Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins
{"title":"Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins","authors":"Tanmoy Pal, Jonas Wessén, Suman Das, Hue Sun Chan","doi":"arxiv-2407.07226","DOIUrl":null,"url":null,"abstract":"Conformational properties of intrinsically disordered proteins (IDPs) are\ngoverned by a sequence-ensemble relationship. To differentiate the impact of\nsequence-local versus sequence-nonlocal features of an IDP's charge pattern on\nits conformational dimensions and its phase-separation propensity, the charge\n\"blockiness'' $\\kappa$ and the nonlocality-weighted sequence charge decoration\n(SCD) parameters are compared for their correlations with isolated-chain radii\nof gyration ($R_{\\rm g}$s) and upper critical solution temperatures (UCSTs) of\npolyampholytes modeled by random phase approximation, field-theoretic\nsimulation, and coarse-grained molecular dynamics. SCD is superior to $\\kappa$\nin predicting $R_{\\rm g}$ because SCD accounts for effects of contact order,\ni.e., nonlocality, on dimensions of isolated chains. In contrast, $\\kappa$ and\nSCD are comparably good, though nonideal, predictors of UCST because\nfrequencies of interchain contacts in the multiple-chain condensed phase are\nless sensitive to sequence positions than frequencies of intrachain contacts of\nan isolated chain, as reflected by $\\kappa$ correlating better with\ncondensed-phase interaction energy than SCD.","PeriodicalId":501022,"journal":{"name":"arXiv - QuanBio - Biomolecules","volume":"22 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Biomolecules","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2407.07226","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Conformational properties of intrinsically disordered proteins (IDPs) are
governed by a sequence-ensemble relationship. To differentiate the impact of
sequence-local versus sequence-nonlocal features of an IDP's charge pattern on
its conformational dimensions and its phase-separation propensity, the charge
"blockiness'' $\kappa$ and the nonlocality-weighted sequence charge decoration
(SCD) parameters are compared for their correlations with isolated-chain radii
of gyration ($R_{\rm g}$s) and upper critical solution temperatures (UCSTs) of
polyampholytes modeled by random phase approximation, field-theoretic
simulation, and coarse-grained molecular dynamics. SCD is superior to $\kappa$
in predicting $R_{\rm g}$ because SCD accounts for effects of contact order,
i.e., nonlocality, on dimensions of isolated chains. In contrast, $\kappa$ and
SCD are comparably good, though nonideal, predictors of UCST because
frequencies of interchain contacts in the multiple-chain condensed phase are
less sensitive to sequence positions than frequencies of intrachain contacts of
an isolated chain, as reflected by $\kappa$ correlating better with
condensed-phase interaction energy than SCD.