Intrinsic thermal expansivity and hydrational properties of amyloid peptide Aβ42 in liquid water

Thermal Lens Measurements of Thermal Expansivity in Thermosensitive Polymer Solutions

The weak absorption of a laser beam generates in a fluid an inhomogeneous refractive index profile acting as a negative lens. This self-effect on beam propagation, known as Thermal Lensing (TL), is extensively exploited in sensitive spectroscopic techniques, and in several all-optical methods for the assessment of thermo-optical properties of simple and complex fluids. Using the Lorentz-Lorenz equation, we show that the TL signal is directly proportional to the sample thermal expansivity α, a feature allowing minute density changes to be detected with high sensitivity in a tiny sample volume, using a simple optical scheme. We took advantage of this key result to investigate the compaction of PniPAM microgels occurring around their volume phase transition temperature, and the temperature-driven formation of poloxamer micelles. For both these different kinds of structural transitions, we observed a significant peak in the solute contribution to α, indicating a decrease in the overall solution density-rather counterintuitive evidence that can nevertheless be attributed to the dehydration of the polymer chains. Finally, we compare the novel method we propose with other techniques currently used to obtain specific volume changes.

Negative Thermal Expansion and Disorder-to-Order Collapse of an Intrinsically Disordered Protein under Marginally Denaturing Conditions

Recent work with intrinsically disordered proteins (IDPs) has projected a myriad of their survival instincts based mainly on the total charge content, the abundance of polar residues, and the paucity of hydrophobic amino acids. This work uses a plant IDP AtPP16-1 (Arabidopsis thaliana phloem protein class 16-1), whose solution NMR structure was determined by us recently, to show legitimate negative thermal expansion (NTE) of the native state. The thermal expansion continues to be negative even as the tertiary structure is perturbed by ultralow levels of urea up to 0.4 M. The NTE of these subdenatured states is called apparent NTE because they are prone to undergo conformational changes with temperature. Hydrodynamic shrinkage of the NTE IDP is also observed by dynamic light scattering (DLS) and NMR-measured global rotational correlation time (τ_c). The protein with denatured tertiary structure but otherwise preserved native-state secondary structure collapses to a dynamically rigid state. The data are mainly based on thermal coefficients of chemical shift and nuclear relaxation measured by heteronuclear NMR. The hydrodynamic shrinkage and collapse under marginally varying solvent compositions that may arise from unstable tertiary structure and dynamic disorder of chain segments across the backbone could be a generic property of IDPs.

Molecular Explanation for the Abnormal Flux of Material into a Hot Spot in Ester Monolayers

Langmuir monolayers of certain surfactants show a negative derivative of the surface pressure with respect to temperature. In these monolayers, a local temperature gradient leads to local yielding of the solid phase to a kinetically flowing liquid, so that the material flows toward the hotter regions that act as sinks. The accumulation of material leads to the formation of nonequilibrium multilamellar bubbles of different sizes. Here we investigate the molecular factors leading to such a peculiar behavior. First, we identify the required structural molecular moieties, and second we vary the composition of the subphase in order to analyze its influence. We conclude that esters appear to be unique in two key aspects: they form monolayers whose compression isotherms shift to lower areas as the temperature increases, and thus collapse into a hot spot; and they bind weakly to the aqueous subphase, i.e., water does not attach to the monolayer at the molecular level, but only supports it. Molecular simulations for a selected system confirm and help explain the observed behavior: surfactant molecules form a weak hydrogen bonding network, which is disrupted upon heating, and also the molecular tilting changes with temperature, leading to changes in the film density.

TMAO and urea in the hydration shell of the protein SNase

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures.

Structures and free energy landscapes of the A53T mutant-type α-synuclein protein and impact of A53T mutation on the structures of the wild-type α-synuclein protein with dynamics

The A53T genetic missense mutation of the wild-type α-synuclein (αS) protein was initially identified in Greek and Italian families with familial Parkinson's disease. Detailed understanding of the structures and the changes induced in the wild-type αS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson's disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type αS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in αS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type α-synuclein proteins in an aqueous solution environment. Results demonstrate that the β-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type αS protein in aqueous solution. The β-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-β component (NAC) and C-terminal regions show a decrease in β-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in α-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in β-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding β-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type αS disappear upon A53T mutation. The A53T mutant-type αS structures are thermodynamically more stable than those of the wild-type αS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type αS protein to aggregate in comparison to the wild-type αS protein is related to the increased β-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the β-sheet forming residues, which are reactive toward aggregation.

Molecular insights into the reversible formation of tau protein fibrils

We computationally and experimentally showed that tau protein fibrils can be formed at high temperature. When cooled, the fibrils dissociate back to monomers. Heparin promotes tau fibril formation and prevents its reversion. Our results revealed the physicochemical mechanism of reversible formation of tau fibrils.

Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study

Amyloid β-protein (Aβ) is central to the pathology of Alzheimer's disease. A 5% difference in the primary structure of the two predominant alloforms, Aβ(1-40) and Aβ(1-42), results in distinct assembly pathways and toxicity properties. Discrete molecular dynamics (DMD) studies of Aβ(1-40) and Aβ(1-42) assembly resulted in alloform-specific oligomer size distributions consistent with experimental findings. Here, a large ensemble of DMD-derived Aβ(1-40) and Aβ(1-42) monomers and dimers was subjected to fully atomistic molecular dynamics (MD) simulations using the OPLS-AA force field combined with two water models, SPCE and TIP3P. The resulting all-atom conformations were slightly larger, less compact, had similar turn and lower β-strand propensities than those predicted by DMD. Fully atomistic Aβ(1-40) and Aβ(1-42) monomers populated qualitatively similar free energy landscapes. In contrast, the free energy landscape of Aβ(1-42) dimers indicated a larger conformational variability in comparison to that of Aβ(1-40) dimers. Aβ(1-42) dimers were characterized by an increased flexibility in the N-terminal region D1-R5 and a larger solvent exposure of charged amino acids relative to Aβ(1-40) dimers. Of the three positively charged amino acids, R5 was the most and K16 the least involved in salt bridge formation. This result was independent of the water model, alloform, and assembly state. Overall, salt bridge propensities increased upon dimer formation. An exception was the salt bridge propensity of K28, which decreased upon formation of Aβ(1-42) dimers and was significantly lower than in Aβ(1-40) dimers. The potential relevance of the three positively charged amino acids in mediating the Aβ oligomer toxicity is discussed in the light of available experimental data.

Thermal stability of the hydrogen-bonded water network in the hydration shell of islet amyloid polypeptide

The effect of temperature on the connectivity of hydrogen bonds in the hydration shells of the islet amyloid polypeptides (IAPPs) is studied by means of computer simulations. The hydrogen-bonded network of hydration water homogeneously envelopes a peptide at low temperature and breaks into an ensemble of small clusters upon heating. This thermal break occurs via a percolation transition, which is not found to be sensitive to the chemical modifications of IAPP (IAPP with and without a disulfide bridge, human and rat IAPP). The radius of gyration of IAPP starts to increase when the hydration water network breaks upon heating. The fluctuations of the number of intra-peptide hydrogen bonds show negative correlation with the fraction of molecules in the largest cluster of hydration water. The thermal stability of the network of hydration water is enhanced upon increasing number of intra-peptide hydrogen bonds, which makes the peptide surface more hydrophobic. The thermal stabilities of the hydrogen-bonded water networks in the hydration shells of IAPPs and of several other biomolecules are found to be rather similar: the network breaks between 300 and 330 K, i.e., in the temperature interval where the biological activity of living organisms is maximal.

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE-rich solutions have stronger TFE-water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF(3) groups. The distribution of cluster sizes in solution supports these conclusions.

Demixing transition of the aqueous solution of amyloidogenic peptides: a REMD simulation study

The aggregation of amyloidogenic peptides in liquid water is studied at various temperatures by replica exchange molecular dynamics (REMD) simulations. The formation of a peptide aggregate upon decreasing the temperature reveals features typical for a first-order demixing phase transition, which is smeared out due to the finite size of the simulation box. Various properties of the ensemble of peptides were used to describe the temperature-induced demixing phase transition, which was found to occur at about 375 K. The hydrational and volumetric properties of the peptides and their aggregates are analyzed.