The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability.


Abstract

Like most extracellular bacterial proteases, Streptomyces griseus protease B (SGPB) and alpha-lytic protease (alphaLP) are synthesized with covalently attached pro regions necessary for their folding. In this article, we characterize the folding free energy landscape of SGPB and compare it to the folding landscapes of alphaLP and trypsin, a mammalian homolog that folds independently of its zymogen peptide. In contrast to the thermodynamically stable native state of trypsin, SGPB and alphaLP fold to native states that are thermodynamically marginally stable or unstable, respectively. Instead, their apparent stability arises kinetically, from unfolding free energy barriers that are both large and highly cooperative. The unique unfolding transitions of SGPB and alphaLP extend their functional lifetimes under highly degradatory conditions beyond that seen for trypsin; however, the penalty for evolving kinetic stability is remarkably large in that each factor of 2.4-8 in protease resistance is accompanied by a cost of ~10(5) in the spontaneous folding rate and ~5-9 kcal/mole in thermodynamic stability. These penalties have been overcome by the coevolution of increasingly effective pro regions to facilitate folding. Despite these costs, kinetic stability appears to be a potent mechanism for developing native-state properties that maximize protease longevity. Study holds ProTherm entries: 16833, 16834, 16835 Extra Details: Streptomyces griseus protease B; protein folding; pro region; kinetic stability; protein evolution

Submission Details

ID: 2gpAU9C6

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:48 p.m.

Version: 1

Publication Details
Truhlar SM;Cunningham EL;Agard DA,Protein Sci. (2004) The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability. PMID:14718653
Additional Information

Study Summary

Number of data points 3
Proteins Anionic trypsin ; Alpha-lytic protease ; Cationic trypsin ; Streptogrisin-B ; Streptogrisin-B ; Alpha-lytic protease
Unique complexes 3
Assays/Quantities/Protocols Experimental Assay: dG_H2O prot_conc:1.75 microM, ionic:: ; Experimental Assay: dG_H2O prot_conc:2 microM, ionic:calcium chloride: 10 mM
Libraries Mutations for sequence IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN ; Mutations for sequence E:ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALVAYGVSVY/I:PICTNCCAGYKGCNYYSANGAFICEGQSDPKKPKACPLNCDPHIAYSKCPR ; Mutations for sequence A:ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVASGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG/B:ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVASGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG/C:ADQVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIESSPGKLQTT/D:ADQVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIESSPGKLQTT

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
4SGB 1989-09-21T00:00:00+0000 2.1 STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEINASE B AND POLYPEPTIDE CHYMOTRYPSIN INHIBITOR-1 FROM RUSSET BURBANK POTATO TUBERS AT 2.1 ANGSTROMS RESOLUTION
1CSO 1999-08-18T00:00:00+0000 1.9 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-ILE18I IN COMPLEX WITH SGPB
1CT0 1999-08-18T00:00:00+0000 1.8 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-SER18I IN COMPLEX WITH SGPB
1CT2 1999-08-18T00:00:00+0000 1.65 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-THR18I IN COMPLEX WITH SGPB
1CT4 1999-08-18T00:00:00+0000 1.6 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-VAL18I IN COMPLEX WITH SGPB
1DS2 2000-01-06T00:00:00+0000 1.7 CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I
1SGD 1999-03-25T00:00:00+0000 1.8 ASP 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5
1SGE 1999-03-25T00:00:00+0000 1.8 GLU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5
1SGN 1999-03-25T00:00:00+0000 1.8 ASN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B
1SGP 1995-05-26T00:00:00+0000 1.4 ALA 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Anionic trypsin Q29463 TRY2_BOVIN
397.8 A,B,C,D Alpha-lytic protease P00778 PRLA_LYSEN
192.0 A,B Alpha-lytic protease P27459 PRLA_ACHLY
100.0 Cationic trypsin P00760 TRY1_BOVIN
100.0 Streptogrisin-B P00777 PRTB_STRGR
91.3 I Streptogrisin-B P84813 POTM1_SOLTU
92.2 I Streptogrisin-B Q00782 IP2X_SOLTU
96.0 I Streptogrisin-B Q41488 IP25_SOLTU
100.0 I Streptogrisin-B P01080 IP2K_SOLTU