# Alicia Oberländer & Giuliano Ballacchino
# ! Paper handed in by Mail !
**Protein of interests: Coxsackie- Adenovirus-Receptor (CAR)**

# Paper for introduction:

> Human coxsackie-adenovirus receptor is colocalized with integrins αvβ3 and αvβ5 on the cardiomyocyte sarcolemma and upregulated in dilated cardiomyopathy implications for cardiotropic viral infections https://pubmed.ncbi.nlm.nih.gov/11457744/

> Unexpected subcellular distribution of a specific isoform
> of the Coxsackie and adenovirus receptor, CAR-SIV, in human pancreatic beta cells
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182664/pdf/125_2018_Article_4704.pdf

> CAR: A virus receptor within the tight junction https://pubmed.ncbi.nlm.nih.gov/15820557/
>-> kein full text/pdf *

> Coxsackievirus-adenovirus receptor (CAR) is essential for early embryonic cardiac development https://pubmed.ncbi.nlm.nih.gov/16079292/

> CAR-diology - A virus receptor in the healthy and diseased heart
https://pubmed.ncbi.nlm.nih.gov/19495568/
-> kein full text/pdf

**Important Paper:**

> The coxsackievirus and adenovirus receptor: virological and biological beauty https://pubmed.ncbi.nlm.nih.gov/32298477/

> The coxsackievirus-adenovirus receptor reveals complex homophilic and heterophilic interactions on neural cells https://pubmed.ncbi.nlm.nih.gov/20181587/

> Isoform-specific regulation and localization of the coxsackie and adenovirus receptor in human airway epithelia https://pubmed.ncbi.nlm.nih.gov/20361046/

> Alternative splicing of viral receptors: A review of the diverse morphologies and physiologies of adenoviral receptors https://pubmed.ncbi.nlm.nih.gov/25621323/

> Genomic organization and chromosomal localization of the human Coxsackievirus B-adenovirus receptor gene https://pubmed.ncbi.nlm.nih.gov/105434![color=#07589e]
> -> kein full text/pdf

# Graphics for Introduction

Abb. 1 

Abb. 2 

Abb. 3 

# Concept for Paper Layout

**1. Introduction**

- What is CAR ?
- Where is it to Find ?
- What are the functions?
- Genetic background
- Binding domains
- Isoforms
- Scientific interests

**2. Main-Part**

- DNA/RNA analysis
- Secondary structure analysis
- Analysis of soluble and conjugated forms
- Three dimensional structure
- Comparison between different Isoforms

**3. Excurs Science - Results?**

- Genetic knockout of CAR
- Hypoxia experiments

**4. Summary and Conclusion (Outcome)**

### Unit 1
- PubMed

### Unit 2
- FASTA Format
- Gene modle
- Find Mutation
### Unit 3
- Homologous Sequences (Ensemble)
- BLAST
- MSA
- Phylogenetic tree based on protein sequences
### Unit 4
- Gen Expression
### Unit 5
- R

# RAW-Data for CAR

**FASTA:** CXADR https://www.ncbi.nlm.nih.gov/gene/1525
**Variant 1 FASTA:** https://www.ncbi.nlm.nih.gov/nuccore/NM_001338.5?report=fasta
**Protein Structure:** https://www.rcsb.org/structure/1JEW
**Protein Structure 2021:** https://alphafold.ebi.ac.uk/entry/P78310
**UniProt:** https://www.uniprot.org/uniprot/P78310 (with isoforms 1-7)

Isoform 1: NP_001329
https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS33519.1

Isoform 2: NP_001193992
https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS56205.1

Clustal Omega comparison (DNA):
https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=clustalo-I20211206-084354-0896-20444255-p2m

Clustal Omega comparison (RNA):
https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=clustalo-I20211206-084807-0534-43301360-p2m


# Programs/ Tools for Data Analysis

**DNA/ RNA / Protein analysis :**

1. BLAST (DNA/RNA)
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

2. BLAST (Protein)
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

3. Clustal Omega
https://www.ebi.ac.uk/Tools/msa/clustalo/

4. UniProt
https://www.uniprot.org

5. ApE
https://jorgensen.biology.utah.edu/wayned/ape/

**Translate tool DNA/RNA <=> Aminoacids:**

1. ExPASy Translate tool
https://web.expasy.org/translate/

**Secondary Structure analysis tool:**

1. NetSurfP - 2.0
https://services.healthtech.dtu.dk/service.php?NetSurfP-2.0

**Three Dimensional Structure Tool:**
1. RSCB Data Bank
https://www.rcsb.org

2. Swiss Model ExPASy
https://swissmodel.expasy.org

3. PyMOL
https://pymol.org/2/

# Resulst/ Notes

Protoytpe 3D modeling with PyMOL:


# Unit 2

**CXADR Ig-like cell adhesion molecule [ Homo sapiens (human)]**
- Chromosom 21 (21q21.1)
- Gen CXADR -> Protein CAR
- 54.000 Nukleotiden
- 8 Exons
- 365 AS
- 46 kDa

FASTA CAR Protein https://www.ncbi.nlm.nih.gov/protein/P78310.1?report=fasta
FASTA CAR Gen https://www.ncbi.nlm.nih.gov/nuccore/NC_000021.9?report=fasta&from=17513016&to=17636213
ORFfinder
https://www.ncbi.nlm.nih.gov/orffinder/
Ergebnis ORF:
30 minimal ORF length
150 minimal ORF length

ENSEMBLE DATA:
https://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000154639;r=21:17513043-17570100;t=ENST00000284878

Consensus CDS DATA:
https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS33519


CONTIG: ein Satz überlappender DNA- oder Protein-Stücke (reads), die von derselben genetischen Quelle stammen

## Gene Modle



**Isoform 1**

**Isoform 2** 346-365 missing

# **Phylogenetic Analysis of different species:**

niedrige Übereinstimmung
https://www.uniprot.org/align/A20211206A084FC58F6BBA219896F365D15F2EB4400E4489

hohe Übereinstimmung https://www.uniprot.org/align/A2021120792C7BAECDB1C5C413EE0E0348724B68200E9D1V

# Unit 4
## Task 1
1. How many experiments?
- 1 https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-58170/?query=Coxsackievirus+and+adenovirus+receptor+
- EMBL-EBI 25,639 Ergebnisse
2. Experiment in other species?
- mouse
3. Cancer cells?
- ES cells
4. Role of gene in disease?
- Myocarditis
6. How many experiments are Mircroarry?
- 1
-> Hyperlink in Minipaper zu Experiment
-> Accesionnumber: E-GEOD-58170

## Task 2

Expression Atlas (32 Uhlens Lab)
https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2836/Results?geneQuery=%5B%7B%22value%22%3A%22ensg00000154639%22%7D%5D
https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2836/Results?geneQuery=%5B%7B%22value%22%3A%22ensg00000154639%22%7D%5D#
# Unit 5