scholarly journals Juggling with fluorescent proteins: Spectrum and structural changes of the mCardinal2 variants

Author(s):  
Tae-Yeon Kim ◽  
Tae-Sung Yoon ◽  
Sunghyun Kang ◽  
Muhammad Afzal
Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1286 ◽  
Author(s):  
Faez Iqbal Khan ◽  
Fakhrul Hassan ◽  
Razique Anwer ◽  
Feng Juan ◽  
Dakun Lai

Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of Agrobacterium tumefaciens C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm2) and PAiRFP2 (726.74 nm2) when compared with Agp2 (535.79 nm2). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.


RSC Advances ◽  
2016 ◽  
Vol 6 (82) ◽  
pp. 78661-78668 ◽  
Author(s):  
Wooseok Ko ◽  
Sanggil Kim ◽  
Seonghyun Lee ◽  
Kyubong Jo ◽  
Hyun Soo Lee

FRET sensors based on fluorescent proteins have been powerful tools for probing protein–protein interactions and structural changes within proteins.


Author(s):  
S. Phyllis Steamer ◽  
Rosemarie L. Devine

The importance of radiation damage to the skin and its vasculature was recognized by the early radiologists. In more recent studies, vascular effects were shown to involve the endothelium as well as the surrounding connective tissue. Microvascular changes in the mouse pinna were studied in vivo and recorded photographically over a period of 12-18 months. Radiation treatment at 110 days of age was total body exposure to either 240 rad fission neutrons or 855 rad 60Co gamma rays. After in vivo observations in control and irradiated mice, animals were sacrificed for examination of changes in vascular fine structure. Vessels were selected from regions of specific interest that had been identified on photomicrographs. Prominent ultrastructural changes can be attributed to aging as well as to radiation treatment. Of principal concern were determinations of ultrastructural changes associated with venous dilatations, segmental arterial stenosis and tortuosities of both veins and arteries, effects that had been identified on the basis of light microscopic observations. Tortuosities and irregularly dilated vein segments were related to both aging and radiation changes but arterial stenosis was observed only in irradiated animals.


Author(s):  
W. Kunath ◽  
E. Zeitler ◽  
M. Kessel

The features of digital recording of a continuous series (movie) of singleelectron TV frames are reported. The technique is used to investigate structural changes in negatively stained glutamine synthetase molecules (GS) during electron irradiation and, as an ultimate goal, to look for the molecules' “undamaged” structure, say, after a 1 e/Å2 dose.The TV frame of fig. la shows an image of 5 glutamine synthetase molecules exposed to 1/150 e/Å2. Every single electron is recorded as a unit signal in a 256 ×256 field. The extremely low exposure of a single TV frame as dictated by the single-electron recording device including the electron microscope requires accumulation of 150 TV frames into one frame (fig. lb) thus achieving a reasonable compromise between the conflicting aspects of exposure time per frame of 3 sec. vs. object drift of less than 1 Å, and exposure per frame of 1 e/Å2 vs. rate of structural damage.


Author(s):  
K. Kovacs ◽  
E. Horvath ◽  
J. M. Bilbao ◽  
F. A. Laszlo ◽  
I. Domokos

Electrolytic lesions of the pituitary stalk in rats interrupt adenohypophysial blood flow and result in massive infarction of the anterior lobe. In order to obtain a deeper insight into the morphogenesis of tissue injury and to reveal the sequence of events, a fine structural investigation was undertaken on adenohypophyses of rats at various intervals following destruction of the pituitary stalk.The pituitary stalk was destroyed electrolytically, with a Horsley-Clarke apparatus on 27 male rats of the R-Amsterdam strain, weighing 180-200 g. Thirty minutes, 1,2,4,6 and 24 hours after surgery the animals were perfused with a glutaraldehyde-formalin solution. The skulls were then opened and the pituitary glands removed. The anterior lobes were fixed in glutaraldehyde-formalin solution, postfixed in osmium tetroxide and embedded in Durcupan. Ultrathin sections were stained with uranyl acetate and lead citrate and investigated with a Philips 300 electron microscope.


Author(s):  
P.L. Moore ◽  
P.L. Sannes ◽  
H.L. Bank ◽  
S.S. Spicer

It is thought that calcium and/or magnesium may play important roles in polymorphonuclear (PMN) leukocyte functions such as chemotaxis, adhesion and phagocytosis. Yet, a clear understanding of the biological roles of these ions has awaited the development of techniques which permit a selective alteration of intracellular ion concentrations. Recently, treatment of cells with the ionophore A23187 has been used to alter intracellular divalent cation concentrations. This ionophore is a lipid soluble antibiotic produced by Streptomyces chartreusensis that complexes with both calcium and magnesium (3) and is believed to carry these ions across biological membranes (4). Biochemical investigations of human PMN leukocytes demonstrate that cells treated with A23187 and extracellular calcium release their lysosomal enzymes into the extracellular medium without rupturing and releasing their soluble cytoplasmic enzymes (5,6). The aim of the present study and and a companion report (7) was to investigate the structural changes that occur in leukocytes during ionophore-induced lysosomal enzyme release.


Author(s):  
Werner J. Niklowitz

After intoxication of rabbits with certain substances such as convulsant agents (3-acetylpyridine), centrally acting drugs (reserpine), or toxic metal compounds (tetraethyl lead) a significant observation by phase microscope is the loss of contrast of the hippocampal mossy fiber layer. It has been suggested that this alteration, as well as changes seen with the electron microscope in the hippocampal mossy fiber boutons, may be related to a loss of neurotransmitters. The purpose of these experiments was to apply the OsO4-zinc-iodide staining technique to the study of these structural changes since it has been suggested that OsO4-zinc-iodide stain reacts with neurotransmitters (acetylcholine, catecholamines).Domestic New Zealand rabbits (2.5 to 3 kg) were used. Hippocampal tissue was removed from normal and experimental animals treated with 3-acetylpyridine (antimetabolite of nicotinamide), reserpine (anti- hypertensive/tranquilizer), or iproniazid (antidepressant/monamine oxidase inhibitor). After fixation in glutaraldehyde hippocampal tissue was treated with OsO4-zinc-iodide stain and further processed for phase and electron microscope studies.


Author(s):  
Ann M. Thomas ◽  
Virginia Shemeley

Those samples which swell rapidly when exposed to water are, at best, difficult to section for transmission electron microscopy. Some materials literally burst out of the embedding block with the first pass by the knife, and even the most rapid cutting cycle produces sections of limited value. Many ion exchange resins swell in water; some undergo irreversible structural changes when dried. We developed our embedding procedure to handle this type of sample, but it should be applicable to many materials that present similar sectioning difficulties.The purpose of our embedding procedure is to build up a cross-linking network throughout the sample, while it is in a water swollen state. Our procedure was suggested to us by the work of Rosenberg, where he mentioned the formation of a tridimensional structure by the polymerization of the GMA biproduct, triglycol dimethacrylate.


Author(s):  
N. Uyeda ◽  
E. J. Kirkland ◽  
B. M. Siegel

The direct observation of structural change by high resolution electron microscopy will be essential for the better understanding of the damage process and its mechanism. However, this approach still involves some difficulty in quantitative interpretation mostly being due to the quality of obtained images. Electron diffraction, using crystalline specimens, has been the method most frequently applied to obtain a comparison of radiation sensitivity of various materials on the quantitative base. If a series of single crystal patterns are obtained the fading rate of reflections during the damage process give good comparative measures. The electron diffraction patterns also render useful information concerning the structural changes in the crystal. In the present work, the radiation damage of potassium tetracyano-platinate was dealt with on the basis two dimensional observation of fading rates of diffraction spots. KCP is known as an ionic crystal which possesses “one dimensional” electronic properties and it would be of great interest to know if radiation damage proceeds in a strongly asymmetric manner.


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