scholarly journals Integrative structural biology ofTetrahymenatelomerase - insights into catalytic mechanism and interaction at telomeres

FEBS Journal ◽  
2016 ◽  
Vol 283 (11) ◽  
pp. 2044-2050 ◽  
Author(s):  
Juli Feigon ◽  
Henry Chan ◽  
Jiansen Jiang
Keyword(s):  
Structural Biology ◽  
Catalytic Mechanism ◽  
Integrative Structural Biology

scholarly journals Advances in integrative structural biology: Towards understanding protein complexes in their cellular context

2021 ◽  
Vol 19 ◽  
pp. 214-225
Author(s):  
Samantha J. Ziegler ◽  
Sam J.B. Mallinson ◽  
Peter C. St. John ◽  
Yannick J. Bomble
Keyword(s):  
Structural Biology ◽  
Protein Complexes ◽  
Cellular Context ◽  
Integrative Structural Biology

scholarly journals Integrative Structural Biology

Science ◽  
2013 ◽  
Vol 339 (6122) ◽  
pp. 913-915 ◽  
Author(s):  
A. B. Ward ◽  
A. Sali ◽  
I. A. Wilson
Keyword(s):  
Structural Biology ◽  
Integrative Structural Biology

scholarly journals Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Iskander Khusainov ◽  
Bulat Fatkhullin ◽  
Simone Pellegrino ◽  
Aydar Bikmullin ◽  
Wen-ti Liu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Structural Biology ◽  
Integrative Structural Biology

scholarly journals Integrative Structural Biology of the Calcium Dependent Type 2 Secretion Pseudopilus

2018 ◽  
Vol 114 (3) ◽  
pp. 229a
Author(s):  
Aracelys Lopez-Castilla ◽  
Benjamin Bardiaux ◽  
Jenny-Lee Thomassin ◽  
Weili Zheng ◽  
Michael Nilges ◽  
...  
Keyword(s):  
Structural Biology ◽  
Calcium Dependent ◽  
Integrative Structural Biology ◽  
Dependent Type ◽  
Type 2 Secretion

scholarly journals Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 370 ◽  
Author(s):  
Linda Cerofolini ◽  
Marco Fragai ◽  
Enrico Ravera ◽  
Christoph A. Diebolder ◽  
Ludovic Renault ◽  
...  
Keyword(s):  
Structural Biology ◽  
Catalytic Mechanism ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Protein Model ◽  
Pros And Cons ◽  
Transient Interactions ◽  
Single Technique ◽  
Nmr Restraints

With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’.

scholarly journals Sortase Transpeptidases: Structural Biology and Catalytic Mechanism

2017 ◽  
pp. 223-264 ◽  
Author(s):  
Alex W. Jacobitz ◽  
Michele D. Kattke ◽  
Jeff Wereszczynski ◽  
Robert T. Clubb
Keyword(s):  
Structural Biology ◽  
Catalytic Mechanism

scholarly journals Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology

Structure ◽  
2019 ◽  
Vol 27 (9) ◽  
pp. 1416-1426.e3 ◽  
Author(s):  
Martin F. Peter ◽  
Anne T. Tuukkanen ◽  
Caspar A. Heubach ◽  
Alexander Selsam ◽  
Fraser G. Duthie ◽  
...  
Keyword(s):  
Structural Biology ◽  
Conformational Changes ◽  
Type Iii Secretion ◽  
Type Iii ◽  
Integrative Structural Biology ◽  
Type Iii Secretion Effector

scholarly journals High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase

2020 ◽  
Vol 117 (8) ◽  
pp. 4071-4077 ◽  
Author(s):  
Yohta Fukuda ◽  
Yu Hirano ◽  
Katsuhiro Kusaka ◽  
Tsuyoshi Inoue ◽  
Taro Tamada
Keyword(s):  
Computational Chemistry ◽  
Structural Biology ◽  
Resting State ◽  
Catalytic Mechanism ◽  
Low Ph ◽  
Intramolecular Electron Transfer ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Electron Transfer Pathway ◽  
Neutron Structure

Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.

scholarly journals Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR

2014 ◽  
Vol 15 (3) ◽  
pp. 117-124 ◽  
Author(s):  
Jeffrey Lengyel ◽  
Eric Hnath ◽  
Marc Storms ◽  
Thomas Wohlfarth
Keyword(s):  
Structural Biology ◽  
X Ray ◽  
X Ray Crystallography ◽  
Integrative Structural Biology
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