AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

Robert T McDonnell; Adrian H Elcock

doi:10.1016/j.str.2024.02.002

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AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

Journal article

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AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

Robert T McDonnell and Adrian H Elcock

Structure (London), Vol.32(5), pp.621-629.e5

02/21/2024

DOI: 10.1016/j.str.2024.02.002

PMCID: PMC11073581

PMID: 38428431

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312685View

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Abstract

The interpretation of experimental studies of co-translational protein folding often benefits from the use of computational methods that seek to model or simulate the nascent chain and its interactions with the ribosome. Building realistic 3D models of ribosome-nascent chain (RNC) constructs often requires expert knowledge, so to circumvent this issue, we describe here AutoRNC, an automated modeling program capable of constructing large numbers of plausible atomic models of RNCs within minutes. AutoRNC takes input from the user specifying any regions of the nascent chain that contain secondary or tertiary structure and attempts to build conformations compatible with those specifications-and with the constraints imposed by the ribosome-by sampling and progressively piecing together dipeptide conformations extracted from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB). Despite using only modest computational resources, we show here that AutoRNC can build plausible conformations for a wide range of RNC constructs for which experimental data have already been reported.

Details

Title: Subtitle: AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes
Creators: Robert T McDonnell - University of Iowa
Adrian H Elcock - Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA. Electronic address: adrian-elcock@uiowa.edu
Resource Type: Journal article
Publication Details: Structure (London), Vol.32(5), pp.621-629.e5
DOI: 10.1016/j.str.2024.02.002
PMID: 38428431
PMCID: PMC11073581
NLM abbreviation: Structure
eISSN: 1878-4186
Publisher: Elsevier BV
Grant note: DOI: 10.13039/100008893, name: University of Iowa; DOI: 10.13039/100000002, name: National Institutes of Health, award: R35 GM122466
Language: English
Electronic publication date: 02/21/2024
Academic Unit: Physics and Astronomy; Biochemistry and Molecular Biology
Record Identifier: 9984563558802771

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