In this study, we have shown that in absence of significant conformational variations in the inhibitor-bound wild-type RT and RT with single resistance mutations, the protein contact network analysis of their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect of small local conformational variations

In this study, we have shown that in absence of significant conformational variations in the inhibitor-bound wild-type RT and RT with single resistance mutations, the protein contact network analysis of their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect of small local conformational variations. of significant conformational variations in the inhibitor-bound wild-type RT and RT with solitary resistance mutations, the protein contact network analysis of their static constructions, along with molecular dynamics simulations, can be a useful approach to understand the practical effect of small local conformational variations. The simple network analysis exposes the localized contact changes that lead to global rearrangement in the communication pattern within RT. Furthermore, these conformational changes possess implications on the overall dynamics of RT. Using numerous measures, we display that a solitary resistance mutation can change the network structure and dynamics of RT to behave more like unbound RT, actually in the presence of the inhibitor. This combined coarse-grained contact network and molecular dynamics approach promises to be a useful tool to analyze structure-function studies of proteins that display large functional changes with negligible variations in their overall conformation. Significance Emergence of resistance against antiretroviral medicines targeting human being immunodeficiency disease-1 remains one of the biggest challenges in the treatment of acquired immunodeficiency syndrome. This is complicated by the fact that conformational changes in reverse transcriptase, resulting from binding of medicines and the emergence of resistance mutations, are delicate. Here, we sophisticated and characterize these small conformational changes using an approach based on network analysis and molecular dynamics. We illustrate that these small conformational changes drastically alter the communication paths between different subdomains and perturb the underlying community structure. Importantly, we clearly display reversal of perturbations in network guidelines, community structure, and dynamics due to presence of resistance mutations, as compared with the wild-type reverse transcriptase bound to drug, therefore distinctly delineating the structural basis of drug resistance. Introduction Human being immunodeficiency disease-1 (HIV-1) has been the underlying cause for the devastating pandemic of acquired immunodeficiency syndrome (AIDS). HIV, being a retrovirus, offers RNA as its genome and needs to undergo the process of reverse transcription for replication and integration into the sponsor genome and to create the viral proteins to make copies of itself inside the sponsor cells (1). Reverse transcription is carried out from the enzyme reverse transcriptase (RT), which is a polymerase encoded from the viral gene and atoms of common residues in all the structures is definitely shown. The right line represents the average RMSD total the residues in all constructions. The shaded areas at the top of MLLT3 the storyline correspond to residues belonging to different subdomains. (ball and stick model) certain to RT (package in atoms of common residues in all the crystal constructions were aligned using Biopython (29,30) and residuewise root mean-square deviation (RMSD) determined using the following equation: is the RMSD for the Cof the is the range between the Catoms of each of the structures and the research structure. Protein contact network generation PCN is usually a graph theoretic representation of the three-dimensional structure of a protein in terms of a set of interconnected nodes and edges. The protein structure as decided from X-ray crystallography or NMR is usually converted into a network in which nodes are the Catoms of the amino acid residues, and the edges or links between nodes are defined based on the cutoff distance between two Catoms (25,26,31). For PCN construction, distances between pairs of all Catoms of the protein with N residues are calculated, giving an N X N distance matrix D. From this distance matrix, an adjacency matrix (A) is usually generated based on following criteria: atom and taken as a node. Many questions in protein science require fine-scale networks in which all atoms and side chains are considered (33,34). The PCN construction was carried out using in-house python scripts, which can be made available freely upon request for academic purposes. Network analysis Network parameters provide metrics that summarize the properties of the topology of the network at both local (node) and global (whole-network) levels. Network parameters like degree, betweenness centrality, eigenvector centrality (EVC), and shortest path of the PCNs were calculated using igraph package (35) of R (36), as explained previously (25). Communities were detected in each of the PCNs using the fast-greedy algorithm (37) as implemented in NetworkX (38). Cytoscape 3.7 (39).The NvpK103NRT and NvpY181CRT MD trajectories show three distinct minima, suggesting an increase in the conformational heterogeneity despite the presence of inhibitor in the binding pocket (Fig.?7 em C /em ; Fig.?S9 em A /em ). with single resistance mutations, the protein contact network analysis of LY2801653 dihydrochloride their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect LY2801653 dihydrochloride of small local conformational variations. The simple network analysis exposes the localized contact changes that lead to global rearrangement in the communication pattern within RT. Furthermore, these conformational changes have implications on the overall dynamics of RT. Using numerous measures, we show that a single LY2801653 dihydrochloride resistance mutation can change the network structure and dynamics of RT to behave more like unbound RT, even in the presence of the inhibitor. This combined coarse-grained contact network and molecular dynamics approach promises to be a useful tool to analyze structure-function studies of proteins that show large functional changes with negligible variations in their overall conformation. Significance Emergence of resistance against antiretroviral drugs targeting human immunodeficiency computer virus-1 remains one of the biggest challenges in the treatment of acquired immunodeficiency syndrome. This is complicated by the fact that conformational changes in reverse transcriptase, resulting from binding of drugs and the emergence of resistance mutations, are delicate. Here, we sophisticated and characterize these small conformational changes using an approach based on network analysis and molecular dynamics. We illustrate that these small conformational changes drastically alter the communication paths between different subdomains and perturb the underlying community structure. Importantly, we clearly show reversal of perturbations in network parameters, community structure, and dynamics due to presence of resistance mutations, as compared with the wild-type reverse transcriptase bound to drug, thereby distinctly delineating the structural basis of drug resistance. Introduction Human immunodeficiency computer virus-1 (HIV-1) has been the underlying cause for the devastating pandemic of acquired immunodeficiency syndrome (AIDS). HIV, being a retrovirus, has RNA as its genome and needs to undergo the process of reverse transcription for replication and integration into the host genome and to produce the viral proteins to make copies of itself inside the host cells (1). Reverse transcription is carried out by the enzyme reverse transcriptase (RT), which is a polymerase encoded by the viral gene and atoms of common residues in all the structures is usually shown. The straight line represents the average RMSD over all the residues in all structures. The shaded regions at the top of the plot correspond to residues belonging to different subdomains. (ball and stick model) bound to RT (box in atoms of common residues in all the crystal structures were aligned using Biopython (29,30) and residuewise root mean-square deviation (RMSD) calculated using the following equation: is the RMSD for the Cof the is the distance between the Catoms of each of the structures and the reference structure. Protein contact network generation PCN is usually a graph theoretic representation of the three-dimensional structure of a protein in terms of a set of interconnected nodes and edges. The protein structure as decided from X-ray crystallography or NMR is usually converted into a network in which nodes are the Catoms of the amino acid residues, and the edges or links between nodes are defined based on the cutoff distance between two Catoms (25,26,31). For PCN construction, distances between pairs of all Catoms of the protein with N residues are calculated, giving an LY2801653 dihydrochloride N X N distance matrix D. From this distance matrix, an adjacency matrix (A) is usually generated based on following criteria: atom and taken as a node. Many questions in protein science require fine-scale networks in which all atoms and side chains.