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Background |
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Protein
Engineering |
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So
why would one want to create an enzyme in the first place? Simply stated,
enzymes are proteins that catalyze reactions with incredible efficiency.
While inorganic catalysts may increase reactions rates by a factor of hundreds
or thousands, organic catalysts may increase reactions rates on the order
of several million (Garrett and Grisham,
1999, p427). Such catalysts are obviously extremely useful. Possibile uses
for engineered enzymes include: |
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- creation of industrial
super-catalysts to withstand heat and pH extremes (Thermogen)
- pharmacy: new drugs; mass production
of old drugs. (example: erythromycin)
- "nanotechnology" -- molecular-sized
machines. (example:
ATP synthase motor)
- new detergents
- mass production of known enzymes
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Protein
engineering is done to modify a gene coding for a protein, in order
to create a new, recombinant protein with a different amino acid sequence
and(hopefully) new structural features or functions (Branden
and Tooze, 1999, p347). Protein engineering can be accomplished by several
different procedures that have varying probablilities of success. For example,
de novo recombinant protein engineering, the random generation of
altered amino acid sequences to create an entirely new protein, generally
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yields a "functionless blob," since proteins depend on specific interactions
between amino |
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acids to determine their
structure and function. A small number of mutations may also be made
to create stepwise changes in the activity of the proteins, although
the changes are neither always predictable nor useful. Recombinant proteins
can also be engineered by recombination of two or more known functional
domains. These domains may or may not retain their original functions
in the new protein.
Back to top
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TIM
a/b barrels |
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The
TIM barrel motif is common to many different enzymes. It was named for triose
phosphate isomerase (TIM), the enzyme in which it was first discovered.
This motif is also found in fructose-1,6-bisphosphate aldolase, Rubisco,
and a number of enzymes in the tryptophan synthesis pathway. It is important
to note that while these enzymes all share the same foundational structure,
many of them carry out different reactions. This trait is suggestive of
divergent evolution -- a phrase used to describe what occurs when several
similar things (animals, bacteria, enzymes) develop different functions
as a result of different environments (Hegyi and
Gerstein, 1998). |
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TIM barrel Chime routine |
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Figure
4 Tertiary structure
of triose phosphate isomerase displays the quintessential TIM barrel motif,
stabilized in part by hydrogen bonds (green). |
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The
TIM barrel motif consists of eight beta sheets and eight alpha helices; these
secondary structural elements are arranged so that the hydrophobic beta sheets
form a central "barrel," while the amphipathic alpha helices comprise the exterior
"shell" (Branden 48-54). The secondary structures
alternate and are connected by loops; unfolded, the protein would have a general
scheme similar to that shown below: |
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The
loops are denoted according to their position relative to the secondary
features; the loop b1a1
refers to the loop between the first beta sheet and the first alpha helix.
In general, the tertiary structure is fairly stable, held in place by a
number of hydrogen bonds. To look at the TIM barrel
using Chime, click here. |
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Figure
5 Secondary
structures in an unfolded TIM barrel. |
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Alchemy
in a Nutshell |
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[Overview]
[Background] [Structural Modification] [Selection]
[ivePRAI] [Implications]
[References] [Links]
[Chime
routine]
Nikki
Jarrett, 11/20/00
Biochemistry
462bH, Dr. D. Bourque
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