Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery.National Institutes of Health (U.S.) (Grant R21-CA-140030-01

The donders model of the circulation in normo- and pathophysiology.

Item does not contain fulltextThe solution of some recent as well as of long standing problems, unanswerable due to experimental inaccessibility or moral objections are addressed. In this report, a model of the closed human cardiovascular loop is developed. This model, using one set of 88 equations, allows variations from normal resting conditions to exercise, as well as to the ultimate condition of a circulation following cardiac arrest. The principal purpose of the model is to evaluate the continuum of physiological conditions to cardiopulmonary resuscitation (CPR) effects within the circulation.Within the model, Harvey's view of the circulation has been broadened to include impedance-defined flow as a unifying concept, and as a mechanism in CPR. The model shows that depth of respiration, sympathetic stimulation of cardiac contractile properties and baroreceptor activity can exert powerful influences on the increase in cardiac output, while heart and respiratory rate increases tend to exert an inhibiting influence, with the pressure and flow curves compatible with accepted references. Impedance-defined flow encompasses both positive and negative effects.The model also demonstrates the limitations to cardiopulmonary resuscitation caused by external force applied to intrathoracic structures, with effective cardiac output being limited by collapse and sloshing. Stroke volumes from 6 to 51 ml are demonstrated. It shows that the clinical inclination to apply high pressures to intrathoracic structures may not be rewarded with improved net flow

A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5 ' exonucleolytic degradation

The removal of the mRNA 5' cap structure by the decapping enzyme DCP2 leads to rapid 5'→3' mRNA degradation by XRN1, suggesting that the two processes are coordinated, but the coupling mechanism is unknown. DCP2 associates with the decapping activators EDC4 and DCP1. Here we show that XRN1 directly interacts with EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively. In D. melanogaster cells, this interaction is mediated by the DCP1 EVH1 domain and a DCP1-binding motif (DBM) in the XRN1 C-terminal region. The NMR structure of the DCP1 EVH1 domain bound to the DBM reveals that the peptide docks at a conserved aromatic cleft, which is used by EVH1 domains to recognize proline-rich ligands. Our findings reveal a role for XRN1 in decapping and provide a molecular basis for the coupling of decapping to 5'→3' mRNA degradation