Assignment 2
Part I:
Identification of a disease
1). Thesequence,
PPGEEQRYTYQVEHPGLDQP, was blasted at the NCBI website and a snap of some of hits are shown below(see Figure 1). By exploring some of the top hits, it was found that the wild type protein associated with the signature sequence blasted is the
HFE hemochromatosis protein [1].
Figure 1. Illustration of of some of the hits found by blasting the fingerprint sequence of the mutated protein.
2). The one letter AA code sequence of the full wild type protein in fasta format is shown below (see Figure 2).
>gi|2088551|gb|AAB82083.1| hereditary hemochromatosis [Homo sapiens] MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEP RTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGY DGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQQVPPLV KVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRY TCQVEHPGLDQPLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE
Figure 2. Sequence of the wild type protein with the fingerprint shown in red.
3).
The single mutation (C282Y)between the wild type sequence and the marker given above can be seen below (see Figure 3). The mutation is located in the signature (fingerprint or marker) of sequence.
In addition to the pC282Y mutation, other mutations had been reported. Some of these mutations are pH63D and pS65C [2]
Figure 3. Illustration of the mutation within the fingerprint sequence.
4). Name of the
inherited
disorder is hereditary hemochromatosis.
Hereditary hemochromatosis is a genetically heterogeneous disease of iron metabolism.
The most common form of the disorder is an adult-onset form that has mainly been associated with the HFE pC282Y/pC282Y genotype. The phenotypic expression of this genotype is very heterogeneous and could be modulated by both environmental factors and modifier genes [3].
5).
The information of the PDB structure that shows the normal, wild type protein
of NOT complexed protein is is shown below (see Figure 4). And the cartoon illustration of the same is shown is figure 5 [3].
Figure 4. General information of the HFE (human) Hemochromatosis protein taken from the pdb website.
Figure 5. Cartoon representation of the HFE (human) Hemochromatosis protein. The black arrows indicates where the mutation takes place.
6). The sequence of the wild type HFE protein was align with the sequence of the histo-compatibility complex (MHC) class I-related (see Figure 6). Even though they are similar in many of their amino acids, it is very unlikely that they have the same function since the histo-compatibility complex (MHC) class I-related no longer has the finger print of the sequence
Figure 6. Alignment of the wild type HFE protein and the histo-compatibility complex (MHC) class I-related. The pink area shows the finger print (marker) of the HFE protein.
| Part 2:
browsing the human genome
|
1) The Human Genome was searched using the wild type sequence corresponding to the fragment of protein given above. the location of the corresponding gene projected on a human karyotype is shown in figure 7. A closer vew of the location of teh gene can be seen on figure 8[4].
Figure 7. Location of the corresponding gene projected on a human karyotype that codes for the HFE (human) Hemochromatosis protein.
Figure 8. Location of the ge that code for the HFE (human) Hemochromatosis protein on chromosome 6
| Part III: Understanding sickle cell anemia |
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1). The marker can just be Pro-Glu-Glu and if glu is replaced for val, then the patient has the desease (see Figure 9).
>sp|P68871|HBB_HUMAN Hemoglobin beta chain - Homo sapiens (Human). VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK EFTPPVQAAYQKVVAGVANALAHKYH
Figure 9. Sequence of of hemoglobin. The marker sequence is in red.
2)
The protein associated with this disease (sickle cell anemia) is hemoglobin.
3)In the first eight amino acids in the beta chain of hemoglobin. The sixth position in the normal beta chain has glutamic acid, while sickle beta chain has valine, this is the sole difference between the two. But, since glu has a negative charge and val is neutral, this single amino acid difference (glu => val) has a great effect on the protein.
4).
The Crystal Structure of Human Deoxy- haemoglobin at 1.74 A Resolution.
Source: PDB ID 4HHB and a teh cartoon interpretation can be seen in figure 10.
Each heme serves as a contact site for binding one molecule of oxygen. The two gold spheres near the top of the molecule are phosphate groups.
Figure 10. Cartoon structure of hemoglobin
Figure 11. Cartoon illustration of hemoglobin demostrating the sites of mutaion for sickle cell anemia.
Mutant sites, Glu6Val residues are highlighted in green.
References
1. NCBI website <http://www.ncbi.nlm.nih.gov/BLAST/>
2. Sandrine Jacolot , Gerald Le Gac , Virginie Scotet , Isabelle Quere , Catherine Mura , and Claude Ferec. HAMP as a modifier gene that increases the phenotypic expression of the HFE pC282Y homozygous genotype. Blood, 1 April 2004, Vol. 103, No. 7, pp. 2835-2840.
3. PBD server <http://www.rcsb.org/pdb/cgi/explore.cgi?pid=269661108591942&page=0&pdbId=1A6Z>
4.
Emsembl (http://www.emsembl.org)
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