TargetSp15+-+Apicomplexan+histone+deacetylase+(Plasmodium+berghei)


 * *Target (protein/gene name): ** Histone deacetylase

 ***NCBI Gene # or RefSeq#: **NCBIGene ID: 3428686 PB000903.02.0

 ***Protein ID (NP or XP #) or Wolbachia#: ** XP_680051.1

 ***Organism (including strain): **//Plasmodium berghei //strain ANKA

 **Etiologic Risk Group (see link below): **Risk Group 2

http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html

 ***/ ****Disease Information** **<span style="font-family: Arial,sans-serif;">(sort of like the Intro to your Mini ****<span style="font-family: Arial,sans-serif;">Research Write ****<span style="font-family: Arial,sans-serif;">up): **Plasmodium berghei is a type of bacteria that can be found to cause malaria in mice. The malaria bacteria is transmitted through female mosquito bites, and the bacteria travels to the liver for reproduction. After a short while, the bacteria then leaves the liver and invades red blood cells that go through the circulatory system. Side effects include anemia and damage to essential host organs, but one side effect found mostly in mice is the cerebral complications.


 * <span style="font-family: Arial,sans-serif;">Link to TDR Targets page (if present): **<span style="font-family: Arial,sans-serif;">N/A


 * <span style="font-family: Arial,sans-serif;">Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) **http://www.ncbi.nlm.nih.gov/gene/3428686

Histone deacetylase is essential in transcription of eukaryotic DNA by removing acetyl groups from histones.
 * <span style="font-family: Arial,sans-serif;">Essentiality of this protein: **http://www.pnas.org/content/93/23/13143.full.pdf http://mcb.asm.org/content/27/13/4784.short

Is it a monomer or multimer as biological unit**<span style="font-family: Arial,sans-serif;">? (make prediction at ** <span style="font-family: Arial,sans-serif; font-size: 10pt;">@http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): Monomeric

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Complex of proteins?: **<span style="font-family: Arial,sans-serif;">No. One protein. 3 amino acids and 12 ligands in ASU

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): **<span style="font-family: Arial,sans-serif;">Apicidin

http://www.pnas.org/content/93/23/13143.full.pdf

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">*EC#: ** 3.5.1.98

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Link to BRENDA EC# page: ** http://www.brenda-enzymes.org/enzyme.php?ecno=3.5.1.98

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">-- ** Show screenshot of BRENDA enzyme mechanism schematic <span style="font-family: Arial,sans-serif; font-size: 10pt;">

<span style="font-family: Arial,sans-serif; font-size: 10pt;">**Enzyme Assay** **<span style="font-family: Arial,sans-serif;">information (spectrophotometric, coupled assay ?, reagents): ** Fluor de Lys kit from BioMol. Uses fluorescence Reagent: acetylated lysine side chains, nuclear or cellular extract

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">-- link to Sigma (or other ****company****<span style="font-family: Arial,sans-serif;">) page for assay (see Sigma links below) ** http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2431080/

-- -or link (or citation) to paper that contains assay information

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">-- links to assay reagents (substrates) pages. ** http://www.enzolifesciences.com/BML-KI104/fluor-de-lys-deacetylase-substrate/

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">--- List cost and quantity of substrate reagents, supplier, and catalog # **
 * **<span style="font-family: Arial,sans-serif; font-size: 10pt; line-height: 1.5;">468.00 USD **
 * **<span style="font-family: Arial,sans-serif; font-size: 10pt; line-height: 1.5;">98 wells **
 * **<span style="font-family: Arial,sans-serif; font-size: 10pt; line-height: 1.5;">Reagant for 100-200 assays **
 * **<span style="font-family: Arial,sans-serif; font-size: 10pt; line-height: 1.5;">Biomol (EnzoLifeSciences) **
 * **<span style="background-color: #ffffff; font-family: Arial,Helvetica,Geneva,sans-serif; font-size: 12px;">BML-AK500-0001 **

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Structure (PDB or Homology model) **

<span style="font-family: Arial,sans-serif; font-size: 10pt;">-- PDB # or closest PDB entry if using homology model: PDB: 3C0Y

<span style="font-family: Arial,sans-serif; font-size: 10pt;">-- For Homology Model option: N/A

Show pairwise alignment of your BLASTP search in NCBI against the PDB

Query Coverage:

Max % Identities:

% Positives

Chain used for homology:

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Current Inhibitors: ** Apicidin http://www.jstor.org/stable/40761?seq=1#page_scan_tab_contents

<span style="font-family: Arial,sans-serif; font-size: 10pt;">**<span style="font-family: Arial,sans-serif;">Expression Information (has it been expressed in bacterial cells): ** <span style="font-family: Arial,sans-serif; font-size: 10pt;">Brenda has no expression in things other than homo sapiens, but the PDB article cited below has an expression in E. coli.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2431080/

<span style="font-family: Arial,sans-serif; font-size: 10pt;">**Purification Method****<span style="font-family: Arial,sans-serif;">: **<span style="font-family: Arial,sans-serif;">Purification of homogeneity by anion-exchange chromatography after dilution with buffer.

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Image of protein (PyMol with features delineated and shown separately): ** <span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): ** code format="sequence" VVLNKHHEMS DQISLNDYYD YYAPDFQLHL QPSSIPNYNS PEHLSKIKMK 60        70         80         90        100 ITENLRNIEH APGVQFSYVP PDFFDSDIDD KSDKNQYELK DDSGGGRAAG 110       120        130 TRGKEHSSTH HLRRKNYEDD FFDMSDRDQG II code <span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">*length of your protein in Amino Acids ** <span style="font-family: Arial,sans-serif; font-size: 10pt;">132 Amino Acids

<span style="font-family: Arial,sans-serif; font-size: 10pt;">**Molecular Weight** **<span style="font-family: Arial,sans-serif;">of your protein in kiloDaltons using the ****<span style="font-family: Arial,sans-serif;">[|Expasy ProtParam] ****<span style="font-family: Arial,sans-serif;">website ** <span style="font-family: Arial,sans-serif; font-size: 10pt;">15.3357 kDa

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Molar ****Extinction coefficient** **<span style="font-family: Arial,sans-serif;">of your protein at 280 nm wavelength: ** <span style="font-family: Arial,sans-serif; font-size: 10pt;">Expasy ProtParam detected no TRP residues so there can be greater than 10% error. <span style="font-family: Arial,sans-serif; font-size: 10pt;">But the extinction coefficient measured at 280 nm in water was 11920 1/M*cm.

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">TMpred graph Image ** (@http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. <span style="font-family: Arial,sans-serif; font-size: 10pt; line-height: 0px; overflow: hidden;">

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">*CDS ****Gene Sequence****<span style="font-family: Arial,sans-serif;">(paste as text only): ** <span style="background-color: #ffffff; font-family: courier,sans-serif; font-size: medium;">gtggtgctgaacaaacatcatgaaatgagcgatcagattagcctgaacgattattatgat tattatgcgccggattttcagctgcatctgcagccgagcagcattccgaactataacagc ccggaacatctgagcaaaattaaaatgaaaattaccgaaaacctgcgcaacattgaacat gcgccgggcgtgcagtttagctatgtgccgccggatttttttgatagcgatattgatgat aaaagcgataaaaaccagtatgaactgaaagatgatagcggcggcggccgcgcggcgggc acccgcggcaaagaacatagcagcacccatcatctgcgccgcaaaaactatgaagatgat ttttttgatatgagcgatcgcgatcagggcattatt

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">*GC% Content for gene: **<span style="font-family: Arial,sans-serif;">46.2%

*CDS Gene Sequence (codon optimized) - copy fromoutputofPrimer DesignProtocol (paste as text only):

*GC% Content for gene (codon optimized): Told not to do until the target was selected.

<span style="font-family: Arial,sans-serif; font-size: 10pt;">Do Not Need this info for Spring (but still copy these lines to your Target page for now)

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): **

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">( ** **<span style="color: #008000; font-family: Arial,sans-serif; font-size: 10pt;">link to DNA Works output ****<span style="color: #008000; font-family: Arial,sans-serif; font-size: 10pt;">text file ****<span style="color: #008000; font-family: Arial,sans-serif; font-size: 10pt;">- **<span style="font-family: Arial,sans-serif; font-size: 10pt;">that should be saved in your Google Docs <span class="m9l40l772" style="font-family: Arial,sans-serif; font-size: 10pt;"> folder after you did the primer design protocol)

<span style="font-family: Arial,sans-serif; font-size: 10pt;">-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not <span class="apple-converted-space" style="font-family: Arial,sans-serif; font-size: 10pt;"> sure how to.

<span style="font-family: Arial,sans-serif; font-size: 10pt;"> **<span style="font-family: Arial,sans-serif;">Primer design results for 'tail' primers (this is just 2 sequences): **

<span style="font-family: Arial,sans-serif; font-size: 10pt;">**