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Trending Papers in biophysics

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2
Authors: Hansen, Simon, et al
Published: Nov 2017
Authors: Hansen, Simon, et al
Published: Nov 2017
Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.
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Daniel Bojar
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Daniel Bojar
216
From Paper: Multiple binding sites for resin-acid derivatives on the voltage-sensor domain of the Shaker potassium channel
Published: Nov 2020
From Paper: Multiple binding sites for resin-acid derivatives on the voltage-sensor domain of the Shaker potassium channel
Published: Nov 2020
  • Based on the concept of the equilibrium potential, it becomes clear what force in natural conditions provides movement ions through the channels. By the formula - i = γ⋅V -ionic current flowing through the channel is proportional to the potential on the membrane, but this formula is not takes into account the concentration gradient and equilibrium potential for and she. For example, at a potential of -95 mV, there will be no current through the K-channels, since this potential is equal to the potassium equilibrium potential, at a potential of +67 mV there will be no current through the Na-channels, at +123 mV - through Ca channels.
  • resin acids have been proposed to primarily bind in a pocket in the periphery of the channel, located between the lipid-facing extracellular ends of the transmembrane segments S3 and S4.
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Esosa Alimele Morgans
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Esosa Alimele Morgans
113
From Paper: Crystal structure of prototype foamy virus (PFV) protease-reverse transcriptase fusion (PR-RT) reveals conformational plasticity: implications for function
Published: Nov 2020
From Paper: Crystal structure of prototype foamy virus (PFV) protease-reverse transcriptase fusion (PR-RT) reveals conformational plasticity: implications for function
Published: Nov 2020
  • Significant spatial and conformational domain rearrangements are required for nucleic acid binding.
  • This offers structural insight into retroviral RT conformational maturation and architecture of immature enzymes.
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Esosa Alimele Morgans
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Esosa Alimele Morgans
220
From Paper: (PDF) The protein folding problem
Published: Jul 2017
From Paper: (PDF) The protein folding problem
Published: Jul 2017
  • A protein’s biological function is determined by its three-dimensional (3D) native structure, which is encoded by its amino acid sequence.
  • Proteins are essential to life, supporting practically all its functions. They are large complex molecules, made up of chains of amino acids, and what a protein does largely depends on its unique 3D structure. Many of the world’s greatest challenges, like developing treatments for diseases or finding enzymes that break down industrial waste, are fundamentally tied to proteins and the role they play. Figuring out what shapes proteins fold into is known as the “protein folding problem” - and has stood as a grand challenge in biology for the past 50 years.
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kusuma .
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236
Authors: David Bauer, Hiroaki Ishikawa, Kimberly Wemmer, Jane Kondev, Wallace F Marshall
Published: Nov 2020
Authors: David Bauer, Hiroaki Ishikawa, Kimberly Wemmer, Jane Kondev, Wallace F Marshall
Published: Nov 2020
  • Taken together all results show that biological noise exists at the level of subcellular structures, with a corresponding effect on cell function, and can provide new insights into the mechanisms of organelle size control.
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Esosa Alimele Morgans
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Esosa Alimele Morgans
7
Published: Aug 2015
Published: Aug 2015
There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide–wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide–wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide–wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.
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Brian Novak
11
Published: Apr 2010
Published: Apr 2010
SIMtoEXP is a software package designed to facilitate the comparison of biomembrane simulations with experimental X-ray and neutron scattering data. It has the following features: (1) Accepts number density profiles from simulations in a standard but flexible format. (2) Calculates the electron density ε(z) and neutron scattering length density ν(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., Fε[qz] and Fν[qz]). The resultant four functions are then displayed graphically. (3) Accepts experimental Fε(qz) and Fν(qz) data for graphical comparison with simulations. (4) Allows for lipids and other large molecules to be parsed into component groups by the user and calculates the component volumes following Petrache et al. (Biophys J 72:2237–2242, 1997). The software then calculates and displays the contributions of each component group as volume probability profiles, ρ(z), as well as the contributions of each component to ε(z) and ν(z).
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Brian Novak
11
Published: Aug 2017
Published: Aug 2017
Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillatoroffers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations. Building on the first-generation Drude polarizable force field for the dipalmitoylphosphatidylcholine 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecule, the present effort was undertaken to improve this initial model and expand the force field to a wider range of phospholipid molecules. New lipids parametrized include dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-snglycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), dipalmitoylphosphatidylethanolamine(DPPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers. A parametrization strategy based on a restrained ensemble−maximum entropy methodology was used to help accurately match the experimental NMR order parameters in the polar headgroup region. All the parameters were developed to be compatible with the remainder of the Drude polarizable force field, which includes water, ions, proteins, DNA, and selected carbohydrates.
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Brian Novak
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