B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 64
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However, as we discuss next, neither assignment can be considered certain without additional data.2. Protein interaction networks need to be interpreted with caution because,as a result of evolution making efficient use of each organism’s geneticinformation, the same protein can be used as part of different proteincomplexes that have different types of functions. Thus, although protein Abinds to protein B and protein B binds to protein C, proteins A and C neednot function in the same process.
For example, we know from detailedbiochemical studies that the functions of Skp1 in the kinetochore and in167Figure 3–80 A network of proteinbinding interactions in a yeast cell.Each line connecting a pair of dots(proteins) indicates a protein–proteininteraction. (From A. Guimerá andM. Sales–Pardo, Mol. Syst. Biol. 2:42,2006. With permission from MacmillanPublishers Ltd.)MBoC6 m3.83/3.73Chapter 3: Proteins168ORIGIN OF REPLICATIONCELL CYCLE REGULATORSOrc2Orc1Swe1Orc3Cdc28Orc6Cks1METHIONINE SYNTHESISCli1Met31Cdc5Orc4Cli2Met32Erd3Orc5Sic1Rpt1Met4Met28Yak1Dla2KINETOCHOREUfb1Okp1Rcy1Grr1Cdc4Cdc34YLR224WE2 ubiquitinconjugatingenzymeHrt3Mit2Ctf19Cbf1Cep3Cbf2Me130Skp2F-boxproteinsYDR131YDR306Mdm30Mcm21Mck1Das1Ctfl3Hrt1Vma4Vma8adaptorprotein 1Tfp1Ram2Skp1Cdc53Ram1Vma2VACUOLAR H+-ATPaseASSEMBLYadaptorprotein 2scaffold protein(cullin)Figure 3–81 A map of some protein–protein interactions of the SCF ubiquitin ligase and other proteins in the yeastS.
cerevisiae. The symbols and/or colors used for the five proteins of the ligase are those in Figure 3–71. Note that 15 differentF-box proteins are shown (purple); those with white lettering (beginning with Y) are known from the genome sequence asopen reading frames. For additional details, see text. (Courtesy of Peter Bowers and David Eisenberg, UCLA-DOE Institute forGenomics and Proteomics, UCLA.)MBoC6 m3.82/3.74vacuolar H+-ATPase assembly (yellow shading) are separate from its function in the SCF ubiquitin ligase.
In fact, only the remaining three functionsof Skp1 illustrated in the diagram—methionine synthesis, cell cycle regulation, and origin of replication (green shading)—involve ubiquitylation.3. In cross-species comparisons, those proteins displaying similar patterns ofinteractions in the two protein interaction maps are likely to have the samefunction in the cell. Thus, as scientists generate more and more highlydetailed maps for multiple organisms, the results will become increasinglyuseful for inferring protein function.
These map comparisons will be a particularly powerful tool for deciphering the functions of human proteins,because a vast amount of direct information about protein function canbe obtained from genetic engineering, mutational, and genetic analyses inexperimental organisms—such as yeast, worms, and flies—that are not feasible in humans.What does the future hold? There are likely to be on the order of 10,000 different proteins in a typical human cell, each of which interacts with 5 to 10 different partners.
Despite the enormous progress made in recent years, we cannot yetclaim to understand even the simplest known cells, such as the small Mycoplasmabacterium formed from only about 500 gene products (see Figure 1–10). How thenSUMMARY169can we hope to understand a human? Clearly, a great deal of new biochemistrywill be essential, in which each protein in a particular interacting set is purified sothat its chemistry and interactions can be dissected in a test tube.
But in addition,more powerful ways of analyzing networks will be needed based on mathematicaland computational tools not yet invented, as we shall emphasize in Chapter 8.Clearly, there are many wonderful challenges that remain for future generationsof cell biologists.SummaryProteins can form enormously sophisticated chemical devices, whose functionslargely depend on the detailed chemical properties of their surfaces.
Binding sitesfor ligands are formed as surface cavities in which precisely positioned amino acidside chains are brought together by protein folding. In this way, normally unreactive amino acid side chains can be activated to make and break covalent bonds.Enzymes are catalytic proteins that greatly speed up reaction rates by binding thehigh-energy transition states for a specific reaction path; they also can perform acidcatalysis and base catalysis simultaneously. The rates of enzyme reactions are oftenso fast that they are limited only by diffusion.
Rates can be further increased only ifenzymes that act sequentially on a substrate are joined into a single multienzymecomplex, or if the enzymes and their substrates are attached to protein scaffolds, orotherwise confined to the same part of the cell.Proteins reversibly change their shape when ligands bind to their surface. Theallosteric changes in protein conformation produced by one ligand affect the binding of a second ligand, and this linkage between two ligand-binding sites providesa crucial mechanism for regulating cell processes. Metabolic pathways, for example, are controlled by feedback regulation: some small molecules inhibit and othersmall molecules activate enzymes early in a pathway.
Enzymes controlled in thisway generally form symmetric assemblies, allowing cooperative conformationalchanges to create a steep response to changes in the concentrations of the ligandsthat regulate them.The expenditure of chemical energy can drive unidirectional changes in proteinshape. By coupling allosteric shape changes to ATP hydrolysis, for example, proteins can do useful work, such as generating a mechanical force or moving for longdistances in a single direction.
The three-dimensional structures of proteins haverevealed how a small local change caused by nucleoside triphosphate hydrolysis isamplified to create major changes elsewhere in the protein. By such means, theseproteins can serve as input–output devices that transmit information, as assembly factors, as motors, or as membrane-bound pumps. Highly efficient proteinmachines are formed by incorporating many different protein molecules into largerassemblies that coordinate the allosteric movements of the individual components.Such machines perform most of the important reactions in cells.Proteins are subjected to many reversible, post-translational modifications, suchas the covalent addition of a phosphate or an acetyl group to a specific amino acidside chain.
The addition of these modifying groups is used to regulate the activity ofa protein, changing its conformation, its binding to other proteins, and its locationinside the cell. A typical protein in a cell will interact with more than five differentpartners. Through proteomics, biologists can analyze thousands of proteins in oneset of experiments. One important result is the production of detailed protein interaction maps, which aim at describing all of the binding interactions between thethousands of distinct proteins in a cell. However, understanding these networks willrequire new biochemistry, through which small sets of interacting proteins can bepurified and their chemistry dissected in detail.
In addition, new computationaltechniques will be required to deal with the enormous complexity.WHAT WE DON’T KNOW• What are the functions of thesurprisingly large amount of unfoldedpolypeptide chain found in proteins?• How many types of protein functionsremain to be discovered? What arethe most promising approaches fordiscovering them?• When will scientists be able totake any amino acid sequence andaccurately predict both that protein’sthree-dimensional conformationsand its chemical properties? Whatbreakthroughs will be needed toaccomplish this important goal?• Are there ways to reveal the detailedworkings of a protein machine that donot require the purification of each ofits component parts in large amounts,so that the machine’s functions canbe reconstituted and dissected usingchemical techniques in a test tube?• What are the roles of the dozensof different types of covalentmodifications of proteins that havebeen found in addition to those listedin Table 3–3? Which ones are criticalfor cell function and why?• Why is amyloid toxic to cellsand how does it contribute toneurodegenerative diseases such asAlzheimer’s disease?170Chapter 3: ProteinsPROBLEMSWhich statements are true? Explain why or why not.One such kelch repeat domain is shown in Figure Q3–1.Would you classify this domain as an “in-line” or “plug-in”type domain?3–1Each strand in a β sheet is a helix with two aminoacids per turn.β7Cβ63–2Intrinsically disordered regions of proteins can beidentified using bioinformatic methods to search genes forencoded amino acid sequences that possess high hydrophobicity and low net charge.β1β53–3Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules.3–5Higher concentrations of enzyme give rise to ahigher turnover number.3–6Enzymes that undergo cooperative allosteric transitions invariably consist of symmetric assemblies of multiple subunits.3–7Continual addition and removal of phosphatesby protein kinases and protein phosphatases is wastefulof energy—since their combined action consumes ATP—but it is a necessary consequence of effective regulation byphosphorylation.Discuss the following problems.3–8Consider the following statement.
“To produceone molecule of each possible kind of polypeptide chain,300 amino acids in length, would require more atoms thanexist in the universe.” Given the size of the universe, do yousuppose this statement could possibly be correct? Sincecounting atoms is a tricky business, consider the problemfrom the standpoint of mass. The mass of the observableuniverse is estimated to be about 1080 grams, give or takean order of magnitude or so. Assuming that the averagemass of an amino acid is 110 daltons, what would be themass of one molecule of each possible kind of polypeptidechain 300 amino acids in length? Is this greater than themass of the universe?3–9A common strategy for identifying distantly relatedhomologous proteins is to search the database using a shortsignature sequence indicative of the particular proteinfunction.
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