Subunit stoichiometry determination by chemical cross-linking

2008 ◽  
Author(s):  
Aubin Penna ◽  
Michael Cahalan
Keyword(s):  
Cross Linking ◽  
Subunit Stoichiometry ◽  
Chemical Cross Linking

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

scholarly journals Structure of cyanobacterial phycobilisome core revealed by structural modeling and chemical cross-linking

2021 ◽  
Vol 7 (2) ◽  
pp. eaba5743
Author(s):  
Haijun Liu ◽  
Mengru M. Zhang ◽  
Daniel A. Weisz ◽  
Ming Cheng ◽  
Himadri B. Pakrasi ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Excitation Energy Transfer ◽  
Energy Coupling ◽  
Regulatory Elements ◽  
Photochemical Activity ◽  
Structural Basis ◽  
Bottom Surface ◽  
Cross Linking ◽  
Orange Carotenoid Protein ◽  
Chemical Cross Linking

In cyanobacteria and red algae, the structural basis dictating efficient excitation energy transfer from the phycobilisome (PBS) antenna complex to the reaction centers remains unclear. The PBS has several peripheral rods and a central core that binds to the thylakoid membrane, allowing energy coupling with photosystem II (PSII) and PSI. Here, we have combined chemical cross-linking mass spectrometry with homology modeling to propose a tricylindrical cyanobacterial PBS core structure. Our model reveals a side-view crossover configuration of the two basal cylinders, consolidating the essential roles of the anchoring domains composed of the ApcE PB loop and ApcD, which facilitate the energy transfer to PSII and PSI, respectively. The uneven bottom surface of the PBS core contrasts with the flat reducing side of PSII. The extra space between two basal cylinders and PSII provides increased accessibility for regulatory elements, e.g., orange carotenoid protein, which are required for modulating photochemical activity.

scholarly journals Enzymatic and Chemical Cross-Linking of Bacterial Cellulose/Fish Collagen Composites—A Comparative Study

2021 ◽  
Vol 22 (7) ◽  
pp. 3346
Author(s):  
Agata Sommer ◽  
Paulina Dederko-Kantowicz ◽  
Hanna Staroszczyk ◽  
Sławomir Sommer ◽  
Marek Michalec
Keyword(s):  
Thermal Stability ◽  
Bacterial Cellulose ◽  
Secondary Alcohol ◽  
Water Vapor Permeability ◽  
Polymer Chains ◽  
Cross Linking ◽  
Vapor Permeability ◽  
Covalent Bonds ◽  
Fish Collagen ◽  
Chemical Cross Linking

This article compares the properties of bacterial cellulose/fish collagen composites (BC/Col) after enzymatic and chemical cross-linking. In our methodology, two transglutaminases are used for enzymatic cross-linking—one recommended for the meat and the other proposed for the fish industry—and pre-oxidated BC (oxBC) is used for chemical cross-linking. The structure of the obtained composites is characterized by scanning electron microscopy, thermogravimetric analysis, X-ray diffraction, and Fourier transform infrared spectroscopy, and their functional properties by mechanical and water barrier tests. While polymer chains in uncross-linked BC/Col are intertwined by H-bonds, new covalent bonds in enzymatically cross-linked ones are formed—resulting in increased thermal stability and crystallinity of the material. The C2–C3 bonds cleavage in D-glucose units, due to BC oxidation, cause secondary alcohol groups to vanish in favor of the carbonyl groups’ formation, thus reducing the number of H-bonded OHs. Thermal stability and crystallinity of oxBC/Col remain lower than those of BC/Col. The BC/Col formation did not affect tensile strength and water vapor permeability of BC, but enzymatic cross-linking with TGGS improved them significantly.

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