membranes & membane proteins
Post on 03-Jun-2018
226 Views
Preview:
TRANSCRIPT
-
8/13/2019 Membranes & Membane Proteins
1/47
Membranes/membrane proteins
Importance of membranes and membraneproteins
General requirements for proteins to residein biological membranes
Different types of membrane proteins
-helical proteins Trans-membrane helix interactions
-
8/13/2019 Membranes & Membane Proteins
2/47
Biological Membranes
Highly selective permeability barriers Amphiphilic organization: Hydrophobic in,
hydrophilic out Fluid mosaic model: liquid and asymmetric
-
8/13/2019 Membranes & Membane Proteins
3/47
Importance of membranes
Compartimentalization: specific chemical environmentpH, redox potential,enzymatic composition, ioncomposition etc.
-
8/13/2019 Membranes & Membane Proteins
4/47
Higher organization
Compartimentalization: specific chemical environmentpH, redox potential,enzymatic composition, ion composition etc.
Lyzosomes contains enzymes fordegradation of macromoleculesat low pH
Organization into organelles
Mitochondrion
-
8/13/2019 Membranes & Membane Proteins
5/47
Membrane structures inorganelles
Inside mitochondria and chloroplasts further compartimentalization
-
8/13/2019 Membranes & Membane Proteins
6/47
Importance of membranes
Chemical insulators: Charge gradient, energy generationProton gradient, energy generationIon gradients, signaling
Peter Mitchell's, Chemiosmotic Theory, Nobel prize 1978
-
8/13/2019 Membranes & Membane Proteins
7/47
Chemiosmotic Theory
-
8/13/2019 Membranes & Membane Proteins
8/47
-
8/13/2019 Membranes & Membane Proteins
9/47
Fundamental importance
-
8/13/2019 Membranes & Membane Proteins
10/47
Fundamental importance
-
8/13/2019 Membranes & Membane Proteins
11/47
Fundamental importance
genomic composition: 20-30% of thegenes code for membrane proteins
pdb statistics, 25.000 structures250 membrane proteins
-
8/13/2019 Membranes & Membane Proteins
12/47
Medical importance
Cytic fybrosis, chloride transporter Virus entry and maturation, receptors
Resistance against cytostatica, multi drugresistance proteins Bacterial infection, adhesins, transporters Certain cancer types Immune system Regulated cell death/apoptosis
-
8/13/2019 Membranes & Membane Proteins
13/47
Economical importance
marketed small molecule drug targets grouped by class
-
8/13/2019 Membranes & Membane Proteins
14/47
Fluid mosaic modelSinger and Nicholson, 1972
-
8/13/2019 Membranes & Membane Proteins
15/47
Integral and PeripheralMembrane Proteins
Integral (yellow): bound by Hydrophobic interactions, can only beremoved by disruption of membranes, examples are cytochromeoxidase, GPCRs, channels.
Peripheral (blue): Bound by electrostatic and H-bond interactions,i.e. mitochondrial cytochrome c .
-
8/13/2019 Membranes & Membane Proteins
16/47
Types of Membrane Proteins
-
8/13/2019 Membranes & Membane Proteins
17/47
-helical and -barrelmembrane proteins
Photosystem I OmpF
-
8/13/2019 Membranes & Membane Proteins
18/47
It costs energy to break hydrogenbonds in hydrophobic environments
It costs ~ 2 kcal/mol to bring one hydrogenbond from water into alkane. (C=O.H-N).
It costs ~6 kcal/mol to bring one hydrated pairof hydrogen bond donor/acceptor into alkane.(C=OH 2O; N-HH 2O).
It thus costs about 4 kcal/mol/peptide bond tomaintain unfolded/unsatisfied hydrogen
bonds in a membrane: It is impossible for anunfolded protein to reside in a membrane.
-
8/13/2019 Membranes & Membane Proteins
19/47
Main-chain hydrogen bonds
membranehydrophobiccore
-helical proteins vs. - barrel proteins
The hydrogen-bonding patterns imply that -barrel proteins have to befolded prior to insertion into the membrane, whereas presence of2ndary structure is sufficient for helical proteins.
-
8/13/2019 Membranes & Membane Proteins
20/47
Localization of and membrane proteins
-helical proteinsbacterial inner membranescell membranesER, golgi complexorganelle membranesinner and outer membranesof chloroplast andmitochondria
viruses
- barrel proteinouter membranes ofGram-negative bacteriaouter membranes ofchloroplasts and mitochondria
-
8/13/2019 Membranes & Membane Proteins
21/47
Polytopic Membrane Proteins:Helical Proteins
Bacteriorhodopsin converts light into electrochemical energy. First structure of membrane protein, done by electron microscopy. 7 Transmembrane helices, almost perpendicular to membrane. Discussed in detail Bioenergetics
-
8/13/2019 Membranes & Membane Proteins
22/47
Main Chain Hydrogen Bondsin -helices
Main chain hydrogen-bond donors andacceptors all participatein hydrogen bonds.
Helical membraneproteins are commonbecause it is easy tosatisfy hydrogen bond
requirements.
Side chains
-
8/13/2019 Membranes & Membane Proteins
23/47
All side chains point outwardsinto membrane: They all need tobe hydrophobic.
helices are readily recognised insequence by stretches ofhydrophobic residues.
Side chainsin transmembrane -helices
Hydrophobic residues in yellow
-
8/13/2019 Membranes & Membane Proteins
24/47
TM Amino acid composition
R K E D Q N H P Y W S T G A M C F L V I0
2
4
6
8
10
12
14
16
TM H. Sapiens (all)
Amino acid residue
a v e r a g e o c c u r e n c e
(adapted from Lui et al. Genome Biol 2002 and with data from Sanger institute)
Hydrophobic residues are overrepresentedCharged and polar residues are
under represented
-
8/13/2019 Membranes & Membane Proteins
25/47
helical proteins Identification of helical membrane proteins Hydrophobicity plots
MALEPETVTVSEVVSPEYLDMRRRFWIALMLTIPVVILEMGGHGLKHFISGNGSSWIQLL
Kyte and Doolittle hydrophobicity scale-4.5 most polar, 4.5 most hydrophobicAla: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900Tyr: -1.300 Val: 4.200
- Take average hydrophobicity of 9 residues(a window) assign that to the central residue.- Shift the window by one residue etc.
Kyte, J. and Doolittle, R. 1982. J . Mol. Biol.
-
8/13/2019 Membranes & Membane Proteins
26/47
Hydropathy plotsMALEPETVTVSEVVSPEYLDMRRRFWIALMLTIPVVILEMGGHGLKHFISGNGSSWIQLL
-
8/13/2019 Membranes & Membane Proteins
27/47
TM regions
http://www.expasy.org/tools/protscale.html
7-8 predicted helices
-
8/13/2019 Membranes & Membane Proteins
28/47
Number of TM regions
TM = Trans Membrane(Adapted from Krogh et al, JMB 2001)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18012
3456789
1011121314151617
Num ber of helices
O c c u r e n c e
i n %
Predicted number of TMhelices in the E. coli genome
-
8/13/2019 Membranes & Membane Proteins
29/47
Number of TM regions
(Adapted from Krogh et al, JMB 2001)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 180
2.55
7.5
1012.5
1517.5
2022.5
2527.5
30
32.535
37.5
num ber of TM helices
o c c u r e n c e
i n %
Predicted number of TM helicesin the E. coli , C. elegans genome
-
8/13/2019 Membranes & Membane Proteins
30/47
Interface residues
Aromatic residues (Trp, Tyr
and Phe) are abundant at thepolar/apolar border
Tyrosine hydroxyl pointoutward
-
8/13/2019 Membranes & Membane Proteins
31/47
Helix angles
bacteriorhodopsin
-
8/13/2019 Membranes & Membane Proteins
32/47
Helix angles
Van den Burg et al. Nature 2004
SecYEG complex
~0-35 o tilt
avarage~ 21 o
-
8/13/2019 Membranes & Membane Proteins
33/47
The hydrophobic effect
The hydrophobic effect gives soluble proteins their compactness.
aqueous
solvent
hydrophobic
polar
ordered solvent
b h l
-
8/13/2019 Membranes & Membane Proteins
34/47
Interaction between helices
What then gives TM proteins their compactness and stability?
aqueous
solvent
hydrophobic
polar
Interaction between helices
-
8/13/2019 Membranes & Membane Proteins
35/47
Polar interactionsFew polar residues in TM regions
Those that are often involved in inter-TM hydrogen bonds
Rhodopsin
Ubarretxena-Belandia and Engelman, Curr. Op. Struc. Biol. 2001
Interaction between helices
-
8/13/2019 Membranes & Membane Proteins
36/47
Glycophorin ATM most often form coiled-coils (left-handed, right-handed)
Knob into holes packingby hydrophobic residues
Close VdW interaction packing
Protein-protein packing moreefficient that lipid protein packing
LIxxGVxxGVxxT
MacKenzie et al. (1997) Science 276 , 131-133.
Helical wheel
-
8/13/2019 Membranes & Membane Proteins
37/47
motifHelix 3.6 residue per turn
Residue n and n+4 point inabout same direction
Heptad repeat, 7 residues
Interaction between helices
-
8/13/2019 Membranes & Membane Proteins
38/47
GXXXG motif
LIxxGxxxG VxxT in glycophorin A
GXXXG (or GG4) very close packing
Formation of C -H --- O hydrogen bonds
In hydrophobic environment C -H --- Oabout half strength of ordinary NH --- O
MacKenzie et al. (1997) Science 276 , 131-133.
-
8/13/2019 Membranes & Membane Proteins
39/47
Identif ing interactions: TOXCAT
-
8/13/2019 Membranes & Membane Proteins
40/47
Identifying interactions: TOXCAT
TOXCAT system: MBP domain-membrane helix-ToxR domain
Oligomerization activates ToxR
Oligomeric ToxR controls expressionof chloramphenicol-acetyl transferase(CAT)
CAT gives resistance againstchloramphenicol Giving resistanceagainst
Russ and Engelman PNAS 1999
-
8/13/2019 Membranes & Membane Proteins
41/47
Other Motifs
-
8/13/2019 Membranes & Membane Proteins
42/47
Other Motifs
SxxSSxxT
SxxxSSxxT
GxxxxxxG
AxxxA
Monotopic membrane proteins
-
8/13/2019 Membranes & Membane Proteins
43/47
Monotopic membrane proteins
Are embedded in but do not traverse themembrane completely
Example: Prostaglandin N-synthase
-
8/13/2019 Membranes & Membane Proteins
44/47
F i P l di S h
-
8/13/2019 Membranes & Membane Proteins
45/47
Function Prostaglandin Synthase
Catalyses synthesis ofProstaglandin H 2 fromarachidonic acid.
The fatty acid is ahydrophobic degradationproduct of lipids.
Prostaglandins are signal
molecules
-
8/13/2019 Membranes & Membane Proteins
46/47
Summarized
-
8/13/2019 Membranes & Membane Proteins
47/47
SummarizedImportance of membrane proteins
Hydrogen bonds satisfied within hydrophobic part of membranes
Side-chains of TM a-helix hydrophobic
Interactions between TM-helices- Polar interaction side chains
- VdW interactions due to close packing
- C-H...O hydrogen bond
Monotopic membrane protein architecture
top related