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

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
3VM9 2012-09-12 1.05 Dimeric horse myoglobin
4TWV 2016-05-04 1.06 Horse heart myoglobin mutant (K45E/K63E/K96E) with Zn-deuteroporphyrin IX
4TWU 2016-05-04 1.08 Horse heart myoglobin mutant (D44K/D60K/E85K) with Zn-deuteroporphyrin IX
4NS2 2014-12-24 1.18 Crystal structure of Horse heart ferric myoglobin; D44K/D60K/E85K mutant
2V1F 2007-06-12 1.2 Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 8.7
2FRF 2006-05-30 1.2 Horse Heart Myoglobin, Nitrite Adduct, Crystal Soak
5AZR 2016-01-20 1.2 Crystal structure of aqua-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin
2V1I 2007-06-12 1.2 Crystal structure of radiation-induced metmyoglobin - aqua ferrous myoglobin at pH 6.8
3RJ6 2012-05-09 1.23 Crystal Structure of Horse heart ferric myoglobin; K45E/K63E/K96E mutant
2V1K 2007-06-12 1.25 Crystal structure of ferrous deoxymyoglobin at pH 6.8
2FRJ 2006-05-30 1.3 Nitrosyl Horse Heart Myoglobin, Nitrite/Dithionite Method
2V1E 2007-06-12 1.3 Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 6.8
2V1H 2007-06-12 1.3 Crystal structure of radiation-induced metmyoglobin - aqua ferrous myoglobin at pH 5.2
2VLX 2009-02-10 1.3 Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III
3WFT 2014-12-03 1.3 Crystal structure of horse heart myoglobin reconstituted with cobalt(II) tetradehydrocorrin
2FRK 2006-05-30 1.3 Nitrosyl Horse Heart Myoglobin, Nitric Oxide Gas Method
2V1G 2007-06-12 1.35 Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 5.2
1GJN 2002-03-01 1.35 Hydrogen Peroxide Derived Myoglobin Compound II at pH 5.2
3WFU 2014-12-03 1.35 Crystal structure of horse heart myoglobin reconstituted with cobalt(I) tetradehydrocorrin
5AZQ 2016-01-20 1.4 Crystal structure of cyano-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin
1DWT 2000-03-03 1.4 Photorelaxed horse heart MYOGLOBIN CO complex
2V1J 2007-06-12 1.4 Crystal structure of radiation-induced metmyoglobin - aqua ferrous myoglobin at pH 8.7
5ZZE 2019-02-20 1.42 Crystal structure of horse myoglobin crystallized by ammonium sulfate
1DWS 2000-03-03 1.45 PHOTOLYZED CARBONMONOXY MYOGLOBIN (HORSE HEART)
1DWR 2000-03-03 1.45 MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH CO
4DC7 2013-01-23 1.5 Crystal Structure of Myoglobin Exposed to Excessive SONICC Imaging Laser Dose.
4DC8 2013-01-23 1.5 Crystal Structure of Myoglobin Unexposed to Excessive SONICC Imaging Laser Dose.
2VLZ 2008-01-29 1.5 Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III
5YL3 2017-12-27 1.5 Crystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5
3LR9 2010-07-07 1.55 X-ray photogenerated ferrous horse heart myoglobin, nitrite adduct
5YCJ 2018-09-19 1.58 Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) imidazole-ligand
5D5R 2015-09-16 1.6 Horse-heart myoglobin - deoxy state
1NZ3 2003-04-08 1.6 K45E-K63E Variant of Horse Heart Myoglobin
2O5S 2007-10-16 1.6 Cobalt horse heart myoglobin, nitrite modified
2O5O 2007-10-16 1.6 Manganese horse heart myoglobin, nitrite modified
2O5T 2007-10-16 1.6 Cobalt horse heart myoglobin, oxidized
2VLY 2008-01-29 1.6 Crystal structure of myoglobin compound III (radiation-induced)
2FRI 2006-05-30 1.6 Horse Heart Myoglobin, Nitrite Adduct, Co-crystallized
3LR7 2010-07-07 1.6 Ferric horse heart myoglobin, nitrite adduct
2VM0 2008-01-29 1.6 Crystal structure of radiation-induced myoglobin compound II generated after annealing of peroxymyoglobin
2O58 2007-10-16 1.65 Horse heart met manganese myoglobin
2O5M 2007-10-16 1.65 Manganese horse heart myoglobin, azide modified
3V2V 2012-11-21 1.65 Nitrite Bound Chlorin Substituted Myoglobin- Method 1
3V2Z 2012-11-21 1.65 Nitrite Bound Chlorin Substituted Myoglobin- Method 2
1NPG 2003-11-11 1.7 MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITROSOETHANE
1MWC 1998-08-19 1.7 WILD TYPE MYOGLOBIN WITH CO
1XCH 1997-09-17 1.7 MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N)
2O5L 2007-10-16 1.7 Manganese horse heart myoglobin, methanol modified
3VAU 2012-04-11 1.7 Myoglobin nitrite structure: nitriheme modified
1WLA 1998-01-14 1.7 MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE
1RSE 1996-12-23 1.7 MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D)
1NZ5 2003-04-08 1.7 The Horse heart myoglobin variant K45E/K63E complexed with Manganese
1HRM 1995-01-26 1.7 THE PROXIMAL LIGAND VARIANT HIS93TYR OF HORSE HEART MYOGLOBIN
1MYG 1994-01-31 1.75 HIGH RESOLUTION X-RAY STRUCTURES OF PIG METMYOGLOBIN AND TWO CD3 MUTANTS MB(LYS45-> ARG) AND MB(LYS45-> SER)
5CMV 2015-09-16 1.8 Ultrafast dynamics in myoglobin: dark-state, CO-ligated structure
5CNF 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 50 ps time delay
5Z7E 2019-01-30 1.8 Horse Heart Myoglobin Mutant - H93M
5CNG 2015-09-16 1.8 ultrafast dynamics in myoglobin: 150 ps time delay
5CNE 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 10 ps time delay
5CN5 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0 ps time delay
5CN4 2015-09-16 1.8 Ultrafast dynamics in myoglobin: -0.1 ps time delay
1BJE 1998-01-28 1.8 H64T VARIANT OF MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE
1MWD 1998-08-19 1.8 WILD TYPE DEOXY MYOGLOBIN
5CNC 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.6 ps time delay
5CN6 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.1 ps time delay
5CN9 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.4 ps time delay
1NZ4 2003-04-08 1.8 The horse heart myoglobin variant K45E/K63E complexed with Cadmium
5CNB 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.5 ps time delay
5CND 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 3 ps time delay
5CN8 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.3 ps time delay
5CN7 2015-09-16 1.8 Ultrafast dynamics in myoglobin: 0.2 ps time delay
1M6M 1998-08-19 1.8 V68N MET MYOGLOBIN
3BA2 2008-11-11 1.8 Cyanide bound Chlorin substituted Myoglobin
1HSY 1995-02-27 1.9 ORIGIN OF THE PH-DEPENDENT SPECTROSCOPIC PROPERTIES OF PENTACOORDINATE METMYOGLOBIN VARIANTS
1MYH 1994-01-31 1.9 HIGH RESOLUTION X-RAY STRUCTURES OF PIG METMYOGLOBIN AND TWO CD3 MUTANTS MB(LYS45-> ARG) AND MB(LYS45-> SER)
1YMB 1994-01-31 1.9 HIGH RESOLUTION STUDY OF THE THREE-DIMENSIONAL STRUCTURE OF HORSE HEART METMYOGLOBIN
5Z7F 2019-01-30 1.9 Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative
1M6C 1998-08-19 1.9 V68N MYOGLOBIN WITH CO
1NPF 2003-11-11 1.9 MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRIC OXIDE
1MYJ 1994-01-31 1.9 DISTAL POLARITY IN LIGAND BINDING TO MYOGLOBIN: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A THREONINE68(E11) MUTANT
3HEN 2009-12-29 1.9 Ferric Horse Heart Myoglobin; H64V/V67R Mutant
2O5Q 2007-10-16 1.9 Manganese horse heart myoglobin, nitric oxide modified
2NSR 2007-11-06 1.9 Nitromethane Modified Horse Heart Myoglobin
3RJN 2012-05-09 1.9 Horse heart myoglobin: D44K/D60K mutant with zinc (II) -deuteroporphyrin dimethyl ester
1NZ2 2003-04-08 1.9 K45E Variant of Horse Heart Myoglobin
1MNO 1998-08-19 1.95 V68N MYOGLOBIN OXY FORM
3HEP 2009-12-29 1.95 Ferric Horse Heart Myoglobin; H64V Mutant, Nitrite Modified
5YCI 2018-09-19 1.97 Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly)
1MDN 1998-09-30 1.98 WILD TYPE MYOGLOBIN WITH CO
2O5B 2007-10-16 2.0 Manganese horse heart myoglobin, reduced
1YMA 1994-01-31 2.0 STRUCTURAL CHARACTERIZATION OF HEME LIGATION IN THE HIS64-->TYR VARIANT OF MYOGLOBIN
3WYO 2014-11-19 2.0 Heterodimeric myoglobin formed by domain swapping
2NSS 2007-11-06 2.0 Nitrobenzene Modified Horse Heart Myoglobin
1YMC 1994-01-31 2.0 THREE-DIMENSIONAL STRUCTURE OF CYANOMET-SULFMYOGLOBIN C
1MYI 1994-01-31 2.0 HIGH RESOLUTION X-RAY STRUCTURES OF PIG METMYOGLOBIN AND TWO CD3 MUTANTS MB(LYS45-> ARG) AND MB(LYS45-> SER)
3HEO 2009-12-29 2.0 Ferric Horse Heart Myoglobin; H64V/V67R mutant, Nitrite Modified
3HC9 2009-12-29 2.0 Ferric Horse Heart Myoglobin; H64V mutant
1AZI 1998-02-25 2.0 MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE
1MNI 1995-04-20 2.07 ALTERATION OF AXIAL COORDINATION BY PROTEIN ENGINEERING IN MYOGLOBIN. BIS-IMIDAZOLE LIGATION IN THE HIS64-->VAL(SLASH)VAL68-->HIS DOUBLE MUTANT
1YCB 1994-01-31 2.1 DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND CARBONMONOXY FORMS OF A THREONINE68 (E11) MUTANT INVESTIGATED BY X-RAY CRYSTALLOGRAPHY AND INFRARED SPECTROSCOPY
2IN4 2006-10-31 2.15 Crystal Structure of Myoglobin with Charge Neutralized Heme, ZnDMb-dme
3WI8 2014-03-26 2.2 Crystal structure of horse heart myoglobin reconstituted with manganese porphycene
1MNJ 1995-04-20 2.2 INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN
1MNK 1995-04-20 2.2 INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN
1MNH 1995-05-08 2.3 INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN
5YCG 2018-09-19 2.4 Ancestral myoglobin aMbWp of Pakicetus relative
1PMB 1990-01-15 2.5 THE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYOGLOBIN BY MOLECULAR REPLACEMENT AND ITS REFINEMENT
1YCA 1994-01-31 2.9 DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND CARBONMONOXY FORMS OF A THREONINE68 (E11) MUTANT INVESTIGATED BY X-RAY CRYSTALLOGRAPHY AND INFRARED SPECTROSCOPY

Relevant UniProtKB Entries

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