| 1. |
- Andersson, Martin E, et al.
(författare)
-
Structural and mutational studies of the carboxylate cluster in iron-free ribonucleotide reductase R2.
- 2004
-
Ingår i: Biochemistry. - 0006-2960. ; 43:24, s. 7966-72
-
Tidskriftsartikel (refereegranskat)abstract
- The R2 protein of ribonucleotide reductase features a di-iron site deeply buried in the protein interior. The apo form of the R2 protein has an unusual clustering of carboxylate side chains at the empty metal-binding site. In a previous study, it was found that the loss of the four positive charge equivalents of the diferrous site in the apo protein appeared to be compensated for by the protonation of two histidine and two carboxylate side chains. We have studied the consequences of removing and introducing charged residues on the local hydrogen-bonding pattern in the region of the carboxylate cluster of Corynebacterium ammoniagenes and Escherichia coli protein R2 using site-directed mutagenesis and X-ray crystallography. The structures of the metal-free forms of wild-type C. ammoniagenes R2 and the mutant E. coli proteins D84N, S114D, E115A, H118A, and E238A have been determined and their hydrogen bonding and protonation states have been structurally assigned as far as possible. Significant alterations to the hydrogen-bonding patterns, protonation states, and hydration is observed for all mutant E. coli apo proteins as compared to wild-type apo R2. Further structural variations are revealed by the wild-type apo C. ammoniagenes R2 structure. The protonation and hydration effects seen in the carboxylate cluster appear to be due to two major factors: conservation of the overall charge of the site and the requirement of electrostatic shielding of clustered carboxylate residues. Very short hydrogen-bonding distances between some protonated carboxylate pairs are indicative of low-barrier hydrogen bonding.
|
|
| 2. |
- Asimakopoulou, Eleni Myrto, et al.
(författare)
-
Development towards high-resolution kHz-speed rotation-free volumetric imaging
- 2024
-
Ingår i: Optics Express. - 1094-4087. ; 32:3, s. 4413-4426
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray multi-projection imaging (XMPI) has the potential to provide rotation-free 3D movies of optically opaque samples. The absence of rotation enables superior imaging speed and preserves fragile sample dynamics by avoiding the centrifugal forces introduced by conventional rotary tomography. Here, we present our XMPI observations at the ID19 beamline (ESRF, France) of 3D dynamics in melted aluminum with 1000 frames per second and 8 µm resolution per projection using the full dynamical range of our detectors. Since XMPI is a method under development, we also provide different tests for the instrumentation of up to 3000 frames per second. As the high-brilliance of 4th generation light-sources becomes more available, XMPI is a promising technique for current and future X-ray imaging instruments.
|
|
| 3. |
- Ren, Hui, et al.
(författare)
-
The crystal structure of human adenylate kinase 6 : An adenylate kinase localized to the cell nucleus
- 2005
-
Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 102:2, s. 8-303
-
Tidskriftsartikel (refereegranskat)abstract
- Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur single-wavelength anomalous dispersion phasing methods and refined to 2.0-A resolution with a free R factor of 21.8%. Sequence analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Enzymatic assays show that human AK6 has properties similar with other AKs, particularly with AK5. Fluorescence microscopy showed that human AK6 is localized predominantly to the nucleus of HeLa cells. The identification of a nuclear-localized AK sheds light on nucleotide metabolism in the nucleus and the energetic communication between mitochondria and nucleus by means of phosphotransfer networks.
|
|
| 4. |
- Soyama, Hitoshi, et al.
(författare)
-
Revealing the origins of vortex cavitation in a Venturi tube by high speed X-ray imaging
- 2023
-
Ingår i: Ultrasonics Sonochemistry. - 1350-4177. ; 101
-
Tidskriftsartikel (refereegranskat)abstract
- Hydrodynamic cavitation is useful in many processing applications, for example, in chemical reactors, water treatment and biochemical engineering. An important type of hydrodynamic cavitation that occurs in a Venturi tube is vortex cavitation known to cause luminescence whose intensity is closely related to the size and number of cavitation events. However, the mechanistic origins of bubbles constituting vortex cavitation remains unclear, although it has been concluded that the pressure fields generated by the cavitation collapse strongly depends on the bubble geometry. The common view is that vortex cavitation consists of numerous small spherical bubbles. In the present paper, aspects of vortex cavitation arising in a Venturi tube were visualized using high-speed X-ray imaging at SPring-8 and European XFEL. It was discovered that vortex cavitation in a Venturi tube consisted of angulated rather than spherical bubbles. The tangential velocity of the surface of vortex cavitation was assessed considering the Rankine vortex model.
|
|
| 5. |
- Su, Xiao Dong, et al.
(författare)
-
A large-scale, high-efficiency and low-cost platform for structural genomics studies
- 2006
-
Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 0907-4449. ; 62:Pt 8, s. 51-843
-
Tidskriftsartikel (refereegranskat)abstract
- A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.
|
|
