Ph at which protein protein interaction occur in vitro
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Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivomethods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Thus, in silico methods which include sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, phylogenetic tree, phylogenetic profile, and gene expression-based approaches were developed. Elucidation of protein interaction networks also contributes greatly to the analysis of signal transduction pathways. Recent developments have also led to the construction of networks having all the protein-protein interactions using computational methods for signaling pathways and protein complex identification in specific diseases.
1. Introduction
Protein-protein interactions (PPIs) handle a wide range of biological processes, including cell-to-cell interactions and metabolic and developmental control [1]. Protein-protein interaction is becoming one of the major objectives of system biology. Noncovalent contacts between the residue side chains are the basis for protein folding, protein assembly, and PPI [2]. These contacts induce a variety of interactions and associations among the proteins. Based on their contrasting structural and functional characteristics, PPIs can be classified in several ways [3]. On the basis of their interaction surface, they may be homo- or heterooligomeric; as judged by their stability, they may be obligate or nonobligate; as measured by their persistence, they may be transient or permanent [4]. A given PPI may be a combination of these three specific pairs. The transient interactions would form signaling pathways while permanent interactions will form a stable protein complex.
Typically proteins hardly act as isolated species while performing their functions in vivo [5]. It has been revealed that over 80% of proteins do not operate alone but in complexes [6]. The substantial analysis of authenticated proteins reveals that the proteins involved in the same cellular processes are repeatedly found to be interacting with each other [7]. The study of PPIs is also important to infer the protein function within the cell. The functionality of unidentified proteins can be predicted on the evidence of their interaction with a protein, whose function is already revealed. The detailed study of PPIs has expedited the modeling of functional pathways to exemplify the molecular mechanisms of cellular processes [4]. Characterizing the interactions of proteins in a given proteome will be phenomenal to figure out the biochemistry of the cell [4]. The result of two or more proteins interacting with a definite functional objective can be established in several ways. The significant properties of PPIs have been marked by Phizicky and Fields [8].
PPIs can
1. Introduction
Protein-protein interactions (PPIs) handle a wide range of biological processes, including cell-to-cell interactions and metabolic and developmental control [1]. Protein-protein interaction is becoming one of the major objectives of system biology. Noncovalent contacts between the residue side chains are the basis for protein folding, protein assembly, and PPI [2]. These contacts induce a variety of interactions and associations among the proteins. Based on their contrasting structural and functional characteristics, PPIs can be classified in several ways [3]. On the basis of their interaction surface, they may be homo- or heterooligomeric; as judged by their stability, they may be obligate or nonobligate; as measured by their persistence, they may be transient or permanent [4]. A given PPI may be a combination of these three specific pairs. The transient interactions would form signaling pathways while permanent interactions will form a stable protein complex.
Typically proteins hardly act as isolated species while performing their functions in vivo [5]. It has been revealed that over 80% of proteins do not operate alone but in complexes [6]. The substantial analysis of authenticated proteins reveals that the proteins involved in the same cellular processes are repeatedly found to be interacting with each other [7]. The study of PPIs is also important to infer the protein function within the cell. The functionality of unidentified proteins can be predicted on the evidence of their interaction with a protein, whose function is already revealed. The detailed study of PPIs has expedited the modeling of functional pathways to exemplify the molecular mechanisms of cellular processes [4]. Characterizing the interactions of proteins in a given proteome will be phenomenal to figure out the biochemistry of the cell [4]. The result of two or more proteins interacting with a definite functional objective can be established in several ways. The significant properties of PPIs have been marked by Phizicky and Fields [8].
PPIs can
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