Protein disorder analysis of Histone Octomer complex in Neucleosome

Author Name: *Bejon Kumar Bhowmick
Author Email: bkb4n@virginia.edu

Abstract

Phosphoproteins are found to be enriched in intrinsic sequence disorder (ID), and this enrichment is related with both cellular location and phosphorylation status. The majority of phosphorylation sites are located outside the structural protein motifs but were mostly located in regions of ID. ID proteins are also very important in certain epigenetic and evolutionary studies. However, few ID proteins were recognized in detection process which remained experimentally laborious and cost effective. Also due to the sensitivity to molecular size, condensation or hydrodynamic attraction, detection process through experiments required much trials and errors. Hence proper computational prediction is an aid to narrow down the screening in small sample pool by which wet lab can practice for error less result. Though, this could be a handy approach but majority of the methods provided contradictory results with one another. Thus, we considered consensus approach and verified the accuracy through real experiments. The sample used was Histone as its widely bearing disordered properties and is easy to handle empirically. Others proteins also could be used in this process.

Keywords

Intrinsic disorder, Consensus method, Histone Neucleosome, Protein structure, Protein function, Evolutionary trend.

Introduction

ID proteins exist as dynamic ensembles in which the atom positions and the backbone Ramachandran angles vary significantly over time with no specific equilibrium values and typically involve non-cooperative conformational changes. In reality, it was hard to define ID and there was no bombastic mark of ubiquitously agreement for ID proteins. Moreover, different parts of proteins are probably ordered under different circumstances [1]. Despite the fact that, ID proteins fail to form fixed 3-D structure under physiological conditions; they carry out critically important biological functions [2,3] attest to the growing interest for these proteins. Prediction of such significant protein feature accurately is very important. We have developed a consensus prediction system with regard to standard scale to predict most accurate ID regions. ID is a very common element of protein structure [4]; the strength of ID prediction is correlated with sequence complexity [5]; and eukaryotes evidently have a much larger fraction of proteins with ID than eubacteria or archaeobacteria.
Distinctive amino acid biases in ordered regions, short ID regions, and long ID regions indicate that the sequences are the determinants for these flexibility categories differ from one another [6].
Predicting ID proteins is important because they are thought to carry out various cellular functions even though they have no stable three-dimensional structure. The structure and function of unknown proteins in nature can be inferred by those proteins whose structures have been determined experimentally. By using novel methods, it can accurately predict ID proteins and their functions from a huge amount of structurally-known sequences. [7]. Currently, more than 200 counter examples in which function depends on non folded or incompletely folded regions of protein have been described. It is suggested that the existence of proteins with protein ID calls for a re-assessment of the protein structure-function paradigm [8]. ID protein has the potential to increase significantly the drug discovery rate for new molecule entities [9]. As many as 50% of eukaryotic proteins are likely to contain functionally important long ID regions. Many proteins are wholly ID but still possess numerous biologically important functions. However, the number of experimentally confirmed ID proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there was a crucial need for novel bioinformatics approach that can be used to combine current knowledge of those (few) experimental results to apply on much larger groups of potential proteins [10].
Structural quality of hub proteins enables them to interact with large numbers of diverse targets. One possibility would be to employ binding regions that have the ability to bind multiple, structurally diverse partners. ID can serve as the structural basis for hub protein promiscuity. They can bind to structured hub proteins; can provide flexible linkers between functional domains with the linkers enabling mechanisms that facilitate binding diversity [11].
Unfolded regions have characteristically high net charge and low hydrophobic traits.

Conclusion

ID regions are implicated with various regulations, but a few ID proteins were experimentally done and huge amounts of such proteins are still undone. Computational methods can be novel ways to determine such ID regions rapidly and efficiently. Thereafter, experimental verifications reduce labor and cost intensity. ID proteins are actively crucial for bio functions and cellular locations. Experimental data are insufficient. And, there is no method solely sufficient to predict ID proteins accurately. Thus, our consensus approach takes the benefit to predict ID proteins more accurately and it will help to analyze functions more pertinently. Histone is a group of proteins present in all cells in all life forms. This family is very important for cellular functions and regulations. With that regard, we identified and analyzed all of the ID parts of Histone complex by our efficient prediction system and interpreted their significant molecular relations. We found that ID regions are conserved, included with various functional relations. The above computational approaches eased to analyze ID regions and to navigate significant biological roles. Just because, even singular processes are undertaken to see the process through, but, hopefully it will be applicable in broad spectra.

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