Experimental evaluation of topological parameters determining protein-folding rates.


Abstract

Recent work suggests that structural topology plays a key role in determining protein-folding rates and pathways. The refolding rates of small proteins that fold without intermediates are found to correlate with simple structural parameters such as relative contact order, long-range order, or the fraction of short-range contacts. To test and evaluate the role of structural topology experimentally, a set of circular permutants of the ribosomal protein S6 from Thermus thermophilus was analyzed. Despite a wide range of relative contact order, the permuted proteins all fold with similar rates. These results suggest that alternative topological parameters may better describe the role of topology in protein-folding rates. Study holds ProTherm entries: 15452 Extra Details: structural topology; contact order; long-range order; protein-folding rates

Submission Details

ID: WvW6DfPE4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:46 p.m.

Version: 1

Publication Details
Miller EJ;Fischer KF;Marqusee S,Proc. Natl. Acad. Sci. U.S.A. (2002) Experimental evaluation of topological parameters determining protein-folding rates. PMID:12149462
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
1CQN 1999-08-08T00:00:00+0000 2.1 PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC ANALYSIS OF THE PHENOMENON. ENGINEERED VERSION OF THE RIBOSOMAL PROTEIN S6 USED AS A STABLE SCAFFOLD TO STUDY OLIGOMERIZATION.
1LOU 1998-11-25T00:00:00+0000 1.95 RIBOSOMAL PROTEIN S6
1QJH 1999-06-24T00:00:00+0000 2.2 Protein Aggregation and Alzheimer's Disease: Crystallographic Analysis of the Phenomenon. Engineered version of the ribosomal protein S6 used as a stable scaffold to study oligomerization.
1RIS 1994-05-31T00:00:00+0000 2.0 CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMOPHILUS
2BVZ 2005-07-05T00:00:00+0000 2.2 Mutant of the Ribosomal Protein S6
2BXJ 2005-07-26T00:00:00+0000 2.4 Double Mutant of the Ribosomal Protein S6
6C5L 2018-01-16T00:00:00+0000 3.2 Conformation of methylated GGQ in the Peptidyl Transferase Center during translation termination (T. thermophilus)
4KVB 2013-05-22T00:00:00+0000 4.2 Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17
4V4I 2007-02-15T00:00:00+0000 3.71 Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.
4V4J 2007-07-18T00:00:00+0000 3.83 Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 30S ribosomal protein S6 P23370 RS6_THETH
100.0 30S ribosomal protein S6 Q5SLP8 RS6_THET8
100.0 30S ribosomal protein S6 P62666 RS6_THET2