Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aß by multiple endoproteolytic cleavages within the ß-sheet domain.

Accumulation of amyloid-beta (Aß), which is associated with Alzheimer's disease, can be caused by excess production or insufficient clearance. Because of its ß-sheet structure, fibrillar Aß is resistant to proteolysis, which would contribute to slow degradation of Aß plaques in vivo. Fibrillar Aß can be internalized by microglia, which are the scavenger cells of the brain, but the fibrils are degraded only slowly in microglial lysosomes. Cathepsin B is a lysosomal protease that has been shown to proteolyze fibrillar Aß. Tripeptidyl peptidase 1 (TPP1), a lysosomal serine protease, possesses endopeptidase activity and has been shown to cleave peptides between hydrophobic residues. Herein, we demonstrate that TPP1 is able to proteolyze fibrillar Aß efficiently. Mass spectrometry analysis of peptides released from fibrillar Aß digested with TPP1 reveals several endoproteolytic cleavages including some within ß-sheet regions that are important for fibril formation. Using molecular dynamics simulations, we demonstrate that these cleavages destabilize fibrillar ß-sheet structure. The demonstration that TPP1 can degrade fibrillar forms of Aß provides insight into the turnover of fibrillar Aß and may lead to new therapeutic methods to increase degradation of Aß plaques.

Free Energy Perturbation Approach for Accurate Crystalline Aqueous Solubility Predictions.

Early assessment of crystalline thermodynamic solubility continues to be elusive for drug discovery and development despite its critical importance, especially for the ever-increasing fraction of poorly soluble drug candidates. Here we present a detailed evaluation of a physics-based free energy perturbation (FEP+) approach for computing the thermodynamic aqueous solubility. The predictive power of this approach is assessed across diverse chemical spaces, spanning pharmaceutically relevant literature compounds and more complex AbbVie compounds. Our approach achieves predictive (RMSE = 0.86) and differentiating power (R2 = 0.69) and therefore provides notably improved correlations to experimental solubility compared to state-of-the-art machine learning approaches that utilize quantum mechanics-based descriptors. The importance of explicit considerations of crystalline packing in predicting solubility by the FEP+ approach is also highlighted in this study. Finally, we show how computed energetics, including hydration and sublimation free energies, can provide further insights into molecule design to feed the medicinal chemistry DMTA cycle.

Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.

Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies. In this chapter, we describe the application of the physics-based UNited RESidue (UNRES) force field developed in our laboratory to study protein aggregation, in both free simulations and simulations of aggregation propagation from an existing template (seed), and illustrate it with the examples of Aß-peptide aggregation and Aß-peptide-assisted aggregation of the peptides derived from the repeat domains of tau (TauRD).

Dependence of the Formation of Tau and Aß Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aß.

One of the hallmarks of Alzheimer's disease is the formation of aggregates of the tau protein, a process that can be facilitated by the presence of fibrils formed by the amyloid ß peptide (Aß). However, the mechanism that triggers tau aggregation is still a matter of debate. The effect of Aß40 fibrils on the aggregation of the repeat domain of tau (TauRD) is investigated here by employing coarse-grained molecular dynamics simulations. The results indicate that the repeat domain of tau has a high affinity for Aß40 fibrils, with the 261GSTENLK267 fragment of tau driving TauRD toward the 16KLVFFA21 fragment in Aß40. Monomeric Aß40, in which the 16KLVFFA21 fragment is rarely found in an extended conformation (as in the fibril), has a low affinity for the TauRD, indicating that the ability of Aß40 fibrils to bind to the TauRD depends on the 16KLVFFA21 fragment of Aß adopting an extended conformation.

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

The implementation of molecular dynamics with the united-residue (UNRES) force field is extended to treat multichain proteins. Constant temperature was maintained in the simulations with Berendsen or Langevin thermostats. The method was tested on three alpha-helical proteins (1G6U and GCN4-p1, each with two chains, and 1C94, with four chains). Simulations were carried out for both the isolated single chains and the multichain complexes. The proteins were folded by starting from the extended conformation with random initial velocities and with the chains parallel to each other. No symmetry constraints or structure information were included for the single chains or the multichain complexes. In the case of single-chain simulations, a high percentage of the trajectories (100% for 1G6U, 90% for GCN4-p1, and 80% for 1C94) converged to nativelike structures (assumed as the experimental structure of a monomer in the multichain complex), showing that, for the proteins studied in this work with the UNRES force field, the interactions between chains are not critical for stabilization of the individual chains. In the case of multichain simulations, the native structures of the 1G6U and GCN4-p1 complexes, but not that of 1C94, are predicted successfully. The association of the subunits does not follow a unique mechanism; the monomers were observed to fold both before and simultaneously with their association.

T cell receptor signaling can directly enhance the avidity of CD28 ligand binding.

T cell activation takes place in the context of a spatial and kinetic reorganization of cell surface proteins and signaling molecules at the contact site with an antigen presenting cell, termed the immunological synapse. Coordination of the activation, recruitment, and signaling from T cell receptor (TCR) in conjunction with adhesion and costimulatory receptors regulates both the initiation and duration of signaling that is required for T cell activation. The costimulatory receptor, CD28, is an essential signaling molecule that determines the quality and quantity of T cell immune responses. Although the functional consequences of CD28 engagement are well described, the molecular mechanisms that regulate CD28 function are largely unknown. Using a micropipet adhesion frequency assay, we show that TCR signaling enhances the direct binding between CD28 and its ligand, CD80. Although CD28 is expressed as a homodimer, soluble recombinant CD28 can only bind ligand monovalently. Our data suggest that the increase in CD28-CD28 binding is mediated through a change in CD28 valency. Molecular dynamic simulations and in vitro mutagenesis indicate that mutations at the base of the CD28 homodimer interface, distal to the ligand-binding site, can induce a change in the orientation of the dimer that allows for bivalent ligand binding. When expressed in T cells, this mutation allows for high avidity CD28-CD80 interactions without TCR signaling. Molecular dynamic simulations also suggest that wild type CD28 can stably adopt a bivalent conformation. These results support a model whereby inside-out signaling from the TCR can enhance CD28 ligand interactions by inducing a change in the CD28 dimer interface to allow for bivalent ligand binding and ultimately the transduction of CD28 costimulatory signals that are required for T cell activation.

A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the ß amyloid peptide (Aß(1-28)).

The ß amyloid (Aß) peptide aggregates to form ß-rich structures that are known to trigger Alzheimer's disease. Experiments suggest that an α-helical intermediate precedes the formation of these aggregates. However, a description at the molecular level of the α-to-ß transition has not been obtained. Because it has been proposed that the transition might be initiated in the amino-terminal region of Aß, we studied the aggregation of the 28-residue amino-terminal fragment of Aß (Aß(1-28)) using molecular dynamics and a coarse-grained force field. Simulations starting from extended and helical conformations showed that oligomerization is initiated by the formation of intermolecular ß-sheets between the residues in the N-terminal regions. In simulations starting from the α-helical conformation, forcing residues 17-21 to remain in the initial (helical) conformation prevents aggregation but allows for the formation of dimers, indicating that oligomerization, initiated along the nonhelical N-terminal regions, cannot progress without the α-to-ß transition propagating along the chains.