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Nanoinformatics: An Emerging Trend in Cancer Therapeutics
Published in Rajesh Singh Tomar, Anurag Jyoti, Shuchi Kaushik, Nanobiotechnology, 2020
Medha Pandya, Snehal Jani, Vishakha Dave, Rakesh Rawal
The investigation of nucleic acids and many protein structures has been done by crystallography, nuclear magnetic resonance, electron microscopy, and many other techniques [52]. Structural biology provides information on the static structures of biomolecules. However, in reality, biomolecules are highly dynamic, and their motion is important to their function. Various experimental techniques are available to help study the dynamics of biomolecules [41]. Computational power continues to increase, and the development of new theoretical methods offers hope of solving scientific problems at the molecular level. All the theoretical methods and computational techniques that are used to model the behavior of molecules are defined as molecular modeling.
Large Dataset Electron Diffraction Patterns for the Structural Analysis of Metallic Nanostructures
Published in Alina Bruma, Scanning Transmission Electron Microscopy, 2020
Arturo Ponce, José Luis Reyes-Rodríguez, Eduardo Ortega, Prakash Parajuli, M. Mozammel Hoque, Azdiar A. Gazder
The described optimal configuration of modern cryo-electron microscopes has pushed the method to near-atomic resolution, with several protein structures already solved under 3-Å´ resolution. Cryo-EM has had such a big impact in the field of structural biology that Nature Methods designated it as Method of the Year 2015 (2016). There are two avenues in structural biology to determine the structure of proteins: single particle technique is performed at high resolution and microelectron diffraction (MicroED). The main damage mechanism that can appear in proteins during the acquisition of images or electron diffraction in the TEM is the ionization damage (radiolysis). Certain conditions must be satisfied to declare that the observed electron DPs are significant for the case of proteins susceptible to beam damage. They must show stability for several milliseconds, i.e. they are the representative patterns registered under rapid acquisition and ultralow-dose irradiation, to preserve not only the initial structure of the protein. In this way, brightness is directly related to the electron current density per unit solid angle of the source. The current density can be measured from the fluorescence screen to convert it to the dose rate on the specimen. However, to determine the dose rate the magnification factor, which is also proportional to the radius of the viewing screen, needs to be considered. In the microscope, this magnification is referred to as the film plane, although there is no film the magnifications still use that plane as a reference. Hence, the magnification of the images recorded using a camera correspond to around 80% of that on the film plane. Therefore, we can relate the current density on the screen to that on the specimen by the following formula (Ortega et al. 2017a): σ=ρ×C×(0.8M)2
A comprehensive review on stability of therapeutic proteins treated by freeze-drying: induced stresses and stabilization mechanisms involved in processing
Published in Drying Technology, 2022
Zhe Wang, Linlin Li, Guangyue Ren, Xu Duan, Jingfang Guo, Wenchao Liu, Yuan Ang, Lewen Zhu, Xing Ren
At present, the main technology to determine the three-dimensional structure of molecules at the atomic resolution level is X-ray crystallography. X-ray is a kind of electromagnetic radiation like light, but it has a shorter wavelength, generally about 0.1 nm. X-rays interact weakly with biological substances, which make it difficult to use them to study individual protein complexes. But when multiple copies of the same protein are arranged in a 3D crystal, information about the protein's atomic structure can be obtained through it. This technique is called X-ray crystallography and is one of the most important tools in structural biology. Taschner et al [87] obtained the three-dimensional crystal structure of anti-idiotypic antibody MMA 383 by X-ray, although the assumed conformation in the crystal is only one of many conformations in the solution. Moreover, although X-ray has high requirements for the purity and crystallinity of proteins, it is still of great significance for the characterization of protein structures. The application of X-ray in the freeze-drying stability of therapeutic proteins needs further study.
Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research
Published in Molecular Physics, 2018
Sabine Van Doorslaer, Bert Cuypers
The above illustrates that many questions are still open in globin research that can only be tackled by an interdisciplinary approach. Because of the close link between structure and function, structural biology tools play a crucial role in this matter. In this review, we focus on the advantages and challenges of using electron paramagnetic resonance (EPR) in globin research. EPR is sometimes also referred to as electron spin resonance or electron magnetic resonance. As early as 1955, EPR has been used to study ferric myoglobin [23]. However, the EPR technique has enormously evolved since then and has become a versatile spectroscopic tool for (bio)material characterisation. After a short introduction into current state-of-the-art EPR and an outline of what (not) to expect from such studies, we will here exemplify the power of this technique in globin research with a number of non-exhaustive examples. Furthermore, in this review, we highlight how globins can be ideal model systems to develop or test new EPR methodologies.