How Peptides Bind to PSD-95/Discs-Large/ZO-1 Domains.

PSD-95/discs-large/ZO-1 (PDZ) domains form a large family of adaptor proteins that bind to the C-terminal tails of their binding partner proteins. Via extensive molecular dynamics simulations and alchemical free energy calculations, we characterized the binding modi of phosphorylated and unphosphorylated EQVSAV peptides and of a EQVEAV phosphate mimic to the hPTP1E PDZ2 and MAGI1 PDZ1 domains. The simulations reproduced the well-known binding characteristics such as tight coordination of the peptidic carboxyl tail and pronounced hydrogen bonding between the peptide backbone and the backbone atoms of a ß-sheet in PDZ. Overall, coordination by hPTP1E PDZ2 appeared tighter than by MAGI1 PDZ1. Simulations of wild-type PDZ and arginine mutants suggest that contacts with Arg79/85 in hPTP1E/MAGI1 are more important for the EQVEAV peptide than for EQVSAV. Alchemical free energy calculations and PaCS-MD simulations could well reproduce the difference in binding free energy between unphosphorylated EQVSAV and EQVEAV peptides and the absolute binding free energy of EQVSAV. However, likely due to small force field inaccuracies, the simulations erroneously favored binding of the phosphorylated peptide instead of its unphosphorylated counterpart, which is in contrast to the experiment.

Is the proteomic composition of the salivary pellicle dependent on the substrate material?

PURPOSE: The use of dental restorative materials is a routine task in clinical dentistry. Upon exposure to the oral cavity, continuous adsorption of salivary proteins and other macromolecules to all surfaces occurs, representing the first step in dental biofilm formation. Different physico-chemical properties of substrate materials potentially influence the composition of the initial biofilm, termed pellicle. This study aimed at characterizing and comparing the individual proteomic composition of the 3-min pellicle formed on bovine enamel and six restorative materials. EXPERIMENTAL DESIGN: After chemical elution, pellicle proteins were identified by nano-LC-HR-MS/MS. Proteomic profiles were analyzed in terms of molecular weights, isoelectric points, molecular functions and compared to saliva to reveal substrate material-specific adsorption patterns. RESULTS: A total of 1348 different pellicle proteins were identified, with 187-686 proteins in individual 3-min pellicles. Unexpectedly, this yielded quite similar distribution patterns independent of the substrate materials. Furthermore, overall similar fold changes were obtained for the major part of commonly enriched or depleted proteins in the pellicles. CONCLUSIONS AND CLINICAL RELEVANCE: The current results point to a minor role of the substrate material on the proteomic composition of the 3-min pellicle and represent core data for understanding the complex surface interactions in the oral cavity.

How phosphorylation of peptides affects their interaction with 14-3-3η domains.

Members of the 14-3-3 domain family have important functions as adapter domains. Via an amphipathic groove on their protein surface they typically bind to disordered C-terminals of other proteins. Importantly, binding partners of 14-3-3 domains usually contain a phosphorylated serine or threonine residue at their binding interface and possess one of three different sequence motifs. Binding of the respective unphosphorylated versions of the peptides is typically strongly disfavored. There is a wealth of structural and thermodynamic data available for the phosphorylated forms but not for the unphosphorylated forms as the binding affinities seem to be too weak to be measurable experimentally. Here, we characterized the mechanistic details that govern the preference for the binding of phosphorylated peptides to 14-3-3η domains by means of molecular dynamics (MD) simulations. We found that the phosphate group is ideally coordinated in the binding pocket whereas the respective unphosphorylated side-chain counterpart is not. Thus, the binding preference results from the tight coordination of the phosphorylated residue at the center of the binding interface. Furthermore, MD simulations of 14-3-3η dimers showed a preference for the simultaneous binding of two phosphorylated peptides in agreement with their experimentally observed cooperativity.

A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling.

Alternative splicing is a potent modifier of protein function. Stromal interaction molecule 1 (Stim1) is the essential activator of store-operated Ca2+ entry (SOCE) triggering activation of transcription factors. Here, we characterize Stim1A, a splice variant with an additional 31 amino acid domain inserted in frame within its cytosolic domain. Prominent expression of exon A is found in astrocytes, heart, kidney, and testes. Full-length Stim1A functions as a dominant-negative regulator of SOCE and ICRAC, facilitating sequence-specific fast calcium-dependent inactivation and destabilizing gating of Orai channels. Downregulation or absence of native Stim1A results in increased SOCE. Despite reducing SOCE, Stim1A leads to increased NFAT translocation. Differential proteomics revealed an interference of Stim1A with the cAMP-SOCE crosstalk by altered modulation of phosphodiesterase 8 (PDE8), resulting in reduced cAMP degradation and increased PIP5K activity, facilitating NFAT activation. Our study uncovers a hitherto unknown mechanism regulating NFAT activation and indicates that cell-type-specific splicing of Stim1 is a potent means to regulate the NFAT signalosome and cAMP-SOCE crosstalk.

Protein Signatures of NK Cell-Mediated Melanoma Killing Predict Response to Immunotherapies.

Despite impressive advances in melanoma-directed immunotherapies, resistance is common and many patients still succumb to metastatic disease. In this context, harnessing natural killer (NK) cells, which have thus far been sidelined in the development of melanoma immunotherapy, could provide therapeutic benefits for cancer treatment. To identify molecular determinants of NK cell-mediated melanoma killing (NKmK), we quantified NK-cell cytotoxicity against a panel of genetically diverse melanoma cell lines and observed highly heterogeneous susceptibility. Melanoma protein microarrays revealed a correlation between NKmK and the abundance and activity of a subset of proteins, including several metabolic factors. Oxidative phoshorylation, measured by oxygen consumption rate, negatively correlated with melanoma cell sensitivity toward NKmK, and proteins involved in mitochondrial metabolism and epithelial-mesenchymal transition were confirmed to regulate NKmK. Two- and three-dimensional killing assays and melanoma xenografts established that the PI3K/AKT/mTOR signaling axis controls NKmK via regulation of NK cell-relevant surface proteins. A "protein-killing-signature" based on the protein analysis predicted NKmK of additional melanoma cell lines and the response of patients with melanoma to anti-PD-1 checkpoint therapy. Collectively, these findings identify novel NK cell-related prognostic biomarkers and may contribute to improved and personalized melanoma-directed immunotherapies. SIGNIFICANCE: NK-cell cytotoxicity assays and protein microarrays reveal novel biomarkers of NK cell-mediated melanoma killing and enable development of signatures to predict melanoma patient responsiveness to immunotherapies.

Deep Proteomic Insights into the Individual Short-Term Pellicle Formation on Enamel-An In Situ Pilot Study.

PURPOSE: Dental pellicle formation starts instantaneously after oral hygiene due to the adsorption of salivary proteins to all orally exposed surfaces. The pellicle acts as a physiological mediator, protects the tooth surface from mechanical damages and reduces acid-induced enamel demineralization. The aim of this pilot study is to identify and characterize individual proteomic profiles of the initial pellicle formed on dental enamel and to compare the profiles with the corresponding saliva to analyze specific adsorption patterns occurring during pellicle formation. EXPERIMENTAL DESIGN: The 3-min pellicle of five subjects formed in situ on bovine enamel is eluted chemically and analyzed separately by nano-mass spectrometry. The analysis of the corresponding saliva is conducted in parallel. RESULTS: Up to 498 pellicle proteins and up to 1032 salivary proteins are identified on an individual level. Comparison of the salivary and pellicle protein profiles demonstrates the pellicle formation to be highly individual. Nineteen proteins are significantly enriched in the 3-min pellicle of all subjects and 22 proteins are significantly depleted indicating that pellicle formation relies on selective adsorption. CONCLUSIONS AND CLINICAL RELEVANCE: The short-term enamel pellicle is composed of several hundreds of adsorbed salivary proteins and reveals a highly individual proteomic profile.