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BMC Biophysics

Asli Yildirim, Nathalie Brenner, Robert Sutherland, Michael Feig
Background: Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied extensively, very little is known how cellular crowding affects the conformational sampling of nucleic acids. Results: The effect of protein crowding on the conformational preferences of DNA (deoxyribonucleic acid) is described from fully atomistic molecular dynamics simulations of systems containing a DNA dodecamer surrounded by protein crowders...
2018: BMC Biophysics
Christian V Hansen, Hans J Schroll, Daniel Wüstner
Background: Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of such processes heavily relies on quantitative fluorescence imaging of suitably tagged proteins. Fluorescence loss in photobleaching (FLIP) is particularly well-suited to study the dynamics of protein aggregation in cellular models of Chorea Huntington and other polyQ diseases, as FLIP gives access to the full spatio-temporal profile of intensity changes in the cell geometry...
2018: BMC Biophysics
Paulina Adamczewski, Valeria Tsoukanova
Background: Propensity of phenylalanine (Phe) for nonpolar environments drives its intercalation into phospholipid membranes, which has been implicated in metabolic and neurological disorders. The knowledge of Phe intercalation parameters can be instrumental in understanding various membrane processes triggered by interactions with Phe, in particular the early events leading to the formation of nucleation/docking sites for the self-assembly of Phe amyloid fibrils at the membrane surface...
2018: BMC Biophysics
Giuseppe Chirico, Alexander Gansen, Sanford H Leuba, Ada L Olins, Donald E Olins, Jeremy C Smith, Katalin Tóth
Background: With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks. Methods: Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered...
2018: BMC Biophysics
Esin B Sözer, C Florencia Pocetti, P Thomas Vernier
Background: Applications of electric-field-induced permeabilization of cells range from cancer therapy to wastewater treatment. A unified understanding of the underlying mechanisms of membrane electropermeabilization, however, has not been achieved. Protocols are empirical, and models are descriptive rather than predictive, which hampers the optimization and expansion of electroporation-based technologies. A common feature of existing models is the assumption that the permeabilized membrane is passive, and that transport through it is entirely diffusive...
2018: BMC Biophysics
Pavel Montes de Oca Balderas, Horacio Montes de Oca Balderas
Background: Astrocytes were conceived for decades only as supporting cells of the brain. However, the observation of Ca2+ waves in astrocyte synctitia, their neurotransmitter receptor expression and gliotransmitter secretion suggested a role in information handling, conception that has some controversies. Synaptic Neuron-Astrocyte metabotropic communication mediated by Inositol tris-phosphate (SN-AmcIP3) is supported by different reports. However, some models contradict this idea and Ca2+ stores are 1000 ± 325 nm apart from the Postsynaptic Density in the Perisynaptic Astrocyte Projections (PAP's), suggesting that SN-AmcIP3 is extrasynaptic...
2018: BMC Biophysics
Ingrid M Weiss, Christina Muth, Robert Drumm, Helmut O K Kirchner
Background: The pathways of thermal instability of amino acids have been unknown. New mass spectrometric data allow unequivocal quantitative identification of the decomposition products. Results: Calorimetry, thermogravimetry and mass spectrometry were used to follow the thermal decomposition of the eight amino acids G, C, D, N, E, Q, R and H between 185 °C and 280 °C. Endothermic heats of decomposition between 72 and 151 kJ/mol are needed to form 12 to 70% volatile products...
2018: BMC Biophysics
Špela Zemljič Jokhadar, Urška Klančnik, Maja Grundner, Tjaša Švelc Kebe, Saša Vrhovec Hartman, Mirjana Liović, Jure Derganc
Background: Cell based carriers are increasingly recognized as a good system for cargo delivery to cells. One of the reasons is their biocompatibility and low toxicity compared to artificial systems. Giant plasma membrane vesicles (GPMV) derive from the cell plasma membrane. Thus they offer the closest approximation to it, which makes them good candidates for potential drug delivery systems. To evaluate the applicability of GPMVs as carriers, we analyzed their basic biophysical properties to test their robustness in the face of changeable physiological conditions, as well as their ability to translocate across the membrane into cells...
2018: BMC Biophysics
Lucas C Wheeler, Michael J Harms
Background: S100A5 is a calcium binding protein found in a small subset of amniote tissues. Little is known about the biological roles of S100A5, but it may be involved in inflammation and olfactory signaling. Previous work indicated that S100A5 displays antagonism between binding of Ca2+ and Cu2+ ions-one of the most commonly cited features of the protein. We set out to characterize the interplay between Ca2+ and Cu2+ binding by S100A5 using isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD), and analytical ultracentrifugation (AUC)...
2017: BMC Biophysics
Baosheng Ge, Xiaoyong Jiang, Yao Chen, Tingting Sun, Qiuxia Yang, Fang Huang
BACKGROUND: Proteins with low sequence identity but almost identical tertiary structure and function have been valuable to uncover the relationship between sequence, tertiary structure, folding mechanism and functions. Two homologous chemokines, CCL11 and CCL24, with low sequence identity but similar tertiary structure and function, provide an excellent model system for respective studies. RESULTS: The kinetics and thermodynamics of the two homologous chemokines were systematically characterized...
2017: BMC Biophysics
H Billur Engin, Daniel Carlin, Dexter Pratt, Hannah Carter
BACKGROUND: RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions...
2017: BMC Biophysics
Efrain H Pinzon, Daniel A Sierra, Miguel O Suarez, Sergio Orduz, Alvaro M Florez
BACKGROUND: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an in silico analysis using different experimental DNA shuffling scenarios...
2017: 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
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
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