Dead-end street of protein folding: thermodynamic rationale of amyloid fibril formation

An increasing number of diseases, including Alzheimer's, have been found to be a result of the formation of amyloid aggregates that are practically independent of the original primary sequence of the protein(s). (Eakin, C. M.; Berman, A. J.; Miranker, A. D. Nat. Struct. Mol. Biol. 2006, 13, 202-208.) Consequently, the driving force of the transformation from original to disordered amyloid fold is expected to lie in the protein backbone, which is common to all proteins. (Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. O.; Riekel, C.; Grothe, R.; Eisenberg, D. Nature 2005, 435, 773-778. Wright, C. F.; Teichmann, S. A.; Clarke, J.; Dobson, C. M. Nature 2005, 438, 878-881.) However, the exact explanation for the existence of such a "dead-end" structure is still unknown. Using systematic first principle calculations on carefully selected but large enough systems modeling the protein backbone we show that the beta-pleated sheet structure, the building block of amyloid fibers, is the thermodynamically most stable supramolecular arrangement of all the possible peptide dimers and oligomers both in vacuum and in aqueous environments. Even in a crystalline state (periodical, tight peptide attechment), the beta-pleated sheet assembly remains the most stable superstructure. The present theoretical study provides a quantum-level explanation for why proteins can take the amyloid state when local structural preferences jeopardize the functional native global fold and why it is a beta-pleated sheetlike structure they prefer.     

Fast fluctuations in protein powders: The role of hydration

An elastic neutron scattering investigation of the molecular dynamics of hydrated lysozyme powders has been undertaken for different water contents h (g water/g Lysozyme). The dry sample exhibits a harmonic behaviour in the whole temperature range, while anharmonic motions arise on hydrated samples at a temperature T_d. Both T_d and the magnitude of the anharmonic motions are markedly hydration dependent. On increasing water content the crossing barrier entropy change increases, while the enthalpy change keeps constant. The estimated average rigidity of the protein structure decreases abruptly immediately below the onset of the enzymatic activation at around 0.2h.     

Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis

Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches.     

Changes in thermodynamic quantities upon contact of two solutes in solvent under isochoric and isobaric conditions

The changes in excess thermodynamic quantities upon the contact of two solutes immersed in a solvent are analyzed using the radial-symmetric and three-dimensional versions of the integral equation theory. A simple model mimicking a solute in water is employed. The solute-solute interaction energy is not included in the calculations. Under the isochoric condition, the solute contact always leads to a positive entropy change irrespective of the solute solvophobicity or solvophilicity. The energy change is negative for solvophobic solutes while it is positive for solvophilic ones. Under the isobaric condition, the contact of solvophobic solutes results in system-volume compression but that of solvophilic ones gives rise to expansion. Effects of the compression and expansion on the changes in enthalpy and entropy are enlarged with rising temperature. When the solute solvophobicity is sufficiently high, the entropy change (multiplied by the absolute temperature) can become negative due to the compression, except at low temperatures with the result of an even larger, negative enthalpy change. The expansion in the case of solvophilic solutes leads to a large, positive entropy change accompanied by an even larger, positive enthalpy change. The changes in enthalpy and entropy are strongly dependent on the temperature. However, the changes in enthalpy and entropy are largely cancelled out and the temperature dependency of the free-energy change is much weaker. The authors also discuss possible relevance to the enthalpy-entropy compensation experimentally known for a variety of physicochemical processes in aqueous solution such as protein folding.     

Insight into the role of hydration on protein dynamics

The potential energy surface of a protein is rough. This intrinsic energetic roughness affects diffusion, and hence the kinetics. The dynamics of a system undergoing Brownian motion on this surface in an implicit continuum solvent simulation can be tuned via the frictional drag or collision frequency to be comparable to that of experiments or explicit solvent simulations. We show that the kinetic rate constant for a local rotational isomerization in stochastic simulations with continuum solvent and a collision frequency of 2 ps(-1) is about 10(4) times faster than that in explicit water and experiments. A further increase in the collision frequency to 60 ps(-1) slows down the dynamics, but does not fully compensate for the lack of explicit water. We also show that the addition of explicit water does not only slow down the dynamics by increasing the frictional drag, but also increases the local energetic roughness of the energy landscape by as much as 1.0 kcal/mol.     

Inherent structure analysis of protein folding

An analysis in terms of the inherent structures (IS, local minima) of the multidimensional potential energy landscape is applied to proteins. Detailed calculations are performed for the 46 bead BLN model, which folds into a four-stranded beta-barrel. Enhanced sampling has allowed determination of 239 199 IS states, believed to encompass nearly all the compact, low-energy states, and of well-averaged thermodynamic quantities at low temperature. The density of states shows distinct lobes for compact and extended states, and entropic barriers for the collapse and local ordering transitions. A two-dimensional scatterplot or density of states clearly shows the multifunnel structure of the energy landscape. The anharmonic vibrational free energy is found to play a crucial role in protein folding. The problem of determining the folding transition in a multifunnel system is discussed, and novel indicators of folding are introduced. A particularly clear picture is obtained through the occupation probabilities, pi, of individual low-lying IS, which become finite below the collapse temperature; it is suggested that poor foldability corresponds to a large "misfolding interval" where the excited state pi>0 exceeds that of the native state p0.     

Understanding the role of the topology in protein folding by computational inverse folding experiments

Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical protein conformations can be obtained starting from simple geometric considerations. We generated a large data set of C-alpha traces made of 65 points, by computationally solving a backbone model that takes into account only topological features of the all-alpha proteins; then, we built corresponding tertiary structures, by using the sequences associated to the crystallographic structures of four small globular all-alpha proteins from PDB, and analysed them in terms of structural and energetic properties. In this way we obtained four poorly populated sets of structures that are reasonably similar to the conformational states typical of the experimental PDB structures. These results show that our computational approach can capture the native topology of all-alpha proteins; furthermore, it generates backbone folds without the influence of the side chains and uses the protein sequence to select a specific fold among the generated folds. This agrees with the recent view that the backbone plays an important role in the protein folding process and that the amino acid sequence chooses its own fold within a limited total number of folds.     

Theoretical investigation of changes in the thermodynamic properties of water in the region near an electrode upon the discharge of an hydroxonium ion

A method for investigating solutions in the region near an electrode has been developed in the framework of the Monte Carlo method. The energies of the reorganization of water upon the transfer of an electron to a hydroxonium ion from the unpolarized surface of an absolutely solid charged electrode in the range of surface charge densities from +0.056 to –0.640 C/m² and upon the reverse process have been calculated. The hydration energies of an H₃O⁺ cation and an H₃O^– radical in the region near an electrode have been calculated. The effective interactions of an ion and a nonpolar molecule with an electrode in a solution have been analyzed.Translated from Teoreticheskaya i Éksperimental/naya Khimiya, Vol. 26, No. 5, pp. 596–600, September–October, 1990.     

In silico analysis of the thermodynamic stability changes of psychrophilic and mesophilic alpha-amylases upon exhaustive single-site mutations

Identifying sequence modifications that distinguish psychrophilic from mesophilic proteins is important for designing enzymes with different thermodynamic stabilities and to understand the underlying mechanisms. The PoPMuSiC algorithm is used to introduce, in silico, all the single-site mutations in four mesophilic and one psychrophilic chloride-dependent alpha-amylases and to evaluate the changes in thermodynamic stability. The analysis of the distribution of the sequence positions that could be stabilized upon mutation shows a clear difference between the three domains of psychrophilic and mesophilic alpha-amylases. Most of the mutations stabilizing the psychrophilic enzyme are found in domains B and C, contrary to the mesophilic proteins where they are preferentially situated in the catalytic domain A. Moreover, the calculations show that the environment of some residues responsible for the activity of the psychrophilic protein has evolved to reinforce favorable interactions with these residues. In the second part, these results are exploited to propose rationally designed mutations that are predicted to confer to the psychrophilic enzyme mesophilic-like thermodynamic properties. Interestingly, most of the mutations found in domain C strengthen the interactions with domain A, in agreement with suggestions made on the basis of structural analyses. Although this study focuses on single-site mutations, the thermodynamic effects of the recommended mutations should be additive if the mutated residues are not close in space.     

Real value prediction of protein folding rate change upon point mutation

Prediction of protein folding rate change upon amino acid substitution is an important and challenging problem in protein folding kinetics and design. In this work, we have analyzed the relationship between amino acid properties and folding rate change upon mutation. Our analysis showed that the correlation is not significant with any of the studied properties in a dataset of 476 mutants. Further, we have classified the mutants based on their locations in different secondary structures and solvent accessibility. For each category, we have selected a specific combination of amino acid properties using genetic algorithm and developed a prediction scheme based on quadratic regression models for predicting the folding rate change upon mutation. Our results showed a 10-fold cross validation correlation of 0.72 between experimental and predicted change in protein folding rates. The correlation is 0.73, 0.65 and 0.79, respectively in strand, helix and coil segments. The method has been further tested with an extended dataset of 621 mutants and a blind dataset of 62 mutants, and we observed a good agreement with experiments. We have developed a web server for predicting the folding rate change upon mutation and it is available at .     

Solvent-induced forces in protein folding reflections on the protein folding problem

It is shown that the solvent induced forces on hydrophilic groups are the strongest ones. The relevance of this finding to protein folding is discussed.     

Bulk properties and hydration numbers of ammonium nitrate and ammonium chloride in solution: A structural and thermodynamic analysis

The apparent volumes of the salts in the systems H₂O-NH₄Cl (298 K) and H₂O-NH₄NO₃ (273 K, 298 K, and 323 K) are reproduced with an accuracy of 0.03–0.01 cm³/mol by the equation ? = ?⁰ + Aw ₂ ^0.5 + Bw ₂, where w ₂ is the salt content (mass fractions). The study shows that there is a correspondence between the critical (for determining the hydration number) structural parameters-the intrinsic volume of the electrolyte and the volume of water in ion hydration shells-and the limiting (at w ₂ = 1) partial molar volumes of the components. The hydration numbers at infinite dilution are 6.9 for NH₄Cl at 298 K and 9.1, 6.7, and 6.4 for NH₄NO₃ at 273 K, 298 K, and 323 K. The water volume in ion hydration shells decreases in the sequence: No ₃ ^? , Cl^?, and NH ₄ ⁺ . The hydration numbers decrease with increasing salt concentration. The study shows that within a simpler model ? = ?⁰ + aw ₂ ^0.5 , the hydration numbers are temperature independent.     

Theoretical analysis of systems of chelation chromatography upon irradiation

The changes that occur under conditions of irradiation in a chromatographic system were considered with the use of a mathematical model for eluents with a wide pH range at constant concentration of complexone. The effect of the concentration of complexone and the behavior of individual components of the mixture under separation were studied at constant pH. The character of the change in the concentrations and pH values in eluates was determined. Experimental data obtained earlier were interpreted on the basis of the above considerations.     

硝基甲苯异构体的液晶溶液热力学性质的色谱法研究

本文用气液色谱方法研究了o-, m-, p-硝基甲苯三种异构体在双(对己氧基苯甲酸)对苯二酚酯(PBH~xB)和双(对庚氧基苯甲酸)对苯二酚酯(PBH~pB)两种向列液晶固定液中无限稀薄条件下的活度系数, 进而求得了超额焓, 超额自由能和超额熵, 同时得到溶解焓和溶解熵, 并对结果进行了分析和讨论。