Biology subjects

Parker, B.

Publications and source records attributed to Parker, B..

4 recordsLinked to original sources

bioRxiv2018

LiF-MS: Mapping unstructured peptide-protein interactions using Ligand-Footprinting Mass Spectrometry

Unstructured peptides, or linear motifs, present a poorly understood molecular language within the context of cellular signaling. These modular regions are often short, unstructured and interact weakly and transiently with folded target proteins. Thus, they are difficult to study with conventional structural biology methods. We present Ligand-Footprinting Mass Spectrometry, or LiF-MS, as a method of mapping the binding sites and dynamic disorder of these peptides on folded protein domains. LiF-MS uses a cleavable crosslinker to mark regions of a protein contacted by a bound linear motif. We demonstrate this method can detect both conformation ensembles and binding orientations of a linear motif in its binding pocket to amino-acid-level detail. Furthermore, marked amino acids can be used as constraints in peptide-protein docking simulations to improve model quality. In conclusion, LiF-MS proves a simple and novel method of elucidating peptide docking structural data not accessible by other methods in the context of a purified system.

biochemistry↗

bioRxiv2018

Mob-family kinase co-activators bind cognate Ndr/Lats kinases through conserved and modular interface

Ndr/Lats kinases bind to Mob coactivator proteins and their complexes play important roles in \"Hippo\" signaling pathways controlling cell proliferation and morphogenesis. All Ndr/Lats kinases have a 70-80 amino acid long unique N-terminal region (NTR) which binds to Mob factors. In order to gain insight into the structural basis of kinase-coactivator binding specificity, we have determined the crystal structure of Cbk1(NTR)-Mob2 and Dbf2(NTR)-Mob1 complexes from yeast (S. cerevisiae). We show that the Ndr/Lats(NTR)-Mob interface is a common structural platform through which kinase-cofactor binding is mediated, albeit amino acid variations in key positions contribute to subgroup and organism-specific differences. We further show that conserved residues at the NTR-Mob interface may participate in novel activation mechanisms likely ubiquitous in Ndr/Lats kinases. Ndr/Lats kinase activation may resemble to that of other AGC kinases but with an extra structural requirement for NTR mediated Mob binding for proper allosteric activation.

biochemistry↗

bioRxiv2018

Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum

The mammalian response to endoplasmic reticulum (ER) stress dynamically affects all layers of gene expression regulation. We quantified transcript and protein abundance along with footprints of ribosomes and non-ribosomal proteins for thousands of genes in cervical cancer cells responding to treatment with tunicamycin or hydrogen peroxide over an eight hour time course. We identify shared and stress-specific significant regulatory events at the transcriptional and post-transcriptional level and at different phases of the experiment. ER stress regulators increase transcription and translation at different times supporting an adaptive response. ER stress also induces translation of genes from serine biosynthesis and one-carbon metabolism indicating a shift in energy production. Discordant regulation of DNA repair genes suggests transcriptional priming in which delayed translation fine-tunes the early change in the transcriptome. Finally, case studies on stress-dependent alternative splicing and protein-mRNA binding demonstrate the ability of this resource to generate hypotheses for new regulatory mechanisms.

systems biology↗

bioRxiv2017

The cost of enforcing marine protected areas to achieve ecological targets

Protected areas are the primary management tool for conserving ecosystems, yet their intended outcomes may often be compromised by poaching. Consequently, many protected areas are ineffective paper parks that contribute little towards conserving ecosystems. Poaching can be prevented through enforcement and engaging with community members so they support protected areas. It is not clear how much needs to be spent on enforcement and engagement to ensure they are frequent enough to be effective at conserving biodiversity. We develop models of enforcement against illegal fishing in marine protected areas. We apply the models to data on fishing rates and fish biomass from a marine protected area in Raja Ampat, Indonesia and explore how frequent enforcement patrols need to be to achieve targets for coral reef fish biomass. Achieving pristine levels of reef fish biomass required almost year-round enforcement of the protected area. Surveillance of the protected area may also be enhanced if local fishers who support the reserve report on poaching. The opportunity for local fishing boats to participate in surveillance was too small for it to have much benefit for total reef fish biomass, which increases slowly. However, specific functional groups of fish have much higher population growth rates and their biomass was predicted to increase markedly with community surveillance. We conclude that budgets for park management must balance the cost of conducting frequent patrols against supporting alternative activities, like education to build community support. Optimized budgets will be much more likely to achieve ecological targets for recovering fish biomasses and will contribute to fiscal sustainability of protected areas.

ecology↗