Next Article in Journal
Specific Magnetic Isolation of E6 HPV16 Modified Magnetizable Particles Coupled with PCR and Electrochemical Detection
Next Article in Special Issue
MT1-MMP Inhibits the Activity of Bst-2 via Their Cytoplasmic Domains Dependent Interaction
Previous Article in Journal
Investigation of Ternary Mixtures Containing 1-Ethyl-3-methylimidazolium Bis(trifluoromethanesulfonyl)azanide, Ethylene Carbonate and Lithium Bis(trifluoromethanesulfonyl)azanide
Previous Article in Special Issue
Copper Homeostasis as a Therapeutic Target in Amyotrophic Lateral Sclerosis with SOD1 Mutations
Article Menu
Issue 5 (May) cover image

Export Article

Open AccessReview
Int. J. Mol. Sci. 2016, 17(5), 671; doi:10.3390/ijms17050671

Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics

1
Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
2
Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Masatoshi Maki
Received: 2 April 2016 / Revised: 18 April 2016 / Accepted: 28 April 2016 / Published: 4 May 2016
(This article belongs to the Special Issue Metalloproteins)
View Full-Text   |   Download PDF [2417 KB, uploaded 4 May 2016]   |  

Abstract

Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity. View Full-Text
Keywords: metalloenzyme; bioinorganic chemistry; structural biology; cytochrome; heme; zinc; iron metalloenzyme; bioinorganic chemistry; structural biology; cytochrome; heme; zinc; iron
Figures

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Rosato, A.; Valasatava, Y.; Andreini, C. Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. Int. J. Mol. Sci. 2016, 17, 671.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top