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Biophysical Chemistry

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https://www.readbyqxmd.com/read/29758467/ligation-events-influence-alg-2-dimerization
#1
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...
May 5, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29753257/salt-induced-effects-on-natural-and-inverse-dppc-lipid-membranes-molecular-dynamics-simulation
#2
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...
May 3, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29753256/new-antineoplastic-agent-based-on-a-dibenzoylmethane-derivative-cytotoxic-effect-and-direct-interaction-with-dna
#3
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...
May 3, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29734136/predicting-neuroblastoma-using-developmental-signals-and-a-logic-based-model
#4
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...
April 30, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29742444/mixing-behaviour-of-asymmetrical-glycerol-diether-bolalipids-with-saturated-and-unsaturated-phosphatidylcholines
#5
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)...
April 25, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29723717/lipopolysaccharides-and-peptidoglycans-modulating-the-interaction-of-au-naparticles-with-cell-membranes-models-at-the-air-water-interface
#6
Rafael Leonardo Cruz Gomes da Silva, Heloiza Fernanda Oliveira da Silva, Luiz Henrique da Silva Gasparotto, Luciano Caseli
Understanding the interactions between nanoparticles and biological surfaces is of great importance for many areas of nanomedicine and calls for detailed studies at the molecular level using simplified models of cellular membranes. In this paper, water-dispersed polyvinylpyrrolidonestabilized gold nanoparticles (AuNPs) were incorporated in floating monolayers of selected lipids at the air-water interface as cell membrane models. Surface pressure-area isotherms showed the condensation of glycoside-free lipid monolayers, suggesting their adsorption on the nanoparticle surface through the hydrophilic head groups...
April 25, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29704770/physical-principles-and-new-applications-of-comet-assay
#7
REVIEW
Katerina Afanasieva, Andrei Sivolob
The comet assay is a sensitive method to assess DNA damages in single cells. The approach consists of an analysis of electrophoretic migration of DNA from nucleoids obtained after cell lysis in a thin layer of agarose. Although the method is widely used the physical mechanisms of DNA track formation remained to be rather elusive for a long time. This review is devoted to our recent results pertaining to this subject, using an original approach based on the kinetic measurements of the comet formation. We argue that linear DNA fragments give an essential contribution into the tail formation in the alkaline conditions and, at neutral pH, when the level of DNA damages is very high...
April 20, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29705275/conformational-studies-of-gram-negative-bacterial-quorum-sensing-acyl-homoserine-lactone-ahl-molecules-the-importance-of-the-n-%C3%A2-%C3%AF-interaction
#8
Goar Sánchez-Sanz, Darren Crowe, Alan Nicholson, Adrienne Fleming, Ed Carey, Fintan Kelleher
A 1 H NMR study shows the presence of intermolecular hydrogen bonds for AHLs in CDCl3 solution. A detailed computational study of the structure of AHLs and the relative stability between the extended conformations (X) and those showing n → π* interactions (np) have been carried out by means of DFT calculations. Solvent effects have been shown to be very important when stabilising np conformations, particularly with polar solvents. This was shown by the shortening of C⋯O intramolecular distances and the increase in the relative energies favouring the np conformation with the dielectric constant of the solvent...
April 17, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29705276/biophysical-evaluation-of-cardiolipin-content-as-a-regulator-of-the-membrane-lytic-effect-of-antimicrobial-peptides
#9
Laura Hernández-Villa, Marcela Manrique-Moreno, Chad Leidy, Małgorzata Jemioła-Rzemińska, Claudia Ortíz, Kazimierz Strzałka
Cardiolipin is an anionic tetra-acyl chained glycerophospholipid that increases lipid packing levels and induces intrinsic negative curvature in membranes. Cardiolipin is found in Staphylococcus aureus (S. aureus) membranes, where increased levels of this lipid are induced at the expense of diacyl phosphatidylglycerol in response to stress. We investigate cardiolipin as an inhibitor of the lytic activity of the cationic antimicrobial peptides LL-37 and ∆M2 in model systems with varying phosphatidylglycerol/cardiolipin ratios...
April 13, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29631151/molecular-dynamics-analysis-of-stabilities-of-the-telomeric-watson-crick-duplex-and-the-associated-i-motif-as-a-function-of-ph-and-temperature
#10
Tomasz Panczyk, Pawel Wolski
This work deals with a molecular dynamics analysis of the protonated and deprotonated states of the natural sequence d[(CCCTAA)3 CCCT] of the telomeric DNA forming the intercalated i-motif or paired with the sequence d[(CCCTAA)3 CCCT] and forming the Watson-Crick (WC) duplex. By utilizing the amber force field for nucleic acids we built the i-motif and the WC duplex either with native cytosines or using their protonated forms. We studied, by applying molecular dynamics simulations, the role of hydrogen bonds between cytosines or in cytosine-guanine pairs in the stabilization of both structures in the physiological fluid...
April 3, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29656216/insights-into-cell-penetrating-peptide-conjugated-gold-nanoparticles-for-internalization-into-bacterial-cells
#11
Munish Kumar, Werner Tegge, Nishima Wangoo, Rahul Jain, Rohit K Sharma
Gold nanoparticles (AuNPs) functionalized with different biomolecules find extensive application in therapy, clinical diagnosis and biomedical imaging. Herein, two derivatives of TAT peptide with sequences YGRKKRRQRRR and YGRKKRRQRRR-(β-ala)3 -Cys-amide were conjugated with tannic acid capped gold nanoparticles which acted as a carrier for cell penetrating peptides (CPPs) into the bacterial cells. The interaction of YGRKKRRQRRR peptide with AuNPs was non-covalent in nature whereas YGRKKRRQRRR-(β-ala)3 -Cys-amide interacted covalently with the AuNPs due to presence of thiol group in cysteine which bind strongly to gold nanoparticles surface...
March 31, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29625337/domain-swapping-between-fabgs-deciphers-the-structural-determinant-for-in-solution-oligomerization-and-substrate-binding
#12
Rupam Biswas, Bina Kumari Singh, Debajyoti Dutta, Amit Basak, Amit Kumar Das
No abstract text is available yet for this article.
March 27, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29605501/amyloid-fibrillation-of-an-intrinsically-disordered-plant-phloem-protein-atpp16-1-under-acidic-condition
#13
D Santi Swarupini, Abani K Bhuyan
Arabidopsis thaliana Phloem Protein 16-1 (AtPP16-1) is a 156-residue intrinsically disordered nucleic acid binding protein which is putatively involved in long-distance systemic transport of RNA to budding regions in plants. Dimerization or oligomerization of the protein at pH higher than about 4.1 leaves no apolar surface exposed for interaction with the dye 8-Anilinonaphthalene-1-sulfonate (ANS). The most stable monomeric state is found near pH 4 where the structure of the protein is determined to have three short β-strands and a single α-helix...
March 26, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29635149/comparison-of-the-thermal-stabilization-of-proteins-by-oligosaccharides-and-monosaccharide-mixtures-measurement-and-analysis-in-the-context-of-excluded-volume-theory
#14
Ilyas Beg, Allen P Minton, Asimul Islam, Md Imtaiyaz Hassan, Faizan Ahmad
The thermal stability of apo α-lactalbumin (α-LA) and lysozyme was measured in the presence of mixtures of glucose, fructose, and galactose. Mixtures of these monosaccharides in the appropriate stoichiometric ratio were found to have a greater stabilizing effect on each of the two proteins than equal weight/volume concentrations of di- tri- and tetrasaccharides with identical subunit composition (sucrose, trehalose, raffinose, and stachyose). The excluded volume model for the effect of a single saccharide on the stability of a protein previously proposed by Beg et al...
March 22, 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29525503/the-importance-of-pk-a-in-an-analysis-of-the-interaction-of-compounds-with-dna
#15
Mouli Saha, Promita Nandy, Mousumi Chakraborty, Piyal Das, Saurabh Das
pKa of a compound is crucial for determining the contributions of different forms of it towards overall binding with DNA. Hence it is important to use correct pKa values in DNA interaction studies. This study takes a look at the importance of pKa values to realize binding of compounds with DNA. Since pKa of a compound determined in the presence of DNA is quite different from that determined in its absence hence, presence of different forms of a compound during interaction with DNA is different from that realized if the determination of pKa is done in normal aqueous solution in absence of DNA...
May 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29524614/protein-polyelectrolyte-coacervation-investigating-its-occurrence-in-the-lysozyme-carboxymethylcellulose-system
#16
Lucas M B Yoshihara, Elizabeth P G Arêas
The coacervation of carboxymethylcellulose (CMC) and hen egg white lysozyme (HEWL) was investigated. The work focused on the effects of pH, ionic strength, I, temperature, T, and mass fraction of the macromolecular components on the coacervation process by spectrophotometry, and on characteristics of the resulting coacervate phase by rheology in the linear and non-linear regimes. Coacervation was found to be highest at HEWL mass fraction ≈0.25 with very slight dependence on pH in the range from 5 to 9. The process was favored at I < 0...
May 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29486387/modulation-of-calcium-and-potassium-permeation-in-plant-tpc-channels
#17
Armando Carpaneto, Antonella Gradogna
Plant two-pore channels (TPCs) are non-selective cation channels permeable both to monovalent potassium and divalent calcium. We previously developed a technique that allowed the simultaneous determination of the fluxes of these two ions across the channel by a combined use of patch-clamp and fluorescence. In this paper we studied how potassium and calcium fluxes were influenced by modification of cytosolic concentrations of K+ and Ca2+ . A decrease in cytosolic calcium from 2 to 0.5 mM led to a shift of the activation curve of about +60 mV; although at positive potentials currents were very similar, calcium ion permeation was significantly reduced and the ratio between the total and calcium-mediated current increased about two-fold...
May 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29331201/impact-of-polymer-geometry-on-the-interactions-of-protein-peg-conjugates
#18
Jonathan Zarzar, Whitney Shatz, Nikhil Peer, Rosalynn Taing, Brian McGarry, Yun Liu, Daniel G Greene, Isidro E Zarraga
The conjugation of high molecular weight polyethylene glycol (PEG) to an active pharmaceutical ingredient (API) is an attractive strategy for the modification of biophysical and biodistribution properties of the API. Indeed, several therapeutic proteins conjugated to PEG have been safely administered in the clinic. While there have been studies on the configuration of these conjugates in solution, investigations on the impact of PEG geometry on protein-PEG conjugate interactions is limited. In this study, we use dynamic light scattering (DLS), rheology, and small-angle neutron scattering (SANS) to investigate the biophysical solution and interaction behavior of a 50kDa Fab protein attached to either a linear or tetrameric (branched) 40kDa PEG molecule...
May 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29477768/inhibition-of-amyloid-fibrillation-of-lysozyme-by-bisdemethoxycurcumin-and-diacetylbisdemethoxycurcumin
#19
Fakhrossadat Mohammadi, Marzieh Moeeni, Afshin Mahmudian, Leila Hassani
Amyloid deposition, arising from the fibrillogenesis of proteins in organs and tissues of the body, causes several neurodegenerative disorders. One therapeutic approach is based on the use of polyphenols and their derivatives for suppressing and inhibiting the accumulation of these toxic fibrils in tissues. In the present study, the anti-amyloidogenic activities of bisdemethoxycurcumin (BDMC), a natural polyphenolic compound, and diacetylbisdemethoxycurcumin (DABC), a synthetic derivative of curcumin, on the amyloid fibrillation of hen egg white lysozyme (HEWL) is studied in depth using thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), circular dichroism spectroscopy (CD), molecular docking and Ligplot calculations...
April 2018: Biophysical Chemistry
https://www.readbyqxmd.com/read/29477767/coupling-electrochemistry-and-tirf-microscopy-with-the-fluorescent-false-neurotransmitter-ffn102-supports-the-fluorescence-signals-during-single-vesicle-exocytosis-detection
#20
Xiaoqing Liu, Lihui Hu, Na Pan, Laurence Grimaud, Eric Labbé, Olivier Buriez, Jérôme Delacotte, Frédéric Lemaître, Manon Guille-Collignon
Applications of the Fluorescent False Neurotransmitter FFN102, an analog of biogenic neurotransmitters and a suitable probe for coupled amperometry and TIRFM (total internal reflexion fluorescence microscopy) investigations of exocytotic secretion, were considered here. The electroactivity of FFN102 was shown to very likely arise from the oxidation of its phenolic group through a CE (Chemical-Electrochemical) mechanism. Evidences that the aminoethyl group of FFN102 is the key recognition element by BON N13 cells were also provided...
April 2018: Biophysical Chemistry
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