Tyrone Evans Hox Proteins sandbox

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(Difference between revisions)

Current revision

Hox Proteins

1 Introduction
2 Role in Development
3 Hox Protein Regulation
4 Interaction with DNA
5 Human Hox Genes^[6]
6 Structural highlights^[7]
7 References

Introduction

Hox Proteins are transcription factors, proteins that are involved in the process of transcribing DNA into RNA. These specific types of proteins are capable of binding to enhancers, a short (50-1500 bp) region of DNA, in pursuit of activating or repressing certain genes. These proteins are named this way because of the mutations that are done within them that cause homeotic transformations, changing of an organ into another^[1] ^[2] .

Role in Development

As mentioned previously, homeotic transformations can alter DNA sequences so that specific proteins will have different functions, and certain genes will be either activated or deactivated. More specifically, if a certain hox protein is responsible for the development of legs on a fly in the middle region of its body, a homeotic transformation can cause this protein to carry out this same function in a different area. In this example, this altered protein can activate the gene for leg development to change the antennae to legs on that fly's head, as seen in multiple experiments. And biologists believe this to be true for Hox genes in flies, mice, humans, and other animals^[3].

Hox Protein Regulation

Hox genes, which hold the instructions for how each protein should be constructed, are regulated by both gap genes and pair-rule genes. Gap genes are responsible for the development of particular sections of an organism, more specifically for embryos of some arthropods. If a mutation occurs with these genes, adjoining body sections can be loss. Pair-rule genes are similar to gap genes but instead of being involved in the development of arthropods, it participates in the segment development of insects. And both of these regulators are ultimately regulated by maternally-supplied mRNA. In a series of events, depending on the amount of said maternally-supplied mRNA either the gap or pair-rule genes are activated, which in turn activate the Hox genes, allowing them to cause a differentiation in the genes that are responsible for the construction of proteins for embryo development^[4]..

Interaction with DNA

A homeodomain is an essential part that all Hox proteins possess. The homeodomain can be found within the homeobox, a DNA sequence found within genes that are responsible of morphogenesis of living organisms. This sequence codes for homeodomain protein products, 60 amino-acid segments, which have specific folding patterns (helix-turn-helix) that allows them to bind with DNA through a core motif. This domain consists of three helical regions folded into a tight spherical structure. There are (Recognition helix) within this domain. The C-terminal helix binds directly with DNA through the use of and between side chains and the outer bases and thymine methyl groups within the major groove of a DNA helix. Ionic bonding can also be observed between the bases of the DNA sequence and the amino acids of the protein dimers. A more specific is the one between LYS 207 and an oxygen atom of a phosphate group. The within homeodomain binds within the of a DNA helix, while the binds within the of a DNA helix^[5].

Human Hox Genes^[6]

The cluster HOX-A corresponds with chromosome 7, regulating genes: HOX-A1, HOX-A2, HOX-A3, HOX-A4, HOX-A5, HOX-A6, HOX-A7, HOX-A9, HOXA-10, HOXA-11, HOXA-13.

The cluster HOX-B corresponds with chromosome 17, regulating genes: HOX-B1, HOX-B2, HOX-B3, HOX-B4, HOX-B5, HOX-B6, HOX-B7, HOX-B8, HOX-B9, HOX-B13.

The cluster HOX-C corresponds with chromosome 12, regulating genes:HOX-C4, HOX-C5, HOX-C6, HOX-C8, HOX-C9, HOX-C10, HOX-C11, HOX-C12, HOX-C13.

And finally, the cluster HOX-D corresponds with chromosome 2, regulating genes:HOX-D1, HOX-D3, HOX-D4, HOX-D8, HOX-D9, HOX-D10, HOX-D11, HOX-D12, HOX-D13.

Structural highlights^[7]

References

↑ "Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.
↑ Ladam, Franck, and Charles G. Sagerström. “Hox Regulation of Transcription – More Complex(es).” Developmental dynamics : an official publication of the American Association of Anatomists 243.1 (2014): 10.1002/dvdy.23997. PMC. Web. 3 Nov. 2015.
↑ Freeman, Quillin, and Allison. Biological Science. 5th ed. Vol. 1. N.p.: Benjamin Cummings, n.d. Print.
↑ Ladam, Franck, and Charles G. Sagerström. “Hox Regulation of Transcription – More Complex(es).” Developmental dynamics : an official publication of the American Association of Anatomists 243.1 (2014): 10.1002/dvdy.23997. PMC. Web. 3 Nov. 2015.
↑ "Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.
↑ "Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.
↑ Berman, Helen M., John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, and Philip E. Bourne. "The Protein Data Bank." RCSB. Nucl. Acids Res. (2000) 28 (1): 235-242 Web.

Proteopedia Page Contributors and Editors (what is this?)

Tyrone Evans, Ann Taylor

Retrieved from "http://52.214.119.220/wiki/index.php/Tyrone_Evans_Hox_Proteins_sandbox"

@@ Line 1: / Line 1: @@
 ==Hox Proteins==
 <StructureSection load='1puf' size='340' side='right' caption='Caption for this structure' scene=''>
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
 == Introduction ==
-Hox Proteins are transcription factors, proteins that are involved in the process of translating, or transcribing, DNA into RNA. These specific types of proteins are capable of binding to enhancers, a short (50-1500 bp) region of DNA, in pursuit of activating or repressing certain genes. These proteins are named this way because of the mutations that are done within them that cause homeotic transformations, changing of an organ into another.
+Hox Proteins are transcription factors, proteins that are involved in the process of transcribing DNA into RNA. These specific types of proteins are capable of binding to enhancers, a short (50-1500 bp) region of DNA, in pursuit of activating or repressing certain genes. These proteins are named this way because of the mutations that are done within them that cause homeotic transformations, changing of an organ into another<ref>"Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.</ref> <ref>Ladam, Franck, and Charles G. Sagerström. “Hox Regulation of Transcription – More Complex(es).” Developmental dynamics : an official publication of the American Association of Anatomists 243.1 (2014): 10.1002/dvdy.23997. PMC. Web. 3 Nov. 2015.</ref>
+.
-== Classification ==
+== Role in Development ==
-If proteins have a major amount of similarity between their sequences, then they are believed to have similar functionality. In hox proteins, if they have parallel homeodomains then the specifics on how these proteins bind with DNA should be identical. But in order to tell the difference between the alike species, three types of classification are used: 1.) Phylogentic Inference Based, 2.) Synteny-Based, and 3.) Sequence Similarity-Based. The Phylogentic Inference Based classification method is used to show shared and unshared characteristics. Synteny-Based classification is a method of tracking mutations in comparable given sequences. The final method of classification, Sequence Similarity-Based, is used for identifying “homologous” or related proteins and genes.
+As mentioned previously, homeotic transformations can alter DNA sequences so that specific proteins will have different functions, and certain genes will be either activated or deactivated. More specifically, if a certain hox protein is responsible for the development of legs on a fly in the middle region of its body, a homeotic transformation can cause this protein to carry out this same function in a different area. In this example, this altered protein can activate the gene for leg development to change the antennae to legs on that fly's head, as seen in multiple experiments. And biologists believe this to be true for Hox genes in flies, mice, humans, and other animals<ref>Freeman, Quillin, and Allison. Biological Science. 5th ed. Vol. 1. N.p.: Benjamin Cummings, n.d. Print.
+</ref>.
-== Hox Protein Regualtion ==
+== Hox Protein Regulation ==
-Hox genes, which hold the instructions for how each protein should be constructed, are regulated by both gap genes and pair-rule genes. Gap genes are responsible for the development of particular sections of an organism, more specifically for embryos of some arthropods. If a mutation occurs with these genes, adjoining body sections can be loss. Pair-rule genes are similar to gap genes but instead of being involved in the development of arthropods, it participates in the segment development of insects. And both of these regulators are ultimately regulated by maternally-supplied mRNA. In a series of events, depending on the amount of said maternally-supplied mRNA either the gap or pair-rule genes are activated, which in turn activate the Hox genes, allowing them to cause a differentiation in the genes that are responsible for the construction of proteins for embryo development.
+Hox genes, which hold the instructions for how each protein should be constructed, are regulated by both gap genes and pair-rule genes. Gap genes are responsible for the development of particular sections of an organism, more specifically for embryos of some arthropods. If a mutation occurs with these genes, adjoining body sections can be loss. Pair-rule genes are similar to gap genes but instead of being involved in the development of arthropods, it participates in the segment development of insects. And both of these regulators are ultimately regulated by maternally-supplied mRNA. In a series of events, depending on the amount of said maternally-supplied mRNA either the gap or pair-rule genes are activated, which in turn activate the Hox genes, allowing them to cause a differentiation in the genes that are responsible for the construction of proteins for embryo development<ref>Ladam, Franck, and Charles G. Sagerström. “Hox Regulation of Transcription – More Complex(es).” Developmental dynamics : an official publication of the American Association of Anatomists 243.1 (2014): 10.1002/dvdy.23997. PMC. Web. 3 Nov. 2015.</ref>..
-	While these Hox proteins can be regulated, they also do a fair amount of regulation that consist of major networks of other genes like those who are responsible for limb formation. Examples of genes that are regulated by Hox proteins in both Drosophila and Mice.
 == Interaction with DNA ==
-A homeodomain is an essential part that all Hox proteins possess. The homeodomain can be found within the homeobox, a DNA sequence found within genes that are responsible of morphogenesis of living organisms. This sequence codes for homeodomain protein products, 60 amino-acid segments, which have specific folding patterns (helix-turn-helix) that allows them to bind with DNA through a 5’-TAAT-3’ core motif.  This domain consist of three helical regions folded into a tight spherical structure (need picture of structure). There are two antiparallel N-terminal helices and one C-terminal helix within this domain. The C-terminal helix binds directly with DNA through the use of hydrogen bonds and hydrophobic interactions between side chains and the outer bases and thymine methyl groups within the major groove of a DNA helix. The <scene name='71/714951/Recognition_helix/1'>Recognition helix</scene> within homeodomain binds within the <scene name='71/714951/Dna_major_groove/1'>major groove</scene> of a DNA helix, while the Amino-terminal tail binds within the <scene name='71/714951/Dna_minor_groove/1'>minor groove</scene> of a DNA helix.
+A homeodomain is an essential part that all Hox proteins possess. The homeodomain can be found within the homeobox, a DNA sequence found within genes that are responsible of morphogenesis of living organisms. This sequence codes for homeodomain protein products, 60 amino-acid segments, which have specific folding patterns (helix-turn-helix) that allows them to bind with DNA through a <scene name='71/714951/Taaat_sequence/1'>5’-TAAAT-3’</scene> core motif.  This domain consists of three helical regions folded into a tight spherical structure. There are <scene name='71/714951/Both_n_and_c-terminal_helices/1'>two antiparallel N-terminal helices and one C-terminal helix</scene> (Recognition helix) within this domain. The C-terminal helix binds directly with DNA through the use of <scene name='71/714951/H_bond_between_gln_and_p/1'>Hydrogen bonds</scene> and <scene name='71/714951/Hydrophobic_interaction/3'>Hydrophobic interactions</scene> between side chains and the outer bases and thymine methyl groups within the major groove of a DNA helix. Ionic bonding can also be observed between the bases of the DNA sequence and the amino acids of the protein dimers. A more specific <scene name='71/714951/Ionic_bond/1'>Ionic interaction</scene> is the one between LYS 207 and an oxygen atom of a phosphate group. The <scene name='71/714951/Recognition_helix/1'>Recognition helix</scene> within homeodomain binds within the <scene name='71/714951/Dna_major_groove/1'>major groove</scene> of a DNA helix, while the <scene name='71/714951/Amino-terminal_tail/1'>Amino-Terminal tail</scene> binds within the <scene name='71/714951/Dna_minor_groove/1'>minor groove</scene> of a DNA helix<ref>"Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.</ref>.
+== Human Hox Genes<ref>"Hox Gene." Wikipedia. Wikimedia Foundation, 14 Aug. 2015. Web. 20 Oct. 2015.</ref> ==
+The cluster HOX-A corresponds with chromosome 7, regulating genes: HOX-A1, HOX-A2, HOX-A3, HOX-A4, HOX-A5, HOX-A6, HOX-A7, HOX-A9, HOXA-10, HOXA-11,   HOXA-13.
+The cluster HOX-B corresponds with chromosome 17, regulating genes: HOX-B1, HOX-B2, HOX-B3, HOX-B4, HOX-B5, HOX-B6, HOX-B7, HOX-B8, HOX-B9, HOX-B13.
+The cluster HOX-C corresponds with chromosome 12, regulating genes:HOX-C4, HOX-C5, HOX-C6, HOX-C8, HOX-C9, HOX-C10, HOX-C11, HOX-C12, HOX-C13.
+And finally, the cluster HOX-D corresponds with chromosome 2, regulating genes:HOX-D1, HOX-D3, HOX-D4, HOX-D8, HOX-D9, HOX-D10, HOX-D11, HOX-D12, HOX-D13.
+== Structural highlights<ref>Berman, Helen M., John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, and Philip E. Bourne. "The Protein Data Bank." RCSB. Nucl. Acids Res. (2000) 28 (1): 235-242 Web.</ref>  ==
+<scene name='71/714951/Taaat_sequence/1'>5’-TAAT-3’</scene>
+<scene name='71/714951/Both_n_and_c-terminal_helices/1'>Two antiparallel N-terminal helices and one C-terminal helix</scene>
+<scene name='71/714951/H_bond_between_gln_and_p/1'>Hydrogen bonds</scene>
+<scene name='71/714951/Hydrophobic_interaction/3'>Hydrophobic interactions</scene>
+<scene name='71/714951/Ionic_bond/1'>Ionic interaction</scene>
+<scene name='71/714951/Recognition_helix/1'>Recognition helix</scene>
-== Human Hox Genes ==
+<scene name='71/714951/Dna_major_groove/1'>Major Groove</scene>
-The cluster HOX-A corresponds with chromosome 7, regulating genes: HOX-A1, HOX-A2, HOX-A3, HOX-A4, HOX-A5, HOX-A6, HOX-A7, HOX-A9, HOXA-10, HOXA-11,   HOXA-13. The cluster HOX-B corresponds with chromosome 17, regulating genes: HOX-B1, HOX-B2, HOX-B3, HOX-B4, HOX-B5, HOX-B6, HOX-B7, HOX-B8, HOX-B9, HOX-B13. The cluster HOX-C corresponds with chromosome 12, regulating genes:HOX-C4, HOX-C5, HOX-C6, HOX-C8, HOX-C9, HOX-C10, HOX-C11, HOX-C12, HOX-C13. And finally, the cluster HOX-D corresponds with chromosome 2, regulating genes:HOX-D1, HOX-D3, HOX-D4, HOX-D8, HOX-D9, HOX-D10, HOX-D11, HOX-D12, HOX-D13.
+<scene name='71/714951/Amino-terminal_tail/1'>Amino-Terminal tail</scene>
-== Structural highlights ==
+<scene name='71/714951/Dna_minor_groove/1'>Minor Groove</scene>
-recognition helix binds to <scene name='71/714951/Dna_major_groove/1'>major groove</scene>
-<scene name='71/714951/Recognition_helix/1'>recognition helix</scene>
-<scene name='71/714951/Dna_minor_groove/1'>minor groove</scene>
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
-</StructureSection>
 == References ==
 <references/>

Tyrone Evans Hox Proteins sandbox

From Proteopedia

Current revision

Hox Proteins

Contents

Introduction

Role in Development

Hox Protein Regulation

Interaction with DNA

Human Hox Genes^[6]

Structural highlights^[7]

References

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox

Tyrone Evans Hox Proteins sandbox

From Proteopedia

Current revision

Hox Proteins

Contents

Introduction

Role in Development

Hox Protein Regulation

Interaction with DNA

Human Hox Genes[6]

Structural highlights[7]

References

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox

Human Hox Genes^[6]

Structural highlights^[7]