scholarly journals Structural insights into the architecture and membrane interactions of the conserved COMMD proteins

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Michael D Healy ◽  
Manuela K Hospenthal ◽  
Ryan J Hall ◽  
Mintu Chandra ◽  
Molly Chilton ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Intracellular Membrane ◽  
X Ray ◽  
X Ray Crystallography ◽  
Terminal Domain ◽  
X Ray Scattering ◽  
Conserved Domain ◽  
Underlying Mechanisms ◽  
Specific Membrane ◽  
Structural Insights

The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.

scholarly journals Opportunities and challenges in neutron crystallography

2020 ◽  
Vol 236 ◽  
pp. 02001
Author(s):  
Nathan Richard Zaccai ◽  
Nicolas Coquelle
Keyword(s):  
X Rays ◽  
Hydrogen Atoms ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Nuclei ◽  
X Ray Scattering ◽  
Data Collection And Analysis ◽  
Analysis Strategies ◽  
Structural Insights ◽  
Neutron Crystallography

Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.

scholarly journals Structural insights into rice SalTol QTL located SALT protein

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Navdeep Kaur ◽  
Amin Sagar ◽  
Pankaj Sharma ◽  
Ashish ◽  
Pratap Kumar Pati
Keyword(s):  
Data Analysis ◽  
Radius Of Gyration ◽  
Relative Positioning ◽  
Salt Stress Tolerance ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Sugar Unit ◽  
Structural Insights

Abstract Salinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 Å). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 Å2 compared to only 240 Å2 for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.

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

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’.

Regulative interactions of the osmosensing C-terminal domain in the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum

2009 ◽  
Vol 390 (8) ◽  
Author(s):  
Reinhard Krämer ◽  
Christine Ziegler
Keyword(s):  
Amino Acid ◽  
Corynebacterium Glutamicum ◽  
Protein Interactions ◽  
Regulation Mechanism ◽  
Protein Protein Interactions ◽  
Molecular Switching ◽  
X Ray ◽  
X Ray Crystallography ◽  
Terminal Domain ◽  
Domain Reorientation

Abstract Activation of the osmoregulated trimeric betaine transporter BetP from Corynebacterium glutamicum was shown to depend mainly on the correct folding and integrity of its 55 amino acid long, partly α-helical C-terminal domain. Reorientation of the three C-terminal domains in the BetP trimer indicates different lipid-protein and protein-protein interactions of the C-terminal domain during osmoregulation. A regulation mechanism is suggested where this domain switches the transporter from the inactive to the active state. Interpretation of recently obtained electron and X-ray crystallography data of BetP led to a structure-function based model of C-terminal molecular switching involved in osmoregulation.

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