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European Biophysics Journal: EBJ

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https://www.readbyqxmd.com/read/28314880/comparative-study-of-the-structure-and-interaction-of-the-pore-helices-of-the-herg-and-kv1-5-potassium-channels-in-model-membranes
#1
Maïwenn Beaugrand, Alexandre A Arnold, Steve Bourgault, Philip T F Williamson, Isabelle Marcotte
The hERG channel is a voltage-gated potassium channel found in cardiomyocytes that contributes to the repolarization of the cell membrane following the cardiac action potential, an important step in the regulation of the cardiac cycle. The lipids surrounding K(+) channels have been shown to play a key role in their regulation, with anionic lipids shown to alter gating properties. In this study, we investigate how anionic lipids interact with the pore helix of hERG and compare the results with those from Kv1...
March 17, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28258312/advantages-of-synchrotron-radiation-circular-dichroism-spectroscopy-to-study-intrinsically-disordered-proteins
#2
Patricia S Kumagai, Ricardo DeMarco, Jose L S Lopes
The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others...
March 3, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28251265/binding-mechanism-of-picogreen-to-dna-characterized-by-magnetic-tweezers-and-fluorescence-spectroscopy
#3
Ying Wang, Helene Schellenberg, Volker Walhorn, Katja Toensing, Dario Anselmetti
Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules...
March 1, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28204854/adsorption-of-dna-binding-proteins-to-functionalized-carbon-nanotube-surfaces-with-and-without-dna-wrapping
#4
Yu Ishibashi, Shusuke Oura, Kazuo Umemura
We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH2 groups (CONH2-SWNT) exhibited very strong interactions between the CONH2-SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces...
February 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28168331/protein-structure-estimation-from-nmr-data-by-matrix-completion
#5
Zhicheng Li, Yang Li, Qiang Lei, Qing Zhao
Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage...
February 6, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28161748/the-swimming-polarity-of-multicellular-magnetotactic-prokaryotes-can-change-during-an-isolation-process-employing-magnets-evidence-of-a-relation-between-swimming-polarity-and-magnetic-moment-intensity
#6
Roger Duarte de Melo, Daniel Acosta-Avalos
Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets...
February 4, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28116476/comparative-stability-of-major-facilitator-superfamily-transport-proteins
#7
Nicola J Harris, Heather E Findlay, Michael R Sanders, Mateusz Kedzierski, Ália Dos Santos, Paula J Booth
Membrane transporters are a vital class of proteins for which there is little available structural and thermodynamic information. The Major Facilitator Superfamily (MFS) is a large group of transport proteins responsible for transporting a wide range of substrates in eukaryotes and prokaryotes. We have used far-UV circular dichroism (CD) to assess whether transporters from this superfamily have the same chemical and thermal stability. We have compared the stability of five different MFS transporters; PepTSo from Shewanella oneidensis and LacY, GalP, GlpT and XylE from Escherichia coli, as well as a known stable mutant of LacY, LacY-C154G...
January 23, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28108814/the-small-neurotoxin-apamin-blocks-not-only-small-conductance-ca-2-activated-k-channels-sk-type-but-also-the-voltage-dependent-kv1-3-channel
#8
Patrick Voos, Mehtap Yazar, René Lautenschläger, Oliver Rauh, Anna Moroni, Gerhard Thiel
Apamin is frequently used as a specific blocker of small-conductance Ca(2+)-activated (SK type) K(+) channels. Here we show that the small neurotoxin is not as specific as anticipated. It is also a high-affinity inhibitor with an IC50 of 13 nM of the Kv1.3 channel; it blocks the latter with potency similar to the Kv1.3 blocker PAP-1. Since SK type channels and Kv1.3 channels are frequently coexpressed in different tissues such as cells of the immune system, apamin must be used with caution as a pharmacological tool...
January 20, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28070661/voltage-gated-sodium-channels-as-targets-for-pyrethroid-insecticides
#9
Linda M Field, T G Emyr Davies, Andrias O O'Reilly, Martin S Williamson, B A Wallace
The pyrethroid insecticides are a very successful group of compounds that have been used extensively for the control of arthropod pests of agricultural crops and vectors of animal and human disease. Unfortunately, this has led to the development of resistance to the compounds in many species. The mode of action of pyrethroids is known to be via interactions with the voltage-gated sodium channel. Understanding how binding to the channel is affected by amino acid substitutions that give rise to resistance has helped to elucidate the mode of action of the compounds and the molecular basis of their selectivity for insects vs mammals and between insects and other arthropods...
January 9, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27604548/relaxation-dynamics-and-thermophysical-properties-of-vegetable-oils-using-time-domain-reflectometry
#10
Anil A Sonkamble, Rahul P Sonsale, Mahesh S Kanshette, Komal B Kabara, Kunal H Wananje, Ashok C Kumbharkhane, Arvind V Sarode
Dielectric relaxation studies of vegetable oils are important for insights into their hydrogen bonding and intermolecular dynamics. The dielectric relaxation and thermo physical properties of triglycerides present in some vegetable oils have been measured over the frequency range of 10 MHz to 7 GHz in the temperature region 25 to 10 °C using a time-domain reflectometry approach. The frequency and temperature dependence of dielectric constants and dielectric loss factors were determined for coconut, peanut, soya bean, sunflower, palm, and olive oils...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27589857/oligomerization-of-the-antimicrobial-peptide-protegrin-5-in-a-membrane-mimicking-environment-structural-studies-by-high-resolution-nmr-spectroscopy
#11
Konstantin S Usachev, Olga A Kolosova, Evelina A Klochkova, Aidar R Yulmetov, Albert V Aganov, Vladimir V Klochkov
Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27557558/study-of-procaine-and-tetracaine-in-the-lipid-bilayer-using-molecular-dynamics-simulation
#12
Seifollah Jalili, Marzieh Saeedi
Despite available experimental results, the molecular mechanism of action of local anesthetics upon the nervous system and contribution of the cell membrane to the process are still controversial. In this work, molecular dynamics simulations were performed to investigate the effect of two clinically used local anesthetics, procaine and tetracaine, on the structure and dynamics of a fully hydrated dimyristoylphosphatidylcholine lipid bilayer. We focused on comparing the main effects of uncharged and charged drugs on various properties of the lipid membrane: mass density distribution, diffusion coefficient, order parameter, radial distribution function, hydrogen bonding, electrostatic potential, headgroup angle, and water dipole orientation...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27473845/conditions-for-homogeneous-preparation-of-stable-monomeric-and-oligomeric-forms-of-activated-vip3a-toxin-from-bacillus-thuringiensis
#13
Thittaya Kunthic, Wahyu Surya, Boonhiang Promdonkoy, Jaume Torres, Panadda Boonserm
Bacillus thuringiensis vegetative insecticidal proteins like Vip3A have been used for crop protection and to delay resistance to existing insecticidal Cry toxins. However, little is known about Vip3A's behavior or its mechanism of action, and a structural model is required. Herein, in an effort to facilitate future crystallization and functional studies, we have used the orthogonal biophysical techniques of light scattering and sedimentation to analyze the aggregation behavior and stability of trypsin-activated Vip3A toxin in solution...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27469622/findings-on-the-interaction-of-the-antimicrobial-peptide-cecropin-melittin-with-a-gold-surface-from-molecular-dynamics-studies
#14
André F Ferreira, Akhilesh Rai, Lino Ferreira, Pedro N Simões
The immobilization of gold nanoparticles (AuNPs) with antimicrobial peptides (AMPs) is a new and promising way to enhance both the activity and targeting capabilities of AMPs. However, a full understanding of the adsorption process underlying these materials is still lacking. Cecropin-melittin is a peptide with a broad antimicrobial activity while displaying low hemolytic properties, whose conjugation with AuNPs has not been studied before. In this context, we report the investigation of the adsorption process of the cecropin-melittin peptide, with (CM-SH) and without (CM) cysteine at its C-terminus, onto a gold surface based on all-atom MD simulations...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27461369/theory-for-nonlinear-dynamic-force-spectroscopy
#15
Oscar Björnham, Magnus Andersson
Dynamic force spectroscopy (DFS) is an experimental technique that is commonly used to assess information on the strength, energy landscape, and lifetime of noncovalent bio-molecular interactions. DFS traditionally requires an applied force that increases linearly with time so that the bio-complex under investigation is exposed to a constant loading rate. However, tethers or polymers can modulate the applied force in a nonlinear manner. For example, bacterial adhesion pili and polymers with worm-like chain properties are structures that show nonlinear force responses...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27457765/role-of-water-in-the-formation-of-macromolecular-structures
#16
REVIEW
Peter L Privalov, Colyn Crane-Robinson
This review shows that water in biological systems is not just a passive liquid solvent but also a partner in the formation of the structure of proteins, nucleic acids and their complexes, thereby contributing to the stability and flexibility required for their proper function. Reciprocally, biological macromolecules affect the state of the water contacting them, so that it is only partly in the normal liquid state, being somewhat ordered when bound to macromolecules. While the compaction of globular proteins results from the reluctance of their hydrophobic groups to interact with water, the collagen superhelix is maintained by water forming a hydroxyproline-controlled frame around this coiled-coil macromolecule...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27444285/application-of-novel-analytical-ultracentrifuge-analysis-to-solutions-of-fungal-mannans
#17
Richard B Gillis, Gary G Adams, David T M Besong, Eva Machová, Anna Ebringerová, Arthur J Rowe, Stephen E Harding, Trushar R Patel
Polysaccharides, the most abundant biopolymers, are required for a host of activities in lower organisms, animals, and plants. Their solution characterization is challenging due to their complex shape, heterogeneity, and size. Here, recently developed data analysis approaches were applied for traditional sedimentation equilibrium and velocity methods in order to investigate the molar mass distribution(s) of a subtype of polysaccharide, namely, mannans from four Candida spp. The molecular weight distributions of these mannans were studied using two recently developed equilibrium approaches: SEDFIT-MSTAR and MULTISIG, resulting in corroboratory distribution profiles...
April 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28039513/actomyosin-interaction-at-low-atp-concentrations
#18
Manuela Maffei, Emanuela Longa, Antonio Sabatini, Alberto Vacca, Stefano Iotti
In vitro motility assay (IVMA) experiments were performed to analyze the movement of actin filaments sliding on a pavement of myosin molecules at different [ATP] and [ADP]. In standard experimental conditions at [ATP] = 2 mM, about 80% of the actin filaments move in unloaded conditions with a constant velocity. However, a fraction of at least 20% static actin filaments is always present. The accepted explanation is the occurrence of damaged "rigor"-like myosin heads that do not undergo the normal ATP-dependent cycling motion...
March 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27942765/stochastic-phenotypic-interconversion-in-tumors-can-generate-heterogeneity
#19
Giuseppina Simone
Phenotype variations define heterogeneity in biological and molecular systems, and play a crucial mechanistic role, and heterogeneity has been demonstrated in tumor cells. In this work, cells from blood of patients affected by colon cancer were analyzed and sorted using a microfluidic assay based on galactose-active moieties and incubated for culturing in severe combined immunodeficiency (SCID) mice. Based on the results of these experiments, a model based on Markov theory is implemented and discussed to explain the equilibrium existing between phenotypes of cell subpopulations sorted using the microfluidic assay...
March 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27450562/molecular-basis-and-quantitative-assessment-of-trf1-and-trf2-protein-interactions-with-tin2-and-apollo-peptides
#20
Umesh Kalathiya, Monikaben Padariya, Maciej Baginski
Shelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate the molecular basis of these interactions, we employed molecular dynamics (MD) simulations of TRF1TRFH-TIN2TBM and TRF2TRFH-TIN2TBM/ApolloTBM complexes and of the isolated proteins...
March 2017: European Biophysics Journal: EBJ
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