docking

1. R.DHANALAKSHMI
MSFBI1504

2. Biomolecular interactions
 All functions of living systems ranging from
primitive bacteria to higher-order organisms,
as well as their interactions with their
environment, are realised through
macromolecular interactions.
 These interactions might be simple or rather
complex with at least one of the partners
being a biological macromolecule, usually a
protein.

3. DIFFERENT TYPES OF
INTERACTION
 The interactions of proteins with other proteins,
small molecules, carbohydrates, lipids or nucleic
acids
 Receptor-ligand interactions
 Antigen-antibody interactions
 Enzymatic interactions, enzyme-inhibitor
interactions

4.  ligand binding such as that of steroid
hormones to their cytoplasmic or nuclear
receptors or the binding of secreted peptide
ligands to transmembrane receptors might
activate a receptor molecule, which induces
a cellular response

5. Reaction kinetics
 protein-ligand interaction include the
concentrations of the partners, the binding
affinity, and the rate constants of association
and dissociation
 Let us consider the following interaction:

6.  The equilibrium association and dissociation
constants describe the extent to which the
reaction is shifted towards the formation of the
products.
 In the case of protein-ligand interactions ,
these characterise the binding affinity between
the components.

7. Protein-ligand interactions
 Reactants by their initials, P and L, and
their protein-ligand complex as PL.

8.  where [P] is the concentration of free ligand
molecules and [PL] is the concentration of
the protein-ligand complex.
 In this simple reaction, the unit of the
dissociation constant is concentration (M,
mol/litre). The lower the dissociation
constant, the stronger the binding

10.  the hydrophobic effect is a complex, noncovalent
interaction in which the hydrophobic part of the
molecule becomes buried from water and thus the
water-accessible a polar surface area of the
macromolecule decreases.
 The interaction is additive; its energy is roughly
proportional to the buried surface area
 The strong binding affinity and high specificity of
protein-ligand interactions result from a high
amount of weak noncovalent interactions. enzyme-
inhibitor complex with a dissociation constant of 10-
13 M.

11. Determination of the binding
constant
 The dissociation constant can be written by
introducing total protein concentration [P]T as
follows,
 where [P], [L] and [PL] are the concentrations of
the free protein, the free ligand and the protein-
ligand complex, respectively, and [P]T is the total
protein concentration

12.  The equation describes a hyperbola. The
saturation curve, as a function of the free
ligand concentration, converges to 1, which
is the asymptote of the hyperbola represents
saturation curves representing
different KD values.
 It is worth noting that the value of KD is
equal to the free ligand concentration
producing 50% saturation.

14.  The dissociation constant can be
determined easily by fitting a hyperbola
to the saturation curve. To obtain the
saturation curve, we need to know the
free (unbound) ligand concentration
 Often, we can experimentally measure
the bound ligand concentration ([PL]),
thus the free ligand concentration can
be calculated from the total ligand
concentration ([L]T) by subtraction

15.  In such a case, the number of molecules in
the complex can be neglected compared to
the total ligand concentration.
 Therefore, the free ligand concentration can
be taken as equal to the total ligand
concentration

16.  Hemoglobin shows high similarity to
myoglobin however, it is a tetramer of four
subunits with oxygen binding ability
 Oxygen binding to hemoglobin is brought
about by a cooperative process. The first
oxygen molecule binds with low affinity, but
induces an allosteric effect, which increases
the binding affinity of further oxygen
molecules and results in a sigmoid-like
saturation curve

17.  The main role of hemoglobin is oxygen
transport in the blood of vertebrates. By
analysing the saturation curves, we can
understand the mechanism of oxygen
transport. In the capillary of the lung, the
partial pressure of oxygen is approximately
100 Hgmm.
 oxygen is released where it is needed, and
this occurs to the necessary extent.

18.  In contrast, myoglobin binds oxygen with
high affinity even at lower partial pressures.
 Its function is probably the storage of
oxygen, as indicated by the fact that it can
be found at high concentrations in striated
muscle tissue, especially in the muscles of
sea mammals that spend long time periods
underwater.

20. Thank you