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Conserved Helix-Flanking Prolines Modulate Intrinsically Disordered Protein
Michael D Crabtree, Wade Borcherds, Anusha Poosapati, Sarah L Shammas, Gary W Daughdrill, Jane Clarke
Mar 26, 2018
Appropriate integration of cellular signals requires a delicate balance of ligand-target binding affinities. Increasing the level of residual structure in intrinsically disordered proteins (IDPs), which are overrepresented in...
Amino Acid Sequence Animals Binding Sites Cloning Molecular Conserved Sequence Escherichia coli Gene Expression Histone-Lysine N-Methyltransferase Humans Intrinsically Disordered Proteins Membrane Proteins Mice Models Molecular Mutation Myeloid-Lymphoid Leukemia Protein Phosphoproteins Proline Protein Binding Protein Conformation alpha-Helical Protein Folding Protein Interaction Domains and Motifs Recombinant Proteins Sequence Alignment Sequence Homology Amino Acid Tumor Suppressor Protein p53
Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins.
Francisco N Newby, Alfonso De Simone, Maho Yagi-Utsumi, Xavier Salvatella, Christopher M Dobson, Michele Vendruscolo
Oct 21, 2015
Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies.
IDP biophysics coupled folding and binding Electrostatics Kinetics phi-value protein dynamic protein electrostatics Protein Folding protein-protein interactions residual structure signaling Apoptosis Regulatory Proteins CREB-Binding Protein Cyclic AMP Response Element-Binding Protein Humans Hydrophobic and Hydrophilic Interactions Intrinsically Disordered Proteins Kinetics Molecular Dynamics Simulation Myeloid Cell Leukemia Sequence 1 Protein Protein Binding Protein Folding Protein Interaction Domains and Motifs Proto-Oncogene Proteins Signal Transduction Static Electricity Thermodynamics
A chain mechanism for flagellum growth.
Bacteria swim by means of long flagella extending from the cell surface. These are assembled from thousands of protein subunits translocated across the cell membrane by an export machinery at the base of each flagellum. Unfolded...
Multi-scale ensemble properties of the Escherichia coli RNA degradosome.
Tom Dendooven, Giulia Paris, Alexander V Shkumatov, Md Saiful Islam, Alister Burt, Marta A Kubańska, Tai Yuchen Yang, Steven W Hardwick, Ben F Luisi
Aug 20, 2021
In organisms from all domains of life, multi-enzyme assemblies play central roles in defining transcript lifetimes and facilitating RNA-mediated regulation of gene expression. An assembly dedicated to such roles, known as the...
RNA condensates RNA metabolism RNA surveillance RNase E colloidal polymer Intrinsically Disordered Protein post-transcriptional gene regulation Ribonuclease riboregulation Catalytic Domain Cryoelectron Microscopy Electrophoretic Mobility Shift Assay Endoribonucleases Escherichia coli Escherichia coli Proteins Gene Expression Regulation Bacterial Intrinsically Disordered Proteins Models Structural Multienzyme Complexes Mutation Polyribonucleotide Nucleotidyltransferase RNA Helicases RNA processing Post-Transcriptional RNA Bacterial Ribonucleases Static Electricity Tomography
A method for partitioning the information contained in a protein sequence between its structure and function.
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the...
Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry.
Lasse Staby, Katherine R Kemplen, Amelie Stein, Michael Ploug, Jane Clarke, Karen Skriver, Pétur O Heidarsson, Birthe B Kragelund
Sep 16, 2021
EF-hand Frequenin IDP NCS-1 Order–disorder interplay Protein Folding Amino Acid Sequence Binding Sites Carrier Proteins Humans Hydrophobic and Hydrophilic Interactions Intrinsically Disordered Proteins Kinetics Ligands Models Molecular Mutation Neuronal Calcium-Sensor Proteins Neuropeptides Protein Domains Protein Stability Thermodynamics
A Small Molecule Stabilizes the Disordered Native State of the Alzheimer's Aβ Peptide.
The stabilization of native states of proteins is a powerful drug discovery strategy. It is still unclear, however, whether this approach can be applied to intrinsically disordered proteins. Here, we report a small molecule that...
GADIS
Tyler S Harmon, Michael D Crabtree, Sarah L Shammas, Ammon E Posey, Jane Clarke, Rohit V Pappu
Aug 19, 2016
Disordered domains in chromatin-binding proteins.
Chromatin comprises proteins, DNA and RNA, and its function is to condense and package the genome in a way that allows the necessary transactions such as transcription, replication and repair to occur in a highly organised and...
Common Functions of Disordered Proteins across Evolutionary Distant Organisms
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence−structure−function relationship. Hence, classic sequence- or structure-based...
Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding...
CRIB effector disorder
CRIB effectors Intrinsically Disordered Proteins Protein Conformation small G-proteins Animals GTP Phosphohydrolases GTP-Binding Proteins Gene Expression Regulation Humans Hydrophobic and Hydrophilic Interactions Membrane Proteins Nonlinear dynamics Polylysine Protein Binding Protein Domains Protein Structure Quaternary Signal Transduction Static Electricity Tumor Suppressor Proteins cdc42 GTP-Binding Protein rac1 GTP-Binding Protein
Role of Non-Native Electrostatic Interactions in the Coupled Folding and Binding of PUMA with Mcl-1
Interplay of Structural Disorder and Short Binding Elements in the Cellular Chaperone Function of Plant Dehydrin ERD14.
Nikoletta Murvai, Lajos Kalmar, Bianka Szalaine Agoston, Beata Szabo, Agnes Tantos, Gyorgy Csikos, András Micsonai, József Kardos, Didier Vertommen, Phuong N Nguyen, Nevena Hristozova, Andras Lang, Denes Kovacs, Laszlo Buday, Kyou-Hoon Han, Andras Perczel, Peter Tompa
Sep 01, 2020
Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed...
cell protection chaperone client protein in-cell NMR intrinsic structural disorder pre-structured motif Arabidopsis Arabidopsis Proteins Escherichia coli Heat-Shock Response Intrinsically Disordered Proteins Microbial Viability Microorganisms Genetically-Modified Molecular Chaperones Protein Binding Protein Domains Proteome
Critical assessment of protein intrinsic disorder prediction.
Intrinsically disordered proteins, defying the traditional protein structure-function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial...
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14.
Nikoletta Murvai, Lajos Kalmar, Beata Szabo, Eva Schad, András Micsonai, József Kardos, László Buday, Kyou-Hoon Han, Peter Tompa, Agnes Tantos
Aug 02, 2021
Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins...
An intrinsically disordered proteins community for ELIXIR.
Norman E Davey, M Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J Edwards, Arne Elofsson, Isabella C Felli, Toby J Gibson, Aleksandras Gutmanas, John M Hancock, Jen Harrow, Desmond Higgins, Cy M Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C Shields, Joel L Sussman, Jonathan A Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio CE Tosatto
Jan 12, 2020
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments...
Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid-Liquid Phase Separation.
Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid-liquid phase separation (LLPS). The sequence of...
Purification of Recombinant α-synuclein
Amberley D Stephens, Dijana Matak-Vinkovic, Ana Fernandez-Villegas, Gabriele S Kaminski Schierle
Nov 23, 2020
The initial state of the intrinsically disordered protein α-synuclein (aSyn), e.g., the presence of oligomers and degradation products, or the presence of contaminants and adducts can greatly influence the aggregation kinetics...
Cell Line Cell Survival Chemical Precipitation Chromatography Gel Chromatography Ion Exchange Chromatography Liquid Escherichia coli Humans Intrinsically Disordered Proteins Microscopy Electron Transmission Protein Aggregates Protein Conformation Protein Conformation beta-Strand Recombinant Proteins Spectrometry Mass Electrospray Ionization ALPHA-SYNUCLEIN
Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence.
Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which...
Parallel and Sequential Pathways of Molecular Recognition of a Tandem-Repeat Protein and Its Intrinsically Disordered Binding Partner.
The Wnt signalling pathway plays an important role in cell proliferation, differentiation, and fate decisions in embryonic development and the maintenance of adult tissues. The twelve armadillo (ARM) repeat-containing protein...
Tcf Armadillo Repeat BETA-CATENIN Fuzzy Complex intrinsic disorder Intrinsically Disordered Protein Protein Folding protein-protein interactions repeat protein tandem-repeat protein Crystallography X-Ray Humans Intrinsically Disordered Proteins Mutagenesis Site-Directed Protein Structure Quaternary Transcription Factor 7-Like 2 Protein beta Catenin
Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein.
Joseph M Rogers, Vladimiras Oleinikovas, Sarah L Shammas, Chi T Wong, David De Sancho, Christopher M Baker, Jane Clarke
Oct 20, 2014
BCL-2 Protein Folding coarse-grained simulation Protein–protein interactions stopped flow Intrinsically Disordered Proteins Kinetics Ligands Molecular Dynamics Simulation Mutant Proteins Mutation Myeloid Cell Leukemia Sequence 1 Protein Protein Binding Protein Folding Protein Structure Secondary Proto-Oncogene Proteins
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