Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination.

Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.

Molecular dynamics simulations and in vitro studies of hybrid decellularized leaf-peptide-polypyrrole composites for potential tissue engineering applications.

Tissue engineering (TE) aims to repair and regenerate damaged tissue by an assimilation of optimal combination of cells specific to the tissue with an appropriate biomaterial. In this work, a new biomaterial for potential cardiac TE applications was developed by utilizing a combination of in silico studies and in vitro experiments. Molecular dynamics (MD) simulations for the formation of the novel composite prepared from the decellularized leaf components cellulose and pectin along with the VEGF derived peptide (NYLTHRQ) and polypyrrole (PPy) was carried out to assess self-assembly, mechanical properties, and interactions with integrin and NPR-C receptors which are commonly found in cells of cardiac tissue. Results of molecular dynamics simulations indicated the successful formation of stable assemblies. MD simulations also revealed that the scaffold successfully interacted with integrin and NPR-C receptors. As a proof of concept, beet leaves were decellularized (DC) and cross-linked with NYLTHRQ and PPy using layer-by-layer assembly. Decellularization (DC) was confirmed by DNA and protein quantification. Incorporation of the NYLTHRQ peptide and polypyrrole was confirmed by FTIR spectroscopy and SEM imaging. The DC-NYLTHRQ-PPy scaffold was seeded with co-cultured cardiomyocytes and vascular smooth muscle cells. The scaffold promoted cell proliferation and adhesion. Actin and Troponin T immunofluorescence staining showed the presence of these critical cardiomyocyte markers. Thus, for the first time we have developed a decellularized leaf-peptide-PPy composite scaffold by a combination of in silico studies and laboratory analyses that may have potential applications in cardiac TE.Communicated by Ramaswamy H. Sarma.

Varying fish scale derived hydroxyapatite bound hybrid peptide nanofiber scaffolds for potential applications in periodontal tissue regeneration.

New peptide based hybrid scaffolds were prepared by blending two different fish scale derived hydroxyapatite with functionalized peptide nanofibers for potential applications in periodontal tissue regeneration. The nanofibers were prepared by self-assembly of the newly designed peptide bolaamphiphile Bis (N-α-amido-glutamic acid) 1,7 heptane tetracarboxylate and functionalized with a segment of the tyrosine rich amylogenin peptide sequence MPLPPHPGHPGYINF followed by polygalacturnonic acid and hydroxyapatite derived from salmon or red-snapper fish scales. The binding interactions of the components of the scaffold was confirmed by FTIR spectroscopy as well as SEM imaging. Hybrids scaffolds with salmon scale derived HaP showed higher mechanical strength and Young's Modulus compared to snapper scale derived scaffolds. Our results indicated that while both the scaffolds supported cell proliferation and efficiently formed cell-scaffold matrices with gingival fibroblasts, we observed greater alignment of the cells in the case of scaffolds that contained snapper scale derived hydroxyapatite. Furthermore, higher differentiation ability into osteoblast like cells was seen in the case of the snapper scale derived HaP based scaffolds. Our studies indicate that the hybrid peptide nanofiber scaffold matrices, particularly those prepared using snapper scales may have significant utility in the development of biomaterials for periodontal tissue regeneration.