Related Experiment Video
Updated: Jul 12, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Protein stability is determined by single-site bias rather than pairwise covariance
Matt Sternke1,2, Katherine W Tripp1, Soumya Prakash Behera1
1T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
None:
The biases revealed in protein sequence alignments have been shown to provide information related to protein structure, stability and function. Recent studies using Potts models show that single-site biases and pair correlations can improve predictions of protein fitness, activity and stability compared to simpler models. Here we use a Potts model to design groups of protein sequences with different amounts of single-site biases and pair correlations and determine the stabilities of sequences from each group. Surprisingly, sequences excluding pair correlations maximize stability compared to sequences that maximize pair correlations, suggesting that pair correlations contribute to other aspects of protein fitness. Consistent with this interpretation, we find that for three enzyme families, activity is greatly increased by maximizing pair correlations. The finding that elimination of covariant residue pairs increases protein stability suggests a route to enhance stability of designed proteins, although this stability may be offset by reduced enzyme activity.
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
RNA Stability
RNA Stability
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Stability of Equilibrium Configuration
A stable equilibrium occurs when a system tends to return to its original position when given a small displacement, and the potential energy is at its minimum. An example of a stable equilibrium is when a cantilever beam is fixed at one end and a weight is attached to the other end. If the weight...

