l
PCN: Adjacent Amino Acid Network: the whole adjacent amino
acid network.
l
HSN Hot Spot Network: the nodes are Hot Spots and the links
are between two nodes in different chains (each amino acid
involves in the interfaces). This network models the 4D
structure.
l
IHSN Induced Hot Spot Network: the induced graph of amino
acids involved in the interfaces. The nodes are Hot Spots (subset
N
0 of the N nodes in PCN) and the links of the induced network
are all links between Hot Spot in the PCN network. This network is given by the Hot Spots and all links between them; thus,
the links between hotspots within the same chain are present
while in the HSN they are not.
l
LRN Long Range Network: For each amino acid i in a single
chain, we take all amino acids j on the same chain with distant
position in the sequence of at least 8 amino acids (this is with the
distance on the sequence |i À j| > 7) that are linked in PCN and
thus we add in the network all links in PCN from i to j and the
amino acids i and j such that |i À j| > 7 . For example, if we
consider the chain A and the amino acid in position 10 then we
add in the network the amino acids of the chain A in position
1, 2, and the 18, 19, and so on that are linked with the amino
acid 10 in PCN. This network models the 3D structure of the
protein.
All these networks have many distinct topological properties
and may be involved in some important structural mechanisms of
the proteins.
The Adjacent Amino Acid Network gives information on the
whole structure of the protein and it is based the sub-networks that
control the 2D, 3D, and the 4D structures. Comparing the four
different networks PCN, HSN, IHSN. and LRN aims at investigating the independency of the structural level coded by each of the
sub-network, that is, to what extent the structural levels have their
own topological characteristics.
We are particularly interested in comparing the topological
properties of the interface with the rest of the protein because the
Hot Spot Network is made of only 10% or less of the total amino
acids of the protein, making the interface potentially fragile. Since
protein oligomers are not more susceptible to mutations than
monomeric proteins, it suggests the existence of a mechanism to
increase the interface robustness and protect it from harm. IHSN
can be compared with the Adjacent Amino Acid Network (PCN)
and with the Hot Spot Networks to study how the protein masks
the position of the interface or to investigate the backup of the
interface, respectively [15]. Backups are additional links that make
the interface more robust to mutation and to special perturbation
120
Claire Lesieur and Laurent Vuillon
PCN: Adjacent Amino Acid Network: the whole adjacent amino
acid network.
l
HSN Hot Spot Network: the nodes are Hot Spots and the links
are between two nodes in different chains (each amino acid
involves in the interfaces). This network models the 4D
structure.
l
IHSN Induced Hot Spot Network: the induced graph of amino
acids involved in the interfaces. The nodes are Hot Spots (subset
N
0 of the N nodes in PCN) and the links of the induced network
are all links between Hot Spot in the PCN network. This network is given by the Hot Spots and all links between them; thus,
the links between hotspots within the same chain are present
while in the HSN they are not.
l
LRN Long Range Network: For each amino acid i in a single
chain, we take all amino acids j on the same chain with distant
position in the sequence of at least 8 amino acids (this is with the
distance on the sequence |i À j| > 7) that are linked in PCN and
thus we add in the network all links in PCN from i to j and the
amino acids i and j such that |i À j| > 7 . For example, if we
consider the chain A and the amino acid in position 10 then we
add in the network the amino acids of the chain A in position
1, 2, and the 18, 19, and so on that are linked with the amino
acid 10 in PCN. This network models the 3D structure of the
protein.
All these networks have many distinct topological properties
and may be involved in some important structural mechanisms of
the proteins.
The Adjacent Amino Acid Network gives information on the
whole structure of the protein and it is based the sub-networks that
control the 2D, 3D, and the 4D structures. Comparing the four
different networks PCN, HSN, IHSN. and LRN aims at investigating the independency of the structural level coded by each of the
sub-network, that is, to what extent the structural levels have their
own topological characteristics.
We are particularly interested in comparing the topological
properties of the interface with the rest of the protein because the
Hot Spot Network is made of only 10% or less of the total amino
acids of the protein, making the interface potentially fragile. Since
protein oligomers are not more susceptible to mutations than
monomeric proteins, it suggests the existence of a mechanism to
increase the interface robustness and protect it from harm. IHSN
can be compared with the Adjacent Amino Acid Network (PCN)
and with the Hot Spot Networks to study how the protein masks
the position of the interface or to investigate the backup of the
interface, respectively [15]. Backups are additional links that make
the interface more robust to mutation and to special perturbation
120
Claire Lesieur and Laurent Vuillon