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Molecular Dynamics Simulations of a Hyperthermophilic and a Mesophilic Protein L30e

Molecular dynamics (MD) simulations were used to study the hyperthermophilic ribosomal protein L30e from archaeon Thermococcus celer at 300 and 350 K, and its mesophilic homologue, yeast L30e, at 300 K in explicit solvent for a period of 5.0 ns. Three trajectories obtained from the MD simulations were stable throughout the simulation period, such as total potential energy, radius of gyration, root-mean-square deviation, and secondary structures assignment. At 300 K, T. celer L30e is less flexible than its mesophilic homologue, and this difference becomes more pronounced at 350 K. Salt bridge networks, one triad and one hexad, are present at the surface of T. celer L30e. The ion pairs forming these salt bridges maintain close contact at a higher temperature, suggesting that these networks contribute to the protein’s hyperthermal stability. By contrast, they found no such networks to be present in yeast L30e. For charged residue I in T. celer L30e, the ΔΔGsolvI value and its corresponding ΔECoulI value possess opposite signs. This indicates that for T. celer L30e, a change in the solvation free energy of a charged residue due to increasing temperature is compensated by a change in the residude’s Coulombic interaction energy with the rest of the protein.

Organisms with an optimal growth temperature between 80 and 110 °C are termed hyperthermophiles, while thermophilic organisms grow optimally between 50 and 80 °C.Optimal growth temperatures for mesophilic organisms range from 20 to 50 °C.Proteins isolated from thermophilic or hyperthermophilic organisms remain stable and active at extreme temperatures, while their mesophilic homologues become denatured.Thermophilic or hyperthermophilic proteins and their mesophilic homologues usually share a high degree of similarity in their sequences and three-dimensional (3D) structures. Proteins that are stable at high temperatures have attracted much interest because they have potential industrial applications; thus, it is important to understand how these thermophilic proteins remain stable at elevated temperatures. Such an understanding may help to elucidate critical principles of protein engineering and inform the design of thermostable proteins for industrial applications.

(a) Structure of T. celer L30e from NMR structure (1GO1). (b) Structure of yeast L30e from NMR structure (1CN7). Figures in both (a) and (b) are drawn using the program PyMOL ( The secondary structure elements in both (a) and (b) are also labeled. N and C in both (a) and (b) indicate the amino and carboxy termini, respectively. (c) The amino acid sequences of T. celer L30e and yeast L30e. The sequences were aligned using the CLUSTAL W program ( The residues in T. celer L30e and yeast L30e are numbered according to those reported in NMR structures.

Comparative studies have revealed several prominent feactures often exhibited by thermophilic proteins compared to their mesophilic homologues, including increased hydrogen bonds, salt bridges, fewer thermolabile residues, decreased number and volume of internal cavities, increased hydrophobicity in protein cores, and increased interface stabilization between oligomeric protein subunits.These studies are based on 3D protein structures available in the Protein Data Bank (PDB) or that have been predicted using homology modeling of thermophilic/mesophilic pairs.The structures of proteins, therefore, play an important role in governing their thermostability. It seems that there are no general rules to determine thermostability, and it is apparent that different proteins attain their thermostabity due to different combinations of the above factors.

Radius of gyration (Rg) of the proteins as functions of time calculated according to eq 3 for T. celer L30e at 300 and 350 K and for yeast L30e at 300 K. Labels for T. celer_300 (red) and T. celer_350 (green) denote the curves for T. celer L30e at 300 and 350 K, respectively. Label for Yeast_300 (blue) denotes the curve for yeast L30e at 300 K.

A whole genome analysis of various hyperthermophileshas revealed a large proportion of charged residues to be present in hyperthermophilic proteins. According to comparative studies, many thermophilic proteins have an increased number of salt bridges compared to analogous mesophilic proteins. Furthermore, there are a large number of salt bridges present on the surface of thermophilic proteins, and these salt bridges may participate in a complex interplay at intraprotein, interdomain, and intersubunit interfaces of oligomeric proteins. Thus, temperature dependency of molecular structures and their dynamics may be factors in charged residue interaction. Molecular dynamics simulation at varying temperatures is a useful tool to investigate the dynamic properties of charged residue interactions at the atomic level. Investigations of the structure and property relationships of proteins at the atomic level, which sometimes proves difficult to achieve in experimental studies, are important because thermostable properties are influenced by protein molecular structures.

The trajectory of the root-mean-square deviation (rmsd) values calculated according to eq 5 for T. celer L30e at 300 and 350 K, and for yeast L30e at 300 K.

This study primarily focuses on the hyperthermophilic ribosomal protein L30e from archaeon Thermococcus celer and its mesophilic homologue from the yeast Saccharomyces cerevisiae.In yeast, L30e, formerly known as L32,is a ubiquitous component of a large subunit in the eukaryotic and archaeal ribosomes, though it has no homologue in prokarya. In yeast, L30e binds to a purine-rich internal loop in its pre-mRNA and mRNA, to autoregulate splicing and translation functions, respectively.T. cele L30e is a single domain protein composed of 100 residues,while yeast L30e consists of 104 residues. The most significant difference between the two proteins is in their thermostabilities. The melting temperature of T. celer L30e is ∼94 °C, while that of yeast is 46 °C.T. celer L30e exhibits reversible thermal denaturation, whereas yeast L30e unfolds irreversibly at temperatures greater than 45 °C.The structure of T. celer L30e was determined both by nuclear magnetic resonance (NMR) spectroscopy and by X-ray crystallography, whereas the structure of yeast L30e was only investigated by NMR spectroscopy in both free and pre-mRNA bound forms. Both proteins present an α/β/α sandwich pattern (Figure 1a and b). The topology of T. celer L30e contains four α-helices and one small 310 helix, as indicated by α5 (Figure 1a), and a mixed β-sheet comprising of four β-strands. Yeast L30e contains four α-helices and four β-strands. Although the aligned amino acid sequences of T. celer L30e and yeast L30e show that both proteins share about 30% sequence identity, the structures of these two proteins are very similar, and the root-mean-square deviation (rmsd) of backbone atoms between these two proteins is about 2.0 Å.

  1. Molecular Dynamics Simulations of a Hyperthermophilic and a Mesophilic Protein L30e Kuei-Jen Lee Journal of Chemical Information and Modeling 2012 52 (1), 7-15 DOI: 10.1021/ci200184y


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