Publications from The Sosnick Group at The University of Chicago
M.C. Baxa, X. Lin, C.D. Mukinay, S. Chakravarthy, J.R. Sacheleben, S. Antilla, N. Hartrampf, J.A. Riback, I.A. Gagnon, B.L. Pentelute, P.L. Clark, T.R. Sosnick, "How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins" Prot Sci 33(5):e4986 (2024).
H. Glauninger, J.A.M. Bard, C.W. Hickernell, E.M. Airoldi, W. Li, R.H. Singer, S. Paul, J. Fei, T.R. Sosnick, E.W.J. Wallace, D.A. Drummond, "Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts" bioRxiv 2024.04.15.589678
S.K. Kik, D. Christopher, H. Glauninger, C.W. Hickernell, J.A.M. Bard, M. Ford, T.R. Sosnick, D.A. Drummond, "An adaptive biomolecular condensation response is conserved across environmentally divergent species" Nat Comm 15, 3127 (2024).
X. Lin, P. Haller, N. Bavi, N. Faruk, E. Perozo, T.R. Sosnick, "Folding of Prestin’s Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility" eLife 12:RP89635
T.R. Sosnick, "AlphaFold developers Demis Hassabis and John Jumper share the 2023 Albert Lasker Basic Medical Research Award" J Clin Invest. 133 (19) (2023).
K.L. Kroll, A.R. French, T.R. Sosnick, R.S. Rock, "LILAC: enhanced actin imaging with an optogenetic Lifeact" Nature Methods 20 (2023).
S. Chen, M. Hassan, R.L. Jernigan, K. Jia, D. Kihara, A. Kloczkowski, S. Kotelnikov, D. Kozakov, J. Liang, A. Liwo, S. Matysiak, J. Meller, C. Micheletti, J.C. Mitchell, S. Mondal, R. Nussinov, K. Okazaki, D. Padhorny, J. Skolnick, T.R. Sosnick, G. Stan, I. Vakser, X. Zou, G.D. Rose, "Protein folds vs. protein folding: Differing questions, different challenges" Proc Natl Acad Sci U S A 120 (1) (2023).
X. Lin, A.M. Zmyslowski, I.A. Gagnon, R.K. Nakamoto, T.R. Sosnick, "Development of in vivo HDX-MS with applications to a TonB-dependent transporter and other proteins" Protein Science 31 (9) (2022).
A.M. Zmyslowski, M.C. Baxa, I.A. Gagnon, T.R. Sosnick, "HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain’s allostery and unfolding upon B12 and TonB binding" Proc Natl Acad Sci U S A 119 (2022).
K.A. Gaffney, R. Guo, M.D. Bridges, S. Muhammednazaar, D. Chen, M. Kim, Z. Yang, A.L. Schilmiller, N.F. Faruk, X. Peng, A.D. Jones, K.H. Kim, L. Sun, W.L. Hubbell, T.R. Sosnick, H. Hong, "Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein" Proc Natl Acad Sci U S A 119 (2022).
X. Peng, M.C. Baxa, N.F. Faruk, J.R. Sachleben, S. Pintscher, I.A. Gagnon, S. Houliston, C.H. Arrowsmith, K.F. Freed, G.J. Rocklin, T.R. Sosnick, "Prediction and Validation of a Protein’s Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence." J Chem Theory Comput, 18 (2022) 550-61.
M.C. Baxa, T.R. Sosnick, "Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis." Muñoz V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376. (2021) 31-63.
K.C. Song, A.V. Molina, R. Chen, I.A. Gagnon, Y.H. Koh, B. Roux, T.R. Sosnick, "Folding and misfolding of potassium channel monomers during assembly and tetramerization" Proc Natl Acad Sci U S A 118 (2021).
M.A. Bowman, J.A. Riback, A. Rodriguez, H. Guo, J. Li, T.R. Sosnick, P.L. Clark, "Properties of protein unfolded states suggest broad selection for expanded conformational ensembles" Proc Natl Acad Sci U S A 117 (2020) 23356-64.
P.L. Clark, K.W. Plaxco, T.R. Sosnick, "Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different" J Mol Biol 432 (2020) 2882-89.
K. Leon, R.L. Cunningham, J.A. Riback, E. Feldman, J. Li, T.R. Sosnick, M. Zhao, K.R. Monk, D. Araç, "Structural basis for adhesion G protein-coupled receptor Gpr126 function" Nat Comm 11:194 (2020).
Z. Wang, J.M. Jumper, K.F. Freed, T.R. Sosnick, "On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations" Biophysical Journal, 117 (2019) 1429-41.
J.A. Riback, M.A. Bowman, A.M. Zmyslowski, K.W. Plaxco, P.L. Clark, T.R. Sosnick, "Commonly used FRET fluorophores promote collapse of an otherwise disordered protein" Proc Natl Acad Sci U S A 116 (2019) 8889-94
J.P. Zayner, T. Mathes, T.R. Sosnick, J.T.M. Kennis, "Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1" ACS Omega 2019, 4(1) 1238-43.
J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics" PLoS Comput Biol 14(12): e1006342
J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours" PLoS Comput Biol. 14(12): e1006578
Z. Wang, J.M. Jumper, S. Wang, K.F. Freed, T.R. Sosnick, "A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations." Biophysical Journal, 115 (2018) 1872-84.
J.R. Riback, M.A. Bowman, A.M. Zmyslowski, C.R. Knoverek, J.M. Jumper, E.B. Haye, K.F. Freed, P.L. Clark, T.R. Sosnick, "Response to Comment on 'Innovative scattering analysis shows hydrophobic disordered proteins are expanded in water'" Science 361 (2018).
J.J. Skinner, S. Wang, J. Lee, C. Ong, R. Sommese, S. Sivaramakrishnan, W. Koelmel, M. Hirschbeck, H. Schindelin, C. Kisker, K. Lorenz, T.R. Sosnick, M.R. Rosner, "Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome." Proc Natl Acad Sci U S A 114 (2017) 13453-8.
J.R. Riback, M.A. Bowman, A.M. Zmyslowski, C.R. Knoverek, J.M. Jumper, J.R. Hinshaw, E.B. Haye, K.F. Freed, P.L. Clark, T.R. Sosnick, "Innovative scattering analysis shows hydrophobic disordered proteins are expanded in water" Science 358 (2017) 238-41.
J.A. Riback*, C.D. Katanski*, J.L. Kear-Scott, E.V. Pilipenko, A.E. Rojek, T.R. Sosnick, D.A. Drummond, "Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response" Cell 168 (2017) 1028-40.
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A.R. French, T.R. Sosnick, R.S. Rock, "Investigations of human myosin VI targeting using optogenetically controlled cargo loading" Proc Natl Acad Sci U S A 114 (2017) E1607-16.
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Z.P. Gates*, M.C. Baxa*, W. Yu, J.A. Riback, H. Li, B. Roux, S.B.H. Kent, T.R. Sosnick, "Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core" Proc Natl Acad Sci U S A 114 (2017) 2241-6.
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B. Basanta, K.K. Chan, P. Barth, T. King, T.R. Sosnick, J.R. Hinshaw, G. Liu, J.K. Everett, R. Xiao, G.T. Montelione, D. Baker, "Introduction of a polar core into the de novo designed protein Top7" Protein Sci 25 (2016) 1299-307.
M.J. Poellmann, T.R. Sosnick, S.C. Meredith, R.C. Lee, "The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme" Macromol Biosci (2016).
J.R. Sachleben, A.N. Adhikari, G. Gawlak, R.J. Hoey, G. Liu, A. Joachimiak, G.T. Montelione, T.R. Sosnick, S. Koide, "Aromatic claw: A new fold with high aromatic content that evades structural prediction" Protein Sci (2016).
J.J. Virtanen, T.R. Sosnick, K.F. Freed, "Erratum: Ionic strength independence of charge distributions in solvation of biomolecules [J. Chem. Phys. 141, 22D503 (2014)]" J Chem Phys 145 (2016) 059903.
W. Yu, M.C. Baxa, I. Gagnon, K.F. Freed, T.R. Sosnick, "Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange" Proc Natl Acad Sci U S A 113 (2016) 4747-52.
M.C. Baxa, W. Yu, A.N. Adhikari, L. Ge, Z. Xia, R. Zhou, K.F. Freed, T.R. Sosnick, "Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar" Proc Natl Acad Sci U S A 112 (2015) 8302-7.
H.M. Watkins, A.J. Simon, T.R. Sosnick, E.A. Lipman, R.P. Hjelm, K.W. Plaxco, "Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions" Proc Natl Acad Sci U S A 112 (2015) 6631-6.
M.C. Baxa, E.J. Haddadian, J.M. Jumper, K.F. Freed, T.R. Sosnick, "Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations" Proc Natl Acad Sci U S A 111 (2014) 15396-401.
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J.J. Skinner, W. Yu, E.K. Gichana, M.C. Baxa, J.R. Hinshaw, K.F. Freed, T.R. Sosnick, "Benchmarking all-atom simulations using hydrogen exchange" Proc Natl Acad Sci U S A 111 (2014) 15975-80.
J.J. Virtanen, T.R. Sosnick, K.F. Freed, "Ionic strength independence of charge distributions in solvation of biomolecules" J Chem Phys 141 (2014) 22D503.
J.P. Zayner, T.R. Sosnick, "Factors that control the chemistry of the LOV domain photocycle" PLoS One 9 (2014) e87074.
A.N. Adhikari, K.F. Freed, T.R. Sosnick, "Simplified protein models: predicting folding pathways and structure using amino acid sequences" Phys Rev Lett 111 (2013) 028103.
Y. Liu, E. Haddadian, T.R. Sosnick, K.F. Freed, H. Gong, "A novel implicit solvent model for simulating the molecular dynamics of RNA" Biophys J 105 (2013) 1248-57.
M. Parisien, X. Wang, G. Perdrizet, 2nd, C. Lamphear, C.A. Fierke, K.C. Maheshwari, M.J. Wilde, T.R. Sosnick, T. Pan, "Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface" Cell Rep 3 (2013) 1703-13.
T.R. Sosnick, M.C. Baxa, "Revealing what gets buried first in protein folding" Proc Natl Acad Sci U S A 110 (2013) 16704-5.
B.T. Walters, L. Mayne, J.R. Hinshaw, T.R. Sosnick, S.W. Englander, "Folding of a large protein at high structural resolution" Proc Natl Acad Sci U S A 110 (2013) 18898-903.
J.P. Zayner, C. Antoniou, A.R. French, R.J. Hause, Jr., T.R. Sosnick, "Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein" Biophys J 105 (2013) 1027-36.
A.N. Adhikari, K.F. Freed, T.R. Sosnick, "De novo prediction of protein folding pathways and structure using the principle of sequential stabilization" Proc Natl Acad Sci U S A 109 (2012) 17442-7.
A.N. Adhikari, J. Peng, M. Wilde, J. Xu, K.F. Freed, T.R. Sosnick, "Modeling large regions in proteins: applications to loops, termini, and folding" Protein Sci 21 (2012) 107-21.
M.C. Baxa, E.J. Haddadian, A.K. Jha, K.F. Freed, T.R. Sosnick, "Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles" J Am Chem Soc 134 (2012) 15929-36.
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M. Parisien, K.F. Freed, T.R. Sosnick, "On docking, scoring and assessing protein-DNA complexes in a rigid-body framework" PLoS One 7 (2012) e32647.
G.A. Perdrizet, 2nd, I. Artsimovitch, R. Furman, T.R. Sosnick, T. Pan, "Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch" Proc Natl Acad Sci U S A 109 (2012) 3323-8.
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A.T. Shandiz, M.C. Baxa, T.R. Sosnick, "A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable" Protein Sci 21 (2012) 819-27.
D. Strickland, Y. Lin, E. Wagner, C.M. Hope, J. Zayner, C. Antoniou, T.R. Sosnick, E.L. Weiss, M. Glotzer, "TULIPs: tunable, light-controlled interacting protein tags for cell biology" Nat Methods 9 (2012) 379-84.
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T.Y. Yoo, A. Adhikari, Z. Xia, T. Huynh, K.F. Freed, R. Zhou, T.R. Sosnick, "The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized)" J Mol Biol 420 (2012) 220-34.
T.Y. Yoo, S.P. Meisburger, J. Hinshaw, L. Pollack, G. Haran, T.R. Sosnick, K. Plaxco, "Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state" J Mol Biol 418 (2012) 226-36.
J.P. Zayner, C. Antoniou, T.R. Sosnick, "The amino-terminal helix modulates light-activated conformational changes in AsLOV2" J Mol Biol 419 (2012) 61-74.
E.J. Haddadian, H. Gong, A.K. Jha, X. Yang, J. Debartolo, J.R. Hinshaw, P.A. Rice, T.R. Sosnick, K.F. Freed, "Automated real-space refinement of protein structures using a realistic backbone move set" Biophys J 101 (2011) 899-909.
L.A. Ralat, V. Kalas, Z. Zheng, R.D. Goldman, T.R. Sosnick, W.J. Tang, "Ubiquitin is a novel substrate for human insulin-degrading enzyme" J Mol Biol 406 (2011) 454-66.
T.R. Sosnick, J.R. Hinshaw, "Biochemistry. How proteins fold" Science 334 (2011) 464-5.
T.R. Sosnick, S.A. Woodson, "New era of molecular structure and dynamics from solution scattering experiments" Biopolymers 95 (2011) 503-4.
T.R. Sosnick, D. Barrick, "The folding of single domain proteins--have we reached a consensus?" Curr Opin Struct Biol 21 (2011) 12-24.
J.J. Virtanen, L. Makowski, T.R. Sosnick, K.F. Freed, "Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering" Biophys J 101 (2011) 2061-9.
N.J. Baird, S.J. Ludtke, H. Khant, W. Chiu, T. Pan, T.R. Sosnick, "Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy" J Am Chem Soc 132 (2010) 16352-3.
N.J. Baird, H. Gong, S.S. Zaheer, K.F. Freed, T. Pan, T.R. Sosnick, "Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion" J Mol Biol 397 (2010) 1298-306.
J. DeBartolo, G. Hocky, M. Wilde, J. Xu, K.F. Freed, T.R. Sosnick, "Protein structure prediction enhanced with evolutionary diversity: SPEED" Protein Sci 19 (2010) 520-34.
D. Strickland, X. Yao, G. Gawlak, M.K. Rosen, K.H. Gardner, T.R. Sosnick, "Rationally improving LOV domain-based photoswitches" Nat Methods 7 (2010) 623-6.
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J.J. Virtanen, L. Makowski, T.R. Sosnick, K.F. Freed, "Modeling the hydration layer around proteins: HyPred" Biophys J 99 (2010) 1611-9.
F. Zhao, J. Peng, J. Debartolo, K.F. Freed, T.R. Sosnick, J. Xu, "A probabilistic and continuous model of protein conformational space for template-free modeling" J Comput Biol 17 (2010) 783-98.
Z. Zheng, T.R. Sosnick, "Protein vivisection reveals elusive intermediates in folding" J Mol Biol 397 (2010) 777-88.
M.C. Baxa, K.F. Freed, T.R. Sosnick, "Psi-constrained simulations of protein folding transition states: implications for calculating φ" J Mol Biol 386 (2009) 920-8.
G.L. Bosco, M. Baxa, T.R. Sosnick, "Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates" Biochemistry 48 (2009) 2950-9.
J. DeBartolo, A. Colubri, A.K. Jha, J.E. Fitzgerald, K.F. Freed, T.R. Sosnick, "Mimicking the folding pathway to improve homology-free protein structure prediction" Proc Natl Acad Sci U S A 106 (2009) 3734-9.
J.R. Horn, T.R. Sosnick, A.A. Kossiakoff, "Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions" Proc Natl Acad Sci U S A 106 (2009) 2559-64.
T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack, Jr., K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek, Jr., T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, I.A. Wilson, "Outcome of a workshop on applications of protein models in biomedical research" Structure 17 (2009) 151-9.
F. Zhao, J. Peng, J. Debartolo, K.F. Freed, T.R. Sosnick, J. Xu, "A Probabilistic Graphical Model for Ab Initio Folding" Res Comput Mol Biol 5541 (2009) 59-73.
M.C. Baxa, K.F. Freed, T.R. Sosnick, "Quantifying the structural requirements of the folding transition state of protein A and other systems" J Mol Biol 381 (2008) 1362-81.
H.S. Chung, A. Shandiz, T.R. Sosnick, A. Tokmakoff, "Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding" Biochemistry 47 (2008) 13870-7.
X. Qu, G.J. Smith, K.T. Lee, T.R. Sosnick, T. Pan, N.F. Scherer, "Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA" Proc Natl Acad Sci U S A 105 (2008) 6602-7.
G.J. Smith, K.T. Lee, X. Qu, Z. Xie, J. Pesic, T.R. Sosnick, T. Pan, N.F. Scherer, "A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics" J Mol Biol 378 (2008) 943-53.
T.R. Sosnick, "Kinetic barriers and the role of topology in protein and RNA folding" Protein Sci 17 (2008) 1308-18.
D. Strickland, K. Moffat, T.R. Sosnick, "Light-activated DNA binding in a designed allosteric protein" Proc Natl Acad Sci U S A 105 (2008) 10709-14.
N.J. Baird, X.W. Fang, N. Srividya, T. Pan, T.R. Sosnick, "Folding of a universal ribozyme: the ribonuclease P RNA" Q Rev Biophys 40 (2007) 113-61.
J.E. Fitzgerald, A.K. Jha, A. Colubri, T.R. Sosnick, K.F. Freed, "Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification" Protein Sci 16 (2007) 2123-39.
J.E. Fitzgerald, A.K. Jha, T.R. Sosnick, K.F. Freed, "Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors" Biochemistry 46 (2007) 669-82.
J. Jacob, R.S. Dothager, P. Thiyagarajan, T.R. Sosnick, "Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature" J Mol Biol 367 (2007) 609-15.
A.D. Pandit, B.A. Krantz, R.S. Dothager, T.R. Sosnick, "Characterizing protein folding transition States using Psi-analysis" Methods Mol Biol 350 (2007) 83-104.
A.T. Shandiz, B.R. Capraro, T.R. Sosnick, "Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state" Biochemistry 46 (2007) 13711-9.
T.N. Wong, T.R. Sosnick, T. Pan, "Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures" Proc Natl Acad Sci U S A 104 (2007) 17995-8000.
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N.J. Baird, N. Srividya, A.S. Krasilnikov, A. Mondragon, T.R. Sosnick, T. Pan, "Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium" RNA 12 (2006) 598-606.
A. Colubri, A.K. Jha, M.Y. Shen, A. Sali, R.S. Berry, T.R. Sosnick, K.F. Freed, "Minimalist representations and the importance of nearest neighbor effects in protein folding simulations" J Mol Biol 363 (2006) 835-57.
M.A. de los Rios, B.K. Muralidhara, D. Wildes, T.R. Sosnick, S. Marqusee, P. Wittung-Stafshede, K.W. Plaxco, I. Ruczinski, "On the precision of experimentally determined protein folding rates and phi-values" Protein Sci 15 (2006) 553-63.
A.D. Pandit, A. Jha, K.F. Freed, T.R. Sosnick, "Small proteins fold through transition states with native-like topologies" J Mol Biol 361 (2006) 755-70.
I. Ruczinski, T.R. Sosnick, K.W. Plaxco, "Methods for the accurate estimation of confidence intervals on protein folding phi-values" Protein Sci 15 (2006) 2257-64.
Z. Shi, K. Chen, Z. Liu, T.R. Sosnick, N.R. Kallenbach, "PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV" Proteins 63 (2006) 312-21.
T.R. Sosnick, B.A. Krantz, R.S. Dothager, M.C. Baxa, "Characterizing the protein folding transition state using psi analysis" Chem Rev 106 (2006) 1862-76.
N.J. Baird, E. Westhof, H. Qin, T. Pan, T.R. Sosnick, "Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding" J Mol Biol 352 (2005) 712-22.
A.K. Jha, A. Colubri, K.F. Freed, T.R. Sosnick, "Statistical coil model of the unfolded state: resolving the reconciliation problem" Proc Natl Acad Sci U S A 102 (2005) 13099-104.
A.K. Jha, A. Colubri, M.H. Zaman, S. Koide, T.R. Sosnick, K.F. Freed, "Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library" Biochemistry 44 (2005) 9691-702.
K.L. Maxwell, D. Wildes, A. Zarrine-Afsar, M.A. De Los Rios, A.G. Brown, C.T. Friel, L. Hedberg, J.C. Horng, D. Bona, E.J. Miller, A. Vallee-Belisle, E.R. Main, F. Bemporad, L. Qiu, K. Teilum, N.D. Vu, A.M. Edwards, I. Ruczinski, F.M. Poulsen, B.B. Kragelund, S.W. Michnick, F. Chiti, Y. Bai, S.J. Hagen, L. Serrano, M. Oliveberg, D.P. Raleigh, P. Wittung-Stafshede, S.E. Radford, S.E. Jackson, T.R. Sosnick, S. Marqusee, A.R. Davidson, K.W. Plaxco, "Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins" Protein Sci 14 (2005) 602-16.
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G.J. Smith, T.R. Sosnick, N.F. Scherer, T. Pan, "Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization" RNA 11 (2005) 234-9.
T. Wong, T.R. Sosnick, T. Pan, "Mechanistic insights on the folding of a large ribozyme during transcription" Biochemistry 44 (2005) 7535-42.
J. Jacob, B. Krantz, R.S. Dothager, P. Thiyagarajan, T.R. Sosnick, "Early collapse is not an obligate step in protein folding" J Mol Biol 338 (2004) 369-82.
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J.E. Kohn, I.S. Millett, J. Jacob, B. Zagrovic, T.M. Dillon, N. Cingel, R.S. Dothager, S. Seifert, P. Thiyagarajan, T.R. Sosnick, M.Z. Hasan, V.S. Pande, I. Ruczinski, S. Doniach, K.W. Plaxco, "Random-coil behavior and the dimensions of chemically unfolded proteins" Proc Natl Acad Sci U S A 101 (2004) 12491-6.
B.A. Krantz, R.S. Dothager, T.R. Sosnick, "Discerning the structure and energy of multiple transition states in protein folding using psi-analysis" J Mol Biol 337 (2004) 463-75.
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W.K. Meisner, T.R. Sosnick, "Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding" Proc Natl Acad Sci U S A 101 (2004) 15639-44.
W.K. Meisner, T.R. Sosnick, "Fast folding of a helical protein initiated by the collision of unstructured chains" Proc Natl Acad Sci U S A 101 (2004) 13478-82.
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T.R. Sosnick, R.S. Dothager, B.A. Krantz, "Differences in the folding transition state of ubiquitin indicated by phi and psi analyses" Proc Natl Acad Sci U S A 101 (2004) 17377-82.
T.R. Sosnick, "Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein"" Science 306 (2004) 411; author reply
T.R. Sosnick, T. Pan, "Reduced contact order and RNA folding rates" J Mol Biol 342 (2004) 1359-65.
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Z. Xie, N. Srividya, T.R. Sosnick, T. Pan, N.F. Scherer, "Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme" Proc Natl Acad Sci U S A 101 (2004) 534-9.
X.W. Fang, N. Srividya, B.L. Golden, T.R. Sosnick, T. Pan, "Stepwise conversion of a mesophilic to a thermophilic ribozyme" J Mol Biol 330 (2003) 177-83.
A. Fernandez, M.Y. Shen, A. Colubri, T.R. Sosnick, R.S. Berry, K.F. Freed, "Large-scale context in protein folding: villin headpiece" Biochemistry 42 (2003) 664-71.
T.R. Sosnick, T. Pan, "RNA folding: models and perspectives" Curr Opin Struct Biol 13 (2003) 309-16.
M.H. Zaman, M.Y. Shen, R.S. Berry, K.F. Freed, T.R. Sosnick, "Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides" J Mol Biol 331 (2003) 693-711.
X.W. Fang, P. Thiyagarajan, T.R. Sosnick, T. Pan, "The rate-limiting step in the folding of a large ribozyme without kinetic traps" Proc Natl Acad Sci U S A 99 (2002) 8518-23.
***Recommended in F1000Prime***
A. Fernandez, T.R. Sosnick, A. Colubri, "Dynamics of hydrogen bond desolvation in protein folding" J Mol Biol 321 (2002) 659-75.
B.A. Krantz, L. Mayne, J. Rumbley, S.W. Englander, T.R. Sosnick, "Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding" J Mol Biol 324 (2002) 359-71.
***Recommended in F1000Prime***
B.A. Krantz, A.K. Srivastava, S. Nauli, D. Baker, R.T. Sauer, T.R. Sosnick, "Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects" Nat Struct Biol 9 (2002) 458-63.
***Recommended in F1000Prime***
Z. Shi, C.A. Olson, N.R. Kallenbach, T.R. Sosnick, "D/H amide isotope effect in model alpha-helical peptides" J Am Chem Soc 124 (2002) 13994-5.
Z. Shi, B.A. Krantz, N. Kallenbach, T.R. Sosnick, "Contribution of hydrogen bonding to protein stability estimated from isotope effects" Biochemistry 41 (2002) 2120-9.
***Recommended in F1000Prime***
T.R. Sosnick, T. Pan, "Getting hotter with RNA" Nat Struct Biol 9 (2002) 795-6.
T.R. Sosnick, R.S. Berry, A. Colubri, A. Fernandez, "Distinguishing foldable proteins from nonfolders: when and how do they differ?" Proteins 49 (2002) 15-23.
M.H. Zaman, R.S. Berry, T.R. Sosnick, "Entropic benefit of a cross-link in protein association" Proteins 48 (2002) 341-51.
X.W. Fang, B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, T. Pan, T.R. Sosnick, "The thermodynamic origin of the stability of a thermophilic ribozyme" Proc Natl Acad Sci U S A 98 (2001) 4355-60.
X.W. Fang, X.J. Yang, K. Littrell, S. Niranjanakumari, P. Thiyagarajan, C.A. Fierke, T.R. Sosnick, T. Pan, "The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits" RNA 7 (2001) 233-41.
B.A. Krantz, T.R. Sosnick, "Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil" Nat Struct Biol 8 (2001) 1042-7.
B.C. Lee, P.A. Croonquist, T.R. Sosnick, W.D. Hoff, "PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation" J Biol Chem 276 (2001) 20821-3.
H. Qin, T.R. Sosnick, T. Pan, "Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA" Biochemistry 40 (2001) 11202-10.
V.M. Shelton, T.R. Sosnick, T. Pan, "Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations" Biochemistry 40 (2001) 3629-38.
T.R. Sosnick, "Characterization of tertiary folding of RNA by circular dichroism and urea" Curr Protoc Nucleic Acid Chem Chapter 11 (2001) Unit 11 5.
X. Fang, K. Littrell, X.J. Yang, S.J. Henderson, S. Siefert, P. Thiyagarajan, T. Pan, T.R. Sosnick, "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" Biochemistry 39 (2000) 11107-13.
B.A. Krantz, T.R. Sosnick, "Distinguishing between two-state and three-state models for ubiquitin folding" Biochemistry 39 (2000) 11696-701.
B.A. Krantz, L.B. Moran, A. Kentsis, T.R. Sosnick, "D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding" Nat Struct Biol 7 (2000) 62-71.
T.R. Sosnick, X. Fang, V.M. Shelton, "Application of circular dichroism to study RNA folding transitions" Methods Enzymol 317 (2000) 393-409.
R.P. Bhattacharyya, T.R. Sosnick, "Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil" Biochemistry 38 (1999) 2601-9.
X. Fang, T. Pan, T.R. Sosnick, "A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme" Biochemistry 38 (1999) 16840-6.
X.W. Fang, T. Pan, T.R. Sosnick, "Mg2+-dependent folding of a large ribozyme without kinetic traps" Nat Struct Biol 6 (1999) 1091-5.
L.B. Moran, J.P. Schneider, A. Kentsis, G.A. Reddy, T.R. Sosnick, "Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking" Proc Natl Acad Sci U S A 96 (1999) 10699-704.
T. Pan, I. Artsimovitch, X.W. Fang, R. Landick, T.R. Sosnick, "Folding of a large ribozyme during transcription and the effect of the elongation factor NusA" Proc Natl Acad Sci U S A 96 (1999) 9545-50.
V.M. Shelton, T.R. Sosnick, T. Pan, "Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding" Biochemistry 38 (1999) 16831-9.
A. Kentsis, T.R. Sosnick, "Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding" Biochemistry 37 (1998) 14613-22.
P.X. Qi, T.R. Sosnick, S.W. Englander, "The burst phase in ribonuclease A folding and solvent dependence of the unfolded state" Nat Struct Biol 5 (1998) 882-4.
S.W. Englander, L. Mayne, Y. Bai, T.R. Sosnick, "Hydrogen exchange: the modern legacy of Linderstrom-Lang" Protein Sci 6 (1997) 1101-9.
T. Pan, T.R. Sosnick, "Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity" Nat Struct Biol 4 (1997) 931-8.
D. Safer, T.R. Sosnick, M. Elzinga, "Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends" Biochemistry 36 (1997) 5806-16.
T.R. Sosnick, M.D. Shtilerman, L. Mayne, S.W. Englander, "Ultrafast signals in protein folding and the polypeptide contracted state" Proc Natl Acad Sci U S A 94 (1997) 8545-50.
W.F. DeGrado, T.R. Sosnick, "Protein minimization: downsizing through mutation" Proc Natl Acad Sci U S A 93 (1996) 5680-1.
S.W. Englander, T.R. Sosnick, J.J. Englander, L. Mayne, "Mechanisms and uses of hydrogen exchange" Curr Opin Struct Biol 6 (1996) 18-23.
T.R. Sosnick, S. Jackson, R.R. Wilk, S.W. Englander, W.F. DeGrado, "The role of helix formation in the folding of a fully alpha-helical coiled coil" Proteins 24 (1996) 427-32.
T.R. Sosnick, L. Mayne, S.W. Englander, "Molecular collapse: the rate-limiting step in two-state cytochrome c folding" Proteins 24 (1996) 413-26.
Y. Bai, T.R. Sosnick, L. Mayne, S.W. Englander, "Protein folding intermediates: native-state hydrogen exchange" Science 269 (1995) 192-7.
G.A. Olah, D.M. Gray, C.W. Gray, D.L. Kergil, T.R. Sosnick, B.L. Mark, M.R. Vaughan, J. Trewhella, "Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study" J Mol Biol 249 (1995) 576-94.
C.J. Unkefer, D.R. Houck, B.M. Britt, T.R. Sosnick, J.L. Hanners, "Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine" Methods Enzymol 258 (1995) 227-35.
T.R. Sosnick, L. Mayne, R. Hiller, S.W. Englander, "The barriers in protein folding" Nat Struct Biol 1 (1994) 149-56.
G.A. Olah, R.D. Mitchell, T.R. Sosnick, D.A. Walsh, J. Trewhella, "Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide" Biochemistry 32 (1993) 3649-57.
T.R. Sosnick, J. Trewhella, "Denatured states of ribonuclease A have compact dimensions and residual secondary structure" Biochemistry 31 (1992) 8329-35.
T.R. Sosnick, D.C. Benjamin, J. Novotny, P.A. Seeger, J. Trewhella, "Distances between the antigen-binding sites of three murine antibody subclasses measured using neutron and X-ray scattering" Biochemistry 31 (1992) 1779-86.