Introduction
Although, molecular and cell biology have made huge advancement towards
the delivery of powerful methodologies for the discovery and
identification of protein-protein interactions, likewise their
sub-cellular localization, yet structural biology alone is able to give
definite answers regarding interaction mechanisms through the uncovering
of atomistic and high-resolution structures of the underlying complexes
[1]. Determination of the structure of such biomolecular
interactions however can be a costly, laborious and time-consuming
endeavor [2]. The gap increment between the universe of determined
3D structures and that of known sequences is a proof that
high‐throughput structural biology remains a fantasy [3], as the gap
increases the more with the consideration of available number of
biomolecular complex structures [4]. By contrast, computational
structural biology has the potential to generate protein–protein
interaction models of high resolution [5].
Timely and accurate segregation of chromosomes in meiosis and mitosis is
crucial for organismal and cellular viability. Sister chromatids
produced through DNA replication during mitosis maintain strong cohesion
till a bioriented arrangement is formed on the mitotic spindle. The loss
of sister chromatid cohesion during the transition from metaphase to
anaphase allows for a successful separation of the sister chromatids
into daughter cells with genetic identity [6]. The sister chromatid
attachment to microtubules is mediated by the kinetochores. Kinetochores
become established on a part of the centromere (a specialized
chromatin), with the presence of CENP-A (a variant of histone H3) as a
major hallmark [7, 8]. The kinetochores at low resolution assume a
laminar structure appearance, with the ends of each microtubule
connected to its outer plate and a dense centromeric chromatin adjacent
to its inner plate [9]. The outer kinetochore plate serves as a host
for the KMN network (Knl1, Mis12 and Ndc80 complexes); an assembly
consisting of ten protein subunits that act as a microtubule receptor
[10, 11]. The inner kinetochore on the other hand serve as a host
for the CCAN (constitutive centromere–associated network), a complex
consisting of sixteen different centromeric proteins (CENPs), most of
which were identified originally in the vertebrates’ CENP-A interactome
[12, 13].
The sixteen CCAN proteins of vertebrates are grouped into different
sub-complexes including, CENP-LN, CENP-C, CENP-OPQUR, CENP-HIKM and
CENP-TWSX [14, 15]. Orthologs of most of the listed sub-complexes
have been recognized in species like fungi and yeast [16, 17]. As a
nucleosomal canonical H3 substitute, the CENP-A accumulates at the
nucleosome of centromeres [18] for the initiation of the CCAN
assembly through the binding to CENP-C and CENP-LN [19, 20]. Several
studies have also established the crucial role of the CCAN in mediating
the outer kinetochore assembly [21, 22]. CENP-T and CENP-C function
as the outer kinetochore structural platform through a direct
interaction with the NDC80 and MIS12 complexes [23, 24].
Many CCAN components are held in place by a cumbersome protein-protein
interaction network [25, 26]. However, the exact way in which the
CCAN complex is assembled by these interactions is yet to be completely
understood. As a core CCAN subunit, CENP-H (Mcm16/Fta3), CENP-I
(Ctf3/Mis6) and CENP-K (Mcm22/Sim4) assemble into a ternary complex and
are likewise crucial for the kinetochore integrity. Chromosomal
congression is compromised upon the loss of any of these proteins
[27] while their localization to the centromere has also been
revealed to be dependent on each other [28]. CENP-M (another subunit
of the CCAN) through in vitro reconstitution has been shown to
form a stable complex with the CENP-HIK via an interaction with the
CENP-I C-terminus. This interaction is essential for chromosomal
alignment and also for the localization of the CENP-IM to the centromere
[29]. Although low-resolution electron microscopy analyses have
shown the overall CENP-HIKM organization, the specific molecular basis
for the complex assembly remains predominantly uncharacterized [29].
With reference to the existing complex structure of the CENP-HIK from
yeast and fungi, we have predicted in this study the organizational
model of the human CENP-HIKM complex, using extensive computational
approaches. Our result also shows great consistency with experimental
inter-model interaction studies from several published literature.