Membrane proteins

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Membrane proteins
Notes based mostly on Branden Tooze,
Introduction to Protein Structure, 2nd Ed.
Chapter 12.
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Classes of membrane proteins

• Single transmembrane helix
• several transmembrane helices
• beta-barrel or channel
• Anchored by one (not-transmembrane) helix or a
  covalently attached fatty acid

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Photosystem I
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Photosystem I Guided tour
Download and display 1JB0.pdb (one jay bee
zero) restrict !protein and !hohcolor
cpkDisplay -gt ball and stickselect
magnesiumlabel rset fontsize 12set fontstroke
2color labels yellow
Find the pseudo 2-fold axis
How many Mg are there?
What are the residue numbers of the special
pair of chlorophylls?
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Photosystem I Guided tour
(select the special pair using select XXX or
YYY)spacefillselect hetero and !hohlabels
offcolor temperature
How are the B-factorsdistributed?
Was NCS 2-fold symmetry enforced during
refinement?
Which side is more ordered? Chain A or chain B?
Guess what 2-fold symmetry was not enforced
during evolution!
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Photosystem I Guided tour
Find the name of the lipid that does not havea
phosphate group.
Unix shortcut use grepgrep HETNAM 1JB0.pdb
Characterize the environmentof the lipid. Could
it have a role in the light harvest process?
select LMGrestrict selectedcenter
selectedselect within (11., LMG) and
proteinDisplay -gt ball_and_stickcolor
cpkselect within (11., LMG) and ligand
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Photosystem I Guided tour
select within (11., LMG) and ligandspacefill
1.5color green select within (11., LMG) and
.MGspacefill 1.5color white select within
(11., LMG) and PQNcolor red select within
(11., LMG) and solventspacefill 1.0color cyan
What is PQN?How close is it to the
nearestmagnesium
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Photosystem I Guided tour
restrict ligandwireframecolor cpkDisplay-gt
ball and stickselect CL1 or CL2wireframe
color greenselect PQNcolor magentaspacefill
1.0select BCRcolor orangespacefill
1.5select .MGspacefill 1.0color white
Light harvesting complex
Trace the path of the electronsfrom the special
pair to the twoquinones.
Are are of the pigmentsconnected to the special
pair?
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Photosystem I Guided tour
restrict PQNspacefill color cpkselect within
(11.,PQN) and proteinwireframe 0.5color
cpkselect within (11.,PQN) and ligand and not
PQNcolor greenwireframe 0.5select within
(11.,PQN) and solvent spacefill 0.6color cyan
Environment of the quinones
Which quinone is more loosely-bound
How does the electron getfrom one quinone to
theother? What protein sidechainforms a bridge?
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Photosystem I Guided tour
Draw a TOPS diagram of chain D residues 24-95 only
Look in scop.berkeley.edu for the fold under
alphabetaWhat fold is this?
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