Tobin R. Sosnick

Research Summary
My research program involves synergistic studies of protein folding and design, protein-RNA interactions, phosphorylation, signaling, and function with both experimental and computational components. The research is based on the premise that rigorous and innovative studies of basic processes have broad implications in many areas of biological research. My lab employs a range of experimental and computational methods including hydrogen exchange (HX), NMR, small-angle X-ray scattering (SAXS), rapid mixing methods, mass spectrometry, molecular dynamics and home-grown coarse-grain folding simulations and modeling. I am a very a strong believer in collaboration, having co-mentored over twenty students and post-doctoral fellows who produce over 60 papers in the last 20 years. I have a history of developing multi-approaches to bear on a problem. Since my Ph.D. in low temperature physics in 1989, I have entered many different areas, including delineating protein and RNA folding pathways and denatured states, de novo structure prediction, and the design of light-sensitive allosteric proteins.
Keywords
Protein Folding, disordered proteins, Simulations, Molecular Dynamics, stress biology, Membrane Proteins, small-angle scattering, NMR Spectroscopy, Hydrogen exchange, optogenetics
Education
  • Harvard University, Cambridge, Ph.D. Applied Physics 1989
  • University of California, San Diego, B.A. Physics 06/1983
Biosciences Graduate Program Association
Publications
  1. Clark PL, Plaxco KW, Sosnick TR. Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different. J Mol Biol. 2020 Apr 17; 432(9):2882-2889. View in: PubMed

  2. Leon K, Cunningham RL, Riback JA, Feldman E, Li J, Sosnick TR, Zhao M, Monk KR, Araç D. Structural basis for adhesion G protein-coupled receptor Gpr126 function. Nat Commun. 2020 01 10; 11(1):194. View in: PubMed

  3. Wang Z, Jumper JM, Freed KF, Sosnick TR. On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations. Biophys J. 2019 10 15; 117(8):1429-1441. View in: PubMed

  4. Zayner JP, Mathes T, Sosnick TR, Kennis JTM. Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1. ACS Omega. 2019 Jan 31; 4(1):1238-1243. View in: PubMed

  5. Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR. Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proc Natl Acad Sci U S A. 2019 04 30; 116(18):8889-8894. View in: PubMed

  6. Jumper JM, Faruk NF, Freed KF, Sosnick TR. Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PLoS Comput Biol. 2018 12; 14(12):e1006342. View in: PubMed

  7. Jumper JM, Faruk NF, Freed KF, Sosnick TR. Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. PLoS Comput Biol. 2018 12; 14(12):e1006578. View in: PubMed

  8. 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. Biophys J. 2018 11 20; 115(10):1872-1884. View in: PubMed

  9. 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. 2018 08 31; 361(6405). View in: PubMed

  10. 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. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13453-13458. View in: PubMed

  11. 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. 2017 10 13; 358(6360):238-241. View in: PubMed

  12. 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. 2017 03 09; 168(6):1028-1040.e19. View in: PubMed

  13. 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. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):2241-2246. View in: PubMed

  14. French AR, Sosnick TR, Rock RS. Investigations of human myosin VI targeting using optogenetically controlled cargo loading. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):E1607-E1616. View in: PubMed

  15. 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 Sci. 2017 02; 26(2):208-217. View in: PubMed

  16. Poellmann MJ, Sosnick TR, Meredith SC, Lee RC. The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme. Macromol Biosci. 2017 02; 17(2). View in: PubMed

  17. Virtanen JJ, Sosnick TR, Freed KF. Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)]. J Chem Phys. 2016 08 07; 145(5):059903. View in: PubMed

  18. Yu W, Baxa MC, Gagnon I, Freed KF, Sosnick TR. Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Proc Natl Acad Sci U S A. 2016 Apr 26; 113(17):4747-52. View in: PubMed

  19. Basanta B, Chan KK, Barth P, King T, Sosnick TR, Hinshaw JR, Liu G, Everett JK, Xiao R, Montelione GT, Baker D. Introduction of a polar core into the de novo designed protein Top7. Protein Sci. 2016 07; 25(7):1299-307. View in: PubMed

  20. 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. Proc Natl Acad Sci U S A. 2015 Jul 07; 112(27):8302-7. View in: PubMed

  21. 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. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):6631-6. View in: PubMed

  22. Virtanen JJ, Sosnick TR, Freed KF. Ionic strength independence of charge distributions in solvation of biomolecules. J Chem Phys. 2014 Dec 14; 141(22):22D503. View in: PubMed

  23. Skinner JJ, Yu W, Gichana EK, Baxa MC, Hinshaw JR, Freed KF, Sosnick TR. Benchmarking all-atom simulations using hydrogen exchange. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15975-80. View in: PubMed

  24. 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. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15396-401. View in: PubMed

  25. Zayner JP, Sosnick TR. Factors that control the chemistry of the LOV domain photocycle. PLoS One. 2014; 9(1):e87074. View in: PubMed

  26. Walters BT, Mayne L, Hinshaw JR, Sosnick TR, Englander SW. Folding of a large protein at high structural resolution. Proc Natl Acad Sci U S A. 2013 Nov 19; 110(47):18898-903. View in: PubMed

  27. Sosnick TR, Baxa MC. Revealing what gets buried first in protein folding. Proc Natl Acad Sci U S A. 2013 Oct 15; 110(42):16704-5. View in: PubMed

  28. Liu Y, Haddadian E, Sosnick TR, Freed KF, Gong H. A novel implicit solvent model for simulating the molecular dynamics of RNA. Biophys J. 2013 Sep 03; 105(5):1248-57. View in: PubMed

  29. 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. Biophys J. 2013 Aug 20; 105(4):1027-36. View in: PubMed

  30. Adhikari AN, Freed KF, Sosnick TR. Simplified protein models: predicting folding pathways and structure using amino acid sequences. Phys Rev Lett. 2013 Jul 12; 111(2):028103. View in: PubMed

  31. 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 Rep. 2013 May 30; 3(5):1703-13. View in: PubMed

  32. Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. A Probabilistic Graphical Model for Ab Initio Folding. Res Comput Mol Biol. 2009; 5541:59-73. View in: PubMed

  33. Adhikari AN, Freed KF, Sosnick TR. De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17442-7. View in: PubMed

  34. 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. J Am Chem Soc. 2012 Sep 26; 134(38):15929-36. View in: PubMed

  35. 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 Sci. 2012 Jun; 21(6):819-27. View in: PubMed

  36. 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). J Mol Biol. 2012 Jul 13; 420(3):220-34. View in: PubMed

  37. Zayner JP, Antoniou C, Sosnick TR. The amino-terminal helix modulates light-activated conformational changes in AsLOV2. J Mol Biol. 2012 May 25; 419(1-2):61-74. View in: PubMed

  38. Parisien M, Freed KF, Sosnick TR. On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PLoS One. 2012; 7(2):e32647. View in: PubMed

  39. 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. Nat Methods. 2012 Mar 04; 9(4):379-84. View in: PubMed

  40. 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. Proc Natl Acad Sci U S A. 2012 Feb 28; 109(9):3323-8. View in: PubMed

  41. 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. J Mol Biol. 2012 May 04; 418(3-4):226-36. View in: PubMed

  42. Adhikari AN, Peng J, Wilde M, Xu J, Freed KF, Sosnick TR. Modeling large regions in proteins: applications to loops, termini, and folding. Protein Sci. 2012 Jan; 21(1):107-21. View in: PubMed

  43. Sosnick TR, Hinshaw JR. Biochemistry. How proteins fold. Science. 2011 Oct 28; 334(6055):464-5. View in: PubMed

  44. Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering. Biophys J. 2011 Oct 19; 101(8):2061-9. View in: PubMed

  45. 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. Biophys J. 2011 Aug 17; 101(4):899-909. View in: PubMed

  46. Sosnick TR, Woodson SA. New era of molecular structure and dynamics from solution scattering experiments. Biopolymers. 2011 Aug; 95(8):503-4. View in: PubMed

  47. Ralat LA, Kalas V, Zheng Z, Goldman RD, Sosnick TR, Tang WJ. Ubiquitin is a novel substrate for human insulin-degrading enzyme. J Mol Biol. 2011 Feb 25; 406(3):454-66. View in: PubMed

  48. Sosnick TR, Barrick D. The folding of single domain proteins--have we reached a consensus? Curr Opin Struct Biol. 2011 Feb; 21(1):12-24. View in: PubMed

  49. Baird NJ, Ludtke SJ, Khant H, Chiu W, Pan T, Sosnick TR. Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc. 2010 Nov 24; 132(46):16352-3. View in: PubMed

  50. Virtanen JJ, Makowski L, Sosnick TR, Freed KF. Modeling the hydration layer around proteins: HyPred. Biophys J. 2010 Sep 08; 99(5):1611-9. View in: PubMed

  51. 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. J Comput Biol. 2010 Jun; 17(6):783-98. View in: PubMed

  52. Strickland D, Yao X, Gawlak G, Rosen MK, Gardner KH, Sosnick TR. Rationally improving LOV domain-based photoswitches. Nat Methods. 2010 Aug; 7(8):623-6. View in: PubMed

  53. 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. J Mol Biol. 2010 Apr 16; 397(5):1298-306. View in: PubMed

  54. Zheng Z, Sosnick TR. Protein vivisection reveals elusive intermediates in folding. J Mol Biol. 2010 Apr 02; 397(3):777-88. View in: PubMed

  55. DeBartolo J, Hocky G, Wilde M, Xu J, Freed KF, Sosnick TR. Protein structure prediction enhanced with evolutionary diversity: SPEED. Protein Sci. 2010 Mar; 19(3):520-34. View in: PubMed

  56. Sosnick T, Charles S, Stubbs G, Yau P, Bradbury EM, Timmins P, Trewhella J. Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies. Biophys J. 1991 Nov; 60(5):1178-89. View in: PubMed

  57. Baxa MC, Freed KF, Sosnick TR. Psi-constrained simulations of protein folding transition states: implications for calculating. J Mol Biol. 2009 Mar 06; 386(4):920-8. View in: PubMed

  58. DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR. Mimicking the folding pathway to improve homology-free protein structure prediction. Proc Natl Acad Sci U S A. 2009 Mar 10; 106(10):3734-9. View in: PubMed

  59. 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. 2009 Apr 07; 48(13):2950-9. View in: PubMed

  60. 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, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. View in: PubMed

  61. Horn JR, Sosnick TR, Kossiakoff AA. Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2559-64. View in: PubMed

  62. Chung HS, Shandiz A, Sosnick TR, Tokmakoff A. Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding. Biochemistry. 2008 Dec 30; 47(52):13870-7. View in: PubMed

  63. Strickland D, Moffat K, Sosnick TR. Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci U S A. 2008 Aug 05; 105(31):10709-14. View in: PubMed

  64. Baxa MC, Freed KF, Sosnick TR. Quantifying the structural requirements of the folding transition state of protein A and other systems. J Mol Biol. 2008 Sep 19; 381(5):1362-81. View in: PubMed

  65. Sosnick TR. Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci. 2008 Aug; 17(8):1308-18. View in: PubMed

  66. 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. Proc Natl Acad Sci U S A. 2008 May 06; 105(18):6602-7. View in: PubMed

  67. Sosnick TR. Characterization of tertiary folding of RNA by circular dichroism and urea. Curr Protoc Nucleic Acid Chem. 2001 May; Chapter 11:Unit 11.5. View in: PubMed

  68. 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. J Mol Biol. 2008 May 09; 378(4):943-53. View in: PubMed

  69. Wong TN, Sosnick TR, Pan T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):17995-8000. View in: PubMed

  70. Shandiz AT, Capraro BR, Sosnick TR. Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state. Biochemistry. 2007 Dec 04; 46(48):13711-9. View in: PubMed

  71. Baird NJ, Fang XW, Srividya N, Pan T, Sosnick TR. Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys. 2007 May; 40(2):113-61. View in: PubMed

  72. Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF. Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification. Protein Sci. 2007 Oct; 16(10):2123-39. View in: PubMed

  73. Jacob J, Dothager RS, Thiyagarajan P, Sosnick TR. Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature. J Mol Biol. 2007 Mar 30; 367(3):609-15. View in: PubMed

  74. 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. 2007 Feb 09; 128(3):613-24. View in: PubMed

  75. 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. 2007 Jan 23; 46(3):669-82. View in: PubMed

  76. Ruczinski I, Sosnick TR, Plaxco KW. Methods for the accurate estimation of confidence intervals on protein folding phi-values. Protein Sci. 2006 Oct; 15(10):2257-64. View in: PubMed

  77. 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. J Mol Biol. 2006 Nov 03; 363(4):835-57. View in: PubMed

  78. Pandit AD, Krantz BA, Dothager RS, Sosnick TR. Characterizing protein folding transition States using Psi-analysis. Methods Mol Biol. 2007; 350:83-104. View in: PubMed

  79. Pandit AD, Jha A, Freed KF, Sosnick TR. Small proteins fold through transition states with native-like topologies. J Mol Biol. 2006 Aug 25; 361(4):755-70. View in: PubMed

  80. Pan T, Sosnick T. RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006; 35:161-75. View in: PubMed

  81. Sosnick TR, Krantz BA, Dothager RS, Baxa M. Characterizing the protein folding transition state using psi analysis. Chem Rev. 2006 May; 106(5):1862-76. View in: PubMed

  82. 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. 2006 Apr; 12(4):598-606. View in: PubMed

  83. 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 Sci. 2006 Mar; 15(3):553-63. View in: PubMed

  84. 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. 2006 May 01; 63(2):312-21. View in: PubMed

  85. Jha AK, Colubri A, Freed KF, Sosnick TR. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc Natl Acad Sci U S A. 2005 Sep 13; 102(37):13099-104. View in: PubMed

  86. 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. J Mol Biol. 2005 Sep 23; 352(3):712-22. View in: PubMed

  87. 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. 2005 Jul 19; 44(28):9691-702. View in: PubMed

  88. Wong T, Sosnick TR, Pan T. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry. 2005 May 24; 44(20):7535-42. View in: PubMed

  89. 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, Vu ND, Edwards AM, Ruczinski I, Poulsen FM, Kragelund BB, Michnick SW, Chiti F, Bai Y, Hagen SJ, Serrano L, Oliveberg M, Raleigh DP, Wittung-Stafshede P, Radford SE, Jackson SE, Sosnick TR, Marqusee S, Davidson AR, Plaxco KW. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci. 2005 Mar; 14(3):602-16. View in: PubMed

  90. Smith GJ, Sosnick TR, Scherer NF, Pan T. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA. 2005 Feb; 11(2):234-9. View in: PubMed

  91. Sosnick TR, Dothager RS, Krantz BA. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci U S A. 2004 Dec 14; 101(50):17377-82. View in: PubMed

  92. Meisner WK, Sosnick TR. Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding. Proc Natl Acad Sci U S A. 2004 Nov 02; 101(44):15639-44. View in: PubMed

  93. Sosnick TR. Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein". Science. 2004 Oct 15; 306(5695):411; author reply 411. View in: PubMed

  94. Sosnick TR, Pan T. Reduced contact order and RNA folding rates. J Mol Biol. 2004 Oct 01; 342(5):1359-65. View in: PubMed

  95. Meisner WK, Sosnick TR. Fast folding of a helical protein initiated by the collision of unstructured chains. Proc Natl Acad Sci U S A. 2004 Sep 14; 101(37):13478-82. View in: PubMed

  96. 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. Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34):12491-6. View in: PubMed

  97. Jacob J, Krantz B, Dothager RS, Thiyagarajan P, Sosnick TR. Early collapse is not an obligate step in protein folding. J Mol Biol. 2004 Apr 23; 338(2):369-82. View in: PubMed

  98. Krantz BA, Dothager RS, Sosnick TR. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J Mol Biol. 2004 Mar 19; 337(2):463-75. View in: PubMed

  99. 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. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2):534-9. View in: PubMed

  100. 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. J Mol Biol. 2003 Aug 15; 331(3):693-711. View in: PubMed

  101. Sosnick TR, Pan T. RNA folding: models and perspectives. Curr Opin Struct Biol. 2003 Jun; 13(3):309-16. View in: PubMed

  102. Fang XW, Srividya N, Golden BL, Sosnick TR, Pan T. Stepwise conversion of a mesophilic to a thermophilic ribozyme. J Mol Biol. 2003 Jul 04; 330(2):177-83. View in: PubMed

  103. Fernández A, Shen MY, Colubri A, Sosnick TR, Berry RS, Freed KF. Large-scale context in protein folding: villin headpiece. Biochemistry. 2003 Jan 28; 42(3):664-71. View in: PubMed

  104. Krantz BA, Mayne L, Rumbley J, Englander SW, Sosnick TR. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol. 2002 Nov 22; 324(2):359-71. View in: PubMed

  105. Shi Z, Olson CA, Kallenbach NR, Sosnick TR. D/H amide isotope effect in model alpha-helical peptides. J Am Chem Soc. 2002 Nov 27; 124(47):13994-5. View in: PubMed

  106. Sosnick TR, Pan T. Getting hotter with RNA. Nat Struct Biol. 2002 Nov; 9(11):795-6. View in: PubMed

  107. Sosnick TR, Berry RS, Colubri A, Fernández A. Distinguishing foldable proteins from nonfolders: when and how do they differ? Proteins. 2002 Oct 01; 49(1):15-23. View in: PubMed

  108. Fernández A, Sosnick TR, Colubri A. Dynamics of hydrogen bond desolvation in protein folding. J Mol Biol. 2002 Aug 23; 321(4):659-75. View in: PubMed

  109. Zaman MH, Berry RS, Sosnick TR. Entropic benefit of a cross-link in protein association. Proteins. 2002 Aug 01; 48(2):341-51. View in: PubMed

  110. Fang XW, Thiyagarajan P, Sosnick TR, Pan T. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8518-23. View in: PubMed

  111. Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nat Struct Biol. 2002 Jun; 9(6):458-63. View in: PubMed

  112. Shi Z, Krantz BA, Kallenbach N, Sosnick TR. Contribution of hydrogen bonding to protein stability estimated from isotope effects. Biochemistry. 2002 Feb 19; 41(7):2120-9. View in: PubMed

  113. Krantz BA, Sosnick TR. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nat Struct Biol. 2001 Dec; 8(12):1042-7. View in: PubMed

  114. Qin H, Sosnick TR, Pan T. Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry. 2001 Sep 18; 40(37):11202-10. View in: PubMed

  115. Lee BC, Croonquist PA, Sosnick TR, Hoff WD. PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation. J Biol Chem. 2001 Jun 15; 276(24):20821-3. View in: PubMed

  116. Shelton VM, Sosnick TR, Pan T. Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations. Biochemistry. 2001 Mar 27; 40(12):3629-38. View in: PubMed

  117. Fang XW, Golden BL, Littrell K, Shelton V, Thiyagarajan P, Pan T, Sosnick TR. The thermodynamic origin of the stability of a thermophilic ribozyme. Proc Natl Acad Sci U S A. 2001 Apr 10; 98(8):4355-60. View in: PubMed

  118. 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. 2001 Feb; 7(2):233-41. View in: PubMed

  119. 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. 2000 Sep 12; 39(36):11107-13. View in: PubMed

  120. Krantz BA, Sosnick TR. Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry. 2000 Sep 26; 39(38):11696-701. View in: PubMed

  121. Sosnick TR, Fang X, Shelton VM. Application of circular dichroism to study RNA folding transitions. Methods Enzymol. 2000; 317:393-409. View in: PubMed

  122. Krantz BA, Moran LB, Kentsis A, Sosnick TR. D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding. Nat Struct Biol. 2000 Jan; 7(1):62-71. View in: PubMed

  123. Fang X, Pan T, Sosnick TR. A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme. Biochemistry. 1999 Dec 21; 38(51):16840-6. View in: PubMed

  124. Shelton VM, Sosnick TR, Pan T. Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry. 1999 Dec 21; 38(51):16831-9. View in: PubMed

  125. Fang XW, Pan T, Sosnick TR. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol. 1999 Dec; 6(12):1091-5. View in: PubMed

  126. 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. Proc Natl Acad Sci U S A. 1999 Sep 14; 96(19):10699-704. View in: PubMed

  127. 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. Proc Natl Acad Sci U S A. 1999 Aug 17; 96(17):9545-50. View in: PubMed

  128. Bhattacharyya RP, Sosnick TR. Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil. Biochemistry. 1999 Feb 23; 38(8):2601-9. View in: PubMed

  129. Pan T, Fang X, Sosnick T. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J Mol Biol. 1999 Feb 26; 286(3):721-31. View in: PubMed

  130. Qi PX, Sosnick TR, Englander SW. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nat Struct Biol. 1998 Oct; 5(10):882-4. View in: PubMed

  131. 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. 1998 Oct 13; 37(41):14613-22. View in: PubMed

  132. Powers CM, Landel R, Sosnick T, Kirby J, Mengel K, Cheney A, Perry J. The effects of patellar taping on stride characteristics and joint motion in subjects with patellofemoral pain. J Orthop Sports Phys Ther. 1997 Dec; 26(6):286-91. View in: PubMed

  133. 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. Nat Struct Biol. 1997 Nov; 4(11):931-8. View in: PubMed

  134. Sosnick TR, Shtilerman MD, Mayne L, Englander SW. Ultrafast signals in protein folding and the polypeptide contracted state. Proc Natl Acad Sci U S A. 1997 Aug 05; 94(16):8545-50. View in: PubMed

  135. 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. 1996 Apr; 24(4):427-32. View in: PubMed

  136. Sosnick TR, Mayne L, Englander SW. Molecular collapse: the rate-limiting step in two-state cytochrome c folding. Proteins. 1996 Apr; 24(4):413-26. View in: PubMed

  137. Safer D, Sosnick TR, Elzinga M. Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends. Biochemistry. 1997 May 13; 36(19):5806-16. View in: PubMed

  138. Englander SW, Mayne L, Bai Y, Sosnick TR. Hydrogen exchange: the modern legacy of Linderstrøm-Lang. Protein Sci. 1997 May; 6(5):1101-9. View in: PubMed

  139. Englander SW, Sosnick TR, Englander JJ, Mayne L. Mechanisms and uses of hydrogen exchange. Curr Opin Struct Biol. 1996 Feb; 6(1):18-23. View in: PubMed

  140. DeGrado WF, Sosnick TR. Protein minimization: downsizing through mutation. Proc Natl Acad Sci U S A. 1996 Jun 11; 93(12):5680-1. View in: PubMed

  141. Unkefer CJ, Houck DR, Britt BM, Sosnick TR, Hanners JL. Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine. Methods Enzymol. 1995; 258:227-35. View in: PubMed

  142. 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. 1993 Apr 13; 32(14):3649-57. View in: PubMed

  143. 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. J Mol Biol. 1995 Jun 09; 249(3):576-94. View in: PubMed

  144. Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding. Nat Struct Biol. 1994 Mar; 1(3):149-56. View in: PubMed

  145. Bai Y, Sosnick TR, Mayne L, Englander SW. Protein folding intermediates: native-state hydrogen exchange. Science. 1995 Jul 14; 269(5221):192-7. View in: PubMed

  146. Thomas J, Van Patten SM, Howard P, Day KH, Mitchell RD, Sosnick T, Trewhella J, Walsh DA, Maurer RA. Expression in Escherichia coli and characterization of the heat-stable inhibitor of the cAMP-dependent protein kinase. J Biol Chem. 1991 Jun 15; 266(17):10906-11. View in: PubMed

  147. 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. 1992 Feb 18; 31(6):1779-86. View in: PubMed

  148. Sosnick TR, Trewhella J. Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry. 1992 Sep 08; 31(35):8329-35. View in: PubMed