Published in J Mol Biol on October 13, 2005
P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci U S A (2006) 2.01
Stabilizing IkappaBalpha by "consensus" design. J Mol Biol (2006) 1.53
Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci (2009) 1.52
Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Arch Biochem Biophys (2007) 1.51
Complex energy landscape of a giant repeat protein. Structure (2013) 1.41
Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A (2009) 1.39
Rational redesign of the folding pathway of a modular protein. Proc Natl Acad Sci U S A (2007) 1.37
Pre-folding IkappaBalpha alters control of NF-kappaB signaling. J Mol Biol (2008) 1.35
Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol (2008) 1.31
Probing a moving target with a plastic unfolding intermediate of an ankyrin-repeat protein. Proc Natl Acad Sci U S A (2007) 1.25
Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry (2010) 1.25
The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol (2008) 1.25
Protein frustratometer: a tool to localize energetic frustration in protein molecules. Nucleic Acids Res (2012) 1.23
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14
Shifting transition states in the unfolding of a large ankyrin repeat protein. Proc Natl Acad Sci U S A (2008) 1.08
The capillarity picture and the kinetics of one-dimensional protein folding. Proc Natl Acad Sci U S A (2008) 1.02
Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A. Proc Natl Acad Sci U S A (2006) 0.98
Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins. Proc Natl Acad Sci U S A (2009) 0.98
Mapping the energy landscape of repeat proteins using NMR-detected hydrogen exchange. J Mol Biol (2008) 0.94
The plastic landscape of repeat proteins. Proc Natl Acad Sci U S A (2007) 0.94
Discrete kinetic models from funneled energy landscape simulations. PLoS One (2012) 0.91
Cooperativity, connectivity, and folding pathways of multidomain proteins. Proc Natl Acad Sci U S A (2008) 0.91
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain. J Mol Biol (2011) 0.90
The folding energy landscape and free energy excitations of cytochrome c. Acc Chem Res (2010) 0.88
Predicted disorder-to-order transition mutations in IκBα disrupt function. Phys Chem Chem Phys (2014) 0.87
Capturing coevolutionary signals inrepeat proteins. BMC Bioinformatics (2015) 0.86
Structural and Energetic Characterization of the Ankyrin Repeat Protein Family. PLoS Comput Biol (2015) 0.86
Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J Biol Chem (2010) 0.86
Modulation of folding kinetics of repeat proteins: interplay between intra- and interdomain interactions. Biophys J (2012) 0.84
Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats. J Biol Chem (2012) 0.83
The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein-folding pathway. Proc Natl Acad Sci U S A (2009) 0.83
Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape. Protein Sci (2009) 0.81
CARPe diem. Biophys J (2014) 0.81
Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c. J Mol Model (2008) 0.79
Single-molecule FRET reveals hidden complexity in a protein energy landscape. Structure (2015) 0.75
Characterization of the unfolded state of repeat proteins. HFSP J (2008) 0.75
A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen. Sci Rep (2015) 0.75
Theory of protein folding. Curr Opin Struct Biol (2004) 7.64
Protein topology determines binding mechanism. Proc Natl Acad Sci U S A (2003) 3.16
Stochastic gene expression as a many-body problem. Proc Natl Acad Sci U S A (2003) 2.94
The experimental survey of protein-folding energy landscapes. Q Rev Biophys (2006) 2.67
Water in protein structure prediction. Proc Natl Acad Sci U S A (2004) 2.35
Theory of structural glasses and supercooled liquids. Annu Rev Phys Chem (2007) 2.34
Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci U S A (2007) 2.33
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.23
P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci U S A (2006) 2.01
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol (2005) 1.99
Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci U S A (2004) 1.93
Absolute rate theories of epigenetic stability. Proc Natl Acad Sci U S A (2005) 1.89
Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution. Protein Sci (2004) 1.89
Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB. Proc Natl Acad Sci U S A (2006) 1.86
Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc (2007) 1.85
An unexpected twist in viral capsid maturation. Nature (2009) 1.80
Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci (2006) 1.75
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci U S A (2009) 1.65
Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J Mol Biol (2006) 1.59
Consequences of localized frustration for the folding mechanism of the IM7 protein. Proc Natl Acad Sci U S A (2007) 1.58
Simple energy landscape model for the kinetics of functional transitions in proteins. J Phys Chem B (2005) 1.57
Role of water mediated interactions in protein-protein recognition landscapes. J Am Chem Soc (2003) 1.56
Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci U S A (2007) 1.54
Stabilizing IkappaBalpha by "consensus" design. J Mol Biol (2006) 1.53
Microscopic theory of network glasses. Phys Rev Lett (2003) 1.52
The physics and bioinformatics of binding and folding-an energy landscape perspective. Biopolymers (2003) 1.52
Optimizing physical energy functions for protein folding. Proteins (2004) 1.49
Self-consistent proteomic field theory of stochastic gene switches. Biophys J (2004) 1.47
Origins of barriers and barrierless folding in BBL. Proc Natl Acad Sci U S A (2008) 1.47
Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol (2008) 1.44
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci U S A (2005) 1.42
A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proc Natl Acad Sci U S A (2005) 1.42
Complex energy landscape of a giant repeat protein. Structure (2013) 1.41
Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A (2009) 1.39
On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A (2011) 1.39
Understanding stochastic simulations of the smallest genetic networks. J Chem Phys (2007) 1.37
Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. J Mol Biol (2002) 1.36
Pre-folding IkappaBalpha alters control of NF-kappaB signaling. J Mol Biol (2008) 1.35
AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. J Phys Chem B (2012) 1.35
Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci (2002) 1.35
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A (2012) 1.33
Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol (2008) 1.31
Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci U S A (2012) 1.25
Folding funnels: the key to robust protein structure prediction. J Comput Chem (2002) 1.25
Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry (2010) 1.25
The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol (2008) 1.25
Mosaic energy landscapes of liquids and the control of protein conformational dynamics by glass-forming solvents. J Phys Chem B (2005) 1.24
Protein frustratometer: a tool to localize energetic frustration in protein molecules. Nucleic Acids Res (2012) 1.23
The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. J Mol Biol (2004) 1.22
An improved grafting technique for mature Arabidopsis plants demonstrates long-distance shoot-to-root transport of phytochelatins in Arabidopsis. Plant Physiol (2006) 1.21
Ligand-induced conformational changes in the acetylcholine-binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. J Biol Chem (2006) 1.20
Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles. Proc Natl Acad Sci U S A (2009) 1.19
Abduction and asylum in the lives of transcription factors. Proc Natl Acad Sci U S A (2010) 1.19
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc (2010) 1.18
Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins. Proc Natl Acad Sci U S A (2011) 1.15
The IkappaBalpha/NF-kappaB complex has two hot spots, one at either end of the interface. Protein Sci (2008) 1.15
Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry. J Am Soc Mass Spectrom (2006) 1.15
Theory of aging in structural glasses. J Chem Phys (2004) 1.14
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14
Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Proc Natl Acad Sci U S A (2003) 1.12
Capillarity theory for the fly-casting mechanism. Proc Natl Acad Sci U S A (2010) 1.11
Restriction versus guidance in protein structure prediction. Proc Natl Acad Sci U S A (2009) 1.11
Two apolipoprotein E mimetic peptides, ApoE(130-149) and ApoE(141-155)2, bind to LRP1. Biochemistry (2004) 1.11
A second molecular biology revolution? The energy landscapes of biomolecular function. Phys Chem Chem Phys (2014) 1.10
Constructing explicit magnetic analogies for the dynamics of glass forming liquids. J Chem Phys (2008) 1.09
Facilitation, complexity growth, mode coupling, and activated dynamics in supercooled liquids. Proc Natl Acad Sci U S A (2008) 1.08
Phenotypic variability of growing cellular populations. Proc Natl Acad Sci U S A (2007) 1.07
Interactions of the NPXY microdomains of the low density lipoprotein receptor-related protein 1. Proteomics (2009) 1.07
Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time. Proc Natl Acad Sci U S A (2011) 1.06
Associative memory Hamiltonians for structure prediction without homology: alpha/beta proteins. Proc Natl Acad Sci U S A (2003) 1.06
Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A (2013) 1.06
Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation. J Mol Biol (2002) 1.05
Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry (2008) 1.05
Minimal models for proteins and RNA from folding to function. Prog Mol Biol Transl Sci (2008) 1.05
Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A. Biochemistry (2005) 1.04
Thrombomodulin tightens the thrombin active site loops to promote protein C activation. Biochemistry (2005) 1.04
Allosteric changes in solvent accessibility observed in thrombin upon active site occupation. Biochemistry (2004) 1.04
Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins. J Am Chem Soc (2006) 1.04
Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins (2004) 1.03
The capillarity picture and the kinetics of one-dimensional protein folding. Proc Natl Acad Sci U S A (2008) 1.02
Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation. Phys Biol (2005) 1.02
A universal origin for secondary relaxations in supercooled liquids and structural glasses. Nat Phys (2009) 1.01
Critical salt bridges guide capsid assembly, stability, and maturation behavior in bacteriophage HK97. Mol Cell Proteomics (2010) 1.01
A variational approach to the stochastic aspects of cellular signal transduction. J Chem Phys (2006) 1.01
The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J (2005) 1.00
Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proc Natl Acad Sci U S A (2008) 0.99
The spectrum of biomolecular states and motions. HFSP J (2008) 0.98
Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA. Proc Natl Acad Sci U S A (2013) 0.98
The dynamic structure of thrombin in solution. Biophys J (2012) 0.98
Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. J Mol Biol (2006) 0.97