Protein charge distribution in proteomes and its impact on translation

PLoS Computational Biology
Rodrigo D RequiãoFernando L Palhano

Abstract

As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel. The following annotated and reviewed proteins in the UniProt database (Swiss-Prot) were analyzed: 551,705 proteins from different organisms and a total of 180 million protein segments. We observed that there were more negative than positive stretches and that super-charged positive sequences (i.e., net charges ≥ 14) were underrepresented in the proteomes. Overall, the proteins were more positively charged at their N-termini and C-termini, and this feature was present in most organisms and subcellular localizations. To investigate whether the N-terminal charges affect the elongation rates, previously published ribosomal profiling data obtained from S. cerevisiae, without translation...Continue Reading

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Citations

Jul 12, 2019·Proceedings of the National Academy of Sciences of the United States of America·Andrea RibaMihaela Zavolan
Feb 20, 2019·Molecular Systems Biology·Basak EraslanJulien Gagneur
May 3, 2019·Proteomics·Leah V SchafferLloyd M Smith
Dec 5, 2019·Preparative Biochemistry & Biotechnology·Biyan WenHuangjin Li
May 26, 2020·Molecular Systems Biology·Marc WeberLuis Serrano
Sep 19, 2018·Proceedings of the National Academy of Sciences of the United States of America·José Arcadio Farías-RicoGunnar von Heijne
Aug 17, 2020·The Biochemical Journal·Rodrigo D RequiãoFernando L Palhano
Jan 8, 2021·Frontiers in Genetics·Shuxia ZhangYoufa Zhou
Feb 20, 2021·Science·Anastassia A VorobievaDavid Baker
Mar 27, 2021·PLoS Computational Biology·Tingzhong TianJianyang Zeng
Mar 29, 2021·The Journal of Biological Chemistry·Géssica C BarrosFernando L Palhano
Jun 4, 2021·The Journal of Physical Chemistry. B·Dmitrii E Makarov, Hagen Hofmann
Jun 17, 2021·Biosensors & Bioelectronics·Rupa HaldavnekarDr Bo Tan
Oct 4, 2017·Journal of the American Chemical Society·Roy GovrinUri Sivan

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