Tobin R. Sosnick - Publications

Affiliations: 
University of Chicago, Chicago, IL 
Area:
studies of protein and RNA folding, function and design
Website:
http://sosnick.uchicago.edu/people/trsosnick.html

152 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR. Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 30992378 DOI: 10.1073/pnas.1813038116  0.6
2018 Jumper JM, Faruk NF, Freed KF, Sosnick TR. Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. Plos Computational Biology. 14: e1006342. PMID 30589846 DOI: 10.1371/journal.pcbi.1006342  0.88
2018 Jumper JM, Faruk NF, Freed KF, Sosnick TR. Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. Plos Computational Biology. 14: e1006578. PMID 30589834 DOI: 10.1371/journal.pcbi.1006578  0.88
2018 Wang Z, Jumper JM, Wang S, Freed KF, Sosnick TR. A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations. Biophysical Journal. PMID 30413241 DOI: 10.1016/j.bpj.2018.10.012  0.88
2018 Riback JA, Bowman MA, Zmyslowski A, Knoverek CR, Jumper J, Kaye EB, Freed KF, Clark PL, Sosnick TR. Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science (New York, N.Y.). 361. PMID 30166460 DOI: 10.1126/science.aar7949  0.88
2017 Skinner JJ, Wang S, Lee J, Ong C, Sommese R, Sivaramakrishnan S, Koelmel W, Hirschbeck M, Schindelin H, Kisker C, Lorenz K, Sosnick TR, Rosner MR. Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome. Proceedings of the National Academy of Sciences of the United States of America. PMID 29208709 DOI: 10.1073/pnas.1711543114  0.6
2017 Riback JA, Bowman MA, Zmyslowski AM, Knoverek CR, Jumper JM, Hinshaw JR, Kaye EB, Freed KF, Clark PL, Sosnick TR. Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science (New York, N.Y.). 358: 238-241. PMID 29026044 DOI: 10.1126/science.aan5774  0.88
2017 Riback JA, Katanski CD, Kear-Scott JL, Pilipenko EV, Rojek AE, Sosnick TR, Drummond DA. Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response. Cell. 168: 1028-1040.e19. PMID 28283059 DOI: 10.1016/j.cell.2017.02.027  0.6
2017 Gates ZP, Baxa MC, Yu W, Riback JA, Li H, Roux B, Kent SB, Sosnick TR. Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193869 DOI: 10.1073/pnas.1609579114  1
2016 Sachleben JR, Adhikari AN, Gawlak G, Hoey RJ, Liu G, Joachimiak A, Montelione GT, Sosnick TR, Koide S. Aromatic Claw: A new fold with high aromatic content that evades structural prediction. Protein Science : a Publication of the Protein Society. PMID 27750371 DOI: 10.1002/pro.3069  0.56
2016 Yu W, Baxa MC, Gagnon I, Freed KF, Sosnick TR. Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Proceedings of the National Academy of Sciences of the United States of America. PMID 27078098 DOI: 10.1073/pnas.1522500113  1
2016 Basanta B, Chan KK, Barth P, King T, Hinshaw JR, Sosnick TR, Liu G, Everett J, Xiao R, Montelione GT, Baker D. Introduction of a polar core into the de novo designed protein Top7. Protein Science : a Publication of the Protein Society. PMID 26873166 DOI: 10.1002/pro.2899  1
2015 Baxa MC, Yu W, Adhikari AN, Ge L, Xia Z, Zhou R, Freed KF, Sosnick TR. Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100906 DOI: 10.1073/pnas.1503613112  1
2015 Watkins HM, Simon AJ, Sosnick TR, Lipman EA, Hjelm RP, Plaxco KW. Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions. Proceedings of the National Academy of Sciences of the United States of America. 112: 6631-6. PMID 25964362 DOI: 10.1073/pnas.1418673112  1
2014 Virtanen JJ, Sosnick TR, Freed KF. Ionic strength independence of charge distributions in solvation of biomolecules. The Journal of Chemical Physics. 141: 22D503. PMID 25494774 DOI: 10.1063/1.4895522  0.88
2014 Skinner JJ, Yu W, Gichana EK, Baxa MC, Hinshaw JR, Freed KF, Sosnick TR. Benchmarking all-atom simulations using hydrogen exchange. Proceedings of the National Academy of Sciences of the United States of America. 111: 15975-80. PMID 25349413 DOI: 10.1073/pnas.1404213111  1
2014 Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proceedings of the National Academy of Sciences of the United States of America. 111: 15396-401. PMID 25313044 DOI: 10.1073/pnas.1407768111  1
2014 Zayner JP, Sosnick TR. Factors that control the chemistry of the LOV domain photocycle. Plos One. 9: e87074. PMID 24475227 DOI: 10.1371/journal.pone.0087074  1
2013 Walters BT, Mayne L, Hinshaw JR, Sosnick TR, Englander SW. Folding of a large protein at high structural resolution. Proceedings of the National Academy of Sciences of the United States of America. 110: 18898-903. PMID 24191053 DOI: 10.1073/pnas.1319482110  1
2013 Sosnick TR, Baxa MC. Revealing what gets buried first in protein folding. Proceedings of the National Academy of Sciences of the United States of America. 110: 16704-5. PMID 24096579 DOI: 10.1073/pnas.1316158110  1
2013 Liu Y, Haddadian E, Sosnick TR, Freed KF, Gong H. A novel implicit solvent model for simulating the molecular dynamics of RNA. Biophysical Journal. 105: 1248-57. PMID 24010668 DOI: 10.1016/j.bpj.2013.07.033  1
2013 Zayner JP, Antoniou C, French AR, Hause RJ, Sosnick TR. Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein. Biophysical Journal. 105: 1027-36. PMID 23972854 DOI: 10.1016/j.bpj.2013.07.010  1
2013 Adhikari AN, Freed KF, Sosnick TR. Simplified protein models: predicting folding pathways and structure using amino acid sequences. Physical Review Letters. 111: 028103. PMID 23889448 DOI: 10.1103/PhysRevLett.111.028103  1
2013 Parisien M, Wang X, Perdrizet G, Lamphear C, Fierke CA, Maheshwari KC, Wilde MJ, Sosnick TR, Pan T. Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. Cell Reports. 3: 1703-13. PMID 23665222 DOI: 10.1016/j.celrep.2013.04.010  1
2013 Adhikari AN, Freed KF, Sosnick TR. Simplified protein models: Predicting folding pathways and structure using amino acid sequences Physical Review Letters. 111. DOI: 10.1103/PhysRevLett.111.028103  0.88
2012 Adhikari AN, Freed KF, Sosnick TR. De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proceedings of the National Academy of Sciences of the United States of America. 109: 17442-7. PMID 23045636 DOI: 10.1073/pnas.1209000109  1
2012 Baxa MC, Haddadian EJ, Jha AK, Freed KF, Sosnick TR. Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles. Journal of the American Chemical Society. 134: 15929-36. PMID 22928488 DOI: 10.1021/ja3064028  1
2012 Shandiz AT, Baxa MC, Sosnick TR. A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable. Protein Science : a Publication of the Protein Society. 21: 819-27. PMID 22528473 DOI: 10.1002/pro.2065  1
2012 Yoo TY, Adhikari A, Xia Z, Huynh T, Freed KF, Zhou R, Sosnick TR. The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized). Journal of Molecular Biology. 420: 220-34. PMID 22522126 DOI: 10.1016/j.jmb.2012.04.013  1
2012 Zayner JP, Antoniou C, Sosnick TR. The amino-terminal helix modulates light-activated conformational changes in AsLOV2. Journal of Molecular Biology. 419: 61-74. PMID 22406525 DOI: 10.1016/j.jmb.2012.02.037  1
2012 Parisien M, Freed KF, Sosnick TR. On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. Plos One. 7: e32647. PMID 22393431 DOI: 10.1371/journal.pone.0032647  1
2012 Strickland D, Lin Y, Wagner E, Hope CM, Zayner J, Antoniou C, Sosnick TR, Weiss EL, Glotzer M. TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nature Methods. 9: 379-84. PMID 22388287 DOI: 10.1038/nmeth.1904  1
2012 Perdrizet GA, Artsimovitch I, Furman R, Sosnick TR, Pan T. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proceedings of the National Academy of Sciences of the United States of America. 109: 3323-8. PMID 22331895 DOI: 10.1073/pnas.1113086109  1
2012 Yoo TY, Meisburger SP, Hinshaw J, Pollack L, Haran G, Sosnick TR, Plaxco K. Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state. Journal of Molecular Biology. 418: 226-36. PMID 22306460 DOI: 10.1016/j.jmb.2012.01.016  1
2012 Adhikari AN, Peng J, Wilde M, Xu J, Freed KF, Sosnick TR. Modeling large regions in proteins: applications to loops, termini, and folding. Protein Science : a Publication of the Protein Society. 21: 107-21. PMID 22095743 DOI: 10.1002/pro.767  1
2012 Debartolo J, Jha A, Freed KF, Sosnick TR. Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States Protein and Peptide Folding, Misfolding, and Non-Folding. 79-98. DOI: 10.1002/9781118183373.ch3  1
2011 Sosnick TR, Hinshaw JR. Biochemistry. How proteins fold. Science (New York, N.Y.). 334: 464-5. PMID 22034424 DOI: 10.1126/science.1214018  1
2011 Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering. Biophysical Journal. 101: 2061-9. PMID 22004761 DOI: 10.1016/j.bpj.2011.09.021  1
2011 Haddadian EJ, Gong H, Jha AK, Yang X, Debartolo J, Hinshaw JR, Rice PA, Sosnick TR, Freed KF. Automated real-space refinement of protein structures using a realistic backbone move set. Biophysical Journal. 101: 899-909. PMID 21843481 DOI: 10.1016/j.bpj.2011.06.063  1
2011 Sosnick TR, Woodson SA. New era of molecular structure and dynamics from solution scattering experiments. Biopolymers. 95: 503-4. PMID 21618464 DOI: 10.1002/bip.21643  1
2011 Ralat LA, Kalas V, Zheng Z, Goldman RD, Sosnick TR, Tang WJ. Ubiquitin is a novel substrate for human insulin-degrading enzyme. Journal of Molecular Biology. 406: 454-66. PMID 21185309 DOI: 10.1016/j.jmb.2010.12.026  1
2011 Sosnick TR, Barrick D. The folding of single domain proteins--have we reached a consensus? Current Opinion in Structural Biology. 21: 12-24. PMID 21144739 DOI: 10.1016/j.sbi.2010.11.002  1
2010 Baird NJ, Ludtke SJ, Khant H, Chiu W, Pan T, Sosnick TR. Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. Journal of the American Chemical Society. 132: 16352-3. PMID 21038867 DOI: 10.1021/ja107492b  1
2010 Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Modeling the hydration layer around proteins: HyPred. Biophysical Journal. 99: 1611-9. PMID 20816074 DOI: 10.1016/j.bpj.2010.06.027  1
2010 Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. A probabilistic and continuous model of protein conformational space for template-free modeling. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 783-98. PMID 20583926 DOI: 10.1089/cmb.2009.0235  1
2010 Strickland D, Yao X, Gawlak G, Rosen MK, Gardner KH, Sosnick TR. Rationally improving LOV domain-based photoswitches. Nature Methods. 7: 623-6. PMID 20562867 DOI: 10.1038/nmeth.1473  1
2010 Baird NJ, Gong H, Zaheer SS, Freed KF, Pan T, Sosnick TR. Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. Journal of Molecular Biology. 397: 1298-306. PMID 20188108 DOI: 10.1016/j.jmb.2010.02.025  1
2010 Zheng Z, Sosnick TR. Protein vivisection reveals elusive intermediates in folding. Journal of Molecular Biology. 397: 777-88. PMID 20144618 DOI: 10.1016/j.jmb.2010.01.056  1
2010 DeBartolo J, Hocky G, Wilde M, Xu J, Freed KF, Sosnick TR. Protein structure prediction enhanced with evolutionary diversity: SPEED. Protein Science : a Publication of the Protein Society. 19: 520-34. PMID 20066664 DOI: 10.1002/pro.330  1
2009 Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. A Probabilistic Graphical Model for Ab Initio Folding. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 5541: 59-73. PMID 23459639 DOI: 10.1007/978-3-642-02008-7_5  1
2009 Baxa MC, Freed KF, Sosnick TR. Psi-constrained simulations of protein folding transition states: implications for calculating. Journal of Molecular Biology. 386: 920-8. PMID 19244613 DOI: 10.1016/j.jmb.2009.01.010  1
2009 DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR. Mimicking the folding pathway to improve homology-free protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 106: 3734-9. PMID 19237560 DOI: 10.1073/pnas.0811363106  1
2009 Bosco GL, Baxa M, Sosnick TR. Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates. Biochemistry. 48: 2950-9. PMID 19220047 DOI: 10.1021/bi802072u  1
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, ... ... Sosnick TR, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/j.str.2008.12.014  1
2009 Horn JR, Sosnick TR, Kossiakoff AA. Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. Proceedings of the National Academy of Sciences of the United States of America. 106: 2559-64. PMID 19196954 DOI: 10.1073/pnas.0809800106  1
2008 Chung HS, Shandiz A, Sosnick TR, Tokmakoff A. Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding. Biochemistry. 47: 13870-7. PMID 19053229 DOI: 10.1021/bi801603e  1
2008 Strickland D, Moffat K, Sosnick TR. Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America. 105: 10709-14. PMID 18667691 DOI: 10.1073/pnas.0709610105  1
2008 Baxa MC, Freed KF, Sosnick TR. Quantifying the structural requirements of the folding transition state of protein A and other systems. Journal of Molecular Biology. 381: 1362-81. PMID 18625237 DOI: 10.1016/j.jmb.2008.06.067  1
2008 Sosnick TR. Kinetic barriers and the role of topology in protein and RNA folding. Protein Science : a Publication of the Protein Society. 17: 1308-18. PMID 18502978 DOI: 10.1110/ps.036319.108  1
2008 Qu X, Smith GJ, Lee KT, Sosnick TR, Pan T, Scherer NF. Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proceedings of the National Academy of Sciences of the United States of America. 105: 6602-7. PMID 18448679 DOI: 10.1073/pnas.0801436105  1
2008 Smith GJ, Lee KT, Qu X, Xie Z, Pesic J, Sosnick TR, Pan T, Scherer NF. A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics. Journal of Molecular Biology. 378: 943-53. PMID 18402978 DOI: 10.1016/j.jmb.2008.01.078  1
2008 Pan T, Sosnick TR. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering Handbook of Rna Biochemistry. 385-397. DOI: 10.1002/9783527619504.ch23  1
2007 Wong TN, Sosnick TR, Pan T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 17995-8000. PMID 17986617 DOI: 10.1073/pnas.0705038104  1
2007 Shandiz AT, Capraro BR, Sosnick TR. Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state. Biochemistry. 46: 13711-9. PMID 17985931 DOI: 10.1021/bi701042e  1
2007 Baird NJ, Fang XW, Srividya N, Pan T, Sosnick TR. Folding of a universal ribozyme: the ribonuclease P RNA. Quarterly Reviews of Biophysics. 40: 113-61. PMID 17931443 DOI: 10.1017/S0033583507004623  1
2007 Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF. Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification. Protein Science : a Publication of the Protein Society. 16: 2123-39. PMID 17893359 DOI: 10.1110/ps.072939707  1
2007 Jacob J, Dothager RS, Thiyagarajan P, Sosnick TR. Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature. Journal of Molecular Biology. 367: 609-15. PMID 17292402 DOI: 10.1016/j.jmb.2007.01.012  1
2007 Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 128: 613-24. PMID 17289578 DOI: 10.1016/j.cell.2006.12.042  1
2007 Fitzgerald JE, Jha AK, Sosnick TR, Freed KF. Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors. Biochemistry. 46: 669-82. PMID 17223689 DOI: 10.1021/bi061575x  1
2007 Pandit AD, Krantz BA, Dothager RS, Sosnick TR. Characterizing protein folding transition States using Psi-analysis. Methods in Molecular Biology (Clifton, N.J.). 350: 83-104. PMID 16957319  1
2006 Ruczinski I, Sosnick TR, Plaxco KW. Methods for the accurate estimation of confidence intervals on protein folding phi-values. Protein Science : a Publication of the Protein Society. 15: 2257-64. PMID 17008714 DOI: 10.1110/ps.062230106  1
2006 Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. Journal of Molecular Biology. 363: 835-57. PMID 16982067 DOI: 10.1016/j.jmb.2006.08.035  1
2006 Pandit AD, Jha A, Freed KF, Sosnick TR. Small proteins fold through transition states with native-like topologies. Journal of Molecular Biology. 361: 755-70. PMID 16876194 DOI: 10.1016/j.jmb.2006.06.041  1
2006 Pan T, Sosnick T. RNA folding during transcription Annual Review of Biophysics and Biomolecular Structure. 35: 161-175. PMID 16689632 DOI: 10.1146/annurev.biophys.35.040405.102053  1
2006 Sosnick TR, Krantz BA, Dothager RS, Baxa M. Characterizing the protein folding transition state using psi analysis. Chemical Reviews. 106: 1862-76. PMID 16683758 DOI: 10.1021/cr040431q  1
2006 Baird NJ, Srividya N, Krasilnikov AS, Mondragón A, Sosnick TR, Pan T. Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. Rna (New York, N.Y.). 12: 598-606. PMID 16581805 DOI: 10.1261/rna.2186506  1
2006 de los Rios MA, Muralidhara BK, Wildes D, Sosnick TR, Marqusee S, Wittung-Stafshede P, Plaxco KW, Ruczinski I. On the precision of experimentally determined protein folding rates and phi-values. Protein Science : a Publication of the Protein Society. 15: 553-63. PMID 16501226 DOI: 10.1110/ps.051870506  1
2006 Shi Z, Chen K, Liu Z, Sosnick TR, Kallenbach NR. 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: 312-21. PMID 16362932 DOI: 10.1002/prot.20788  1
2005 Jha AK, Colubri A, Freed KF, Sosnick TR. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proceedings of the National Academy of Sciences of the United States of America. 102: 13099-104. PMID 16131545 DOI: 10.1073/pnas.0506078102  1
2005 Baird NJ, Westhof E, Qin H, Pan T, Sosnick TR. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. Journal of Molecular Biology. 352: 712-22. PMID 16115647 DOI: 10.1016/j.jmb.2005.07.010  1
2005 Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry. 44: 9691-702. PMID 16008354 DOI: 10.1021/bi0474822  1
2005 Wong T, Sosnick TR, Pan T. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry. 44: 7535-42. PMID 15895996 DOI: 10.1021/bi047560l  1
2005 Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT, Hedberg L, Horng JC, Bona D, Miller EJ, Vallée-Bélisle A, Main ER, Bemporad F, Qiu L, Teilum K, ... ... Sosnick TR, et al. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Science : a Publication of the Protein Society. 14: 602-16. PMID 15689503 DOI: 10.1110/ps.041205405  1
2005 Smith GJ, Sosnick TR, Scherer NF, Pan T. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. Rna (New York, N.Y.). 11: 234-9. PMID 15613536 DOI: 10.1261/rna.7180305  1
2004 Sosnick TR, Dothager RS, Krantz BA. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proceedings of the National Academy of Sciences of the United States of America. 101: 17377-82. PMID 15576508 DOI: 10.1073/pnas.0407683101  1
2004 Meisner WK, Sosnick TR. Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding. Proceedings of the National Academy of Sciences of the United States of America. 101: 15639-44. PMID 15505204 DOI: 10.1073/pnas.0404895101  1
2004 Sosnick TR. Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein". Science (New York, N.Y.). 306: 411; author reply 41. PMID 15486276 DOI: 10.1126/science.1100962  1
2004 Sosnick TR, Pan T. Reduced contact order and RNA folding rates. Journal of Molecular Biology. 342: 1359-65. PMID 15364565 DOI: 10.1016/j.jmb.2004.08.002  1
2004 Meisner WK, Sosnick TR. Fast folding of a helical protein initiated by the collision of unstructured chains. Proceedings of the National Academy of Sciences of the United States of America. 101: 13478-82. PMID 15347811 DOI: 10.1073/pnas.0404057101  1
2004 Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW. Random-coil behavior and the dimensions of chemically unfolded proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12491-6. PMID 15314214 DOI: 10.1073/pnas.0403643101  1
2004 Jacob J, Krantz B, Dothager RS, Thiyagarajan P, Sosnick TR. Early collapse is not an obligate step in protein folding. Journal of Molecular Biology. 338: 369-82. PMID 15066438 DOI: 10.1016/j.jmb.2004.02.065  1
2004 Krantz BA, Dothager RS, Sosnick TR. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. Journal of Molecular Biology. 337: 463-75. PMID 15003460 DOI: 10.1016/j.jmb.2004.01.018  1
2004 Xie Z, Srividya N, Sosnick TR, Pan T, Scherer NF. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 101: 534-9. PMID 14704266 DOI: 10.1073/pnas.2636333100  1
2003 Zaman MH, Shen MY, Berry RS, Freed KF, Sosnick TR. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. Journal of Molecular Biology. 331: 693-711. PMID 12899838 DOI: 10.1016/S0022-2836(03)00765-4  1
2003 Sosnick TR, Pan T. RNA folding: models and perspectives. Current Opinion in Structural Biology. 13: 309-16. PMID 12831881 DOI: 10.1016/S0959-440X(03)00066-6  1
2003 Fang XW, Srividya N, Golden BL, Sosnick TR, Pan T. Stepwise conversion of a mesophilic to a thermophilic ribozyme. Journal of Molecular Biology. 330: 177-83. PMID 12823959 DOI: 10.1016/S0022-2836(03)00582-5  1
2003 Fernández A, Shen MY, Colubri A, Sosnick TR, Berry RS, Freed KF. Large-scale context in protein folding: villin headpiece. Biochemistry. 42: 664-71. PMID 12534278 DOI: 10.1021/bi026510i  1
2003 Zaman MH, Sosnick TR, Berry RS. Temperature dependence of reactions with multiple pathways Physical Chemistry Chemical Physics. 5: 2589-2594. DOI: 10.1039/b212671k  1
2002 Krantz BA, Mayne L, Rumbley J, Englander SW, Sosnick TR. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. Journal of Molecular Biology. 324: 359-71. PMID 12441113 DOI: 10.1016/S0022-2836(02)01029-X  1
2002 Shi Z, Olson CA, Kallenbach NR, Sosnick TR. D/H amide isotope effect in model alpha-helical peptides. Journal of the American Chemical Society. 124: 13994-5. PMID 12440888 DOI: 10.1021/ja027740n  1
2002 Sosnick TR, Pan T. Getting hotter with RNA. Nature Structural Biology. 9: 795-6. PMID 12402034 DOI: 10.1038/nsb1102-795  1
2002 Sosnick TR, Berry RS, Colubri A, Fernández A. Distinguishing foldable proteins from nonfolders: when and how do they differ? Proteins. 49: 15-23. PMID 12211012 DOI: 10.1002/prot.10193  1
2002 Fernández A, Sosnick TR, Colubri A. Dynamics of hydrogen bond desolvation in protein folding. Journal of Molecular Biology. 321: 659-75. PMID 12206781 DOI: 10.1016/S0022-2836(02)00679-4  1
2002 Zaman MH, Berry RS, Sosnick TR. Entropic benefit of a cross-link in protein association. Proteins. 48: 341-51. PMID 12112701 DOI: 10.1002/prot.10165  1
2002 Fang XW, Thiyagarajan P, Sosnick TR, Pan T. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proceedings of the National Academy of Sciences of the United States of America. 99: 8518-23. PMID 12084911 DOI: 10.1073/pnas.142288399  1
2002 Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature Structural Biology. 9: 458-63. PMID 11979278 DOI: 10.1038/nsb794  1
2002 Shi Z, Krantz BA, Kallenbach N, Sosnick TR. Contribution of hydrogen bonding to protein stability estimated from isotope effects. Biochemistry. 41: 2120-9. PMID 11841202 DOI: 10.1021/bi011307t  1
2002 Sosnick T, Pan T, Fang X, Shelton V, Thiyagarajan P, Littrel K. Metal ions and the thermodynamics and kinetics of tertiary RNA folding Indian Journal of Chemistry - Section a Inorganic, Physical, Theoretical and Analytical Chemistry. 41: 54-64.  1
2001 Sosnick TR. Characterization of tertiary folding of RNA by circular dichroism and urea. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.5. PMID 18428831 DOI: 10.1002/0471142700.nc1105s04  1
2001 Krantz BA, Sosnick TR. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nature Structural Biology. 8: 1042-7. PMID 11694889 DOI: 10.1038/nsb723  1
2001 Qin H, Sosnick TR, Pan T. Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry. 40: 11202-10. PMID 11551219 DOI: 10.1021/bi010076n  1
2001 Lee BC, Croonquist PA, Sosnick TR, Hoff WD. PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation. The Journal of Biological Chemistry. 276: 20821-3. PMID 11319215 DOI: 10.1074/jbc.C100106200  1
2001 Shelton VM, Sosnick TR, Pan T. Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations. Biochemistry. 40: 3629-38. PMID 11297430 DOI: 10.1021/bi002646+  1
2001 Fang XW, Golden BL, Littrell K, Shelton V, Thiyagarajan P, Pan T, Sosnick TR. The thermodynamic origin of the stability of a thermophilic ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 98: 4355-60. PMID 11296284 DOI: 10.1073/pnas.071050698  1
2001 Fang XW, Yang XJ, Littrell K, Niranjanakumari S, Thiyagarajan P, Fierke CA, Sosnick TR, Pan T. The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. Rna (New York, N.Y.). 7: 233-41. PMID 11233980 DOI: 10.1017/S1355838201001352  1
2000 Fang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, Thiyagarajan P, Pan T, Sosnick TR. 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: 11107-13. PMID 10998249 DOI: 10.1021/bi000724n  1
2000 Krantz BA, Sosnick TR. Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry. 39: 11696-701. PMID 10995237 DOI: 10.1021/bi000792+  1
2000 Sosnick TR, Fang X, Shelton VM. Application of circular dichroism to study RNA folding transitions. Methods in Enzymology. 317: 393-409. PMID 10829292  1
2000 Krantz BA, Moran LB, Kentsis A, Sosnick TR. D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding. Nature Structural Biology. 7: 62-71. PMID 10625430 DOI: 10.1038/71265  1
1999 Fang X, Pan T, Sosnick TR. A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme. Biochemistry. 38: 16840-6. PMID 10606517 DOI: 10.1021/bi991700n  1
1999 Shelton VM, Sosnick TR, Pan T. Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry. 38: 16831-9. PMID 10606516 DOI: 10.1021/bi991699s  1
1999 Fang XW, Pan T, Sosnick TR. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nature Structural Biology. 6: 1091-5. PMID 10581546 DOI: 10.1038/70016  1
1999 Moran LB, Schneider JP, Kentsis A, Reddy GA, Sosnick TR. Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. Proceedings of the National Academy of Sciences of the United States of America. 96: 10699-704. PMID 10485889 DOI: 10.1073/pnas.96.19.10699  1
1999 Pan T, Artsimovitch I, Fang XW, Landick R, Sosnick TR. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proceedings of the National Academy of Sciences of the United States of America. 96: 9545-50. PMID 10449729 DOI: 10.1073/pnas.96.17.9545  1
1999 Bhattacharyya RP, Sosnick TR. Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil. Biochemistry. 38: 2601-9. PMID 10029555 DOI: 10.1021/bi982209j  1
1998 Qi PX, Sosnick TR, Englander SW. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nature Structural Biology. 5: 882-4. PMID 9783747 DOI: 10.1038/2321  1
1998 Kentsis A, Sosnick TR. 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: 14613-22. PMID 9772190 DOI: 10.1021/bi981641y  1
1998 Englander SW, Sosnick TR, Mayne LC, Shtilerman M, Qi PX, Bai Y. Fast and Slow Folding in Cytochrome c Accounts of Chemical Research. 31: 737-744.  1
1997 Pan T, Sosnick TR. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nature Structural Biology. 4: 931-8. PMID 9360610 DOI: 10.1038/nsb1197-931  1
1997 Sosnick TR, Shtilerman MD, Mayne L, Englander SW. Ultrafast signals in protein folding and the polypeptide contracted state. Proceedings of the National Academy of Sciences of the United States of America. 94: 8545-50. PMID 9238013 DOI: 10.1073/pnas.94.16.8545  1
1997 Safer D, Sosnick TR, Elzinga M. Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends. Biochemistry. 36: 5806-16. PMID 9153421 DOI: 10.1021/bi970185v  1
1997 Englander SW, Mayne L, Bai Y, Sosnick TR. Hydrogen exchange: the modern legacy of Linderstrøm-Lang. Protein Science : a Publication of the Protein Society. 6: 1101-9. PMID 9144782 DOI: 10.1002/pro.5560060517  1
1996 Sosnick TR, Jackson S, Wilk RR, Englander SW, DeGrado WF. The role of helix formation in the folding of a fully alpha-helical coiled coil. Proteins. 24: 427-32. PMID 9162943 DOI: 10.1002/(SICI)1097-0134(199604)24:4<427::AID-PROT2>3.0.CO;2-B  1
1996 Sosnick TR, Mayne L, Englander SW. Molecular collapse: the rate-limiting step in two-state cytochrome c folding. Proteins. 24: 413-26. PMID 9162942 DOI: 10.1002/(SICI)1097-0134(199604)24:4<413::AID-PROT1>3.0.CO;2-F  1
1996 Englander SW, Sosnick TR, Englander JJ, Mayne L. Mechanisms and uses of hydrogen exchange. Current Opinion in Structural Biology. 6: 18-23. PMID 8696968 DOI: 10.1016/S0959-440X(96)80090-X  1
1996 DeGrado WF, Sosnick TR. Protein minimization: downsizing through mutation. Proceedings of the National Academy of Sciences of the United States of America. 93: 5680-1. PMID 8650151 DOI: 10.1073/pnas.93.12.5680  1
1995 Unkefer CJ, Houck DR, Britt BM, Sosnick TR, Hanners JL. Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine. Methods in Enzymology. 258: 227-35. PMID 8524153 DOI: 10.1016/0076-6879(95)58049-2  1
1995 Olah GA, Gray DM, Gray CW, Kergil DL, Sosnick TR, Mark BL, Vaughan MR, Trewhella J. Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study. Journal of Molecular Biology. 249: 576-94. PMID 7783213 DOI: 10.1006/jmbi.1995.0320  1
1995 Bai Y, Sosnick TR, Mayne L, Englander SW. Protein folding intermediates: native-state hydrogen exchange. Science (New York, N.Y.). 269: 192-7. PMID 7618079  1
1994 Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding. Nature Structural Biology. 1: 149-56. PMID 7656032  1
1993 Olah GA, Mitchell RD, Sosnick TR, Walsh DA, Trewhella J. Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide. Biochemistry. 32: 3649-57. PMID 8385485  1
1992 Sosnick TR, Benjamin DC, Novotny J, Seeger PA, Trewhella J. Distances between the antigen-binding sites of three murine antibody subclasses measured using neutron and X-ray scattering. Biochemistry. 31: 1779-86. PMID 1737031  1
1992 Sosnick TR, Trewhella J. Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry. 31: 8329-35. PMID 1525171  1
1991 Sokol PE, Silver RN, Sosnick TR, Snow WM. Comment on "Final-state effects on the deep-inelastic response of liquid 4He" Physical Review Letters. 67: 524. PMID 10044916  0.72
1991 Sosnick TR, Snow WM, Silver RN, Sokol PE. Deviations from the impulse approximation in liquid 4He: An experimental test at Q=23 Å -1. Physical Review. B, Condensed Matter. 43: 216-228. PMID 9996206  0.72
1991 Sokol PE, Silver RN, Sosnick TR, Snow WM. Comment on final-state effects on the deep-inelastic response of liquid 4 Physical Review Letters. 67: 524. DOI: 10.1103/PhysRevLett.67.524  1
1991 Sosnick TR, Snow WM, Silver RN, Sokol PE. Deviations from the impulse approximation in liquid He4: An experimental test at Q=23 -1 Physical Review B. 43: 216-228. DOI: 10.1103/PhysRevB.43.216  1
1990 Sosnick TR, Snow WM, Sokol PE. Deep-inelastic neutron scattering from liquid 4He. Physical Review. B, Condensed Matter. 41: 11185-11202. PMID 9993539  0.72
1990 Herwig KW, Sokol PE, Sosnick TR, Snow WM, Blasdell RC. Density dependence of the momentum distribution in normal liquid 4He. Physical Review. B, Condensed Matter. 41: 103-110. PMID 9992743  0.72
1990 Sosnick TR, Snow WM, Sokol PE. Deep-inelastic neutron scattering from liquid He4 Physical Review B. 41: 11185-11202. DOI: 10.1103/PhysRevB.41.11185  1
1990 Herwig KW, Sokol PE, Sosnick TR, Snow WM, Blasdell RC. Density dependence of the momentum distribution in normal liquid He4 Physical Review B. 41: 103-110. DOI: 10.1103/PhysRevB.41.103  1
1989 Sosnick TR, Snow WM, Sokol PE, Silver RN. Momentum distributions in liquid 4He Epl. 9: 707-712. DOI: 10.1209/0295-5075/9/7/016  1
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