No Arabic abstract
Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimers and Parkinsons disease. In contrast to that of folded proteins, the thermodynamic stability of amyloid fibrils is not well understood: specifically the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using simulations of a coarse-grained protein model we delineate the enthalpic and entropic contributions dominating amyloid fibril elongation, predicting a characteristic temperature-dependent enthalpic signature. We confirm this thermodynamic signature by performing calorimetric experiments and a meta-analysis over published data. From these results, we can also elucidate the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability.
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to include these disordered species when discussing the thermodynamic equilibrium behavior of the system. Here, we initiate such a task by considering a mixture of monomeric proteins and the corresponding aggregates in the disordered form (micelles) and in the fibrillar form (amyloid fibrils). Starting with a model on the respective binding free energies for these species, we calculate their concentrations at thermal equilibrium. We then discuss how the incorporation of the disordered structure furthers our understanding on the various amyloid promoting factors observed empirically, and on the kinetics of fibrilization.
We study the two-filament insulin fibrils structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed structural model, while the elasticity measurement suggests that stretching the fibril may involve hydrogen bond breakage. Our work illustrates an attempt to correlate nanoscale measurements with microscopic information on the quaternary protein structure.
Elongation is a fundament process in amyloid fiber growth, which is normally characterized by a linear relationship between the fiber elongation rate and the monomer concentration. However, in high concentration regions, a sub-linear dependence was often observed, which could be explained by a universal saturation mechanism. In this paper, we modeled the saturated elongation process through a Michaelis-Menten like mechanism, which is constituted by two sub-steps -- unspecific association and dissociation of a monomer with the fibril end, and subsequent conformational change of the associated monomer to fit itself to the fibrillar structure. Typical saturation concentrations were found to be $7-70mu M$ for A$beta$40, $alpha$-synuclein and etc. Furthermore, by using a novel Hamiltonian formulation, analytical solutions valid for both weak and strong saturated conditions were constructed and applied to the fibrillation kinetics of $alpha$-synuclein and silk fibroin.
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA l_P~150 base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale l_D~10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than l_P, it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around 100 base pairs.
Shining a tightly-focused but low-powered laser beam on an absorber dispersed in a biological fluid gives rise to spectacular growth of dendritic patterns. These result from localized drying of the fluid because of efficient absorption and conduction of optical energy by the absorber. We have carried out experiments in several biologically relevant fluids and have analyzed patterns generated by different types of absorbers. We observe that the growth velocity of branches in the dendritic patterns can decrease below the value expected for natural drying.