Peripheral membrane protein

Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure. Proteins with GPI anchors are an exception to this rule and can have purification properties similar to those of integral membrane proteins.

The reversible attachment of proteins to biological membranes has shown to regulate cell signaling and many other important cellular events, through a variety of mechanisms. David S. Cafiso Structure and interactions of C2 domains at membrane surfaces. In: cite book |author=Tamm LK (Editor) |title=Protein-Lipid Interactions: From Membrane Domains to Cellular Networks| url=http://books.google.com/books?vid=ISBN3527311513 | pages=pp.403-22 | publisher=John Wiley & Sons |location=Chichester |year= 2005 | isbn=3-527-31151-3] For example, the close association between many enzymes and biological membranes may bring them into close proximity with their lipid substrate(s).cite journal |author=Ghosh M, Tucker, DE. "et al" |title=Properties of group IV phospholipase A₂ family (review) |journal=Prog. Lipid. Res. |volume=45 |issue=6 |pages=487–510 |year= 2006 |pmid=16814865 |doi=10.1016/j.plipres.2006.05.003] Membrane binding may also promote rearrangement, dissociation, or conformational changes within many protein structural domains, resulting in an activation of their biological activity.cite journal |author=Guruvasuthevan RT, Craig JW "et al" |title=Evidence that membrane insertion of the cytosolic domain of Bcl-xL is governed by an electrostatic mechanism | journal=J. Mol. Biol. | volume=359 | issue=4 | pages=1045-1058 |year= 2006 |pmid=16650855 | doi = 10.1016/j.jmb.2006.03.052 ] Additionally, the positioning of many proteins are localized to either the inner or outer surfaces or leaflets of their resident membrane.cite journal |author=Takida S and Wedegaertner PB |title=Exocytic pathway-independent plasma membrane targeting of heterotrimeric G proteins |journal=FEBS Letters |volume=567 | pages=209–213 |year= 2004 |pmid=15178324 |doi=10.1016/j.febslet.2004.04.062] This facilitates the assembly of multi-protein complexes by increasing the probability of any appropriate protein-protein interactions.

:1. interaction by an amphipathic α-helix parallel to the membrane plane (in-plane membrane helix)2. interaction by a hydrophic loop3. interaction by a covalently bound membrane lipid ("lipidation")4. electrostatic or ionic interactions with membrane lipids ("e.g." through a calcium ion)
]

Binding of peripheral proteins to the lipid bilayer

Peripheral membrane proteins may interact with other proteins or directly with the lipid bilayer. In the latter case, they are then known as "amphitropic" proteins.cite journal |author=Johnson J, Cornell R |title=Amphitropic proteins: regulation by reversible membrane interactions (review) |journal=Mol Membr Biol |volume=16 |issue=3 |pages=217-35 |year= 2002 |pmid=10503244 | doi = 10.1080/096876899294544 ] Some proteins, such as G-proteins and certain protein kinases, interact with transmembrane proteins and the lipid bilayer simultaneously. Some polypeptide hormones, antimicrobial peptides, and neurotoxins accumulate at the membrane surface prior to locating and interacting with their cell surface receptor targets, which may themselves be peripheral membrane proteins.

The Phospholipid bilayer that forms the cell surface membrane consists of a hydrophobic inner core region sandwiched between two regions of hydrophilicity, one at the inner surface and one at the outer surface of the cell membrane (see lipid bilayer article for a more detailed structural description of the cell membrane). The inner and outer surfaces, or interfacial regions, of model phospholipid bilayers have been shown to have a thickness of around 8 to 10 Å, although this may be wider in biological membranes that include large amounts of gangliosides or lipopolysaccharides.cite book | last = McIntosh | first = TJ | coauthors = Vidal A, Simon SA |title = The energetics of peptide-lipid interactions: modification by interfacial dipoles and cholesterol. "In" Current Topics in Membranes (52) | pages= pp. 205–253 | publisher = Academic Press | year = 2003 | id = ISBN 978-0126438710] The hydrophobic inner core region of typical biological membranes may have a thickness of around 27 to 32 Å, as estimated by Small angle X-ray scattering (SAXS).cite journal |author=Mitra K, Ubarretxena-Belandia I, Taguchi T, Warren G, Engelman D |title=Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol |journal=Proc Natl Acad Sci U S A |volume=101 |issue=12 |pages=4083–8 |year=2004 |pmid=15016920 |doi=10.1073/pnas.0307332101] The boundary region between the hydrophobic inner core and the hydrophilic interfacial regions is very narrow, at around 3Å, (see lipid bilayer article for a description of its component chemical groups). Moving outwards away from the hydrophobic core region and into the interfacial hydrophilic region, the effective concentration of water rapidly changes across this boundary layer, from nearly zero to a concentration of around 2M.cite journal |author=Marsh D |title=Polarity and permeation profiles in lipid membranes |journal=Proc Natl Acad Sci U S A |volume=98 |issue=14 |pages=7777–82 |year=2001 |pmid=11438731 |doi=10.1073/pnas.131023798] cite journal |author=Marsh D |title=Membrane water-penetration profiles from spin labels |journal=Eur Biophys J |volume=31 |issue=7 |pages=559–62 |year=2002 |pmid=12602343 |doi=10.1007/s00249-002-0245-z] The phosphate groups within phospholipid bilayers are fully hydrated or saturated with water and are situated around 5 Å outside the boundary of the hydrophobic core region (see Figures ).cite journal |author=Nagle J, Tristram-Nagle S |title=Structure of lipid bilayers |journal=Biochim Biophys Acta |volume=1469 |issue=3 |pages=159–95 |year=2000 |pmid=11063882]

Some water-soluble proteins associate with lipid bilayers "irreversibly" and can form transmembrane alpha-helical or beta-barrel channels. Such transformations occur in pore forming toxins such as colicin A, alpha-hemolysin, and others. They may also occur in BcL-2 like proteins which has been shown to play a role in cellular apoptosis , in some amphiphilic antimicrobial peptides , and in certain annexins . These proteins are usually described as peripheral as one of their conformational states is water-soluble or only loosely associated with a membrane.cite journal |author=Goñi F |title=Non-permanent proteins in membranes: when proteins come as visitors (Review) |journal=Mol Membr Biol |volume=19 |issue=4 |pages=237-45 |year= 2002|pmid=12512770 | doi = 10.1080/0968768021000035078 ]

Membrane binding mechanisms

The association of a protein with a lipid bilayer may involve significant changes within tertiary structure of a protein. These may include the folding of regions of protein structure that were previously unfolded or a re-arrangement in the folding or a refolding of the membrane-associated part of the proteins . It also may involve the formation or dissociation of protein quaternary structures or oligomeric complexes, and specific binding of ions, ligands, or regulatory lipids.

Typical amphitropic proteins must interact strongly with the lipid bilayer in order to perform their biological functions. These include the enzymatic processing of lipids and other hydrophobic substances, membrane anchoring, and the binding and transfer of small nonpolar compounds between different cellular membranes. These proteins may be anchored to the bilayer as a result of hydrophobic interactions between the bilayer and exposed nonpolar residues at the suface of a protein, by specific non-covalent binding interactions with regulatory lipids , or through their attachment to covalently-bound lipid anchors.

It has been shown that the membrane binding affinities of many peripheral proteins depend on the specific lipid composition of the membrane with which they are associated. cite journal |author=McIntosh T, Simon S |title=Roles of bilayer material properties in function and distribution of membrane proteins |journal=Annu Rev Biophys Biomol Struct |volume=35 |issue= |pages=177–98 |year=2006 |pmid=16689633|url= http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.35.040405.102022?journalCode=biophys |doi=10.1146/annurev.biophys.35.040405.102022 ]

Non-specific hydrophobic association

Amphitropic proteins associate with lipid bilayers via various hydrophobic anchor structures. Such as amphiphilic α-helixes, exposed nonpolar loops, post-translationally acylated or lipidated amino acid residues, or acyl chains of specifically bound regulatory lipids such as phosphatidylinositol phosphates. Hydrophobic interactions have been shown to be important even for highly cationic peptides and proteins, such as the polybasic domain of the MARCKS protein or histactophilin, when their natural hydrophobic anchors are present.

Covalently bound lipid anchors

Lipid anchored proteins are covalently attached to different fatty acid acyl chains on the cytoplasmic side of the cell membrane via palmitoylation, myristoylation, or prenylation. At the cell surface, on the opposite side of the cell membrane lipid anchored proteins are covalently attached to the lipids glycosylphosphatidylinositol (GPI) and cholesterol.cite book | last = Silvius | first = JR | title = Lipidated peptides as tools for understanding the membrane interactions of lipid-modified proteins. "In" Current Topics in Membranes (52) | pages= pp. 371–395 | publisher = Academic Press | year = 2003 | id = ISBN 978-0126438710] cite book | last = Baumann | first = NA | coauthors = Mennon AK | title = Lipid modifications of proteins. "In" DE Vance and JE Vance (Eds.) Biochemistry of Lipids, Lipoproteins and Membranes | pages = pp. 37–54 | edition = 4th ed. | publisher = Elsevier Science | year = 2002 | id = ISBN 978-0444511393] Protein association with membranes through the use of acylated residues is a reversible process, as the acyl chain can be buried in a protein's hydrophobic binding pocket after dissociation from the membrane. This process occurs within the beta-subunits of G-proteins . Perhaps because of this additional need for structural flexibility, lipid anchors are usually bound to the highly flexible segments of proteins tertiary structure that are not well resolved by protein crystalographic studies.

pecific protein-lipid binding

Some cytosolic proteins are recruited to different cellular membranes by recognizing certain types of lipid found within a given membrane.cite journal |author= Cho, W. and Stahelin, R.V. |year=2005|title= Membrane-protein interactions in cell signaling and membrane trafficking|journal=Annual Review of Biophysics and Biomolecular Structure|volume= 34|pages= 119–151|month=June |doi=10.1146/annurev.biophys.33.110502.133337 |url= http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.33.110502.133337?cookieSet=1&journalCode=biophys |accessdate=2007-01-23 | pmid = 15869386 ] Binding of a protein to a specific lipid occurs via specific membrane-targeting structural domains that occur within the protein and have specific binding pockets for the lipid head groups of the lipids to which they bind. This is a typical biochemical protein-ligand interaction, and is stabilized by the formation of intermolecular hydrogen bonds, van der Waals interactions, and hydrophobic interactions between the protein and lipid ligand. Such complexes are also stabilized by the formation of ionic bridges between the aspartate or glutamate residues of the protein and lipid phosphates via interveening calcium ions (Ca²⁺). Such ionic bridges can occur and are stable when ions (such as Ca²⁺) are already bound to a protein in solution, prior to lipid binding. The formation of ionic bridges is seen in the protein-lipid interaction between both protein C2 type domains and annexins.

Protein-lipid electrostatic interactions

Any positively charged protein will be attracted to a negatively charged membrane by nonspecific electrostatic interactions. However, not all peripheral peptides and proteins are cationic, and only certain sides of membrane are negatively charged. These include the cytoplasmic side of plasma membranes, the outer leaflet of outer bacterial membranes and mitochondrial membranes. Therefore, electrostatic interactions play an important role in membrane targeting of electron carriers such as cytochrome c, cationic toxins such as charybdotoxin, and specific membrane-targeting domains such as some PH domains, C1 domains, and C2 domains.

Electrostatic interactions are strongly dependent on the ionic strength of the solution. These interactions are relatively weak at the physiological ionic strength (0.14M NaCl): ~3 to 4 kcal/mol for small cationic proteins, such as cytochrome c, charybdotoxin or hisactophilin.cite journal|journal= Biophys J.|year= 1997 |month=Oct|volume=73|issue=4|pages=1717–27|title=Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles.|author=Ben-Tal N, Honig B, Miller C, McLaughlin S.|pmid = 9336168] cite book | last = Sankaram | first=MB | coauthors = Marsh D | title = Protein-lipid interactions with peripheral membrane proteins. In: Protein-lipid interactions (Ed. A. Watts) | pages = 127–162 | publisher = Elsevier | year = 1993 | id = ISBN 0-4448-1575-9 ] cite journal |author=Hanakam F, Gerisch G, Lotz S, Alt T, Seelig A |title=Binding of hisactophilin I and II to lipid membranes is controlled by a pH-dependent myristoyl-histidine switch |journal=Biochemistry |volume=35 |issue=34 |pages=11036–44 |year=1996 |pmid=8780505 |doi=10.1021/bi960789j]

patial position in membrane

Orientations and penetration depths of many amphitropic proteins and peptides in membranes are studied using site-directed spin labeling,cite journal |author=Malmberg N, Falke J |title=Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains |journal=Annu Rev Biophys Biomol Struct |volume=34 |issue= |pages=71–90 |year= 2005|pmid=15869384 |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.34.040204.144534?journalCode=biophys |doi=10.1146/annurev.biophys.34.040204.144534] chemical labeling, measurement of membrane binding affinities of protein mutants,cite journal |author=Spencer A, Thuresson E, Otto J, Song I, Smith T, DeWitt D, Garavito R, Smith W |title=The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis |journal=J Biol Chem |volume=274 |issue=46 |pages=32936–42 |year=1999 |pmid=10551860 |doi=10.1074/jbc.274.46.32936] fluorescence spectroscopy,cite journal |author=Lathrop B, Gadd M, Biltonen R, Rule G |title=Changes in Ca2+ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A2 |journal=Biochemistry |volume=40 |issue=11 |pages=3264–72 |year=2001 |pmid=11258945 |doi=10.1021/bi001901n] solution or solid-state NMR spectroscopy,cite journal |author=Kutateladze T, Overduin M |title=Structural mechanism of endosome docking by the FYVE domain |journal=Science |volume=291 |issue=5509 |pages=1793–6 |year=2001 |pmid=11230696 |doi=10.1126/science.291.5509.1793] ATR FTIR spectroscopy,cite journal |author=Tatulian S, Qin S, Pande A, He X |title=Positioning membrane proteins by novel protein engineering and biophysical approaches |journal=J Mol Biol |volume=351 |issue=5 |pages=939–47 |year=2005 |pmid=16055150 |doi=10.1016/j.jmb.2005.06.080] X-ray or neutron diffraction, and computational methods.cite journal |author=Murray D, Honig B |title=Electrostatic control of the membrane targeting of C2 domains |journal=Mol Cell |volume=9 |issue=1 |pages=145–54 |year=2002 |pmid=11804593 |doi=10.1016/S1097-2765(01)00426-9] cite journal |author=Efremov R, Nolde D, Konshina A, Syrtcev N, Arseniev A |title=Peptides and proteins in membranes: what can we learn via computer simulations? |journal=Curr Med Chem |volume=11 |issue=18 |pages=2421–42 |year=2004 |pmid=15379706] cite journal |author=Lomize A, Pogozheva I, Lomize M, Mosberg H |title=Positioning of proteins in membranes: a computational approach |journal=Protein Sci |volume=15 |issue=6 |pages=1318–33 |year=2006 |pmid=16731967 |doi=10.1110/ps.062126106] [cite web | author=Lomize A, Lomize M, Pogozheva I |title=Comparison with experimental data | work=Orientations of Proteins in Membranes | publisher = University of Michigan | url=http://opm.phar.umich.edu/about.php?subject=experiments | accessdate=2007-02-08]

Two distinct membrane-association modes of proteins have been identified. Typical water-soluble proteins have no exposed nonpolar residues or any other hydrophobic anchors. Therefore, they remain completely in aqueous solution and do not penetrate into the lipid bilayer, which would be energetically costly. Such proteins interact with bilayers only electrostatically, for example, ribonuclease and poly-lysine interact with membranes in this mode. However, typical amphitropic proteins have various hydrophobic anchors that penetrate the interfacial region and reach the hydrocarbon interior of the membrane. Such proteins "deform" the lipid bilayer, decreasing the temperature of lipid fluid-gel transition. cite journal |author=Papahadjopoulos D, Moscarello M, Eylar E, Isac T |title=Effects of proteins on thermotropic phase transitions of phospholipid membranes |journal=Biochim Biophys Acta |volume=401 |issue=3 |pages=317–35 |year=1975 |pmid=52374 |doi=10.1016/0005-2736(75)90233-3] The binding is usually a strongly exothermic reaction.cite journal |author=Seelig J |title=Thermodynamics of lipid-peptide interactions |journal=Biochim Biophys Acta |volume=1666 |issue=1-2 |pages=40–50 |year=2004 |pmid=15519307] Association of amphiphilic α-helices with membranes occurs similarly.cite journal | author = Darkes MJM, Davies SMA, Bradshaw JP| title = Interaction of tachykinins with phospholipid membranes: A neutron diffraction study | journal = Physica B | year = 1997 | volume = 241 | pages = 1144–7 | url=http://adsabs.harvard.edu/abs/1998PhyB..241.1144D | doi = 10.1016/S0921-4526(97)00811-9] cite journal|pmid= 10388560|journal=J Mol Biol|year=1999 |month=July 2|volume=290| issue=1|pages=99–117|title=An amphipathic alpha-helix at a membrane interface: a structural study using a novel X-ray diffraction method|author=Hristova K, Wimley WC, Mishra VK, Anantharamiah GM, Segrest JP, White SH.|doi= 10.1006/jmbi.1999.2840] Intrinsically unstructured or unfolded peptides with nonpolar residues or lipid anchors can also penetrate the interfacial region of the membrane and reach the hydrocarbon core, especially when such peptides are cationic and interact with negatively charged membranes.cite journal|journal=Biophys J.| year= 2004 |month=Nov|volume=87|issue=5|pages=3221–33|title=Membrane position of a basic aromatic peptide that sequesters phosphatidylinositol 4,5 bisphosphate determined by site-directed spin labeling and high-resolution NMR.|author=Ellena JF, Moulthrop J, Wu J, Rauch M, Jaysinghne S, Castle JD, Cafiso DS. |pmid= 15315949 |doi=10.1529/biophysj.104.046748] cite journal |author=Marcotte I, Dufourc E, Ouellet M, Auger M |title=Interaction of the neuropeptide met-enkephalin with zwitterionic and negatively charged bicelles as viewed by 31P and 2H solid-state NMR |journal=Biophys J |volume=85 |issue=1 |pages=328–39 |year=2003 |pmid=12829487 |doi=10.1021/bi0341859] cite journal |author=Zhang W, Crocker E, McLaughlin S, Smith S |title=Binding of peptides with basic and aromatic residues to bilayer membranes: phenylalanine in the myristoylated alanine-rich C kinase substrate effector domain penetrates into the hydrophobic core of the bilayer |journal=J Biol Chem |volume=278 |issue=24 |pages=21459–66 |year=2003 |pmid=12670959 |doi=10.1074/jbc.M301652200]

Categories of peripheral proteins

Enzymes

Peripheral enzymes participate in metabolism of different membrane components, such as lipids (phospholipases and cholesterol oxidases), cell wall oligosaccharides (glycosyltransferase and transglycosidases), or proteins (signal peptidase and palmitoyl protein thioesterases). Lipases can also digest lipids that form micelles or nonpolar droplets in water.

ee also

* Membrane proteins
* Lipoproteins
* Transmembrane proteins
* Antimicrobial peptides

References

General references

*cite book |author=Lukas K. Tamm (Editor) |title=Protein-Lipid Interactions: From Membrane Domains to Cellular Networks| url=http://books.google.com/books?vid=ISBN3527311513 |publisher=John Wiley & Sons |location=Chichester |year= |isbn=3-527-31151-3 |oclc= |doi=
*cite journal|author= Cho, W. and Stahelin, R.V. |year=2005|title= Membrane-protein interactions in cell signaling and membrane trafficking|journal=Annual Review of Biophysics and Biomolecular Structure|volume= 34|pages= 119–151|month=June |doi=10.1146/annurev.biophys.33.110502.133337 |url= http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.33.110502.133337?cookieSet=1&journalCode=biophys |accessdate=2007-01-23
*cite journal|url=http://taylorandfrancis.metapress.com/index/KH5DWA8PT5Q20XCP.pdf|author=Goni F.M. |year=2002|title= Non-permanent proteins in membranes: when proteins come as visitors|journal=Mol. Membr. Biol|volume= 19|pages=237–245|doi= 10.1080/0968768021000035078
*cite journal |author=Johnson J, Cornell R |title=Amphitropic proteins: regulation by reversible membrane interactions (review) |journal=Mol Membr Biol |volume=16 |issue=3 |pages=217–35 |year= 1999|pmid=10503244 |url=http://taylorandfrancis.metapress.com/index/KQLBWVAQT24PRXUJ.pdf |doi=10.1080/096876899294544
*Seaton B.A. and Roberts M.F. Peripheral membrane proteins. pp. 355-403. In "Biological Membranes" (Eds. K. Mertz and B.Roux), Birkhauser Boston, 1996.
*Benga G. Protein-lipid interactions in biological membranes, pp.159-188. In "Structure and Properties of Biological Membranes", vol. 1 (Ed. G. Benga) Boca Raton CRC Press, 1985.
*Kessel A. and Ben-Tal N. 2002. Free energy determinants of peptide association with lipid bilayers. In "Current Topics in Membranes" 52: 205-253.
*cite journal |author=Malmberg N, Falke J |title=Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains |journal=Annu Rev Biophys Biomol Struct |volume=34 |issue= |pages=71–90 |year= 2005|pmid=15869384 |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.34.040204.144534?journalCode=biophys |doi=10.1146/annurev.biophys.34.040204.144534
*cite journal |author=McIntosh T, Simon S |title=Roles of bilayer material properties in function and distribution of membrane proteins |journal=Annu Rev Biophys Biomol Struct |volume=35 |issue= |pages=177–98 |year=2006 |pmid=16689633|url= http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.35.040405.102022?journalCode=biophys |doi=10.1146/annurev.biophys.35.040405.102022

External links

*
* [http://www.mrc-lmb.cam.ac.uk/genomes/dolop/ DOLOP] Genomics-oriented database of bacterial lipoproteins
* [http://www.cryst.bbk.ac.uk/peptaibol/home.shtml Peptaibol database]
* [http://aps.unmc.edu/AP/main.php Antimicrobial Peptide Database]