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The human "magnesome": Detecting magnesium binding sites on human proteins

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Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein covalent structure whether a human chain is or not involved in magnesium binding. This is mainly due to little information on the structural characteristics of magnesium binding sites in proteins and protein complexes. Magnesium binding features, differently from those of other divalent cations such as calcium and zinc, are elusive. Here we address a question that is relevant in protein annotation: how many human proteins can bind Mg2+? Our analysis is performed taking advantage of the recently implemented Bologna Annotation Resource (BAR-PLUS), a non hierarchical clustering method that relies on the pair wise sequence comparison of about 14 millions proteins from over 300.000 species and their grouping into clusters where annotation can safely be inherited after statistical validation. After cluster assignment of the latest version of the human proteome, the total number of human proteins for which we can assign putative Mg binding sites is 3,751. Among these proteins, 2,688 inherit annotation directly from human templates and 1,063 inherit annotation from templates of other organisms. Protein structures are highly conserved inside a given cluster. Transfer of structural properties is possible after alignment of a given sequence with the protein structures that characterise a given cluster as obtained with a Hidden Markov Model (HMM) based procedure. Interestingly a set of 370 human sequences inherit Mg2+ binding sites from templates sharing less than 30% sequence identity with the template. We describe and deliver the "human magnesome", a set of proteins of the human proteome that inherit putative binding of magnesium ions. With our BAR-hMG, 251 clusters including 1,341 magnesium binding protein structures corresponding to 387 sequences are sufficient to annotate some 13,689 residues in 3,751 human sequences as "magnesium binding". Protein structures act therefore as three dimensional seeds for structural and functional annotation of human sequences. The data base collects specifically all the human proteins that can be annotated according to our procedure as "magnesium binding", the corresponding structures and BAR+ clusters from where they derive the annotation (http://bar.biocomp.unibo.it/mg).
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RESEARCH Open Access
The human magnesome: detecting magnesium
binding sites on human proteins
Damiano Piovesan
1
, Giuseppe Profiti
1,2
, Pier Luigi Martelli
1
, Rita Casadio
1,2*
From NETTAB 2011 Workshop on Clinical Bioinformatics
Pavia, Italy. 12-14 October 2011
Abstract
Background: Magnesium research is increasing in molecular medicine due to the relevance of this ion in several
important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein
covalent structure whether a human chain is or not involved in magnesium binding. This is mainly due to little
information on the structural characteristics of magnesium binding sites in proteins and protein complexes. Magnesium
binding features, differently from those of other divalent cations such as calcium and zinc, are elusive. Here we address
a question that is relevant in protein annotation: how many human proteins can bind Mg
2+
? Our analysis is performed
taking advantage of the recently implemented Bologna Annotation Resource (BAR-PLUS), a non hierarchical clustering
method that relies on the pair wise sequence comparison of about 14 millions proteins from over 300.000 species and
their grouping into clusters where annotation can safely be inherited after statistical validation.
Results: After cluster assignment of the latest version of the human proteome, the total number of human
proteins for which we can assign putative Mg binding sites is 3,751. Among these proteins, 2,688 inherit
annotation directly from human templates and 1,063 inherit annotation from templates of other organisms. Protein
structures are highly conserved inside a given cluster. Transfer of structural properties is possible after alignment of
a given sequence with the protein stru ctures that characterise a given cluster as obtained with a Hidden Markov
Model (HMM) based procedure. Interestingly a set of 370 human sequences inherit Mg
2+
binding sites from
templates sharing less than 30% sequence identity with the template.
Conclusion: We describe and deliver the human m agnesome, a set of proteins of the human proteome that
inherit putative binding of magnesium ions. With our BAR-hMG, 251 clusters including 1,341 magnesium binding
protein structures corresponding to 387 sequences are sufficient to annotate some 13,689 residues in 3,751 human
sequences as magnesium binding. Protein structures act therefore as three dimensional seeds for structural and
functional annotation of human sequences. The data base collects specifically all the human proteins that can be
annotated according to our procedure as magnesium binding, the corresponding structures and BAR+ clusters
from where they derive the annotation (http://bar.biocomp.unibo.it/mg).
Background
Magnes ium is the most abundant divalent alkaline ion in
living cel ls and it i s an indispensable element for many
biological processes. Magnesium deficiency in humans is
responsible for many diseases including o steoporosis [1]
or metabolic syndrome (MetS), a combination of different
metabolic diso rders that increase the risk of developing
cardiovascular diseases and diabetes [2]. Magnesium is
characterised by specific chemico-physical properties: it is
redox inert, it has a small ionic radius and is consequently
endowed with a high charge density [3,4]. In cells magne-
sium ions have both structural and functional roles. Mag-
nesium plays a key role in stabilising protein structures,
phosphate groups of membrane lipids and negatively
charged phosphates of nucleic acids. Concomitantly, it is
* Correspondence: casadio@biocomp.unibo.it
1
Biocomputing Group, Department of Biology, University of Bologna,
Bologna, 40126, Italy
Full list of author information is available at the end of the article
Piovesan et al. BMC Bioinformatics 2012, 13(Suppl 14):S10
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© 2012 Piov esan et al.; l icensee BioMed Central Ltd. This is an ope n access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0) , which permits unrestricted use, distribution , and
reproduction in any medium, provided the original work is proper ly cited.
also involved in catalytic roles, such as the activation/inhi-
bition of many enzymes [3,4].
Observations on the structural geometry of Mg
2+
binding sites in proteins known with atomic resolution
may be derived from PROCOGNATE, a cognate ligand
domain mapping for enzymes [5] and from the Protein
Data Bank [PDB, http://www.rcsb.org]. Typical magne-
sium binding sites on proteins show three or fewer
direct binding contacts with c arbonyl oxygen atoms of
the backbone and/or protein side chains, with a ten-
dency to bind water molecules given the octahedral
coordination geometry of the divalent cation [3,6]. It is
known that Mg
2+
binding sites are less specific than
those of other divalent cations such as Zn
2+
and Ca
2+
,
andthatinparticularconditions,Zn
2+
can dislocate
Mg
2+
from its pocket [3,7]. Apparently metal binding
sites on proteins seem to satisfy constraints related to
the physiological availabi lity of the ions [4]. Magnesium
binds weakly to proteins and enzymes (Ka 10
5
M
-1
)[8]
and its binding a ffinity app ears to be d epend ent on its
high cellular concentration. Free Mg
2+
concentration is
higher than that of any other ion (0.5-1mM, [4]). As a
consequence magnesium binding sites are less conserved
through evolution than those of others divalent cations
[4] and their detection is therefore difficult. Mg
2+
bind-
ing s equence motifs have been described to be con-
served in similar RNA and DNA polymerases [9,10].
Three dimensional Mg
2+
binding pockets derived from
70 Mg
2+
binding prote ins solved at atomic resolut ion
were recognised in protein structures by implementing a
structural alphabet [11].
In this work we describe how to assign putative Mg
2+
binding sites to human proteins that lack structural infor-
mation and also to pro teins that share less than 30%
sequence identity w ith any a vailable Mg
2+
binding pro-
tein template. This is possible within o ur BAR-PLUS
annotation resource (BAR+), a non hierarchical cluster-
ing method that has been recently described and relies
on the pair wise sequence comparison of about 14 mil-
lions proteins, including 998 complete proteomes of dif-
ferent species and Homo sapiens [12,13]. This paper to
our kno wledge describes the first large scale investigation
of magnes ium binding sites at the human proteome level.
The results highlight that residu es involved in magne-
sium binding in p rotein structures (derived from the
PDB) falling into the same BAR+ cluster are conserved
and can be transferred to all the human sequences shar-
ing the same cluster on the basis of structure to sequence
alignment with a cluster specific hidden Markov model
(HMM). Magnesium binding sites within a given cluster
are also conserved when pair-wise sequence identity
among the target and the template/s i s less than 30%. A
data base (BAR-hMG) is made available from where for a
given human input sequence the predicted magnesium
binding site/s can be retrieved with the corresponding
structural template/s and the annotating BAR+ cluster.
Methods
The dataset of Mg
2+
binding protein structures
A list of 4,710 magnesium binding protein structures was
retrieved from the Ligand-Expo database [14] by search-
ing MG as Mg
2+
ligand identifier. The Expo databa se is
a data warehouse that integrates databases, services and
tools related to small molecules bound to macromole-
cules and based o n PDB. It allows users to extract ligand
information directly from the P DB, to perform chemical
substructure searches of PDB ligands using a gra phical
interface and also to browse other relevant small mole-
cule resources on the Web. It is updated daily and there-
fore provides the most current information on small
molecules present in the PDB. Its reliability is based on
the reliability of the structures from where information is
derived and ultimately on the resolution of the electron
density map of the molecule. Our set includes PDBs with
an average Resolution (R) factor of 0.23 nm. The list of
magnesium binding residues and corresponding positions
in the sequence for each PDB w as obtained parsing bot h
the LINK and SITE fields on the coordinate files [15].
In order to guarantee that magnesium is part of a biologi-
cally significant PDB structure, we filtered out fragments
and chimeric structures by constraining the coverage of
the template PDB structure to its UniProtKB correspond-
ing sequence (without signal peptide, when present) to be
70%. This bound guarantees a satisfactory overlapping
of the sequence to its structure and this is essential in
building by homology procedures. Applying this criter-
ion, we ended up with 1,341 PDB templates. For each
PDB structure the reference sequence and the corre-
sponding U niProtKB [ 16] accession are obtained from
the Sifts web server [17]. In case of m ultiple PDBs con-
taining different magnesium bindin g site s and referring
to the same sequence, all the sites are mapped into the
protein sequence. Human sequences are collected from
UniProtKB (release 2011_02), including also splicing iso-
forms, for a total of 110,464 sequences. Most of these
sequences are annotated in UniProtKB in an automatic
way and lack any expe rimental evidence. When frag-
ments are filtered o ut, the total number of human
sequences adopted for our analysis is 84,520.
The BAR-PLUS annotation resource
BAR+ is an annotation resource based on the notion that
sequences with high identity value to a counterpart can
inheritfromthisthesamefunction/sandstructure,if
available (http://bar.b iocomp.unibo.it/bar2.0/). The
method has been recently described [13]. Briefly, an
extensive BLAST alignment [18] was performed for some
13,495,736 sequences in a GRID environment [13]. The
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sequence similarity network was built b y connecting two
proteins only if their sequence identity is 40% with an
overlap (Coverage, COV) 90%. 913,762 clusters were
obtained by splitting of the connected components of the
similarity network. Mapping of PDB, Pfam functional
domains (http://pfam.sanger.ac.uk/) and GO terms (Gene
Ontology terms, http://www.geneontology.org/) as listed
in the UniProtKB protein files allows different annotation
types within each cluster. Enrichment of Pfam domains
[http://www.sanger.ac.uk/resources/databases/pfam.html]
and GO terms [http://www.geneontology.org/] for eac h
cluster was statistically validated (by computing a Bonfer-
roni corrected P-value and by selecting its significance
threshold with a bootstrapping procedure) [13]. Only
when P<0.01, terms are transferred from one pr otein to
ano ther one in the same cluster and annotati on is inher-
ited by all the sequences in the cluster. When a sequence
falls into a validated cluster it can inherit in a validated
manner functional and structural annotation (PDB
+/SCOP +/Pfam +/GOterms +/). Stand alone sequences
are called Singletons (30.4% of the total protein universe).
Clusters can contain distantly related proteins that by
this procedure can be annotated with high confidence.
We verified that the magnesium containing 1,341 PDB
structures were in BAR+ clusters and when not present,
we included them in the corresponding cluster. In any
case we verified that backbone structure was conserved
in the same cluster (average Root Mean Square Deviation
(RMSD) was about 2.0±0.2 Å) (for the definition of
RSMD see: http://cnx.org/content/m11608/latest/). The
human s equences were then aligned agai nst BAR+ clus-
ters and only those satisfying the BAR+ constraints
(ID40% and COV90%) were retained. Out of the
84,520 human sequences aligned towards BAR+ with the
required criteria, some 61,106 fell into 22,8 58 clusters
and some 2,791 aligned with singletons. The remaining
portion of the human p roteome (alig ned with sequences
contained in BAR+ clusters with lower sequence identity
and coverage th an tho se required for a va lidated transfer
of annotation) is not considered in the present analysis.
In BAR+, each cluster endowed with structure/s is char-
acterised by a computed cluster Hidden Markov Model
(HMM) that is derived from a structure-to-sequence
alignment within the cluster and can be adopted to
model the cluster sequences on the structure template/s
of the cluster [12]. We to ok advantage of the cluster
HMM bo th for structural alignments of the newly intro-
duced PDB structures and for sequence-to-structure
alignment.
Selection of the human magnesome
Out of the above selected 61,106 human sequences, w e
focused on the subset that comprises all the chains
included in 251 clusters endowed with magnesium
containing PDB structures. In our clusters, we deal with
1,341 PDBs. We therefore checked all the PDB files, the
corresponding UniProtKB files and the related literature.
From this effort we were able to verify that for onl y 119
structures (9% of the total) in 21 clusters there is no
published observation supporting so far any functional
or st ructural role of MG. Within the cluste rs, sequences
could also safely inherit validated Pfam functional
domains and GO functional terms (Mol ecular Function,
Biological Process and Cellular Component, http://www.
geneontology.org/).
Binding positions were transferred from the template/s
to the target after pair-wisealignment/sbasedonthe
cluster HMM. 251 clusters contain Mg binding templates
and there from an equivalent number of HMM models
were used to transfer Mg binding position/s to the
human sequences in the clusters. 1 41 clusters contain
827 magnesium b inding protein structures derived from
non human species (25 different Eukaryota, 42 different
bacteria, 9 different Archaea and 1 virus). 110 clusters
contain 514 human templates.
Results and discussion
Finding Magnesium binding sites with BAR+
When a human sequence has a counterpart in BAR+
with sequence identity 40% over at least 90% of the
alignment length, it falls into the same cluster of the
similar chain. In t he example of Figure 1, when human
sequence P09936 is aligned towards the BAR+ data base,
the result web page identifies cluster #4791 that com-
prises 213 sequences from Eukaryotes with an average
length of 232 residues (Standard D eviation (SD)=4.8%)
and 3 P DB structures with magnes ium and chloride ions
as ligands (1CMX_A from Saccharomyces cerivisiae;
2ETL_A and 1XD3_A from Homo sapiens). The three
templates are however highly similar (the average root
mean square deviation is 1.62+/-0.35Å). Here we focus
only on magnesium bi nding site s and for clarity we show
only the structure of the human Ubiquitin hydrolase
UCH-L3(1XD3_A).Asshown,thestructurecontains3
Mg ions. The Site field of the corresponding PDB file
indicates that of the three Magnesium ions one is coordi-
nated only by water molecules and it is not considered in
our analysis. The remaining two are coordinated by four
and two residues, respectively (the remaining coordina-
tion sites are probably occupied by water). With the clus-
ter HMM based alignment only the coordination sites
including residues of the template/s are transferred to
the human sequences falling into the cluster. From the
cluster, the human sequence inherited all the validated
features that are reported in the corresponding web page:
validated GO terms, the SCOP classification, and the
Pfam domain PF01088 (Ubiquitin carboxyl-termin al
hydrolase, family 1) . BAR+ g ives the HMM based target/
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Figure 1 A BAR+ cluster with a magnesium binding template. The BAR+ output. When the query is the U niProtKB accession code P15374,
the corresponding annotation cluster comprises 213 sequences from Eukaryotes with an average length of 232 residues and 3 PDB structures.
Only one of them (human Ubiquitin hydrolase UCH-L3, PDB:1XD3_A) is shown using PyMol (http://www.pymol.org) with the three Mg ions. Of
the three ions (as shown in the inset where the PDB SITE fields are reported) only two are coordinated by lateral side chains (in red in the
protein structure representation). The cluster contains 26 validated GO terms and 1 validated Pfam term (PF01088, Ubiquitin carboxyl-terminal
hydrolase, family 1) that are also inherited by the human query sequence. See text for details.
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template alignment for computational modelling of the
3D structure of all the other sequences in the cluster.
Among these, 4 are from Homo sapiens and inherit all
the cluster s pecif ic annotation, includ ing the Mg binding
sites.
Bound Mg in this structure i s not as yet supported b y
any experimental observation highlighting a specific
functional role. The whole BAR-hMG data base contains
21 out of 251 clusters with templates binding Mg with-
out any experimental (still) determined functional or
structural role. This information can be retrieved for
each template f rom the correspon ding PDB and Uni-
ProtKB files and the quoted literature therein. It should
be considered that Mg ions may play a role on protein
stability still not fully described or even a role in pro-
tein-protein interaction that is at the basis of many rele-
vant biological processes. In many instances the
formation of protein complexes ha s not yet been recog-
nized due to its transient characteristics. Therefore the
question is still open and we therefore included also
these cases in our data set f or a comprehensive analysis
of putative Mg binding sites. Clusters containing tem-
plates where Mg has a documented structural and func-
tional role are labelled with a yellow star, and a yellow
star and the corresponding EC number, respectively. For
this reason no label is present in the figure.
Annotation of Mg
2+
binding sites in human proteins
A structural analysis of the magnesium containing 1,341
PDB templates indicates that the ion can be present in
different ways. For this reason we list our annotation
results considering that the ion co-crystallises w ith the
protein chain either alone (Mg) or concomitantly with
other ions (Mg and Ions) or ligands (Mg and Ligands)
or with other ion s and ligands (MG, Ions and Ligands) .
In some instances PDB structures can combine two or
more of the binding mod es (Mixed). Results are listed
by splitting human sequences that inherited annotation
from human templates (2,688) from those that inherit
annotation from stru ctures of other organisms (1,063).
TheresultsareshowninTable1and2,respectively,
where the number of sequences with low sequence iden-
tity to the cluster templates is also reported. Clusters are
split depending on the role of bound Mg ion: functional,
structural, not yet determined.
The number of PDB human protein structures with
bound magnesium (514) univocally identifies 172 tem-
plate sequences; within the BAR+ environment this
number reaches 2,688 (Annotation inherited from
human templates). Some other 1,063 human sequences
inherit annotation within BAR+ clust ers where the
structural templates are from other organisms (Table 2)
(Annotation inherited from other organisms).
When more PDB structures fall into the same cluster
(Tabl e 1 and 2) their RMSDs are very low (<1 Å) for all
the groups. This indicates that the BAR+ clusters pre-
serve the structural specificity. Therefore when a target
sequence falls into a cluster characterised by Mg bind-
ing, the corresponding site annotation can be safely
inherited. This is so also for very distantly related
sequences (sequence identity <30%, l ast column) that
are in the same cluster.
In BAR-hMG some 3,751 human se quences are anno-
tated as Mg binding. About 98% of this set is annotated
for the first time. For these sequences the corresponding
UniProtKB entry neither has any information on Mg
binding nor contains any GO term related to Mg
binding.
Characteristics o f Mg
2+
binding sites can be detected
from a simple counting on the retrieved 1,341 PDB
structures contained in the 251 clusters of the BAR-
hMG data b ase. Results (shown in Figure 2) are split
Table 1 Human sequences annotated with human structural templates
Cluster
(#)
PDB
(#)
Cluster RMSD
(Å)
Template
sequence
(#)
Annotated
sequence
(#)
Newly annotated
sequence (#)
Annotated sequence
(ID<30%)*
$^°
Mg 8 1 0 9 - 9 55 54 1
Mg and Ions 7 1 0 9 0.30 8 53 52 6
Mg and Ligands 24 4 2 73 0.77 32 159 158 33
Mg , Ions and
Ligands
22 5 4 57 0.52 31 1948 1947 19
Mixed 22 6 4 366 0.68 92 473 455 120
Total 83 17 10 514 172 2688 2666 179
Human sequences that inherit annotation from human structural templates are listed as a function of the different typologies of magnesium binding in the PDB
files. The table lists the number of clusters, of structural templates, of annotated sequences (sequences that inherit Mg binding positions) according to our
procedure, of sequences never annotated before as Mg binding proteins according to UniProtKB and of *sequences annotated when the target/template identity
is below the 30%. Three different types of clusters are identified a nd listed in the first column: $ cluster with structures binding MG with a recognized functional
role and whit an EC number, ^ clusters with structures binding MG with a recognized structural role (without an EC number), ° cluster containing structures (119
out of 1,341) binding MG without recognized physiological role.
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into binding sites stabilised by lateral side chains and by
backbone c arbonyl groups. The highest frequenc y is
observed for Asp and Glu residues. Similar frequency
distribution is obtained when counting is done on the
newly annotated human sequences (Figure 2). Here
binding is referred only to the residue type.
Localising the human Mg
2+
binding sequences
In Table 3 we list the most populated cellular localiza-
tions (Cellular Component of the Gene Ontology) of the
human sequences (the human magnesome) sorted out
according to the different magnesium binding modes.
For each GO term, the number of human sequences is
reported. The selected terms are those that are the most
distant f rom the ontology root in the corresponding
BAR+ cluster of each sequence. Similarly GO terms of
biological process and molecular function can be
obtained for each sequence (data not shown; the data
can be retrieved when a sequence falls into a validated
cluster).
The Human Magnesome database
The Human Magnesome is a dat a b ase of human
sequences generated after annotation with the procedure
here described. The main page allows a sequence search
either with a UniprotKB accession code or the FASTA
format of the s equence. When the sequen ce is present
in the database it is returned with the putative magne-
sium binding sites, the structural templates from where
it inherits magnesium binding and the number of mag-
nesium ions present in the structural templates. Differ-
ent colors are displayed when the binding residues are
identical, similar or different to the template reference/s.
Residue substitution is scored with Blosum62 matrix. In
Figure 3 a typical output is shown. The data base is
available at http://bar.biocomp.unibo.it/mg.
Table 2 Human sequences annotated with structural templates from other organisms
Cluster
(#)
PDB
(#)
Cluster RMSD
(Å)
Template
sequence
(#)
Annotated
sequence
(#)
Newly annotated
sequence (#)
Annotated sequence
(ID<30%)*
$^°
Mg 12 10 0 75 0.73 33 105 105 24
Mg and Ions 5 5 0 160 0.38 10 51 50 22
Mg and Ligands 20 22 3 81 0.86 54 359 352 51
Mg , Ions and
Ligands
12 6 2 66 0.52 23 278 276 28
Mixed 21 17 6 445 0.83 95 270 243 66
Total 70 60 11 827 215 1063 1026 191
Table legend is as in Table 1.
Figure 2 Frequency distribution of Magnesium binding residues in PDB templates and in anno tated human sequenc es. Distribution of
the frequency of residues coordinating magnesium ions in the PDB structures (1,341, blue color: Mg is coordinated by the backbone carbonyl
oxygen, red color: Mg is coordinated by the lateral side chain) and in the putatively annotated human sequences (3,751, yellow color).
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Conclusion
In this work we address the problem of annotating mag-
nesium binding sites in proteins starting from their
sequence. We take advanta ge of an annotation resource
recently introduced (BAR+, [13]), where functional and
structural features derived from PDB structures are
implemented into HMM models that allows sequence to
template alignment even when sequence identity is
below 30%. T his procedure is based on the notion of
cluster, a set of sequences retrieved as connected com-
ponents of a graph where two pro teins are linked
tog ether when they share a sequence identi ty greater or
equal than 40% in at least 90% of the pair wise align-
ment length. By restricting our analysis to clust ers con-
taining human sequences and magnesium binding PDB
structures, we align with the cluster HMMs some 3,751
Table 3 Localising the human magnesium binding sequences
Sequence (#) GO terms (Cellular Component) Sequence (#) GO terms (Cellular Component)
Mg Mg + Ions + Ligands
23 endoplasmic reticulum lumen 1817 cell surface
21 cell body 117 endoplasmic reticulum part
Mg + Ions 92 dendrite cytoplasm
33 site of polarized growth 56 mitochondrial matrix
13 membrane-bounded organelle 48 cell division site
Mg + Ligands 47 ruffle
118 azurophil granule 44 cell septum
37 cytoplasmic mRNA processing body 44 membrane raft
19 cytoplasmic membrane-bounded vesicle 37 endoplasmic reticulum
16 intracellular 24 cell leading edge
15 intracellular membrane-bounded organelle 23 plasma membrane enriched fraction
14 mitochondrion 22 internal side of plasma membrane
11 neuron projection 15 cell cortex
11 cell part 15 intracellular membrane-bounded organelle
For explanation see text.
Figure 3 The Human Magnesome output. A typical output of the human magnesome site (BAR-hMG). The test sequence inherits, after cluster
based HMM alignment to the corresponding templates (listed in the inset), five binding residues (K 21, S 22, T 40, D 63 and T 64). The residues
are color coded depending on the BLOSUM 62 alignment scoring matrix. From the result page is also possible to retrieve the matching BAR+
cluster page and the corresponding UniProtKB page of the target entry. The green color in the output indicates residues identical to the original
template/s. Similar residues are highlighted in yellow. The yellow star indicates that the protein is located in a cluster where Mg binds to PDB
templates (listed) in a documented structural way. Cluster HMM can be downloaded.
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human s equences that fall in the same clusters and
inherit by this the magnesium b inding feature. Some
370 human sequences share an identity to the template
less than 30%.
We theref ore prove feasible that magnesi um binding
sites can be inherited from a given template when t he
sequence falls inside a well annot ated cluster from
where it deri ves also v alidated Pfam functional domain s
and GO functional terms. Presently we can annotate
some 5% of the human genome as inheriting the cap-
ability of binding magnesium ions. All the a nalysed
sequences, their binding sites, and the corresponding
clusters from where they derive annotation are included
in the Human Magnesome data set (BAR-hMG), freely
available at http://bar.biocomp.unibo.it/mg.
Acknowledgements
RC thanks the following grants: PRIN 2009 project 009WXT45Y (Italian
Ministry for University and Research: MIUR), COST BMBS Action TD1101
(European Union RTD Framework Programme), and PON project
PON01_02249 (Italian Ministry for University and Research: MIUR). DP is a
recipient of a PHD fellowship from the Ministry of the Italian University and
Research. GP is a recipient of a research contract from Health Science and
Technologies-ICIR.
This article has been published as part of BMC Bioinformatics Volume 13
Supplement 14, 2012: Selected articles from Research from the Eleventh
International Workshop on Network Tools and Applications in Biology
(NETTAB 2011). The full contents of the supplement are available online at
http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S14
Author details
1
Biocomputing Group, Department of Biology, University of Bologna,
Bologna, 40126, Italy.
2
Health Science and Technologies-ICIR, University of
Bologna, Bologna, 40126, Italy.
Authors contributions
DP carried out all the calculations. GP developed the web site. RC, DP, GP
and PM conceived the study, analyzed the data and wrote the manuscript.
All the authors have read and approved the final manuscript.
Competing interests
The authors declare that they have no competing interests.
Published: 7 September 2012
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doi:10.1186/1471-2105-13-S14-S10
Cite this article as: Piovesan et al .: The human magnesome: detecting
magnesium binding sites on human proteins. BMC Bioinformatics 2012
13(Suppl 14):S10.
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... In support of this, it has been reported that disruption of Mg 2+ -dependent processes occurs with increased Mn 2+ import under conditions of low environmental magnesium (97). Magnesium is fundamental in stabilizing protein, lipid and nucleic acid structures (101) and is involved in many catalytic mechanisms (25). It is the most common metal found in enzymes according to systematic analyses of reported protein structures, appearing in 16% of all enzymes (12,101). ...
... Magnesium is fundamental in stabilizing protein, lipid and nucleic acid structures (101) and is involved in many catalytic mechanisms (25). It is the most common metal found in enzymes according to systematic analyses of reported protein structures, appearing in 16% of all enzymes (12,101). For comparison, manganese is identified as a co-factor in approximately 6% of all enzymes with known structure, while iron is a co-factor in 8% (12,102). ...
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... This docking program has been trained to predict heme coordination, with a selfdocking accuracy of 62% on a small set of complexes (31/50 heme structures that exhibited iron-nitrogen coordination). 68 While zinc is often used to cleave peptide or protein amide bonds and iron is used for its redox properties, magnesium (and manganese) ions are often used by enzymes involved in nucleic acids 69 biochemistry, as well as by human ubiquitin hydrolase 70 and pyruvate carboxylase. 71 Complicating matters, some proteins feature more than one magnesium and/or manganese ion in their catalytic site. ...
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