Pressure effect on the stability and the conformational dynamics of the D‐Galactose/D‐Glucose‐binding protein from <i>Escherichia coli</i>

Heřman, Petr; Staiano, Maria; Varriale, Antonio; Champdoré, Marcella de; Rossi, Mosè; Gryczyński, Zygmunt; D’Auria, Sabato

doi:10.1002/prot.20753

Cited by 8 publications

(9 citation statements)

References 34 publications

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“…The dependencies of the fluorescence characteristics of BADAN linked to the GGBP/H152C-Glc complex on the denaturant concentration are a sigmoidal curve and generally correspond to the denaturation curves of the GGBP/H152C holoform obtained based on intrinsic UV fluorescence data. This indicates a one-step unfolding of the GGBP/H152C complex with glucose, which is consistent with the literature data on the preferential stabilization of the C-terminal domain of the protein during the interaction of GGBP with glucose [39,[58][59][60][61].…”

Section: Unfolding Of Ggbp/h152c In Ligand-free and Ligand-bound Statessupporting

confidence: 92%

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

Fonin

Silonov

Antifeeva

et al. 2021

IJMS

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The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated “PICT” (planar intramolecular charge transfer state) and solvated “TICT” (twisted intramolecular charge transfer state) excited states. While “TICT” state can be formed both as a result of the “PICT” state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained.

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Section: Unfolding Of Ggbp/h152c In Ligand-free and Ligand-bound Statessupporting

confidence: 92%

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

Fonin

Silonov

Antifeeva

et al. 2021

IJMS

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“…Although much has been learned from simulation studies of thermal40–43 and chemical denaturation44–46 of proteins, simulations of pressure effects on proteins have been limited 47–55. Most notably, Paschek and Garcia have employed extensive replica exchange MD simulations to explore structure and stability of an α‐helical peptide56 and protein‐G fragment57 as well as of the 20 amino acid protein Trp‐cage 58.…”

Section: Introductionmentioning

confidence: 99%

Studying pressure denaturation of a protein by molecular dynamics simulations

et al. 2010

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Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies.

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“…In our previous work (12), we applied steady-state and time-resolved fluorescence spectroscopy to investigate the effects of moderate pressure (up to 2000 bar) on the structure and function of D-galactose/D-glucose binding protein (GGBP) from Escherichia coli, the primary receptor for a high-affinity transport complex of the two sugars and for chemotaxis toward glucose and galactose (13). This protein can be a good candidate for its use as an implantable biosensor for glucose determination, e.g.…”

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confidence: 96%

Pressure Affects the Structure and the Dynamics of thed-Galactose/d-Glucose-Binding Protein fromEscherichia coliby Perturbing the C-Terminal Domain of the Protein

et al. 2006

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The effect of the pressure on the structure and stability of the D-galactose/D-glucose binding protein from Escherichia coli in the absence (GGBP) and in the presence (GGBP/Glc) of glucose was studied by Fourier transform infrared (FT-IR) spectroscopy and molecular dynamic (MD) simulations. FT-IR spectroscopy experiments showed that the protein beta-structures are more resistant than alpha-helices structures to pressure value increases. In addition, the infrared data indicated that the binding of glucose stabilizes the protein structure against high pressure values, and the protein structure does not completely unfold up to pressure values close to 9000 bar. MD simulations allow a prediction of the most probable configuration of the protein, consistent with the increasing pressures on the two systems. The detailed analysis of the structures at molecular level confirms that, among secondary structures, alpha-helices are more sensitive than beta-structures to the destabilizing effect of high pressure and that glucose is able to preserve the structure of the protein in the complex. Moreover, the evidence of the different resistance of the two domains of this protein to high pressure is investigated and explained at a molecular level, indicating the importance of aromatic amino acid in protein stabilization.

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Pressure effect on the stability and the conformational dynamics of the D‐Galactose/D‐Glucose‐binding protein from Escherichia coli

Cited by 8 publications

References 34 publications

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

Studying pressure denaturation of a protein by molecular dynamics simulations

Pressure Affects the Structure and the Dynamics of thed-Galactose/d-Glucose-Binding Protein fromEscherichia coliby Perturbing the C-Terminal Domain of the Protein

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