X-ray data processing

Powell, Harold R.

doi:10.1042/bsr20170227

Cited by 30 publications

(22 citation statements)

References 64 publications

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“…Currently, the main methods for high-resolution structure determination of proteins are X-ray crystallography and nuclear magnetic resonance (NMR), with cryo-electron microscopy (cryo-EM) joining the group, fueled by technological advances in recent years enabling sub-1.5 Å resolution [39]. Of these methods, X-ray crystallography is the one most inherently linked to symmetry operations because symmetry underlies both diffraction data collection and processing [40] as well as nearly all calculations needed to arrive at the final model of the structure [41]. Moreover, cryo-EM utilizes symmetry during image processing and averaging to achieve a higher signal-to-noise ratio [42].…”

Section: High-resolution Structure Determination Of Homo-oligomersmentioning

confidence: 99%

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Gaber

Pavšič

2021

IJMS

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Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.

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Section: High-resolution Structure Determination Of Homo-oligomersmentioning

confidence: 99%

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Gaber

Pavšič

2021

IJMS

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“…The most widely implemented methods include nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, neutron diffraction, cryo-EM, and spectroscopic techniques. X-ray crystallography has been the most powerful tool in resolving structures of macromolecules at atomic resolution since its birth over a century ago (Shi, 2014;Powell, 2017;Wang and Wang, 2017;Standfuss, 2019). More than 138,000 molecular structures, reported with this technique, have been deposited in the Protein Data Bank (PDB) since its establishment in 1971, endowing X-ray crystallography with the dominant role in structural biology.…”

Section: Pre-structural Age Their Existence and Their Functionmentioning

confidence: 99%

Research journey of respirasome

Zong

et al. 2020

Protein Cell

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Respirasome, as a vital part of the oxidative phosphorylation system, undertakes the task of transferring electrons from the electron donors to oxygen and produces a proton concentration gradient across the inner mitochondrial membrane through the coupled translocation of protons. Copious research has been carried out on this lynchpin of respiration. From the discovery of individual respiratory complexes to the report of the high-resolution structure of mammalian respiratory supercomplex I 1 III 2 IV 1 , scientists have gradually uncovered the mysterious veil of the electron transport chain (ETC). With the discovery of the mammalian respiratory mega complex I 2 III 2 IV 2 , a new perspective emerges in the research field of the ETC. Behind these advances glitters the light of the revolution in both theory and technology. Here, we give a short review about how scientists 'see' the structure and the mechanism of respirasome from the macroscopic scale to the atomic scale during the past decades.

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“…Datasets were collected on the BL-7A synchrotron at the Pohang Light Source (PLS) Facility in South Korea [48]. The datasets were indexed, processed, and scaled using a HKL-2000 software package [49,50], as summarized in Table 1. For assessing the effect of mosaicity by freezing, the X-ray data of the HEWL crystals were collected at room temperature (see Supplementary Materials: Table S1).…”

Section: X-ray Diffraction and Analysismentioning

confidence: 99%

Enhancing Protein Crystallization under a Magnetic Field

Ryu

Cho

et al. 2020

Crystals

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High-quality crystals are essential to ensure high-resolution structural information. Protein crystals are controlled by many factors, such as pH, temperature, and the ion concentration of crystalline solutions. We previously reported the development of a device dedicated to protein crystallization. In the current study, we have further modified and improved our device. Exposure to external magnetic field leads to alignment of the crystal toward a preferred direction depending on the magnetization energy. Each material has different magnetic susceptibilities depending on the individual direction of their unit crystal cells. One of the strategies to acquire a large crystal entails controlling the nucleation rate. Furthermore, exposure of a crystal to a magnetic field may lead to new morphologies by affecting the crystal volume, shape, and quality.

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X-ray data processing

Cited by 30 publications

References 64 publications

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Research journey of respirasome

Enhancing Protein Crystallization under a Magnetic Field

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