3.5 │ Structural and kinetic properties of complexes created by
histone H1 subtypes and interacting protein
In order to determine the types of complexes formed by histone H1
subtypes with interacting partners, the kinetic and structural
parameters of binary interactions were evaluated. They include twelve
proteins indicated in the APID database as displaying physical
association with histone H1 subtypes, also annotated in the BioGRID and
IntAct database (Figure 5). To discriminate a type of formed complexes,
an occurrence of amino acid residues in the contact binding sites and
its location in the secondary structure motifs were analyzed using
BIPSPI and GOR method, respectively. Due to that the contact between
proteins is reflected by increased proportion of differently structured
amino acids 39, the interface residues were grouped
according to the biochemical and structural properties of side chain
into hydrophobic (non-polar - Ala, Ile, Leu, Met, Phe, Pro, Trp, Val),
polar (uncharged - Asn, Cys, Gly, Gln, Ser, Thr, Tyr) and charged (Asp,
Arg, Glu, His, Lys). As it is seen in the Figure 5, in all interfaces of
histone H1 subtypes prevailed are amino acid residues with charged (Arg,
Glu and Lys) and polar (Asn, Gly, Ser and Thr) side chain. Only one
amino acid containing a hydrophobic property is a residue of Ala that
occur at a ratio amounting from 0.11 to 0.25 to the other residues.
Thus, histone H1 subtypes favor the polar and charged interactions,
mostly found in non-obligate 40 and usually transient41 complexes. Because the transient complexes are weak
associated and poorly optimized 2, they might have at
most a few hydrophobic residues which generally predominated in the
obligate interaction. 42 A specificity of H1
interactions is likely determined by large residues of Arg, Glu and Lys
that make a side chain to side chain contact, compared to other
residues, as Ser and Thr, which favor main chain to side chain contact.43 A complement of amino acid residues in the
interfaces of H1-interacting proteins is essentially similar. For
between protein-protein contact responsible are charged and polar
residues, mainly Arg, Glu, Lys, Ser and Thr, which in a 75% of
interactions are the sole residues of the interface. Occasionally, a
residue of hydrophobic Leu and Met supplements an interacting surface.
Such a transient type of histone H1-partner protein interaction inferred
from a character of the interfaces residues was confirmed by
determination of their positioning in the secondary structure elements.
Whereas the regular secondary structures, i.e. α-helix and β-sheets, are
stabilized by hydrogen bonds between backbone atoms in not sequence
specific mode, they are less important in formation the transient
protein-protein interfaces. 44 Compared to them, the
non-regular elements, i.e. coils, loops and turns, are enriched in the
transient interactions and specify this type of protein complex.41,42 However, both helical and non-regular secondary
structures participating in various proportions in the transient
interactions 42 may form the mixed motifs
characteristic of heterodimeric interfaces. 45 The
contact sites of histone H1 subtypes and their partnering proteins are
completely devoid of β-sheets but participation of α-helices is
frequently observed. Although some of the binding sites are more
abundant in the α-helix fraction, the overall number of non-regular
elements is higher. They occur in a 63.9% and 62.26% in the interfaces
of histone H1 subtypes and their interacting proteins, respectively
(Figure 6). In terms of the binding affinity, transient complexes can
display a weak and strong interactions, commonly measured by difference
in their equilibrium dissociation constant (Kd).46 To define a strength of histone H1 subtypes-partner
protein interactions, the binding affinity of emerging complexes was
determined using the ISLAND predictor. The resulted values of
Kd for all complexes stay in the nanomolar range, from
10-8 to 10-7 (Table 7). According to
the categorization of the binding affinities proposed by Veresov47, the complexes created by histone H1 subtypes
should be classified as medium – strong transient, for which
Kd takes a value between 10-8 and
10-6. Thus, histone H1 subtypes together with partner
proteins fall in the transient interactions by forming a medium unstable
complexes. They are capable of temporal association and dissociation in
dependence on the effects caused by specific stabilizers and triggers,
respectively, that determine a characteristic conformational state.48