Metal Ion — Ligand Interactions for the Tetracycline Derivative Antibiotics: A Structural Approach

1977 ◽  
pp. 375-396
Author(s):  
John J. Stezowski
Keyword(s):  
Metal Ion ◽  
Structural Approach ◽  
Ligand Interactions ◽  
Tetracycline Derivative

scholarly journals MeLAD: an integrated resource for metalloenzyme-ligand associations

2019 ◽  
Author(s):  
Gen Li ◽  
Yu Su ◽  
Yu-Hang Yan ◽  
Jia-Yi Peng ◽  
Qing-Qing Dai ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Metal Binding ◽  
Metal Ion ◽  
Structural Data ◽  
Structural Similarity ◽  
Functional Class ◽  
Supplementary Information ◽  
Biological Processes ◽  
Ligand Interactions ◽  
Data Source

Abstract Motivation Metalloenzymes are attractive targets for therapeutic intervention owing to their central roles in various biological processes and pathological situations. The fast-growing body of structural data on metalloenzyme-ligand interactions is facilitating efficient drug discovery targeting metalloenzymes. However, there remains a shortage of specific databases that can provide centralized, interconnected information exclusive to metalloenzyme-ligand associations. Results We created a Metalloenzyme-Ligand Association Database (MeLAD), which is designed to provide curated structural data and information exclusive to metalloenzyme-ligand interactions, and more uniquely, present expanded associations that are represented by metal-binding pharmacophores (MBPs), metalloenzyme structural similarity (MeSIM) and ligand chemical similarity (LigSIM). MeLAD currently contains 6086 structurally resolved interactions of 1416 metalloenzymes with 3564 ligands, of which classical metal-binding, non-classical metal-binding, non-metal-binding and metal water-bridging interactions account for 63.0%, 2.3%, 34.4% and 0.3%, respectively. A total of 263 monodentate, 191 bidentate and 15 tridentate MBP chemotypes were included in MeLAD, which are linked to different active site metal ions and coordination modes. 3726 and 52 740 deductive metalloenzyme-ligand associations by MeSIM and LigSIM analyses, respectively, were included in MeLAD. An online server is provided for users to conduct metalloenzyme profiling prediction for small molecules of interest. MeLAD is searchable by multiple criteria, e.g. metalloenzyme name, ligand identifier, functional class, bioinorganic class, metal ion and metal-containing cofactor, which will serve as a valuable, integrative data source to foster metalloenzyme related research, particularly involved in drug discovery targeting metalloenzymes. Availability and implementation MeLAD is accessible at https://melad.ddtmlab.org. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies

Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 135
Author(s):  
Yanchun Lin ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Metal Binding ◽  
Metal Ion ◽  
Photochemical Oxidation ◽  
Structural Proteomics ◽  
Binding Studies ◽  
Ligand Interactions ◽  
Amino Acid Labeling

Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), “fast photochemical oxidation of proteins” (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including “protein–ligand interactions by mass spectrometry, titration and HD exchange” (PLIMSTEX) and “ligand titration, fast photochemical oxidation of proteins and mass spectrometry” (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.

Cysteine Interactions in Glutathione Mediated Assembly of Silver Nanoparticles in the Presence of Metal Ions

2012 ◽  
Vol 18-19 ◽  
pp. 63-76 ◽  
Author(s):  
Can Serkan Keskin ◽  
Semra Yılmazer Keskin ◽  
Abdil Özdemir
Keyword(s):  
Silver Nanoparticles ◽  
Optical Properties ◽  
Complex Formation ◽  
Metal Ions ◽  
Metal Ion ◽  
Variable Degree ◽  
Ordered Structures ◽  
Vis Spectroscopy ◽  
Ligand Interactions ◽  
New Material

We Report Herein Results of an Investigation of the Assembly of Silver Nanoparticles Mediated by Glutathione (GSH) and Cysteine (Cys) Interaction in the Presence of Metal Ions: Ag+, Cd2+, Co2+, Cu2+, Fe3+, Hg2+, Ni2+, Pb2+, Zn2+. The Silver Nanoparticles Produce Well-Ordered Structures upon Interaction with Glutathione in Variable Acidic Ph Condition and Exhibit Pronounced Changes in their Optical Properties Arising due to Electromagnetic Interaction. The Effect of Selected Metal Ions on the Nature of Complexation as Well as the Variation in the Optical Response due to Variable Degree of Complex Formation Amongst the Particles Have Been Investigated. The Changes in Optical Properties of the Silver Nanoparticles Have Been Accounted for the Complex Formation among the Aggsh, Cys and Metal Ions. The Complexes Have Been Characterized by UV-Vis Spectroscopy, FTIR, and AFM Studies. It Has Been Observed that the New Absorption Peaks Appear and Intensifies Depending on the Cys and Metal Ion Interaction. The Aggsh Nanoparticles Provided a Simple and Rapid Strategy to Detect Cys with the Aid of Metal Ions in Aqueous Solution. Different Metal Ions Give Different UV-Vis Spectra Profile and Show Different Sensitivity. This New Material Allows a Quantitative Assay of Cys down to the Concentration of 1× 10−5 M in Co2+ Ion Complexation. The Mechanism by which Metal Ions Can Bind with both the GSH Modified Ag Nanoparticles and Cys Molecule through Cooperative Metal–ligand Interactions Is Discussed.

A Generic Synthesis Route for Matrix Assisted Self-Assembly of Metal-Oxo Clusters in Organosilica Sol-Gels

2002 ◽  
Vol 726 ◽  
Author(s):  
Mukti S. Rao ◽  
Bakul C. Dave
Keyword(s):  
Metal Ions ◽  
Self Assembly ◽  
Metal Ion ◽  
Sol Gel ◽  
Modified Silica ◽  
Organically Modified ◽  
The Matrix ◽  
Ligand Interactions ◽  
Organically Modified Silica ◽  
Metal Oxo Clusters

AbstractThe use of an organically modified silica sol-gel matrix containing ligating groups that assist in the formation of metal-oxo clusters is described. The metal-ligand interactions can be tuned by change in external environment such that: a) under overload metal ion concentrations, the sol-gel matrix sequesters the metal ions to promote the growth of 4-7 nm size metal-oxo clusters within the porous structure of the matrix, b) a change in pH releases the metal ions from the bound metal-oxo clusters, thereby making the sol-gel matrix behave as ferritin analogues. These characteristics of the matrix assisted self-assembly of metal-oxo clusters are shown using UVVis, TEM, AES, and EDX data.

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