Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/089706

PolyCut: a computer programme for assignments of MSn signals of metallo-biomolecules by considering the entire isotope patterns

Shi, Z.·Sze, C. M.
View original source ↗Export metadata ↓

Abstract

A computer programme PolyCut has been written to assist mass spectrometry-based bioinorganic studies via top-down and bottom-up approaches in positive and negative ion modes. PolyCut is designed to cope with metalloproteins, metallo-polymers and biomolecules with heavy element(s) as one (or more) of the charging agents at defined but different oxidation states. It does automatic assignment by considering the entire experimental and simulated isotopic patterns of an ion rather than reading only the mono-isotopic and average m/z values (and/or mass values). The calculation of chemical formula and the simulation of isotopic pattern for an ion at various charge states require PolyCut to be informed of the user-defined elements, the user-defined abundance of isotopes for each element, the user-defined oxidation state of an element, the user-defined residues and sequence of a polymer, and the user-defined fragmentation (or digestion). The programme successfully assisted MSn studies of two copper proteins coordinated to platinum(II) centres (a functional group possessing an intrinsic positive charge rather than a neutral organic modification), published as J. Biol. Inorg. Chem. 2009, 14(2), 163-165; Metallomics 2013, 5(8), 946-954; and [more]. Besides polypeptides, polynucleotides and polysaccharides, PolyCut can be extended to other polymers using user-defined monomer residues. For the metallo-community.\n\nAbbreviations

Explore related subjects

biochemistryPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Shi, Z., Sze, C. M.. 2016-11-26. PolyCut: a computer programme for assignments of MSn signals of metallo-biomolecules by considering the entire isotope patterns. https://doi.org/10.1101/089706

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Functional Reconstitution of Human OATP1B1 and OATP1B3 in Proteoliposomes: Effect of Bicarbonate Gradients and Substrate-specific Stimulation on Transport

The hepatic organic anion transporting polypeptides OATP1B1 and OATP1B3 are critical for the clearance of widely prescribed drugs, hepatotoxins, and endogenous metabolites. However, the thermodynamic driving force governing their transport has remained a subject of debate due to the complexity of cellular models. Here, we report a defined, reconstituted proteoliposome system to study the transport kinetics of isolated human OATP1B1 and OATP1B3. Through direct functional assays, real-time counter-ion tracking, and a novel ABCG2-OATP1B1 functional co-reconstitution, we identify an outwardly directed bicarbonate gradient as a thermodynamic driving force for concentrative substrate uptake. In contrast we find no evidence for the proposed role of reduced glutathione efflux as a possible driving force. Targeted mutagenesis experiments revealed that the conserved TM3 residue His115 is needed to couple the bicarbonate gradient to concentrative substrate uptake, mechanistically linking substrate antiport to local pH-sensitive bicarbonate processing. We also investigated the substrate-specific stimulatory effect of the green tea catechin epigallocatechin gallate (EGCG) on OATP1B3 transport, confirming that this effect is intrinsic to OATP1B3, substrate specific, and does not need the involvement of other cellular proteins. Our findings define the energetic basis of OATP1B1 and OATP1B3 hepatic xenobiotic clearance.

biochemistry↗
bioRxiv2026

Mapping the sequence determinants of constitutive activity in GPCRs

G protein-coupled receptors (GPCRs) signal not only in response to ligands but also in their absence. This basal, or constitutive, activity has distinct physiological consequences and is the only functional measurement available for orphan receptors. It is also hard to compare receptors because each is reported relative to its own baseline. Here, we measure basal activity on a single scale across the human GPCR family. Pairing a barcoded library of all human GPCRs with a transcriptional cAMP reporter, we scored 901 receptor constructs in one pool experiment. Basal activity forms a continuous distribution, and many of the highest-scoring recipes have prior reports of ligand-independent activity, with orphan being strongly represented. We then exhaustively mutated one of them, GPR161, and measured its effects on protein abundance, surface expression, and cAMP signaling. Of the 528 positions, only 10 specifically alter signaling independent of expression. Constraints on basal signaling are dominated by reepotro biogenesis, which requires multiphenotype scanning to resolve. Together, these datasets place basal activity on a common scale across the GPCR family and provide a template for dissecting it at residue resolution.

biochemistry↗
bioRxiv2026

Aggregate Deep Visual Proteomics reveals selective organization of α-synuclein inclusions

-Synuclein inclusions, the lesions typical of Parkinson's disease, have been interpreted as protective deposits, toxic species or failed degradation products, each predicting a different composition and correlating that enrichment with neuron dysfunction and eventual degeneration. Distinguishing them requires measuring what an inclusion concentrates relative to the cell that built it. Here we developed Aggregate Deep Visual Proteomics, which uses ultrasensitive mass spectrometry to profile laser-microdissected inclusions against the remainder of the same cell or a matched host. In HEK293 cells, iPSC-derived dopaminergic neurons and post-mortem patient brain, each inclusion concentrated a selective subset of its cell's proteome, independent of abundance and dominated by membrane, in neurons largely presynaptic. Inclusions took up whole assemblies, with subunits moving together in 421 of 438 complexes, and the V-ATPase alone was enriched in all three systems. Degradation cargo stayed with the receptors that route it, consistent with sequestration and failed degradation acting together. Neuritic and somatic inclusions differed, the former rich in UBQLN2 and the latter in intermediate filaments. In the cell line, phosphorylated -synuclein was tenfold higher in the inclusion than in the rest of the cell, with about one third of the rise already present before an inclusion was visible. Measured against its host, the composition of an inclusion becomes a readout of how it formed and a source of candidate markers and therapeutic targets.

biochemistry↗