Motivation: Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms? Results: A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms. Availability: The database of 373 structurally well-aligned protein pairs is available at

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Mechanical unfolding of proteins L and G, which have similar structures, is considered in this work, and the question arises what changes happen in the unfolding pathways under the action of mechanical force. Molecular dynamics simulations with explicit water (134 trajectories) demonstrate that the mechanical unfolding with constant force occurs through at least two pathways in both proteins. These pathways practically coincide for both proteins and under different constant extensional forces (600, 700, 800, 900, and 1050 pN) and at different temperatures (320, 350, and 400 K at F=1050 pN). Go-like modeling of forced unfolding of proteins L and G does not agree with experimental results that protein G is more mechanically resistant than protein L. At the same time, molecular dynamics simulations of forced unfolding of proteins L and G with explicit water demonstrate that protein G is more mechanically resistant than protein L. Our investigation demonstrates that mechanical stable elements are the same for both proteins, namely, the N-terminal beta-hairpin. This result agrees with experimental data on denaturant unfolding for protein L but not for protein G.