Metalloproteins: Structural Aspects


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1st Edition

The expression of the detoxification proteins iso-allosterically controlled by a class of heavy metal sensing proteins cease to inhibit expression of the detoxification genes in the presence of the heavy metals. Protein folding is a subject that has attracted the attention of scientists from various disciplines. The protein folding problem can be divided into two categories: the first is the attempt to predict the three dimensional structure of a protein in its native state from a knowledge of the primary sequence and the second would be to understand the relationship between the protein sequence and its mechanism of folding.

De Novo design of proteins is a useful technique for understanding the factors that influence metalloprotein structure and stability. Through much of the 's we designed and characterized a series of -helical coiled coil peptides. The peptide was designed using the repeated heptad approach. This design leads to a pH dependent structure. Protonation of the Glutamate residues at pH values above 7 lead to salt bridges that result in a three helical aggregate. At low pH the system is a two stranded coiled coil.

The hydrophobic residues are arranged in layers. Substitution of Leucine residues in a layer usually with cysteine leads to a soft metal binding site. The orientation of the Cysteine in the core is dependent on the type of site "a" or "d" that has been modified. In all of the studies, the chosen metals do not bind to TRI and only form stable complexes with cysteine substituted peptides.

In many cases the geometrical preference of the peptide and the metal are different. Our interest is to investigate impact on protein structure and folding that results from the interplay between the metal and the peptide geometry ie. Matzapetakis, M. We also study enzymes with an S-adenosylmethionine cofactor linked to a [4Fe-4S] cluster, which catalyze radical-based chemical reactions. Some of these are involved in the post-translational maturation of the metal-containing active sites of the already mentioned gas-processing metalloenzymes, which is crucial for their activity.

Another important focus of our research consists of the study of metalloproteins functioning in FeS cluster biogenesis. More recently, we have become interested in proteins that use the oxygen-sensing function of FeS clusters to regulate gene transcription. Another recent activity is the design of artificial metalloenzymes. The majority of the investigated proteins are very sensitive to oxygen, necessitating their study under anaerobic conditions inside glove boxes.

Manipulations under controlled atmospheres using glove boxes for anaerobic cell growth, protein purification, manual crystallization, automated crystallization, crystal manipulation and automated crystal visualization. The information is distributed under different tabs within the page. By hovering the mouse over the book icons, a sentence of the article supporting the annotation appears in a box Figure 2.

Coordination Sphere tab : each ligand is now associated with a relative solvent accessibility and with a secondary structure element.

Metalloprotein

Sequence tab : this tab was not present in the previous version. It displays the sequence alignment of all the members of the protein superfamily of the query MFS Figure 1. A structural superposition of the putative sites in the apo-structures with the metal-binding pattern to the query MFS can be downloaded. It is also possible to download the alignment of all the sequences. The user can move along the alignment by shifting it right or left to inspect its different regions, or by showing more or less sequences.

A color code highlights the protein residues forming the MFS as well as the position and interactions of the metal-binding residues.

Introduction

It details the modifications of the query MFS with respect to the physiologically relevant site s. The new Information on the site table reports the Physiological relevance of the site highlighted with a red circle. Each physiological site has an associated function that is detailed in a further new table Information on the function s of the site , also highlighted with a red circle When an annotation is based on the literature, it is possible to display the sentence of the article that supports the functional annotation by hovering the mouse on the book icon.

The book icon links to the article entry on PubMed. We have extended the previous version of MetalPDB to provide extensive statistics on its contents, providing both structural and functional information. Several different pages, which can be accessed via the Statistics drop-down menu of the navigation bar, are available: Summary , which lists the number of sites, atoms and PDB structures contained in MetalPDB on a per-metal basis;.

Metals in PDB , which provides an overview of the fractional occurrence of metal-binding structures in different repositories or for different macromolecule types, a histogram of the number of MFS with a given nuclearity number of metal ions per site , and a statistics of the most common coordination geometries observed in MetalPDB;. Per Geometry , which provides statistics per each coordination geometry defined in FindGeo By clicking on the geometry of interest, the user enters a page describing which metals were assigned that geometry in MetalPDB and how many different metal-binding patterns adopted that geometry for each metal;.

Metal domains , which provides an overview of the fractional occurrence of metal-binding domains in domain databases, in total and on a per-metal basis. Per metal , which enables two different kinds of analyses: coordination geometries or metal ligand distributions.

In the Geometries section, MetalPDB reports the occurrence of all regular coordination geometries Figure 3A , the distribution of aminoacidic ligands for each geometry, and the number of different metal-binding patterns observed for the selected metal as a function of the coordination geometry. In the Ligands section, MetalPDB reports the statistics on the presence of aminoacidic or nucleic ligands in the coordination sphere of the selected metal Figure 3B , the distribution of metal to donor atom distances Figure 3C , and data on non-bonded interactions between aminoacidic ligands and other aminoacids of the protein so-called second-sphere interactions ;.

Metals in enzymes , which reports on the presence of metal sites in enzymes as well as on the occurrence of the different metal ions among the six EC classes and on the distribution of the six EC classes among metalloproteins on a per-metal basis note that we include both catalytic and non-catalytic MFSs for any protein that has a EC number associated ;. Metal substitutions in sites , which reports on the distribution of the different metal ions replacing any given metal in all the sites for example showing that the most common replacement for Ni is Zn, whereas for Mg it is Ca ; this statistics is derived from the comparison of equistructural groups.

Example of statistics for zinc coordination spheres in the PDB. A Pie chart displaying the coordination geometries of zinc sites; B histogram reporting the occurrence of residues in the first coordination sphere of zinc ions; C distances between zinc ions and different donor atoms.

NII catalog › Details for: Metalloproteins: structural aspects

All these pages are updated every time the database content is updated to the newest PDB release. Several of the statistics listed above, in particular those involving ligands and metal-binding patterns, address only metalloproteins. The number of structurally characterized metal-binding sites in biological macromolecules is still experiencing a significant growth.

In parallel, we expanded the options available to users for interacting with MetalPDB as well as the amount and complexity of precomputed structural and functional information displayed in the pages of MetalPDB. In the next releases of MetalPDB, we will continue to improve the functional information, also by enabling queries and statistics that target functional aspects directly. An important advancement is the functional annotation of individual MFSs, which is only partial at present.

We gratefully acknowledge the technical help of Enrico Morelli.


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Maria Laura Vieri is thanked for the functional annotation of some copper-binding sites. We thank Dr Serena Lorenzini for an initial version of some of the statistics pages.


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Funding for open access charge: European Commission [H]. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search.

Background

Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents. MetalPDB in a database of metal sites in biological macromolecular structures Valeria Putignano. Sacconi 6, Sesto Fiorentino, Italy. Oxford Academic. Google Scholar. Antonio Rosato. Lucia Banci. Claudia Andreini.

Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects
Metalloproteins: Structural Aspects Metalloproteins: Structural Aspects

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