scaffold for efficient light harvesting. Despite numerous investigations, a consensus regarding the spatial structure of chlorosomal antennae has not yet been reached. For the first time, we demonstrated by coherent femtosecond spectroscopy at cryogenic temperature that the very low-frequency (~101  cm-1 ) vibrations of bacteriochlorophyll c pigments in isolated Chloroflexus aurantiacus chlorosomes are sensitive to their oligomerisation extent which depends on the light intensity during the growth of the cell cultures...
May 22, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29807308/checkpoint-for-helicity-conservation-in-fluorescence-at-the-nanoscale-energy-and-helicity-transfer-hfret-from-a-rotating-donor-dipole
#14
László Bene, Miklós Bagdány, László Damjanovich
Orientation factor (κ2 ) for FRET from a rotating donor dipole, transferred helicity of the donor field and torque exerted on the acceptor by the donor have been investigated in the framework of classical electrodynamics. It is shown that for rotating dipole, κ2 is significantly higher as compared to linear dipole independently of the orientation distribution of the donor and acceptor and whether the static or the dynamic rotational regimes are used for averaging κ2 . By this property of κ2 , FRET serves as an example for a phenomenon where local field interference may take place in a "natural" way for emitters possessing rotating dipoles in their excited states by nature...
August 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29804029/the-effects-of-varying-the-substituent-and-dna-sequence-on-the-stability-of-4-substituted-dna-naphthalimide-complexes
#15
Elizabeth A Jolley, Laura K E Hardebeck, Yi Ren, Miranda S Adams, Michael Lewis, Brent M Znosko
DNA duplexes are stabilized by many interactions, one of which is stacking interactions between the nucleic acid bases. These interactions are useful for designing small molecules that bind to DNA. Naphthalimide intercalators have been shown to be valuable anti-cancer agents that stack between the DNA bases and exhibit stabilizing effects. There is a continued need to design intercalators that will exhibit these stabilizing effects while being more selective toward DNA binding. This work investigates 4-substituted naphthalimides with varying functional groups and their interactions with nucleic acid duplexes...
August 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29758467/ligation-events-influence-alg-2-dimerization
#16
Michael T Henzl
ALG-2 dimerization was studied using Förster resonance-energy-transfer. D162C variants of ALG-2des23 were covalently modified with Alexa Fluor 488 and Alexa Fluor 647. When samples of the two labeled protein-preparations are combined, the sensitized emission from AF647 serves as a sensitive probe of dimer formation. At 25 °C, in the absence of divalent ions, the wild-type homodimer, ΔGF122 homodimer, and heterodimer display dissociation constants of 7.1, 26, and 4.5 nM, respectively. At 35 °C, subunit interaction is weaker, indicating that dimer formation is exothermic...
August 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29753257/salt-induced-effects-on-natural-and-inverse-dppc-lipid-membranes-molecular-dynamics-simulation
#17
Seyed Mojtaba Rezaei Sani, Mojdeh Akhavan, Seifollah Jalili
Molecular dynamics (MD) simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer and its neutral inverse-phosphocholine equivalent (DPCPe) were performed to find salt-induced effects on their surface structure and the nature of ion-lipid interactions. We found that the area per lipid is not considerably affected by the inversion, but the deuterium order parameter of carbon atoms in the region of carbonyl carbons changes dramatically. MD simulations indicate that Ca2+ ions can bind to the surface of both DPPC and DPCPe membranes, but K+ ions do not bind to them...
August 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29753256/new-antineoplastic-agent-based-on-a-dibenzoylmethane-derivative-cytotoxic-effect-and-direct-interaction-with-dna
#18
Fernanda R Nascimento, Tiago A Moura, Jefferson V P B Baeta, Bruno C Publio, Pollyanna M F Ferreira, Anésia A Santos, Andressa A P França, Marcio S Rocha, Gaspar Diaz-Muñoz, Marisa A N Diaz
Melanoma accounts for only 4% of all skin cancers but is among the most lethal cutaneous neoplasms. Dacarbazine is the drug of choice for the treatment of melanoma in Brazil through the public health system mainly because of its low cost. However, it is an alkylating agent of low specificity and elicits a therapeutic response in only 20% of cases. Other drugs available for the treatment of melanoma are expensive, and tumor cells commonly develop resistance to these drugs. The fight against melanoma demands novel, more specific drugs that are effective in killing drug-resistant tumor cells...
August 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29742444/mixing-behaviour-of-asymmetrical-glycerol-diether-bolalipids-with-saturated-and-unsaturated-phosphatidylcholines
#19
Sindy Müller, Annette Meister, Christian Otto, Gerd Hause, Simon Drescher
Liposomes have received attention as a promising class of drug delivery vehicles. To date, many approaches have been tried developing liposomes for oral use. However, no liposomal formulation is on the market so far that is approved for oral application. In this study, we investigate the miscibility of two glycerol diether bolalipids with classical saturated and unsaturated phosphatidylcholines by means of differential scanning calorimetry (DSC), transmission electron microscopy (TEM), and dynamic light scattering (DLS)...
July 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29734136/predicting-neuroblastoma-using-developmental-signals-and-a-logic-based-model
#20
Jennifer C Kasemeier-Kulesa, Santiago Schnell, Thomas Woolley, Jennifer A Spengler, Jason A Morrison, Mary C McKinney, Irina Pushel, Lauren A Wolfe, Paul M Kulesa
Genomic information from human patient samples of pediatric neuroblastoma cancers and known outcomes have led to specific gene lists put forward as high risk for disease progression. However, the reliance on gene expression correlations rather than mechanistic insight has shown limited potential and suggests a critical need for molecular network models that better predict neuroblastoma progression. In this study, we construct and simulate a molecular network of developmental genes and downstream signals in a 6-gene input logic model that predicts a favorable/unfavorable outcome based on the outcome of the four cell states including cell differentiation, proliferation, apoptosis, and angiogenesis...
July 2018: Biophysical Chemistry
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