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Sosnick, Tobin R.
One or more keywords matched the following properties of Sosnick, Tobin R.
PropertyValue
keywords Protein Folding
overview My research program involves synergistic studies of protein folding and design, protein-RNA interactions, phosphorylation, signaling, and function with both experimental and computational components. The research is based on the premise that rigorous and innovative studies of basic processes have broad implications in many areas of biological research. My lab employs a range of experimental and computational methods including hydrogen exchange (HX), NMR, small-angle X-ray scattering (SAXS), rapid mixing methods, mass spectrometry, molecular dynamics and home-grown coarse-grain folding simulations and modeling. I am a very a strong believer in collaboration, having co-mentored over twenty students and post-doctoral fellows who produce over 60 papers in the last 20 years. I have a history of developing multi-approaches to bear on a problem. Since my Ph.D. in low temperature physics in 1989, I have entered many different areas, including delineating protein and RNA folding pathways and denatured states, de novo structure prediction, and the design of light-sensitive allosteric proteins.
One or more keywords matched the following items that are connected to Sosnick, Tobin R.
Item TypeName
Academic Article Mechanisms and uses of hydrogen exchange.
Academic Article The role of helix formation in the folding of a fully alpha-helical coiled coil.
Academic Article Molecular collapse: the rate-limiting step in two-state cytochrome c folding.
Academic Article The burst phase in ribonuclease A folding and solvent dependence of the unfolded state.
Academic Article Hydrogen exchange: the modern legacy of Linderstrøm-Lang.
Academic Article Distinguishing between two-state and three-state models for ubiquitin folding.
Academic Article Ultrafast signals in protein folding and the polypeptide contracted state.
Academic Article Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil.
Academic Article Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity.
Academic Article Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.
Academic Article Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding.
Academic Article D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding.
Academic Article Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking.
Academic Article Dynamics of hydrogen bond desolvation in protein folding.
Academic Article A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme.
Academic Article Entropic benefit of a cross-link in protein association.
Academic Article Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil.
Academic Article Distinguishing foldable proteins from nonfolders: when and how do they differ?
Academic Article Large-scale context in protein folding: villin headpiece.
Academic Article Contribution of hydrogen bonding to protein stability estimated from isotope effects.
Academic Article Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects.
Academic Article Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.
Academic Article Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme.
Academic Article Discerning the structure and energy of multiple transition states in protein folding using psi-analysis.
Academic Article Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding.
Academic Article Fast folding of a helical protein initiated by the collision of unstructured chains.
Academic Article Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins.
Academic Article Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein".
Academic Article Characterizing protein folding transition States using Psi-analysis.
Academic Article PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV.
Academic Article Methods for the accurate estimation of confidence intervals on protein folding phi-values.
Academic Article Folding of a universal ribozyme: the ribonuclease P RNA.
Academic Article The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
Academic Article Random-coil behavior and the dimensions of chemically unfolded proteins.
Academic Article Kinetic barriers and the role of topology in protein and RNA folding.
Academic Article Quantifying the structural requirements of the folding transition state of protein A and other systems.
Academic Article Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding.
Academic Article Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state.
Academic Article Psi-constrained simulations of protein folding transition states: implications for calculating.
Academic Article Characterizing the protein folding transition state using psi analysis.
Academic Article On the precision of experimentally determined protein folding rates and phi-values.
Academic Article Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.
Academic Article Small proteins fold through transition states with native-like topologies.
Academic Article Protein vivisection reveals elusive intermediates in folding.
Academic Article The folding of single domain proteins--have we reached a consensus?
Academic Article Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification.
Academic Article A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable.
Academic Article De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.
Academic Article Biochemistry. How proteins fold.
Academic Article Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding.
Academic Article Protein structure prediction enhanced with evolutionary diversity: SPEED.
Academic Article Modeling large regions in proteins: applications to loops, termini, and folding.
Academic Article The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).
Academic Article Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature.
Academic Article The barriers in protein folding.
Academic Article Protein folding intermediates: native-state hydrogen exchange.
Academic Article The rate-limiting step in the folding of a large ribozyme without kinetic traps.
Academic Article Early collapse is not an obligate step in protein folding.
Academic Article Differences in the folding transition state of ubiquitin indicated by phi and psi analyses.
Academic Article Statistical coil model of the unfolded state: resolving the reconciliation problem.
Academic Article Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Academic Article Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates.
Academic Article Mimicking the folding pathway to improve homology-free protein structure prediction.
Academic Article Simplified protein models: predicting folding pathways and structure using amino acid sequences.
Academic Article Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Academic Article Folding of a large protein at high structural resolution.
Academic Article Revealing what gets buried first in protein folding.
Academic Article Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions.
Academic Article Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.
Academic Article Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.
Academic Article Introduction of a polar core into the de novo designed protein Top7.
Academic Article Aromatic claw: A new fold with high aromatic content that evades structural prediction.
Academic Article Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.
Academic Article Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.
Academic Article A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.
Academic Article Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
Academic Article Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.
Academic Article On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.
Academic Article Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.
Academic Article Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.
Academic Article Folding and misfolding of potassium channel monomers during assembly and tetramerization.
Academic Article Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.
Academic Article Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.
Academic Article HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain's allostery and unfolding upon B12 and TonB binding.
Academic Article Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation.
Academic Article How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins.
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  • Protein Folding