scholarly journals Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments

Author(s):  
Stefan Hörer ◽  
Dirk Reinert ◽  
Katja Ostmann ◽  
Yvette Hoevels ◽  
Herbert Nar
2019 ◽  
Vol 19 (4) ◽  
pp. 2380-2387 ◽  
Author(s):  
Phillip Nowotny ◽  
Johannes Hermann ◽  
Jianing Li ◽  
Angela Krautenbacher ◽  
Kai Klöpfer ◽  
...  

2012 ◽  
Vol 22 (3) ◽  
pp. 147-155 ◽  
Author(s):  
Aiya Chantarasiri ◽  
Vithaya Meevootisom ◽  
Duangnate Isarangkul ◽  
Suthep Wiyakrutta

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 975
Author(s):  
Brigitte Walla ◽  
Daniel Bischoff ◽  
Robert Janowski ◽  
Nikolas von den Eichen ◽  
Dierk Niessing ◽  
...  

Protein crystallization can serve as a purification step in biotechnological processes but is often limited by the non-crystallizability of proteins. Enabling or improving crystallization is mostly achieved by high-throughput screening of crystallization conditions and, more recently, by rational crystal contact engineering. Two selected rational crystal contact mutations, Q126K and T102E, were transferred from the alcohol dehydrogenases of Lactobacillus brevis (LbADH) to Lactobacillus kefir (LkADH). Proteins were expressed in E. coli and batch protein crystallization was performed in stirred crystallizers. Highly similar crystal packing of LkADH wild type compared to LbADH, which is necessary for the transfer of crystal contact engineering strategies, was achieved by aligning purification tag and crystallization conditions, as shown by X-ray diffraction. After comparing the crystal sizes after crystallization of LkADH mutants with the wild type, the mean protein crystal size of LkADH mutants was reduced by 40–70% in length with a concomitant increase in the total amount of crystals (higher number of nucleation events). Applying this measure to the LkADH variants studied results in an order of crystallizability T102E > Q126K > LkADH wild type, which corresponds to the results with LbADH mutants and shows, for the first time, the successful transfer of crystal contact engineering strategies.


2020 ◽  
Vol 15 (11) ◽  
pp. 2000010
Author(s):  
Phillip Grob ◽  
Max Huber ◽  
Brigitte Walla ◽  
Johannes Hermann ◽  
Robert Janowski ◽  
...  

Author(s):  
Kristen Scicluna ◽  
Grant Dewson ◽  
Peter E. Czabotar ◽  
Richard W. Birkinshaw

The Atg8 protein family comprises the GABA type A receptor-associated proteins (GABARAPs) and microtubule-associated protein 1 light chains 3 (MAP1LC3s) that are essential mediators of autophagy. The LC3-interacting region (LIR) motifs of autophagy receptors and adaptors bind Atg8 proteins to promote autophagosome formation, cargo recruitment, and autophagosome closure and fusion to lysosomes. A crystal structure of human GABARAPL2 has been published [PDB entry 4co7; Ma et al. (2015), Biochemistry, 54, 5469–5479]. This was crystallized in space group P21 with a monoclinic angle of 90° and shows a pseudomerohedral twinning pathology. This article reports a new, untwinned GABARAPL2 crystal form, also in space group P21, but with a 98° monoclinic angle. No major conformational differences were observed between the structures. In the structure described here, the C-terminal Phe117 binds into the LIR docking site (LDS) of a neighbouring molecule within the asymmetric unit, as observed in the previously reported structure. This crystal contact blocks the LDS for co-crystallization with ligands. Phe117 of GABARAPL2 is normally removed during biological processing by Atg4 family proteases. These data indicate that to establish interactions with the LIR, Phe117 should be removed to eliminate the crystal contact and liberate the LDS for co-crystallization with LIR peptides.


Author(s):  
R.A. Milligan ◽  
P.N.T. Unwin

A detailed understanding of the mechanism of protein synthesis will ultimately depend on knowledge of the native structure of the ribosome. Towards this end we have investigated the low resolution structure of the eukaryotic ribosome embedded in frozen buffer, making use of a system in which the ribosomes crystallize naturally.The ribosomes in the cells of early chicken embryos form crystalline arrays when the embryos are cooled at 4°C. We have developed methods to isolate the stable unit of these arrays, the ribosome tetramer, and have determined conditions for the growth of two-dimensional crystals in vitro, Analysis of the proteins in the crystals by 2-D gel electrophoresis demonstrates the presence of all ribosomal proteins normally found in polysomes. There are in addition, four proteins which may facilitate crystallization. The crystals are built from two oppositely facing P4 layers and the predominant crystal form, accounting for >80% of the crystals, has the tetragonal space group P4212, X-ray diffraction of crystal pellets demonstrates that crystalline order extends to ~ 60Å.


1997 ◽  
Vol 503 ◽  
Author(s):  
H. Jiang ◽  
M. K. Davis ◽  
R. K. Eby ◽  
P. Arsenovic

ABSTRACTPhysical properties and structural parameters have been measured for ropes of nylon 6 as a function of the number of use operations. The fractional content of the α crystal form, sound velocity, birefringence, tensile strength and length all increase systematically and significantly with increasing the number of use operations. The fractional content of the γ crystal form and fiber diameter decrease with use. These trends indicate that the measurement of such properties and structural parameters, especially the length, provide a possible basis for establishing a reliable, rapid, and convenient nondestructive characterization method to predict the remaining service life of nylon 6 ropes.


Author(s):  
Aditi Rathee ◽  
Anil Panwar ◽  
Seema Kumari ◽  
Sanjay Chhibber ◽  
Ashok Kumar

Introduction:: Enzymatic degradation of peptidoglycan, a structural cell wall component of Gram-positive bacteria, has attracted considerable attention being a specific target for many known antibiotics. Methods:: Peptidoglycan hydrolases are involved in bacterial lysis through peptidoglycan degradation. β-N-acetylglucosaminidase, a peptidoglycan hydrolase, acts on O-glycosidic bonds formed by N-acetylglucosamine and N-acetyl muramic acid residues of peptidoglycan. Aim of present study was to study the action of β-N-acetylglucosaminidase, on methicillin- resistant Staphylococcus aureus (MRSA) and other Gram-negative bacteria. Results:: We investigated its dynamic behaviour using molecular dynamics simulation and observed that serine and alanine residues are involved in catalytic reaction in addition to aspartic acid, histidine, lysine and arginine residues. When simulated in its bound state, the RMSD values were found lesser than crystal form in the time stamp of 1000 picoseconds revealing its stability. Structure remained stably folded over 1000 picoseconds without undergoing any major change further confirming the stability of complex. Conclusion:: It can be concluded that enzymes belonging to this category can serve as a tool in eradicating Gram-positive pathogens and associated infections.


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