Ribosome exit tunnel can entropically stabilize alpha-helices.

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys (2008) 7.77

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol (2010) 2.14

Inhibition of 2A-mediated 'cleavage' of certain artificial polyproteins bearing N-terminal signal sequences. Biotechnol J (2010) 1.57

Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS Comput Biol (2006) 1.50

Atomic structure of anthrax protective antigen pore elucidates toxin translocation. Nature (2015) 1.35

Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32

Protein folding under confinement: a role for solvent. Proc Natl Acad Sci U S A (2007) 1.30

Protein folding in confined and crowded environments. Arch Biochem Biophys (2007) 1.30

Thermodynamics and kinetics of protein folding under confinement. Proc Natl Acad Sci U S A (2008) 1.26

Ribosomal features essential for tna operon induction: tryptophan binding at the peptidyl transferase center. J Bacteriol (2007) 1.22

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

Control of translocation through the Sec61 translocon by nascent polypeptide structure within the ribosome. J Biol Chem (2008) 1.04

Factors governing helix formation in peptides confined to carbon nanotubes. Nano Lett (2008) 1.03

Ligand-driven vectorial folding of ribosome-bound human CFTR NBD1. Mol Cell (2011) 0.97

Polytopic membrane protein folding at L17 in the ribosome tunnel initiates cyclical changes at the translocon. J Cell Biol (2011) 0.96

Computational studies of molecular machines: the ribosome. Curr Opin Struct Biol (2012) 0.96

Confinement effects on the kinetics and thermodynamics of protein dimerization. Proc Natl Acad Sci U S A (2009) 0.95

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins (2009) 0.93

Kinetic analysis of ribosome-bound fluorescent proteins reveals an early, stable, cotranslational folding intermediate. J Biol Chem (2011) 0.93

Mechanisms of CFTR Folding at the Endoplasmic Reticulum. Front Pharmacol (2012) 0.90

Large facilities and the evolving ribosome, the cellular machine for genetic-code translation. J R Soc Interface (2009) 0.88

Non-bulk-like solvent behavior in the ribosome exit tunnel. PLoS Comput Biol (2010) 0.88

Smoothing of the GB1 hairpin folding landscape by interfacial confinement. Biophys J (2012) 0.85

The ribosome in action: Tuning of translational efficiency and protein folding. Protein Sci (2016) 0.83

The cell-free integration of a polytopic mitochondrial membrane protein into liposomes occurs cotranslationally and in a lipid-dependent manner. PLoS One (2012) 0.82

Free energy of nascent-chain folding in the translocon. J Am Chem Soc (2011) 0.82

Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome. Methods (2010) 0.80

Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement. J Phys Chem Lett (2015) 0.79

Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein. Sci Rep (2016) 0.77

Directionality in protein fold prediction. BMC Bioinformatics (2010) 0.77

Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework. Biochem Cell Biol (2010) 0.77

Thermodynamic stability of polypeptides folding within modeled ribosomal exit tunnel: a density functional study. Eur Phys J E Soft Matter (2010) 0.76

Does mRNA structure contain genetic information for regulating co-translational protein folding? Zool Res (2017) 0.75

The structural basis of ribosome activity in peptide bond synthesis. Science (2000) 18.82

Coiled coils: new structures and new functions. Trends Biochem Sci (1996) 8.63

Optimized Monte Carlo data analysis. Phys Rev Lett (1989) 7.03

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell (2001) 6.97

The ribosomal exit tunnel functions as a discriminating gate. Cell (2002) 4.57

Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry (1996) 4.39

Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers (1991) 3.51

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14

Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell (2004) 3.03

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol (1999) 2.14

Conformational studies of poly-L-alanine in water. Biopolymers (1968) 2.02

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations. Proc Natl Acad Sci U S A (2003) 1.99

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

Secondary structure formation of a transmembrane segment in Kv channels. Biochemistry (2005) 1.62

A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. Science (1987) 1.54

A nascent secretory protein may traverse the ribosome/endoplasmic reticulum translocase complex as an extended chain. J Biol Chem (1996) 1.51

The elasticity of alpha-helices. J Chem Phys (2005) 1.38

Ergodic behavior in supercooled liquids and in glasses. Phys Rev A Gen Phys (1989) 1.36

The machinery of membrane protein assembly. Curr Opin Struct Biol (2004) 1.34

Different conformations of nascent polypeptides during translocation across the ER membrane. BMC Cell Biol (2000) 1.34

Three-dimensional structures of translating ribosomes by Cryo-EM. Mol Cell (2004) 1.21

Signal sequence recognition and protein targeting. Curr Opin Struct Biol (1999) 1.18

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

Location of exit channel for nascent protein in 80S ribosome. Nature (1986) 1.04

From peptide-bond formation to cotranslational folding: dynamic, regulatory and evolutionary aspects. FEBS Lett (2005) 1.02

A crevice adjoining the ribosome tunnel: hints for cotranslational folding. FEBS Lett (2005) 0.89

Kinetics of the coil-to-helix transition on a rough energy landscape. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.88

Nonlinear elasticity of an alpha -helical polypeptide. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.82

Helical polymer in cylindrical confining geometries. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.78

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

Watching proteins fold one molecule at a time. Proc Natl Acad Sci U S A (2003) 3.25

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

Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci U S A (2006) 2.27

Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22

Two-state folding observed in individual protein molecules. J Am Chem Soc (2004) 2.14

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

Protein-protein association in polymer solutions: from dilute to semidilute to concentrated. Biophys J (2006) 1.40

Separating the contribution of translational and rotational diffusion to protein association. J Am Chem Soc (2005) 1.39

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

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

Common crowding agents have only a small effect on protein-protein interactions. Biophys J (2009) 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

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein. Nat Commun (2011) 1.30

Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back. Annu Rev Phys Chem (2011) 1.27

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

Protein folding, protein collapse, and tanford's transfer model: lessons from single-molecule FRET. J Am Chem Soc (2009) 1.13

Using fluorescence correlation spectroscopy to study conformational changes in denatured proteins. Biophys J (2008) 1.13

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

Kinetics of loop formation in polymer chains. J Phys Chem B (2008) 1.10

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci U S A (2013) 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

The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature (2012) 1.06

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