Topic 149

disordered intrinsically proteins idps residues structural biophysics protein conformational molecular idp simulations ensembles idrs folding interactions sequence interaction binding regions disorder amino structure experimental conformations nmr domains dynamics computational proteome ensemble how their coarse residue biophysical functional md hydrophobic different partners key experimentally contacts idr electrostatic folded specificity tertiary stability biological dynamic recognition saxs acids description formation many agreement complex understanding polymer ray grained nuclear affinity acid dynamical propensity them regulation solvent simple state kinetics structures scanning ordered function transient properties native make sequences context pathways allosteric experiments adopt allostery switch large domain cellular good phosphorylated motifs characterize spectroscopy helix

61 items. Top items listed below.

Intrinsically disordered protein ensembles shape evolutionary rates revealing conformational patterns 149 91 21 8 5

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein 149 91 78 8

Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins 149 91 78 8

Evolution of an interaction between disordered proteins resulted in increased heterogeneity of the binding transition state 149 78 8

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway 149 91 78 8

Probing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment 149 78 8

Molecular details of protein condensates probed by microsecond-long atomistic simulations 149 78 8

Protein Plasticity and its Role in Cellular Functions 149 8 3

Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins 149 8

Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics 149 105 13 4

Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence 149 78 8

NSP 11 of SARS-CoV-2 is an Intrinsically Disordered Protein 149 78 8

Integrating multiple experimental data to determine conformational ensembles of an intrinsically disordered protein 149 91 78 8

Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27 149 91 8

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins 149 91 78 26 8 4

Distance-based metrics for comparing conformational ensembles of intrinsically disordered proteins 149 91 8 4

Intrinsically disordered protein mutations can drive cancer and their targeted interference extends therapeutic options 149 142 14 9

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations 149 91 78 8

Structural and dynamic characterization of the C-terminal tail of ErbB2: disordered but not random 149 63 8 3

Predicting substitutions to modulate disorder and stability in coiled-coils 149 91 8

Conformational ordering of intrinsically disordered peptides for targeting translation initiation 149 63 8

Unexpected Specificity within Dynamic Transcriptional Protein-Protein Complexes 149 63 8 3

Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments 149 91 78 8

Identifying molecular features that are associated with biological function of intrinsically disordered protein regions 149

SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region 149 78 8

Identifying Sequence Perturbations to an Intrinsically Disordered Protein that Determine Its Phase Separation Behavior 78 8

Criticality in the conformational phase transition among self-similar groups in intrinsically disordered proteins: probed by salt-bridge dynamics 149 91 78 8

Intrinsic disorder in the T cell receptor creates cooperativity and controls ZAP70 binding 149 8

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ 149 91 78 8

How and why plants and humans N-glycans are different: Insight from molecular dynamics into the "glycoblocks" architecture of complex carbohydrates 149 91 8

Investigating the conformational ensembles of intrinsically-disordered proteins with a simple physics-based model 149 91 38 8 4

Short Peptides as Predictors for the Structure of Polyarginine Sequences in Disordered Proteins. 149 91 78 8

A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation 149 78 8

Experimentally determined long intrinsically disordered protein regions are now abundant in the Protein Data Bank 149 111 4

Disordered Proteins Enable Histone Chaperoning on the Nucleosome 149 8 3

Computational investigation for modelling the protein-protein interaction of TasA(28-261)with TapA(33-253); a decisive process in biofilm formation by Bacillus subtilis 149 8

Intrinsically disordered linkers control tethered kinases via effective concentration 149 8

Physical modelling of multivalent interactions in the nuclear pore complex 149 78 8

SWOTein: A structure-based approach to predict stability Strengths and Weaknesses of prOTEINs 149 91 63 8 4

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA 78 8

Conformational states of the cytoprotective protein Bcl-xL 91 78 63 8 3

Charge Interactions in a Highly Charge-depleted Protein 149 91 8

Unraveling molecular interactions in a phase-separating protein by atomistic simulations 78 8

A kinetic ensemble of the Alzheimer's Aβ peptide 91 78 38 8 4

Biophysical basis of cellular multi-specificity encoded in a model molecular switch 149 8 3

Sequence dependent co-phase separation of RNA-protein mixtures elucidated using molecular simulations 78 8

Order and disorder - an integrative structure of the full-length human growth hormone receptor 78 8

Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance 149 8

A large accessory protein interactome is rewired across environments 149 8

A High Accurate Machine Learning Meta-Strategy for the Prediction of Intrinsically Disorder Proteins 105 26 4

Multivalent interactions between eIF4G1, Pub1 and Pab1 drive the formation of protein condensates 149 78 8 3

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution 91 78 8

Structural basis of client specificity in mitochondrial membrane-protein chaperones 149 8

DIP/Dpr interactions and the evolutionary design of specificity in protein families 149 8

Using a simple cellular assay to map NES motifs in cancer-related proteins, gain insight into CRM1-mediated NES export, and search for NES-harbouring micropeptides 149 63 8

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations 78 8

A designer FG-Nup that reconstitutes the selective transport barrier of the Nuclear Pore Complex 149 78 8

Charge-Driven Phase Condensation of RNA and Proteins Suggests Broad Role of Phase Separation in Cytoplasmic Environments 78 8

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme 91 78 4

Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding 91 8 3

State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane 163 91 82 8 3

Epistasis shapes the fitness landscape of an allosteric specificity switch 149 63 8

Hydropathy patterning complements charge patterning to describe conformational preferences of disordered proteins 6

Diversification of DNA-binding specificity via permissive and specificity-switching mutations in the ParB/Noc protein family 149 8

Structure of Biomolecular Condensates from Dissipative Particle Dynamics Simulations 78 8

Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease 78 8

Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation 149 63 8

Extreme Fuzzy Association of an Intrinsically Disordered Protein with Acidic Membranes 78 8

Probing acetylated-α-synuclein monomer-aggregate complexes by NMR elucidates mechanism of fibril seeding 78 54 8 3

Mutational Survivorship Bias: The case of PNKP 149

Dynamic Order in Allosteric Interactions 149 8

Impact of phosphorylation on thermal stability of proteins 149 8

The electrostatic allostery could be the trigger for the changes in dynamics for the PDZ domain of PICK1 63 8 3

Refinement of protein structure via contact based potentials in replica exchange simulations 91 38 26 4

Monomeric amyloid beta-peptide (1-42) significantly populates compact fibril-like conformations 78 8

Beta Turn Propensity and Polymer Scaling Exponent Identify Intrinsically Disordered Proteins that Phase Separate 7

Multiple random phosphorylations in clock proteins provide long delays and switches 149 38 8

The intrinsically disordered N-terminus of the voltage-dependent anion channel 91 78 8

Automated and statistically corrected identification of flexible multivalent IDP-bound assemblies in electron micrographs 111 8 4

Structural model of the proline-rich domain of huntingtin exon-1 fibrils 78 8

Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors 134 31 8 3

The relation between intrinsic protein conformational changes and ligand binding 91 8

Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture 149 31 8 3

Critical Assessment of Protein Intrinsic Disorder Prediction 105 26 4

FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution 105 91 26 4

Programmed trade-offs in protein folding networks 149 129 8

SurA is a "Groove-y" Chaperone That Expands Unfolded Outer Membrane Proteins 8

Dynamics of chromosomal target search by a membrane-integrated one-component receptor 127 8 3

The Structural Basis of Rubisco Phase Separation in the Pyrenoid 51 8 3

Insights into actin polymerization and nucleation using a coarse grained model 111 51 8

Aggregation and Disaggregation Features of the Human Proteome 45

Membrane bending by protein phase separation 78 8

Ancient evolutionary origin of intrinsically disordered cancer risk regions 40 9 5

When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses 103 1

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens 37 1

Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates 136 49 8

Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone 78 8

Dynamics in Natural and Designed Elastins and Their Relation to Elastic Fiber Structure and Recoil 78 8

Discovering loop conformational flexibility in T4 lysozyme mutants through Artificial Intelligence aided Molecular Dynamics 91 8 4