Stopped-flow fluorescence spectroscopy is a highly sensitive method for measuring rapid enzyme kinetics. A wide range of fluorophores can be employed, and fluorescence and fluorescence polarization can be measured. Thus, binding, conformational changes, and catalysis can, in principle, be measured, making it helpful in probing the entire kinetic landscape of a reaction. In this chapter, we use the bacterial RNA processing enzyme ribonuclease P (RNase P) as a model system to illustrate the determination of the kinetic constants for substrate binding and cleavage, thus allowing mechanistic questions regarding the effects of reaction conditions, mutations, or drug binding to be answered.
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http://dx.doi.org/10.1007/978-1-0716-3918-4_27 | DOI Listing |
Curr Opin Struct Biol
December 2024
Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France. Electronic address:
Advances in the characterization of intrinsically disordered proteins (IDPs) have unveiled a remarkably complex and diverse interaction landscape, including coupled folding and binding, highly dynamic complexes, multivalent interactions, and even interactions between entirely disordered proteins. Here we review recent examples of IDP binding mechanisms elucidated by experimental techniques such as nuclear magnetic resonance spectroscopy, single-molecule Förster resonance energy transfer, and stopped-flow fluorescence. These techniques provide insights into the structural details of transition pathways and complex intermediates, and they capture the dynamics of IDPs within complexes.
View Article and Find Full Text PDFMethods Enzymol
November 2024
MAX IV Laboratory, Lund University, Lund, Sweden. Electronic address:
Int J Mol Sci
November 2024
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119899, Russia.
Cation-pumping membrane pyrophosphatases (mPPases; EC 7.1.3.
View Article and Find Full Text PDFBiophys Chem
January 2025
Chemistry Department of Lomonosov Moscow State University, Moscow, Russia; Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Moscow, Russia. Electronic address:
Non-canonical nucleic acid structures possess an ability to interact selectively with proteins, thereby exerting influence over various intracellular processes. Numerous studies indicate that genomic G-quadruplexes and i-motifs are involved in the regulation of transcription. These structures are formed temporarily during the unwinding of the DNA double helix; and their direct determination is a rather difficult task.
View Article and Find Full Text PDFACS Omega
October 2024
Biophysics Division, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 St., 02-093 Warsaw, Poland.
The structural changes induced by the addition of sodium dodecyl sulfate (SDS) in chymotrypsin and chymotrypsinogen were studied by the stopped-flow kinetic method with tryptophan fluorescence observation of the transients. Four fluorescence excitation wavelengths were used: 222, 260, 280, and 295 nm. It was found that the recorded transients were dependent on the excitation wavelength.
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