Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions

Meersman, Filip; Dobson, Christopher M.; Heremans, Karel

doi:10.1039/b517761h

Cited by 147 publications

(123 citation statements)

References 51 publications

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“…One difference between effects of heat activation on germination by an HP of 150 MPa and nutrients is that there was essentially no effect of heat activation on 150-MPa germination by GerA, in contrast to an ϳ40% stimulation in L-valine germination rate via GerA by heat activation. However, since HP can cause conformational changes in proteins (53)(54)(55) in addition to triggering GR-dependent germination, an HP of 150 MPa could also activate GRs, with GerA being most responsive to activation by this HP. (iii) While the loss of GerD greatly reduces rates of GR-dependent germination, gerD spores required heat activation times similar to those of wild-type spores for maximal germination rates.…”

Section: Discussionmentioning

confidence: 99%

The Effects of Heat Activation on Bacillus Spore Germination, with Nutrients or under High Pressure, with or without Various Germination Proteins

Luu

Cruz-Mora

Setlow

et al. 2015

Appl Environ Microbiol

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bNutrient germination of spores of Bacillus species occurs through germinant receptors (GRs) in spores' inner membrane (IM) in a process stimulated by sublethal heat activation. Bacillus subtilis spores maximum germination rates via different GRs required different 75°C heat activation times: 15 min for L-valine germination via the GerA GR and 4 h for germination with the L-asparagine-glucose-fructose-K ؉ mixture via the GerB and GerK GRs, with GerK requiring the most heat activation. In some cases, optimal heat activation decreased nutrient concentrations for half-maximal germination rates. Germination of spores via various GRs by high pressure (HP) of 150 MPa exhibited heat activation requirements similar to those of nutrient germination, and the loss of the GerD protein, required for optimal GR function, did not eliminate heat activation requirements for maximal germination rates. These results are consistent with heat activation acting primarily on GRs. However, (i) heat activation had no effects on GR or GerD protein conformation, as probed by biotinylation by an external reagent; (ii) spores prepared at low and high temperatures that affect spores' IM properties exhibited large differences in heat activation requirements for nutrient germination; and (iii) spore germination by 550 MPa of HP was also affected by heat activation, but the effects were relatively GR independent. The last results are consistent with heat activation affecting spores' IM and only indirectly affecting GRs. The 150-and 550-MPa HP germinations of Bacillus amyloliquefaciens spores, a potential surrogate for Clostridium botulinum spores in HP treatments of foods, were also stimulated by heat activation. Spores of Bacillus species can remain dormant for long periods in the absence of suitable growth conditions (1, 2). However, if specific nutrients are sensed, spores can rapidly become metabolically active in the process of germination followed by outgrowth. The specific nutrients that trigger spore germination are termed germinants, and these molecules are sensed by germinant receptors (GRs) located in spores' inner membrane (IM). Bacillus subtilis spores have three functional GRs: GerA, which responds to L-alanine or L-valine alone, and GerB and GerK, which together are essential for germination with a mixture of L-asparagine, Dglucose, D-fructose, and K ϩ (termed AGFK), with all four components of the mixture required; neither GerB nor GerK alone triggers germination with any nutrient germinant (1, 3). There is also a variant of the GerB GR, termed GerB*, that responds to L-asparagine alone, although GerB* action can be stimulated by glucose via GerK (3). All GRs in B. subtilis spores appear to be located together in a small cluster in the IM termed the germinosome, and formation of this structure is dependent on the GerD protein, which is also in the IM (2, 4). Since gerD spores do not form a germinosome and exhibit extremely slow GR-dependent germination (4), germinosome formation may be essential for rapid GR-dependent germinatio...

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Section: Discussionmentioning

confidence: 99%

The Effects of Heat Activation on Bacillus Spore Germination, with Nutrients or under High Pressure, with or without Various Germination Proteins

Luu

Cruz-Mora

Setlow

et al. 2015

Appl Environ Microbiol

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“…Proteins can denaturate-unfolding their structure and losing their activity-as a consequence of changes in the environmental conditions. Experimental data show that for many proteins the native folded state is stable in a limited range of temperatures T and pressures P [3][4][5][6][7][8] and that partial folding is T modulated also in "intrinsically disordered proteins" [9]. By hypothesizing that proteins have only two different states, folded (f) and unfolded (u), and that the f⟷u process is reversible at any moment, Hawley proposed a theory [10] that predicts a close stability region (SR) with an elliptic shape in the T-P plane, consistent with the experimental data [11].…”

mentioning

confidence: 99%

Contribution of Water to Pressure and Cold Denaturation of Proteins

2015

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The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering. DOI: 10.1103/PhysRevLett.115.108101 PACS numbers: 87.15.Cc, 87.15.A-, 87.15.kr Water plays an essential role in driving the folding of a protein and in stabilizing the tertiary protein structure in its native state [1,2]. Proteins can denaturate-unfolding their structure and losing their activity-as a consequence of changes in the environmental conditions. Experimental data show that for many proteins the native folded state is stable in a limited range of temperatures T and pressures P [3][4][5][6][7][8] and that partial folding is T modulated also in "intrinsically disordered proteins" [9]. By hypothesizing that proteins have only two different states, folded (f) and unfolded (u), and that the f⟷u process is reversible at any moment, Hawley proposed a theory [10] that predicts a close stability region (SR) with an elliptic shape in the T-P plane, consistent with the experimental data [11].Cold and P denaturation of proteins have been related to the equilibrium properties of the hydration water [12][13][14][15][16][17][18][19][20][21][22][23]. However, the interpretations of the mechanism are still controversial [8,[24][25][26][27][28][29][30][31][32][33][34][35][36][37]. High-T denaturation is easily understood in terms of thermal fluctuations that disrupt the compact protein conformation: the open protein structure increases the entropy S minimizing the global Gibbs free energy G ≡ H − TS, where H is the total enthalpy. High-P unfolding can be explained by the loss of internal cavities in the folded states of proteins [36], while denaturation at negative P has been experimentally observed [38] and simulated [38,39] recently. Cold and P unfolding can be thermodynamically justified assuming an enthalpic gain of the solvent upon the denaturation process, without specifying the origin of this gain from molecular interactions [40]. Here, we propose a molecular-interactions model for proteins solvated by explicit water, based on the "many-body" water model [32,[41][42][43][44][45]. We demonstrate how the cold-and P-denaturation mechanisms can emerge as a competition between different free energy contributions coming from water, one from hydration water and another from bulk water. Moreover, we sh...

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“…15 High pressure is thought to change the protein conformation and force the penetration of water molecules into the protein interior, especially into cavities, leading to denaturing of the protein. 16 In this study, we used PCT, which uses alternating cycles of atmospheric and high pressure, up to tens of kpsi (1 kpsi = 6.895 MPa). 17 Recent studies have shown enhanced digestion speed using trypsin, chymotrypsin, and pepsin under pressure cycl-ing.…”

Section: Introductionmentioning

confidence: 99%

Pressure Cycling Technology-assisted Protein Digestion for Efficient Proteomic Analysis

Choi¹,

Lee²,

Kwon³

et al. 2011

Bulletin of the Korean Chemical Society

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In typical proteomic analysis, trypsin digestion is one of the most time-consuming steps. Conventional proteomic sample preparation methods use an overnight trypsin digestion method. In this study, we compared high-pressure cycling technology (PCT) during enzyme digestion for proteome analysis to the conventional method. We examined the effect of PCT on enzyme activity at temperatures of 25, 37, and 50 o C. Although a fast digestion (1 h) was used for the standard protein mixture analysis, the PCT-assisted method with urea showed better results for protein sequence coverage and the number of peptides identified compared with the conventional method. There was no significant difference between temperatures for PCT-assisted digestion; however, we selected PCT-assisted digestion with urea at 25 o C as an optimized method for fast enzyme digestion, based on peptide carbamylation at these conditions. The optimized method was used for stem cell proteome analysis. We identified 233, 264 and 137 proteins using the conventional method with urea at 37 o C for 16h, the PCT-assisted digestion with urea at 25 o C for 1 h, and the non-PCT-assisted digestion with urea at 25 o C for 1 h, respectively. A comparison of these results suggests that PCT enhanced the enzyme digestion by permitting better access to cleavage sites on the proteins.

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Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions

Cited by 147 publications

References 51 publications

The Effects of Heat Activation on Bacillus Spore Germination, with Nutrients or under High Pressure, with or without Various Germination Proteins

The Effects of Heat Activation on Bacillus Spore Germination, with Nutrients or under High Pressure, with or without Various Germination Proteins

Contribution of Water to Pressure and Cold Denaturation of Proteins

Pressure Cycling Technology-assisted Protein Digestion for Efficient Proteomic Analysis

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