Principles and methods used to grow and optimize crystals of protein–metallodrug adducts, to determine metal binding sites and to assign metal ligands

Metallomics ◽  
2017 ◽  
Vol 9 (11) ◽  
pp. 1534-1547 ◽  
Author(s):  
Irene Russo Krauss ◽  
Giarita Ferraro ◽  
Andrea Pica ◽  
José A. Márquez ◽  
John R. Helliwell ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Biological Macromolecules ◽  
Metal Ligands ◽  
Metal Binding Sites

Examples from the literature and experience in our own laboratory on the characterization of the interactions between biological macromolecules and metal-based drugs are provided.

Biophysical and physiological characterization of ZraP from Escherichia coli, the periplasmic accessory protein of the atypical ZraSR two-component system

2015 ◽  
Vol 472 (2) ◽  
pp. 205-216 ◽  
Author(s):  
Isabelle Petit-Härtlein ◽  
Kevin Rome ◽  
Eve de Rosny ◽  
Florian Molton ◽  
Carole Duboc ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Zinc Binding ◽  
Accessory Protein ◽  
Two Component System ◽  
Physiological Characterization ◽  
Metal Binding Sites ◽  
Two Component ◽  
Zinc Resistance

ZraP is an octamer containing four interfacial metal-binding sites contributing to dimer stability. Zinc binding enhances its chaperone properties and zinc-bound ZraP represses the expression of the zraPSR operon. None of the Zra proteins are involved in zinc resistance.

scholarly journals Check your metal - not every density blob is a water molecule

2014 ◽  
Vol 70 (a1) ◽  
pp. C1483-C1483
Author(s):  
Heping Zheng ◽  
Mahendra Chordia ◽  
David Cooper ◽  
Ivan Shabalin ◽  
Maksymilian Chruszcz ◽  
...  
Keyword(s):  
Coordination Chemistry ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Structures ◽  
Data Bank ◽  
Careful Examination ◽  
Biological Macromolecules ◽  
Metal Binding Sites ◽  
Heterogeneous Chemical

Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemistry; (2) agreement of experimental B-factors and occupancy; and (3) the composition and motif of the metal binding environment. Due to additional strain introduced by macromolecular backbones, the patterns of coordination of metal binding sites in metal-containing macromolecules are more complex and diverse than those found in inorganic or organometallic chemistry. These complications make a comprehensive library of "permitted" coordination chemistry in protein structures less feasible, and the usage of global parameters such as the bond valence method more practical, in the determination and validation of metal binding environments. Although they are relatively infrequent, there are also cases where the experimental B-factor or occupancy of a metal ion suggests careful examination. We have developed a web-based tool called CheckMyMetal [1](http://csgid.org/csgid/metal_sites/) for the quick validation of metal binding sites. Moreover, the acquired knowledge of the composition and spatial arrangement (motif) of the coordinating atoms around the metal ion may also help in the modeling of metal binding sites in macromolecular structures. All of the studies described herein were performed using the NEIGHBORHOOD SQL database [2], which connects information about all modeled non-solvent heterogeneous chemical motifs in PDB structure by vectors describing all contacts to neighboring residues and atoms. NEIGHBORHOOD has broad applications for the validation and data mining of ligand binding environments in the PDB.

scholarly journals Cross-π-conjugated enediyne with multitopic metal binding sites

RSC Advances ◽  
2020 ◽  
Vol 10 (63) ◽  
pp. 38612-38616
Author(s):  
Djawed Nauroozi ◽  
Benjamin Wurster ◽  
Rüdiger Faust
Keyword(s):  
Structural Characterization ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Binding Sites

Synthesis and structural characterization of a geminal enediyne molecule with three imine metal binding sites based on diazafluorenemethylidene in a cross-π-conjugated fashion is reported.

Localization and functional characterization of metal-binding sites in phytochelatin synthases

Planta ◽  
2003 ◽  
Vol 218 (2) ◽  
pp. 300-308 ◽  
Author(s):  
Thomas Maier ◽  
Chao Yu ◽  
Gerhard K�llertz ◽  
Stephan Clemens
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Functional Characterization ◽  
Metal Binding Sites
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