T. Sosnick

发表

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

Abhishek K. Jha, K. Freed, S. Koide, 2005, Biochemistry.

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.

R. Berry, K. Freed, M. Zaman, 2003, Journal of molecular biology.

Towards petascale ab initio protein folding through parallel scripting

Glen M. Hocky, I. Foster, M. Wilde, 2009 .

Mimicking the folding pathway to improve homology-free protein structure prediction

James E. Fitzgerald, Abhishek K. Jha, K. Freed, 2009, Proceedings of the National Academy of Sciences.

A novel implicit solvent model for simulating the molecular dynamics of RNA.

H. Gong, K. Freed, T. Sosnick, 2013, Biophysical journal.

Light-activated DNA binding in a designed allosteric protein

K. Moffat, T. Sosnick, D. Strickland, 2008, Proceedings of the National Academy of Sciences.

Protein folding intermediates: native-state hydrogen exchange.

T. Sosnick, Yawen Bai, Y. Bai, 1995, Science.

Introduction of a polar core into the de novo designed protein Top7

D. Baker, Gaohua Liu, G. Montelione, 2016, Protein science : a publication of the Protein Society.

Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study.

J. Trewhella, T. Sosnick, D. Gray, 1995, Journal of molecular biology.

HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain’s allostery and unfolding upon B12 and TonB binding

T. Sosnick, A. Zmyslowski, Michael C. Baxa, 2022, bioRxiv.

The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection

D. Baker, G. Varani, T. Sosnick, 2007, Cell.

Hydrogen exchange: The modern legacy of Linderstrøm‐Lang

T. Sosnick, Y. Bai, L. Mayne, 1997, Protein science : a publication of the Protein Society.

How Proteins Fold

Tobin R Sosnick, T. Sosnick, James R. Hinshaw, 2011, Science.

Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.

T. Pan, T. Sosnick, R. Landick, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme.

T. Pan, T. Sosnick, N. Scherer, 2004, Proceedings of the National Academy of Sciences of the United States of America.

The barriers in protein folding

T. Sosnick, L. Mayne, S. Englander, 1994, Nature Structural Biology.

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics.

T. Pan, T. Sosnick, N. Scherer, 2008, Journal of molecular biology.

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA

T. Pan, T. Sosnick, N. Scherer, 2008, Proceedings of the National Academy of Sciences.

Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.

Abhishek K. Jha, K. Freed, T. Sosnick, 2012, Journal of the American Chemical Society.

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

J. Jumper, K. Freed, T. Sosnick, 2014, Proceedings of the National Academy of Sciences.

Early collapse is not an obligate step in protein folding.

Robin S. Dothager, T. Sosnick, P. Thiyagarajan, 2004, Journal of molecular biology.

Random-coil behavior and the dimensions of chemically unfolded proteins.

Robin S. Dothager, V. Pande, I. Ruczinski, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Statistical coil model of the unfolded state: resolving the reconciliation problem.

Abhishek K. Jha, K. Freed, A. Colubri, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.

James E. Fitzgerald, Abhishek K. Jha, K. Freed, 2007, Biochemistry.

Distinguishing between two-state and three-state models for ubiquitin folding.

T. Sosnick, B. Krantz, 2000 .

Differences in the folding transition state of ubiquitin indicated by phi and psi analyses.

Robin S. Dothager, T. Sosnick, B. Krantz, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Differences in the folding transition state of ubiquitin indicated by φ and ψ analyses

Robin S. Dothager, T. Sosnick, B. Krantz, 2004 .

Molecular collapse: The rate‐limiting step in two‐state cytochrome c folding

T. Sosnick, L. Mayne, S. Englander, 1996, Proteins.

Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding.

T. Sosnick, L. Mayne, S. Englander, 2002, Journal of molecular biology.

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

Joshua A. Riback, J. Jumper, K. Freed, 2017, Science.

Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamics

J. Jumper, K. Freed, T. Sosnick, 2016 .

Mechanisms and uses of hydrogen exchange.

L Mayne, S W Englander, T. Sosnick, 1996, Current opinion in structural biology.

Protein structure prediction enhanced with evolutionary diversity: SPEED

Michael Wilde, Jinbo Xu, Karl F Freed, 2010, Protein science : a publication of the Protein Society.

Modeling large regions in proteins: Applications to loops, termini, and folding

Michael Wilde, Jinbo Xu, Jian Peng, 2012, Protein science : a publication of the Protein Society.

On Docking, Scoring and Assessing Protein-DNA Complexes in a Rigid-Body Framework

Karl F. Freed, Tobin R. Sosnick, Marc Parisien, 2012, PloS one.

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.

T. Pan, T. Sosnick, K. Littrell, 2000, Biochemistry.

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

K. Freed, T. Sosnick, Michael C. Baxa, 2016, Proceedings of the National Academy of Sciences.

Erratum: Random-coil behavior and the dimensions of chemically unfolded proteins (Proceedings of The National Academy of Sciences of The United States of America (August 24, 2004) 101, 34 (12491-12496))

Vijay S. Pande, Ingo Ruczinski, Kevin W. Plaxco, 2005 .

Fast folding of a helical protein initiated by the collision of unstructured chains.

T. Sosnick, W. Meisner, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine.

C. Unkefer, T. Sosnick, D. Houck, 1995, Methods in enzymology.

Quantifying the structural requirements of the folding transition state of protein A and other systems.

K. Freed, T. Sosnick, Michael C. Baxa, 2008, Journal of molecular biology.

Automated real-space refinement of protein structures using a realistic backbone move set.

Abhishek K. Jha, Xiaojing Yang, H. Gong, 2011, Biophysical journal.

Inverse Protein Folding of Ubiquitin on the Illinois Bio-Grid

Abhishek K. Jha, G. Laszewski, K. Freed, 2006 .

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

Joshua A. Riback, K. Plaxco, T. Sosnick, 2018, Proceedings of the National Academy of Sciences.

Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1

Josiah P. Zayner, T. Sosnick, J. Kennis, 2019, ACS omega.

Factors That Control the Chemistry of the LOV Domain Photocycle

Josiah P. Zayner, T. Sosnick, 2014, PloS one.

Expression in Escherichia coli and characterization of the heat-stable inhibitor of the cAMP-dependent protein kinase.

J. Trewhella, T. Sosnick, S. M. Van Patten, 1991, The Journal of biological chemistry.

The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme.

T. Sosnick, S. Meredith, M. Poellmann, 2017, Macromolecular bioscience.

A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.

Sheng Wang, J. Jumper, K. Freed, 2018, Biophysical journal.

Aromatic claw: A new fold with high aromatic content that evades structural prediction

Aashish N. Adhikari, Gaohua Liu, G. Montelione, 2017, Protein science : a publication of the Protein Society.

Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.

Corissa L. Lamphear, T. Pan, M. Wilde, 2013, Cell reports.

Structural basis for adhesion G protein-coupled receptor Gpr126 function

Joshua A. Riback, T. Sosnick, Minglei Zhao, 2019, Nature Communications.

Methods for the accurate estimation of confidence intervals on protein folding φ‐values

I. Ruczinski, K. Plaxco, T. Sosnick, 2006, Protein science : a publication of the Protein Society.

Aβ Fibrils Can Act as Aqueous Pores: a Molecular Dynamics Study

K. Freed, T. Sosnick, E. Haddadian, 2018, bioRxiv.

The role of helix formation in the folding of a fully alpha-helical coiled coil.

W. DeGrado, T. Sosnick, S. Englander, 1996, Proteins.

Contribution of hydrogen bonding to protein stability estimated from isotope effects.

Zhengshuang Shi, N. Kallenbach, T. Sosnick, 2002, Biochemistry.

LILAC: Enhanced actin imaging with an optogenetic Lifeact

T. Sosnick, R. Rock, A. R. French, 2022, bioRxiv.

Characterization of Tertiary Folding of RNA by Circular Dichroism and Urea

T. Sosnick, 2001, Current protocols in nucleic acid chemistry.

Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding.

A. Kentsis, T. Sosnick, 1998, Biochemistry.

Local Backbone Preferences and Nearest‐Neighbor Effects in the Unfolded and Native States

Abhishek K. Jha, K. Freed, T. Sosnick, 2012 .

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

T. Pan, T. Sosnick, I. Artsimovitch, 2012, Proceedings of the National Academy of Sciences.

RNA folding during transcription.

Tao Pan, T. Pan, T. Sosnick, 2006, Annual review of biophysics and biomolecular structure.

Folding of a large protein at high structural resolution

Tobin R Sosnick, S Walter Englander, Leland Mayne, 2013, Proceedings of the National Academy of Sciences.

Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response

Joshua A. Riback, D. Drummond, T. Sosnick, 2017, Cell.

Distances between the antigen-binding sites of three murine antibody subclasses measured using neutron and X-ray scattering.

J. Novotný, D. Benjamin, J. Trewhella, 1992, Biochemistry.

Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature.

Robin S. Dothager, T. Sosnick, P. Thiyagarajan, 2007, Journal of molecular biology.

Modeling the hydration layer around proteins: HyPred.

Lee Makowski, Karl F Freed, Tobin R Sosnick, 2010, Biophysical journal.

PAS Domain Receptor Photoactive Yellow Protein Is Converted to a Molten Globule State upon Activation*

T. Sosnick, W. Hoff, Byoung-Chul Lee, 2001, The Journal of Biological Chemistry.

Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions

R. Hjelm, K. Plaxco, T. Sosnick, 2015, Proceedings of the National Academy of Sciences.

Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state.

K. Plaxco, T. Sosnick, L. Pollack, 2012, Journal of molecular biology.

Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide.

J. Trewhella, T. Sosnick, D. Walsh, 1993, Biochemistry.

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

W. Chiu, T. Pan, S. Ludtke, 2010, Journal of the American Chemical Society.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures

Tao Pan, Tobin R Sosnick, T. Pan, 2007, Proceedings of the National Academy of Sciences.

Mg2+-dependent folding of a large ribozyme without kinetic traps

T. Pan, T. Sosnick, X. Fang, 1999, Nature Structural Biology.

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding.

T. Pan, T. Sosnick, V. Shelton, 1999, Biochemistry.

Folding of Prestin’s Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility

Nabil F. Faruk, T. Sosnick, E. Perozo, 2023, bioRxiv.

Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity

T. Pan, T. Sosnick, 1997, Nature Structural Biology.

Pathway modulation, circular permutation and rapid RNA folding under kinetic control.

T. Pan, T. Sosnick, X. Fang, 1999, Journal of molecular biology.

Rationally improving LOV domain–based photoswitches

Xiaolan Yao, Tobin R. Sosnick, Kevin H. Gardner, 2010, Nature Methods.

Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes.

Nabil F. Faruk, K. Freed, T. Sosnick, 2022, Journal of chemical theory and computation.

Application of circular dichroism to study RNA folding transitions.

T. Sosnick, X. Fang, X. Fang, 2000, Methods in enzymology.

Investigations of human myosin VI targeting using optogenetically controlled cargo loading

T. Sosnick, R. Rock, A. French, 2017, Proceedings of the National Academy of Sciences.

Investigations of human myosin VI targeting using optogenetically-controlled cargo loading

T. Sosnick, R. Rock, A. French, 2017, bioRxiv.

Optogenetically controlled cargo shows full length human myosin VI integrates activation signals in vivo and in vitro

T. Sosnick, R. Rock, A. French, 2016 .

Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome

Hermann Schindelin, Kristina Lorenz, Sheng Wang, 2017, Proceedings of the National Academy of Sciences.

The amino-terminal helix modulates light-activated conformational changes in AsLOV2.

Josiah P. Zayner, T. Sosnick, C. Antoniou, 2012, Journal of molecular biology.

Folding of a universal ribozyme: the ribonuclease P RNA

T. Pan, T. Sosnick, X. Fang, 2007, Quarterly Reviews of Biophysics.

Foldingof a universal ribozyme: theribonuclease PRNA

T. Pan, T. Sosnick, X. Fang, 2007 .

The thermodynamic origin of the stability of a thermophilic ribozyme

T. Pan, B. Golden, T. Sosnick, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein.

Josiah P. Zayner, T. Sosnick, Ronald J. Hause, 2013, Biophysical journal.

Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.

Lee Makowski, Karl F Freed, Tobin R Sosnick, 2011, Biophysical journal.

Protein folding: Defining a “standard” set of experimental conditions and a preliminary kinetic data set of two‐state proteins

Kevin W Plaxco, Ingo Ruczinski, Fabrizio Chiti, 2005, Protein science : a publication of the Protein Society.

Development of in vivo HDX‐MS with applications to a TonB‐dependent transporter and other proteins

T. Sosnick, A. Zmyslowski, Isabelle A. Gagnon, 2022, Protein science : a publication of the Protein Society.

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Joshua A. Riback, T. Sosnick, P. Clark, 2020, Proceedings of the National Academy of Sciences.

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

Karl F Freed, Tobin R Sosnick, John M Jumper, 2018, PLoS Comput. Biol..

Reduced Cβ statistical potentials can outperform all‐atom potentials in decoy identification

James E Fitzgerald, Karl F Freed, Andres Colubri, 2007, Protein science : a publication of the Protein Society.

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.

Andrej Sali, Min-Yi Shen, Andrés Colubri, 2006, Journal of molecular biology.

TULIPs: Tunable, light-controlled interacting protein tags for cell biology

Josiah P. Zayner, Tobin R. Sosnick, Eric L. Weiss, 2012, Nature Methods.

RNA folding: models and perspectives.

Tao Pan, Tobin R Sosnick, T. Pan, 2003, Current opinion in structural biology.

Small proteins fold through transition states with native-like topologies.

Abhishek K. Jha, K. Freed, T. Sosnick, 2006, Journal of molecular biology.

Hydrogen exchange: The modern legacy of Linderstrøm‐Lang

T. Sosnick, Yawen Bai, Y. Bai, 1997, Protein science : a publication of the Protein Society.

Ubiquitin is a novel substrate for human insulin-degrading enzyme.

T. Sosnick, V. Kalas, Wei-Jen Tang, 2011, Journal of molecular biology.

Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide.

J. Trewhella, T. Sosnick, D. Walsh, 1993, Biochemistry.

D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding

Alex Kentsis, Tobin R. Sosnick, A. Kentsis, 2000, Nature Structural Biology.

A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme.

T. Pan, T. Sosnick, X. Fang, 1999, Biochemistry.

Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends.

T. Sosnick, D. Safer, M. Elzinga, 1997, Biochemistry.

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

Karl F Freed, Tobin R Sosnick, John M Jumper, 2018, PLoS Comput. Biol..

Dimensional Scaling of the Large Majority of Chemically Unfolded Proteins Is Indistinguishable from Random Coil Behavior

I. Ruczinski, K. Plaxco, T. Dillon, 2004 .

Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil

T. Sosnick, B. Krantz, 2001, Nature Structural Biology.

The folding of single domain proteins--have we reached a consensus?

Tobin R Sosnick, Doug Barrick, D. Barrick, 2011, Current opinion in structural biology.

Folding and misfolding of potassium channel monomers during assembly and tetramerization

Kevin C. Song, B. Roux, T. Sosnick, 2021, Proceedings of the National Academy of Sciences.

Momentum Distributions in Liquid Helium

P. Sokol, T. Sosnick, W. Snow, 1989 .

Kinetic barriers and the role of topology in protein and RNA folding

Tobin R Sosnick, T. Sosnick, 2008, Protein science : a publication of the Protein Society.

A “Link‐Psi” strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable

T. Sosnick, Ali T Shandiz, Michael C. Baxa, 2012, Protein science : a publication of the Protein Society.

Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates.

Gerra L. Bosco, T. Sosnick, Michael C. Baxa, 2009, Biochemistry.

Psi-constrained simulations of protein folding transition states: implications for calculating.

K. Freed, T. Sosnick, Michael C. Baxa, 2009, Journal of molecular biology.

Simulations of protein folding transition states using ψ-values

K. Freed, T. Sosnick, Michael C. Baxa, 2009 .

Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state.

T. Sosnick, B. Capraro, Ali T Shandiz, 2007, Biochemistry.

Discerning the structure and energy of multiple transition states in protein folding using psi-analysis.

Tobin R Sosnick, Robin S. Dothager, T. Sosnick, 2004, Journal of molecular biology.

Ionic strength independence of charge distributions in solvation of biomolecules.

K. Freed, T. Sosnick, J. Virtanen, 2014, The Journal of chemical physics.

Denatured states of ribonuclease A have compact dimensions and residual secondary structure.

J. Trewhella, T. Sosnick, 1992, Biochemistry.

Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein

Anthony L. Schilmiller, Nabil F. Faruk, A. D. Jones, 2021, Proceedings of the National Academy of Sciences.

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization.

Tao Pan, Tobin R Sosnick, Norbert F Scherer, 2005, RNA.

Fast and Slow Folding in Cytochrome c

Yawen Bai, Leland Mayne, Tobin R. Sosnick, 1998 .

Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking.

A. Kentsis, T. Sosnick, J. Schneider, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Reduced contact order and RNA folding rates.

T. Pan, T. Sosnick, 2004, Journal of molecular biology.

The rate-limiting step in the folding of a large ribozyme without kinetic traps

T. Pan, T. Sosnick, X. Fang, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Large-scale context in protein folding: villin headpiece.

Ariel Fernández, Andrés Colubri, R Stephen Berry, 2003, Biochemistry.

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.

T. Pan, H. Gong, K. Freed, 2010, Journal of molecular biology.

RNA Structure and Folding Analyzed Using Small‐Angle X‐Ray Scattering

T. Sosnick, N. Baird, J. West, 2014 .

The role of helix formation in the folding of a fully α‐helical coiled coil

Tobin R. Sosnick, William F. DeGrado, S. Walter Englander, 1996 .

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein

Kevin W Plaxco, Joshua A. Riback, Tobin R Sosnick, 2018 .

Dynamics of hydrogen bond desolvation in protein folding.

Ariel Fernández, Andrés Colubri, Tobin R Sosnick, 2002, Journal of molecular biology.

Sequential Activation and Local Unfolding Control Poly(A)-Binding Protein Condensation

Joshua A. Riback, T. Sosnick, J. Sachleben, 2022, bioRxiv.

Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.

Tao Pan, Eric Westhof, Tobin R Sosnick, 2005, Journal of molecular biology.

Characterizing the protein folding transition state using psi analysis.

Robin S. Dothager, T. Sosnick, Michael C. Baxa, 2006, Chemical reviews.

Erratum to “Discerning the Structure and Energy of Multiple Transition States in Protein Folding using ψ-Analysis” [J. Mol. Biol. (2004) 337, 463–475]

Robin S. Dothager, T. Sosnick, B. Krantz, 2005 .

Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.

T. Sosnick, Michael C. Baxa, 2021, Methods in molecular biology.

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar

Ruhong Zhou, Wookyung Yu, Karl F. Freed, 2015, Proceedings of the National Academy of Sciences.

The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).

T. Huynh, R. Zhou, K. Freed, 2012, Journal of molecular biology.

Characterizing protein folding transition States using Psi-analysis.

Robin S. Dothager, T. Sosnick, B. Krantz, 2007, Methods in molecular biology.

Benchmarking all-atom simulations using hydrogen exchange

Wookyung Yu, Karl F. Freed, Tobin R. Sosnick, 2014, Proceedings of the National Academy of Sciences.

Prediction and Validation of a Protein’s Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence

Nabil F. Faruk, K. Freed, C. Arrowsmith, 2021, Journal of chemical theory and computation.

Ultrafast signals in protein folding and the polypeptide contracted state.

L Mayne, S W Englander, T. Sosnick, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

Joshua A. Riback, B. Roux, T. Sosnick, 2017, Proceedings of the National Academy of Sciences.

Entropic benefit of a cross‐link in protein association

R. Berry, T. Sosnick, M. Zaman, 2002, Proteins.

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

Karl F Freed, Tobin R Sosnick, Aashish N. Adhikari, 2012, Proceedings of the National Academy of Sciences.

The burst phase in ribonuclease A folding and solvent dependence of the unfolded state

Tobin R. Sosnick, S. Walter Englander, T. Sosnick, 1998, Nature Structural Biology.

Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Thoughput Protein Simulation

Karl F. Freed, Tobin R. Sosnick, John M. Jumper, 2017, bioRxiv.

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding.

Andrei Tokmakoff, Tobin R Sosnick, T. Sosnick, 2008, Biochemistry.

An adaptive biomolecular condensation response is conserved across environmentally divergent species

T. Sosnick, Michael Ford, Hendrik Glauninger, 2023, bioRxiv.

Distinguishing between two-state and three-state models for ubiquitin folding.

T. Sosnick, B. Krantz, 2000, Biochemistry.

Water as a good solvent for unfolded proteins: Folding and collapse are fundamentally different.

K. Plaxco, T. Sosnick, P. Clark, 2020, Journal of molecular biology.

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.

J. Jumper, K. Freed, T. Sosnick, 2019, Biophysical journal.

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

Joshua A. Riback, J. Jumper, K. Freed, 2018, Science.

The importance of measuring the solvent quality of unfolded proteins

Joshua A. Riback, K. Plaxco, T. Sosnick, 2019, Acta Crystallographica Section A: Foundations and Advances.

PII structure in the model peptides for unfolded proteins: Studies on ubiquitin fragments and several alanine‐rich peptides containing QQQ, SSS, FFF, and VVV

Zhengshuang Shi, Kang Chen, Zhigang Liu, 2005, Proteins.

New era of molecular structure and dynamics from solution scattering experiments

T. Sosnick, S. Woodson, 2011, Biopolymers.

Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation

Nabil F. Faruk, T. Sosnick, Xiangda Peng, 2023, International journal of molecular sciences.

Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.

A. S. Krasilnikov, T. Pan, A. Mondragón, 2006, RNA.

Stepwise conversion of a mesophilic to a thermophilic ribozyme.

T. Pan, B. Golden, T. Sosnick, 2003, Journal of molecular biology.

The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits.

S. Niranjanakumari, T. Pan, T. Sosnick, 2001, RNA.

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling

Feng Zhao, Jian Peng, Jinbo Xu, 2010, J. Comput. Biol..

Principal determinants leading to transition state formation of a protein–protein complex, orientation trumps side-chain interactions

T. Sosnick, A. Kossiakoff, J. R. Horn, 2009, Proceedings of the National Academy of Sciences.

A Probabilistic Graphical Model for Ab Initio Folding

Feng Zhao, Jian Peng, Jinbo Xu, 2009, RECOMB.

The Role a-Helical of Helix Formation in the Folding of a Fully Coiled Coil

Tobin R. Sosnick, William F. DeGrado, S. Walter Englander, 1996 .

Simplified protein models: predicting folding pathways and structure using amino acid sequences.

Aashish N. Adhikari, Karl F. Freed, Tobin R. Sosnick, 2013, Physical review letters.

Protein minimization: downsizing through mutation.

W. DeGrado, T. Sosnick, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar

Aashish N. Adhikari, R. Zhou, K. Freed, 2015, Proceedings of the National Academy of Sciences.

On the precision of experimentally determined protein folding rates and ϕ‐values

Kevin W Plaxco, Ingo Ruczinski, Tobin R Sosnick, 2006, Protein science : a publication of the Protein Society.

Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

Joshua A. Riback, B. Roux, T. Sosnick, 2017, Proceedings of the National Academy of Sciences.

Saxs Confirms that FRET Dyes Promote Collapse of an Otherwise Fully Disordered Protein

Joshua A. Riback, K. Plaxco, T. Sosnick, 2018 .

Outcome of a workshop on applications of protein models in biomedical research.

Roland L. Dunbrack, David T. Jones, M. Levitt, 2009, Structure.

Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects

R. Sauer, T. Sosnick, B. Krantz, 2002, Nature Structural Biology.