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.