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BMC Biophysics

Sara Carozza, Jamie Culkin, John van Noort
BACKGROUND: Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion...
2017: BMC Biophysics
Daniel Šmít, Coralie Fouquet, Mohamed Doulazmi, Frédéric Pincet, Alain Trembleau, Martin Zapotocky
BACKGROUND: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available...
2017: BMC Biophysics
Ranja Sarkar
BACKGROUND: Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state...
2017: BMC Biophysics
Clemens Sill, Ralf Biehl, Bernd Hoffmann, Aurel Radulescu, Marie-Sousai Appavou, Bela Farago, Rudolf Merkel, Dieter Richter
BACKGROUND: Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from open to close when Fe(3+) is present in the solution and can be bound. The binding mechanism was assumed to relate on thermal domain fluctuations of the cleft domains prior to binding. We used Small Angle Neutron Scattering and Neutron Spin Echo Spectroscopy to determine the lactoferrin structure and domain dynamics in solution...
2016: BMC Biophysics
Chien Y Lin, Jung Y Huang, Leu-Wei Lo
BACKGROUND: The first step in many cellular signaling processes occurs at various types of receptors in the plasma membrane. Membrane cholesterol can alter these signaling pathways of living cells. However, the process in which the interaction of activated receptors is modulated by cholesterol remains unclear. METHODS: In this study, we measured single-molecule optical trajectories of epidermal growth factor receptors moving in the plasma membranes of two cancerous cell lines and one normal endothelial cell line...
2016: BMC Biophysics
Yareni A Ayala, Bruno Pontes, Diney S Ether, Luis B Pires, Glauber R Araujo, Susana Frases, Luciana F Romão, Marcos Farina, Vivaldo Moura-Neto, Nathan B Viana, H Moysés Nussenzveig
BACKGROUND: The viscoelastic properties of cells have been investigated by a variety of techniques. However, the experimental data reported in literature for viscoelastic moduli differ by up to three orders of magnitude. This has been attributed to differences in techniques and models for cell response as well as to the natural variability of cells. RESULTS: In this work we develop and apply a new methodology based on optical tweezers to investigate the rheological behavior of fibroblasts, neurons and astrocytes in the frequency range from 1Hz to 35Hz, determining the storage and loss moduli of their membrane-cortex complex...
2016: BMC Biophysics
Philipp Kynast, Philippe Derreumaux, Birgit Strodel
BACKGROUND: Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature. METHODS: In this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field...
2016: BMC Biophysics
Julia Simundza
The editors of BMC Biophysics would like to thank all our reviewers who have contributed to the journal in Volume 8 (2015).
2015: BMC Biophysics
Christopher H Bohrer, Elijah Roberts
BACKGROUND: Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiation and elongation are inhibited by the buildup of positive supercoiling. It has therefore been proposed that intermittent binding of gyrase plays a role in transcriptional bursting. Considering that transcription is one of the most fundamental cellular processes, it is desirable to be able to account for the buildup and release of positive supercoiling in models of transcription...
2015: BMC Biophysics
Jia Bai, Zeting Zhang, Maili Liu, Conggang Li
BACKGROUND: The pathological hallmark of Parkinson's disease is the deposition of cytoplasmic neuronal inclusions termed Lewy bodies. The major component of Lewy bodies is amyloid fibrils of α-synuclein. To investigate what causes α-synuclein aggregation is essential to understand its pathological roles in Parkinson's disease. Various metal ions, including iron and copper, have been implicated in the pathogenesis of Parkinson's disease. Divalent metal ions can regulate α-synuclein fibrillation rate, however, few studies have been performed to investigate how trivalent metal ions interact with α-synuclein and their effect on α-synuclein fibrillation...
2015: BMC Biophysics
Aarón Ayllón Benítez, José Ginés Hernández Cifre, Francisco Guillermo Díaz Baños, José García de la Torre
BACKGROUND: The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain...
2015: BMC Biophysics
Elfriede Friedmann
BACKGROUND: We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which requires a substantial knowledge in mathematical theory. Using our new developed analytical and numerical techniques together with modern experiments, we analyze and quantify various types of diffusive effects in intra- and inter-cellular signaling. The complexity of these models necessitates suitable numerical methods to perform the simulations precisely and within an acceptable period of time...
2015: BMC Biophysics
Jorine M Eeftens, Jaco van der Torre, Daniel R Burnham, Cees Dekker
BACKGROUND: Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer that is anchored between a glass surface and a magnetic bead. Whereas the relevant force regime for many biological processes is above 20pN, problems arise at these higher forces, since the molecule of interest can detach from the attachment points at the surface or the bead...
2015: BMC Biophysics
Ramiro Magno, Verônica A Grieneisen, Athanasius Fm Marée
BACKGROUND: The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and attach to substrates. The acquired shape of cells and tissues is a consequence of (i) internal cytoskeletal processes, such as actin polymerisation and cortical myosin contraction, (ii) adhesion molecules within the cell membrane that interact with substrates and neighbouring cells, and (iii) processes that regulate cell volume...
2015: BMC Biophysics
Wenxiao Pan, Michael Daily, Nathan A Baker
BACKGROUND: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. METHODS: We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries...
2015: BMC Biophysics
Phuong H Nguyen, Anna M Popova, Kálmán Hideg, Peter Z Qin
BACKGROUND: Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-directed spin labeling and paramagnetic NMR. Among spin labels developed, the class of rigid labels have limited or no independent motions between the radical bearing moiety and the target, and afford a number of advantages in measuring distances and monitoring local dynamics within the parent bio-molecule...
2015: BMC Biophysics
Christoph Roethlein, Markus S Miettinen, Zoya Ignatova
BACKGROUND: Time-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions...
2015: BMC Biophysics
Richard P Sear, Ignacio Pagonabarraga, Andrew Flaus
The cell contains highly dynamic structures exploiting physical principles of self-organisation at the mesoscale (100 nm to 10 μm). Examples include non-membrane bound cytoplasmic bodies, cytoskeleton-based motor networks and multi-scale chromatin organisation. The challenges of mesoscale self-organisation were discussed at a CECAM workshop in July 2014. Biologists need approaches to observe highly dynamic, low affinity, low specificity associations and to perturb single structures, while biological physicists and biomathematicians need to work closely with biologists to build and validate quantitative models...
2015: BMC Biophysics
Catherine J Potenski
The editors of BMC Biophysics would like to thank all our reviewers who have contributed to the journal in Volume 7 (2014).
2015: BMC Biophysics
Hui Ye, Austen Curcuru
BACKGROUND: Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged...
2015: BMC Biophysics
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