Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 54

The authors of the ConSurf package assumed that biologically active residues
(including residues responsible for ligand binding) are conservative in character -
thus, their tool searches for such conservative residues and analyzes their ability
to bind ligands.
The FOD method (“fuzzy oil drop”) as described in preceding chapter exploits
observable differences in hydrophobicity as a useful criterion for identification of
binding pockets.
The SuMo package starts with a protein-ligand complex and derives similarity met-
rics to determine which site is most likely responsible for binding the specific ligand.
Although each of these packages applies different methods, results are usually
presented in the form of a ranked list, suggesting the most probable solutions to
each problem. In our analysis we will always focus on the topmost (i.e. highest
ranked) and bottommost (i. e. lowest ranked) solution from each list. The technique
based on “fuzzy oil drop” model identifies only one binding area due to the form of
the criterion used for recognition.

4.2 The Object of Comparative Analysis

4.2.1 Ligands - The Recognition of Their Binding

Cavity in Proteins

For our comparative study we have selected proteins which form complexes with
NAD + and FMN. When choosing ligands we considered their size (preferring large
molecules) as well as the relative differences in stability of protein-ligand com-
plexes. Both selected ligands are classified as nucleotide-like. FMN yields a stable
complex, while NAD + is only transiently associated with the given protein (enzyme)
as its complexation is rather weak (Kamburov et al. 2011 ; Tsai et al. 2009 ) .
Analysis of selected proteins (enzymes) results in a comparative assessment of
the accuracy of various software packages. Moreover, it also enables us to conclude
of the relation between the stability of each protein-ligand complex and its biological
role, as well as the properties of the binding pocket itself.
Flavin mononucleotide (FMN), or ribo fl avin-5 ¢ -phosphate (produced from
riboflavin (vitamin B2) by the enzyme riboflavin kinase) acts as prosthetic group of
various oxidoreductases (including NADH dehydrogenase). In NADH dehydroge-
nase FMN plays the role of electron carrier by being alternately oxidized (FMN)
and reduced (FMNH2). FMN is a stronger oxidizing agent than NAD + due to its
participation in both one- and two-electron transfers. It also acts as a cofactor in
optical receptors sensitive to blue light (Joosten and van Berkel 2007 ) .
NAD + is a dinucleotide consisting of adenosine monophosphate and nicotin-
amide linked by an anhydrous bridge . NAD + binds one proton and two electrons
which act upon the amide moiety of nicotinamide (Pollak et al. 2007 ) . A second
proton is expelled into the reaction environment. Following reduction, NAD +
(NADH) is oxidized by complex I of the respiratory chain. As a result of electron