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Biophysics and the Challenges of Emerging Threats

  • Conference proceedings
  • © 2009

Overview

Editors:
  1. Joseph D. Puglisi

    1. SMRL & Dept. of Structural Biology D105A Fairchild Science Building, Stanford University, Stanford, USA

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  • Presents state of the art information on NMR spectroscopy, and its place in the broader field of biophysics
  • No other monograph presents such a wide range of topics, including NMR spectroscopy, protein folding, X-ray crystallography, spectroscopy and applications

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Table of contents (8 papers)

  1. Front Matter

    Pages i-vii
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  2. A Simple Model for Protein Folding

    • Eric R. Henry, William A. Eaton
    Pages 1-20

  3. Complementarity of Hydrophobic/Hydrophilic Properties In Protein—Ligand Complexes: A New Tool to Improve Docking Results

    • Timothy V. Pyrkov, Anton O. Chugunov, Nikolay A. Krylov, Dimitry E. Nolde, Roman G. Efremov
    Pages 21-41

  4. Structures of Cvnh Family Lectins

    • Angela M. Gronenborn
    Pages 43-50

  5. Biophysical Approaches To Study Dna Base Flipping

    • Saulius KlimaŠauskas, Zita LiutkeviČiŪtĖ, Dalia DaujotytĖ
    Pages 51-64

  6. The Diversity of Nuclear Magnetic Resonance Spectroscopy

    • Corey W. Liu, Viktor Y. Alekseyev, Jeffrey R. Allwardt, Alexander J. Bankovich, Barbara J. Cade-Menun, Ronald W. Davis et al.
    Pages 65-81

  7. Improved Dye Stability in Single-Molecule Fluorescence Experiments

    • Colin EcheverrÍa Aitken, R. Andrew Marshall, Joseph D. Pugi
    Pages 83-99

  8. The Evaluation of Isotope Editing and Filtering for Protein—Ligand Interaction Elucidation by Nmr

    • Ian M. Robertson, Leo Spyracopoulos, Brian D. Sykes
    Pages 101-119

  9. Ribosome: an Ancient Cellular Nano-Machine for Genetic Code Translation

    • Ada Yonath
    Pages 121-155

  10. Back Matter

    Pages 157-179
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Keywords

About this book

Single-molecule techniques eliminate ensemble averaging, thus revealing transient or rare species in heterogeneous systems [1–3]. These approaches have been employed to probe myriad biological phenomena, including protein and RNA folding [4–6], enzyme kinetics [7, 8], and even protein biosynthesis [1, 9, 10]. In particular, immobilization-based fluorescence te- niques such as total internal reflection fluorescence microscopy (TIRF-M) have recently allowed for the observation of multiple events on the millis- onds to seconds timescale [11–13]. Single-molecule fluorescence methods are challenged by the instability of single fluorophores. The organic fluorophores commonly employed in single-molecule studies of biological systems display fast photobleaching, intensity fluctuations on the millisecond timescale (blinking), or both. These phenomena limit observation time and complicate the interpretation of fl- rescence fluctuations [14, 15]. Molecular oxygen (O) modulates dye stability. Triplet O efficiently 2 2 quenches dye triplet states responsible for blinking. This results in the for- tion of singlet oxygen [16–18]. Singlet O reacts efficiently with organic dyes, 2 amino acids, and nucleobases [19, 20]. Oxidized dyes are no longer fluor- cent; oxidative damage impairs the folding and function of biomolecules. In the presence of saturating dissolved O , blinking of fluorescent dyes is sup- 2 pressed, but oxidative damage to dyes and biomolecules is rapid. Enzymatic O -scavenging systems are commonly employed to ameliorate dye instability. 2 Small molecules are often employed to suppress blinking at low O levels.

Editors and Affiliations

  • SMRL & Dept. of Structural Biology D105A Fairchild Science Building, Stanford University, Stanford, USA

    Joseph D. Puglisi

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