bar-headed gooes hemoglobin

Sequence, structure and function analysis the bar-headed goose hemoglobin

Hemoglobin is one of the most well studied proteins in the last century. The sequence, structure and function of several vertebrates have been investigated during the past 50 years. More than 200 hundreds of hemoglobin protein sequences have been deposited into the Swiss-Prot database. Three-dimensional structures wild type and mutants from dozens of species have been solved. This provides us a good opportunity to study the relationship among sequence, structure and function of hemoglobins.

Bar-headed goose is a special species of migration birds. They live in the Qinghai lake during summer time and fly to India all way along over the Tibetan plateau in autumn and come back in spring. Interestingly, close relative of bar-headed goose, the graylag goose lives in the low land of Indian all year around and do not migrate. Sequence alignment of bar-headed goose hemoglobin with that of graylag goose shows that there are only 4 substitutions. The Pro 119 in the alpha subunit of graylag goose has been changed to Ala in bar-headed goose. This residue is located in the surface of the alpha/beta interface. In 1983, Perutz proposed that this substitution reduces the contact between the alpha and beta subunit and increases the oxygen affinity, due to the relation of the tension status in the deoxy form (Perutz, 1983). During the past decade, a research group at Peking University has solved the crystal structure of both deoxy and oxy form of bar-headed goose, as well as the oxy form of the graylag goose hemoglobin (Zhang et al. 1996; Liang et al., 2001a; Liang et al., 2001b). We will use this example to learn how to analyze the sequence and structure of hemoglobin molecules.

Exercises

Find literature on bar-headed goose hemoglobin from PubMed.
Find protein sequences of bar-headed goose and graylag goose hemoglobin from Swiss-Prot make sequence alignment to compare the differences between these two molecules.
Find protein sequences which share 90% similarity with bar-headed hemoglobin alpha chain, make multiple sequence alignment and construct a phylogenetic tree for the above protein sequences using the maximum parsimony method.
Retrieve three-dimensional structure oxy (1A4F) and deoxy (1HV4) form of bar-headed goose hemoglobin, compare the difference of the heme molecule with Swiss-PDB Viewer.
Make superimposition for the alpha and beta subunit of bar-headed goose (1A4F) and greylag goose (1FAW) hemoglobin, find out the differences of the substitution site (Pro119-Ala119), measure the contact distance between the side chain of this residues and the side chain of Ile55 of the beta subunit.
Make a summary about the sequence, structure and function of bar-headed goose hemoglobin.
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References:

An Overview of Hemoglobin (revised April 10, 2002)
Shuchismita Dutta and David S. Goodsell, May 2003, Hemoglobin, Molecule of the Month, PDB
Hardison R. Hemoglobins from bacteria to man: evolution of different patterns of gene expression. J Exp Biol. 1998 Apr;201(Pt 8):1099-117.
[Abstract | PDF]
Perutz MF. Species adaptation in a protein molecule. Mol Biol Evol. 1983 Dec;1(1):1-28.
[Abstract | PDF]
Jessen TH, Weber RE, Fermi G, Tame J, Braunitzer G. Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6519-22.
[Abstract | PDF]
Liang Y, Hua Z, Liang X, Xu Q, Lu G. The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity. J Mol Biol. 2001 Oct 12;313(1):123-37.
[Abstract | PDF]
Burmester T, Ebner B, Weich B, Hankeln T. Cytoglobin: A Novel Globin Type Ubiquitously Expressed in Vertebrate Tissues. Mol. Biol. Evol. 2002 Apr; 19(4):416-421.
[Abstract | PDF]
" Zhang J, Hua Z, Tame JR, Lu G, Zhang R, Gu X. The crystal structure of a high oxygen affinity species of haemoglobin. J Mol Biol. 1996 Jan 26;255(3):484-93.
[Abstract]
Xu LM, Analysis of Bar-headed goose hemoglobin. Homework of the ABC course (in Chinese).
[PDF]

The pictures of bar-headed goose and greylag goose were downloaded from several web pages. Thanks to the original authors to make these beautiful pictures available on the Internet.

Applied Bioinformatics Course

Sequence, structure and function analysis the bar-headed goose hemoglobin

Exercises

References: