Biomedical Engineering Reference
In-Depth Information
1.3.5
Proteins Interacting With DNA act as Switches of DNA Effector or Actuator
Function—Understanding Stability and Functional Outcomes of the Complexes by
Examining the DNA Sequence Physical Properties
Through interactions with other molecules, DNA possesses mechanisms that can act
as
switches of effector or actuator function
. For example, DNA has the ability to bind small
molecules. When small planar molecules possess appropriate functional group arrays and
geometries, including multiple fused aromatic rings, they can intercalate into the DNA
helix. In the intercalation process, two planar DNA base pairs stacked on top of one
another in the interior of the double helix move apart from each other as the double helix
unwinds. When separation is sufficient, this allows the planar intercalating molecule to
insert itself and 'stack' with the adjacent planar base pairs at the thermodynamically most
favorable 0.34 nm Van der Waals interaction distance observed for stacked base pairs in
DNA. Investigators have demonstrated that the intercalation process can involve a limited
sequence specificity in certain systems involving more complex ligands. Following inter-
calation, the optical properties of the intercalating ligand are often very different and the
physical properties and intelligent properties of DNA can be changed (161). The same con-
sequences can result from sequence-specific binding for some nonintercalating ligands
that bind within the major and minor grooves of DNA.
Another more biological mechanism leading to a potential
switch of effector or actuator
function
in DNA is the binding of sequence-specific proteins to specific conserved DNA
binding sites. This class of interactions, found in all cells, has evolved as a critical part of
the underlying biological mechanism involved in the transcriptional regulation of specific
genes being copied into mRNA for subsequent protein synthesis. In many instances of
complex genomic regulation in cells, the initial DNA sequence-specific protein(s) binding
their DNA recognition sites are followed by subsequent protein-protein recognition and
binding events. The assembly of regulatory multiprotein complexes upon the initial
DNA-protein complexes brings about a change in the transcriptional status of the regu-
lated gene(s). Given these facts, our understanding of the basis for the energetic stability
of sequence-specific DNA-protein complexes is an important first step in being able to
manipulate the intelligent properties of DNA and its
actuation
or
switching
by proteins.
However, understanding why a specific protein sequence, correctly folded in solution, rec-
ognizes and interacts favorably with a particular DNA sequence is well beyond the abil-
ity of any current theory to provide adequate insights or answers (162). An important
activity on the pathway to this understanding has been the cataloging into databases of
members of the different classes of DNA-protein complexes whose 3-D structures have
been obtained from experimental NMR and x-ray crystallography studies (163). The ulti-
mate goal envisioned for the database is that the study of DNA-protein interaction classes
will facilitate an understanding of the 'universe' of DNA-protein interaction types. In
turn, this understanding will enable the discovery of important structural and energetic
rules underlying these interactions.
One of the insights that has resulted from analysis of these high-resolution structure
databases has been a general recognition of how proteins in sequence-specific DNA-pro-
tein complexes distort their DNA recognition sites. An example of this type of DNA dis-
tortion is shown in Figure 1.48 where an x-ray structure of the bacteriophage cro protein
is presented on the right in the form of a ribbon diagram of its secondary structure. It is
depicted binding to its 14-bp DNA recognition sequence (164). Note that at either end of
the DNA region contacted by the protein dimer, the DNA helix axis bends to the right.
Distortion of DNA binding sites by sequence-specific recognition proteins is a commonly
observed phenomenon (165,166). It has led to the calculation of a DNA physical property
parameter called the protein deformability (PD). The magnitude of any local PD region in
