Molecular Recognition of Oligopeptides and Protein Surfaces - Designing Receptors for the Next Generation of Biosensors - page 77

chain. The -sheet, on the other hand, is stabilized by a hydrogen bond network

between two neighboring strands, which are either oriented in the same (parallel
b

b

-sheet). Those parts of the polypep-
tide chain which do not feature any special secondary structure are called random
coil. The folding of the secondary structure elements and the exact spatial position-
ing of each atom of the protein is called its tertiary structure . It can be determined
by X-ray crystal structure analysis or by NMR spectroscopy. If a functional peptide
unit consists of more than one polypeptide strand, the orientation of the different
strands relative to each other is called the quaternary structure .
Due to the structural diversity of proteins it is possible to interact with them in a
manifold of different ways [ 26 ]. While the overwhelming majority of known
enzyme inhibitors are small molecules which competitively bind to the active
center of the target protein (either reversibly or irreversibly) and thus prevent the
binding of the actual substrate, in recent years other ways to influence proteins and
especially enzymes are coming more and more to the fore. These novel approaches
offer great potential for the development of new therapeutic strategies [ 27 ]. Within
this chapter we will focus on selected examples of protein surface recognition by
chemical ligands. Such interactions also allow the biological functions of a given
protein to be influenced [ 28 - 30 ]. For example, protein-protein interactions can be
prevented by a chemical ligand which binds to the area of the protein surface
responsible for its interaction with another protein. Enzymes can be inhibited by
surface binding ligands too if the conformation of the protein is altered upon
binding or if the ligand blocks access of the substrate to the active site (non-
competitive inhibition).

-sheet) or in opposite directions (antiparallel

b

2.1 Anionic Ligands

In recent years more and more multivalent chemical peptide receptors were devel-
oped for the recognition of peptide surfaces. In particular Hamilton has synthesized
and applied various tetravalent ligands for the recognition of protein surfaces
[ 31 - 33 ]. Templates such as porphyrin, calix[4]arene, or rigid aromatic scaffolds
were used to combine linear or cyclic peptidic side chains. Equipped with anionic
side chains such as tetravalent ligands are then able to bind to positively charged
protein surfaces with high affinity. Tetravalent 36 (Fig. 11 ), for example, binds to
Cytochrome c, which features a strongly cationic surface (p I

¼ 10), with a binding

10 6 M 1 .
Hayashida developed the cyclophane-based anionic, trivalent resorcinol-
derivative 37, depicted in Fig. 12 , which is able to form stable complexes with
histones in aqueous solution [ 34 , 35 ]. As determined by changes of the fluorescence
properties of the integrated dansyl-label upon binding, the affinity is as high as
K

constant of K

10 6 M 1 . Acetylated, neutral histones, on the other hand, are not bound by 37,
which clearly stresses the importance of electrostatic interactions for the recogni-
tion of the positively charged histone surface.