The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus

1999 ◽  
Vol 55 (4) ◽  
pp. 801-809 ◽  
Author(s):  
Stephen W. White ◽  
Keith S. Wilson ◽  
Krzysztof Appelt ◽  
Isao Tanaka
Keyword(s):  
High Resolution ◽  
Protein Interactions ◽  
Bacillus Stearothermophilus ◽  
Helical Structure ◽  
Structural Basis ◽  
Hydrophobic Core ◽  
Salt Bridges ◽  
Medium Resolution ◽  
High Resolution Structure ◽  
Resolution Structure

Protein HU is a ubiquitous prokaryotic protein which controls the architecture of genomic DNA. It binds DNA non-specifically and promotes the bending and supercoiling of the double helical structure. HU is involved in many DNA-associated cellular processes, including replication, transcription and the packaging of DNA into chromosome-like structures. Originally determined at medium resolution, the crystal structure of HU has now been refined at 2.0 Å resolution. The high-resolution structure shows that the dimeric molecule is essentially a compact platform for two flexible and basic arms which wrap around the DNA molecule. To maximize the protein's stability, non-secondary structural regions are reduced to a minimum, there is an extensive aromatic hydrophobic core and several salt bridges and hydrogen-bonded water molecules knit together crucial regions. Based on the original medium-resolution structure of HU, several proposals were made concerning the structural basis of HU's ability to bind, bend and supercoil DNA. Each of these proposals is fully supported by the high-resolution structure. Most notably, the surfaces of the molecule which appear to mediate protein–DNA and protein–protein interactions have the ideal shapes and physicochemical properties to perform these functions.

Improving the convergence rate of a hybrid input–output phasing algorithm by varying the reflection data weight

2018 ◽  
Vol 74 (1) ◽  
pp. 36-43 ◽  
Author(s):  
Hongxing He ◽  
Wu-Pei Su
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
Sharp Decrease ◽  
Projection Algorithm ◽  
Reflection Data ◽  
Error Metrics ◽  
Medium Resolution ◽  
Data Weighting ◽  
High Resolution Structure ◽  
Resolution Structure

In an iterative projection algorithm proposed forab initiophasing, the error metrics typically exhibit little improvement until a sharp decrease takes place as the iteration converges to the correct high-resolution structure. Related to that is the small convergence probability for certain structures. As a remedy, a variable weighting scheme on the diffraction data is proposed. It focuses on phasing low- and medium-resolution data first. The weighting shifts to incorporate more high-resolution reflections when the iteration proceeds. It is found that the precipitous drop in error metrics is replaced by a less dramatic drop at an earlier stage of the iteration. It seems that once a good configuration is formed at medium resolution, convergence towards the correct high-resolution structure is almost guaranteed. The original problem of phasing all diffraction data at once is reduced to a much more manageable one due to the dramatically smaller number of reflections involved. As a result, the success rate is significantly enhanced and the speed of convergence is raised. This is illustrated by applying the new algorithm to several structures, some of which are very difficult to solve without data weighting.

scholarly journals Structural Basis for Cytoplasmic Dynein-1 Regulation by Lis1

2021 ◽  
Author(s):  
John P Gillies ◽  
Janice M Reimer ◽  
Eva P Karasmanis ◽  
Indrajit Lahiri ◽  
Zaw Min Htet ◽  
...  
Keyword(s):  
High Resolution ◽  
Cytoplasmic Dynein ◽  
Motor Domain ◽  
Structural Basis ◽  
Neurodevelopmental Disease ◽  
Microtubule Motor ◽  
High Resolution Structure ◽  
Resolution Structure

The lissencephaly 1 gene, LIS1, is mutated in patients with the neurodevelopmental disease lissencephaly. The Lis1 protein is conserved from fungi to mammals and is a key regulator of cytoplasmic dynein-1, the major minus-end-directed microtubule motor in many eukaryotes. Lis1 is the only dynein regulator that binds directly to dynein's motor domain, and by doing so alters dynein's mechanochemistry. Lis1 is required for the formation of fully active dynein complexes, which also contain essential cofactors: dynactin and an activating adaptor. Here, we report the first high-resolution structure of the yeast dynein-Lis1 complex. Our 3.1Å structure reveals, in molecular detail, the major contacts between dynein and Lis1 and between Lis1's β-propellers. Structure-guided mutations in Lis1 and dynein show that these contacts are required for Lis1's ability to form fully active human dynein complexes and to regulate yeast dynein's mechanochemistry and in vivo function. We present a model for the conserved role of Lis1 in regulating dynein from yeast to humans.

scholarly journals Structural basis for cytoplasmic dynein-1 regulation by Lis1

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
John P Gillies ◽  
Janice M Reimer ◽  
Eva P Karasmanis ◽  
Indrajit Lahiri ◽  
Zaw Min Htet ◽  
...  
Keyword(s):  
High Resolution ◽  
Cytoplasmic Dynein ◽  
Motor Domain ◽  
Structural Basis ◽  
Neurodevelopmental Disease ◽  
Molecular Detail ◽  
Microtubule Motor ◽  
High Resolution Structure ◽  
Resolution Structure

The lissencephaly 1 gene, LIS1, is mutated in patients with the neurodevelopmental disease lissencephaly. The Lis1 protein is conserved from fungi to mammals and is a key regulator of cytoplasmic dynein-1, the major minus-end-directed microtubule motor in many eukaryotes. Lis1 is the only dynein regulator known to bind directly to dynein's motor domain, and by doing so alters dynein's mechanochemistry. Lis1 is required for the formation of fully active dynein complexes, which also contain essential cofactors: dynactin and an activating adaptor. Here, we report the first high-resolution structure of the yeast dynein–Lis1 complex. Our 3.1Å structure reveals, in molecular detail, the major contacts between dynein and Lis1 and between Lis1's ß-propellers. Structure-guided mutations in Lis1 and dynein show that these contacts are required for Lis1's ability to form fully active human dynein complexes and to regulate yeast dynein's mechanochemistry and in vivo function.

scholarly journals High-resolution structure determination by continuous-rotation data collection in MicroED

2014 ◽  
Vol 11 (9) ◽  
pp. 927-930 ◽  
Author(s):  
Brent L Nannenga ◽  
Dan Shi ◽  
Andrew G W Leslie ◽  
Tamir Gonen
Keyword(s):  
High Resolution ◽  
Data Collection ◽  
Structure Determination ◽  
Continuous Rotation ◽  
High Resolution Structure ◽  
Resolution Structure
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