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Sosnick, Tobin R.
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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 Actins
Concept Avidin
Concept Bacillus
Concept Cyclic AMP
Concept Algorithms
Concept Amino Acid Sequence
Concept Calmodulin
Concept Anilino Naphthalenesulfonates
Concept Anions
Concept Antibodies, Monoclonal
Concept Computer Simulation
Concept Cytoplasmic Granules
Concept Base Sequence
Concept Cations, Divalent
Concept Cell Nucleus
Concept Deuterium
Concept Bayes Theorem
Concept Bacteriorhodopsins
Concept Biotin
Concept Carbon Isotopes
Concept Bacillus subtilis
Concept Endoribonucleases
Concept Cattle
Concept Cell Membrane
Concept Chromatography, Gel
Concept Cobamides
Concept Cross-Linking Reagents
Concept Cysteine
Concept Hydrogen
Concept Dinitrocresols
Concept Cytochrome c Group
Concept Insulin
Concept Insulysin
Concept Diethyl Pyrocarbonate
Concept Diffusion
Concept Disulfides
Concept Dithiothreitol
Concept Cations, Monovalent
Concept Fluoresceins
Concept Energy Transfer
Concept Ethylenediamines
Concept Cell Biology
Concept Ribonuclease T1
Concept Escherichia coli
Concept Fourier Analysis
Concept Gait
Concept Light
Concept Magnesium
Concept Microfilament Proteins
Concept Actin Cytoskeleton
Concept Molecular Sequence Data
Concept Micrococcal Nuclease
Concept Hot Temperature
Concept Heat-Shock Proteins
Concept HeLa Cells
Concept Neutrons
Concept Oxidation-Reduction
Concept Patella
Concept Endopeptidases
Concept Bacteriophage lambda
Concept Muramidase
Concept Femur
Concept Flavin Mononucleotide
Concept Repressor Proteins
Concept RNA Probes
Concept Ribosomes
Concept RNA Polymerase I
Concept Sodium
Concept Ribonuclease, Pancreatic
Concept DNA-Directed RNA Polymerases
Concept Sulfates
Concept Hydrogen Bonding
Concept Cluster Analysis
Concept Transcription, Genetic
Concept Software
Concept Sequence Homology, Amino Acid
Concept Drug Design
Concept Hair Cells, Auditory, Outer
Concept X-Rays
Concept Acrylamide
Concept Water
Concept Leucine Zippers
Concept Observer Variation
Concept Molecular Probes
Concept Neurofilament Proteins
Concept Gene Expression
Concept Walking
Concept Crystallography, X-Ray
Concept Avena
Concept Aptamers, Nucleotide
Concept src Homology Domains
Concept Myosin Heavy Chains
Concept Bacteriophage T7
Concept 5' Untranslated Regions
Concept Internet
Concept Catalytic Domain
Concept Polyethylene Glycols
Concept Transglutaminases
Concept Ribonucleases
Concept Sodium Chloride
Concept HEK293 Cells
Concept Static Electricity
Concept Temperature
Concept Zebrafish
Concept Zinc
Concept Protein Interaction Domains and Motifs
Concept Magnesium Chloride
Concept Acid Anhydride Hydrolases
Concept Inovirus
Concept Amyloid beta-Peptides
Concept Cell Polarity
Concept GTP-Binding Proteins
Concept Dimerization
Concept Euryarchaeota
Concept Molecular Motor Proteins
Concept Structural Homology, Protein
Concept History, 20th Century
Concept Kv1.2 Potassium Channel
Concept Escherichia coli Proteins
Concept Cryptochromes
Concept Cell Line, Tumor
Concept PDZ Domains
Concept Drug Discovery
Concept Alzheimer Disease
Concept Artificial Intelligence
Concept Carbon
Concept Cochlea
Concept Data Interpretation, Statistical
Concept Fluorescent Dyes
Concept Horses
Concept Lactoglobulins
Concept Protons
Concept Hydroxyl Radical
Concept Troponin C
Concept Computational Biology
Concept Fluorescence Resonance Energy Transfer
Concept Ribonuclease P
Concept PQQ Cofactor
Concept Molecular Dynamics Simulation
Academic Article Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine.
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 Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding.
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 PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation.
Academic Article Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations.
Academic Article Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil.
Academic Article Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering.
Academic Article Pathway modulation, circular permutation and rapid RNA folding under kinetic control.
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 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 Application of circular dichroism to study RNA folding transitions.
Academic Article The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits.
Academic Article Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA.
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 Getting hotter with RNA.
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 Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization.
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 RNA folding: models and perspectives.
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 A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics.
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 Reduced contact order and RNA folding rates.
Academic Article Outcome of a workshop on applications of protein models in biomedical research.
Academic Article Characterization of tertiary folding of RNA by circular dichroism and urea.
Academic Article Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.
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 Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures.
Academic Article Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.
Academic Article New era of molecular structure and dynamics from solution scattering experiments.
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 Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.
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 Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.
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 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 effects of patellar taping on stride characteristics and joint motion in subjects with patellofemoral pain.
Academic Article The rate-limiting step in the folding of a large ribozyme without kinetic traps.
Academic Article Stepwise conversion of a mesophilic to a thermophilic ribozyme.
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 A novel implicit solvent model for simulating the molecular dynamics of RNA.
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 Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)].
Academic Article Aromatic claw: A new fold with high aromatic content that evades structural prediction.
Academic Article A Probabilistic Graphical Model for Ab Initio Folding.
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 Investigations of human myosin VI targeting using optogenetically controlled cargo loading.
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 Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1.
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.
Academic Article Molecular dynamics study of water channels in natural and synthetic amyloid-ß fibrils.
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 Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.
Academic Article Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.
Academic Article Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes.
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 Development of in vivo HDX-MS with applications to a TonB-dependent transporter and other proteins.
Academic Article LILAC: enhanced actin imaging with an optogenetic Lifeact.
Academic Article Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation.
Concept Machine Learning
Concept Protein Domains
Concept Protein Conformation, alpha-Helical
Concept Molecular Docking Simulation
Academic Article Folding of Prestin's Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility.
Academic Article AlphaFold developers Demis Hassabis and John Jumper share the 2023 Albert Lasker Basic Medical Research Award.
Academic Article An adaptive biomolecular condensation response is conserved across environmentally divergent species.
Academic Article Folding of prestin's anion-binding site and the mechanism of outer hair cell electromotility.
Academic Article HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker.
Academic Article How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins.
Academic Article An adaptive biomolecular condensation response is conserved across environmentally divergent species.
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