Conformational strain in the hydrophobic core and its implications for protein folding and design.


Abstract

We have designed de novo 13 divergent spectrin SH3 core sequences to determine their folding properties. Kinetic analysis of the variants with stability similar to that of the wild type protein shows accelerated unfolding and refolding rates compatible with a preferential stabilization of the transition state. This is most likely caused by conformational strain in the native state, as deletion of a methyl group (Ile-->Val) leads to deceleration in unfolding and increased stability (up to 2 kcal x mol(-1)). Several of these Ile-->Val mutants have negative phi(-U) values, indicating that some noncanonical phi(-U) values might result from conformational strain. Thus, producing a stable protein does not necessarily mean that the design process has been entirely successful. Strained interactions could have been introduced, and a reduction in the buried volume could result in a large increase in stability and a reduction in unfolding rates. Study holds ProTherm entries: 15221, 15222, 15223, 15224, 15225, 15226, 15227, 15228, 15229, 15230, 15231, 15232, 15233, 15234, 15235, 15236, 15237, 15238, 15239 Extra Details: kinetic analysis; transition state; methyl group; strained interactions

Submission Details

ID: Q7yXM39L

Submitter: Connie Wang

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

Version: 1

Publication Details
Ventura S;Vega MC;Lacroix E;Angrand I;Spagnolo L;Serrano L,Nat. Struct. Biol. (2002) Conformational strain in the hydrophobic core and its implications for protein folding and design. PMID:12006985
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
3THK 2011-08-19T00:00:00+0000 1.7 Structure of SH3 chimera with a type II ligand linked to the chain C-terminal
2FOT 2006-01-13T00:00:00+0000 2.45 Crystal structure of the complex between calmodulin and alphaII-spectrin
3F31 2008-10-30T00:00:00+0000 2.3 Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain
3FB2 2008-11-18T00:00:00+0000 2.3 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a.
5FW9 2016-02-12T00:00:00+0000 1.55 Human Spectrin SH3 domain D48G, E7Y, K60Y
5FWB 2016-02-12T00:00:00+0000 1.5 Human Spectrin SH3 domain D48G, E7F, K60F
5FWC 2016-02-12T00:00:00+0000 1.4 Human Spectrin SH3 domain D48G, E7A, K60A
6ZEH 2020-06-16T00:00:00+0000 1.3 Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580)
1AEY 1997-03-02T00:00:00+0000 0 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, SOLUTION NMR, 15 STRUCTURES
1AJ3 1997-05-14T00:00:00+0000 0 SOLUTION STRUCTURE OF THE SPECTRIN REPEAT, NMR, 20 STRUCTURES

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Spectrin alpha chain, non-erythrocytic 1 P07751 SPTN1_CHICK
100.0 Spectrin alpha chain, non-erythrocytic 1 Q13813 SPTN1_HUMAN
100.0 Spectrin alpha chain, non-erythrocytic 1 P16546 SPTN1_MOUSE
100.0 Spectrin alpha chain, non-erythrocytic 1 P16086 SPTN1_RAT