Alpha-helix stability and the native state of myoglobin.


Abstract

Native proteins fold to form structures that contain secondary-structure regular patterns in the peptide backbone, such as alpha-helix, beta-structure, and turns with high frequency. The role of this secondary structure in stabilizing the native folded state is presently unclear. Alanine substitutions at helical sites in myoglobin show no correlation with the helical propensity of the side chains involved. In an effort to demonstrate a relationship between the effect of a side chain on stabilizing secondary structure and the native structure, we have carried out site-directed changes in the sequence of the helical protein sperm whale myoglobin. Fully buried hydrophobic side chains were exchanged for similar side chains at sites corresponding to midhelical positions in the native state. The results show a positive correlation between the alpha-helix-forming ability of the substituted side chain and the stability of the mutant proteins, when differences between the size of the side chains are taken into account. If, in addition, each type of amino acid substitution is averaged over different sites, the helix propensities of the amino acids account for much of the residual variation. This implies that the stability of the native state of a protein is coupled to that of secondary structural elements in the structure. In magnitude, the net contribution of propensity differences is smaller than hydrophobic effects, but not negligible in terms of the net free energy of unfolding. Study holds ProTherm entries: 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 13271, 13272, 13273, 13274, 13275, 13276, 13277, 13278, 13279, 13280, 13281, 13282, 13283, 13284, 13285, 13286, 13287, 13288, 13289, 13290, 13291, 13292, 13293 Extra Details: hydrophobic effects; alpha-helix stability; myoglobin;,secondary structure; free energies of unfolding

Submission Details

ID: KWAPVSvc3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:14 p.m.

Version: 1

Publication Details
Lin L;Pinker RJ;Kallenbach NR,Biochemistry (1993) Alpha-helix stability and the native state of myoglobin. PMID:8251481
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
6BMG 2017-11-14T00:00:00+0000 1.88 Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
5YCJ 2017-09-07T00:00:00+0000 1.58 Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) imidazole-ligand
5YCI 2017-09-07T00:00:00+0000 1.97 Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly)
1BVD 1994-12-16T00:00:00+0000 1.4 STRUCTURE OF A BILIVERDIN APOMYOGLOBIN COMPLEX (FORM B) AT 98 K
1OFJ 1998-01-30T00:00:00+0000 1.8 RECOMBINANT SPERM WHALE MYOGLOBIN L29H/H64L/D122N MUTANT (WITH INITIATOR MET)
1BVC 1994-12-16T00:00:00+0000 1.5 STRUCTURE OF A BILIVERDIN APOMYOGLOBIN COMPLEX (FORM D) AT 118 K
5UTD 2017-02-14T00:00:00+0000 1.78 Sperm whale myoglobin V68A/I107Y with nitrite
2W6W 2008-12-19T00:00:00+0000 1.99 Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon
1NAZ 2002-11-30T00:00:00+0000 1.04 structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A)
1FCS 1993-04-20T00:00:00+0000 1.6 CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.3 Myoglobin P02180 MYG_BALPH
90.8 Myoglobin P68278 MYG_PHOPH
90.8 Myoglobin P68277 MYG_PHODA
90.8 Myoglobin P68279 MYG_TURTR
90.8 Myoglobin P68276 MYG_DELDE
90.8 Myoglobin Q0KIY7 MYG1_STEAT
91.4 Myoglobin P02173 MYG_ORCOR
90.9 Myoglobin P02179 MYG_BALAC
92.1 Myoglobin P02174 MYG_GLOME
91.4 Myoglobin P02181 MYG_INIGE
91.4 Myoglobin Q0KIY3 MYG_PENEL
92.2 Myoglobin P02178 MYG_MEGNO
92.9 Myoglobin P02177 MYG_ESCRO
92.9 Myoglobin Q0KIY2 MYG_BALED
92.9 Myoglobin Q0KIY1 MYG_BALBO
96.8 Myoglobin P02184 MYG_KOGSI
96.8 Myoglobin Q0KIY5 MYG_KOGBR
100.0 Myoglobin P02185 MYG_PHYMC
90.1 Myoglobin P02182 MYG_ZIPCA
90.1 Myoglobin Q0KIY0 MYG_MESST
90.1 Myoglobin P02183 MYG_MESCA