Top 3 Biorxiv Papers Today in Biophysics


1.998 Mikeys
#1. Sensitive Detection of Protein Binding to the Plasma Membrane with Dual-Color Z-Scan Fluorescence
Isaac Angert, Siddarth Reddy Karuka, Jared Hennen, Yan Chen, Joseph Peter Albanesi, Louis Mansky, Joachim Müller
Delicate and transitory protein engagement at the plasma membrane (PM) is crucial to a broad range of cellular functions including cell motility, signal transduction, and virus replication. Here we describe a dual color (DC) extension of the fluorescence z-scan technique which has proven successful for quantification of peripheral membrane protein binding to the PM in living cells. We demonstrate that the co-expression of a second distinctly colored fluorescent protein provides a soluble reference species, which delineates the extent of the cell cytoplasm and lowers the detection threshold of z-scan PM binding measurements by an order of magnitude. DC z-scan generates an intensity profile for each detection channel that contains information on the axial distribution of the peripheral membrane and reference protein. Fit models for DC z-scan are developed and verified using simple model systems. Next, we apply the quantitative DC z-scan technique to investigate the binding of two peripheral membrane protein systems for which...
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Sample Sizes : [500]
Authors: 7
Total Words: 11430
Unqiue Words: 2757

1.997 Mikeys
#2. A novel function of M. tuberculosis chaperonin paralog GroEL1 in copper homeostasis
MOHAMED YOUSUF ANSARI, SAKSHI DHINGRA BATRA, HINA OJHA, FNU ASHISH, JAYA S TYAGI, SHEKHAR C MANDE
Mycobacterial GroELs namely GroEL1 and GroEL2 belong to the family of molecular chaperones, chaperonins. Chaperonins in Escherichia coli are termed as GroEL and GroES which are encoded by essential genes and are involved in cellular protein folding. GroEL1 has a characteristic Histidine-rich C-terminus contrary to its essential paralog GroEL2 and E. coli GroEL which have hydrophobic (GGM) repeats. Since Histidine richness is likely to be involved in metal binding, in this study we have attempted to decipher the role of GroEL1 protein in chelating metals and the consequent role on M. tuberculosis physiology. Using isothermal titration calorimetry (ITC), we found that GroEL1 binds copper, nickel and cobalt, with the highest binding affinity to copper. Since copper is known to be toxic at higher concentration, we cultured Wild Type M. tuberculosis H37Rv, groEL1 knock-out and groEL1-complemented strain with increasing concentrations of copper. We found that M. tuberculosis groEL1 knock out strain is more sensitive to copper than the...
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biorxivpreprint: A novel function of M. tuberculosis chaperonin paralog GroEL1 in copper homeostasis https://t.co/SNwiknV9hz #bioRxiv
biorxiv_biophys: A novel function of M. tuberculosis chaperonin paralog GroEL1 in copper homeostasis https://t.co/jtw7MrnACX #biorxiv_biophys
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Authors: 6
Total Words: 11623
Unqiue Words: 3215

1.996 Mikeys
#3. Structural Interpretation of Hydrogen-Deuterium Exchange with Maximum-Entropy Simulation Reweighting
Richard T Bradshaw, Fabrizio Marinelli, José D Faraldo-Gómez, Lucy R Forrest
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules in native environments without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of measured HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post-hoc to the resulting ensemble, such that averaged peptide-deuteration levels, as predicted by an empirical model of a value called the protection factor, agree with target values within a given level of uncertainty. We evaluate this approach,...
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Authors: 4
Total Words: 12173
Unqiue Words: 3329

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