Tobin R. Sosnick, PhD

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.

Harvard University
Cambridge
Ph.D. - Applied Physics
1989

University of California
San Diego
B.A. - Physics
1983

Folding and misfolding of potassium channel monomers during assembly and tetramerization.
Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proc Natl Acad Sci U S A. 2021 Aug 24; 118(34).
PMID: 34413192

Molecular dynamics study of water channels in natural and synthetic amyloid-ß fibrils.
Natesh SR, Hummels AR, Sachleben JR, Sosnick TR, Freed KF, Douglas JF, Meredith SC, Haddadian EJ. Molecular dynamics study of water channels in natural and synthetic amyloid-ß fibrils. J Chem Phys. 2021 Jun 21; 154(23):235102.
PMID: 34241272

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.
Bowman MA, Riback JA, Rodriguez A, Guo H, Li J, Sosnick TR, Clark PL. Properties of protein unfolded states suggest broad selection for expanded conformational ensembles. Proc Natl Acad Sci U S A. 2020 09 22; 117(38):23356-23364.
PMID: 32879005

Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.
Clark PL, Plaxco KW, Sosnick TR. Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different. J Mol Biol. 2020 04 17; 432(9):2882-2889.
PMID: 32044346

Structural basis for adhesion G protein-coupled receptor Gpr126 function.
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.
PMID: 31924782

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.
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.
PMID: 31587831

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.
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.
PMID: 30992378

Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1.
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.
PMID: 31459397

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
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.
PMID: 30589846

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
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.
PMID: 30589834

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