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Biophysical Chemistry

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https://www.readbyqxmd.com/read/28941814/sequence-selective-binding-of-c8-conjugated-pyrrolobenzodiazepines-pbds-to-dna
#1
Mohammad A Basher, Khondaker Miraz Rahman, Paul J M Jackson, David E Thurston, Keith R Fox
DNA footprinting and melting experiments have been used to examine the sequence-specific binding of C8-conjugates of pyrrolobenzodiazepines (PBDs) and benzofused rings including benzothiophene and benzofuran, which are attached using pyrrole- or imidazole-containing linkers. The conjugates modulate the covalent attachment points of the PBDs, so that they bind best to guanines flanked by A/T-rich sequences on either the 5'- or 3'-side. The linker affects the binding, and pyrrole produces larger changes than imidazole...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28916410/kinetic-stability-and-sequence-structure-studies-of-urine-derived-bence-jones-proteins-from-multiple-myeloma-and-light-chain-amyloidosis-patients
#2
Luis M Blancas-Mejía, Emily B Martin, Angela Williams, Jonathan S Wall, Marina Ramirez-Alvarado
It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM)...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28893424/quantifying-the-influence-of-5-rna-modifications-on-rna-polymerase-i-activity
#3
Francis D Appling, Aaron L Lucius, David A Schneider
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28887045/the-molten-globule-residual-structure-is-critical-for-reflavination-of-glucose-oxidase
#4
Katarína Garajová, Martina Zimmermann, Martina Petrenčáková, Lenka Dzurová, Michal Nemergut, Ľudovít Škultéty, Gabriel Žoldák, Erik Sedlák
Glucose oxidase (GOX) is a homodimeric glycoprotein with tightly bound one molecule of FAD cofactor per monomer of the protein. GOX has numerous applications, but the preparation of biotechnologically interesting GOX sensors requires a removal of the native FAD cofactor. This process often leads to unwanted irreversible deflavination and, as a consequence, to the low enzyme recovery. Molecular mechanisms of reversible reflavination are poorly understood; our current knowledge is based only on empiric rules, which is clearly insufficient for further development...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28887044/biochemical-and-biophysical-properties-of-positively-supercoiled-dna
#5
Yingting Liu, Andrea M Berrido, Zi-Chun Hua, Yuk-Ching Tse-Dinh, Fenfei Leng
In this paper we successfully developed a procedure to generate the (+) supercoiled (sc) plasmid DNA template pZXX6 in the milligram range. With the availability of the (+) sc DNA, we are able to characterize and compare certain biochemical and biophysical properties of (+) sc, (-) sc, and relaxed (rx) DNA molecules using different techniques, such as UV melting, circular dichroism, and fluorescence spectrometry. Our results show that (+) sc, (-) sc, and rx DNA templates can only be partially melted due to the fact that these DNA templates are closed circular DNA molecules and the two DNA strands cannot be completely separated upon denaturation at high temperatures...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28882384/two-ion-theory-of-energy-coupling-in-atp-synthesis-rectifies-a-fundamental-flaw-in-the-governing-equations-of-the-chemiosmotic-theory
#6
Sunil Nath
The vital coupled processes of oxidative phosphorylation and photosynthetic phosphorylation synthesize molecules of adenosine-5'-triphosphate (ATP), the universal biological energy currency, and sustain all life on our planet. The chemiosmotic theory of energy coupling in oxidative and photophosphorylation was proposed by Mitchell >50years ago. It has had a contentious history, with part of the accumulated body of experimental evidence supporting it, and part of it in conflict with the theory. Although the theory was strongly criticized by many prominent scientists, the controversy has never been resolved...
August 19, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28843429/ultracompact-states-of-native-proteins
#7
Leandro Grille Coronel, Juan P Acierno, Mario R Ermácora
A statistical analysis of circa 20,000 X-ray structures evidenced the effects of temperature of data collection on protein intramolecular distances and degree of compaction. Identical chains with data collected at cryogenic ultralow temperatures (≤160K) showed a radius of gyration (Rg) significantly smaller than at moderate temperatures (≥240K). Furthermore, the analysis revealed the existence of structures with a Rg significantly smaller than expected for cryogenic temperatures. In these ultracompact cases, the unusually small Rg could not be specifically attributed to any experimental parameter or crystal features...
August 18, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28941815/effect-of-protonation-on-the-mechanism-of-phosphate-monoester-hydrolysis-and-comparison-with-the-hydrolysis-of-nucleoside-triphosphate-in-biomolecular-motors
#8
Hammad Ali Hassan, Sadaf Rani, Tabeer Fatima, Farooq Ahmad Kiani, Stefan Fischer
Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the OaH bond of the attacking water molecule, and the POl bond of the substrate (Oa and Ol stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of OaH and POl bonds occurs simultaneously, whereas in the sequential mechanism, the OaH and POl bonds break at different stages of the reaction...
August 15, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28851547/key-factors-regulating-protein-carbonylation-by-%C3%AE-%C3%AE-unsaturated-carbonyls-a-structural-study-based-on-a-retrospective-meta-analysis
#9
Giulio Vistoli, Chiara Mantovani, Silvia Gervasoni, Alessandro Pedretti, Giancarlo Aldini
Protein carbonylation represents one of the most important oxidative-based modifications involving nucleophilic amino acids and affecting protein folding and function. Protein carbonylation is induced by electrophilic carbonyl species and is an highly selective process since few nucleophilic residues are carbonylated within each protein. While considering the great interest for protein carbonylation, few studies investigated the factors which render a nucleophilic residue susceptible to carbonylation. Hence, the present study is aimed to delve into the factors which modulate the reactivity of cysteine, histidine and lysine residues towards α,β unsaturated carbonyls by a retrospective analysis of the available studies which identified the adducted residues for proteins, the structure of which was resolved...
August 15, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818312/thermodynamic-and-spectroscopic-study-of-al-3-interaction-with-glycine-l-cysteine-and-tranexamic-acid-in-aqueous-solution
#10
Paola Cardiano, Fausta Giacobello, Ottavia Giuffrè, Silvio Sammartano
In this paper a thermodynamic and spectroscopic study on the interaction between Al(3+) and glycine (Gly), l-cysteine (Cys), tranexamic acid (Tranex) is reported. Speciation models have been obtained by processing potentiometric titration data to determine stability constants of the species formed in aqueous solution at T=298.15K, 0.15≤I/molL(-1)≤1 in NaCl. Thermodynamic formation parameters have been obtained from calorimetric titration data, at T=298.15K, I=0.15molL(-1) using NaCl as ionic medium. Al(3+)-Cys system was also investigated by spectrophotometric and (1)H NMR measurements...
August 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818314/comparison-of-disaggregative-effect-of-a-type-egcg-dimer-and-egcg-monomer-on-the-preformed-bovine-insulin-amyloid-fibrils
#11
Rong-Zu Nie, Wei Zhu, Jin-Ming Peng, Zhen-Zhen Ge, Chun-Mei Li
In the present study, the disruptive effects of epigallocatechin-3-gallate (EGCG) and A-type dimeric epigallocatechin-3-gallate (A-type EGCG dimer) on the preformed bovine insulin amyloid fibrils were studied by several biophysical methods including thioflavin-T (ThT) fluorescence assay, 1-anilinonaphthalene-8-sulfonic (ANS) fluorescence assay, Congo red (CR) binding assay, dynamic light scattering (DLS), transmission electron microscopy (TEM), Gel electrophoresis (SDS-PAGE) and Bradford assay. Our results demonstrated that A-type EGCG dimer showed significantly more potential disaggregative effects on the bovine insulin amyloid fibrils than EGCG...
July 31, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28941613/sibpa-under-the-tuscan-sun-introduction-to-the-sibpa-xxiii-special-issue
#12
EDITORIAL
Daniela Giacomazza, Cristiano Viappiani, Enrico Di Cera, Carlo Musio
The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIII National Congress in the gorgeous Tuscan town of Cortona, Italy, on September 18-21, 2016. This special issue features a selection of contributions from the Congress in the areas of molecular, applied, cellular and computational biophysics. Cutting-edge developments in nanoscale biophysics were introduced for the first time in the program. SIBPA continues its successful promotion of biophysical disciplines at the national and international levels, with added strength from its partnership with Biophysical Chemistry and Elsevier...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28818313/controlled-single-cell-cyclic-compression-and-transcription-analysis-a-pilot-study
#13
Paola Gavazzo, Loredana Petecchia, Paolo Facci, Massimo Vassalli, Federica Viti
An innovative platform for the study of the molecular mechanisms at the basis of mechanotransduction has been implemented, developing an experimental approach capable of providing controlled dynamic compression stimuli and retrieving the biomolecular response with single-cell sensitivity. The system provides the ability to perform compression-release cycles on single cells with controlled forces in the nN range and a user-defined repetition rate. Experimental procedures to perform qPCR from a small set of single cells were finely tuned...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28774748/investigation-on-different-chemical-stability-of-mitochondrial-hsp60-and-its-precursor
#14
Caterina Ricci, Rita Carrotta, Giacoma Cinzia Rappa, Maria Rosalia Mangione, Fabio Librizzi, Pier Luigi San Biagio, Heinz Amenitsch, Maria Grazia Ortore, Silvia Vilasi
In the large class of molecules that maintain protein homeostasis, called molecular chaperones, chaperonins constitute a subclass that specifically assist the correct folding of newly synthesized proteins. Among them, Hsp60 is composed of a double heptameric ring structure with a large central cavity where the unfolded protein binds via hydrophobic interactions and is supported, in this function, by the co-chaperonin Hsp10. Hsp60 is typically located in the mitochondria, but in some pathological situations, such as cancers and chronic inflammatory diseases, Hsp60 accumulates in the cytoplasm...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28739150/plasma-assisted-surface-treatments-of-biomaterials
#15
L Minati, C Migliaresi, L Lunelli, G Viero, M Dalla Serra, G Speranza
The biocompatibility of an implant depends upon the material it is composed of, in addition to the prosthetic device's morphology, mechanical and surface properties. Properties as porosity and pore size should allow, when required, cells penetration and proliferation. Stiffness and strength, that depend on the bulk characteristics of the material, should match the mechanical requirements of the prosthetic applications. Surface properties should allow integration in the surrounding tissues by activating proper communication pathways with the surrounding cells...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28733103/broadband-diffuse-optical-characterization-of-elastin-for-biomedical-applications
#16
Sanathana Konugolu Venkata Sekar, Joo Sin Beh, Andrea Farina, Alberto Dalla Mora, Antonio Pifferi, Paola Taroni
Elastin is a key structural protein of dynamic connective tissues widely found in the extracellular matrix of skin, arteries, lungs and ligaments. It is responsible for a range of diseases related to aging of biological tissues. The optical characterization of elastin can open new opportunities for its investigation in biomedical studies. In this work, we present the absorption spectra of elastin using a broadband (550-1350nm) diffuse optical spectrometer. Distortions caused by fluorescence and finite bandwidth of the laser source on estimated absorption were effectively accounted for in measurements and data analysis and compensated...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28712764/nucleocytoplasmic-transport-in-cells-with-progerin-induced-defective-nuclear-lamina
#17
Gianmarco Ferri, Barbara Storti, Ranieri Bizzarri
Recent data indicate that nuclear lamina (NL) plays a relevant role in many fundamental cellular functions. The peculiar role of NL in cells is dramatically demonstrated by the Hutchinson-Gilford progeria syndrome (HGPS), an inherited laminopathy that causes premature, rapid aging shortly after birth. In HGPS, a mutant form of Lamin A (progeria) leads to a dysmorphic NL structure, but how this perturbation is transduced into cellular changes is still largely unknown. Owing to the close structural relationship between NL and the Nuclear Pore Complex (NPC), in this work we test whether HGPS affects passive and active nucleo-cytoplasmic shuttling of cargoes by means of an established model based of fluorescence recovery after photobleaching...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28711348/impact-of-molecular-flexibility-on-the-site-energy-shift-of-chlorophylls-in-photosystem-ii
#18
Daniele Narzi, Emanuele Coccia, Marco Manzoli, Leonardo Guidoni
Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28705333/interdisciplinarity-in-norbert-wiener-a-mathematician-philosopher-of-our-time
#19
Leone Montagnini
The paper focuses on interdisciplinarity in Norbert Wiener looking at his scientific work from a unitary point of view. It begins with a bird's-eye view of the history of the term "interdisciplinarity", pointing out how the word was the result of a movement of ideas that took place in US science along the whole Twentieth century. This way, the Wiener's conceptions and practices concerning interdisciplinarity are compared with their historical context, showing analogies and peculiarities. For Wiener, interdisciplinary research by very small groups whose members have a very broad interdisciplinary basis is an essential prerequisite for new fundamental ideas for invention and discoveries...
October 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28697974/a-possible-desensitized-state-conformation-of-the-human-%C3%AE-7-nicotinic-receptor-a-molecular-dynamics-study
#20
L Chiodo, T E Malliavin, L Maragliano, G Cottone
The determination of the conformational states corresponding to diverse functional roles of ligand gated ion channels is subject of intense investigation with various techniques, from X-rays structure determination to electrophysiology and computational modeling. Even with a certain number of structures becoming recently available, only few major structural features distinguishing conductive open channel from the non conductive resting protein have been highlighted, while high-resolution details are still missing...
October 2017: Biophysical Chemistry
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