Amyloid-like aggregates of a plant protein: a case of a sweet-tasting protein, monellin.
(25/2376)
We report here a novel case of amyloid-like aggregation of a plant protein. A sweet-tasting protein, monellin, experiences an irreversible heat denaturation at pH 2.5 and 85 degrees C. Addition of 100 mM NaCl couples this process with protein aggregation. The aggregates were structured as regular fibers with approximately 10 nm width and capable of binding to Congo red, similarly to well-known amyloid fibrils. The amyloid-like aggregation process was also successfully monitored with a calorimetric method. This work supports the universality of the amyloid-like aggregation, not restricted to some special categories of protein. (+info)
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.
(26/2376)
The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted. (+info)
Understanding beta-hairpin formation.
(27/2376)
The kinetics of formation of protein structural motifs (e.g., alpha-helices and beta-hairpins) can provide information about the early events in protein folding. A recent study has used fluorescence measurements to monitor the folding thermodynamics and kinetics of a 16-residue beta-hairpin. In the present paper, we obtain the free energy surface and conformations involved in the folding of an atomistic model for the beta-hairpin from multicanonical Monte Carlo simulations. The results suggest that folding proceeds by a collapse that is downhill in free energy, followed by rearrangement to form a structure with part of the hydrophobic cluster; the hairpin hydrogen bonds propagate outwards in both directions from the partial cluster. Such a folding mechanism differs from the published interpretation of the experimental results, which is based on a helix-coil-type phenomenological model. (+info)
Intrinsic beta-sheet propensities result from van der Waals interactions between side chains and the local backbone.
(28/2376)
The intrinsic secondary structure-forming propensities of the naturally occurring amino acids have been measured both experimentally in host-guest studies and statistically by examination of the protein structure databank. There has been significant progress in understanding the origins of intrinsic alpha-helical propensities, but a unifying theme for understanding intrinsic beta-sheet propensities has remained elusive. To this end, we modeled dipeptides by using a van der Waals energy function and derived Ramachandran plots for each of the amino acids. These data were used to determine the entropy and Helmholtz free energy of placing each amino acid in the beta-sheet region of phi-psi space. We quantitatively establish that the dominant cause of intrinsic beta-sheet propensity is the avoidance of steric clashes between an amino acid side chain and its local backbone. Standard implementations of coulombic and solvation effects are seen to be less important. (+info)
Association of ethanol with lipid membranes containing cholesterol, sphingomyelin and ganglioside: a titration calorimetry study.
(29/2376)
The association of ethanol at physiologically relevant concentrations with lipid bilayers of different lipid composition has been investigated by use of isothermal titration calorimetry (ITC). The liposomes examined were composed of combinations of lipids commonly found in neural cell membranes: dimyristoyl phosphatidylcholine (DMPC), ganglioside (GM(1)), sphingomyelin and cholesterol. The calorimetric results show that the interaction of ethanol with fluid lipid bilayers is endothermic and strongly dependent on the lipid composition of the liposomes. The data have been used to estimate partitioning coefficients for ethanol into the fluid lipid bilayer phase and the results are discussed in terms of the thermodynamics of partitioning. The presence of 10 mol% sphingomyelin or ganglioside in DMPC liposomes enhances the partitioning coefficient by a factor of 3. Correspondingly, cholesterol (30 mol%) reduces the partitioning coefficient by a factor of 3. This connection between lipid composition and partitioning coefficient correlates with in vivo observations. Comparison of the data with the molecular structure of the lipid molecules suggests that ethanol partitioning is highly sensitive to changes in the lipid backbone (glycerol or ceramide) while it appears much less sensitive to the nature of the head group. (+info)
Interaction mode specific reorganization of gel phase monoglyceride bilayers by beta-lactoglobulin.
(30/2376)
The interaction between beta-lactoglobulin and sonicated aqueous dispersions of the gel phase forming monoglyceride monostearoylglycerol were studied using isothermal titration calorimetry, direct binding experiments, differential scanning calorimetry, leakage of a fluorescent dye and solid-state (31)P- and (2)H-NMR. In the absence of a charged amphiphile, monostearoylglycerol forms a precipitate. Under these conditions, no interaction with beta-lactoglobulin was observed. In the presence of the negatively charged amphiphile dicetylphosphate, the gel phase monostearoylglycerol formed stable and closed, probably unilamellar, vesicles with an average diameter of 465 nm. beta-Lactoglobulin interacts with these bilayer structures at pH 4, where the protein is positively charged, as well as at pH 7 where the protein is negatively charged. Under both conditions of pH, the binding affinity of beta-lactoglobulin is in the micromolar range as observed with ITC and the direct binding assay. At pH 4, two binding modes were found, one of which is determined with ITC while the direct binding assay determines the net result of both. The first binding mode is observed with ITC and is characterized by a large binding enthalpy, a decreased enthalpy of the MSG L(beta) to L(alpha) phase transition and leakage of a fluorescent dye. These characteristics are explained by a beta-lactoglobulin induced partial L(beta) to coagel phase transition that results from a specific electrostatic interaction between the protein and the charged amphiphile. This explanation is confirmed by solid-state (2)H-NMR using 1-monostearoylglycerol with a fully deuterated acyl chain. Upon interaction with beta-lactoglobulin, the isotropic signal in the (2)H-NMR spectrum of the monostearoylglycerol-dicetylphosphate mixture partially transforms into a broad anisotropic signal which could be assigned to coagel formation. The second binding mode probably results from an aspecific electrostatic attraction between the negatively charged bilayer and the positively charged protein and causes the precipitation of the dispersion. At pH 7, only the first binding mode is observed. (+info)
Ice-binding surface of fish type III antifreeze.
(31/2376)
We employed computational techniques, including molecular docking, energy minimization, and molecular dynamics simulation, to investigate the ice-binding surface of fish type III antifreeze protein (AFP). The putative ice-binding site was previously identified by mutagenesis, structural analysis, and flatness evaluation. Using a high-resolution x-ray structure of fish type III AFP as a model, we calculated the ice-binding interaction energy of 11 surface patches chosen to cover the entire surface of the protein. These various surface patches exhibit small but significantly different ice-binding interaction energies. For both the prism ice plane and an "ice" plane in which water O atoms are randomly positioned, our calculations show that a surface patch containing 14 residues (L19, V20, T18, S42, V41, Q9, P12, A16, M21, T15, Q44, I13, N14, K61) has the most favorable interaction energy and corresponds to the previously identified ice-binding site of type III AFP. Although in general agreement with the earlier studies, our results also suggest that the ice-binding site may be larger than the previously identified "core" cluster that includes mostly hydrophilic residues. The enlargement mainly results from the inclusion of peripheral hydrophobic residues and K61. (+info)
The maximal affinity of ligands.
(32/2376)
We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of approximately -1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin-avidin. (+info)