PFDB: A standardized protein folding database with temperature correction

• Published in: Scientific reports Vol. 9; no. 1; p. 1588
• Main Authors: Manavalan, Balachandran, Kuwajima, Kunihiro, Lee, Jooyoung
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07.02.2019; Nature Publishing Group
• Subjects: 119/118; 631/114/129/2044; 631/114/2164; Humanities and Social Sciences; multidisciplinary; Protein folding; Science; Science (multidisciplinary); Temperature; Temperature effects
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-36992-y

We constructed a standardized protein folding kinetics database (PFDB) in which the logarithmic rate constants of all listed proteins are calculated at the standard temperature (25 °C). A temperature correction based on the Eyring–Kramers equation was introduced for proteins whose folding kinetics were originally measured at temperatures other than 25 °C. We verified the temperature correction by comparing the logarithmic rate constants predicted and experimentally observed at 25 °C for 14 different proteins, and the results demonstrated improvement of the quality of the database. PFDB consists of 141 (89 two-state and 52 non-two-state) single-domain globular proteins, which has the largest number among the currently available databases of protein folding kinetics. PFDB is thus intended to be used as a standard for developing and testing future predictive and theoretical studies of protein folding. PFDB can be accessed from the following link: http://lee.kias.re.kr/~bala/PFDB .