Predicting Conformational Properties of Intrinsically Disordered Proteins from Sequence
- 22 July 2020
- book chapter
- protocol
- Published by Springer Science and Business Media LLC
- Vol. 2141, 347-389
- https://doi.org/10.1007/978-1-0716-0524-0_18
Abstract
Intrinsically disordered proteins (IDPs) can adopt a range of conformations from globules to swollen coils. This large range of conformational preferences for different IDPs raises the question of how conformational preferences are encoded by sequence. Global compositional features of a sequence such as the fraction of charged residues and the net charge per residue engender certain conformational biases. However, more specific sequence features such as the patterning of oppositely charged residues, expansion driving residues, or residues that can undergo posttranslational modifications can also influence the conformational ensembles of an IDP. Here, we outline how to calculate important global compositional features and patterning metrics that can be used to classify IDPs into different conformational classes and predict relative changes in conformation for sequences with the same amino acid composition. Although increased effort has been devoted to determining conformational properties of IDPs in recent years, quantitative predictions of conformation directly from sequence remain difficult and often inaccurate. Thus, if quantitative predictions of conformational properties are desired, then sequence-specific simulations must be performed.Keywords
This publication has 111 references indexed in Scilit:
- Solution Model of the Intrinsically Disordered Polyglutamine Tract-Binding Protein-1Biophysical Journal, 2012
- Fractal dimension of an intrinsically disordered protein: Small‐angle X‐ray scattering and computational study of the bacteriophage λ N proteinProtein Science, 2011
- The N0‐binding region of the vesicular stomatitis virus phosphoprotein is globally disordered but contains transient α‐helicesProtein Science, 2011
- Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?Protein Science, 2010
- Proline-Rich Salivary Proteins Have Extended ConformationsBiophysical Journal, 2010
- Sequence Determinants of Compaction in Intrinsically Disordered ProteinsBiophysical Journal, 2010
- Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin LigaseStructure, 2010
- ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutionsJournal of Computational Chemistry, 2008
- The N Terminus of Saccharomyces cerevisiae Msh6 Is an Unstructured Tether to PCNAMolecular Cell, 2007
- Predicting intrinsic disorder from amino acid sequenceProteins, 2003