Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties

2021 ◽  
Vol 77 (5) ◽  
pp. 690-702
Author(s):  
Pandian Ramesh ◽  
Selvarajan Sigamani Sundaresan ◽  
Nagaraj Shobana ◽  
Thangaraj Vinuchakkaravarthy ◽  
Kandasamy Sivakumar ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Crystal Structure Analysis ◽  
Oxygen Molecule ◽  
Amino Acid Sequences ◽  
Physical Parameters ◽  
Oxygen Binding ◽  
Binding Properties ◽  
Form Analysis ◽  
Inverse Transition

Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1.66 Å (turkey monoclinic structure; TMS) and 1.39 Å (turkey orthorhombic structure; TOS). Comparison of the amino-acid sequences of ostrich and turkey Hb with those from other avian species revealed no difference in the number of charged residues, but variations were observed in the numbers of hydrophobic and polar residues. Amino-acid-composition-based computation of various physical parameters, in particular their lower inverse transition temperatures and higher average hydrophobicities, indicated that the structures of ostrich and turkey Hb are likely to be highly ordered when compared with other avian Hbs. From the crystal structure analysis, the liganded state of ostrich Hb was confirmed by the presence of an oxygen molecule between the Fe atom and the proximal histidine residue in all four heme regions. In turkey Hb (both TMS and TOS), a water molecule was bound instead of an oxygen molecule in all four heme regions, thus confirming that they assumed the aqua-met form. Analysis of tertiary- and quaternary-structural features led to the conclusion that ostrich oxy Hb and turkey aqua-met Hb adopt the R-/RH-state conformation.

scholarly journals 1P165 Ancestral myoglobins : amino acid sequences, syntheses and oxygen-binding properties(5. Heme protein,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

2006 ◽  
Vol 46 (supplement2) ◽  
pp. S188
Author(s):  
Manabu Ishida ◽  
Atsushi Yasuda ◽  
Iori Yamasaki ◽  
Yuta Murakami ◽  
Motonori Ota ◽  
...  
Keyword(s):  
Amino Acid ◽  
Poster Session ◽  
Heme Protein ◽  
Amino Acid Sequences ◽  
Oxygen Binding ◽  
Binding Properties ◽  
Meeting Program

scholarly journals The Possibility of Common Amino Acid Sequences in High-Sulphur Protein Fractions from Wool

1969 ◽  
Vol 22 (5) ◽  
pp. 1197 ◽  
Author(s):  
RL Darskus ◽  
JM Gillespie ◽  
H Lindley
Keyword(s):  
Amino Acid ◽  
High Voltage ◽  
Paper Electrophoresis ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Protein Fractions ◽  
Common Amino Acid ◽  
Amino Acid Compositions ◽  
Merino Wool ◽  
Derivatives Of

S-Carboxymethyl derivatives of the high-sulphur components of reduced Merino wool have been subdivided by chromatography into 17 fractions, the amino acid compositions of which are reported. Tryptic, chymotryptic, and thermolysin digests of each fraction have been studied by high-voltage paper electrophoresis at pH 3�5 and 6�5. The results suggest that the high-sulphur proteins consist of families of proteins probably containing common structural features. Evidence is presented that the heterogeneity of high-sulphur proteins is not artefactual.

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

2011 ◽  
Vol 6 (4) ◽  
pp. 545-557 ◽  
Author(s):  
Malay Choudhury ◽  
Takahiro Oku ◽  
Shoji Yamada ◽  
Masaharu Komatsu ◽  
Keita Kudoh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Structural Features ◽  
Lipid Binding ◽  
Japanese Eel ◽  
Amino Acid Sequences ◽  
Novel Genes ◽  
Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Subunit II (b') and Not Subunit I (b) of Photosynthetic ATP Synthases is Equivalent to Subunit b of the ATP Synthases from Nonphotosynthetic Eubacteria. Evidence for a New Assignment of b-Type F0 Subunits

1997 ◽  
Vol 52 (11-12) ◽  
pp. 789-798 ◽  
Author(s):  
Hans-Jürgen Tiburzy ◽  
Richard J. Berzborn
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Structural Feature ◽  
Atp Synthase ◽  
Primary Structure ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
E Coli ◽  
Subunit B ◽  
Atp Synthases

Abstract Subunit I of chloroplast ATP synthase is reviewed until now to be equivalent to subunit b of Escherichia coli ATP synthase, whereas subunit II is suggested to be an additional subunit in photosynthetic ATP synthases lacking a counterpart in E. coli. After publication of some sequences of subunits II a revision of this assignment is necessary. Based on the analysis of 51 amino acid sequences of b-type subunits concerning similarities in primary structure, iso­electric point and a discovered discontinuous structural feature, our data provide evidence that chloroplast subunit II (subunit b' of photosynthetic eubacteria) and not chloroplast subunit I (subunit b of photosynthetic eubacteria) is the equivalent of subunit b of nonphoto­ synthetic eubacteria, and therefore does have a counterpart in e.g. E. coli. In consequence, structural features essential for function should be looked for on subunit II (b').

Comparison of Naturally Occurring Vitamin K-Dependent Proteins:  Correlation of Amino Acid Sequences and Membrane Binding Properties Suggests a Membrane Contact Site†

Biochemistry ◽  
1997 ◽  
Vol 36 (17) ◽  
pp. 5120-5127 ◽  
Author(s):  
John F. McDonald ◽  
Amit M. Shah ◽  
Ruth A. Schwalbe ◽  
Walter Kisiel ◽  
Björn Dahlbäck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Vitamin K ◽  
Membrane Binding ◽  
Amino Acid Sequences ◽  
Contact Site ◽  
Binding Properties ◽  
Naturally Occurring ◽  
Membrane Contact

scholarly journals Structural analyses of the deduced amino acid sequences of a novel type heme–copper terminal oxidase, cytochrome aco3, from alkalophilic Bacillus YN-2000

2001 ◽  
Vol 47 (12) ◽  
pp. 1075-1081 ◽  
Author(s):  
Kimitoshi Denda ◽  
Akira Oshima ◽  
Yoshihiro Fukumori
Keyword(s):  
Amino Acid ◽  
Cytochrome C ◽  
Basic Amino Acid ◽  
Structural Features ◽  
Thermophilic Bacterium ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Bacterium Bacillus ◽  
Alkalophilic Bacillus

Cytochrome aco3 from a facultatively alkalophilic bacterium, Bacillus YN-2000, was found to be alkaline- and heat-tolerant. To better understand the structural features of Bacillus YN-2000 cytochrome aco3, the gene encoding this enzyme was cloned and sequenced. Nucleotide sequence analyses of the region neighboring the acoI (subunit I) gene revealed that the acoII (subunit II) and acoIII (subunit III) genes were concomitantly clustered upstream and downstream of the acoI gene, respectively, forming an operon with transcriptional polarity. The deduced amino acid sequence of subunit I was highly similar to that of cytochrome caa3 from thermophilic bacterium Bacillus PS3 in which the heme a3 could be replaced with heme o. Furthermore, a marked paucity of basic amino acid residues was found in the cytochrome c-binding subunit II, which might be a result of the adaptation to a highly alkaline external milieu.Key words: cytochrome c oxidase, alkalophile, thermostability, heme o, Bacilli.

From membrane to molecule to the third amino acid from the left with a membrane transport protein

1997 ◽  
Vol 30 (4) ◽  
pp. 333-364 ◽  
Author(s):  
H. RONALD KABACK ◽  
JIANHUA WU
Keyword(s):  
Amino Acid ◽  
Molecular Mechanisms ◽  
Biological Membranes ◽  
Structural Features ◽  
Energy Transduction ◽  
Transport Protein ◽  
Amino Acid Sequences ◽  
Lactose Permease ◽  
Flagellar Motor ◽  
Secondary Transport

The mechanism of energy transduction in biological membranes is a fascinating unsolved problem in biology. It has been recognized for some time that the driving force for a variety of seemingly unrelated phenomena (e.g. secondary active transport, oxidative phosphorylation, rotation of the bacterial flagellar motor) is a bulk-phase, transmembrane electrochemical ion gradient. However, insight into the molecular mechanisms by which free energy stored in such gradients is transduced into work or into chemical energy is just beginning. Nonetheless, gene sequencing and analyses of deduced amino-acid sequences suggest that many biological machines involved in energy transduction, secondary transport proteins in particular (Henderson, 1990; Marger & Saier, 1993), fall into families encompassing proteins from archaea to the mammalian central nervous system, thereby raising the possibility that the members may have common basic structural features and mechanisms. In addition, many of these proteins play important roles in human disease (e.g. diabetes mellitus, glucose/galactose malabsorption, some forms of drug abuse, stroke, antibiotic resistance), as well as the mechanism of action of certain psychotropic drugs.The focus of this review is on recent observations with a specific secondary transport protein, the lactose permease (lac permease) of Escherichia coli, as a representative of a huge number of proteins that catalyse similar reactions in virtually all biological membranes.

Analysis of Interhexameric Contact Regions in Two Dodecameric Hemocyanins at Subdohain Resolution by Combination of Data from Electron Microscopy, X-Ray Diffraction and Amino-Acid Sequence Studies

1990 ◽  
Vol 48 (1) ◽  
pp. 266-267
Author(s):  
Felix de Haas ◽  
Jan F. L. van Breemen ◽  
Martha M. C. Bijlholt ◽  
Ernst F. J. van Bruggen
Keyword(s):  
Amino Acid ◽  
Molecular Assembly ◽  
Oxygen Binding ◽  
X Ray Diffraction ◽  
Biological Macromolecule ◽  
Binding Properties ◽  
X Ray ◽  
Simulation Procedure ◽  
Cancer Pagurus ◽  
The Difference

Hemocyanin is a biological macromolecule which occurs freely dissolved in the hemolymph of certain invertebrates. The function of this copper containing protein is the transport of oxygen through the organism. In fulfilling this task hemocyanin has developed a similar mechanism as hemoglobin in binding oxygen reversibly and cooperatively. The hemocyanin of arthropods consists of one or more hexamers of subunits with a molecular weight of approx. 75 000. Depending on the species 3-15 types of monomeric subunits occur, which differ in amino-acid composition and in their oxygen binding properties. Each type of subunit fulfills a specific role in the architecture of that hemocyanin. In nature arthropodan hemocyanin is found as a one-hexameric, two-hexameric (dodecameric), four-hexameric or eight-hexameric molecular assembly depending on the species. In this work we focus on the difference in organization of the hexamers in the dodecamer of two different species i.e. the tarantula Eurypelma californicum (a chelicerate) and the crab Cancer pagurus (a crustacean). Eurypelma hemocyanin is made from 7 different subunits called a - g, whereas Cancer hemocyanin consists of 3 subunit types termed α, β, and γ .By image analysis of electron micrographs of the two-hexameric half hemocyanin molecules from Eurypelma and the two-hexameric whole hemocyanin molecules from Cancer, computer averaged projections of these dodecamers were obtained as shown in fig. 1. They differ clearly in their interhexameric contacts. To analyse this difference in more detail these projections were used as a reference in a simulation procedure.

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