Origin of conformational dynamics in a globular protein.
Abstract
Protein structures are dynamic, undergoing motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual core-residue substitutions in DANCER-3, a streptococcal protein G domain β1 variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how dynamics can appear in a stable globular fold, a critical step in the molecular evolution of dynamics-linked functions.
Submission Details
ID: fXeywkaX4
Submitter: Marc Mayer
Submission Date: May 9, 2020, 11:10 a.m.
Version: 2
Publication Details
Damry AM, Mayer MM, Broom A, Goto NK, Chica RA,Communication Biology (2019) Origin of conformational dynamics in a globular protein. PMID:31799435Additional Information
This is an updated version of study HciYX5Lf3.
Study Summary
Structure view and single mutant data analysis
Study data
| Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
|---|
Data Distribution
Studies with similar sequences (approximate matches)
Correlation with other assays (exact sequence matches)
Relevant PDB Entries
| Structure ID | Release Date | Resolution | Structure Title |
|---|---|---|---|
| 6L9D | 2019-11-08T00:00:00+0000 | 1.73 | X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11S |
| 6L9B | 2019-11-08T00:00:00+0000 | 1.95 | X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A |
| 1MPE | 2002-09-12T00:00:00+0000 | 0 | Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G |
| 1PN5 | 2003-06-12T00:00:00+0000 | 0 | NMR structure of the NALP1 Pyrin domain (PYD) |
| 3MP9 | 2010-04-26T00:00:00+0000 | 1.2 | Structure of Streptococcal protein G B1 domain at pH 3.0 |
| 2IGH | 1992-08-26T00:00:00+0000 | 0 | DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR |
| 2N7J | 2015-09-12T00:00:00+0000 | 0 | Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings |
| 6CNE | 2018-03-08T00:00:00+0000 | 1.2 | Selenomethionine variant (V29SeM) of protein GB1 |
| 2GB1 | 1991-05-15T00:00:00+0000 | 0 | A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G |
| 2K0P | 2008-02-11T00:00:00+0000 | 0 | Determination of a Protein Structure in the Solid State from NMR Chemical Shifts |