Choosing an enzyme/protein for the Enzyme Report in BCMB8010:

The assignment is to create a web report on an enzyme or protein of your choice. The details of the assignment can be found HERE. In order to complete the project you will need to collect a variety of data on an enzyme/protein and assemble it into a clear and concise report submitted as an ABSRACT web page, the body of the REPORT as a pdf file (posted on your web site and linked to the abstract page) linked to the abstract page.

Your choice of the protein is VERY important. You should try to choose a protein that either employs an interesting structural motif, interesting enzymatic mechanism, undergoes a conformational change in the process of carrying out its function, or has an allosteric transition between two or more conformations. Be certain to choose a protein for which there is structural information about the substrate or ligand interaction. Do not choose a static protein structure for which there is little additional information. Creativity in your choice of a protein is as important as the creativity in designing your web presentation. As you search for an enzyme for the report you should be consulting the protein structure data bank (PDB) at: http://www.rcsb.org/pdb/.  You need to check that there are available structures in PDB and download the corresponding coordinate files. The main question that you should be asking is: does it look like there are good structures with substrate analogs or inhibitors that would provide insight into the enzyme/protein mechanism? To evaluate this you should look at the citations that can be found liked to the top page of the website for your given protein. I will describe this process in class. 

Each student MUST CHOOSE A DIFFERENT PROTEIN. If two students choose the same protein, then the first student to email their protein choice to me will get to use that protein. You are not allowed to choose one of the proteins that were chosen in the last three years. A list of these proteins can be found below. You need to get my OK for your enzyme choice by sending me an email containing the name of the protein and the PDB accession codes for the structures that you will be using in the report. I will reply to you if your choice of the protein is OK. The list of the proteins used in the reports in the last two years is as follows:

Excluded Protein Families:
All serine proteases (i.e. trypsin, chymotrypsin etc.)
All glycosidases (both inverting and retaining)
All protein kinases (unless you come up with something REALLY novel)

2005
Nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator
Peptide-MHC complexes
Family 31 alpha-glycosidase
neutral endopeptidase (Neprilysin) complexed with phosphoramidon
glucosamine 6-P synthase complexed with L-Glutamate
Sterol carrier protein
Mdm2-inhibitor complex
Aspartate aminotransferase
Isocitrate Dehydrogenase (complexed with Isocitrate, NADP+, and Calcium)
acetyl coenzyme-A carboxylase
photosynthetic oxygen evolving center (PSII)
Lysine 5,6-aminomutase
Shiga-like toxin I
Cyclic Nucleotide Phosphodiesterase
Erk2
L-proline dehydrogenase
Cyclophilin A
Myc-Max complex with DNA
DnaK
Brca2-Dss1 complex
Lac repressor
Methyl-Coenzyme M reductase
Cathepsin K
Seratonin N-acetyltransferase
Stat1/DNA complex
Streptavidin in complex with Biotin
Hydrogenase Maturating Endopeptidase, Hybd
Plasmepsin II
Glutamate (AMPA) receptor
Obelin
Complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2
Blood Group A/B Transferases
Human cardiac troponin C
Glutathione S-transferase
Angiotensin converting enzyme
Poly(A) polymerase
CENP-B protein-DNA complex

2006
Clathrin
Glucose-6-phosphate dehydrogenase
P. falciparum enoyl acyl carrier protein reductase
Glycogen synthase kinase-3 beta
Glutamate decarboxylase
Bradyrhizobium japonicum FixL heme domain (BjFixLH)
Vascular Endothelial Growth Factor (VEGF) complex with tyrosine kinase receptors
Matrix metalloproteinase neutrophil collagenase (MMP-8)
Tryptophan synthase
Interleukin 10 (IL-10) interaction with receptor
Bordetella Pertussis (whooping cough) toxin
Hepatitis C Viral NS3
Decarboxylase catalytic antibody 21D8-hapten complex
Porphobilinogen synthase
Phosphotidylinositide-3-kinase
Apocarotenoid cleavage oxygenase
Serpin-protease complex
Methylmalonyl-CoA mutase
Phosphatidylinositol-phospholipase C
Histidinol-phosphate aminotransferase
Farnesoid X receptor (FXR), a nuclear bile acid receptor
IgE-high affinity receptor complex
Glucose-6-phosphate isomerase
Glutamate degydrogenase
Estrogen receptor
Serine hydroxymethyltransferase
Histidine ammonia lyase
Plasma alpha-antithrombin-III (bound to a pentasaccharide)
UDP-glucose dehydrogenase

2007
histone methyltransferase
Insulin receptor
Vaccinia Virus: VCP, complement control
protein complexed with heparin
Paramyxovirus Neuraminidase
Laccase
alpha-bungarotoxin
kanamycin nucleotidyl transferase
HMG CoA reductase
Histone acetyltransferase
adenosine deaminase
UDP-3-O-acyl-glucosamine N-acyltransferase
sialic acid synthase (NeuB)
Cre recombinanse
Clostridium botulinum neurotoxin
Phenylalanine Hydroxylase
leucine aminopeptidase
serum transferring
beta-secretase
Myb trascription factor
Semicarbazide-sensitive amine oxidase
Aurora kinase A
Murray Valley Encephalitis Virus NS5 2'-O
Methyltransferase
HLA class I histocompatibility antigen
complexed with Telomerase
beta-galactosidase
phosphoenolpyruvate carboxylase
aconitase
Plasmodium falciparum lactate dehydrogenase
ABO blood group transferase enzymes
Photolyase
acetylcholinesterase
bacterial HU histone-like protein
Glycine Cleavage T Protein (gcvt)
Topoisomerase I
CDC13
Cathepsin B
Taq Polymerase
NAD(P) Transhydrogenase
Human macrophage elastase (MMP-12)
pyruvate kinase
farnesyltransferase
insulin-degrading enzyme (IDE)
trichodiene synthase