Prospects for Atomic Resolution and Neutron Crystallography in Drug Design

2004 ◽  
Vol 5 (2) ◽  
pp. 173-178 ◽  
Author(s):  
L. Coates ◽  
D. A.Myles
IUCrJ ◽  
2016 ◽  
Vol 3 (5) ◽  
pp. 296-297 ◽  
Author(s):  
M. P. Blakeley

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5554
Author(s):  
Yen-Hua Huang ◽  
Qingdan Du ◽  
Zhihao Jiang ◽  
Gordon J. King ◽  
Brett M. Collins ◽  
...  

Cyclotides have attracted great interest as drug design scaffolds because of their unique cyclic cystine knotted topology. They are classified into three subfamilies, among which the bracelet subfamily represents the majority and comprises the most bioactive cyclotides, but are the most poorly utilized in drug design applications. A long-standing challenge has been the very low in vitro folding yields of bracelets, hampering efforts to characterize their structures and activities. Herein, we report substantial increases in bracelet folding yields enabled by a single point mutation of residue Ile-11 to Leu or Gly. We applied this discovery to synthesize mirror image enantiomers and used quasi-racemic crystallography to elucidate the first crystal structures of bracelet cyclotides. This study provides a facile strategy to produce bracelet cyclotides, leading to a general method to easily access their atomic resolution structures and providing a basis for development of biotechnological applications.


IUCrJ ◽  
2015 ◽  
Vol 2 (4) ◽  
pp. 464-474 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Samar S. Hasnain ◽  
Svetlana V. Antonyuk

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e.≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e.≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochromec′, are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.


2018 ◽  
Vol 61 (10) ◽  
pp. 4412-4420 ◽  
Author(s):  
Francesco Manzoni ◽  
Johan Wallerstein ◽  
Tobias E. Schrader ◽  
Andreas Ostermann ◽  
Leighton Coates ◽  
...  

2012 ◽  
Vol 125 (3) ◽  
pp. 1056-1059 ◽  
Author(s):  
M. G. Cuypers ◽  
S. A. Mason ◽  
M. P. Blakeley ◽  
E. P. Mitchell ◽  
M. Haertlein ◽  
...  

Author(s):  
M. Kelly ◽  
D.M. Bird

It is well known that strain fields can have a strong influence on the details of HREM images. This, for example, can cause problems in the analysis of edge-on interfaces between lattice mismatched materials. An interesting alternative to conventional HREM imaging has recently been advanced by Pennycook and co-workers where the intensity variation in the annular dark field (ADF) detector is monitored as a STEM probe is scanned across the specimen. It is believed that the observed atomic-resolution contrast is correlated with the intensity of the STEM probe at the atomic sites and the way in which this varies as the probe moves from cell to cell. As well as providing a directly interpretable high-resolution image, there are reasons for believing that ADF-STEM images may be less suseptible to strain than conventional HREM. This is because HREM images arise from the interference of several diffracted beams, each of which is governed by all the excited Bloch waves in the crystal.


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