7. Following biochemistry within the cell

2021 ◽  
pp. 93-110
Author(s):  
Mark Lorch
Keyword(s):  
Green Fluorescent Protein ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Motor Proteins ◽  
Fluorescent Protein ◽  
Patch Clamping ◽  
Signal To Noise ◽  
Single Molecule Studies ◽  
Technical Challenges ◽  
Green Fluorescent

This chapter presents key advances in the study of individual molecules within cells. When one applies this individualistic methodology to biochemicals, one enters the realms of single-molecule biophysics. There are of course formidable technical challenges associated with single-molecule studies, not least of which is the signal-to-noise problem. The chapter discusses patch clamping, nanoscopes, and optical tweezers. Patch clamping provided insights into the protein machinery that controls the flow of ions in and out of cells. The chapter also examines cytokinesis, cytoskeletons, and motor proteins, and the use of Green Fluorescent Protein (GFP).

Single-Molecule Microscopy of the Green Fluorescent Protein Using Simultaneous Two-Color Excitation

ChemPhysChem ◽  
2001 ◽  
Vol 2 (6) ◽  
pp. 392-396 ◽  
Author(s):  
Gregor Jung ◽  
Jens Wiehler ◽  
Boris Steipe ◽  
Christoph Bräuchle ◽  
Andreas Zumbusch
Keyword(s):  
Green Fluorescent Protein ◽  
Single Molecule ◽  
Fluorescent Protein ◽  
Single Molecule Microscopy ◽  
Green Fluorescent

scholarly journals Single-Molecule Imaging and Computational Microscopy Approaches Clarify the Mechanism of the Dimerization and Membrane Interactions of Green Fluorescent Protein

2019 ◽  
Vol 20 (6) ◽  
pp. 1410 ◽  
Author(s):  
Xiaohua Wang ◽  
Kai Song ◽  
Yang Li ◽  
Ling Tang ◽  
Xin Deng
Keyword(s):  
Molecular Dynamics ◽  
Green Fluorescent Protein ◽  
Single Molecule ◽  
Fluorescent Protein ◽  
Hydrophobic Interactions ◽  
Site Directed Mutagenesis ◽  
Single Amino Acid ◽  
Single Mutation ◽  
Functional Protein ◽  
Green Fluorescent

Green fluorescent protein (GFP) is widely used as a biomarker in living systems; however, GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes, fused to naturally-oligomeric proteins, or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry, as well as interactions between proteins fused to FPs. Introduction of a single mutation, A206K, has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization, thereby contributing to its monomerization. Nevertheless, a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies, facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.

scholarly journals Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding

2017 ◽  
Vol 114 (42) ◽  
pp. 11052-11056 ◽  
Author(s):  
Ziad Ganim ◽  
Matthias Rief
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Optical Sensors ◽  
Structural Integrity ◽  
Fluorescent Protein ◽  
Single Molecule Fluorescence ◽  
Extended States ◽  
Green Fluorescent ◽  
Ensemble Experiments

Green fluorescent protein (GFP) variants are widely used as genetically encoded fluorescent fusion tags, and there is an increasing interest in engineering their structure to develop in vivo optical sensors, such as for optogenetics and force transduction. Ensemble experiments have shown that the fluorescence of GFP is quenched upon denaturation. Here we study the dependence of fluorescence on protein structure by driving single molecules of GFP into different conformational states with optical tweezers and simultaneously probing the chromophore with fluorescence. Our results show that fluorescence is lost during the earliest events in unfolding, 3.5 ms before secondary structure is disrupted. No fluorescence is observed from the unfolding intermediates or the ensemble of compact and extended states populated during refolding. We further demonstrate that GFP can be mechanically switched between emissive and dark states. These data definitively establish that complete structural integrity is necessary to observe single-molecule fluorescence of GFP.

scholarly journals Improved Green Fluorescent Protein Reporter Gene-Based Microplate Screening for Antituberculosis Compounds by Utilizing an Acetamidase Promoter

2003 ◽  
Vol 47 (12) ◽  
pp. 3682-3687 ◽  
Author(s):  
Chartchai Changsen ◽  
Scott G. Franzblau ◽  
Prasit Palittapongarnpim
Keyword(s):  
Green Fluorescent Protein ◽  
High Throughput ◽  
High Throughput Screening ◽  
Antimicrobial Agents ◽  
Fluorescent Protein ◽  
Signal To Noise Ratio ◽  
Enhanced Fluorescence ◽  
Signal To Noise ◽  
Green Fluorescent ◽  
Fluorescent Protein Reporter

ABSTRACT The green fluorescent protein (GFP) gene offers many advantages as a viability reporter for high-throughput antimicrobial drug screening. However, screening for antituberculosis compounds by using GFP driven by the heat shock promoter, hsp60, has been of limited utility due to the low signal-to-noise ratio. Therefore, an alternative promoter was evaluated for its enhanced fluorescence during microplate-based culture and its response to 18 established antimicrobial agents by using a green fluorescent protein microplate assay (GFPMA). Mycobacterium tuberculosis strains H37Rv, H37Ra, and Erdman were transformed with pFPCA1, which contains a red-shifted gfp gene driven by the acetamidase promoter of M. smegmatis mc2155. The pFPCA1 transformants achieved higher levels of GFP-mediated fluorescence than those carrying the hsp60 construct, with signal-to-noise ratios of 20.6 to 27.8 and 3.8 to 4.5, respectively. The MICs of 18 established antimicrobial agents for all strains carrying pFPCA1 in the GFPMA were within 1 to 2 twofold dilutions of those determined by either the fluorometric or the visual microplate Alamar Blue assay (MABA). No significant differences in MICs were observed between wild-type and pFPCA1 transformants by MABA. The optimized GFPMA is sufficiently simple, robust, and inexpensive (no reagent costs) to be used for routine high-throughput screening for antituberculosis compounds.

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