Pressure–temperature phase diagrams of biomolecules

Smeller, László

doi:10.1016/s0167-4838(01)00332-6

Cited by 365 publications

(316 citation statements)

References 97 publications

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“…Such a reentrant phase diagram was observed not only in water soluble polymers [58][59][60] but also in biomacromolecules. 61 We have discussed the reason for the convexity of the phase diagram in previous work. 18,19 According to the Clapeyron-Clausius equation, the derivative of pressure with respect to temperature is…”

Section: Phase Behaviors Of Polymer Gels and Block Copolymer Aqueous mentioning

confidence: 97%

Small-angle neutron scattering on polymer gels: phase behavior, inhomogeneities and deformation mechanisms

Shibayama

2010

Polym J

198

139

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Recent developments in small-angle neutron scattering (SANS) investigations on polymer gels are reviewed by encompassing (i) volume phase transition and microphase separation, (ii) inhomogeneities in polymer gels, (iii) pressure dependence of hydrophobic interaction and (iv) structural characterization of super-tough gels. These developments owe much to the understanding of gel inhomogeneities and advances in the precision analyses of SANS, such as the contrast variation method coupled with singular value decomposition and the accurate evaluation of incoherent scattering intensity. As one of the fruitful outcomes, deformation mechanisms in various types of super-tough gels are elucidated.

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Section: Phase Behaviors Of Polymer Gels and Block Copolymer Aqueous mentioning

confidence: 97%

Small-angle neutron scattering on polymer gels: phase behavior, inhomogeneities and deformation mechanisms

Shibayama

2010

Polym J

198

139

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“…Biopolymers such as proteins remain stable and functional only in a limited pressure and temperature range [31,32,33]. Increasing temperature lead to structural changes differing from the native folded state.…”

Section: Introductionmentioning

confidence: 99%

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

Paschek

Nonn

Geiger

2005

Phys. Chem. Chem. Phys.

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We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between 260 K and 420 K at pressures of 1 bar, 3000 bar, and 4500 bar. The simulations reveal a hydrophobically collapsed state at low pressures and high temperatures. At 3000 bar and about 260 K and at 4500 bar and about 260 K, however, a transition to a swelled state is observed. The transition is driven by a smaller volume and a remarkably strong lower enthalpy of the swelled state, indicating a steep positive slope of the corresponding transition line. The swelling is stabilized almost completely by the energetically favorable state of water in the polymers hydrophobic first hydration shell at low temperatures. Although surprising, this finding is consistent with the observation of a positive heat capacity of hydrophobic solvation. Moreover, the slope and location of the observed swelling transition for the collapsed hydrophobic chain coincides remarkably well with the cold denaturation transition of proteins.

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“…For many proteins this state retains a relatively compact fold, at least near neutral pH and in the absence of denaturants, and is thus distinct from the unfolded states produced thermally or by chemical denaturants wherein both secondary and tertiary structures are largely lost (14)(15)(16)(17)(18)(19)(20). The pressure-denatured state is often labeled as the "unfolded state" (10), but here we reserve the term "unfolded" to describe a state with little tertiary or secondary structure.…”

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confidence: 99%

Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure

Lerch

López

Yang

et al. 2015

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

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Application of hydrostatic pressure shifts protein conformational equilibria in a direction to reduce the volume of the system. A current view is that the volume reduction is dominated by elimination of voids or cavities in the protein interior via cavity hydration, although an alternative mechanism wherein cavities are filled with protein side chains resulting from a structure relaxation has been suggested [López CJ, Yang Z, Altenbach C, Hubbell WL (2013) Proc Natl Acad Sci USA 110(46):E4306-E4315]. In the present study, mechanisms for elimination of cavities under high pressure are investigated in the L99A cavity mutant of T4 lysozyme and derivatives thereof using site-directed spin labeling, pressure-resolved double electronelectron resonance, and high-pressure circular dichroism spectroscopy. In the L99A mutant, the ground state is in equilibrium with an excited state of only ∼3% of the population in which the cavity is filled by a protein side chain [Bouvignies et al. (2011) Nature 477(7362):111-114]. The results of the present study show that in L99A the native ground state is the dominant conformation to pressures of 3 kbar, with cavity hydration apparently taking place in the range of 2-3 kbar. However, in the presence of additional mutations that lower the free energy of the excited state, pressure strongly populates the excited state, thereby eliminating the cavity with a native side chain rather than solvent. Thus, both cavity hydration and structure relaxation are mechanisms for cavity elimination under pressure, and which is dominant is determined by details of the energy landscape.DEER | EPR | conformational exchange | protein structural dynamics P roteins in solution exist in conformational equilibria that cannot be appreciated from structures observed in crystal lattices (1-5). The members of a folded conformational ensemble may have distinct functions and hence are of interest in elucidating mechanisms of protein action (5-7). The free-energy differences between the conformations can range from zero to a few kilocalories per mole; the higher free-energy states are referred to as "invisible" or "excited" (E) states owing to their low equilibrium populations. The structural transition between the native ground state (G) and the E state may involve rigid body motion of the peptide backbone (5, 8) or local unfolding (9).For a complete understanding of molecular mechanisms underlying function, characterization of functionally relevant conformational substates is required. However, in the case of E states, low populations and short lifetimes present a challenge for biophysical characterization. The elegant high-resolution NMR studies from Akasaka (10, 11) and coworkers suggest that application of hydrostatic pressure on the order of a few kilobars may solve this problem by reversibly populating functional E states, making them amenable for study by spectroscopic methods. For example, high-pressure NMR has been used to identify and characterize E states crucial to ligand binding in ubiquitin (12) and d...

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Pressure–temperature phase diagrams of biomolecules

Cited by 365 publications

References 97 publications

Small-angle neutron scattering on polymer gels: phase behavior, inhomogeneities and deformation mechanisms

Small-angle neutron scattering on polymer gels: phase behavior, inhomogeneities and deformation mechanisms

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure

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