Published in Biochemistry on December 31, 2012
Cofactor molecules induce structural transformation during infectious prion formation. Structure (2013) 1.05
Comparing the energy landscapes for native folding and aggregation of PrP. Prion (2016) 0.75
The role of Cys179-Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations. J Mol Model (2014) 0.75
An in vitro approach to identify the key amino acids in the low susceptibility of rabbit PrP to misfolding. J Virol (2017) 0.75
The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study. J Mol Model (2013) 0.75
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75
Prions. Proc Natl Acad Sci U S A (1998) 27.80
Synthetic mammalian prions. Science (2004) 7.35
Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol (2003) 6.50
NMR structure of the mouse prion protein domain PrP(121-231). Nature (1996) 6.37
Self-replication and scrapie. Nature (1967) 6.01
Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad Sci U S A (2000) 5.55
NMR solution structure of the human prion protein. Proc Natl Acad Sci U S A (2000) 4.80
Structure of the recombinant full-length hamster prion protein PrP(29-231): the N terminus is highly flexible. Proc Natl Acad Sci U S A (1997) 4.10
Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci U S A (2004) 3.64
Structural determinants of allosteric ligand activation in RXR heterodimers. Cell (2004) 3.36
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
Emerging ideas on the molecular basis of protein and peptide aggregation. Curr Opin Struct Biol (2003) 2.85
Protein aggregation diseases: pathogenicity and therapeutic perspectives. Nat Rev Drug Discov (2010) 2.58
Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure. Proc Natl Acad Sci U S A (2007) 2.55
Beta-sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange. Proc Natl Acad Sci U S A (2007) 2.14
From conversion to aggregation: protofibril formation of the prion protein. Proc Natl Acad Sci U S A (2004) 2.14
Prediction of amyloid fibril-forming proteins. J Biol Chem (2000) 2.12
Allosteric determinants in guanine nucleotide-binding proteins. Proc Natl Acad Sci U S A (2003) 1.91
Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88
Prion protein NMR structure and species barrier for prion diseases. Proc Natl Acad Sci U S A (1997) 1.86
Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci U S A (2010) 1.85
Folding of prion protein to its native alpha-helical conformation is under kinetic control. J Biol Chem (2001) 1.84
Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci (2002) 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
Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
The α-helical C-terminal domain of full-length recombinant PrP converts to an in-register parallel β-sheet structure in PrP fibrils: evidence from solid state nuclear magnetic resonance. Biochemistry (2010) 1.53
Structural mobility of the human prion protein probed by backbone hydrogen exchange. Nat Struct Biol (1999) 1.41
Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci (2006) 1.35
Prion protein NMR structures of chickens, turtles, and frogs. Proc Natl Acad Sci U S A (2005) 1.34
Hot spots in prion protein for pathogenic conversion. Proc Natl Acad Sci U S A (2007) 1.31
Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc Natl Acad Sci U S A (2004) 1.31
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc? Biochemistry (2002) 1.24
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol (2007) 1.22
Evidence for the role of PrP(C) helix 1 in the hydrophilic seeding of prion aggregates. Proc Natl Acad Sci U S A (1999) 1.19
CD and NMR studies of prion protein (PrP) helix 1. Novel implications for its role in the PrPC-->PrPSc conversion process. J Biol Chem (2003) 1.13
High-resolution structure of infectious prion protein: the final frontier. Nat Struct Mol Biol (2012) 1.09
cDNA cloning of turtle prion protein. FEBS Lett (2000) 1.01
Structural and hydration properties of the partially unfolded states of the prion protein. Biophys J (2007) 0.99
Delineating common molecular mechanisms in Alzheimer's and prion diseases. Trends Biochem Sci (2006) 0.98
Prion proteins with pathogenic and protective mutations show similar structure and dynamics. Biochemistry (2009) 0.97
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Biophys J (2002) 0.96
On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model. Proteins (2009) 0.93
Structural domains and main-chain flexibility in prion proteins. Biochemistry (2009) 0.93
Toward the molecular basis of inherited prion diseases: NMR structure of the human prion protein with V210I mutation. J Mol Biol (2011) 0.90
Dynamics of a truncated prion protein, PrP(113-231), from (15)N NMR relaxation: order parameters calculated and slow conformational fluctuations localized to a distinct region. Protein Sci (2009) 0.89
Peptides and proteins in neurodegenerative disease: helix propensity of a polypeptide containing helix 1 of the mouse prion protein studied by NMR and CD spectroscopy. Biopolymers (1999) 0.89
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion (2011) 0.87
Conformational properties of beta-PrP. J Biol Chem (2009) 0.87
Codon 129 polymorphism of the human prion protein influences the kinetics of amyloid formation. J Gen Virol (2006) 0.86
The H187R mutation of the human prion protein induces conversion of recombinant prion protein to the PrP(Sc)-like form. Biochemistry (2010) 0.84
Three-dimensional NMR structure of a self-folding domain of the prion protein PrP(121-231) Trends Biochem Sci (1997) 0.84
Chicken prion tandem repeats form a stable, protease-resistant domain. Biochemistry (1999) 0.82
Why are prion diseases precluded by non-mammals? Trends Biochem Sci (2007) 0.79
Navigating the folding routes. Science (1995) 7.34
Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A (1990) 3.79
Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A (2005) 3.29
Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (2003) 3.18
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci U S A (1993) 3.08
The nature of folded states of globular proteins. Biopolymers (1992) 2.91
Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66
Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci (1999) 2.41
Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22
Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03
Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A (2006) 2.01
Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A (2002) 1.99
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. J Am Chem Soc (2007) 1.90
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A (2006) 1.90
Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88
Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85
Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. Proc Natl Acad Sci U S A (1996) 1.79
Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol (2001) 1.78
Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci (2002) 1.77
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci U S A (2003) 1.76
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
Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1995) 1.73
Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63
Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins (2001) 1.61
Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. J Mol Biol (2001) 1.61
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60
Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. Proc Natl Acad Sci U S A (2005) 1.59
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58
Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57
Charge density of divalent metal cations determines RNA stability. J Am Chem Soc (2007) 1.56
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A (2008) 1.52
Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol (1998) 1.50
Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc (2003) 1.44
Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem (2011) 1.43
Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42
Collapse transition in proteins. Phys Chem Chem Phys (2008) 1.41
Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41
Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A (1999) 1.38
Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. Structure (2010) 1.37
Ribosome exit tunnel can entropically stabilize alpha-helices. Proc Natl Acad Sci U S A (2005) 1.36
RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J Mol Biol (2005) 1.36
Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci (2006) 1.35
Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des (1998) 1.34
Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proc Natl Acad Sci U S A (2004) 1.34
Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol (2004) 1.33
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci U S A (2008) 1.33
Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32
Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A (2005) 1.32
Exploring the energy landscape in proteins. Proc Natl Acad Sci U S A (1993) 1.32
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31
Size, shape, and flexibility of RNA structures. J Chem Phys (2006) 1.31
Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc Natl Acad Sci U S A (2004) 1.31
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry (2004) 1.26
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24
Persistence length changes dramatically as RNA folds. Phys Rev Lett (2005) 1.23
Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol (2004) 1.23
Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol (2007) 1.22
Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22
Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol (2006) 1.22
Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20
Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B (2007) 1.20
Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol (2005) 1.19
Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci (2002) 1.19
Factors governing the foldability of proteins. Proteins (1996) 1.18
Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol (1997) 1.18
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A (2009) 1.16
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol (2002) 1.16
Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A (2009) 1.15
Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Fold Des (1998) 1.14
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc (2008) 1.13
Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization. J Mol Biol (2004) 1.12
Dynamic transition in tRNA is solvent induced. J Am Chem Soc (2006) 1.11
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 1.10
Kinetics of loop formation in polymer chains. J Phys Chem B (2008) 1.10
Annealing function of GroEL: structural and bioinformatic analysis. Biophys Chem (2003) 1.10
Compression and stretching of a self-avoiding chain in cylindrical nanopores. Phys Rev Lett (2008) 1.09
Entropic stabilization of proteins by TMAO. J Phys Chem B (2011) 1.09
Probing the mechanisms of fibril formation using lattice models. J Chem Phys (2008) 1.08
Kinetics of interior loop formation in semiflexible chains. J Chem Phys (2006) 1.08
Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. J Phys Chem B (2009) 1.08
Counterion charge density determines the position and plasticity of RNA folding transition states. J Mol Biol (2006) 1.07
Minimal models for proteins and RNA from folding to function. Prog Mol Biol Transl Sci (2008) 1.05
Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci U S A (2009) 1.04
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. Proc Natl Acad Sci U S A (2008) 1.04
Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J Am Chem Soc (2009) 1.04
Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins (1995) 1.04
Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. Phys Rev Lett (2010) 1.03
Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol (2008) 1.03
Effect of finite size on cooperativity and rates of protein folding. J Phys Chem A (2006) 1.03
Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. J Am Chem Soc (2008) 1.03
Factors governing helix formation in peptides confined to carbon nanotubes. Nano Lett (2008) 1.03
How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? J Chem Phys (2009) 1.02
Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. Proc Natl Acad Sci U S A (2006) 1.02
Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments. Phys Rev Lett (2011) 1.01
Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol (2008) 1.01
Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry (2009) 1.00