Kinetics of conformational sampling in ubiquitin.

PubWeight™: 1.07‹?› | Rank: Top 10%

🔗 View Article (PMID 22113802)

Published in Angew Chem Int Ed Engl on October 05, 2011

Authors

David Ban1, Michael Funk, Rudolf Gulich, Dalia Egger, T Michael Sabo, Korvin F A Walter, R Bryn Fenwick, Karin Giller, Fabio Pichierri, Bert L de Groot, Oliver F Lange, Helmut Grubmüller, Xavier Salvatella, Martin Wolf, Alois Loidl, Reiner Kree, Stefan Becker, Nils-Alexander Lakomek, Donghan Lee, Peter Lunkenheimer, Christian Griesinger

Author Affiliations

1: Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Articles citing this

Chemical exchange in biomacromolecules: past, present, and future. J Magn Reson (2014) 1.24

Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling. Proc Natl Acad Sci U S A (2013) 0.99

Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc (2013) 0.97

Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. J Am Chem Soc (2012) 0.97

Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. J Biomol NMR (2013) 0.97

Ligand binding to anion-binding exosites regulates conformational properties of thrombin. J Biol Chem (2013) 0.93

NMR studies of nucleic acid dynamics. J Magn Reson (2013) 0.91

Using Protein Motion to Read, Write, and Erase Ubiquitin Signals. J Biol Chem (2015) 0.86

Allosteric switch regulates protein-protein binding through collective motion. Proc Natl Acad Sci U S A (2016) 0.83

Internal protein dynamics on ps to μs timescales as studied by multi-frequency (15)N solid-state NMR relaxation. J Biomol NMR (2013) 0.83

Chemical shifts in biomolecules. Curr Opin Struct Biol (2013) 0.81

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges. Front Genet (2014) 0.80

Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins. J Magn Reson (2012) 0.79

ORIUM: optimized RDC-based Iterative and Unified Model-free analysis. J Biomol NMR (2013) 0.79

Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy. J Biomol NMR (2013) 0.78

3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers. Cell Logist (2012) 0.78

Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR. Protein Sci (2015) 0.78

Speeding-up exchange-mediated saturation transfer experiments by Fourier transform. J Biomol NMR (2015) 0.77

Population shuffling between ground and high energy excited states. Protein Sci (2015) 0.75

Cold-induced changes in the protein ubiquitin. PLoS One (2012) 0.75

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin. PLoS Comput Biol (2017) 0.75

Combining experimental and simulation data of molecular processes via augmented Markov models. Proc Natl Acad Sci U S A (2017) 0.75

Articles by these authors

Molecular anatomy of a trafficking organelle. Cell (2006) 11.47

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33

Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A (2007) 3.96

Anatomy and dynamics of a supramolecular membrane protein cluster. Science (2007) 3.75

Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein. Proc Natl Acad Sci U S A (2005) 3.48

Molecular-level secondary structure, polymorphism, and dynamics of full-length alpha-synuclein fibrils studied by solid-state NMR. Proc Natl Acad Sci U S A (2005) 3.37

NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00

Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature (2004) 2.84

A review on continuous wave functional near-infrared spectroscopy and imaging instrumentation and methodology. Neuroimage (2013) 2.83

Structure of the human voltage-dependent anion channel. Proc Natl Acad Sci U S A (2008) 2.69

Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des (2010) 2.67

Membrane protein sequestering by ionic protein-lipid interactions. Nature (2011) 2.40

Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR. Nature (2006) 2.34

Effect of sodium chloride on a lipid bilayer. Biophys J (2003) 2.24

Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21

Crystal structure of the endosomal SNARE complex reveals common structural principles of all SNAREs. Nat Struct Biol (2002) 2.21

Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J (2006) 2.19

Mechanoenzymatics of titin kinase. Proc Natl Acad Sci U S A (2008) 2.17

Generalized correlation for biomolecular dynamics. Proteins (2006) 2.17

Staged percutaneous coronary intervention and minimally invasive valve surgery: results of a hybrid approach to concomitant coronary and valvular disease. J Thorac Cardiovasc Surg (2011) 2.15

β-synuclein aggregates and induces neurodegeneration in dopaminergic neurons. Ann Neurol (2013) 2.10

Pre-fibrillar alpha-synuclein variants with impaired beta-structure increase neurotoxicity in Parkinson's disease models. EMBO J (2009) 2.09

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem (2010) 2.08

Atomic model of the type III secretion system needle. Nature (2012) 2.02

Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. J Am Chem Soc (2005) 2.02

Predicting free energy changes using structural ensembles. Nat Methods (2009) 1.93

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nat Struct Biol (2002) 1.92

The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol (2003) 1.80

Defining long-range order and local disorder in native alpha-synuclein using residual dipolar couplings. J Am Chem Soc (2005) 1.75

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc (2009) 1.75

Force spectroscopy of single biomolecules. Chemphyschem (2002) 1.73

Noninvasive determination of the optical properties of adult brain: near-infrared spectroscopy approach. J Biomed Opt (2004) 1.70

Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys J (2004) 1.70

Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A (2008) 1.67

The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr Opin Struct Biol (2005) 1.65

Model-free analysis of protein backbone motion from residual dipolar couplings. J Am Chem Soc (2002) 1.65

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR (2007) 1.65

Measurement and modeling of microlenses fabricated on single-photon avalanche diode arrays for fill factor recovery. Opt Express (2014) 1.63

Photonic textiles for pulse oximetry. Opt Express (2008) 1.63

A ligand-induced switch in the periplasmic domain of sensor histidine kinase CitA. J Mol Biol (2008) 1.61

Structural polymorphism of 441-residue tau at single residue resolution. PLoS Biol (2009) 1.61

Single-molecule FRET measures bends and kinks in DNA. Proc Natl Acad Sci U S A (2008) 1.58

Structure and function of water channels. Curr Opin Struct Biol (2002) 1.55

Sites of tau important for aggregation populate {beta}-structure and bind to microtubules and polyanions. J Biol Chem (2005) 1.54

A concept for rapid protein-structure determination by solid-state NMR spectroscopy. Angew Chem Int Ed Engl (2005) 1.53

Structural characterization of copper(II) binding to alpha-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease. Proc Natl Acad Sci U S A (2005) 1.50

Multistep binding of divalent cations to phospholipid bilayers: a molecular dynamics study. Angew Chem Int Ed Engl (2004) 1.50

Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. J Am Chem Soc (2007) 1.49

The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli. J Biol Chem (2003) 1.48

Full correlation analysis of conformational protein dynamics. Proteins (2008) 1.47

Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem (2006) 1.46

Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition. J Am Chem Soc (2011) 1.45

Topotecan/cisplatin compared with cisplatin/etoposide as first-line treatment for patients with extensive disease small-cell lung cancer: final results of a randomized phase III trial. J Thorac Oncol (2012) 1.45

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43

Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol (2013) 1.41

Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol (2009) 1.41

NMR of alpha-synuclein-polyamine complexes elucidates the mechanism and kinetics of induced aggregation. EMBO J (2004) 1.41

Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nat Struct Mol Biol (2011) 1.41

Interaction of urea with amino acids: implications for urea-induced protein denaturation. J Am Chem Soc (2007) 1.39

Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat Struct Mol Biol (2013) 1.38

Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods (2009) 1.38

Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin. Angew Chem Int Ed Engl (2009) 1.38

Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J (2002) 1.37

Structural properties of pore-forming oligomers of alpha-synuclein. J Am Chem Soc (2009) 1.36

A structural link between inactivation and block of a K+ channel. Nat Struct Mol Biol (2008) 1.36

Protein refolding is required for assembly of the type three secretion needle. Nat Struct Mol Biol (2010) 1.36

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. J Am Chem Soc (2011) 1.35

A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J Biomol NMR (2006) 1.34

Anle138b: a novel oligomer modulator for disease-modifying therapy of neurodegenerative diseases such as prion and Parkinson's disease. Acta Neuropathol (2013) 1.34

Measurement of brain activity by near-infrared light. J Biomed Opt (2005) 1.34

Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33

Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33