B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 63
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These are proteins withbinding sites for multiple other proteins, and they serve both to link together specific sets of interacting proteins and to position them at specific locations inside acell. At one extreme are rigid scaffolds, such as the cullin in SCF ubiquitin ligase(see Figure 3–71). At the other extreme are the large, flexible scaffold proteinsthat often underlie regions of specialized plasma membrane. These include theFigure 3–77 How “protein machines” carry out complex functions.These machines are made of individual proteins that collaborate to performa specific task (Movie 3.13).
The movement of these proteins is oftencoordinated by the hydrolysis of a bound nucleotide such as ATP or GTP.Directional allosteric conformational changes of proteins that are driven in thisway often occur in a large protein assembly in which the activities of severaldifferent protein molecules are coordinated by such movements within thecomplex.ADP PiADP + PiPi ADPADP + PiPROTEIN FUNCTION165unstructuredregionscaffold proteinrapidcollisionsstructureddomain+productreactingproteinsscaffold readyfor reuseDiscs-large protein (Dlg), a protein of about 900 amino acids that is concentratedin special regions beneath the plasma membrane in epithelial cells and at synapses.
Dlg contains binding sites for at least seven other proteins, interspersedwith regions of more flexible polypeptide chain. An ancient protein, conserved inorganisms as diverse as sponges, worms, flies, and humans, Dlg derives its namefrom the mutant phenotype of the organism in which it was first discovered; thecells in the imaginal discs of a Drosophila embryo with a mutation in the Dlg genefail to stop proliferating when they should, and they produce unusually large discswhose epithelial cells can form tumors.Although incompletely studied,and a large number of similar scaffoldMBoC6 Dlgm3.80c/3.71proteins are thought to function like the protein that is schematically illustrated inFigure 3–78.
By binding a specific set of interacting proteins, these scaffolds canenhance the rate of critical reactions, while also confining them to the particularregion of the cell that contains the scaffold. For similar reasons, cells also makeextensive use of scaffold RNA molecules, as discussed in Chapter 7.Many Proteins Are Controlled by Covalent Modifications ThatDirect Them to Specific Sites Inside the CellWe have thus far described only a few ways in which proteins are post-translationally modified.
A large number of other such modifications also occur, more than200 distinct types being known. To give a sense of the variety, Table 3–3 presentsTABLE 3–3 Some Molecules Covalently Attached to Proteins Regulate ProteinFunctionModifying groupSome prominent functionsPhosphate on Ser, Thr,or TyrDrives the assembly of a protein into larger complexes(see Figure 15–11)Methyl on LysHelps to create distinct regions in chromatin throughforming either mono-, di-, or trimethyl lysine in histones(see Figure 4–36)Acetyl on LysHelps to activate genes in chromatin by modifyinghistones (see Figure 4–33)Palmityl group on CysThis fatty acid addition drives protein association withmembranes (see Figure 10–18)N-acetylglucosamine onSer or ThrControls enzyme activity and gene expression in glucosehomeostasisUbiquitin on LysMonoubiquitin addition regulates the transport ofmembrane proteins in vesicles (see Figure 13–50)A polyubiquitin chain targets a protein for degradation(see Figure 3–70)Ubiquitin is a 76-amino-acid polypeptide; there are at least 10 other ubiquitin-related proteins inmammalian cells.Figure 3–78 How the proximity createdby scaffold proteins can greatly speedreactions in a cell.
In this example, longunstructured regions of polypeptide chainin a large scaffold protein connect a seriesof structured domains that bind a set ofreacting proteins. The unstructured regionsserve as flexible “tethers” that greatly speedreaction rates by causing a rapid, randomcollision of all of the proteins that are boundto the scaffold. (For specific examples ofprotein tethering, see Figure 3–54 andFigure 16–18; for scaffold RNA molecules,see Figure 7–49B.)166Chapter 3: Proteins(A) A SPECTRUM OF COVALENT MODIFICATIONS PRODUCES A REGULATORY PROTEIN CODEMOLECULAR SIGNALS DIRECT ADDITION OF COVALENT MODIFICATIONSand/orand/orNand/orand/orCPROTEIN XTHE CODE IS READBIND TOMOVE TOPROTEINS orNUCLEUSY AND ZorMOVE TOMOVE TOorPROTEASOMEPLASMAFOR DEGRADATIONMEMBRANE(B) SOME KNOWN MODIFICATIONS OF PROTEIN p53CN50 amino acidsPphosphateAcacetylUubiquitinSUMOa few of the modifying groups with known regulatory roles. As in phosphateand ubiquitin additions described previously, these groups are added and thenremoved from proteins according to the needs of the cell.A large number of proteins are now known to be modified on more than oneamino acid side chain, with different regulatory events producing a different pattern of such modifications.
A striking example is the protein p53, which plays acentral part in controlling a cell’s response to adverse circumstances (see Figure17–62). Through one of four different types of molecular additions, this proteincan be modified at 20 different sites. Because an enormous number of differentcombinations of these 20 modifications are possible, the protein’s behavior canin principle be altered in a hugenumberof ways.
Such modifications will oftenMBoC6e4.44/3.72create a site on the modified protein that binds it to a scaffold protein in a specificregion of the cell, thereby connecting it—via the scaffold—to the other proteinsrequired for a reaction at that site.One can view each protein’s set of covalent modifications as a combinatorialregulatory code. Specific modifying groups are added to or removed from a protein in response to signals, and the code then alters protein behavior—changingthe activity or stability of the protein, its binding partners, and/or its specific location within the cell (Figure 3–79).
As a result, the cell is able to respond rapidlyand with great versatility to changes in its condition or environment.A Complex Network of Protein Interactions Underlies Cell FunctionThere are many challenges facing cell biologists in this information-rich era whena large number of complete genome sequences are known. One is the need todissect and reconstruct each one of the thousands of protein machines that existin an organism such as ourselves. To understand these remarkable protein complexes, each will need to be reconstituted from its purified protein parts, so thatwe can study its detailed mode of operation under controlled conditions in a testtube, free from all other cell components. This alone is a massive task. But we nowknow that each of these subcomponents of a cell also interacts with other sets ofmacromolecules, creating a large network of protein–protein and protein–nucleicacid interactions throughout the cell.
To understand the cell, therefore, we willneed to analyze most of these other interactions as well.Figure 3–79 Multisite protein modificationand its effects. (A) A protein that carriesa post-translational addition to more thanone of its amino acid side chains canbe considered to carry a combinatorialregulatory code. Multisite modificationsare added to (and removed from) a proteinthrough signaling networks, and theresulting combinatorial regulatory code onthe protein is read to alter its behavior inthe cell. (B) The pattern of some covalentmodifications to the protein p53.PROTEIN FUNCTIONWe can gain some idea of the complexity of intracellular protein networksfrom a particularly well-studied example described in Chapter 16: the many dozens of proteins that interact with the actin cytoskeleton to control actin filamentbehavior (see Panel 16–3, p.
905).The extent of such protein–protein interactions can also be estimated moregenerally. An enormous amount of valuable information is now freely available inprotein databases on the Internet: tens of thousands of three-dimensional proteinstructures plus tens of millions of protein sequences derived from the nucleotidesequences of genes. Scientists have been developing new methods for miningthis great resource to increase our understanding of cells. In particular, computer-based bioinformatics tools are being combined with robotics and other technologies to allow thousands of proteins to be investigated in a single set of experiments. Proteomics is a term that is often used to describe such research focusedon the analysis of large sets of proteins, analogous to the term genomics describingthe large-scale analysis of DNA sequences and genes.A biochemical method based on affinity tagging and mass spectroscopyhas proven especially powerful for determining the direct binding interactionsbetween the many different proteins in a cell (discussed in Chapter 8).
The resultsare being tabulated and organized in Internet databases. This allows a cell biologist studying a small set of proteins to readily discover which other proteins in thesame cell are likely to bind to, and thus interact with, that set of proteins. Whendisplayed graphically as a protein interaction map, each protein is represented bya box or dot in a two-dimensional network, with a straight line connecting thoseproteins that have been found to bind to each other.When hundreds or thousands of proteins are displayed on the same map, thenetwork diagram becomes bewilderingly complicated, serving to illustrate theenormous challenges that face scientists attempting to understand the cell (Figure 3–80).
Much more useful are small subsections of these maps, centered on afew proteins of interest.We have previously described the structure and mode of action of the SCFubiquitin ligase, using it to illustrate how protein complexes are constructed frominterchangeable parts (see Figure 3–71). Figure 3–81 shows a network of protein–protein interactions for the five proteins that form this protein complex in a yeastcell. Four of the subunits of this ligase are located at the bottom right of this figure.The remaining subunit, the F-box protein that serves as its substrate-binding arm,appears as a set of 15 different gene products that bind to adaptor protein 2 (theSkp1 protein).
Along the top and left of the figure are sets of additional proteininteractions marked with yellow and green shading: as indicated, these proteinsets function at the origin of DNA replication, in cell cycle regulation, in methionine synthesis, in the kinetochore, and in vacuolar H+-ATPase assembly. Weshall use this figure to explain how such protein interaction maps are used, andwhat they do and do not mean.1.
Protein interaction maps are useful for identifying the likely function ofpreviously uncharacterized proteins. Examples are the products of thegenes that have thus far only been inferred to exist from the yeast genomesequence, which are the three proteins in the figure that lack a simplethree-letter abbreviation (white letters beginning with Y). The three in thisdiagram are F-box proteins that bind to Skp1; these are therefore likely tofunction as part of the ubiquitin ligase, serving as substrate-binding armsthat recognize different target proteins.
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