scholarly journals Atomic resolution structure of serine protease proteinase K at ambient temperature

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Tetsuya Masuda ◽  
Mamoru Suzuki ◽  
Shigeyuki Inoue ◽  
Changyong Song ◽  
Takanori Nakane ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Serine Protease ◽  
Atomic Resolution ◽  
Proteinase K ◽  
Resolution Structure

scholarly journals Atomic resolution structure of serine protease proteinase K at ambient temperature

2017 ◽  
Author(s):  
Tetsuya Masuda ◽  
Mamoru Suzuki ◽  
Shigeyuki Inoue ◽  
Changyong Song ◽  
Takanori Nakane ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Active Sites ◽  
Atomic Resolution ◽  
Proteinase K ◽  
Water Molecules ◽  
Specific Substrate ◽  
Hydrogen Atoms ◽  
X Ray Crystallography ◽  
Chain Conformations ◽  
Resolution Structure

AbstractAtomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.

scholarly journals CryoEM structure of the antibacterial target PBP1b at 3.3 Å resolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nathanael A. Caveney ◽  
Sean D. Workman ◽  
Rui Yan ◽  
Claire E. Atkinson ◽  
Zhiheng Yu ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Acid Anhydride ◽  
Atomic Resolution ◽  
Inherent Difficulty ◽  
Penicillin Binding Proteins ◽  
Antibiotic Development ◽  
Class A ◽  
Membrane Mimetic ◽  
Antibacterial Target ◽  
Resolution Structure

AbstractThe pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates.

scholarly journals MicroED Structures from Micrometer Thick Protein Crystals

2017 ◽  
Author(s):  
Michael W. Martynowycz ◽  
Calina Glynn ◽  
Jennifer Miao ◽  
M. Jason de la Cruz ◽  
Johan Hattne ◽  
...  
Keyword(s):  
Theoretical Calculations ◽  
Protein Structures ◽  
Atomic Resolution ◽  
Proteinase K ◽  
Protein Crystals ◽  
Molecular Replacement ◽  
Varying Thickness ◽  
Order Of Magnitude ◽  
Human Prion Protein ◽  
Do So

AbstractTheoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibility for an even broader range of MicroED experiments.SummaryAtomic resolution protein structures can be determined by MicroED from crystals that surpass the theoretical maximum thickness limit by an order of magnitude.

scholarly journals A resolution record for cryoEM

2021 ◽  
Vol 10 ◽  
Author(s):  
Jonathan Ashmore ◽  
Bridget Carragher ◽  
Peter B Rosenthal ◽  
William Weis
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Structure Determination ◽  
Test Specimen ◽  
Structural Information ◽  
Atomic Resolution ◽  
Fast Growing ◽  
Cryo Electron Microscopy ◽  
New Instrument ◽  
Resolution Structure

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

SAT0012 Proteinase K-Like Serine Protease PCSK9 Influence on the Dyslipidemia Observed in Rheumatoid Arthritis Patients

2015 ◽  
Vol 74 (Suppl 2) ◽  
pp. 653.3-654
Author(s):  
B.T. Segura ◽  
R. Lόpez Mejías ◽  
F. Genre ◽  
B. Ubilla ◽  
E. Delgado-Frías ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Serine Protease ◽  
Proteinase K

A Covalent Modification of NADP+Revealed by the Atomic Resolution Structure of FprA, aMycobacterium tuberculosisOxidoreductase†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (28) ◽  
pp. 8807-8818 ◽  
Author(s):  
Roberto T. Bossi ◽  
Alessandro Aliverti ◽  
Debora Raimondi ◽  
Federico Fischer ◽  
Giuliana Zanetti ◽  
...  
Keyword(s):  
Covalent Modification ◽  
Atomic Resolution ◽  
Resolution Structure

scholarly journals Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

2015 ◽  
Vol 1 (11) ◽  
pp. e1501087 ◽  
Author(s):  
Chaowei Shi ◽  
Pascal Fricke ◽  
Lin Lin ◽  
Veniamin Chevelkov ◽  
Melanie Wegstroth ◽  
...  
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Caulobacter Crescentus ◽  
Heavy Atom ◽  
Cytoskeletal Proteins ◽  
Atomic Resolution ◽  
Hydrophobic Core ◽  
X Ray Crystallography ◽  
Wide Range ◽  
Resolution Structure

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

Atomic Resolution Structure of Human HBP/CAP37/Azurocidin

1998 ◽  
Vol 54 (4) ◽  
pp. 598-609 ◽  
Author(s):  
Solveig Karlsen ◽  
Lars Fogh Iversen ◽  
Ingrid Kjøller Larsen ◽  
Hans Jacob Flodgaard ◽  
Jette Sandholm Kastrup
Keyword(s):  
Atomic Resolution ◽  
Resolution Structure
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