4.7 Article

Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

MobiDB: intrinsically disordered proteins in 2021

Damiano Piovesan et al.

Summary: The latest version of MobiDB database provides more flexibility and visualization tools, allowing users to search and download large datasets more quickly.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin

Kristina Kastano et al.

Summary: Low complexity regions (LCRs) are common in protein sequences, less evolutionarily conserved and facilitate protein interactions in eukaryotes, especially those with complex tissue distribution. Evolutionary studies can evaluate the importance and function of LCRs, and multiple modes of LCR-mediated protein-protein interactions can be detected with a large hub protein like HTT when sufficient protein interaction data is available.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Biophysics

The protein disorder cycle

Vladimir N. Uversky

Summary: This mini-review highlights the interplay between order and disorder in proteins, showing that folding, non-folding, and misfolding are intertwined on multiple levels within the cell. Proteins exhibit heterogeneous spatio-temporal structural organization with components undergoing order-to-disorder and disorder-to-order transitions for functionality. In addition to intrinsic forms of disorder, proteins also face extrinsic disorder from their functional partners, forming a multileveled protein disorder cycle.

BIOPHYSICAL REVIEWS (2021)

Article Biochemical Research Methods

Disentangling the complexity of low complexity proteins

Pablo Mier et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Biochemical Research Methods

Atypical structural tendencies among low-complexity domains in the protein data bank proteome

Sean M. Cascarina et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

Tsai-Chen Chen et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Biochemistry & Molecular Biology

Predicting Secondary Structure Propensities in IDPs Using Simple Statistics from Three-Residue Fragments

Alejandro Estana et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Review Biochemistry & Molecular Biology

Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins

Greta Bianchi et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Chemistry, Physical

Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins

Wai Shing Tang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Multidisciplinary Sciences

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor

Albert Escobedo et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

SCOPe: classification of large macromolecular structures in the structural classification of proteinsextended database

John-Marc Chandonia et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

Alejandro Estana et al.

STRUCTURE (2019)

Article Chemistry, Multidisciplinary

A General Strategy to Access Structural Information at Atomic Resolution in Polyglutamine Homorepeats

Annika Urbanek et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Multidisciplinary Sciences

Developing a molecular dynamics force field for both folded and disordered protein states

Paul Robustelli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemistry & Molecular Biology

Context characterization of amino acid homorepeats using evolution, position, and order

Pablo Mier et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2017)

Article Multidisciplinary Sciences

The Protein Structure Context of PolyQ Regions

Franziska Totzeck et al.

PLOS ONE (2017)

Review Biochemistry & Molecular Biology

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

M. Madan Babu

BIOCHEMICAL SOCIETY TRANSACTIONS (2016)

Article Biochemistry & Molecular Biology

Intrinsically disordered proteins: emerging interaction specialists

Peter Tompa et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Low complexity and disordered regions of proteins have different structural and amino acid preferences

Bandana Kumari et al.

MOLECULAR BIOSYSTEMS (2015)

Article Biochemistry & Molecular Biology

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

Zhenling Peng et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2015)

Review Biochemistry & Molecular Biology

Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

Christopher J. Oldfield et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Review Chemistry, Multidisciplinary

Classification of Intrinsically Disordered Regions and Proteins

Robin van der Lee et al.

CHEMICAL REVIEWS (2014)

Article Chemistry, Multidisciplinary

A Crystal Structure of an Oligoproline PPII-Helix, at Last

Patrick Wilhelm et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Multidisciplinary Sciences

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

Rahul K. Das et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Chemistry, Multidisciplinary

Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution

Valery Ozenne et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemistry & Molecular Biology

Protein tandem repeats - the more perfect, the less structured

Julien Jorda et al.

FEBS JOURNAL (2010)

Article Biochemical Research Methods

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Peter J. A. Cock et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Molecular principles of the interactions of disordered proteins

Balint Meszaros et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)