scholarly journals Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Marcelo V. Liberato ◽  
Rodrigo L. Silveira ◽  
Érica T. Prates ◽  
Evandro A. de Araujo ◽  
Vanessa O. A. Pellegrini ◽  
...  
Keyword(s):  
Large Scale ◽  
Catalytic Domain ◽  
Glycoside Hydrolases ◽  
Induced Fit ◽  
X Ray ◽  
X Ray Crystallography ◽  
Enzymatic Mechanism ◽  
X Ray Scattering ◽  
Large Amplitude Motions ◽  
Dynamics Simulations

Abstract Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.

scholarly journals Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy

2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Lassa Virus ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Ray Scattering

Liquid Structure of 1-Propanol by Molecular Dynamics Simulations and X-Ray Scattering

2004 ◽  
Vol 33 (6/7) ◽  
pp. 797-809 ◽  
Author(s):  
Isao Akiyama ◽  
Masaya Ogawa ◽  
Keiichi Takase ◽  
Toshiyuki Takamuku ◽  
Toshio Yamaguchi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

The nature of the scattering tail in Cu–Ni–Fe and Invar alloys investigated by anomalous small-angle X-ray scattering

1991 ◽  
Vol 24 (6) ◽  
pp. 1027-1034 ◽  
Author(s):  
J. P. Simon ◽  
O. Lyon
Keyword(s):  
Small Angle ◽  
Large Scale ◽  
Concentration Fluctuations ◽  
X Ray ◽  
Invar Alloys ◽  
X Ray Scattering ◽  
Angle Measurements ◽  
Two Systems ◽  
Fe Alloys ◽  
Ray Scattering

A large rapidly decreasing intensity called the `scattering tail' is generally observed at the smallest recorded angles during small-angle measurements of metallic alloys. Since this tail was interpreted as caused by a bimodal phase separation in Cu–Ni–Fe alloys and by long-wavelength concentration fluctuations in Invar alloys, these two systems were re-examined with anomalous X-ray scattering. The variation of the alloying atomic contrasts allows a discrimination between the different types of particles or defects. In neither of the two systems can the tails be interpreted as caused by large-scale concentration fluctuations. In Cu–Ni–Fe alloys, the tail is due to some kind of superficial defect (surface roughness etc.). In Invar alloys, the tail is probably due to residual impurity particles.

scholarly journals Exploiting the full quantum crystallography

2018 ◽  
Vol 96 (7) ◽  
pp. 599-605 ◽  
Author(s):  
Lou Massa ◽  
Chérif F. Matta
Keyword(s):  
Quantum Mechanics ◽  
Electron Density ◽  
Mathematical Structure ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Fundamental Value ◽  
Quantum Crystallography ◽  
Ray Scattering

Quantum crystallography (QCr) is a branch of crystallography aimed at obtaining the complete quantum mechanics of a crystal given its X-ray scattering data. The fundamental value of obtaining an electron density matrix that is N-representable is that it ensures consistency with an underlying properly antisymmetrized wavefunction, a requirement of quantum mechanical validity. However, X-ray crystallography has progressed in an impressive way for decades based only upon the electron density obtained from the X-ray scattering data without the imposition of the mathematical structure of quantum mechanics. Therefore, one may perhaps ask regarding N-representability “why bother?” It is the purpose of this article to answer such a question by succinctly describing the advantage that is opened by QCr.

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’.

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