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The main challenge in using gemcitabine, a nucleoside analogue anti-cancer, includes resistance of some patients to this compound due to the genetic mutations on deoxycytidine kinase (dCK) that are found in a fraction of the human population. Here, we investigated the dynamics behavior and ligand binding properties of the wild type (WT) dCK and its characterized double mutant using a combination of bioinformatics tools and molecular dynamics (MD) simulation studies. Root-mean-square deviation (RMSD) values of the WT and mutant enzyme in complex with both ligands (deoxycytidine/gemcitabine) demonstrated that the WT enzyme forms a more stable complex with gemcitabine, as compared with its natural ligand (deoxycytidine). However, the stability of the double mutant-deoxycytidine complex is greater, when compared with gemcitabine. It was also found that Arg131 as a critical residue can affect the binding pattern of the enzyme to ligands in a manner that the WT enzyme can interact with both ligands, while, the mutant enzyme cannot establish efficient interaction with gemcitabine, and shows high affinity to deoxycytidine. These data together indicate that gemcitabine can interact with the WT enzyme in a competitive manner, while double mutant can be considered as a resistant variant against gemcitabine. The interaction of anti-cancer gemcitabine with deoxycytidine kinase (dCK) was compared with its natural analogue; deoxycytidine. The dynamics behavior of the representative drug-resistant mutant of deoxycytidine kinase (dCK) was investigated in comparison with the wild type enzyme. The results of this study explain the mechanism of resistance of resistant variant against gemcitabine. [ABSTRACT FROM AUTHOR]

In this study we analyzed the sequence and structure of the human DISC1-Ndel1 complex using bioinformatics tools and molecular dynamics simulation studies. Multiple sequence alignment between the homologue protein sequences in primates shows that corresponding positions of residues in Ndel1 are highly conserved, while the DISC1 has variable conservation lines demonstrating its tolerability against various mutations during evolutionary time scale. In comparison with the mouse variant, structural analysis has shown that the evolutionary inserted charged residues in the human DISC1 (E 8 3 7 -R 8 3 8 ) can establish intra-chain electrostatic interactions with the K 8 1 9 -E 8 2 0 dipeptide that may result in more stability of the DISC1 chain. According to MD simulation studies, the compactness for the human variant of the DISC1-Ndel1 is considerably lower than that of the mouse variant. Analysis of structural fluctuation shows that a fragment at the N-terminus side of the human DISC1 has more residual fluctuation. However, the Ndel1 chain of the human variant has globally more flexibility compared with the mouse variant. Considering the identical amino acid sequence of the Ndel1 chains of human and mouse, it concluded that there is a competition between the inter-chain and intra-chain electrostatic interaction in the human DISC1 that directs the complex to weaker inter-chain interactions with the expense of strengthening the intra-chain stabilizing interaction in complex. Human DISC1-Ndel1complex has important neurobiological roles. The interacting fragment of DISC1 shows a degree of variability within primates, and that of Ndel1 is highly conserved. Occurrence of more charged residues in human DISC1 leads to strengthening the intra-chain electrostatics interaction. [ABSTRACT FROM AUTHOR]

We compared the binding properties and dynamics of three experimentally reviewed isoforms of human dihydrofolate reductase (DHFR). The cytoplasmic variants including isoforms1 and 2 (iso1 and iso2) are produced by alternative splicing; while the mitochondrial form is located in the mitochondria. The iso1 as the canonical sequence contains 187 residues, and iso2 differs from the iso1, where it has 1–52 residues missing at the N-terminus of canonical sequence. Here, the structural models of the iso2 and mitochondrial forms were constructed by the MODELLER program using the crystal structure of the iso1 as the template. Bioinformatics analysis on ligand-bearing structures demonstrates that mitochondrial variant forms more stable complex with ligands compared with iso1 and 2, indicating their different binding properties. The root mean square fluctuation (RMSF) data suggest that C-terminus of iso1 contains two representative highly flexible fragments, while iso2 contains a highly flexible fragment at N-terminus end. Interestingly, both ends of mitochondrial variant have a degree of rigidity. Finally, the observation of differences in structural dynamics and binding properties predicts that the simultaneous existence of enzyme isoforms is a way to increase the speed of the enzyme maneuver in response to various environmental conditions. This prediction needs to be tested experimentally. [ABSTRACT FROM AUTHOR]

In order to determine the preference or avoidance of the first and second positions of individual dipeptides for adopting different structural conformations, we randomly select defined structural groups of proteins from protein data bank and statistically analyzed the distribution of all 400 possible dipeptides in different secondary structural elements. Considering different combinations of α-helix (α), β strand (β) and coil (c) including αα, αβ, αc, ββ, βα, βc, cc, cα, cβ conformations, we found that some dipeptides are randomly distributed in these conformations, while others have non-random distribution for a given conformation. Finally, we provide new set of data containing preference and avoidance tendencies that originate from the neighbor effect for each amino acid according to the context of secondary structural element. The output of current work can provide novel data for different fields of structural bioinformatics as well as experiments involving site-directed mutagenesis. [ABSTRACT FROM AUTHOR]