The influence of dipeptide composition on protein thermostability

In this work, the influence of dipeptide composition on protein thermostability was studied. After comparing the normalized dipeptide composition between mesophilic proteins and (hyper)thermophilic proteins, we concluded that when organism optimal growth temperature increased, for archaeal proteins, the compositions of VK, KI, YK, IK, KV, KY, and EV increased significantly and the compositions of DA, AD, TD, DD, DT, HD, DH, DR, and DG decreased significantly; and for bacterial proteins, the compositions of KE, EE, EK, YE, VK, KV, KK, LK, EI, EV, RK, EF, KY, VE, KI, KG, EY, FK, KF, FE, KR, VY, MK, WK, and WE increased significantly and the compositions of WQ, AA, QA, MQ, AW, QW, QQ, RQ, QH, HQ, AD, AQ, WL, QL, HA, and DA decreased significantly. So these characteristic dipeptides are correlative to protein thermostability. At the same time, the influence of single amino acid composition on protein thermostability was also studied for comparison. We found that the influence of single amino acid composition could be deduced from the influence of dipeptide composition. So we thought that the influence of dipeptide composition on protein thermostability is larger than the influence of amino acid composition. The characteristic dipeptides not only describe the dipeptides that influence protein thermostability significantly but also show the relationship among significant single amino acids that influence protein thermostability. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.