Topic 8

biophysics binding biochemistry proteins structural protein membrane structure domain structures molecular microscopy interactions conformational bound cryo domains residues dynamics simulations site mechanism complex terminal molecule complexes crystal formation interaction conformation electron substrate resolution assembly molecules form force membranes surface bind em lipid its catalytic affinity fluorescence here active conserved binds transmembrane biochemical energy into atomic helix conformations cellular properties forms helical biophysical dynamic transport residue disordered state hydrophobic ray eukaryotic kinetic chemical kinetics reveal enzyme ligand filaments spectroscopy like folding peptide amino actin substrates basis subunits formed essential allosteric loop outer nmr native sites subunit function recognition interface how reveals

3046 items. Top items listed below.

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

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

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

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

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

Evolution of structural dynamics in bilobed proteins 63 8 3

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

Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation 34 8 3

Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation 51 8 3

Cholesterol sensing by CD81 is important for hepatitis C virus entry 91 63 8 3

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

Allosteric communications between domains modulate activity of matrix metalloprotease-1 91 63 8

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

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

Structure of the ancestral TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium 51 8 3

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

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

Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein 51 8

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

Conformational state switching and pathways of chromosome dynamics in cell cycle 7

Structural basis of Rgg protein binding to their regulatory pheromones and target DNA promoters 51 8 3

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

Network analysis reveals how lipids and other cofactors influence membrane protein allostery 82 8

Insulin-Induced Conformational Changes in the Full-Length Insulin Receptor: Structural Insights Gained from Molecular Modeling Analyses 91 8

The flexibility of ACE2 in the context of SARS-CoV-2 infection 36 1

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning 111 51 8 4

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

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Atomistic Mechanism of Force Generation, Translocation, and Coordination in a Viral Genome Packaging Motor 51 8

Membrane bending by protein phase separation 78 8

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

Discovery of 20 novel ribosomal leaders in bacteria and archaea 49 31 8

Proteins and Ions Compete for Membrane Interaction: the case of Lactadherin 78 8 3

Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein 8 3

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR 78 8

HIV-1 Gag protein with or without p6 specifically dimerizes on the viral RNA packaging signal 8 3

The cryo-electron microscopy structure of the human CDK-activating kinase 119 51 8 3

Towards the molecular architecture of the peroxisomal receptor docking complex 8 3

Structural basis for the recognition of the 2019-nCoV by human ACE2 36 1

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

Functional anatomy of the full length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis 63 8

Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs 51 8 3

Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation 44 1

Real-Time Observation of Structure and Dynamics during the Liquid-to-Solid Transition of FUS LC 78 8

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

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA 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 Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor 163 91 78 63 8 3

SepF is the FtsZ-anchor in Archaea: implications for cell division in the Last Universal Common Ancestor 8 3

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs 134 49 31 9 3

A sodium-dependent communication pathway across class A G-protein coupled receptors 91 63 8 3

Cotranslational protein folding can promote the formation of correct folding intermediate 91 78 8

Cryo-EM structure of the fully-loaded asymmetric anthrax lethal toxin in its heptameric pre-pore state 51 8 3

High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism 63 8

Cryo-EM structures reveal a multistep mechanism of Hsp90 activation by co-chaperone Aha1 51 7 3

Clathrin senses membrane curvature 151 34 8

Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein 36 1

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

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data 111 105 26 4

Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions 55 8 3

TMEM70 forms oligomeric scaffolds within mitochondrial cristae promoting in situ assembly of mammalian ATP synthase proton channel 8 3

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

A Glu-Glu-Tyr sequence in the cytoplasmic tail of the M2 protein renders IAV susceptible to restriction of HA-M2 association in primary human macrophages 41 34 8 3

A conformational switch driven by phosphorylation regulates Ykt6 activity in macroautophagy 34 8 3

Structural Determinants of Cholesterol Recognition in Helical Integral Membrane Proteins 8

A Molecular View of Lipid-mediated Activation Process of Apolipoprotein E 91 8

Understanding the photophysics and structural organization of photosynthetic proteins using model lipid membranes assembled from natural plant thylakoids 117 78 8

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

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data 38 8

Long-range coupled motions underlie ligand recognition by a chemokine receptor 91 63 8

Molecular mechanism for direct actin force-sensing by α-catenin 55 51 8 3

Structural basis of mechano-chemical coupling by the mitotic kinesin KIF14 51 8 3

Structural basis for the activation of CDK7 by MAT1 and Cyclin H 119 63 8 3

Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics 24 1

Structural studies of Cardiovirus 2A protein reveal the molecular basis for RNA recognition and translational control 51 8 3

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

Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling 55 38 8

Same, Same, but Different: Molecular Analyses of Streptococcus pneumoniae Immune Evasion Proteins Identifies new Domains and Reveals Structural Differences between PspC and Hic Variants 121 114 12 9 8

Actin-binding compounds, discovered by FRET-based high-throughput screening, differentially affect skeletal and cardiac muscle 55 8

Predicting global dynamics of spatial microbial communities from local interaction rules 158 99 38 17 5

Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation 119 31 8 3

Single-particle cryo-EM at atomic resolution 111 51 8 4

The extent of protein hydration dictates the preference for heterogeneous or homogeneous nucleation generating either parallel or antiparallel β-sheet α-synuclein aggregates 78 8

Cooperativity of membrane-protein and protein-protein interactions control membrane remodeling by epsin 1 and regulate clathrin-mediated endocytosis 78 34 8 3

Various miRNAs are involved in efficient HCV replication 41 8 3

Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins 8

Coarse-grained molecular simulations of the binding of the SARS-CoV 2 spike protein RBD to the ACE2 receptor 36 1

Structures, conformations and distributions of SARS-CoV-2 spike protein trimers on intact virions 36 1

Transport mechanism of class-3 P4 ATPase lipid flippases 63 8 3

Saccharomyces cerevisiae Ecm2 Modulates the Catalytic Steps of pre-mRNA Splicing 51 49 8 3

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

New functional identity of the essential inner membrane protein YejM: the cardiolipin translocator is also a metalloenzyme 79 52 8 3

Determining the domain-level reaction-diffusion properties of cellular proteins by incorporating genetic engineering to FRAP-based framework 8

Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae 69 34 3

Mechanism of Dynamic Binding of Replication Protein A to ssDNA 91 8

Single-molecule spectroscopy reveals dynamic allostery mediated by the substrate-binding domain of a AAA+ machine 91 8 3

Cryo-EM structure of the MgtE Mg2+ channel pore domain in Mg2+-free conditions reveals cytoplasmic pore opening 51 8 3

Structural basis of SARS-CoV-2 spike protein induced by ACE2 36 1

A predictive model of antibody binding in the presence of IgG-interacting bacterial surface proteins 79 8

Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate. 51 8