Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate.


Abstract

Protein intermediates in equilibrium with native states may play important roles in protein dynamics but, in cases, can initiate harmful aggregation events. Investigating equilibrium protein intermediates is thus important for understanding protein behaviour (useful or pernicious) but it is hampered by difficulties in gathering structural information. We show here that the phi-analysis techniques developed to investigate transition states of protein folding can be extended to determine low-resolution three-dimensional structures of protein equilibrium intermediates. The analysis proposed is based solely on equilibrium data and is illustrated by determination of the structure of the apoflavodoxin thermal unfolding intermediate. In this conformation, a large part of the protein remains close to natively folded, but a 40 residue region is clearly unfolded. This structure is fully consistent with the NMR data gathered on an apoflavodoxin mutant designed specifically to stabilise the intermediate. The structure shows that the folded region of the intermediate is much larger than the proton slow-exchange core at 25 degrees C. It also reveals that the unfolded region is made of elements whose packing surface is more polar than average. In addition, it constitutes a useful guide to rationally stabilise the native state relative to the intermediate state, a far from trivial task.

Submission Details

ID: iXZDYnHP

Submitter: Shu-Ching Ou

Submission Date: Nov. 22, 2018, 10:41 p.m.

Version: 1

Publication Details
Campos LA;Bueno M;Lopez-Llano J;Jiménez MA;Sancho J,J Mol Biol (2004) Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate. PMID:15504414
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
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
2KQU 2010-06-02 F98N apoflavodoxin from Anabaena PCC 7119
5LJP 2017-08-02 1.1 E20K/I59A/E72K/I92A/D126K/A142V FLAVODOXIN FROM ANABAENA
1OBO 2003-04-24 1.2 W57L flavodoxin from Anabaena
1RCF 1995-01-26 1.4 STRUCTURE OF THE TRIGONAL FORM OF RECOMBINANT OXIDIZED FLAVODOXIN FROM ANABAENA 7120 AT 1.40 ANGSTROMS RESOLUTION
2V5V 2007-10-16 1.88 W57E Flavodoxin from Anabaena
3ESZ 2009-02-10 1.94 K2AK3A Flavodoxin from Anabaena
2V5U 2007-10-16 1.99 I92A FLAVODOXIN FROM ANABAENA
1FLV 1993-10-31 2.0 STRUCTURE OF THE OXIDIZED LONG CHAIN FLAVODOXIN FROM ANABAENA 7120 AT 2 ANGSTROMS RESOLUTION
1FTG 1996-12-23 2.0 STRUCTURE OF APOFLAVODOXIN: CLOSURE OF A TYROSINE/TRYPTOPHAN AROMATIC GATE LEADS TO A COMPACT FOLD
1QHE 1999-05-20 2.0 ENERGETICS OF A HYDROGEN BOND (CHARGED AND NEUTRAL) AND OF A CATION-PI INTERACTION IN APOFLAVODOXIN
1DX9 2000-04-10 2.05 W57A Apoflavodoxin from Anabaena
1OBV 2003-04-24 2.1 Y94F flavodoxin from Anabaena
3ESX 2009-02-10 2.31 E16KE61KD126KD150K Flavodoxin from Anabaena
3ESY 2009-02-10 2.39 E16KE61K Flavodoxin from Anabaena

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Flavodoxin P0A3E0 FLAV_NOSSO
100.0 Flavodoxin P0A3D9 FLAV_NOSS1