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Biophysical Chemistry

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https://read.qxmd.com/read/30780079/cooperative-energetic-effects-elicited-by-the-yeast-shwachman-diamond-syndrome-protein-sdo1-and-guanine-nucleotides-modulate-the-complex-conformational-landscape-of-the-elongation-factor-like-1-efl1-gtpase
#1
Axel Luviano, Roberto Cruz-Castañeda, Nuria Sánchez-Puig, Enrique García-Hernández
One of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (human EFL1, yeast Efl1) GTPase and the Shwachman-Diamond syndrome protein (human SBDS, yeast Sdo1) to release the eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes. However, the nature of such conformational changes or the mechanism by which they are prompted are still largely unknown...
February 13, 2019: Biophysical Chemistry
https://read.qxmd.com/read/30753970/r-and-r2-quaternary-structures-of-carbonmonoxyhemoglobins-differential-effect-of-inositol-hexakisphosphate-on-their-affinity-for-ellman-s-reagent
#2
Kehinde O Okonjo, Adedayo A Fodeke, Orighomisan B Atolaiye, Abimbola M Olatunde, Chijioke J Ajaelu, Oluwatoyin Ajelabi, Abisola T Adediji, Ayorinde M Adebayo, Onyinyechi V Uhuo, Oyebamiji J Babalola
The reaction of 5,5'-dithiobis(2-nitrobenzoate), DTNB, with hemoglobin sulfhydryl groups is linked to three negatively contributing Bohr effect groups: His2β is present in all avian hemoglobins but absent in some mammalian hemoglobins; His77β and His143β are absent in avian but present in nearly all mammalian hemoglobins. To probe the consequences of these differences, we determined the influence of inositol hexakisphosphate (inositol-P6 ) on the DTNB affinities of avian and mammalian carbonmonoxyhemoglobins...
February 6, 2019: Biophysical Chemistry
https://read.qxmd.com/read/30659995/chemical-characterization-of-liposomes-containing-nutraceutical-compounds-tyrosol-hydroxytyrosol-and-oleuropein
#3
Claudia Bonechi, Alessandro Donati, Gabriella Tamasi, Alessio Pardini, Hanzadah Rostom, Gemma Leone, Stefania Lamponi, Marco Consumi, Agnese Magnani, Claudio Rossi
Tyrosol, hydroxytyrosol and oleuropein are among the major phenolic compounds in fruits, leaves and oils from Olea europaea L. These natural antioxidants molecules revealed several beneficial effects on human health, but a low bioavailability and accessibility to targeted site. Liposomes are drug/nutraceutical delivery carriers, used for driving bioactive molecules to desired target tissues, decreasing potential side effects and protecting the encapsulated molecule from enzymatic metabolic processes. In this study, zwitterionic liposomes containing tyrosol, hydroxytyrosol and oleuropein were synthesized and characterized for their size and surface charge...
January 14, 2019: Biophysical Chemistry
https://read.qxmd.com/read/30660935/contribution-of-3-t-and-3-tt-overhangs-to-the-thermodynamic-stability-of-model-sirna-duplexes
#4
Jolanta Lisowiec-Wachnicka, Brent M Znosko, Anna Pasternak
Herein, we report comprehensive thermodynamic studies on 36 RNA/DNA duplexes designed as siRNA mimics to determine the energetic contribution of 3'T and 3'TT dangling ends. The thermodynamic effect induced by the presence of 3'T overhangs on the stability of RNA duplexes ranges from -0.28 to -0.92 kcal/mol and strongly depends on the type and orientation of the adjacent base pair. Further extension of the 3'-dangling end length, by a second T residue, results in additional stabilization of 0.14 to 0.21 kcal/mol...
January 7, 2019: Biophysical Chemistry
https://read.qxmd.com/read/30639535/ab-initio-model-for-the-chlorophyll-lutein-exciton-coupling-in-the-lhcii-complex
#5
Daniil Khokhlov, Aleksandr Belov
2Ag - state of lutein plays a crucial role in photoprotection of higher plants. Due to its multiconfigurational nature, accurate description of this electronic state and respective transition properties is a formidable task. In this paper, applicability of various CASSCF and RASSCF formulations for description of the 2Ag - state is discussed. It is shown that inclusion of the entire π-system of lutein into the active space is required for accurate calculation of transition properties. Exciton coupling in the chlorophyll-lutein dimer involved in non-photochemical quenching in the LHCII complex was calculated to provide a connection between pigment interactions and non-photochemical quenching regulation...
January 3, 2019: Biophysical Chemistry
https://read.qxmd.com/read/30685627/photophysical-and-thermodynamic-evaluation-on-the-in-vitro-and-in-silico-binding-profile-of-camptothecin-with-dna
#6
Riju K Thomas, Surya Sukumaran, C Sudarsanakumar
Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies...
December 24, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30597448/on-empirical-decomposition-of-volumetric-data
#7
Tigran V Chalikian, Robert B Macgregor
Volumetric characterization of proteins and their recognition events has been instrumental in providing information on the role of intra- and intermolecular interactions, including hydration, in stabilizing biomolecules. The credibility of molecular models and interpretation schemes used to rationalize experimental data are essential for the validity of microscopic insights derived from volumetric results. Current empirical schemes used to interpret volumetric data suffer from a lack of theoretical and computational substantiation...
December 23, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30594881/interfacial-vibrational-spectroscopy-and-brewster-angle-microscopy-distinguishing-the-interaction-of-terpineol-in-cell-membrane-models-at-the-air-water-interface
#8
Guilherme Nuñez Jaroque, Patrícia Sartorelli, Luciano Caseli
In this paper, γ-terpineol, a known monoterpene with biological activity, including in lipidic interfaces, was incorporated in Langmuir monolayers of selected phospholipids as a model for cellular membranes. Surface pressure-area isotherms showed that selected amounts of γ-terpineol expand DPPC and DPPE monolayers and decreased the monolayer elasticity, confirming the lipid/compound interaction. Characterization with vibrational spectroscopy and Brewster angle microscopy pointed that γ-terpineol adsorbs on the polar heads of the phospholipids, affecting the gauche conformations of the aliphatic chains, and different patterns were observed for DPPC and DPPE monolayers, indicating a characteristic molecular accommodation of γ-terpineol along the polar head of the phospholipids...
December 20, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30576976/molecular-mechanisms-for-the-destabilization-of-model-membranes-by-islet-amyloid-polypeptide
#9
Madhihalli Basavaraju Divakara, Denis Martinez, Ashwini Ravi, Veer Bhavana, Venkata Ramana, Birgit Habenstein, Antoine Loquet, Mysore Sridhar Santosh
Misfolding of human islet amyloid polypeptide (hIAPP) into insoluble aggregates is associated with Type 2 diabetes. It has been suggested that hIAPP toxicity may be due to its accumulation in pancreatic islets, causing membrane disruption and cell permeabilization, however the molecular basis underlying its lipid association are still unclear. Here, we combine solid-state NMR, fluorescence and bright field microscopy to investigate hIAPP - lipid membrane interactions. Real-time microscopy highlights a time-dependent penetration of hIAPP oligomers toward the most buried layers of the lipid vesicles until the membrane disrupts...
December 14, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30551070/detection-of-mg-2-dependent-coaxial-stacking-rearrangements-in-a-bulged-three-way-dna-junction-by-single-molecule-fret
#10
Michael P Leveille, Thao Tran, Gianna Dingillo, Brian Cannon
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge...
December 5, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30529877/robustness-of-frequency-vs-amplitude-coding-of-calcium-oscillations-during-changing-temperatures
#11
Luis Aguilera, Frank T Bergmann, Giovanni Dalmasso, Sinan Elmas, Tobias Elsässer, Ruth Großeholz, Pascal Holzheu, Priyata Kalra, Ursula Kummer, Sven Sahle, Nadine Veith
Intracellular calcium oscillations have been widely studied. It is assumed that information is conveyed in the frequency, amplitude and shape of these oscillations. In particular, calcium signalling in mammalian liver cells has repeatedly been reported to display frequency coding so that an increasing amount of stimulus is translated into an increasing frequency of the oscillations. However, recently, we have shown that calcium oscillations in fish liver cells rather exhibit amplitude coding with increasing stimuli being translated into increasing amplitudes...
November 26, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30513446/dna-recognition-by-linear-indole-biphenyl-dna-minor-groove-ligands
#12
Noa Erlitzki, Abdelbasset A Farahat, Arvind Kumar, David W Boykin, Gregory M K Poon
Linear heterocyclic cations are interesting DNA minor groove ligands due to their lack of isohelical curvature classically associated with groove-binding compounds. We determined the DNA binding properties of four related dications harboring a linear indole-biphenyl core: the diamidine DB1883, a ditetrahydropyrimidine derivative (DB1804), and their monocationic counterparts (DB1944 and DB2627). These compounds exhibit heterogeneity in binding in accordance with their structures. Whereas the monocations exhibit salt-sensitive 1:1 binding to the duplex 5'-CGCGAATTCGCG-3' (A2 T2 ), the dications show a marked preference for a salt-insensitive 2:1 complex...
November 26, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30465941/rational-cyclization-based-minimization-of-entropy-penalty-upon-the-binding-of-nrf2-derived-linear-peptides-to-keap1-a-new-strategy-to-improve-therapeutic-peptide-activity-against-sepsis
#13
Ke Chen, Liuliu Huang, Bin Shen
Nrf2 is a critical regulator of innate immune response and survival during sepsis, which is constitutively degraded through binding to the Keap1 adapter protein of E3 ubiquitin ligase. Two linear peptides DLG and ETG derived from, respectively, the low-affinity and high-affinity motifs of Nrf2 binding site exhibit self-binding affinity to Keap1 central hole (active pocket); they can be exploited as therapeutic self-inhibitory peptides to disrupt the Nrf2-Keap1 interaction. Molecular dynamics simulation and binding energetics decomposition reveal that the two peptides possess large flexibility and intrinsic disorder in unbound free state, and thus would incur a considerable entropy penalty upon binding to Keap1...
January 2019: Biophysical Chemistry
https://read.qxmd.com/read/30448627/the-maximum-entropy-production-requirement-for-proton-transfers-enhances-catalytic-efficiency-for-%C3%AE-lactamases
#14
Davor Juretić, Željana Bonačić Lošić, Domagoj Kuić, Juraj Simunić, Andrej Dobovišek
Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. When ranked by their evolutionary distance from putative common ancestor, three β-lactamases considered in this study show correspondingly increased catalytic constant, catalytic efficiency, and overall entropy production. The acylation and deacylation steps with concomitant proton shuttles are the most important contributors to overall entropy production...
January 2019: Biophysical Chemistry
https://read.qxmd.com/read/30388712/mixing-behaviour-of-bilayer-forming-phosphatidylcholines-with-single-chain-alkyl-branched-bolalipids-effect-of-lateral-chain-length
#15
Sindy Müller, Maximilian Kind, Kai Gruhle, Gerd Hause, Annette Meister, Simon Drescher
Liposomes are a promising class of drug delivery vehicles. However, no liposomal formulation has been approved for an oral application so far, due to stability issues of the liposomes in the gastrointestinal tract. Herein, we investigate the miscibility of three novel single-chain alkyl-branched bolalipids PC-C32(1,32Cn)-PC (n = 3, 6, 9) with either saturated or unsaturated phosphatidylcholines by means of differential scanning calorimetry (DSC), transmission electron microscopy (TEM) of stained samples, vitrified specimens, or replica of freeze-fractured samples, and dynamic light scattering (DLS)...
January 2019: Biophysical Chemistry
https://read.qxmd.com/read/30352336/singlet-oxygen-quenching-and-chain-breaking-antioxidant-properties-of-a-quercetin-dimer-able-to-prevent-age-related-macular-degeneration
#16
Mario C Foti, Riccardo Amorati, Andrea Baschieri, Concetta Rocco
A dimer of quercetin prepared through a Mannich reaction protects pyridinium bisretinoid A2E from photooxidation at 430 nm in aqueous medium at pH 7.4. In the presence of light and O2 , A2E is quickly attacked by 1 O2 produced in situ (by excited A2E) to give nonaoxirane and other oxygenated compounds which can be involved in diseases of the macula. Peroxyl radicals might have only a marginal role on the photooxidation of A2E. The dimer is actually a potent quencher of 1 O2 with a rate constant kQ of 8...
December 2018: Biophysical Chemistry
https://read.qxmd.com/read/30343111/hofmeister-effect-on-catalytic-properties-of-chymotrypsin-is-substrate-dependent
#17
Eva Dušeková, Katarína Garajová, Rukiye Yavaşer, Rastislav Varhač, Erik Sedlák
Effect of Hofmeister sodium salts, sulfate, chloride, bromide and perchlorate, on catalytic properties and stability of chymotrypsin has been studied by absorbance and circular dichroism spectroscopies. To address Hofmeister effect on activity of chymotrypsin, two different substrates, N-benzoyl-L-tyrosine ethyl ester and amide N-succinyl-L-phenylalanine-p-nitroanilide, were used. Catalytic activity of chymotrypsin is dependent on salt concentration and position of anion in Hofmeister series. The enzyme activity for both substrates is only slightly affected by chaotropic anions and increases with kosmotropic nature of anions...
December 2018: Biophysical Chemistry
https://read.qxmd.com/read/30265962/thermal-unfolding-of-homodimers-and-heterodimers-of-different-skeletal-muscle-isoforms-of-tropomyosin
#18
Alexander M Matyushenko, Sergey Y Kleymenov, Denis S Susorov, Dmitrii I Levitsky
We applied differential scanning calorimetry (DSC) to investigate the structural properties of three isoforms of tropomyosin (Tpm), α, β, and γ, expressed from different genes in human skeletal muscles. We compared specific features of the thermal unfolding of αα, ββ, and γγ Tpm homodimers, as well as of αβ and γβ Tpm heterodimers. The results show that the thermal stability of γγ homodimer is much higher than that of αα homodimer which, in turn, is much more thermostable than the ββ homodimer...
December 2018: Biophysical Chemistry
https://read.qxmd.com/read/30500608/electroactive-fluorescent-false-neurotransmitter-ffn102-partially-replaces-dopamine-in-pc12-cell-vesicles
#19
Lihui Hu, Alexandra Savy, Laurence Grimaud, Manon Guille-Collignon, Frédéric Lemaître, Christian Amatore, Jérôme Delacotte
In the last decade, following fluorescent dyes and protein tags, pH sensitive false fluorescent neurotransmitters (FFN) were introduced and were valuable for labeling secretory vesicles and monitoring exocytosis at living cells. In particular, the synthetic analog of neurotransmitters FFN102 was shown to be an electroactive probe. Here, we show that FFN102 is suitable to be used as a bioanalytic probe at the widely used PC12 cell model. FFN102 was uptaken in the secretory vesicles of PC12 cells, partially replacing the endogenous dopamine stored in these vesicles...
November 12, 2018: Biophysical Chemistry
https://read.qxmd.com/read/30245351/bohr-effect-and-oxygen-affinity-of-carp-eel-and-human-hemoglobin-quantitative-analyses-provide-rationale-for-the-root-effect
#20
Kehinde Onwochei Okonjo
The functional properties of most fish hemoglobins are more complex than those of human hemoglobin. This complexity arises in the form of the Root effect, in which the oxygen affinity of such fish hemoglobins decreases rapidly with pH relative to that of human hemoglobin. Cooperative ligand binding is also diminished below pH ≈ 6.5. The Bohr effect, determined by acid-base titration, has been reported for the Root effect carp and anodic eel hemoglobins. Unlike for mammalian hemoglobins, the Wyman equation for the Bohr effect fails to account quantitatively for these Bohr data...
November 2018: Biophysical Chemistry
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