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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 Models, Chemical
Concept Models, Molecular
Concept Models, Genetic
Concept Models, Theoretical
Concept Models, Statistical
Concept Models, Biological
Academic Article Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends.
Academic Article Distinguishing between two-state and three-state models for ubiquitin folding.
Academic Article Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations.
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 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 Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA.
Academic Article Large-scale context in protein folding: villin headpiece.
Academic Article D/H amide isotope effect in model alpha-helical peptides.
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 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 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 The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
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 Reduced contact order and RNA folding rates.
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 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 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 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 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 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 Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.
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 Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study.
Academic Article Stepwise conversion of a mesophilic to a thermophilic ribozyme.
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 The amino-terminal helix modulates light-activated conformational changes in AsLOV2.
Academic Article Simplified protein models: predicting folding pathways and structure using amino acid sequences.
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 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 A Probabilistic Graphical Model for Ab Initio Folding.
Academic Article Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.
Academic Article Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
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.

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