Summary of EMBRACE Workshop in membrane bioinformatics

websterhissΒιοτεχνολογία

1 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

55 εμφανίσεις

Summary of
the
EMBRACE Workshop
o
n
membrane bioinformatics

A

workshop
o
n "membrane bioinformatics on the web" was organi
sed as part
of the
EMBRACE

Network of Excellence

at Stockholm University, Aug 22
-
23,
2007. T
he workshop was aimed at scientists
interested in membrane proteins,
and provided an introduction to web
-
services in general and the EMBRACE
project in particular. It also provided an overview of state of the art methods
for membrane protein structure pred
ictions. A number of leading scientist
s

within the field of membrane protein bioinformatics presented and discussed
their latest results. The workshop ended with a practical dem
o
nstrati
on o
f

how
web

services from the EMBRACE project cou
ld

be used to analy
s
e
membrane protein sequences.


The focus of the workshop was how to obtain structural models of membrane
proteins. Most state of the art topology prediction methods were presented by
their develope
rs
.
Another focus was on the changed view of membrane
prot
ein structures

highlighted by recent data
. For a long time the general view
was that membrane proteins in principle existed in a two
-
dimensional space,
with the TM helices perpendi
cularly penetrating the membrane
. But as the
increasing amount of solved 3D
structures shows, TM proteins are often too
complex to fit into the constraints of topology, where all transmembrane
segments are helices of between 15
-
35 residues and all loop regions in
between are situated on opposite sides of the membrane.


We have in

a set of recent papers analyzed membrane protein structures and
shown that membrane proteins certainly can
’t

be seen as constrained into two
dimensions (Granseth:2005). Instead it is clear that membrane proteins
contain a similar amount of structural comp
lexity as globular proteins have.
For instance
,

a common feature is reentrant regions (Viklund:2006) or Z
-
coordinates (Granseth, 2006).
F
inally
,

web

services and the EMBRACE
project were introdu
ced
to

a general audience,
man
y of wh
om

had never
heard about
it before.

Short
s
ummary of presentations



Arne Elofsson
opened the workshop with an introduction to

the field
and

to

the EMBRACE project.



This was followed by a description by
Per Larsson
on

how to use
Taverna to
a
ccess SOAP based Web Services



Rita Casa
dio

discussed how to use automated, web
-
based, method
s

to
do
genome
-
scale
annotation of membrane proteins. She also
discussed different topology prediction methods and benchmarks.



David Jones

talked about his methods aimed at structure prediction of
membr
ane proteins. In particular he described the development of the
MEMSAT
-
3 method.



Costas Papaloukas introduced a novel challe
nge for membrane protein
structu
re predictions, the prediction of Z
-
coordinates. He also showed
applications of these prediction
s

i
n estimations of helix lengths etc.



Håkan Viklund talked about prediction of reentrant regions and in
particular about his new predictor, OCTOPUS.



Th
e first day
ended with a ni
ce dinner and boat
-
cruise.



Andreas Bernsel discusse
d

how experiments in the G
unnar von Heijne
lab w
ere

used to derive a biolo
g
ical hydrophobicity scale.



Gunnar von Heij
ne discussed large scale experi
ments to determine the
topology of all membrane proteins in yeast and E.
c
oli.



Anna Johansson talked about simulations of membrane pr
oteins
.




Dmitrij Frishman talked about s
tructural genomics of membrane
proteins:
fold space and target selection.




Jonathan Mullins talked about a number of ongoing projects.



Patrick Barth
t
alked about how to obtain high
-
resolution prediction and
design o
f membrane p
rotein structures using ROSETTA




Björn Wallner followed this talk by describin
g

methods to improve
coarse grained mode
lling in Rosetta
-
Membrane.



Arne Elofsson discussed the evolution of membrane protein structure



Finally
,

Per Larsson demonstra
ted how to use Taverna and EMBRACE
created web

services for membrane protein predictions. The particular
problem was to run prodiv
-
TMHMM and Zpred through Taverna.


References:

Håkan Viklund, Erik Granseth and Arne Elofsson "Reentrant regions in

alpha
-
he
lical transmembrane proteins are divided in 3 structural

classes and
abundant in small residues" J. Mol. Biol. 2006

361(3):591
-
603


Erik Granseth, Håkan Viklund and Arne Elofsson "ZPRED: Predicting the

distance to the membrane center for residues in al
pha
-
helical membrane

proteins", Bioinformatics 2006 22(14):e191
-
196


Erik Granseth, Gunnar von Heijne, Arne Elofsson "A Study of the

Membrane
-
Water Interface Region of Membrane Proteins" J. Mol. Biol

2005 346(1):377
-
85