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European Biophysics Journal: EBJ

Marvin A Soriano-Ursúa, Martiniano Bello, Christian F Hernández-Martínez, Iván Santillán-Torres, Ruth Guerrero-Ramírez, José Correa-Basurto, José-Antonio Arias-Montaño, José G Trujillo-Ferrara
The design of beta2 adrenoceptor (β2 AR) agonists is attractive because of their wide-ranging applications in medicine, and the details of agonist interactions with β2 AR are interesting because it is considered a prototype for G-protein coupled receptors. Preclinical studies for agonist development have involved biological assays with guinea pigs due to a similar physiology to humans. Boron-containing Albuterol derivatives (BCADs) designed as bronchodilators have improved potency and efficacy compared with their boron-free precursor on guinea pig β2 ARs (gpβ2 ARs), and two of the BCADs (BR-AEA and boronterol) conserve these features on cells expressing human β2 ARs (hβ2 ARs)...
November 1, 2018: European Biophysics Journal: EBJ
Thomas Heimburg
No abstract text is available yet for this article.
October 5, 2018: 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
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
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...
October 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...
October 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...
October 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...
October 2018: European Biophysics Journal: EBJ
Haram Kim, Emre Brookes, Weiming Cao, Borries Demeler
Sedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture...
October 2018: European Biophysics Journal: EBJ
Tayler L Williams, Gary E Gorbet, Borries Demeler
Recent developments in the UltraScan-III software make it possible to model multi-speed analytical ultracentrifugation sedimentation velocity experiments using finite-element solutions of the Lamm equation. Using simulated data, we demonstrate here how these innovations can be used to enhance the resolution of sedimentation velocity experiments when compared to single-speed experiments. Using heterogeneous systems covering as much as five orders of magnitude in molar mass and fivefold in anisotropy, we compare results from runs performed at multiple speeds to those obtained from single-speed experiments, fitted individually and analyzed globally over multiple speeds, and quantify resolution for sample heterogeneous in size and anisotropy...
October 2018: European Biophysics Journal: EBJ
Courtney N Johnson, Gary E Gorbet, Heidi Ramsower, Julio Urquidi, Lorenzo Brancaleon, Borries Demeler
The new Beckman Coulter Optima AUC instrument, which features multi-wavelength detection that couples the hydrodynamic separation of colloidal mixtures to spectral deconvolution of interacting and non-interacting solutes present in a mixture, was used to analyze the composition of human serum albumin (HSA) bound to metallo-protoporphyrin. We present new methods implemented in UltraScan that permit Optima AUC-derived multi-wavelength data to be spectrally decomposed in the same fashion as has been made possible for the Cölfen detector earlier...
October 2018: European Biophysics Journal: EBJ
Andreas Hoffmann, Kerstin Grassl, Janine Gommert, Christian Schlesak, Alexander Bepperling
The accurate determination of protein concentration is an important though non-trivial task during the development of a biopharmaceutical. The fundamental prerequisite for this is the availability of an accurate extinction coefficient. Common approaches for the determination of an extinction coefficient for a given protein are either based on the theoretical prediction utilizing the amino acid sequence or the photometric determination combined with a measurement of absolute protein concentration. Here, we report on an improved SV-AUC based method utilizing an analytical ultracentrifuge equipped with absorbance and Rayleigh interference optics...
October 2018: European Biophysics Journal: EBJ
Jennifer M Crowther, Jane R Allison, Grant A Smolenski, Alison J Hodgkinson, Geoffrey B Jameson, Renwick C J Dobson
Milk components, such as proteins and lipids, have different physicochemical properties depending upon the mammalian species from which they come. Understanding the different responses of these milks to digestion, processing, and differences in their immunogenicity requires detailed knowledge of these physicochemical properties. Here we report on the oligomeric state of β-lactoglobulin from caprine milk, the most abundant protein present in the whey fraction. At pH 2.5 caprine β-lactoglobulin is predominantly monomeric, whereas bovine β-lactoglobulin exists in a monomer-dimer equilibrium at the same protein concentrations...
October 2018: European Biophysics Journal: EBJ
Gary E Gorbet, Subhashree Mohapatra, Borries Demeler
A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space-time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution's boundary conditions, and changes in the associated time-invariant noise...
October 2018: European Biophysics Journal: EBJ
Emre Brookes, Mattia Rocco
The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release...
October 2018: European Biophysics Journal: EBJ
Jennifer M K Wakefield, Richard B Gillis, Gary G Adams, Caitlin M A McQueen, Stephen E Harding
The heterogeneity and molecular weight of a chitosan of low molecular weight (molar mass) and low degree of acetylation (0.1) for potential use as a consolidant for decayed archaeological wood were examined by sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge before and after depolymerisation. Sedimentation velocity before depolymerisation revealed a uniform distribution of sedimentation coefficient with little concentration dependence. SEDFIT-MSTAR analysis revealed a weight average molecular weight Mw of (14...
October 2018: European Biophysics Journal: EBJ
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