Peptides: A Package for Data Mining of Antimicrobial Peptides

Osorio, Daniel; Rondón-Villarreal, Paola; Torres, Rodrigo

doi:10.32614/rj-2015-001

Cited by 299 publications

(258 citation statements)

References 27 publications

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“…Gravy score for each protein was calculated as a sum of the values assigned to each amino acid in a protein sequence: arginine (-4.5), lysine (-3.9), asparagine (-3.5), aspartate (-3.5), glutamine (-3.5), glutamate (-3.5), histidine (-3. Isoelectric points and molecular weights were calculated using R package Peptides [79].…”

Section: Discussionmentioning

confidence: 99%

Aggregation and Disaggregation Features of the Human Proteome

Määttä

Rettel

Helm

et al. 2020

Preprint

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Protein aggregates have negative implications in disease. While reductionist experiments have increased our understanding of aggregation processes, the systemic view in biological context is still limited. To extend this understanding, we used mass spectrometry-based proteomics to characterize aggregation and disaggregation in human cells after non-lethal heat shock. Aggregation-prone proteins were enriched in nuclear proteins, high proportion of intrinsically disordered regions, high molecular mass, high isoelectric point and hydrophilic amino acids. During recovery, most aggregating proteins disaggregated with a rate proportional to the aggregation propensity: larger loss in solubility was counteracted by faster disaggregation. High amount of intrinsically disordered regions also resulted in faster disaggregation. However, other characteristics enriched in aggregating proteins did not correlate with the disaggregation rates. In addition, we analyzed changes in protein thermal stability after heat shock. Soluble remnants of aggregated proteins were more thermally stable compared to control condition. Our results provide a rich resource of heat stress-related protein solubility data, propose novel roles for intrinsically disordered regions in protein quality control and reveal a protection mechanism to repress protein aggregation in heat stress.

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Section: Discussionmentioning

confidence: 99%

Aggregation and Disaggregation Features of the Human Proteome

Määttä

Rettel

Helm

et al. 2020

Preprint

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“…For each allele, we trained neural-network classifiers (one hidden layer with 50 units) (by using Theano (Theano Development Team, 2016); 5-fold cross-validation) to differentiate MS 9-mers from random decoy 9-mers by using different input feature schemes: dummy encoding, BLOSUM62, PMBEC (Kim et al, 2009), biochemical properties (Bremel and Homan, 2010), and peptide-level features (Osorio et al, 2014); we averaged the results of these models to obtain a single prediction (called MSIntrinsic). We made a second prediction (MSIntrinsicEC) by adding expression and MS-trained cleavability.…”

Section: Methodsmentioning

confidence: 99%

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

et al. 2017

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SUMMARY Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of subdominant binding motifs and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural-network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on data-sets of peptides with measured affinities. We thus demonstrate a strategy for systematically learning the rules of endogenous antigen presentation.

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“…The physicochemical properties of the CDR3 amino acid sequences were calculated using the R package Peptides (32, 33), and clustering analysis of the Ig gene sequences was carried out using Levenstein distance on the CDR3 regions using R scripts available on our website (34). …”

Section: Methodsmentioning

confidence: 99%

Transitional B Cells in Early Human B Cell Development – Time to Revisit the Paradigm?

Martin

Townsend

et al. 2016

Front. Immunol.

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The B cell repertoire is generated in the adult bone marrow by an ordered series of gene rearrangement processes that result in massive diversity of immunoglobulin (Ig) genes and consequently an equally large number of potential specificities for antigen. As the process is essentially random, the cells exhibiting excess reactivity with self-antigens are generated and need to be removed from the repertoire before the cells are fully mature. Some of the cells are deleted, and some will undergo receptor editing to see if changing the light chain can rescue an autoreactive antibody. As a consequence, the binding properties of the B cell receptor are changed as development progresses through pre-B ≫ immature ≫ transitional ≫ naïve phenotypes. Using long-read, high-throughput, sequencing we have produced a unique set of sequences from these four cell types in human bone marrow and matched peripheral blood, and our results describe the effects of tolerance selection on the B cell repertoire at the Ig gene level. Most strong effects of selection are seen within the heavy chain repertoire and can be seen both in gene usage and in CDRH3 characteristics. Age-related changes are small, and only the size of the CDRH3 shows constant and significant change in these data. The paucity of significant changes in either kappa or lambda light chain repertoires implies that either the heavy chain has more influence over autoreactivity than light chain and/or that switching between kappa and lambda light chains, as opposed to switching within the light chain loci, may effect a more successful autoreactive rescue by receptor editing. Our results show that the transitional cell population contains cells other than those that are part of the pre-B ≫ immature ≫ transitional ≫ naïve development pathway, since the population often shows a repertoire that is outside the trajectory of gene loss/gain between pre-B and naïve stages.

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Peptides: A Package for Data Mining of Antimicrobial Peptides

Cited by 299 publications

References 27 publications

Aggregation and Disaggregation Features of the Human Proteome

Aggregation and Disaggregation Features of the Human Proteome

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

Transitional B Cells in Early Human B Cell Development – Time to Revisit the Paradigm?

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