Myoglobins engineered with artificial cofactors serve as artificial metalloenzymes and models of natural enzymes

2021 ◽  
Author(s):  
Koji Oohora ◽  
Takashi Hayashi
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Artificial Metalloenzymes ◽  
Endogenous Amino Acid

Metalloenzymes naturally achieve various reactivities by assembling of limited types of cofactors with endogenous amino acid residues. Enzymes containing metal porphyrinoid cofactors such as heme, cobalamin and F430 exert precise...

scholarly journals Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation

2015 ◽  
Vol 44 (15) ◽  
pp. 5495-5551 ◽  
Author(s):  
Oleksandr Koniev ◽  
Alain Wagner
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Bond Forming ◽  
Recent Advances ◽  
Bond Forming Reactions ◽  
Endogenous Amino Acid

Recent advances in bond-forming bioconjugation reactions of native amino acid residues with emphasis on the most practically relevant methodologies.

Substrate Recognition by Vitamin K-Dependent Carboxylase

1987 ◽  
Vol 57 (01) ◽  
pp. 017-019 ◽  
Author(s):  
Magda M W Ulrich ◽  
Berry A M Soute ◽  
L Johan M van Haarlem ◽  
Cees Vermeer
Keyword(s):  
Amino Acid ◽  
Vitamin K ◽  
Substrate Recognition ◽  
Bovine Liver ◽  
Amino Acid Residues

SummaryDecarboxylated osteocalcins were prepared and purified from bovine, chicken, human and monkey bones and assayed for their ability to serve as a substrate for vitamin K-dependent carboxylase from bovine liver. Substantial differences were observed, especially between bovine and monkey d-osteocalcin. Since these substrates differ only in their amino acid residues 3 and 4, it seems that these residues play a role in the recognition of a substrate by hepatic carboxylase.

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>

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