Thermal denaturation and folding rates of single domain proteins: size matters
Mai Suan Li, D. K. Klimov, D. Thirumalai
Abstract
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/TF ~ N-1, where TF is the folding transition temperature and DeltaT is the folding transition width. This finding is consistent with finite size effects expected for the systems undergoing a phase transition from a disordered to an ordered phase. The dependence of the folding rates kF on N for lattice models and the dataset of 57 proteins and peptides shows that kF = kF0 exp(-CNbeta) provides a good fit, if 0 < beta <= 2/3 and C is a constant. We find that kF = kF0 exp(-1.1N0.5) with kF0 =(0.4x10-6 s)-1 can estimate optimal protein folding rates to within an order of magnitude in most cases. By using this fit for a set of proteins with beta-sheet topology we find that kF0 is approximately equal to kU0, the prefactor for unfolding rates. The maximum ratio of kU0/kF0 is 10 for this class of proteins.
Create a lesson
Related papers
SaltyMeta: a curated benchmark and protein language model-informed web tool for salty peptide prediction
Wanchao Chen, Wen Li, Yanan He et al.
Exploring Optimal Parameters for Ligand-Based Virtual Screening in Early Drug Discovery
Temitope Sobodu, Victor Chibuzor Johnson, Ryan Kern et al.
Synthesizing State-of-the-Art Structure Predictions from Soup of Co-folding Models
Hyosoon Jang, Taewon Kim, Sungsoo Ahn
Sequence-Informed Geometric Evaluation of RNA 3D Structures
Andrea Zerio, Yighua Yao, Alessandro Micheli et al.
Multi-ligand simultaneous docking of Carica papaya leaf phytochemicals, Carpaine and Rutin, reveals multi-mechanism inhibition of cancer proteins BCL-2 and WWP1
Merla Sudha, Asmita Saha, Belaguppa Manjunath Ashwin Desai et al.
Predicting directional flexibility in proteins
Vsevolod Viliuga, Leif Seute, Matteo Tadiello et al.