Abstract

Proteins from hyperthermophilic microorganisms possess unique structurefunction properties for surviving high temperatures and for exhibiting optimal activity. In an attempt to understand the structural and energetic factors that are responsible for the thermal stability, molecular dynamics (MD) simulations were performed on Sso7d and Sac7d chromosomal proteins from S. solfataricus and S. acidocaldarius respectively. Consistent with experimental data, the proteins are quite stable at 300 and 360 K, but were found to undergo denaturation at higher temperature. Both proteins exhibit similar hierarchical unfolding pathways, which is explained based on the calculated intramolecular interaction energies. Differential dynamic behaviors of these proteins were examined, and possible roles of enzymatic activity of Sso7d are proposed. Structural, energetic, dynamic and solvation properties that influence the stability of these proteins will be discussed. The importance of hydrophobic interactions on their thermal stability will be presented using calculations on a mutant (F31A in Sso7d). These proteins are also capable of binding to DNA in a nonspecific fashion, and upon binding, melting temperature of the DNA was found to increase by about 40 K. MD simulations were also performed on protein-DNA complexes to investigate the stability of the oligonucleotide. Possible factors that facilitate the stability of these binary complexes in extraordinary thermal conditions will be discussed based on intra- and intermolecular interaction energies, correlated movements between the protein and DNA, solvation properties, and other structural parameters.

Abstract

Computational approaches are being successfully utilized for the design of small molecules that could be potential substrates for various biological targets both in academia and pharmaceutical industry. Over the past two decades or so, various computational techniques have been developed and improvements on the existing methodologies were proposed to accomplish high accuracy/ predictability of molecular properties. Consideration of the flexible nature of proteins in structure based drug design studies has been a bottleneck mainly due to the huge demand of computational and actual time. Hence most of the docking studies consider the biological macromolecules to be rigid and allow only the conformational changes of the small molecules. Similarly, the ligand based drug design approaches tend to focus more on the global minima of the small molecules. This could lead to incorrect model and hence false predictions since this approximation may not be true in cases where the global minima essentially is not the bioactive conformer – the conformer that binds to the target. Recently, advanced methods have been proposed to consider the flexible nature of the molecules. Molecular dynamics (MD) simulations have been shown to be a straightforward means to include the flexibility of both ligands and biomolecular targets. MD simulations are invaluable computational methods that are extensively used for deriving information of the structure, dynamics and energetic properties of various biomolecules including proteins, nucleic acids and lipids. The need for consideration of dynamic nature of the biomolecular targets will be demonstrated and the advantages of MD simulations to overcome this limitation will be discussed. Basic principles of MD simulations will be discussed and an introduction to biomolecular force fields will be given. Illustrated examples of the applications of MD simulations to ligand based and structure based drug design approaches will be presented.