Chem 835 REPORT PAGE

Each student will write a report on an enzyme or protein, for up to 100 points toward their final grade.

Enzymes or Proteins available for reports:

  • BAR-1 (b-Catenin/Armadillo-Related) from Caenorhabditis elegans(development, oxidative stress, cancer)
  • CENP-A (Centromere Protein A) from Homo sapiens (maintains centromere position)
  • DAF-2, from Caenorhabditis elegans (longevity, metabolism, development)
  • Engrailed homeodomain from Drosophila melanogaster (developmental transcription factor)
  • Forkhead box (FOXO), from human (transcription factor; longevity)
  • HER-2, from human (breast cancer associated; blocked by Herceptin)
  • LexA, from Escherichia coli (SOS response, antibiotic resistance)
  • Methionine Sulfoxide Reductase A (MsrA) from human lens (oxidative stress response; life span enhancer)
  • MspA, from Mycobacterium smegmatis (outer membrane protein; antibiotic resistance)
  • PhoPQ-Activated Gene P (PagP) from Salmonella typhimurium (transfers palmitate to lipid A)
  • Solute Carrier Family 24 member 5 (SLC24A5) from Homo sapiens (malignant skin melanoma, European/African human skin color difference)
  • Stathmin, from mice (microtubule synthesis, boldness suppression)
  • TOR (Target of Rapamycin) Kinase from Caenorhabditis elegans (longevity, metabolism, development)
  • Werner’s Syndrome Helicase, from human (longevity)

·       Or, one of the enzymes at the Human Ageing Genomic Resources site.

Each Report should include the following:

·       Common name of the enzyme or protein,

·       Enzyme Commission name with an explanation as to the meaning of its numbering,

·       Function of the enzyme or protein,

·       Substrates, products, and cofactors that the enzyme utilizes,

·       Cluster of Orthologous Group (COG or KOG) to which it belongs,

·       Family names of other members of the same COG or KOG,

·       Brief overview of the process in which it particpates (include citations to reviews of the process or protein that have been published within the past five years),

·       Primary structure of the enzyme or protein,

·       Results of a sequence search for enzymes or proteins with similar sequence,

·       Citation describing its tertiary structure if there is one,

·       Referenced description of its quaternary structure,

·       Citations and descriptions of 3 recent studies of the enzyme,

·       List of 3 labs currently studying the enzyme.

Potential Web Sources

There are several important sources on the world wide web that you may find helpful in developing your report. Visit each one to find out what they have to offer. I think you will find it incredible.

·       Collection of Electronic Research Tools:

o      San Diego Supercomputer Research Tools maintained by Christopher M. Smith

o      Biochemistry & Molecular Biology sites collection from Harvard University

·       Enzyme Commission names:

o      Enzyme nomenclature program from the Swiss Institute of Bioinformatics

·       Protein sequence and sequence similarity searches:

o      BLAST from the National Center for Biotechnology Information at the National Library of Medicine. Try the PSI- and PHI-BLAST. You will need to paste in your protein's sequence.

o      SWISS-PROT from the Swiss Institute of Bioinformatics

o      BLITZ from the European Bioinformatics Institute

·       Tertiary structures:

o      Protein Data Bank from the Research Collaboratory for Structural Bioinformatics

o      SWISS-PROT from the Swiss Institute of Bioinformatics

·       Metabolic pathways:

o      BRaunschweig ENzyme DAtabase for information about 40,000 enzyme in over 4460 organisms from Dietmar Schomburg's group at the University of Cologne

o      Biochemical Pathways at the Swiss Institute of Bioinformatics site sponsored by Roche Applied Science

o      Metabolic Pathways for over 150 organisms from the BioCyc Knowledge Library

·       Research Article Search Engines:

o      PubMed from the National Center for Biotechnology Information at the National Library of Medicine

o      World of Science from Information Science Institute. To use this subscripted site, you will need to log on from one of UNL's computers.

·       Popular search engines:

o      Google from Google

o      Yahoo from Yahoo

o      MSN from Microsoft Inc.

 

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