PFDB: A standardized protein folding database with temperature correction

Balachandran Manavalan,Jooyoung Lee,Kunihiro Kuwajima

doi:10.1038/s41598-018-36992-y

Abstract

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.

Highlights

Protein folding is one of the most difficult problems in biophysics and molecular biology
We added new protein data into the protein folding kinetics database (PFDB) from our own collection based on extensive literature search, which resulted in the entry size of 141 globular proteins in our dataset; whose size is the biggest among the currently available protein folding datasets
We developed a new temperature correction method for the proteins whose kinetic folding and unfolding experiments had been carried out at a temperature different from the standard temperature (25 °C)

Summary

Introduction

Protein folding is one of the most difficult problems in biophysics and molecular biology. We added new protein data into the PFDB from our own collection based on extensive literature search, which resulted in the entry size of 141 globular proteins in our dataset; whose size is the biggest among the currently available protein folding datasets.

Results

Conclusion