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Zinc binuclear clusters are motifs found in transcriptional
regulatory proteins in fungi. An early zinc binuclear
cluster was originally thought to be similar to previously
described zinc fingers, with four cysteines forming a
tetrahedral zinc binding site (Johnston, 1987; PMID 3299106).
Subsequent structural studies demonstrated that the zinc
binulear cluster consists of 6 cysteine residues that
are bound to two zinc atoms (Pan, 1990; PMID 2107541,
Marmorstein, PMID: 1557122). This documentary was prepared
by Paul Craig while on sabbatical at University of California,
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is
the enzyme that initiates the second (payoff) stage of
glycolysis. GAPDH catalyzes the reaction that converts
glyceraldehyde 3-phosphate (GAP) into 1,3 bisphosphoglycerate
(1,3 BPG) (and the reverse reaction in gluconeogenesis).
GAPDH oxidizes and phosphorylates GAP to produce 1,3-BPG.
In this reaction, phosphorylation adds an inorganic phosphate
tCo the carbony carbon of GAP, which also requires the
oxidation of that carbonyl group (and reduction of NAD+
to NADH). This documentary was prepared by Murtaza Mogri,
while he was a student in Philip Bourne's Pharmacology
207 course (Using Internet Resources in Molecular Biology),
Fall quarter, 2001-2002 academic year.
Four kinases take part in glycolysis: hexokinase, phosphofructokinase,
phosphoglycerate kinase and pyruvate kinase. The structures
of all four of these kinases have been determined in Baker's
yeast (Saccharomyces cerevisiae). This documentary
was prepared by Laura Tripi in Paul Craig's Biochemistry
Conformation & Dynamics Course at RIT, Fall quarter
2002-2003 academic year.
- The Link
- Science and Art
This extraordinary documentary compares modern art with
modern science. It includes an explanation of the principles
of modern art and demonstrates their connection to science,
both by appearance and with quotes revealing the intent
of the artists themselves. Jonah Olson created this documentary
while on a summer internship in David Goodsell's lab at
The Scripps Institute.
Cyclin Dependent Kinase
Human Cyclin Dependent Kinase 2 is one of several cyclin
dependent kinases that play important roles in the cell
cycle. While CDK2 is involved in a number of reactions
which allow the cell cycle to progress, this documentary
focuses on its phosphorylation of histone H1 during S
phase. In particular, it details the structural properties
of CDK2 that are most important for its role in this reaction,
as well as how the protein interacts with other factors
and how it relates to other CDKs and similar molecules.
Seth Staples prepared this documentary for Paul Craig's
Biochemistry Conformation & Dynamics Course at RIT,
Fall quarter 2002-2003 academic year.
- MAP Kinase P38
MAP Kinase P38 is a member of a very large family known
as the MAPK (mitogen-activated protein kinase) family
or sometimes also called the ERK (extracellular regulated-kinase)
family. This documentary is built around PDB file 1BL6,
though it does briefly mention some other structures.
Evan Santo is a junior in the Bioinformatics program at
RIT; he prepared this documentary for Paul Craig's Biochemistry
Conformation & Dynamics Course, Fall quarter 2002-2003
- MAP Kinase P38
This documentary focuses on the same topic as Evan Santo's
earlier work, but is built around a different PDB strucutre:
1A9U. The author is Stephen Mosher, a junior Biotechnology
major at RIT.
Pyruvate kinase catalyzes the final reaction of glycolysis,
converting phosphoenolpyruvate to pyruvate and generating
ATP from the energy that is released in that reaction.
Mark Gaffney, a Biochemistry major at RIT, prepared this
documentary, which includes some very nice molecular visualization
of basic features of proteins: helices, sheets and the
- Protein Kinase A
Protein kinase A is a serine/threonine kinase which is
involved in signal transduction pathway initiated by epinephrine.
It is one of the most thoroughly studied kinases and has
served as a prototype for studying the protein kinase
family (A conserved helix motif complements the protein
kinase core. (Veron M, Radzio-Andzelm E, Tsigelny I, Ten
Eyck LF, Taylor SS.
Proc Natl Acad Sci U S A 1993 Nov 15;90(22):10618-22).
The author of the documentary is James Thompson, who prepared
it for Biochemistry Conformation & Dynamics at RIT,
- UV Repair Proteins
Alex Vecchio prepared this fine documentary on proteins involved DNA repair after exposure to ultraviolet radiation in prokaryotes for the course, "Conformation & Dynamics " at the Rochester Institute of Technology. His documentary includes three structures: EXCINUCLEASE UVRABC COMPONENT UVRB (PDB file 1D9X); EXCINUCLEASE UVRABC COMPONENT UVRB (PDB 1D9Z; the same enzyme in complex with ATP); and EXCINUCLEASE ABC SUBUNIT C (PDB file 1KFT).
- Carbamoyl Phosphate Synthetase
Carbamoyl phosphate synthetase (CPS) participates in two different pathways: pyrimidine synthesis and the urea cycle. In this documentary, Laura Grell from the Bioinformatics program at RIT, describes the metabolic role of CPS in eukaryotes and prokaryotes, and provides detailed structural information on CPS from E. coli (PDB file 1A9X).
- 8-Amino-7-Oxononanoate Synthase
A team of three undergraduate students at RIT (Robert Saccente, Nathan Hartzell and Ryan Meath) combined excellent writing with stunning molecular visualization to describe 8-AMINO-7-OXONANOATE SYNTHASE (PDB structure 1DJE), one of the enzymes in the biosynthetic pathway for biotin in E. coli. These students also employed the combinatorial extension tool (http://cl.sdsc.edu/ce.html) to structurally align the PLP-bound enzyme with the product bound enzyme; and also to align the enzyme with another PLP-dependent enzyme that has extremely weak sequence homology. The students even contacted Dr. Robert Baxter, the corresponding author on the original publications, to get his explanation of some of the finer details of the mechanism.
- Ubiquitin Conjugating Enzyme
UbcH10 or Human Ubiquitin Conjugating Enzyme functions in ubiquitin-mediated proteolysis in cell cycle progression. Ubiquination functions to tag a protein by a covalent interaction between an ubiquitin protein and a lysine residue on a protein. Jonathan Keeling, Erin Wells and Christian Heine (from the Conformation & Dynamics course at RIT in 2004) do a nice job of comparing published static images with molecular visualizations of the enzyme. In addition to a discussion of family relationships, their molecular visualizations are very appealing and described in expert detail.
- Antifreeze Polypeptide from Winter Flounder
Ice crystals can act like miniscule razors inside cells, puncturing membranes as they grow. Organisms, such as the winter flounder, that live in subfreezing conditions have antifreeze polypeptides (PDB structure 1WFA) that prevent ice crystal formation. Erin Topley, Jeff Gagnon and Elaine Vonderembse (undergraduates at RIT) combine a high quality of science with a beautiful artistic perspective. In addition, they employed the Combinatorial Extension tool to demonstrate structural homology between the antifreeze protein in winter flounder and a polypeptide chain from an aberrant cytochrome c oxidase, which was extracted from the thermophilic bacterium Thermus thermophilus.
- T7 RNA Polymerase
Bradley Tebbetts, a biotechnology student at RIT, presents a detailed description of the structure and mechanism of T7 RNA Polymerase (PDB structure 1H38). His documentary includes a comparision to the more complex RNA polymerases from prokaryotic and eukaryotic organisms.
- Tyrosyl-tRNA Synthetase
The Protein Data Bank now contains Tyrosyl-tRNA synthetase structures from archaea (1J1U), eubacteria (1JII) and animalia (1Q11), enabling Alex Vecchio to compare the three structures for similarities and differences, as well as the role of this enzyme in expansion of genetic code expression through the kingdoms.
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