Topic 78

biophysics lipid membrane disordered membranes separation phase simulations formation liquid condensates amyloid bilayer proteins protein intrinsically aggregation lipids fibrils bilayers oligomers dynamics molecular interactions properties coarse condensate biomolecular conformational assembly binding form nmr grained formed aggregates biophysical vesicles fibril ordered structural beta spectroscopy curvature hydrophobic self domains membraneless force condensation forms llps transition peptide charged droplets residues md nucleation into multivalent separated forming experiments molecules structure energy state domain surface mechanism like idps here assemble atomistic microscopy conformation neurodegenerative concentration polymer oligomer free process find structures solution terminal organelles composition helical cellular model aggregate atom dynamic kinetics plasma propensity ensemble

292 items. Top items listed below.

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

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

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

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

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

Cholesterol in membranes facilitates aggregation of amyloid beta protein at physiologically low concentrations 78 32 8

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

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

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

Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates 78 8

Physical mechanisms of amyloid nucleation on fluid membranes 78 8

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

Membrane bending by protein phase separation 78 8

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

Structure of Biomolecular Condensates from Dissipative Particle Dynamics Simulations 78 8

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

All protein aggregates will thermodynamically order 78 8

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

Heterogeneous aggregation of amyloid-β 42 from single-molecule spectroscopy 78 32 8

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

C subunit of the ATP synthase is an amyloidogenic channel-forming peptide: possible implications in mitochondrial pathogenesis 78 8 3

Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion 78 8

Widespread occurrence of the droplet state of proteins in the human proteome 78 8

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

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

Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies 78 54 8 3

Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy 78 51 8

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

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

Lipid droplet biogenesis is driven by a liquid-liquid phase separation. 69 34 8 3

Rapid formation of peptide/lipid co-aggregates by the amyloidogenic seminal peptide PAP248-286 78 8

Lipid membranes from naked mole-rat brain lipids are cholesterol-rich, highly phase-separated, and sensitive to amyloid-induced damage 78 8

Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation 78 8

Biomolecular condensates undergo a generic shear-mediated liquid-to-solid transition 78 8 3

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

Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks 78 8

Structural Insights on Fusion Mechanisms of Extracellular Vesicles with Model Plasma Membrane 78 8

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

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions 78 8

Melatonin alters fluid phase co-existence in POPC/DPPC/cholesterol membranes 78 8 3

Oligonucleotides can act as superscaffolds that enhance liquid-liquid phase separation of intracellular mixtures 78 8

Structure-function properties in disordered condensates 78 8

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

Membrane interactions accelerate the self-aggregation of huntingtin exon 1 fragments in a polyglutamine length-dependent manner 78 8

Phosphatidylserine prevents the generation of a protein-free giant plasma membrane domain in yeast 78 34 8 3

Mesoscopic Liquid Clusters Represent a Distinct Condensate of Mutant p53 78 8 3

Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation 78 8

Decoding the physical principles of two-component biomolecular phase separation 78 8

3D-Visualization of Amyloid-β Oligomer and Fibril Interactions with Lipid Membranes by Cryo-Electron Tomography 78 8 3

Coupling between lipid miscibility and phosphotyrosine driven protein condensation at the membrane 78 34 8 3

Coexistence of long and short DNA constructs within adhesion plaques 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

Membrane-mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins 163 78 8

Modulation of host lipid membrane elasticity and dipole potential induced by bacterial membrane vesicles 78 8 3

GPCR Oligomerisation Modulation by Conformational State and Lipid Interactions Revealed by MD Simulations and Markov Models 91 78 8 3

Integrated multi-omics reveals common properties underlying stress granule and P-body formation 78 49 8 3

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

Receptor-independent membrane mediated pathways of serotonin action 78 7 3

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

Megadalton-sized dityrosine aggregates of α-synuclein retain high degrees of structural disorder and internal dynamics. 78 8

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

Polymer Stiffness Regulates Multivalent Binding and Liquid-Liquid Phase Separation 78 8

Modelling fibrillogenesis of collagen-mimetic molecules 78 8

The Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor 163 91 78 63 8 3

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

Surface condensation of a pioneer transcription factor on DNA 78 8

Phe-Gly Motifs Drive Fibrillization of TDP-43's Prion-Like Domain Droplets 78 8

Super-elasticity of plasma- and synthetic membranes by coupling of membrane asymmetry and liquid-liquid phase separation 78 8

Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein 78 8 3

Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange Between Membranes 78 8

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

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

Rapid Generation of Protein Condensate Phase Diagrams Using Combinatorial Droplet Microfluidics 78 18 8

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

Nucleation-dependent aggregation kinetics of Yeast Sup35 fragment GNNQQNY 78 8

Effect of cholesterol vs. ergosterol on DPPC bilayer properties: insights from atomistic simulations 78 8

Asymmetric phospholipids impart novel biophysical properties to lipid bilayers allowing environmental adaptation 78 8

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

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

Simulation of FUS protein condensates with an adapted coarse-grained model 78 8

Kinetic analysis reveals the rates and mechanisms of protein aggregation in a multicellular organism 78 38 8

Sequence dependence of biomolecular phase separation 78 8

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

Transport Phenomena in Fluid Films with Curvature Elasticity 78 8

Impact of nanoscale hindrances on the relationship between lipid packing and diffusion in model membranes 78 8

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

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

Lipopolysaccharide Simulations are Sensitive to Phosphate Charge and Ion Parameterization 78 8

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

Kindlin2-mediated phase separation underlies integrin adhesion formation 78 8 3

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

Endophilin Recruitment via GPCR Interactions Enables Membrane Curvature Generation in the Absence of Anionic Lipids 163 78 8 3

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities 78 8

Calcium ions promote membrane fusion by forming negative-curvature inducing clusters on specific anionic lipids 78 8

Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes 78 8

Assembly of bacterial cell division protein FtsZ into dynamic biomolecular condensates 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

ATP regulates TDP-43 pathogenesis by specifically binding to an inhibitory component of a delicate network controlling LLPS 78 8 3

Assessing the Extent of Structural and Dynamic Modulation of Membrane Lipids due to Pore Forming Toxins: Insights from Molecular Dynamics Simulations 78 8

Annexin A4 trimers are recruited by high membrane curvatures in Giant Plasma Membrane Vesicles 78 8