Published in PLoS Comput Biol on January 06, 2016
Allostery: An Overview of Its History, Concepts, Methods, and Applications. PLoS Comput Biol (2016) 0.84
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol (2005) 7.73
AAA+ superfamily ATPases: common structure--diverse function. Genes Cells (2001) 5.83
Posttranslational quality control: folding, refolding, and degrading proteins. Science (1999) 5.55
The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature (2000) 4.46
Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines. Nature (2005) 4.05
Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell (2003) 3.95
AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem (2011) 3.60
Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol (2008) 3.41
ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol Cell (2001) 3.36
Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell (2003) 3.33
The nature of folded states of globular proteins. Biopolymers (1992) 2.91
Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome. J Mol Biol (1995) 2.53
On helicases and other motor proteins. Curr Opin Struct Biol (2008) 2.43
Single-molecule protein unfolding and translocation by an ATP-fueled proteolytic machine. Cell (2011) 2.40
Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell (2005) 2.33
ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell (2011) 2.31
Crystal and solution structures of an HslUV protease-chaperone complex. Cell (2000) 2.29
ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle. Cell (2011) 2.27
A corrected quaternary arrangement of the peptidase HslV and atpase HslU in a cocrystal structure. J Struct Biol (2001) 2.17
Point mutations alter the mechanical stability of immunoglobulin modules. Nat Struct Biol (2000) 2.12
The ClpXP protease unfolds substrates using a constant rate of pulling but different gears. Cell (2013) 2.06
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU. Structure (2001) 2.02
Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A (2002) 1.99
Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J Biol Chem (2002) 1.97
Protein unfolding by a AAA+ protease is dependent on ATP-hydrolysis rates and substrate energy landscapes. Nat Struct Mol Biol (2008) 1.95
Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J (2001) 1.95
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95
A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-kappaB. Nat Struct Mol Biol (2005) 1.91
ClpX and MuB interact with overlapping regions of Mu transposase: implications for control of the transposition pathway. Genes Dev (1997) 1.85
The ATP-dependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome. Nat Struct Biol (1997) 1.81
Mutational studies on HslU and its docking mode with HslV. Proc Natl Acad Sci U S A (2000) 1.79
The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate. J Biol Chem (1990) 1.77
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci U S A (2007) 1.74
Crystal structure of ClpX molecular chaperone from Helicobacter pylori. J Biol Chem (2003) 1.72
Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis. J Biol Chem (2003) 1.61
Six-fold rotational symmetry of ClpQ, the E. coli homolog of the 20S proteasome, and its ATP-dependent activator, ClpY. FEBS Lett (1996) 1.60
Mechanically unfolding the small, topologically simple protein L. Biophys J (2005) 1.57
Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase. J Biol Chem (2005) 1.53
Substrate recognition by the ClpA chaperone component of ClpAP protease. J Biol Chem (2000) 1.45
High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell (2012) 1.35
Coarse-grained sequences for protein folding and design. Proc Natl Acad Sci U S A (2003) 1.35
Glycine-alanine repeats impair proper substrate unfolding by the proteasome. EMBO J (2006) 1.34
At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease. J Struct Biol (1998) 1.34
Stepwise unfolding of a β barrel protein by the AAA+ ClpXP protease. J Mol Biol (2011) 1.33
Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A (2013) 1.33
ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence. Proc Natl Acad Sci U S A (2002) 1.30
Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine. Nat Struct Mol Biol (2012) 1.26
Slippery substrates impair function of a bacterial protease ATPase by unbalancing translocation versus exit. J Biol Chem (2013) 1.22
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. Proc Natl Acad Sci U S A (2009) 1.21
Complementation and reconstitution of fluorescence from circularly permuted and truncated green fluorescent protein. Biochemistry (2009) 1.16
Asymmetric nucleotide transactions of the HslUV protease. J Mol Biol (2008) 1.16
Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine. Cell (2014) 1.15
Intermediates and the folding of proteins L and G. Protein Sci (2004) 1.13
Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc Natl Acad Sci U S A (2009) 1.11
ClpA and ClpX ATPases bind simultaneously to opposite ends of ClpP peptidase to form active hybrid complexes. J Struct Biol (2004) 1.10
Matching simulation and experiment: a new simplified model for simulating protein folding. J Comput Biol (2000) 1.03
Translocation of a knotted polypeptide through a pore. J Chem Phys (2008) 1.03
Mechanochemical basis of protein degradation by a double-ring AAA+ machine. Nat Struct Mol Biol (2014) 1.02
Mechanical unfolding revisited through a simple but realistic model. J Chem Phys (2006) 1.02
Force-induced change in protein unfolding mechanism: discrete or continuous switch? J Phys Chem B (2011) 0.99
Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore. J Chem Phys (2005) 0.99
Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore. Phys Rev Lett (2012) 0.99
Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein. Proc Natl Acad Sci U S A (2007) 0.96
Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine. Nat Chem Biol (2015) 0.95
Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations. Proc Natl Acad Sci U S A (2009) 0.92
Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. J Am Chem Soc (2015) 0.89
Docking of components in a bacterial complex. Nature (2000) 0.89
Critical clamp loader processing by an essential AAA+ protease in Caulobacter crescentus. Proc Natl Acad Sci U S A (2013) 0.89
From structure to function: the convergence of structure based models and co-evolutionary information. Phys Chem Chem Phys (2014) 0.88
Prediction of the translocation kinetics of a protein from its mechanical properties. Biophys J (2006) 0.87
The molecular mechanism underlying mechanical anisotropy of the protein GB1. Biophys J (2012) 0.84
The I domain of the AAA+ HslUV protease coordinates substrate binding, ATP hydrolysis, and protein degradation. Protein Sci (2012) 0.84
Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling. Biophys J (2010) 0.84
Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase. Proc Natl Acad Sci U S A (2011) 0.82
Periodic forces trigger a complex mechanical response in ubiquitin. J Mol Biol (2009) 0.80
Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines. J Chem Phys (2013) 0.78
Mechanism of transient binding and release of substrate protein during the allosteric cycle of the p97 nanomachine. J Am Chem Soc (2013) 0.78
Protein unfolding by biological unfoldases: insights from modeling. Biophys J (2014) 0.78
ClpX shifts into high gear to unfold stable proteins. Cell (2013) 0.77
Computer simulation of I27 translocation through ClpY reveals a critical role of protein mechanical strength and local stability. Conf Proc IEEE Eng Med Biol Soc (2007) 0.77
Protein unfolding under force: crack propagation in a network. Biophys J (2011) 0.77