Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

Contact Us
If you have any questions or feedback please contact us.

Thomas T. Perkins

TitleDirector-Faculty
InstitutionUniversity of Colorado Boulder
DepartmentJILA
Phone303/492-5291

    Collapse Research 
    Collapse research activities and funding
    R01HL117138     (LEINWAND, LESLIE ANNE)Aug 20, 2013 - Jan 31, 2022
    NIH/NHLBI
    Molecular characterization of cardiomyopathy mutations in human cardiac myosin
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT. High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy. Nano Lett. 2018 10 10; 18(10):6318-6325. PMID: 30234311.
      View in: PubMed
    2. Heenan PR, Perkins TT. FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via a Bayesian Algorithm. Biophys J. 2018 Sep 04; 115(5):757-762. PMID: 30122292.
      View in: PubMed
    3. Heenan PR, Yu H, Siewny MGW, Perkins TT. Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy. J Chem Phys. 2018 Mar 28; 148(12):123313. PMID: 29604885.
      View in: PubMed
    4. Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS Nano. 2018 Jan 23; 12(1):198-207. PMID: 29244486.
      View in: PubMed
    5. Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem. 2018 01 05; 19(1):19-23. PMID: 29069529.
      View in: PubMed
    6. Edwards DT, Faulk JK, LeBlanc MA, Perkins TT. Force Spectroscopy with 9-µs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry. Biophys J. 2017 Dec 19; 113(12):2595-2600. PMID: 29132641.
      View in: PubMed
    7. Okoniewski SR, Uyetake L, Perkins TT. Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA. Nucleic Acids Res. 2017 Oct 13; 45(18):10775-10782. PMID: 28977580.
      View in: PubMed
    8. Walder R, LeBlanc MA, Van Patten WJ, Edwards DT, Greenberg JA, Adhikari A, Okoniewski SR, Sullan RMA, Rabuka D, Sousa MC, Perkins TT. Rapid Characterization of a Mechanically Labile a-Helical Protein Enabled by Efficient Site-Specific Bioconjugation. J Am Chem Soc. 2017 07 26; 139(29):9867-9875. PMID: 28677396.
      View in: PubMed
    9. Yu H, Siewny MG, Edwards DT, Sanders AW, Perkins TT. Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. Science. 2017 Mar 03; 355(6328):945-950. PMID: 28254940.
      View in: PubMed
    10. Okoniewski SR, Carter AR, Perkins TT. A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization. Methods Mol Biol. 2017; 1486:77-107. PMID: 27844426.
      View in: PubMed
    11. Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT. Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes. Nucleic Acids Res. 2016 07 08; 44(12):5849-60. PMID: 27220465; PMCID: PMC4937329.
    12. Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution. J Struct Biol. 2017 01; 197(1):13-25. PMID: 26804584.
      View in: PubMed
    13. Edwards DT, Faulk JK, Sanders AW, Bull MS, Walder R, LeBlanc MA, Sousa MC, Perkins TT. Optimizing 1-µs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope. Nano Lett. 2015 Oct 14; 15(10):7091-8. PMID: 26421945; PMCID: PMC4663051 [Available on 10/14/16].
    14. He C, Hu C, Hu X, Hu X, Xiao A, Perkins TT, Li H. Direct Observation of the Reversible Two-State Unfolding and Refolding of an a/ß Protein by Single-Molecule Atomic Force Microscopy. Angew Chem Int Ed Engl. 2015 Aug 17; 54(34):9921-5. PMID: 26136291.
      View in: PubMed
    15. Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. Opt Express. 2015 Jun 29; 23(13):16554-64. PMID: 26191667.
      View in: PubMed
    16. Churnside AB, Perkins TT. Ultrastable atomic force microscopy: improved force and positional stability. FEBS Lett. 2014 Oct 01; 588(19):3621-30. PMID: 24801176.
      View in: PubMed
    17. Bull MS, Sullan RM, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. ACS Nano. 2014 May 27; 8(5):4984-95. PMID: 24670198.
      View in: PubMed
    18. Perkins TT. Ångström-precision optical traps and applications. Annu Rev Biophys. 2014; 43:279-302. PMID: 24773015.
      View in: PubMed
    19. Berweger S, Nguyen DM, Muller EA, Bechtel HA, Perkins TT, Raschke MB. Nano-chemical infrared imaging of membrane proteins in lipid bilayers. J Am Chem Soc. 2013 Dec 11; 135(49):18292-5. PMID: 24251914.
      View in: PubMed
    20. Paik DH, Roskens VA, Perkins TT. Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method. Nucleic Acids Res. 2013 Oct; 41(19):e179. PMID: 23935118; PMCID: PMC3799452.
    21. Sullan RM, Churnside AB, Nguyen DM, Bull MS, Perkins TT. Atomic force microscopy with sub-picoNewton force stability for biological applications. Methods. 2013 Apr 01; 60(2):131-41. PMID: 23562681; PMCID: PMC3669665.
    22. Montange RK, Bull MS, Shanblatt ER, Perkins TT. Optimizing bead size reduces errors in force measurements in optical traps. Opt Express. 2013 Jan 14; 21(1):39-48. PMID: 23388894.
      View in: PubMed
    23. Churnside AB, Sullan RM, Nguyen DM, Case SO, Bull MS, King GM, Perkins TT. Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. Nano Lett. 2012 Jul 11; 12(7):3557-61. PMID: 22694769; PMCID: PMC3397142.
    24. Paik DH, Perkins TT. Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts. Methods Mol Biol. 2012; 875:335-56. PMID: 22573450.
      View in: PubMed
    25. Paik DH, Perkins TT. Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy. Angew Chem Int Ed Engl. 2012 Feb 20; 51(8):1811-5. PMID: 22162006.
      View in: PubMed
    26. Paik DH, Perkins TT. Overstretching DNA at 65 pN does not require peeling from free ends or nicks. J Am Chem Soc. 2011 Mar 16; 133(10):3219-21. PMID: 21207940.
      View in: PubMed
    27. Churnside AB, King GM, Perkins TT. Label-free optical imaging of membrane patches for atomic force microscopy. Opt Express. 2010 Nov 08; 18(23):23924-32. PMID: 21164738; PMCID: PMC3158999.
    28. Perkins TT, Li HW. Single-molecule studies of RecBCD. Methods Mol Biol. 2010; 587:155-72. PMID: 20225148.
      View in: PubMed
    29. Paik DH, Seol Y, Halsey WA, Perkins TT. Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond. Nano Lett. 2009 Aug; 9(8):2978-83. PMID: 19492836.
      View in: PubMed
    30. Carter AR, Seol Y, Perkins TT. Precision surface-coupled optical-trapping assay with one-basepair resolution. Biophys J. 2009 Apr 08; 96(7):2926-34. PMID: 19348774; PMCID: PMC2711297.
    31. King GM, Carter AR, Churnside AB, Eberle LS, Perkins TT. Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions. Nano Lett. 2009 Apr; 9(4):1451-6. PMID: 19351191; PMCID: PMC2953871.
    32. Carter AR, King GM, Perkins TT. Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D. Opt Express. 2007 Oct 01; 15(20):13434-45. PMID: 19550612.
      View in: PubMed
    33. Seol Y, Li J, Nelson PC, Perkins TT, Betterton MD. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. Biophys J. 2007 Dec 15; 93(12):4360-73. PMID: 17766363; PMCID: PMC2098713.
    34. Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, Goodrich JA. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J Mol Biol. 2007 Sep 21; 372(3):619-32. PMID: 17681538.
      View in: PubMed
    35. Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT. Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl Opt. 2007 Jan 20; 46(3):421-7. PMID: 17228390.
      View in: PubMed
    36. Seol Y, Carpenter AE, Perkins TT. Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating. Opt Lett. 2006 Aug 15; 31(16):2429-31. PMID: 16880845.
      View in: PubMed
    37. Nugent-Glandorf L, Perkins TT. Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection. Opt Lett. 2004 Nov 15; 29(22):2611-3. PMID: 15552661.
      View in: PubMed
    38. Perkins TT, Li HW, Dalal RV, Gelles J, Block SM. Forward and reverse motion of single RecBCD molecules on DNA. Biophys J. 2004 Mar; 86(3):1640-8. PMID: 14990491; PMCID: PMC1303999.
    39. Perkins TT, Dalal RV, Mitsis PG, Block SM. Sequence-dependent pausing of single lambda exonuclease molecules. Science. 2003 Sep 26; 301(5641):1914-8. PMID: 12947034; PMCID: PMC1539570.
    Perkins's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _

    Copyright © 2017 The Regents of the University of Colorado, a body corporate. All rights reserved. (Harvard PROFILES RNS software version: 2.10.0)