Supplementary Application to NIGMS R35-R35GM118139, ?Structural Dynamics of Molecular Motors and the Ribosome?, Yale E. Goldman, PI Protein synthesis and active transport of vesicular cargoes are vital to development of all tissues and to the targeted delivery of organelles, proteins, and signaling molecules in eukaryotes. Accordingly, defects in protein expression and transport are linked to developmental, neurodegenerative, pigmentation, immunological, and other diseases. Knowing the detailed mechano-chemistry and structural dynamics of the ribosome and motor proteins is essential for understanding and interpreting their roles in the cell. We have developed a number of powerful new biophysical tools that reveal the modulation of structural dynamics and reaction kinetics of the protein synthesis elongation cycle and molecular motors under applied mechanical force, discriminate models of energy transduction and elucidate the essential rotational motions of conformational transitions of specific domains within the elongation factors and motor proteins. We will apply these unique tools to investigate the rhythm of protein synthesis in bacteria and eukaryotes and mechanisms that functionally modulate it and the divergent biochemical and mechanical properties of myosins-I, V, VI and X, and dynein isoforms. Understanding functional properties that have that have not yet been approached at the mechanistic detail is now possible. The R35 parent grant of this supplemental application combined and extended three NIGMS grants, and so has a number of aims.
Our Aims i n protein synthesis are to determine the mechanisms of modulation of protein synthesis rate of 1) downstream mRNA 2o structure and 2) upstream Shine-Delgarno (SD) sequences.
Aim 3) is to develop a eukaryotic single molecule FRET platform for detailed study of peptide elongation in higher organisms.
Aim 4) is to define how read-through of premature stop codons takes place and the mechanisms of small molecule enhancers of read-through, which are promising therapies in many diseases. For myosins I, V, VI and X, to 5) test the thermal search hypothesis, determine their flexibility and solve the mechanisms of their high directionality; 6) determine the mechanical force- dependence and the energetics of their mechanical stroke using an ultra-high-speed optical trap; 7) determine the dynamics of ATP association and ADP and Pi dissociation from the motors under force; 8) Determine the rotational motions of motor heads and lever arms that generate force and cargo translocation; 9) determine motor force and force regulation on intracellular cargos, and 10) determine how many kinesin motors are actively engaged on intracellular cargos and their spatial distributions. Overall, these studies will lead to a much more general view of the mechanisms and characteristics of the ribosome and molecular motors in vitro and in live cells leading to a more rigorous understanding of their functions in cell biology and disease. The present supplemental application is for purchase of replacement for a crucial preparative and analytical instrument used extensively throughout these studies, a fast protein liquid chromatography (FPLC) workstation.

Public Health Relevance

(Public Health Relevance) Protein synthesis on the ribosome and intracellular motility and cell division, based on the molecular motors are crucial for development and maintenance of all of the organs in the body. The specific cellular machines to be studied here, the ribosome, myosins, kinesin and cytoplasmic dyneins, are required for appropriate neuronal development, sensorineural function in hearing and eyesight, the immune response and cell division. Thus errors of expression or function lead to severe developmental neurological, cardiovascular, immunological deficits, and play roles in cancer cell division and metastasis, muscular dystrophy, cystic fibrosis and many other diseases. The studies proposed here will give fundamental information on how gene expression, cellular development, and transport motors function and may eventually lead to therapeutic targets in these diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Unknown (R35)
Project #
3R35GM118139-03S1
Application #
9707995
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Gindhart, Joseph G
Project Start
2016-07-15
Project End
2021-06-30
Budget Start
2018-07-01
Budget End
2019-06-30
Support Year
3
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of Pennsylvania
Department
Physiology
Type
Schools of Medicine
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Woody, Michael S; Capitanio, Marco; Ostap, E Michael et al. (2018) Electro-optic deflectors deliver advantages over acousto-optical deflectors in a high resolution, ultra-fast force-clamp optical trap. Opt Express 26:11181-11193
Caporizzo, Matthew A; Fishman, Claire E; Sato, Osamu et al. (2018) The Antiparallel Dimerization of Myosin X Imparts Bundle Selectivity for Processive Motility. Biophys J 114:1400-1410
Lippert, Lisa G; Dadosh, Tali; Hadden, Jodi A et al. (2017) Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk. Proc Natl Acad Sci U S A 114:E4564-E4573
Lewis, John H; Jamiolkowski, Ryan M; Woody, Michael S et al. (2017) Deconvolution of Camera Instrument Response Functions. Biophys J 112:1214-1220
Hendricks, Adam G; Goldman, Yale E (2017) Measuring Molecular Forces Using Calibrated Optical Tweezers in Living Cells. Methods Mol Biol 1486:537-552
Jamiolkowski, Ryan M; Chen, Chunlai; Cooperman, Barry S et al. (2017) tRNA Fluctuations Observed on Stalled Ribosomes Are Suppressed during Ongoing Protein Synthesis. Biophys J 113:2326-2335
Woody, Michael S; Lewis, John H; Greenberg, Michael J et al. (2016) MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation. Biophys J 111:273-282
Lippert, Lisa G; Hallock, Jeffrey T; Dadosh, Tali et al. (2016) NeutrAvidin Functionalization of CdSe/CdS Quantum Nanorods and Quantification of Biotin Binding Sites using Biotin-4-Fluorescein Fluorescence Quenching. Bioconjug Chem 27:562-8
Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E (2016) Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc 4:042004
Chen, Chunlai; Cui, Xiaonan; Beausang, John F et al. (2016) Elongation factor G initiates translocation through a power stroke. Proc Natl Acad Sci U S A 113:7515-20

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