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This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding.
All of the residues observed in Figure 5 and Figure 6 are obtained from the apo structure, 2HNP.pdb.
All of the residues observed in Figure 1a are obtained from the apo structure, indicating that the information for binding is already present in the unbound structure.
Images from the apo data set were indexed, integrated, and scaled with HKL2000 and with XDS for the complex.
Displacement of cis-protomer contacts from the apo state is rate-limiting for closure and ATP hydrolysis.
In this study, they show that a temperature-dependent kinetic barrier limits the conformational changes from the apo to the closed form of TRAP1.
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This study highlights the regional plasticity of the receptor and characterizes unique conformations spanning the entire receptor sequence stabilized by functionally selective ligands, all of which differ from the profile for the apo receptor.
The connecting loop between the G′ and G′′ strands spanning residues Thr586-Gly589 runs across the central region of the groove and the following sequence forms a short β-strand G′′ which inserts into N2 domain (Fig. 3A), making regions BbpAsp338 Gly355 and BbpThr365 Tyr387 deviate significantly from the apo-form (Fig. 3B).
The structures were determined by molecular replacement using one subunit from the apo-GlgE structure [Protein Data Bank (PDB) entry 3ZSS] as input to PHASER.
The absence of lactose from the apo-Gal3C samples (used to determine the crystal structures of apo-Gal3C and glycerol-bound Gal3C) was verified using NMR spectroscopy.
Prior to the MR calculation, the side chain of residue 170 was truncated to glycine, all water molecules were removed from the apo-GES-2 model, and the atomic displacement parameters were set to a uniform value of 20.0 Å.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com