BME
225
–
Protein
Function
in
Biology
and
Bioinformatics
Please
direct
any
enquiries
to
Dietlind
Gerloff
(gerloff@soe.ucsc.edu;
9x4833;
PSB320)
Notes (Oct 29, 2007):
Protein-Protein Interactions
Seth Rubin (Dept of Chemistry & Biomedical Sciences)
Fri Nov 2, 2p in PSB305
- check out
the
BME281G www-page for more details.
Course
description
Course
reviewing
functional
roles
of
proteins
and
computational
methods
used
to
predict
functional
aspects
of
proteins.
The
primary
focus
will
be
on
molecular
function
(catalysis
of
biochemical
reactions;
physical
interactions
with
DNA,
RNA,
or
other
proteins;
ion
channels
etc.)
and
structure-function
relationships.
Wider-reaching
notions
of
function
(pathways,
interaction
networks)
will
be
considered
peripherally,
as
the
context
in
which
molecular
function
occurs.
The
course
will
include
lectures,
(computational)
lab
work,
and
discussions
of
topical
publications.
Prerequisite(s):
Biochemistry
100A
or
higher
(or
equivalent
knowledge)
and/or
Chemistry
200B;
BME205B
and
BME220B
are
recommended
but
not
required.
Enrollment
is
restricted
to
graduate
students;
students
not
satisfying
the
prerequisite
requirement
may
seek
instructor's
permission
to
enroll
with
additional
reading
assignments.
Course
times
and
location
TUE
2-3:45p
and
THU
1-2:45p -
Class
room: PSB305
(Physical
Sciences
Building)
Lecture Topics and Slides:
As the course progresses, I will keep a list of the topics we
discussed here.
A list with suggested predicton servers and/or methods to
investigate during your BME225 research assignment can be
found here (posted
Oct 16). (Provisional)
Overall Course
Outline
and
Structure The
course
will
generally
involve
one
taught
session
(lecture)
and
one
applied/practical
session
(computational
lab
exercises;
paper
discussions;
student
presentations)
per
week. The
course
is
loosely
structured
in
a
biological
part
(overviewing
the
diversity
of
natural
protein
function
on
behalf
of
examples,
and
the
wetlab
methods
used
for
functional
characterization)
and
a
bioinformatics
part
(reviewing
current
strategies
and
methods
to
predict
function).
An
overview
of
due
dates
for
assignments
etc
(as
discussed
briefly
in
class
during
week
1)
can
be
found
here.
The
topics
tenatively
scheduled
for
each
week
are: By
comparison
to
protein
structure
the
term
"protein
function"
is
far
less
well
defined.
Researchers
will
use
the
term
vaguely
and
differently
depending
on
their
background
and
interests.
What
schemes
are
there
to
sub-classify
the
wide
variety
of
functions
carried
out
by
proteins
in
their
natural
environment
-
what
are
their
strengths
and
weaknesses? Week
2
+
3:
Enzymes The
best
understood
type
of
molecular
function
is
catalysis
of
a
biochemical
reaction.
We
also
know
the
3D-structures
of
many
enzymes.
Can
we
understand
their
mechanisms
(better)
by
looking
at
these
structures
–
are
there
commonalities
that
may
be
useful
for
predicting
enzyme
function?
Interactions
between
proteins
and
DNA
and/or
RNA
are
crucial
to
all
transcriptional
regulation.
Best
understood
and
characterized
are
specific
interactions,
e.g.
recognition
of
a
promoter
sequence
by
a
transcription
factor.
Additionally
there
are
a
variety
of
more
"generic"
DNA/RNA-binding
events
that
are
of
great
importance,
e.g.
for
discarding
unwanted
RNA
molecules
etc.
Do
3D-structures
provide
enough
information
to
"break
the
recognition
code"â
How
much
constraint
is
imposed
onto
evolutionary
sequence
variation
by
this
type
of
function? Due
to
an
(even)
greater
variety
in
shape
and
physicochemical
properties
in
protein
partners,
the
diversity
in
protein-protein
interactions
is
almost
ungraspable
(for
us
bioinformaticians).
Issues
to
consider
and
discuss
here
are:
transient
versus
permanent
interactions,
conformational
changes
(including
those
triggered
by
post-translational
modifications)
,
specific
versus
unspecific
interactions.
Where
may
lie
clues
for
prediction
methods
basing
on
sequence
and/or
structure? There
are
many
other
types
of
protein
function
that
may
be
considered
variations
or
combinations
of
the
types
discussed
previously,
or
not.
Our
knowledge
of
molecular
protein
function
is
generally
limited
to
"well-behaved"
proteins,
i.e.
those
adopting
well-defined
3D-structures,
typically
at
a
minimum
energy
state.
What
other
proteins
are
there
and
are
their
functions
not
also
molecular
in
nature?
What
clues
toward
protein
function
can
be
gained
by
proteomic
(experimental
high-throughput)
methods? Where
these
have
not
been
mentioned
during
the
previous
weeks,
a
selection
of
existing
computational
strategies
to
tackle
protein
function
prediction
will
be
reviewed
and
discussed.
Why
is
prediction
of
function
so
difficult?
This
part
of
the
course
will
include
student
presentations
and
discussions
guided
by
the
instructor. Evaluation
(revised
Oct
4,
2007)
Students
will
be
evaluated
based
on
their
performance
on 1.
Two
homework
assignments
(20%
each) 2.
An
individual
project
involving
literature
and
WWW/computational
research,
evaluated
based
on
a
summary
report/paper*
(max
10
pages;
research
to
be
carried
out
before
Week
8)
(40%) 3.
A
presentation
of
the
project
results
to
the
class
(10%) 4.
Participation
in
class
(10%) *:
Note
that
students
involved
in
thesis/rotation
research
are
not
required
to
submit
a
written
project
report
but
can
opt
Week
1:
Protein
function
–
general
overview
and
classification
schemes
Week
4:
DNA/RNA-protein
interactions
Week
5
+
6:
Protein-protein
interactions
Week
7:
Other
functions
and
consideration
of
a
wider
context
Week
8-10:
Computational
methods
for
function
prediction