http://www.physmathcentral.com/ The latest research articles published by PhysMath Central 2010-03-05T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: Cellular oxygen sensing is fundamental to all mammalian cells to adequately respond to a shortage of oxygen by increasing the expression of genes that will ensure energy homeostasis. The transcription factor Hypoxia-Inducible-Factor-1 (HIF-1) is the key regulator of the response because it coordinates the expression of hypoxia inducible genes. The abundance and activity of HIF-1 are controlled through posttranslational modification by hydroxylases, the cellular oxygen sensors, of which the activity is oxygen dependent. Methods: Fluorescence resonance energy transfer (FRET) was established to determine the assembly of the HIF-1 complex and to study the interaction of the alpha-subunit of HIF-1 with the O2-sensing hydroxylase. New software was developed to improve the quality and reliability of FRET measurements. Results: FRET revealed close proximity between the HIF-1 subunits in multiple cells. Data obtained by sensitized FRET in this study were fully compatible with previous work using acceptor bleaching FRET. Interaction between the O2-sensing hydroxylase PHD1 and HIF-1alpha was demonstrated and revealed exclusive localization of O2-sensing in the nucleus. The new software FRET significantly improved the quality and speed of FRET measurements. Conclusion: FRET measurements do not only allow following the assembly of the HIF-1 complex under hypoxic conditions but can also provide important information about the process of O2-sensing and its localisation within a cell.MCS codes: 92C30, 92C05, 92C40 http://www.physmathcentral.com/1757-5036/3/5 Christoph Wotzlaw Silke Gneuss Rebecca Konietzny Joachim Fandrey PMC Biophysics 2010, 3:5 2010-03-05T00:00:00Z ${item.identifier} PMC Biophysics 1757-5036 3 5 2010-03-05T00:00:00Z PDF The voltage-dependent anion channel (VDAC, also known as mitochondrial porin) is the major transport channel mediating the transport of metabolites, including ATP, across the mitochondrial outer membrane. Biochemical data demonstrate the binding of the cytosolic protein hexokinase-I to VDAC, facilitating the direct access of hexokinase-I to the transported ATP. In human cells, three hVDAC isoforms have been identified. However, little is known on the distribution of these isoforms within the outer membrane of mitochondria and to what extent they colocalize with hexokinase-I. In this study we show that whereas hVDAC1 and hVDAC2 are localized predominantly within the same distinct domains in the outer membrane, hVDAC3 is mostly uniformly distributed over the surface of the mitochondrion. We used two-color stimulated emission depletion (STED) microscopy enabling a lateral resolution of ~40 nm to determine the detailed sub-mitochondrial distribution of the three hVDAC isoforms and hexokinase-I. Individual hVDAC and hexokinase-I clusters could thus be resolved which were concealed in the confocal images. Quantitative colocalization analysis of two-color STED images demonstrates that within the attained resolution, hexokinase-I and hVDAC3 exhibit a higher degree of colocalization than hexokinase-I with either hVDAC1 or hVDAC2. Furthermore, a substantial fraction of the mitochondria-bound hexokinase-I pool does not colocalize with any of the three hVDAC isoforms, suggesting a more complex interplay of these proteins than previously anticipated. This study demonstrates that two-color STED microscopy in conjunction with quantitative colocalization analysis is a powerful tool to study the complex distribution of membrane proteins in organelles such as mitochondria.PACS: 87.16.Tb, 87.85.Rs http://www.physmathcentral.com/1757-5036/3/4 Daniel Neumann Johanna Buckers Lars Kastrup Stefan Hell Stefan Jakobs PMC Biophysics 2010, 3:4 2010-03-05T00:00:00Z ${item.identifier} PMC Biophysics 1757-5036 3 4 2010-03-05T00:00:00Z PDF The mammalian cell nucleus contains a variety of organelles or nuclear bodies which contribute to key nuclear functions. Promyelocytic leukemia nuclear bodies (PML NBs) are involved in the regulation of apoptosis, antiviral responses, the DNA damage response and chromatin structure, but their precise biochemical function in these nuclear pathways is unknown. One strategy to tackle this problem is to assess the biophysical properties of the component parts of these macromolecular assemblies in living cells. In this study we determined PML NB assembly dynamics by live cell imaging, combined with mathematical modeling. For the first time, dynamics of PML body formation were measured in cells lacking endogenous PML. We show that all six human nuclear PML isoforms are able to form nuclear bodies in PML negative cells. All isoforms exhibit individual exchange rates at NBs in PML positive cells but PML I, II, III and IV are static at nuclear bodies in PML negative cells, suggesting that these isoforms require additional protein partners for efficient exchange. PML V turns over at PML NBs very slowly supporting the idea of a structural function for this isoform. We also demonstrate that SUMOylation of PML at Lysine positions K160 and/or K490 are required for nuclear body formation in vivo. We propose a model in which the isoform specific residence times of PML provide both, structural stability to function as a scaffold and flexibility to attract specific nuclear proteins for efficient biochemical reactions at the surface of nuclear bodies.MCS code: 92C37 http://www.physmathcentral.com/1757-5036/3/3 Peter Brand Thorsten Lenser Peter Hemmerich PMC Biophysics 2010, 3:3 2010-03-05T00:00:00Z ${item.identifier} PMC Biophysics 1757-5036 3 3 2010-03-05T00:00:00Z PDF Polymerization of actin into filaments can push membranes forming extensions like filopodia or lamellipodia, which are important during processes such as cell motility and phagocytosis. Similarly, small organelles or pathogens can be moved by actin polymerization. Such actin filaments can be arranged in different patterns and are usually hundreds of nanometers in length as revealed by various electron microscopy approaches. Much shorter actin filaments are involved in the motility of apicomplexan parasites. However, these short filaments have to date not been visualized in intact cells. Here, we investigated Plasmodium sporozoites, the motile forms of the malaria parasite that are transmitted by the mosquito, using cryogenic electron tomography. We detected filopodia-like extensions of the plasma membrane and observed filamentous structures in the supra-alveolar space underneath the plasma membrane. However, these filaments could not be unambiguously assigned as actin filaments. In silico simulations of EM data collection and tomographic reconstruction identify the limits in revealing the filaments due to their length, concentration and orientation.PACS Codes: 87.64.Ee http://www.physmathcentral.com/1757-5036/3/6 Mikhail Kudryashev Simone Lepper Wolfgang Baumeister Marek Cyrklaff Friedrich Frischknecht PMC Biophysics 2010, 3:6 2010-03-05T00:00:00Z ${item.identifier} PMC Biophysics 1757-5036 3 6 2010-03-05T00:00:00Z PDF Stochastic backgrounds or relic gravitons, if ever detected, will constitute a prima facie evidence of physical processes taking place during the earliest stages of the evolution of the plasma. The essentials of the stochastic backgrounds of relic gravitons are hereby introduced and reviewed. The pivotal observables customarily employed to infer the properties of the relic gravitons are discussed both in the framework of the ΛCDM paradigm as well as in neighboring contexts. The complementarity between experiments measuring the polarization of the Cosmic Microwave Background (such as, for instance, WMAP, Capmap, Quad, Cbi, just to mention a few) and wide band interferometers (e.g. Virgo, Ligo, Geo, Tama) is emphasized. While the analysis of the microwave sky strongly constrains the low-frequency tail of the relic graviton spectrum, wide-band detectors are sensitive to much higher frequencies where the spectral energy density depends chiefly upon the (poorly known) rate of post-inflationary expansion.PACS codes: 04.30.-w, 14.70.Kv, 04.80.Nn, 98.80.-k http://www.physmathcentral.com/1754-0410/4/1 Massimo Giovannini PMC Physics A 2010, 4:1 2010-02-19T00:00:00Z ${item.identifier} PMC Physics A 1754-0410 4 1 2010-02-19T00:00:00Z PDF The Debye-Hückel limiting law (DHL) has often been used to estimate rate constants of diffusion-controlled reactions under different ionic strengths. Two main approximations are adopted in DHL: one is that the solution of the linearized Poisson-Boltzmann equation for a spherical cavity is used to estimate the excess electrostatic free energy of a solution; the other is that details of electrostatic interactions of the solutes are neglected. This makes DHL applicable only at low ionic strengths and dilute solutions (very low substrate/solute concentrations). We show in this work that through numerical solution of the Poisson-Nernst-Planck equations, diffusion-reaction processes can be studied at a variety of conditions including realistically concentrated solutions, high ionic strength, and certainly with non-equilibrium charge distributions. Reaction rate coefficients for the acetylcholine-acetylcholinesterase system are predicted to strongly depend on both ionic strength and substrate concentration. In particular, they increase considerably with increase of substrate concentrations at a fixed ionic strength, which is open to experimental testing. This phenomenon is also verified on a simple model, and is expected to be general for electrostatically attracting enzyme-substrate systems.PACS Codes: 82.45.Tv, 87.15.VvMSC Codes: 92C30 http://www.physmathcentral.com/1757-5036/3/1 Benzhuo Lu J. Andrew McCammon PMC Biophysics 2010, 3:1 2010-01-18T00:00:00Z doi:10.1186/1757-5036-3-1 PMC Biophysics 1757-5036 3 1 2010-01-18T00:00:00Z XML Ca2+ binding proteins are essential for regulating the role of Ca2+ in cell signaling and maintaining Ca2+ homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca2+ binding proteins and are known to influence Ca2+ binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca2+ binding and protein stability using de novo designed Ca2+ binding proteins. The approach of de novo design was chosen to avoid the complications of cooperative binding and Ca2+-induced conformational change associated with natural proteins. We show that when the number of negatively charged coordination residues increased from 2 to 5 in a relatively restricted Ca2+-binding site, Ca2+ binding affinities increased by more than 3 orders of magnitude and metal selectivity for trivalent Ln3+ over divalent Ca2+ increased by more than 100-fold. Additionally, the thermal transition temperatures of the apo forms of the designed proteins decreased due to charge repulsion at the Ca2+ binding pocket. The thermal stability of the proteins was regained upon Ca2+ and Ln3+ binding to the designed Ca2+ binding pocket. We therefore observe a striking tradeoff between Ca2+/Ln3+ affinity and protein stability when the net charge of the coordination residues is varied. Our study has strong implications for understanding and predicting Ca2+-conferred thermal stabilization of natural Ca2+ binding proteins as well as for designing novel metalloproteins with tunable Ca2+ and Ln3+ binding affinity and selectivity.PACS codes: 05.10.-a http://www.physmathcentral.com/1757-5036/2/11 Anna Wilkins Maniccia Wei Yang Julian Johnson Shunyi Li Harianto Tjong Huan-Xiang Zhou Lev Shaket Jenny Yang PMC Biophysics 2009, 2:11 2009-12-21T00:00:00Z doi:10.1186/1757-5036-2-11 PMC Biophysics 1757-5036 2 11 2009-12-21T00:00:00Z XML We combine all the available experimental information on Bs mixing, including the very recent tagged analyses of Bs → J/Ψϕ by the CDF and DØ collaborations. We find that the phase of the Bs mixing amplitude deviates more than 3σ from the Standard Model prediction. While no single measurement has a 3σ significance yet, all the constraints show a remarkable agreement with the combined result. This is a first evidence of physics beyond the Standard Model. This result disfavours New Physics models with Minimal Flavour Violation with the same significance.PACS Codes: 12.15.Ff, 12.15.Hh, 14.40.Nb http://www.physmathcentral.com/1754-0410/3/6 Marcella Bona Marco Ciuchini Enrico Franco Vittorio Lubicz Guido Martinelli Fabrizio Parodi Maurizio Pierini Carlo Schiavi Luca Silvestrini Viola Sordini Achille Stocchi Vincenzo Vagnoni PMC Physics A 2009, 3:6 2009-12-18T00:00:00Z doi:10.1186/1754-0410-3-6 PMC Physics A 1754-0410 3 6 2009-12-18T00:00:00Z XML Absolute angle-differential cross-section data are presented for excitation of the 3p54s manifold in argon by electron impact. The investigation focuses on the near-threshold region, where previous studies have revealed persistent disparities between measurements and theoretical predictions. For the present experiment, the time-of-flight (TOF) technique is employed. This method allows for scattered electrons to be measured over a broad range of energies with a constant transmission, thereby eliminating a potential major source of error in relating relative intensities of elastic and inelastic transitions inherent to other experimental techniques. The present experimental data are compared to theoretical results obtained in relativistic distorted-wave and various R-matrix (close-coupling) approaches, as well as to other recently published experimental data.PACS Codes: 34.80.Dp http://www.physmathcentral.com/1754-0429/2/3 Subhendu Mondal Julian Lower Stephen Buckman Robert McEachran Gustavo Garcia Oleg Zatsarinny Klaus Bartschat PMC Physics B 2009, 2:3 2009-12-18T00:00:00Z doi:10.1186/1754-0429-2-3 PMC Physics B 1754-0429 2 3 2009-12-18T00:00:00Z XML Intrinsic noise is a common phenomenon in biochemical reaction networks and may affect the occurence and amplitude of sustained oscillations in the states of the network. To evaluate properties of such oscillations in the time domain, it is usually required to conduct long-term stochastic simulations, using for example the Gillespie algorithm. In this paper, we present a new method to compute the amplitude distribution of the oscillations without the need for long-term stochastic simulations. By the derivation of the method, we also gain insight into the structural features underlying the stochastic oscillations. The method is applicable to a wide class of non-linear stochastic differential equations that exhibit stochastic oscillations. The application is exemplified for the MAPK cascade, a fundamental element of several biochemical signalling pathways. This example shows that the proposed method can accurately predict the amplitude distribution for the stochastic oscillations even when using further computational approximations.PACS Codes: 87.10.Mn, 87.18.Tt, 87.18.VfMSC Codes: 92B05, 60G10, 65C30 http://www.physmathcentral.com/1757-5036/2/10 Moritz Lang Steffen Waldherr Frank Allgower PMC Biophysics 2009, 2:10 2009-11-17T00:00:00Z doi:10.1186/1757-5036-2-10 PMC Biophysics 1757-5036 2 10 2009-11-17T00:00:00Z XML