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Claire Shoemake
Definitions
Protein is used
interchangeably with
receptor
The implication is that
the drug target (receptor)
being considered is
protein in nature
Protein Classification
PDB ID
1.
2.
3.
4.
1.
2.
3.
4.
X-ray Crystallography
http://en.wikipedia.org/wiki/X-ray_crystallography
5.
5.
6.
6.
It is calculated in the same manner as the R value, but from a subset of the data set aside for the calculation of free R,
and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because
it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced
during refinement.
As a rule of thumb, free R should not exceed the R value by more than 0.05; that is, if the R value is 0.20, free R should
not significantly exceed 0.25. Free R values exceeding 0.40 raise serious doubts about the model.
The R Value
The R value is used to assess progress in the refinement of a model from
X-ray crystallographic data, and can be used as one factor in evaluating
the quality of a model. R is a measure of error between the observed
intensities from the diffraction pattern and the predicted intensities that
are calculated from the model. R values of 0.20 or less are taken as
evidence that the model is reliable.
As a rule of thumb, models with R values substantially exceeding
(resolution/10) should be treated with caution. Thus, if the resolution of
a model is 2.5 , that model's R value should not exceed 0.25.
Completely erroneous models (e.g. random models) give R values of 0.40
to 0.60.
However, R values themselves must be treated with caution. Unlike the
Free R, acceptable R values can be achieved despite serious errors in the
model
Kleywegt, GJ, AT Brnger. 1996. Checking your imagination: applications of the free R value. Structure
4:897-904.
The related entries section of the pdb file is valuable since it provides the researcher with
additional information regarding further structural information that may be available
about the protein, or receptor of interest.
In this case, three further depositions, with pdb IDs 1O86 (ACE + lisinopril), 1O8A (the
unbound form of ACE), and 1UZE (ACE + enalaprilat) are available.
It is of interest from a drug design point of view to visualise and compare these depositions
in order to identify whether or not the tertiary structure of the ACE is in any way ligand
dependant
The term heteroatom is used in pdb files to designate all atoms that do not form part of the
protein i.e. all atoms that do not form part of the primary structure of the protein. This part of
the pdb file indicates all the heteroatoms (excluding water molecules) that form part of the
protein (ACE):ligand (captopril) complex.
The areas highlighted in blue are searchable, and lead to windows in which the structures of
the heteroatoms may be found.
In this case the presence of the Zn atom indicates the fact that ACE is a metalloprotease; MCO is
the code given by the authors for captopril. HOH indicates water.
Parts of which are shown above. In this case, the entry shows which amino acids form helix 1 on the ACE.
The temperature factor or B-factor can be thought of as a measure of how much an atom oscillates or vibrates around the position specified in
the model. Atoms at side-chain termini are expected to exhibit more freedom of movement than main-chain atoms, and this movement
amounts to spreading each atom over a small region of space. Occupancy is one of several parameters included in refinement. The occupancy
nj of atom j is a measure of the fraction of molecules in the crystal in which atom j actually occupies the position specified in the model.
If all molecules in the crystal are precisely identical, then occupancies for all atoms are 1.00.
This part of the pdb file shows the last amino acid in the primary amino acid sequence of the protein. Its end is indicated
by the TER entry encircled above.
The pdb file then continues to describe the first in the series of heteroatoms included in this entry- that is of those atoms
which are not part of the protein molecule. The first is NAG or N-acetylglucosamine. As indicated previously, two NAG
molecules were crystallised in this protein:ligand complex.
The coordinates for the metal ion (Zn) and the bound ligand molecule (Captopril) designated, as previously indicated
through a code identifier MCO are indicated above.
For each atom in the chemical component, lists to how many and to which other
atoms that atom is bonded. The list of CONECT records is concluded with an END record.
In this case, the table above lists the amino acids on the ACE
which make contact with captopril. The bond length, the contact
Surface area, and the nature of the bond are also indicated. The
Table above left is a glossary which explains the terms used in
the table above.
Hydrogen bonds play an important role in binding ligands to the ligand binding pocket of a receptor. They are different
from hydrophobic or Van der Waals interactions. These latter are more numerous and are considered to be largely
responsible for ligand stabilisation within a binding pocket. Hydrogen bonds, on the other hand, are associated with
selectivity. This means that a ligand and its cognate receptor recognise each other on the basis of the hydrogen bonds
they are capable of forging between them.
This is very important from a drug design point of view where selectivity is of paramount importance. Pdb files
conveniently list the hydrogen bonds forged between protein and ligand in a separate table in the LPC section of the file.
In the above table, the first section on the extreme left describes the ligand atoms which are involved in hydrogen bond
contacts with the protein amino acid side chains. In the first entry for example, Oxygen atom no1 (in the pdb entry) is
forging a hydrogen bond with the hydroxyl group of tyrosine520 of the ACE. The protein atom section consequently
describes the receptor atoms which forge hydrogen bond contacts with the ligand atoms. This hydrogen bond is 2.7 long
and occupies a total surface area of 19.42
The classification section (Class in the table above) is discussed later on.