Pressure‐induced changes in the solution structure of the GB1 domain of protein G

Abstract

The solution structure of the GB1 domain of protein G at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy-minimised low-pressure structure using (1)H chemical shifts. Two separate changes can be characterised: a compression/distortion, which is linear with pressure; and a stabilisation of an alternative folded state. On application of pressure, linear chemical shift changes reveal that the backbone structure changes by about 0.2 A root mean square, and is compressed by about 1% overall. The alpha-helix compresses, particularly at the C-terminal end, and moves toward the beta-sheet, while the beta-sheet is twisted, with the corners closest to the alpha-helix curling up towards it. The largest changes in structure are along the second beta-strand, which becomes more twisted. This strand is where the protein binds to IgG. Curved chemical shift changes with pressure indicate that high pressure also populates an alternative structure with a distortion towards the C-terminal end of the helix, which is likely to be caused by insertion of a water molecule.

Simulating protein unfolding under pressure with a coarse-grained model

“…51 The experiments show a less distorted structure at a pressure which is probably less than that corresponding to our results at large values of ssm . According to the nuclear magnetic resonance experiments reported, 51 only one water molecule has been included into the hydrophobic core of the structure at 2 kbar. Probably, at higher pressures the larger structural fluctuations in the pressure unfolded state make it difficult to obtain relevant information about the structure present.…”

“…The folding of this protein at room pressure happens as a cooperative, two-state process, which has been proved both experimentally 47,48 and computationally. 49,50 There are also some structural results for this protein at relatively high pressures 51 (about 2 kbar), where the native structure is started to be affected by the injection of a water molecules inside one of its cavities.…”

Insights into Folate/FAD-dependent tRNA Methyltransferase Mechanism

“…Crystallography and NMR at high pressure revealed that compression of proteins is heterogeneous, involving local expansion, and that buried water molecules are the preferred sites of internal motion of proteins (26, 39 -41). Moreover, several structures of enzymes determined under high pressure revealed that their active sites and cavities in their immediate vicinity are particularly affected by hydrostatic pressure and that the necessary enlargement of the active site upon catalysis is favored by a contraction of these neighboring cavities (42)(43)(44)(45). In addition, spectroscopic studies performed under high pressure highlight the relative malleable nature of chromophore binding sites (24,28,46).…”

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

“…68 For the a priori determination of the forward and backward rates ∆G 1 and ∆G 2 , we ran independent equilibrium simulation runs for 100 ns of each protein using the same particle number and forcefields as well as the same electrostatics. Subsequently, we analyzed the H-bond kinetics using the GROMACS tool g_hbond for the forward and backward transition energies of the H-bonds between protein-protein and protein-solvent and the H-bond autocorrelation analysis of Luzar et al 57,58 In the main text and the supplementary material, the abbreviation RMSD Cα−Cα stands for the root-mean square deviation of peptide backbone conformations from the backbone of the corresponding native structure (see Figure 1 for the PDB-identification numbers and structures 39,41,47 ). We identified the folded state of the protein by a cutoff in the RMSD Cα−Cα lower than 0.3 nm to the native structure.…”