Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.

Abstract

Artificial sequences of the 153 amino acids have been designed to fit the main-chain framework of the sperm whale myoglobin (Mb) structure based on a knowledge-based 3D-1D compatibility method. The previously designed artificial globin (DG1) folded into a monomeric, compact, highly helical and globular form with overall dimensions similar to those of the target structure, but it lacked structural uniqueness at the side-chain level [Isogai, Y., Ota, M., Fujisawa, T. , Izuno, H., Mukai, M., Nakamura, H., Iizuka, T., and Nishikawa, K. (1999) Biochemistry 38, 7431-7443]. In this study, we redesigned hydrophobic sites of DG1 to improve the structural specificity. Several Leu and Met residues in DG1 were replaced with beta-branched amino acids, Ile and Val, referring to the 3D profile of DG1 to produce three redesigned globins, DG2-4. These residue replacements resulted in no significant changes of their compactness and alpha-helical contents in the absence of denaturant, whereas they significantly affected the dependence of the secondary structure on the concentration of guanidine hydrochloride. The analyses of the denaturation curves revealed higher global stabilities of the designed globins than that of natural apoMb. Among DG1-4, DG3, in which 11 Leu residues of DG1 are replaced with seven Ile and four Val residues, and one Met residue is replaced with Val, displayed the lowest stability but the most cooperative folding-unfolding transition and the most dispersed NMR spectrum with the smallest line width. The present results indicate that the replacements of Leu (Met) with the beta-branched amino acids at appropriate sites reduce the freedom of side-chain conformation and improve the structural specificity at the expense of stability. Study holds ProTherm entries: 7974 Extra Details: hydrophobic; beta-branched amino acids; compactness;,alpha-helical contents; structural specificity

Submission Details

ID: tyqnMEcQ

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:35 p.m.

Version: 1

Publication Details
Isogai Y;Ishii A;Fujisawa T;Ota M;Nishikawa K,Biochemistry (2000) Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties. PMID:10801318
Additional Information

Study Summary

Number of data points 1
Proteins Myoglobin ; Myoglobin
Unique complexes 1
Assays/Quantities/Protocols Experimental Assay: dG_H2O
Libraries Mutations for sequence GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG

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 UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Myoglobin P68083 MYG_EQUBU
100.0 Myoglobin P68082 MYG_HORSE
91.6 Myoglobin P02181 MYG_INIGE
92.2 Myoglobin P02169 MYG_LEPMU
90.9 Myoglobin P02166 MYG_PERPO
90.9 Myoglobin P02189 MYG_PIG
90.8 Myoglobin Q0KIY1 MYG_BALBO
90.8 Myoglobin Q0KIY2 MYG_BALED
90.8 Myoglobin P02177 MYG_ESCRO
90.3 Myoglobin P02183 MYG_MESCA
90.3 Myoglobin Q0KIY0 MYG_MESST
90.3 Myoglobin P02167 MYG_NYCCO
90.3 Myoglobin P02165 MYG_TUPGL
90.9 Myoglobin P11343 MYG_LUTLU
90.3 Myoglobin P02163 MYG_ROUAE
90.1 Myoglobin P02178 MYG_MEGNO