Biophysics and the Challenges of Emerging Threats (NATO Science for Peace and Security Series B: Physics and Biophysics)

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. front-matter......Page 2 A Simple Model for Protein Folding......Page 9 Complementarity of Hydrophobic/Hydrophilic Properties In Protein—Ligand Complexes: A New Tool to Improve Docking Results......Page 29 Structures of Cvnh Family Lectins......Page 50 Biophysical Approaches To Study Dna Base Flipping......Page 58 The Diversity of Nuclear Magnetic Resonance Spectroscopy......Page 72 Improved Dye Stability in Single-Molecule Fluorescence Experiments......Page 89 The Evaluation of Isotope Editing and Filtering for Protein—Ligand Interaction Elucidation by Nmr......Page 106 Ribosome: an Ancient Cellular Nano-Machine for Genetic Code Translation......Page 125 Course Abstracts, Author Index......Page 160 A collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 8th Course: Biophysics and the Challenges of Emerging Threats Proceedings of the NATO Advanced Study Institute on Biophysics and the Challenges of Emerging ThreatsErice, Sicily, Italy19-30 June 2007