scholarly journals Time-resolved cryoEM using Spotiton

Author(s):  
Venkata P. Dandey ◽  
William C. Budell ◽  
Hui Wei ◽  
Daija Bobe ◽  
Kashyap Maruthi ◽  
...  

AbstractWe present an approach for preparing cryoEM grids to study short-lived molecular states. Using piezo electric dispensing, two independent streams of ~50 pL sample drops are deposited within 10 ms of each other onto a nanowire EM grid surface, and the mixing reaction stops when the grid is vitrified in liquid ethane, on the order of ~100 ms later. We demonstrate the utility of this approach for four biological systems where short-lived states are of high interest.

2019 ◽  
Vol 88 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Christopher M. Dobson

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.


1993 ◽  
Vol 47 (10) ◽  
pp. 1604-1608 ◽  
Author(s):  
Ruixia Song ◽  
Kuang-Pang Li

Benzo(a)pyrene (BP) in liposomes and microsomes exhibits overlapping excimer bands peaked at 495 and 520 nm, respectively, in contrast to the single band of pyrene at 480 nm. Since BP is asymmetrical and pyrene is symmetrical, the dual maxima imply that the BP molecules in the excimer must be oriented either parallel or anti-parallel to each other. Time-resolved studies of BP oxidation by cytochrome P-450 show that the 520-nm component dissipates much faster than the 495-nm component during the first 30 min of metabolism, indicating that the initial P-450-BP interaction may be BP orientation sensitive. The binding of BP to the porphyrin group of a heme protein (e.g., hemoglobin or myoglobin) appears to be stronger under oxygen saturation than under CO2 saturation conditions. The transfer of BP between the membrane and the porphyrin group, as measured by means of excimer/monomer ratios, appears to be significantly different from that of pyrene. As the liposome-to-protein ratio increases, the excimer/monomer of BP steadily decreases, whereas that of pyrene increases and reaches a plateau. The significance of this phenomenon in their mechanisms of metabolism will have to be investigated further.


2021 ◽  
Author(s):  
Andrew V. Anzalone ◽  
Miguel Jimenez ◽  
Virginia W. Cornish

Cellular barcodes offer critical tools for tracking cellular identity in biological systems. Although genetically encoded fluorescent barcodes are ideal for real-time tracking, their scalability is constrained by the broad, overlapping emission spectra characteristic of fluorescent proteins (FPs). Here, we describe a palette of genetically encoded fluorescent barcodes called FRAME- tags, which break this scalability barrier by encoding barcode identity as unique FP expression ratios. FRAME-tags use -1 programmed ribosomal frameshifting RNA motifs to precisely control the translational output of multiple FPs from a single mRNA, leading to extremely narrow and resolvable ratios of the corresponding cellular fluorescence distributions. With this platform, we constructed 20 resolvable FRAME-tags in yeast using just two FPs, and further demonstrated that 100 or more distinguishable FRAME-tags could be made by the addition of a third FP. We used FRAME-tags to map the dynamic fitness landscape of yeast co-cultures, and to characterize the expression pattern of 20 yeast promoters in multiplex across diverse conditions. FRAME-tags offer a valuable new tool for cellular barcoding that enables time- resolved characterization of complex biological systems using widely available fluorescence detection techniques and a minimal number of spectral channels.


2020 ◽  
Author(s):  
Rajdip Chowdhury ◽  
Zhunzhun Yu ◽  
Stefanie V. Kohlhepp ◽  
Xiang Yin ◽  
Abraham Mendoza

<div><div><div><p>Flexible, small and strong alkyl ligations created upon external light stimuli can open new avenues for medicinal and biological research. Herein, we have found that NADH and analogues can drive photo-couplings without auxiliary photocatalysts. The time- resolved alkyl photo-ligation between redox-active carboxylate derivatives and electron-poor olefins displays a surprising moisture and air-tolerance, and unusually high coupling rates in dilute conditions. This work sets the conceptual basis for further biocompatible C-C coupling reactions promoted by visible-light in combination with NADH, the ubiquitous reductant of biological systems.</p></div></div></div>


1992 ◽  
Vol 96 (13) ◽  
pp. 5243-5254 ◽  
Author(s):  
James W. Lewis ◽  
Robert A. Goldbeck ◽  
David S. Kliger ◽  
Xiaoliang Xie ◽  
Robert C. Dunn ◽  
...  

2020 ◽  
Author(s):  
Rajdip Chowdhury ◽  
Zhunzhun Yu ◽  
Stefanie V. Kohlhepp ◽  
Xiang Yin ◽  
Abraham Mendoza

<div><div><div><p>Flexible, small and strong alkyl ligations created upon external light stimuli can open new avenues for medicinal and biological research. Herein, we have found that NADH and analogues can drive photo-couplings without auxiliary photocatalysts. The time- resolved alkyl photo-ligation between redox-active carboxylate derivatives and electron-poor olefins displays a surprising moisture and air-tolerance, and unusually high coupling rates in dilute conditions. This work sets the conceptual basis for further biocompatible C-C coupling reactions promoted by visible-light in combination with NADH, the ubiquitous reductant of biological systems.</p></div></div></div>


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