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Search Results to Tobin R. Sosnick

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One or more keywords matched the following properties of Sosnick, Tobin R.

keywords Membrane Proteins
keywords Protein Folding
keywords disordered proteins
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
Concept Bacterial Outer Membrane Proteins
Concept Bacterial Proteins
Concept Fungal Proteins
Concept DNA-Binding Proteins
Concept Microfilament Proteins
Concept Nerve Tissue Proteins
Concept Protein Denaturation
Concept Plant Proteins
Concept Protein Binding
Concept Protein Conformation
Concept Protein Processing, Post-Translational
Concept Proteins
Concept Repressor Proteins
Concept Protein Kinases
Concept Staphylococcal Protein A
Concept Protein Engineering
Concept Protein Renaturation
Concept Mitogen-Activated Protein Kinases
Concept Zebrafish Proteins
Concept Neurofilament Proteins
Concept Protein Structure, Tertiary
Concept RNA-Binding Proteins
Concept Phosphatidylethanolamine Binding Protein
Concept Protein Transport
Concept Protein Structure, Secondary
Concept Protein Interaction Mapping
Concept Receptors, G-Protein-Coupled
Concept bcl-2-Associated X Protein
Concept Saccharomyces cerevisiae Proteins
Concept Databases, Protein
Concept Recombinant Proteins
Concept Protein Interaction Domains and Motifs
Concept Viral Proteins
Concept GTP-Binding Proteins
Concept Sequence Analysis, Protein
Concept Antifreeze Proteins
Concept Molecular Motor Proteins
Concept Structural Homology, Protein
Concept Mutant Proteins
Concept Escherichia coli Proteins
Concept Protein Interaction Maps
Concept Arthropod Proteins
Concept Intracellular Signaling Peptides and Proteins
Concept Proto-Oncogene Proteins c-fyn
Concept Viral Regulatory and Accessory Proteins
Concept Protein Stability
Concept Protein Unfolding
Concept Carrier Proteins
Concept Membrane Transport Proteins
Concept Vesicular Transport Proteins
Concept Poly(A)-Binding Proteins
Concept Protein Kinase Inhibitors
Concept Maltose-Binding Proteins
Academic Article Mechanisms and uses of hydrogen exchange.
Academic Article Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide.
Academic Article Protein minimization: downsizing through mutation.
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 Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends.
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 Denatured states of ribonuclease A have compact dimensions and residual secondary structure.
Academic Article PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation.
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 The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits.
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 D/H amide isotope effect in model alpha-helical peptides.
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 The thermodynamic origin of the stability of a thermophilic 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 Mechanistic insights on the folding of a large ribozyme during transcription.
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 Expression in Escherichia coli and characterization of the heat-stable inhibitor of the cAMP-dependent protein kinase.
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 RNA folding during transcription.
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 Light-activated DNA binding in a designed allosteric protein.
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 Outcome of a workshop on applications of protein models in biomedical research.
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 A probabilistic and continuous model of protein conformational space for template-free modeling.
Academic Article Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.
Academic Article Protein vivisection reveals elusive intermediates in folding.
Academic Article Rationally improving LOV domain-based photoswitches.
Academic Article Ubiquitin is a novel substrate for human insulin-degrading enzyme.
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 Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.
Academic Article De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.
Academic Article Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state.
Academic Article Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch.
Academic Article TULIPs: tunable, light-controlled interacting protein tags for cell biology.
Academic Article On docking, scoring and assessing protein-DNA complexes in a rigid-body framework.
Academic Article Biochemistry. How proteins fold.
Academic Article Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.
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 Modeling the hydration layer around proteins: HyPred.
Academic Article Automated real-space refinement of protein structures using a realistic backbone move set.
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 Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study.
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 Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions.
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 The amino-terminal helix modulates light-activated conformational changes in AsLOV2.
Academic Article Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.
Academic Article Simplified protein models: predicting folding pathways and structure using amino acid sequences.
Academic Article Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.
Academic Article Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Academic Article Benchmarking all-atom simulations using hydrogen exchange.
Academic Article Ionic strength independence of charge distributions in solvation of biomolecules.
Academic Article Folding of a large protein at high structural resolution.
Academic Article Revealing what gets buried first in protein folding.
Academic Article Factors that control the chemistry of the LOV domain photocycle.
Academic Article Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein.
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 The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme.
Academic Article Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.
Academic Article Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response.
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 Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome.
Academic Article Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".
Academic Article Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
Academic Article Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
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 Structural basis for adhesion G protein-coupled receptor Gpr126 function.
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.

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