https://docs.google.com/spreadsheets/d/1AsYRLlrRLd6I8abxNHfuz1OtFTSqYZ87_kefBMsxhMo/edit?gid=0#gid=0
Answer any of the following questions by Shuguang Zhang:
This is because humans do not directly integrate the DNA molecules from our food into our DNA. The various components of a food including carbohydrates, fats, proteins and carbohydrates are broken down into simpler and simpler molecules by the digestive system. So that they can be absorbed and used in the vital functions of the organism.
There are some assumptions regarding the origin of these elements, among which the natural chemical processes of the Earth stand out. This was during a primitive period when they were subjected to gases such as methane, ammonia, hydrogen, among others. This is known as prebiotic synthesis. Chemical panspermia and synthesis by hydrothermal environments are also considered.
In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins.
Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions.
Flagellin A https://www.uniprot.org/uniprotkb/Q46113/entry?
For this case, I considered flagellin A (FlaA) as my protein. This protein is crucial in microbiology because it forms the bacterial flagellum, which facilitates bacterial motility and host colonization. Therefore, it is an important factor in virulence and pathogenicity studies.
MGFRINTNVAALNAKANADLNSKSLDASLSRLSSGLRINSAADDASGMAIKDSLRSQANTLGQAISNGNDALGILQTADKAMDEQLKILDTIKTKATQAAQDGQSLKTRTMLQADINRLMEELDNIANTTSFNGKQLLSGNFINQEFQIGASSNQTVKASIGATQSSKIGLTRFETGSRISVGGEVQFTLKNYNGIDDFKFQKVVISTSVGTGLGALADEINKNADKTGVRATFTVETRGMGAVRAGATSDDFAINGVKIGKVDYKDGDANGALVSAINSVKDTTGVEASIDENGKLLLTSREGRGIKIEGNIGRGAFINPNMLENYGRLSLVKNDGKDILISGTNLSAIGFGTGNMISQASVSLRESKGQIDANVADAMGFNSANKGNILGGYSSVSAYMSSTGSGFSSGSGFSVGSGKNYSTGFANTIAISAASQLSAVYNVSAGSGFSSGSNLSQFATMKTSAGNTLGVKDETAGVTTLKGAMAVMDIAETAITNLDQIRADIGSVQNQVTSTINNITVTQVNVKAAESQIRDVDFAAESANYSKANILAQSGSYAMAQANSVQQNVLRLLQ
575 amino acids
A: most repeated - 67
pBLAST and ClustalOmega results
Sequences producing significant alignments: 100
It is of the bacterial flagellin family, which are the major structural proteins of the bacterial flagellum.
LINK: https://www.rcsb.org/3d-view/6X80
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Deposited: 2020-06-01 Released: 2020-07-08
Author(s): [Kreutzberger, M.A.B.](https://www.rcsb.org/search?q=audit_author.name:Kreutzberger, M.A.B.), [Wang, F.](https://www.rcsb.org/search?q=audit_author.name:Wang, F.), [Egelman, E.H.](https://www.rcsb.org/search?q=audit_author.name:Egelman, E.H.)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Resolution: 3.50 Å → average good
Yes, just one: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
This is a structural protein and FlaA belongs to the flagellin-like fold family
Open the structure of your protein in any 3D molecule visualization software:
Visualize the protein as "cartoon", "ribbon" and "ball and stick".
Color the protein by secondary structure. Does it have more helices or sheets?
Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?
A higher amount of hydrophobic residues is observed which could indicate that the nature of this protein aligns mostly to this. This could be related to flagellum assembly as well. However, polar domains are also present which maintain the solubility of the protein.
It may present some regions or surfaces where interactions with other proteins or molecules (such as other flagellin subunits during flagellum assembly) may occur.