Protein stability and dynamics in the pressure–temperature plane

Meersman, Filip; Smeller, László; Heremans, Karel

doi:10.1016/j.bbapap.2005.11.019

Cited by 90 publications

(72 citation statements)

References 88 publications

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“…3). This discrepancy may be due to the difference in temperature between the FTIR studies (25.4°C) and the TTET experiments (5°C), because it is commonly observed that reaction volumes for protein folding are strongly temperature dependent (2,3). The volume decrease upon formation of intramolecular helical hydrogen bonds is further in agreement with results on collagen folding, which showed a volume decrease upon triple helix formation (38).…”

Section: Effect Of Pressure On the Elementary Rate Constants For Helisupporting

confidence: 79%

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Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Neumaier

Büttner

Bachmann

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Volume changes associated with protein folding reactions contain valuable information about the folding mechanism and the nature of the transition state. However, meaningful interpretation of such data requires that overall volume changes be deconvoluted into individual contributions from different structural components. Here we focus on one type of structural element, the α-helix, and measure triplet-triplet energy transfer at high pressure to determine volume changes associated with the helix-coil transition. Our results reveal that the volume of a 21-amino-acid alanine-based peptide shrinks upon helix formation. Thus, helices, in contrast with native proteins, become more stable with increasing pressure, explaining the frequently observed helical structures in pressureunfolded proteins. Both helix folding and unfolding become slower with increasing pressure. per molecule) for removing one residue. Thus, addition or removal of a helical residue proceeds through a transitory high-energy state with a large volume, possibly due to the presence of unsatisfied hydrogen bonds, although steric effects may also contribute.protein stability | helix dynamics | protein dynamics U nderstanding the effect of pressure on protein stability and dynamics provides insight into fundamental principles and mechanisms of protein folding (1). For most proteins, increasing pressure shifts the folding equilibrium toward the unfolded state, which, according to Le Chatelier's principle, shows that the native state has a larger volume than the unfolded state (2-4). The origin of the volume increase upon folding has been discussed controversially for a long time. The major obstacle in the interpretation of volume changes is opposing contributions from different effects. Analysis of high-resolution X-ray structures suggested that formation of intramolecular hydrogen bonds and van der Waals interactions in the native state lead to a decrease in atomic volumes and thus to a decrease in protein volume upon folding (5). Further, water around hydrophobic groups has a larger volume than bulk water, which also leads to a decrease in volume upon burial of hydrophobic groups in the native protein (6). On the other hand, formation of ordered water structures around charged groups (7) and solvation of the peptide backbone decrease the water volume (6), which leads to a volume increase upon folding. Recent experimental results suggested that volume changes associated with transfer of groups from solvent to the protein interior upon folding are small and that the formation of void volumes in native proteins is the major origin of the volume increase upon folding (8).Volume changes associated with the formation of protein folding transition states are only poorly characterized. Highpressure stopped-flow experiments on tendamistat (9) and cold shock protein (10), as well as pressure-jump experiments on coldshock protein (10) and an ankyrin repeat domain (11), revealed that volumes of protein folding transition states are close to the volume of the native...

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Section: Effect Of Pressure On the Elementary Rate Constants For Helisupporting

confidence: 79%

“…For most proteins, increasing pressure shifts the folding equilibrium toward the unfolded state, which, according to Le Chatelier's principle, shows that the native state has a larger volume than the unfolded state (2)(3)(4). The origin of the volume increase upon folding has been discussed controversially for a long time.…”

mentioning

confidence: 99%

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Neumaier

Büttner

Bachmann

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…In this section, we summarize the main theoretical calculations given by Hawley [14] and reviewed by Smeller et al [15] and Meersman et al [16], predicting a close stability region in the P − T plane for proteins, consistent with experiments ( Fig. 1) [1,2,4,5,7,17].…”

Section: Protein Phase Diagrammentioning

confidence: 60%

Understanding the role of hydrogen bonds in water dynamics and protein stability

2011

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The mechanisms of cold and pressure denaturation of proteins are a matter of debate, but it is commonly accepted that water plays a fundamental role in the process. It has been proposed that the denaturation process is related to an increase of hydrogen bonds among hydration water molecules. Other theories suggest that the causes of denaturation are the density fluctuations of surface water, or the destabilization of hydrophobic contacts as a consequence of water molecule inclusions inside the protein, especially at high pressures. We review some theories that have been proposed to give insight into this problem, and we describe a coarse-grained model of water that compares well with experiments for proteins' hydration water. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations in an attempt to understand how the interplay of water cooperativity and interfacial hydrogen bonds affects protein stability.

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“…liptical shape in many cases. 14 The situation may be different in some occasions, depending specially on the values of the system compressibility, 15 but the ellipsoidal phase-diagram is considered rather general. The folded state occupies the internal area of the ellipse, and can be lost by increasing (or decreasing) temperature, pressure, or a combination of both.…”

Section: Introductionmentioning

confidence: 99%

Simulating protein unfolding under pressure with a coarse-grained model

Perezzan

Rey

2012

The Journal of Chemical Physics

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We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the formation of the native contacts. The pressure is taken into account in a qualitative, mean field approach, acting on the parameters describing the native stabilizing interactions. The model has been tested by simulating the thermodynamic and structural behavior of protein GB1 with a parallel tempering Monte Carlo algorithm. At low effective pressures, the model reproduces the standard two-state thermal transition between the native and denatured states. However, at large pressures a new state appears. Its structural characteristics have been analyzed, showing that it corresponds to a swollen version of the native structure. This swollen state is at equilibrium with the native state at low temperatures, but gradually transforms into the thermally denatured state as temperature is increased. Therefore, our model predicts a downhill transition between the swollen and the denatured states. The analysis of the model permits us to obtain a phase diagram for the pressure-temperature behavior of the simulated system, which is compatible with the known elliptical shape of this diagram for real proteins.

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Protein stability and dynamics in the pressure–temperature plane

Cited by 90 publications

References 88 publications

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Understanding the role of hydrogen bonds in water dynamics and protein stability

Simulating protein unfolding under pressure with a coarse-grained model

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