Bioinformatic Techniques on Marine Genomics 10.13 Conclusions and New Frontiers 303
Part B | 10.13
hibit tubulin polymerization or interrupt microtubule
depolymerization would be useful in the treatment of
cancer. In recent decades, several compounds, mostly
natural products, targeting tubulin have been discovered
and developed; some of them are already in clinical use,
such as epothilone, paclitaxel, and vindesine.
Recent studies reveal that the antitubulin agents targeting the colchicine sites could, in addition to their antimitotic action, shut down the blood supply to tumors
by disassembling the microtubules of abnormal vasculatures and changing the endothelial cell morphology,
which would consequently cause nutrient starvation of
tumor cells and eventually lead to apoptosis. These
vascular-disrupting agents, e.g., combretastatin (CA4),
provide a promising new approach in the treatment of
cancer and are currently under clinical evaluation for
single-drug cancer therapy or multidrug treatment in
combination with other cytotoxic drugs and antiangiogenic agents.
10.11.1 CBM4-2 Carbohydrate Binding
Module from a Thermostable
Rhodothermus marinus Xylanase
The family of CBM4-2 structures was calculated using
hybrid distance geometry/simulated annealing protocol
following methods similar to those used by Sorimachi
et al. [10.30] and Simpson et al. [10.31]. The final set
of restraints contained 1654 nonredundant unambiguous NOEs and ambiguous NOEs, 93 æ, 72 ø1, and
1 ø2 restraints, and 65 pairs of hydrogen bond restraints, plus 177 backbone dihedral restraints based
on chemical shifts from TALOS. Almost all hydrogen
bond restraints were limited to those expected from
the regular secondary structure, except for Ala4-Ile164
and Asn79-Ala4, which contribute to tertiary structure,
together with Trp28-Val25, Val36-Gly33, and Trp69Asn67, which are involved in â-turns. The final restraint
set had 12:8 restraints per residue. The first 12 models
had a very similar energy and showed no NOE violations greater than 0:2 Å and no angle violations greater
than 5
ı . Hence, these models were selected to represent the solution structure of CBM4-2. The average
structure was calculated from these 12 structures (by
selecting the lowest energy structure and superimposing the remaining 11 on this one) and was subsequently
subjected to restrained energy minimization to yield
the minimized average structure. The 12 best structures
and the average structure have been deposited with the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank (PDB ID 1k42 (ensemble) and 1k45
(minimized average)).
10.12 The Polymerase Chain Reaction: A Marine Perspective
A major step in the widespread application and development of the polymerase chain reaction was undoubtedly
the early use of the heat stable DNA polymerase Taq.
Owing to commercial interest in manufacturing different heat stable polymerases, a larger number of enzymes
from hot springs and marine environments were subsequently reported. The fidelity of these enzymes also
differed, and one enzyme, that from the marine thermophile Pyrococcus furiosus, named Pfu, was found to
have superior copying fidelity and is now a widely used
polymerase chain reaction PCR reagent. P. furiosus was
isolated from geothermally heated marine sediments on
Vulcano Island, Italy, and is a good example of marine biodiversity providing useful solutions to analytical
methods. The widespread use of PCR and high throughput sequencing has allowed us to realize that the vast
majority of marine microbes remain to be isolated and
studied even though their genes are now accessible.
10.13 Conclusions and New Frontiers
It is clear that once a significant advance has been
made in physics, mathematics or chemistry, it is often
decades before optimization, improved instrumentation, and increased awareness allow the use of these
new techniques in biotechnology. It would, therefore,
be interesting to look into the world of physics and
mathematics today and asks our colleagues in those disciplines what the key breakthroughs have been in the
last few years, so that we might deliberately accelerate their uptake into both mainstream biotechnology
and biotechnology of the sea. Recent reports have highlighted the problems arising from the need to handle,
Part B | 10.13
hibit tubulin polymerization or interrupt microtubule
depolymerization would be useful in the treatment of
cancer. In recent decades, several compounds, mostly
natural products, targeting tubulin have been discovered
and developed; some of them are already in clinical use,
such as epothilone, paclitaxel, and vindesine.
Recent studies reveal that the antitubulin agents targeting the colchicine sites could, in addition to their antimitotic action, shut down the blood supply to tumors
by disassembling the microtubules of abnormal vasculatures and changing the endothelial cell morphology,
which would consequently cause nutrient starvation of
tumor cells and eventually lead to apoptosis. These
vascular-disrupting agents, e.g., combretastatin (CA4),
provide a promising new approach in the treatment of
cancer and are currently under clinical evaluation for
single-drug cancer therapy or multidrug treatment in
combination with other cytotoxic drugs and antiangiogenic agents.
10.11.1 CBM4-2 Carbohydrate Binding
Module from a Thermostable
Rhodothermus marinus Xylanase
The family of CBM4-2 structures was calculated using
hybrid distance geometry/simulated annealing protocol
following methods similar to those used by Sorimachi
et al. [10.30] and Simpson et al. [10.31]. The final set
of restraints contained 1654 nonredundant unambiguous NOEs and ambiguous NOEs, 93 æ, 72 ø1, and
1 ø2 restraints, and 65 pairs of hydrogen bond restraints, plus 177 backbone dihedral restraints based
on chemical shifts from TALOS. Almost all hydrogen
bond restraints were limited to those expected from
the regular secondary structure, except for Ala4-Ile164
and Asn79-Ala4, which contribute to tertiary structure,
together with Trp28-Val25, Val36-Gly33, and Trp69Asn67, which are involved in â-turns. The final restraint
set had 12:8 restraints per residue. The first 12 models
had a very similar energy and showed no NOE violations greater than 0:2 Å and no angle violations greater
than 5
ı . Hence, these models were selected to represent the solution structure of CBM4-2. The average
structure was calculated from these 12 structures (by
selecting the lowest energy structure and superimposing the remaining 11 on this one) and was subsequently
subjected to restrained energy minimization to yield
the minimized average structure. The 12 best structures
and the average structure have been deposited with the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank (PDB ID 1k42 (ensemble) and 1k45
(minimized average)).
10.12 The Polymerase Chain Reaction: A Marine Perspective
A major step in the widespread application and development of the polymerase chain reaction was undoubtedly
the early use of the heat stable DNA polymerase Taq.
Owing to commercial interest in manufacturing different heat stable polymerases, a larger number of enzymes
from hot springs and marine environments were subsequently reported. The fidelity of these enzymes also
differed, and one enzyme, that from the marine thermophile Pyrococcus furiosus, named Pfu, was found to
have superior copying fidelity and is now a widely used
polymerase chain reaction PCR reagent. P. furiosus was
isolated from geothermally heated marine sediments on
Vulcano Island, Italy, and is a good example of marine biodiversity providing useful solutions to analytical
methods. The widespread use of PCR and high throughput sequencing has allowed us to realize that the vast
majority of marine microbes remain to be isolated and
studied even though their genes are now accessible.
10.13 Conclusions and New Frontiers
It is clear that once a significant advance has been
made in physics, mathematics or chemistry, it is often
decades before optimization, improved instrumentation, and increased awareness allow the use of these
new techniques in biotechnology. It would, therefore,
be interesting to look into the world of physics and
mathematics today and asks our colleagues in those disciplines what the key breakthroughs have been in the
last few years, so that we might deliberately accelerate their uptake into both mainstream biotechnology
and biotechnology of the sea. Recent reports have highlighted the problems arising from the need to handle,