Intrinsic Volumetric Properties of Trialanine Isomers in Aqueous Solution

Mitra, Lally; Oleinikova, Alla; Winter, Roland

doi:10.1002/cphc.200800553

Cited by 8 publications

(14 citation statements)

References 38 publications

(9 reference statements)

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“…2. Similarly to the experimental studies, 11 V app increases upon heating indicating positive apparent thermal expansion coefficient of peptides. The contribution DV to the apparent peptide volume V app accounts for the difference between the water densities in the hydration shell and in bulk and increases upon heating faster than V app .…”

Section: Resultssupporting

confidence: 75%

“…The advantage of this approach is that it can be combined with the experimental measurements of the apparent properties of biomolecules. 11 There are three main factors determining the effect of a surface on water properties: the missing neighbor effect, direct surface-water interactions and the unavoidable rearrangement of hydrogen bonds near any boundary. The importance of these factors strongly depends on the thermodynamic state of water and on the character of the surface-water interaction.…”

Section: Introductionmentioning

confidence: 99%

“…Hydration water was found to make a large or even a major contribution to the apparent thermal expansion coefficient of biomolecules in water. [9][10][11] In the case of relatively hydrophobic peptides, such as the Ab 42 peptide and the elastin-like peptide, the intrinsic negative thermal expansion coefficient a p of peptides was completely masked by a huge positive thermal expansivity of hydration water, resulting in the positive values of the apparent thermal expansion coefficients of peptides. For a small polar Ab 16-22 peptide, a positive a p was found.…”

Section: Introductionmentioning

confidence: 99%

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Volumetric properties of human islet amyloid polypeptide in liquid water

Brovchenko

Andrews

Oleinikova

2010

Phys. Chem. Chem. Phys.

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The volumetric properties of human islet amyloid polypeptide (hIAPP) in water were studied in a wide temperature range by computer simulations. The intrinsic density rho(p) and the intrinsic thermal expansion coefficient alpha(p) of hIAPP were evaluated by taking into account the difference between the volumetric properties of hydration and bulk water. The density of hydration water rho(h) was found to decrease almost linearly with temperature upon heating and its thermal expansion coefficient was found to be notably higher than that of bulk water. The peptide surface exposed to water is more hydrophobic and its rho(h) is smaller in conformation with a larger number of intrapeptide hydrogen bonds. The two hIAPP peptides studied (with and without disulfide bridge) show negative alpha(p), which is close to zero at 250 K and decreases to approximately -1.5 x 10(-3) K(-1) upon heating to 450 K. The analysis of various structural properties of peptides shows a correlation between the intrinsic peptide volumes and the number of intrapeptide hydrogen bonds. The obtained negative values of alpha(p) can be attributed to the shrinkage of the inner voids of the peptides upon heating.

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Section: Resultssupporting

confidence: 75%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Volumetric properties of human islet amyloid polypeptide in liquid water

Brovchenko

Andrews

Oleinikova

2010

Phys. Chem. Chem. Phys.

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“…At 25 °C (and somewhat lower pH values) the evaluated number of monomers is in the range of 70−80. A typical volumetric thermal expansion of proteins in the range of 1 × 10 −3 /K (see, e.g., ref (33)), which was not taken into account for the evaluation at the two different temperatures, cannot explain the large difference of about 25%. Nevertheless, because the number of monomers was derived from extrapolating the SAXS curves to Q →0 and under the assumption that all the protein molecules build nanoparticles, these values should be interpreted with caution.…”

Section: Resultsmentioning

confidence: 99%

Amelogenin Nanoparticles in Suspension: Deviations from Spherical Shape and pH-Dependent Aggregation

et al. 2009

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It is well-known that amelogenin self-assembles to form nanoparticles, usually referred to as amelogenin nanospheres, despite the fact that not much is known about their actual shape in solution. In the current paper, we combine SAXS and DLS to study the three-dimensional shape of the recombinant amelogenins rP172 and rM179. Our results show for the first time that amelogenins build oblate nanoparticles in suspension using experimental approaches that do not require the proteins to be in contact with a support material surface. The SAXS studies give evidence for the existence of isolated amelogenin nano-oblates with aspect ratios in the range of 0.45−0.5 at pH values higher than pH 7.2 and show an aggregation of these nano-oblates at lower pH values. The role of the observed oblate shape in the formation of chain-like structures at physiological conditions is discussed as a key factor in the biomineralization of dental enamel.

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“…They have all used nonunique protein volume definitions and/or decomposed the thermal expansion into different contributions, such as the “intrinsic,” “hydrational,” and/or “thermal” components, which introduces several additional subjective parameters. 17 , 43 − 45 …”

Section: Introductionmentioning

confidence: 99%

Infinitely Dilute Partial Molar Properties of Proteins from Computer Simulation

Ploetz

Smith

2014

J. Phys. Chem. B

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A detailed understanding of temperature and pressure effects on an infinitely dilute protein’s conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method’s feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.

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Intrinsic Volumetric Properties of Trialanine Isomers in Aqueous Solution

Cited by 8 publications

References 38 publications

Volumetric properties of human islet amyloid polypeptide in liquid water

Volumetric properties of human islet amyloid polypeptide in liquid water

Amelogenin Nanoparticles in Suspension: Deviations from Spherical Shape and pH-Dependent Aggregation

Infinitely Dilute Partial Molar Properties of Proteins from Computer Simulation

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