Question: Based on the article below, please write a detailed review on your und

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Question: Based on the article below, please write a detailed review on your understanding of Peptides and Proteins.
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I. INTRODUCTION

Biological membranes are constructed of hundreds of different

lipids differing in their fatty acid side chains, backbone

arrangements, and hydrophilic headgroups. When

grouped by the latter, it is clear that a few of these lipids,

and particularly the phospholipids phosphatidylcholine

(PC), phosphatidylserine (PS), and phosphatidylethanolamine

(PE), along with the sphingolipid sphingomyelin

(Sph) and cholesterol predominate in mammalian cells, and

thus are largely responsible for the bilayer structure in

which other lipids are dissolved. Oddly, we know a lot

about the functional significance of some rather rare membrane

lipids, such as the phosphatidylinositols, but our understanding

of the significance of the various structural

phospholipids is very limited, with one exception: PS. Exposed

PS at the cell surface in multicellular animals has

important physiological causes and consequences, and we

are beginning to acquire substantial information about the

molecular basis of these causes and consequences. It is our

purpose here to review the current status of investigations

into these physiological aspects of PS exposure in cells.

The critical aspect of PS that underlies its known physiological

functions is not its creation or destruction, but its location:

the exposure of PS at the surface of mammalian cells is

physiologically significant because it is normally completely

absent from the leaflet of the bilayer that faces the extracellular

space. There are two basic enzymatic activities that

regulate the distribution of PS between the two leaflets. One

is responsible for removing PS from the external leaflet by

ATP-dependent active transport; the relevant proteins are

members of the type IV subfamily of P-type ATPases. Constant

surveillance of the external leaflet by such enzymes

establishes a normal plasma membrane distribution in

which virtually all of the PS (and most of the PE) is in the

inner leaflet. The second enzymatic activity regulating the

distribution of PS between leaflets catalyzes rapid and nonspecific

exchange of phospholipids between the two sides of

the bilayer. This activity, termed the scramblase, is essential

for physiological processes because the exchange of phospholipids

between the two leaflets of a bilayer is slow. The

molecular basis of this activity is just beginning to come to

light, and this review will discuss recent developments, including

both what is known about the biophysics and biochemistry

of such movements, and the properties of the

molecules which have been associated with this activity.

With these two simple activities as the focus for the regulation

of lipid asymmetry and PS distribution, the most important

physiological question is how PS exposure is translated

into physiological consequences. This problem is twofold:

how is the presence of PS on the surface sensed by

actors in the extracellular milieu, and how is that recognition

translated into downstream consequences of PS exposure?

Given the many different kinds of physiological responses

that are triggered by PS exposure, it might be expected

that there would be a similar wide variety in the

mechanisms that operate in these different pathways. Remarkably,

this is not the case, and much of what we have

learned about the molecules that operate in one pathway

has proven useful in understanding another.

. Peptides and Proteins

By definition, integral membrane proteins interrupt the continuity

of the bilayer structure and as such might increase the chance that a phospholipid molecule may flip from one

leaflet to the other leaflet. Whereas in lipid vesicles the exchange

of lipids between the two leaflets requires days or

more, transbilayer movement of PC in erythrocyte membranes

occurs with a halftime of 4–5 h. The de novo synthesis

of lipids during membrane biogenesis is confined to

the cytoplasmic leaflet of the membrane. To avoid a mass

imbalance between the two membrane leaflets, rapid transbilayer

movement of lipids on a timescale of seconds is

required during growth and division of cells. From the foregoing,

it may be speculated that membrane-spanning domains

of integral membrane proteins meet this requirement

by enhancing the flip rate of phospholipids. In a systematic

investigation of this possibility, Kol et al. (137) constructed

_ -helical peptides and measured their ability to induce flop

of fluorescent-labeled phosphatidylglycerol (C6NBD-PG)

in vesicles composed of E. coli phospholipids. These peptides

consisted of 16 hydrophobic amino acids, flanked by

positively charged lysine- or uncharged, hydrophobic

tryptophan residues, KALP23 [GKKL(AL)8KKA] and

WALP23 [GWWL(AL)8WWA], respectively. Induced lipid

flip rates were linearly dependent on peptide concentration,

indicating that the activity is caused by monomers, and

were modulated by the lipid composition (137). Similarly,

proteoliposomes reconstituted with a bacterial integral

membrane protein (Lep) or the potassium channel, KscA,

exhibit a three- to fourfold increase in flop rate of C6NBDPG,

respectively (136). Activity is confined to the _ -helical

transmembrane segments of these proteins. In contrast,

MsbA, an E. coli inner membrane protein with six transmembrane

helices, does not mediate transbilayer diffusion

of C6NBD-PG, indicating that facilitating flip-flop is not a

general characteristic of (E. coli ) membrane proteins. Single

_ -helical peptides are more effective in stimulating flip-flop

than the transmembrane proteins when reconstituted at the

same protein-lipid ratio (135).

A different class of flip-flop enhancing peptides is presented

by the antimicrobial peptides. The antimicrobial properties

of these naturally occurring peptides are based on a selective

disruption of the permeability barrier of bacterial membranes

by formation of lipidic pores . A wellknown

example of this group is the antimicrobial peptide

Magainin2 (175). In contrast to the hydrophobic synthetic

helices described above, this highly charged, 23-amino acidlong

peptide forms an amphipilic helix that can lie along the

membrane surface through interaction with acidic phospholipids.

Above a threshold peptide-lipid ratio, pentameric

structures form spontaneously, generating a transient

transmembrane pore that permits leakage of solutes and

bidirectional flip-flop of lipids. The five peptide helices are

spaced by intercalated lipids to form a toroidal lipidic pore

in which transversal migration of phospholipids is reduced

to lateral diffusion. A few of these transient pores present

per unit time would be sufficient to explain a rapid exchange

of a significant fraction of the phospholipids

between the two monolayers. A similar mechanism has

been proposed for bee venom melittin (176) and mastoparan-

X, a peptidic toxin from Vespa xanthoptera (177).

An extensive discussion of the possible mechanisms of peptide-

facilitated flip-flop with a focus on the comparison between

hydrophobic and amphipatic helical peptides has

been presented by Anglin et al. (12).

The pro-apoptotic proteins of the BCL2 family use the same

principle of pore formation as the antimicrobial peptides to

disrupt the permeability barrier of the outer mitochondrial

membrane (OMM) during apoptosis (77, 277). After triggering

the cell death program, caspase-mediated cleavage of

the pro-apototic protein Bid results in the formation of cBid

(caspase-cleaved Bid) and subsequently tBid (truncated

fragment Bid). tBid binds via its BH3 domain to a Bax-type

protein that inserts into the OMM. Subsequent oligomerization

of tBid/Bax takes place forming a toroidal lipidic

pore, sufficiently sized to allow release of prodeath molecules

such as cytochrome c from the mitochondrial intermembrane

space. Concomitantly, pore formation permits a

rapid transversal migration of lipids, which may facilitate in

the exposure of cardiolipin in the outer leaflet.

A third protein-mediated mechanism of accelerated transbilayer

lipid movement occurs in rod outer segment disc

membranes (117, 317). Triton X-100 solubilized disc membrane

proteins reconstituted in proteoliposomes increases

the transbilayer mobility of phospholipid analogs (182),

and quantitative analysis reveals that rhodopsin is responsible

for enhanced flip-flop. Neither 11-cis -retinal nor a

disc-specific cofactor is required for activity, and flip is nonselective

for lipid polar headgroup. Interestingly, reconstituted

opsin also enhanced flip rates of a glycosylphosphatidylinositol,

but not an oligosaccharide diphosphate

dolichol, raising questions on the mechanism as well as

substrate limitations of the flip-flop process. The half-time

for flip-flop of NBD-lipids is _ 10 s, much faster than the

rates seen with transmembrane helices that operate through

transient disturbances of the bilayer structure. Rhodopsin

belongs to a subfamily of G protein-coupled receptors

(GPCR) characterized by seven membrane-spanning _ -helices

that can include stably associated water molecules

(11). These waters may provide a hydrophilic path for passage

of the lipid polar headgroup, while acyl chains remain

in the hydrophobic core of the membrane.

Similar structural features, including the presence of waters

in the transmembrane region, are present in other members

of this subfamily, such as the _ 1-adrenergic receptor. Indeed,

scrambling activity could also be demonstrated for

this receptor when it was reconstituted into proteoliposomes

(182). Given the widespread presence of these proteins

in plasma membranes of many different cell types and

the importance of bound water molecules in their normal

function (11), an important question is how cells control the

scrambling activity of these proteins to maintain lipid

asymmetry, since phospholipids do not rapidly rearrange in

animal cell membranes which generally contain receptors

from this family. It therefore seems unlikely that lipid

scrambling is a function of GPCR in general, and scrambling

abnormalities have not been reported in cells lacking

these proteins.

Explanation / Answer

Biological membranes are made up of

Chemical Composition Of Plasma Membrane

Lipids

Physiological aspects of PS exposure in cells.

There are two basic enzymatic activities that regulate the distribution of PS between the two leaflets.

Proteins

Facilitated Diffusion of Molecules

Membrane lipids and the cytoskeleton, once regarded as simple and static structures, have recently been recognized as significant players in signal transduction. Signal transduction is initiated by protein-protein interactions between ligands, receptors and kinases. Lipid micro domains on the cell surface-lipid rafts take part in this process.20 different families of trans membrane protein receptors interact with different ligands to receive extracellular stimuli.Proteins involved in the signal transduction are organized in specific domains at the plasma membrane.They orient the downstream members of signaling pathways.

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