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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
© SOT 2018
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
© SOT 2018
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)
© SOT 2018
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
© SOT 2018
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
© SOT 2018
Undergraduate Educator Network Webinar
Search in PDB “arsenic methyltransferase”
I. Protein Data Bank
http://www.rcsb.org/pdb/home/home.do
© SOT 2018
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
Undergraduate Educator Network Webinar
Explore entry 4FSD (with arsenic ligand)
http://www.rcsb.org/pdb/explore/explore.do?structureId=4FSD
Undergraduate Educator Network Webinar
3D view – identify residues involved in binding
http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=4FSD&bionumber=1
Undergraduate Educator Network Webinar
Sequence view
http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=4FSD
Undergraduate Educator Network Webinar
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
© SOT 2018
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/
Undergraduate Educator Network Webinar
https://www.ebi.ac.uk/Tools/msa/clustalo/
Note conservation surrounding binding pocket residues
Residues involved in function (co-ordination of ligands, arsenic)
© SOT 2018
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
© SOT 2018
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
© SOT 2018
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