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Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

https://doi.org/10.1101/734822
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cphc.201700450openalex-snapshot
Lipid Internal Dynamics Probed in Nanodiscs
inferredcites →https://doi.org/10.1002/jcc.20906openalex-snapshot
Fast procedure for reconstruction of full‐atom protein models from reduced representations
inferredcites →https://doi.org/10.1007/978-1-0716-0270-6_15openalex-snapshot
Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach
inferredcites →https://doi.org/10.1007/s00232-010-9296-8openalex-snapshot
Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations
inferredcites →https://doi.org/10.1007/s13361-013-0782-yopenalex-snapshot
Interpretation and Deconvolution of Nanodisc Native Mass Spectra
inferredcites →https://doi.org/10.1016/bs.pmbts.2019.12.006openalex-snapshot
How to learn from inconsistencies: Integrating molecular simulations with experimental data
inferredcites →https://doi.org/10.1016/j.bbamem.2012.12.011openalex-snapshot
Modified lipid and protein dynamics in nanodiscs
inferredcites →https://doi.org/10.1016/j.bpj.2013.07.020openalex-snapshot
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments
inferredcites →https://doi.org/10.1016/j.bpj.2015.06.032openalex-snapshot
Small-Angle X-Ray Scattering of the Cholesterol Incorporation into Human ApoA1-POPC Discoidal Particles
inferredcites →https://doi.org/10.1016/j.softx.2015.06.001openalex-snapshot
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
inferredcites →https://doi.org/10.1016/j.str.2010.10.006openalex-snapshot
SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions
inferredcites →https://doi.org/10.1016/s0001-8686(97)00312-6openalex-snapshot
Analysis of small-angle scattering data from colloids and polymer solutions: modeling and least-squares fitting
inferredcites →https://doi.org/10.1016/s0006-3495(02)75333-2openalex-snapshot
Structure of Gel Phase DMPC Determined by X-Ray Diffraction
inferredcites →https://doi.org/10.1016/s0014-5793(03)01400-5openalex-snapshot
Phospholipid phase transitions in homogeneous nanometer scale bilayer discs
inferredcites →https://doi.org/10.1016/s0076-6879(09)64011-8openalex-snapshot
Reconstitution of Membrane Proteins in Phospholipid Bilayer Nanodiscs
inferredcites →https://doi.org/10.1021/acs.analchem.5b00140openalex-snapshot
Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles
inferredcites →https://doi.org/10.1021/acs.jctc.5b00668openalex-snapshot
Molecular Models of Nanodiscs
inferredcites →https://doi.org/10.1021/acs.jctc.5b00935openalex-snapshot
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
inferredcites →https://doi.org/10.1021/acs.jctc.6b00944openalex-snapshot
Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
inferredcites →https://doi.org/10.1021/acs.jctc.7b00643openalex-snapshot
On the Calculation of Acyl Chain Order Parameters from Lipid Simulations
inferredcites →https://doi.org/10.1021/acs.jpcb.5b02101openalex-snapshot
Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations
inferredcites →https://doi.org/10.1021/acs.jpcb.5b08463openalex-snapshot
Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations
inferredcites →https://doi.org/10.1021/acs.jpcb.6b07753openalex-snapshot
All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10
inferredcites →https://doi.org/10.1021/acs.jpclett.5b02399openalex-snapshot
Structural Properties of Protein–Detergent Complexes from SAXS and MD Simulations
inferredcites →https://doi.org/10.1021/acs.langmuir.8b01503openalex-snapshot
Comprehensive Study of the Self-Assembly of Phospholipid Nanodiscs: What Determines Their Shape and Stoichiometry?
inferredcites →https://doi.org/10.1021/bi000060hopenalex-snapshot
Utilization of Site-Directed Spin Labeling and High-Resolution Heteronuclear Nuclear Magnetic Resonance for Global Fold Determination of Large Proteins with Limited Nuclear Overhauser Effect Data
inferredcites →https://doi.org/10.1021/ja031580dopenalex-snapshot
Ensemble Approach for NMR Structure Refinement against1H Paramagnetic Relaxation Enhancement Data Arising from a Flexible Paramagnetic Group Attached to a Macromolecule
inferredcites →https://doi.org/10.1021/ja0393574openalex-snapshot
Directed Self-Assembly of Monodisperse Phospholipid Bilayer Nanodiscs with Controlled Size
inferredcites →https://doi.org/10.1021/ja1030613openalex-snapshot
Elliptical Structure of Phospholipid Bilayer Nanodiscs Encapsulated by Scaffold Proteins: Casting the Roles of the Lipids and the Protein
inferredcites →https://doi.org/10.1021/ja310901fopenalex-snapshot
Optimized Phospholipid Bilayer Nanodiscs Facilitate High-Resolution Structure Determination of Membrane Proteins
inferredcites →https://doi.org/10.1021/jp051385gopenalex-snapshot
Thermotropic Phase Transition in Soluble Nanoscale Lipid Bilayers
inferredcites →https://doi.org/10.1021/jp072320bopenalex-snapshot
Assembly of Lipids and Proteins into Lipoprotein Particles
inferredcites →https://doi.org/10.1021/nl025623kopenalex-snapshot
Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins
inferredcites →https://doi.org/10.1038/nmeth.4067openalex-snapshot
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
inferredcites →https://doi.org/10.1038/nsmb.2026openalex-snapshot
Cryo-EM structure of the ribosome–SecYE complex in the membrane environment
inferredcites →https://doi.org/10.1038/nsmb.3345openalex-snapshot
Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I
inferredcites →https://doi.org/10.1039/c0cp01074jopenalex-snapshot
Small-angle scattering from phospholipid nanodiscs: derivation and refinement of a molecular constrained analytical model form factor
inferredcites →https://doi.org/10.1039/c0cp01865aopenalex-snapshot
Rotamer libraries of spin labelled cysteines for protein studies
inferredcites →https://doi.org/10.1039/c2sm26007gopenalex-snapshot
GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid
inferredcites →https://doi.org/10.1039/c3sm51727fopenalex-snapshot
Self-assembling peptides form nanodiscs that stabilize membrane proteins
inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
Canonical sampling through velocity rescaling
inferredcites →https://doi.org/10.1063/1.439059openalex-snapshot
Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances
inferredcites →https://doi.org/10.1063/1.4937786openalex-snapshot
Bayesian ensemble refinement by replica simulations and reweighting
inferredcites →https://doi.org/10.1073/pnas.0403643101openalex-snapshot
Random-coil behavior and the dimensions of chemically unfolded proteins
inferredcites →https://doi.org/10.1073/pnas.95.5.2267openalex-snapshot
Protein hydration in solution: Experimental observation by x-ray and neutron scattering
inferredcites →https://doi.org/10.1093/bioinformatics/bts172openalex-snapshot
Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables
inferredcites →https://doi.org/10.1093/bioinformatics/btt055openalex-snapshot
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
inferredcites →https://doi.org/10.1093/nar/gkw389openalex-snapshot
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles
inferredcites →https://doi.org/10.1101/gr.9.11.1106openalex-snapshot
Exploring Expression Data: Identification and Analysis of Coexpressed Genes
inferredcites →https://doi.org/10.1107/s0021889813026022openalex-snapshot
WillItFit: a framework for fitting of constrained models to small-angle scattering data
inferredcites →https://doi.org/10.1107/s0021889893001335openalex-snapshot
On the shape of the radial distribution function of an assembly of monodisperse ellipsoidal scatterers
inferredcites →https://doi.org/10.1107/s0021889895007047openalex-snapshot
CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
inferredcites →https://doi.org/10.1107/s0021889899015216openalex-snapshot
SAXS experiments on absolute scale with Kratky systems using water as a secondary standard
inferredcites →https://doi.org/10.1107/s0909049513010431openalex-snapshot
Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution
inferredcites →https://doi.org/10.1107/s1399004713027466openalex-snapshot
Stealth carriers for low-resolution structure determination of membrane proteins in solution
inferredcites →https://doi.org/10.1107/s1600576714013156openalex-snapshot
Update for BayesApp: a web site for analysis of small-angle scattering data
inferredcites →https://doi.org/10.1107/s160057671500254xopenalex-snapshot
Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)
inferredcites →https://doi.org/10.1107/s1600576716016514openalex-snapshot
SEC-SANS: size exclusion chromatography combined in situ with small-angle neutron scattering
inferredcites →https://doi.org/10.1107/s1600576717018441openalex-snapshot
Interpretation of solution scattering data from lipid nanodiscs
inferredcites →https://doi.org/10.1107/s2059798318007180openalex-snapshot
Introducing SEC–SANS for studies of complex self-organized biological systems
inferredcites →https://doi.org/10.1126/sciadv.aar8521openalex-snapshot
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
inferredcites →https://doi.org/10.1126/science.aat4010openalex-snapshot
Biophysical experiments and biomolecular simulations: A perfect match?
inferredcites →https://doi.org/10.1371/journal.pone.0039492openalex-snapshot
Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements
inferredcites →https://doi.org/10.1529/biophysj.104.046896openalex-snapshot
Molecular Dynamics Simulations of Discoidal Bilayers Assembled from Truncated Human Lipoproteins

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1021/acs.jpclett.9b03154openalex-snapshot
Small-Angle X-ray Scattering Curves of Detergent Micelles: Effects of Asymmetry, Shape Fluctuations, Disorder, and Atomic Details
inferred← citeshttps://doi.org/10.3390/molecules25204783openalex-snapshot
Combining Experimental Data and Computational Methods for the Non-Computer Specialist
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