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European Biophysics Journal: EBJ

Tie Liu, Zhaoshun Wang, Peng Guo, Na Ding
The oncogenic mutation V600E in B-Raf activation loop (A-loop) has been frequently observed to cause drug resistance in colorectal cancer chemotherapy. Here, the molecular mechanism of V600E-induced conformational flipping of B-Raf activation loop (A-loop) is investigated systematically via continuum electrostatic analysis. It is found that substitution of the electroneutral Val600 residue with negatively charged glutamic acid Glu600 electrostatically destabilizes the inactive DFG-out conformation of B-Raf kinase and promotes its shifting to active DFG-in conformation...
September 14, 2018: European Biophysics Journal: EBJ
Olwyn Byron, Ivo Nischang, Trushar R Patel
Analytical ultracentrifugation (AUC) remains a highly versatile and widely applicable tool for the analysis of macromolecules and their interactions. The current state-of-the-art was demonstrated at a recent international meeting held in Glasgow, Scotland, in July 2017, the 23rd International Analytical Ultracentrifugation Workshop and Symposium. This special issue showcases the reports made at the meeting, which concerned the application of AUC to a wide range of topics in biochemical and polymer science including antibody and membrane protein characterisation, and protein-carbohydrate interactions...
September 14, 2018: European Biophysics Journal: EBJ
Hirohisa Tamagawa, Kota Ikeda
According to standard membrane theory, the generation of membrane potential is attributed to transmembrane ion transport. However, there have been a number of reports of membrane behavior in conflict with the membrane theory of cellular potential. Putting aside the membrane theory, we scrutinized the generation mechanism of membrane potential from the view of the long-dismissed adsorption theory of Ling. Ling's adsorption theory attributes the membrane potential generation to mobile ion adsorption. Although Ling's adsorption theory conflicts with the broadly accepted membrane theory, we found that it well reproduces experimentally observed membrane potential behavior...
September 11, 2018: European Biophysics Journal: EBJ
T C Sabari Girisun, C Jeganathan, N Pavithra, S Anandan
Structurally modified bacteriorhodopsin (BR) was prepared by simple surfactant treatment using Cetyl trimethylammonium bromide (cationic; CTAB), Sodium dodecyl sulphate (anionic; SDS) and Triton X-100 (nonionic; TX-100). In the UV-visible absorption spectrum, the characteristic absorption band of native BR at 560 nm is hyperchromically (CTAB, due to induced aggregation), bathochromically (SDS, BR solubilisation and partial unfolding) and hypsochromically (TX-100, BR monomerizes) shifted after chemical treatment and the structural modifications were further confirmed by Raman spectra...
September 3, 2018: European Biophysics Journal: EBJ
Guy Channell, Vlad Dinu, Gary G Adams, Stephen E Harding
In establishing the sources of data variability within sedimentation velocity analysis in the analytical ultracentrifuge and their relative importance, recent studies have demonstrated that alignment of the sample cells to the centre of rotation is the most significant contributing factor to overall variability, particularly for the characterisation of low levels of protein aggregation. Accurate mechanical and optical alignment tools have been recently designed. In this study, we (1) confirm the effect of misalignment observed by others on the estimated amounts of bovine serum albumin (BSA) monomer and dimer, and the sedimentation coefficient value for the BSA dimer; and (2) demonstrate the high performance of a mechanical alignment tool and the usefulness of a simple and complementary enhanced manual alignment protocol which should be useful for situations where these tools are not available...
August 29, 2018: European Biophysics Journal: EBJ
Etske Bijl, Thom Huppertz, Hein van Valenberg, Carl Holt
The white appearance of skim milk is due to strong light scattering by colloidal particles called casein micelles. Bovine casein micelles comprise expressed proteins from four casein genes together with significant fractions of the total calcium, inorganic phosphate, magnesium and citrate ions in the milk. Thus, the milk salts are partitioned between the casein micelles, where they are mostly in the form of nanoclusters of an amorphous calcium phosphate sequestered by caseins through their phosphorylated residues, with the remainder in the continuous phase...
August 21, 2018: European Biophysics Journal: EBJ
Wei Feng, Jinwen Li, Yanjun Liang, Yongqiang Zhang, Shu Jie Li
Tom40, the central component of the preprotein translocase of the mitochondrial outer membrane (TOM complex), forms the import pore that facilitates the translocation of preproteins across the outer membrane. Though the function of Tom40 has been intensively studied, the details of the interactions between presequence peptides and Tom40 remain unclear. In this study, we expressed rat Tom40 in Escherichia coli and purified it from inclusion bodies before investigating the refolded protein by fluorescence spectroscopy and circular dichroism (CD) spectroscopy...
August 18, 2018: European Biophysics Journal: EBJ
Ruslan Garifullin, Dmitriy S Blokhin, Rezeda A Akhmadishina, Natalia V Petrova, Alexandra M Kusova, Vladimir V Klochkov, Timur I Abdullin
Chemical modification of therapeutic peptides is an important approach to improving their physicochemical and pharmacokinetic properties. The triphenylphosphonium (TPP) cation has proved to be a powerful modifier; however, its effects on peptide structure and activity remain uncharacterized. In this study, cytoprotective tetrapeptides based on the YRFK opioid motif with L- or D-Arg residues were linked to (triphenylphosphonio)carboxylic acids with ethylene and pentylene spacers (TPP-3 and TPP-6 groups, respectively)...
August 13, 2018: European Biophysics Journal: EBJ
Aalishaa A Azam, Jean M Kinder, G Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R Ault, Peter J F Henderson, Babur Z Chowdhry, Bruce D Alexander, Stephen E Harding, Mary K Phillips-Jones
Despite the importance of membrane proteins in cellular processes, studies of these hydrophobic proteins present major technical challenges, including expression and purification for structural and biophysical studies. A modified strategy of that proposed previously by Saidijam et al. (2005) and others, for the routine expression of bacterial membrane proteins involved in environmental sensing and antimicrobial resistance (AMR), is proposed which results in purification of sufficient proteins for biophysical experiments...
July 31, 2018: European Biophysics Journal: EBJ
Stephen E Harding
The analytical ultracentrifuge (AUC) invented by T. Svedberg has now become an extremely versatile and diverse tool in Biochemistry and Polymer Science for the characterisation of the sizes, shapes and interactions of particles ranging in size from a few nanometres to tens of microns, or in molecular weight, M (molar mass) terms from a few hundred daltons to hundreds of megadaltons. We illustrate this diversity by reviewing recent work on (1) small lignin-like isoeugenols of M ~ 0.4-0.9 kDa for archaeological wood conservation, (2) protein-like association of a functional amino-cellulose M = 3...
July 28, 2018: European Biophysics Journal: EBJ
Meike Pedersen, Shirin Jamali, Ipsita Saha, Rainer Daum, Mourad Bendjennat, Saveez Saffarian
Interferometric Photo-Activation-Localization-Microscopy (iPALM) localizes single fluorescent molecules with 20 nm lateral and 10 nm axial resolution. We present a method utilizing glass coverslip lithography for correlative imaging between iPALM and scanning electron microscopy (SEM). Using iPALM on HIV Gag-Dendra virus-like particles (VLPs) we localized the position of HIV Gag proteins. Based on these localizations we reconstructed the central cavity of the VLPs along with imperfections within the HIV Gag lattice...
July 24, 2018: European Biophysics Journal: EBJ
J García de la Torre, J G Hernández Cifre, A I Díez Peña
In the prediction of sedimentation profiles in analytical ultracentrifugation, the counterflow due to diffusion must be taken into account for a proper analysis of experimental data in the determination of molecular properties. This is usually achieved by numerical solution of the Lamm equation. This paper presents an alternative approach, in which the displacement of the solute in the cell, resulting from the opposite effects of ultracentrifugal force and diffusional drift, is described by Brownian dynamics simulation of the solute particles...
July 20, 2018: European Biophysics Journal: EBJ
Dalila Khemili, Carmen Valenzuela, Fatima Laraba-Djebari, Djelila Hammoudi-Triki
Neurotoxins of scorpion venoms modulate ion channels. Voltage-gated potassium (KV ) channels regulate the membrane potential and are involved in the activation and proliferation of immune cells. Macrophages are key components of the inflammatory response induced by scorpion venom. The present study was undertaken to investigate the effect of Androctonus australis hector (Aah) venom on KV channels in murine resident peritoneal macrophages. The cytotoxicity of the venom was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) -based assay and electrophysiological recordings were performed using the whole-cell patch clamp technique...
July 13, 2018: European Biophysics Journal: EBJ
Robert T Wright, David Hayes, Peter J Sherwood, Walter F Stafford, John J Correia
The goal of this work is to develop a preclinical method for quantitative hydrodynamic and thermodynamic analysis of therapeutic proteins in crowded environments like human serum. The method utilizes tracer amounts of fluorescently labeled monoclonal antibodies and the Aviv AU-FDS optical system. We have performed sedimentation velocity experiments as a function of mAb, human serum albumin and human IgG concentration to extract self- and cross-term hydrodynamic nonideality effects. SV measurements are consistently complicated by weak mAb-mAb and mAb-IgG interactions (Wright et al...
July 12, 2018: European Biophysics Journal: EBJ
Emilie Vanhove, Marc Vanhove
Equilibrium titration curves have been used to determine the affinity of biomolecules using a variety of platforms and technologies. Such measurements, however, are experimentally limited by the time that is needed for the system to reach the equilibrium, which may exceed the time during which the studied biomolecules are stable. We propose here a kinetic model to analyze titration curves obtained prior to full equilibration of the system.
July 10, 2018: European Biophysics Journal: EBJ
Sagheer A Onaizi
Protein fouling is a serious problem in many food, pharmaceutical and household industries. In this work, the removal of rubisco protein fouling from cellulosic surfaces using a protease (subtilisin A) has been investigated experimentally and mathematically. The cellulosic surfaces were prepared using self-assembled monolayers (SAMs) on a surface plasmon resonance biosensor (chip) surface after conjugating cellulose to α-lipoic acid. Rubisco adsorption on the prepared cellulosic SAMs was found to be irreversible, leading to the creation of a tough protein fouling...
July 9, 2018: European Biophysics Journal: EBJ
Khair Bux, Syed Abid Ali, Syed Tarique Moin
Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein...
July 4, 2018: European Biophysics Journal: EBJ
Abbas Yousefpour, Sepideh Amjad-Iranagh, Fatemeh Goharpey, Hamid Modarress
In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane...
July 3, 2018: European Biophysics Journal: EBJ
André Matagne, Christopher M Dobson
This tribute to the life and work of Nico van Nuland highlights his interdisciplinary application of biophysical methods, especially high-resolution NMR spectroscopy and molecular dynamics simulations, to improve significantly our understanding of the structure, stability, dynamics and folding of proteins, and particularly of protein-protein interactions. His work as a colleague, team leader and collaborator highlights the importance of building scientific communities and of maintaining them, and of educating new generations of scientists...
September 2018: European Biophysics Journal: EBJ
Konstantin A Okotrub, Nikolay V Surovtsev
We applied a Raman spectroscopy approach to investigate the effect of a cryoprotectant on the redox state of cytochromes on freezing yeast cells. The redox activity of cytochromes was studied using time-resolved photobleaching of the resonance Raman lines. It is found that ice formation causes a drastic change in the redox state of cytochromes in cells frozen without cryoprotectant, whereas in the presence of glycerol the effects of ice formation are more gradual. The photobleaching rate of cells frozen in glycerol solution shows a gradual slowing with temperature decrease and an abrupt slowdown below - 48 °C...
September 2018: European Biophysics Journal: EBJ
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