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Biophysical Chemistry

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https://www.readbyqxmd.com/read/28735167/first-observation-of-metal-ion-induced-structural-fluctuations-of-%C3%AE-helical-peptides-by-using-diffracted-x-ray-tracking
#1
Daiki Usui, Satomi Inaba, Hiroshi Sekiguchi, Yuji C Sasaki, Toshiki Tanaka, Masayuki Oda
In order to analyze protein structural dynamics, we designed simple model peptides whose structures changed from random-coil to helix-bundle structures by forming stable hydrophobic core in the presence of metal ions. The strategy involved destabilizing a de novo designed three helix-bundle protein by substituting the residues present in its hydrophobic core with histidine and small amino acids. The conformational changes of peptides induced upon binding of Zn(2+) to histidine were analyzed using circular dichroism spectroscopy, which revealed peptides, HA and HG, to be good candidates for further analyses...
July 14, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28733103/broadband-diffuse-optical-characterization-of-elastin-for-biomedical-applications
#2
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...
July 14, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28711675/molecular-dynamics-simulations-of-t-2410-and-t-2429-hiv-fusion-inhibitors-interacting-with-model-membranes-insight-into-peptide-behavior-structure-and-dynamics
#3
I C V C Mavioso, V C R de Andrade, A J Palace Carvalho, A M T Martins do Canto
T-2410 and T-2429 are HIV fusion inhibitor peptides (FI) designed to present a higher efficiency even against HIV strains that developed resistance against other FIs. Similar peptides were shown to interact with model membranes both in the liquid disordered phase and in the liquid ordered state. Those results indicated that such interaction is important to function and could be correlated with their effectiveness. Extensive molecular dynamics simulations were carried out to investigate the interactions between both T-2410 and T-2429 with bilayers of pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and a mixture of POPC/cholesterol (Chol) (1:1)...
July 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28711348/impact-of-molecular-flexibility-on-the-site-energy-shift-of-chlorophylls-in-photosystem-ii
#4
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...
July 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28710920/thermodynamics-and-kinetics-of-rna-tertiary-structure-formation-in-the-junctionless-hairpin-ribozyme
#5
Neil A White, Charles G Hoogstraten
The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation...
July 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28697449/binding-kinetics-of-mutant-p53r175h-with-wild-type-p53-and-p63-a-surface-plasmon-resonance-and-atomic-force-spectroscopy-study
#6
Ilaria Moscetti, Anna Rita Bizzarri, Salvatore Cannistraro
The oncogenic mutant p53R175H, one of the most frequently occurring in human cancers and usually associated with poor prognosis and chemo resistance, can exert a dominant negative effect over p53 family members, namely wild type p53, p63 and p73, inhibiting their oncosuppressive function. Novel anticancer strategies based on drugs able to prevent the formation of complexes between p53R175H and the p53 family members call for a deeper knowledge on the molecular mechanisms of their interaction. To this aim, p53R175H/p63 and p53R175H/p53 complexes were investigated in vitro by using Surface Plasmon Resonance and Atomic Force Spectroscopy, two emerging and complementary techniques able to provide interaction kinetic information, in near physiological conditions and without any labelling...
July 5, 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
#7
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...
June 30, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28697448/in-silico-analyses-of-the-effects-of-a-point-mutation-and-a-pharmacological-chaperone-on-the-thermal-fluctuation-of-phenylalanine-hydroxylase
#8
Daichi Hayakawa, Noriyuki Yamaotsu, Izumi Nakagome, Shin-Ichiro Ozawa, Tomoki Yoshida, Shuichi Hirono
Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism due to mutations in phenylalanine hydroxylase (PAH). Recently, small compounds, known as pharmacological chaperones (PhCs), have been identified that restore the enzymatic activity of mutant PAHs. Understanding the mechanism of the reduction in enzymatic activity due to a point mutation in PAH and its restoration by PhC binding is important for the design of more effective PhC drugs. Thermal fluctuations of an enzyme can alter its activity...
June 30, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28712764/nucleocytoplasmic-transport-in-cells-with-progerin-induced-defective-nuclear-lamina
#9
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...
June 28, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28705333/interdisciplinarity-in-norbert-wiener-a-mathematician-philosopher-of-our-time
#10
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...
June 28, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28697447/dynamical-regimes-of-lipids-in-additivated-liposomes-with-enhanced-elasticity-a-field-cycling-nmr-relaxometry-approach
#11
Carla C Fraenza, Esteban Anoardo
We study the molecular dynamics of lipids in binary large unilamellar liposomes suspended in D2O composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) or soy phosphatidylcholine (SPC) additivated with different percentiles of sodium deoxycholate (SDC). We use the fast field-cycling proton NMR relaxometry technique over a wide timescale and at diverse temperatures. A model previously validated in different formulations is here employed for the relaxometric analysis of elastic vesicles. A new dynamical regime is observed for the first time in additivated DMPC and additivated/non-additivated SPC liposomes...
June 27, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28688734/first-moves-towards-photoautotrophic-synthetic-cells-in-vitro-study-of-photosynthetic-reaction-centre-and-cytochrome-bc1-complex-interactions
#12
Emiliano Altamura, Rosa Fiorentino, Francesco Milano, Massimo Trotta, Gerardo Palazzo, Pasquale Stano, Fabio Mavelli
Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly "synthetic cells") can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles...
June 26, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28684254/high-contrast-brillouin-and-raman-micro-spectroscopy-for-simultaneous-mechanical-and-chemical-investigation-of-microbial-biofilms
#13
S Mattana, M Alunni Cardinali, S Caponi, D Casagrande Pierantoni, L Corte, L Roscini, G Cardinali, D Fioretto
Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample...
June 24, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28651101/competitive-ligands-facilitate-dissociation-of-the-complex-of-bifunctional-inhibitor-and-protein-kinase
#14
Taavi Ivan, Erki Enkvist, Hedi Sinijarv, Asko Uri
Dissociation of the complex of a ligand and a protein usually follows the kinetic profile of the first order process and the rate of dissociation is not affected by the presence of competitive ligands. We discovered that dissociation of the complex between a bifunctional ligand and a protein kinase (the catalytic subunit of cAMP-dependent protein kinase), an enzyme possessing 2 different substrate binding sites, was accelerated (facilitated) over 50-fold in the presence of competitive ligands at higher concentrations...
June 20, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28673509/discovery-of-a-new-mexiletine-derived-agonist-of-the-herg-k-channel
#15
Roberta Gualdani, Maria Maddalena Cavalluzzi, Francesco Tadini-Buoninsegni, Giovanni Lentini
The human Ether-a-go-go Related Gene (hERG) potassium channel plays a central role in the rapid component (IKr) of cardiac action potential repolarization phase. A large number of structurally different compounds block hERG and cause a high risk of arrhythmias. Among the drugs that block hERG channel, a few compounds have been identified as hERG channel activators. Such compounds may be useful, at least in theory, for the treatment of long term QT syndrome. Here we describe a new activator of hERG channel, named MC450...
June 19, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28648894/compositional-analysis-of-endogenous-porphyrins-from-helicobacter-pylori
#16
A Battisti, P Morici, G Signore, F Ghetti, A Sgarbossa
Bacteria able to accumulate porphyrins can be inactivated by visible light irradiation thanks to the photosensitizing properties of this class of aromatic pigments (photodynamic therapy, PDT). Since the bacterial resistance to antibiotic is growing, PDT is becoming a valid alternative. In this context, the pathogen Helicobacter pylori (Hp) is a suitable target for PDT since it spontaneously produces and accumulates porphyrins. It is then important to understand the spectroscopic behavior of these endogenous species to exploit them as photosensitizers, thus improving the results given by the application of PDT in the treatment of Hp infections...
June 19, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28654813/conformational-flexibility-and-base-pairing-tendency-of-the-tobacco-carcinogen-o6-4-oxo-4-3-pyridyl-butyl-guanine
#17
Katie A Wilson, Kariann G Szemethy, Stacey D Wetmore
The present work uses DFT calculations to characterize the conformational and hydrogen-bonding properties of O6-[4-oxo-4-(3-pyridyl)butyl]guanine (POB-G), a DNA adduct caused by tobacco. POB-G is found to adopt many isoenergetic conformations that allow for discrete interactions between the bulky moiety and the adducted G and/or pairing base. The calculated structure and stability of the hydrogen-bonded pairs between the Watson-Crick or Hoogsteen face of POB-G and the canonical DNA nucleobases fully rationalize the previously reported mutational spectra...
June 10, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28628895/a-composite-polynomial-approach-for-analyzing-the-indefinite-self-association-of-macromolecules-studied-by-sedimentation-equilibrium
#18
LETTER
Damien Hall
A different approach is described for analyzing sedimentation equilibrium experiments of indefinitely self-associating systems. The procedure involves application of conservation of mass criteria, along with local evaluation of the weight average molar mass, to generate a polynomial based on a composite pseudo-independent variable. The outlined method does not depend upon non-linear regression to generate a solution, but instead requires evaluation of the roots of a high-order polynomial.
June 10, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28601005/the-isolated-twenty-three-residue-long-n-terminal-region-of-the-glutamine-synthetase-inactivating-factor-binds-to-its-target
#19
José L Neira, Francisco J Florencio, M Isabel Muro-Pastor
Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS type I is regulated by protein-protein interactions with a 65-residue-long protein (IF7). IF7 binds initially to GS through residues at its N terminus. In this work, we studied the conformational preferences of the N-terminal region of IF7 (IF7pep, residues Ala7-Ala29), its binding to GS and its functional properties. Isolated IF7pep populated a nascent helix in aqueous solution...
June 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28622937/antibodies-under-pressure-a-small-angle-x-ray-scattering-study-of-immunoglobulin-g-under-high-hydrostatic-pressure
#20
Nico König, Michael Paulus, Karin Julius, Julian Schulze, Matthias Voetz, Metin Tolan
In the present work two subclasses of the human antibody Immunoglobulin G (IgG) have been investigated by Small-Angle X-ray Scattering under high hydrostatic pressures up to 5kbar. It is shown that IgG adopts a symmetric T-shape in solution which differs significantly from available crystal structures. Moreover, high-pressure experiments verify the high stability of the IgG molecule. It is not unfolded by hydrostatic pressures of up to 5kbar but a slight increase of the radius of gyration was observed at elevated pressures...
May 26, 2017: Biophysical Chemistry
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