bmb 170 lecture 15 lipids and membranes, nov 14, 2017 · glycine zippers (gxxxgxxxg) are strongly...
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BMB 170 Lecture 15Lipids and Membranes, Nov 14, 2017
• Lipids• Bilayers• Membrane proteins
• Membrane protein structure websites:– Stephen White lab at UC Irvine
• “Membrane Proteins of Known 3D Structure)• http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html
S.J. Singer’s fluid mosaic modelSinger & Nicolson Science (1972) 175, 720-31 Lipid/Protein ratios
myelin 3disk memb(eye) 1E. coli 0.4purple memb 0.2
Integral membrane proteins and the phospholipid bilayer
Fig 4.27
Membrane Proteins - Overview• Lots of processes
– transport and transduction processes that mediate the flow of matter– energy and information across the membrane bilayer
• Poorly characterized relative to water-soluble proteins– experimental challenges of mimicking the membrane and water-
bilayer interfaces
• Constitute an estimated ~20-30% of all proteins, yet only <1000 distinct structures are available (116 10/06; 133 10/07; 174 10/08; 204 10/09; 261 12/10; 722 10/2017)
• ~50% of drug targets
• Corollary - lots of opportunities for research
doubling time ~ 3 years
Tuesday, Nov 15, 2016: 115374 (105570 last year) protein structures
Membrane protein types
Apolar membrane interior
2 kinds of secondary structure• α-helical - found in
cytoplasmic membranes and ER derived organelles
• β-sheets - all bacterial outer membrane proteins and outer membranes of mitochondria and chloroplasts
• The need is to satisfy the hydrogen bonding capabilities of peptide bonds
Bacterial export
Review: Wickner & Scheckman (2005) Science 310:1452
Protein translocation channel (1rhz)
• Universally conserved• Passive conduit• Opens in two directions• Hydrophilic interior• Recognizes signal sequence• Sets topology
Review: Clemons et al Curr Op Struct Bio (2004)14(4):390-6van den Berg et al Nature (2004) 427:36-44
Model for translocation
(+)
(-)
Modeling Translocation
P. Tian and I. Andricioaei (2006) Biophys J
16Å diameter ball can be pulled through the
channel.
See also J. Gumbart and K. Schulten (2006) Biophys J
Co-translation complex
Becker..Beckmann (2009) Science 326:1369
Mammalian Ribosome/Sec61 complex to 3.4Å
Voorhees, Fernández, Scheres, Hegde Cell (2014)157:1632-43
Other membrane insertasesYidC Structure
Kumazaki..Nureki Nature (2014) 509:516 (3wo6)
TatC Structures
Ramasamy..Clemons Structure (2013) 21:777 (4hts) Rollauer..Lea, Berks Nature (2012) 492:210 (4b4a)
Membrane partitioning governed by hydrophobicity• Ideal TM helices were tested
for membrane insertion with single amino acid substitutions
• Strong preferences for certain amino acids
• Membrane insertion purely driven by hydrophobicity
Review: White & von Heijne Curr Op Str Bio (2005) 15:378-86von Heijne Lab: Hessa et al Nature (2005) 433:377-81
N=window size (~21)
Hydropathy analysis of TM helices
White Lab, UC Irvinehttp://blanco.biomol.uci.edu/hydrophobicity_scales.html
http://www.cbs.dtu.dk/services/TMHMM-2.0/
von Heijne lab: Krogh et al. JMB (2001) 305:567-80
Active role for translocon?
• Partitioning model only works at steady state
• Translocon must open in relation to hydrophobic peptide
Zhang & Miller (2010) PNAS 107:5399
Removing proteins• Essential process• Bacterial components
somewhat understood• Much more complicated
in eukaryotes– Linked to many diseases– Deshaies lab
Akiyama (2009) J Biochem 146:449
Positive inside rule
• Noted by von Heijne
• TMs generally have a more positive charge on the cytoplasmic side
von Heijne (1986) EMBO J 5:3021
Genome TM prediction
von Heijne lab: Krogh et al. JMB (2001) 305:567
P. falciparum (Malaria) 2 chromosomes
• Histograms of predicted numbers of TM helices from different genomes
• Orientation preferences– Nin is favored– Nin/Cin favored
Global topology of E. coli inner membrane
• Used GFP and PhoA C-terminal fusions to establish topology
• 737 genes possible identified 601
• Data strengthens TMHMM models
• A few examples of dual topology!
• Using homology can identify 30% of all bacterial proteins (51K/660K)
• Extended it to Yeastvon Heijne lab: Daley et al Science (2005) 308:1321-3
Kim et al PNAS (2006)103(30):11142-7
Cin
Cout
Inverted repeat domains
• Common feature of some membrane proteins
• Evolutionary implications– Small Multidrug Resistant
transporter family (4TM)– Bacterial/Archael
Transporter family(5TM)– Drug/Metabolite Exporter
family (10TM)
Pornillos & Chang FEBS Letters (2006)580:358-62
YdgE/YdgF
EmrE
Route of integration
van Lehn..Miller (2015) eLifealso Woodall, Yin & Bowie (2015) Nature Comm
Glycine zippers (GXXXGXXXG) are strongly overrepresented in TM helices and provide a strong driving force for right-handed helical packing
Kim et al. PNAS (2005)102:14278; Lemmon et al. Biochemistry(1992) 31:12719
“Glycine” zippers at helix-helix interfaces
Affects of proline kinks
WT P50A
• In rhodopsin studies by Bowie et al– P50A mutation did not
remove kink– ΔΔGu = +0.1 kcal/mol
Evolution link to kinks• Not all kinks have
prolines• Proteins have lost
prolines but kept kinks
XHel
ix
P
P
Compensating Mutations
Modern day Proline kink
Y
Modern day non-proline kink
Proline peaks
80 aligned rhodopsins
40 aligned reaction centers
10 MPs (Bowie lab):
• 39 total kinks
• 22 kinks at proline
• 17 non-proline kinks. Of these, 14 show a peak of prolines in the alignment
• No proline peaks not associated with a kink
PRC Chain M: Proline frequency in 40 aligned sequences
0
5
10
15
20
25
30
35
40
45
50
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300
Residue Number
Num
ber
of P
rolin
es
A147 Kink 13o
A153 Kink 34o
P165 Kink 49o
T277 Wide turn 35o
Rhodopsin: Proline frequency in TM Helices from 80 aligned sequences
05
1015202530354045505560657075808590
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310
Residue Number
Num
ber
of P
rolin
es
P303 Kink 46o
P53 Kink 20o
T92 Wide
turn 48o
P215 Wide turn 34o
P267 Kink 44o
P291 Kink 20o
A117 Kink 20o
GPCR classes show different patterns
0102030405060708090
30 50 70 90 110 130 150 170 190 210 230 250 270 290 310
Num
ber
of P
rolin
es
Rhodopsin
Residue Number
A B C D E F G
0
10
20
30
40
50
60
70
120 145 170 195 220 245 270 295 320 345 370 395
Num
ber
of P
rolin
es
Secretin
A B C D E F G
Interfacial preference for Tyr and Trp (esp. in β-barrel MPs)
20 Å
Cowen et al Nature (1992)358:727-33 (1pho)Review: Schultz Curr Op Struct Bio (2000) 10:443-7
Polar aromatics at the interface
“…the hydrophobic force is the energetically dominant force for containment, adhesion, etc., in all life processes. This means that the entire nature of life as we know it is a slave to the hydrogen-bonded structure of liquid water.”
proteinwater
Charles Tanford Protein Science (1997) 6:1358-66
What happens when a protein leaves water (membrane proteins)?
-1 0 +1
Asp Ile
hydrophobicity
buriedsurfacewater-soluble proteins
buried / surfaceTM region, 16 α-helical mps
Spencer & Rees Annu Rev Biophys Biomol Struct (2002) 31:207-33Rees et al Science (1989) 245:510-3
Hydrophobicity scale: Eisenberg et al Faraday Symp Chem Soc (1982) 17:109-20
Hydrophobicities of buried/surface residues
In table, relative packing efficiency is the occupied volume of atoms relative to well packed soluble structures. Lower than 100% indicates a tighter packing.
Gerstein & Chothia Science (1999) 285:1682-3
Packing efficiency of buried atoms
Diacylglycerolkinase in detergent unfolding by CD
Two state model for analysis of SDS denaturation
∆G = 16 kcal/mole for membrane part
Temp dependence still unknown
• much more difficult to study (irreversible) (PROBABLY NOT TRUE ANYMORE…)
• denatured state is not completely unfolded (helices remain intact)
• detergents often destabilizing
• stability-enhancing mutants– common, unlike soluble proteins– Bowie COSB (2001)11:397-402
Membrane Protein Stability
Lau & Bowie Biochemistry (1997)36:5884
Faham et al JMB (2004)335:297-305
Bacteriorhodopsin B helixAlanine scanning to test contribution to stability
Surface residues make relatively small contribution to protein stability
destabilizingsomewhat destabilizingminimal affectstabilizing (25%)
Membrane protein stability
water membrane
• membrane proteins and water soluble proteins have similar– interior apolarities– packing densities– surface areas– patterns of residue conservation– stabilities
• and differ in – surface polarities– helix-helix packing distributions– tertiary folds
Membrane protein - water-soluble protein comparison
Slovic et al. PNAS (2004) 101:1828
Water-solubilization of KcsA
• Designed computationally then made it – confirmed binding to known inhibitors
• Different surface hydrophobicity for different solvents - same internal packing
• Water soluble proteins are membrane proteins with built-in detergent
Reviewed in Borgese et al (2007) COCB 19:368
Tail-anchored protein targeting
Cyanobacterial Get3Nostoc. PCC 7120 All4481 (3IGF)
S. cerevisiae Get3 (2WOJ)
Synechocystis PCC 6803,Hohmann-Marriott et al. 2009
Fusion
Organelle fusion
Review: Wickner & Schekman (2008) NSMB 15:658
• low pH of endosomes induces conformational change
• Eventual coiled-coil leads to fusion
Wiley & Skehel labs: Bullough et al Nature (1994) 371:37-43
Fusion peptide Membrane
fusion
Dengue low pH fusion
Harrison lab: Modis et al Nature (2004) 427:313-9 (1ok8)
This fusion is a general feature of viruses Class I: myxo/paramyxo (flu/measles), retroviruses (HIV), filoviruses (Ebola)Class II: flaviviruses (Dengue & West Nile) and alphaviruses (Semliki Forest)
low pH
C
Fusion Peptide
Lipid Anchoring
• Cytosolic face– Fatty acid
• Myristoyl (C14)– Amino group of N-terminal
glycine• Palmitoyl (C16)
– Cys residue – regulated?– Prenylation
• Polyisoprenoid– Farnesyl (C15) or geranylgeranyl
(C20)– Modified C-terminal Cys (CXXY)
• Outside– Glycosylphosphatidylinositol
• GPI- anchor• Most common in • Amide linkage to C-terminal
residue of protein• Lipid raft localization
GPI Review :Paulick & Bertozzi (2008) Biochemistry 47:6991