Undergraduate Educator Network Webinar

Introduction to Protein Structure through Homology Modeling Using Bioinformatics

Woon-Kai Low, PhDAssociate ProfessorSt. John’s University, College of Pharmacy &Health SciencesQueens, NY, 11439loww@stjohns.edu

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Undergraduate Educator Network Webinar

3 credits (one semester) Associated lab (1 credit, 3 hours/week) Students:

– 3rd year toxicology majors (BS) http://www.stjohns.edu/academics/schools-and-colleges/college-pharmacy-and-health-

sciences/programs-and-majors/biomedical-sciences-bachelor-science

– 2nd year Clinical Laboratory Sciences (BS) http://www.stjohns.edu/academics/schools-and-colleges/college-pharmacy-and-health-

sciences/programs-and-majors/clinical-laboratory-sciences-bachelor-science

Molecular Toxicogenomics

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Undergraduate Educator Network Webinar

Introduction to the molecular and genetic basis for human diversity

Impact on toxicological and pharmacological response

Scientific basis of personalized (precision medicine)

Molecular Toxicogenomics(3 credits, one semester)

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Undergraduate Educator Network Webinar

Introduction (and review) of amino acids, and the four levels of protein structure

Introduction to the concept of homology Introduction to bioinformatics

Lab #2: Protein Structure and Homology

Image Source: Getty Images © SOT 2018

Undergraduate Educator Network Webinar

Resources (Part I):

Ajees, A. A., et al. (2012). "Structure of an As(III) S-adenosylmethionine methyltransferase: insights into the mechanism of arsenic biotransformation." Biochemistry 51(27): 5476-5485.https://www.ncbi.nlm.nih.gov/pubmed/22712827

Undergraduate Educator Network Webinar

Resources (Part II):RCSB PDB protein data bank

http://www.rcsb.org/pdb/home/home.do

Universal Protein Resource (UniProt)

http://www.uniprot.org/

Clustal Omega (sequence comparison software)

http://www.ebi.ac.uk/Tools/msa/clustalo/

NCBI National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/

BLAST (Basic local alignment search tool)

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome

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Undergraduate Educator Network Webinar

I. PDB entry for structure of arsenic methyltransferase (Cyanidioschyzon sp.)

II. UniProKB entries for arsenic methyltransferase

III. Sequence alignment of arsenic methyltransferase from different species using Clustal Omega

IV. NCBI BLAST using arsenic methyltrasferase Students maintain record of activities in lab

notebook

Student Activities

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Undergraduate Educator Network Webinar

Search in PDB “arsenic methyltransferase”

I. Protein Data Bank

http://www.rcsb.org/pdb/home/home.do

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Undergraduate Educator Network Webinar

Results – no structure for human protein (2 hits associated with Homo sapiens are related proteins)

I. Protein Data Bank

http://www.rcsb.org/pdb/home/home.do© SOT 2018

Undergraduate Educator Network Webinar

3 search hits from Cyanidioschyzon sp. (algae)

Ajees, A. A., et al. (2012). Biochemistry 51(27): 5476-5485.http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=37EECA42

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Explore entry 4FSD (with arsenic ligand)

http://www.rcsb.org/pdb/explore/explore.do?structureId=4FSD

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3D view – identify residues involved in binding

http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=4FSD&bionumber=1

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Sequence view

http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=4FSD

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II. Universal Protein Knowledgebase

Explore entries for arsenic methyltransferase from human, rat and mouse

Collect sequences for each in FASTA format

http://www.uniprot.org/uniprot/?query=AS3MT&sort=score

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Undergraduate Educator Network Webinar

III. Clustal Sequence Alignment Using AS3MT

sequences from human, rat, mouse and Cyanidioschyzonsp.

https://www.ebi.ac.uk/Tools/msa/clustalo/

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https://www.ebi.ac.uk/Tools/msa/clustalo/

Note conservation surrounding binding pocket residues

Residues involved in function (co-ordination of ligands, arsenic)

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Undergraduate Educator Network Webinar

IV. BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome

Undergraduate Educator Network Webinar

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome

Explore the BLAST results

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Undergraduate Educator Network Webinar

Final lab report – questions Bioinformatics – databases and their utility

(PDB vs. UniProtKB) Homology – evolutionary conservation of amino

acid sequence and protein function Clustal alignment results vs. BLAST search

results

Post-Lab Activities

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