Lodish H. - Molecular Cell Biology (5ed, Freeman, 2003) (794361), страница 28
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In Chapter 10 we considerthe mechanism by which the gene segments that correspondto domains became shuffled in the course of evolution, resulting in their appearance in many proteins. The modularapproach to protein architecture is particularly easy to recognize in large proteins, which tend to be mosaics of different domains and thus can perform different functionssimultaneously.The epidermal growth factor (EGF) domain is one example of a module that is present in several proteins (Figure 3-8).EGF is a small, soluble peptide hormone that binds to cells inthe embryo and in skin and connective tissue in adults, causing them to divide. It is generated by proteolytic cleavage between repeated EGF domains in the EGF precursor protein,which is anchored in the cell membrane by a membranespanning domain.
EGF modules are also present in otherproteins and are liberated by proteolysis; these proteins include tissue plasminogen activator (TPA), a protease that isused to dissolve blood clots in heart attack victims; FIGURE 3-7 Tertiary and quaternarylevels of structure in hemagglutinin (HA),a surface protein on influenza virus. Thislong multimeric molecule has three identicalsubunits, each composed of two polypeptidechains, HA1 and HA2. (a) Tertiary structure ofeach HA subunit constitutes the folding of itshelices and strands into a compact structurethat is 13.5 nm long and divided into twodomains. The membrane-distal domain isfolded into a globular conformation. Themembrane-proximal domain has a fibrous,stemlike conformation owing to the alignmentof two long helices (cylinders) of HA2 with strands in HA1.
Short turns and longerloops, which usually lie at the surface of themolecule, connect the helices and strands ina given chain. (b) Quaternary structure of HAis stabilized by lateral interactions betweenthe long helices (cylinders) in the fibrousdomains of the three subunits (yellow, blue,and green), forming a triple-stranded coiledcoil stalk. Each of the distal globular domainsin HA binds sialic acid (red) on the surface oftarget cells. Like many membrane proteins,HA contains several covalently linkedcarbohydrate chains (not shown).HA2DISTAL65Neu protein, which takes part in embryonic differentiation;and Notch protein, a receptor protein in the plasma membrane that functions in developmentally important signaling(Chapter 14).
Besides the EGF domain, these proteins contain domains found in other proteins. For example, TPA possesses a trypsin domain, a common feature in enzymes thatdegrade proteins.EGFNeuEGFprecursorTPA▲ FIGURE 3-8 Schematic diagrams of various proteinsillustrating their modular nature. Epidermal growth factor(EGF) is generated by proteolytic cleavage of a precursor proteincontaining multiple EGF domains (green) and a membranespanning domain (blue).
The EGF domain is also present in Neuprotein and in tissue plasminogen activator (TPA). These proteinsalso contain other widely distributed domains indicated by shapeand color. [Adapted from I. D. Campbell and P. Bork, 1993, Curr. Opin.Struct. Biol. 3:385.]66CHAPTER 3 • Protein Structure and FunctionProteins Associate into Multimeric Structuresand Macromolecular AssembliesMultimeric proteins consist of two or more polypeptides orsubunits. A fourth level of structural organization, quaternarystructure, describes the number (stoichiometry) and relativepositions of the subunits in multimeric proteins.
Hemagglutinin, for example, is a trimer of three identical subunits heldtogether by noncovalent bonds (Figure 3-7b). Other multimeric proteins can be composed of any number of identical ordifferent subunits. The multimeric nature of many proteinsis critical to mechanisms for regulating their function. In addition, enzymes in the same pathway may be associated assubunits of a large multimeric protein within the cell, therebyincreasing the efficiency of pathway operation.The highest level of protein structure is the associationof proteins into macromolecular assemblies.
Typically, suchstructures are very large, exceeding 1 mDa in mass, approaching 30–300 nm in size, and containing tens to hundreds of polypeptide chains, as well as nucleic acids in someTABLE 3-1cases. Macromolecular assemblies with a structural functioninclude the capsid that encases the viral genome and bundlesof cytoskeletal filaments that support and give shape to theplasma membrane. Other macromolecular assemblies act asmolecular machines, carrying out the most complex cellularprocesses by integrating individual functions into one coordinated process. For example, the transcriptional machinethat initiates the synthesis of messenger RNA (mRNA) consists of RNA polymerase, itself a multimeric protein, and atleast 50 additional components including general transcription factors, promoter-binding proteins, helicase, and otherprotein complexes (Figure 3-9).
The transcription factorsand promoter-binding proteins correctly position a polymerase molecule at a promoter, the DNA site that determineswhere transcription of a specific gene begins. After helicaseunwinds the double-stranded DNA molecule, polymerase simultaneously translocates along the DNA template strandand synthesizes an mRNA strand. The operational details ofthis complex machine and of others listed in Table 3-1 arediscussed elsewhere.Selected Molecular MachinesMachine*Main ComponentsCellular LocationFunctionReplisome (4)Helicase, primase, DNA polymeraseNucleusDNA replicationTranscription initiationcomplex (11)Promoter-binding protein, helicase,general transcription factors (TFs), RNApolymerase, large multisubunit mediatorcomplexNucleusRNA synthesisSpliceosome (12)Pre-mRNA, small nuclear RNAs(snRNAs), protein factorsNucleusmRNA splicingNuclear porecomplex (12)Nucleoporins (50–100)Nuclear membraneNuclear importand exportRibosome (4)Ribosomal proteins (50) and fourrRNA molecules (eukaryotes) organizedinto large and small subunits; associatedmRNA and protein factors (IFs, EFs)Cytoplasm/ER membraneProtein synthesisChaperonin (3)GroEL, GroES (bacteria)Cytoplasm,mitochondria,endoplasmicreticulumProtein foldingProteasome (3)Core proteins, regulatory (cap) proteinsCytoplasmProtein degradationPhotosystem (8)Light-harvesting complex (multipleproteins and pigments), reaction center(multisubunit protein with associatedpigments and electron carriers)Thylakoid membranein plant chloroplasts,plasma membrane ofphotosynthetic bacteriaPhotosynthesis(initial stage)MAP kinasecascades (14)Scaffold protein, multiple differentprotein kinasesCytoplasmSignal transductionSarcomere (19)Thick (myosin) filaments, thin (actin)filaments, Z lines, titin/nebulinCytoplasm ofmuscle cellsContraction*Numbers in parentheses indicate chapters in which various machines are discussed.3.1 • Hierarchical Structure of ProteinsMembers of Protein Families Have a CommonEvolutionary AncestorGeneral transcription factors+67+RNA polymeraseMediatorcomplexDNAPromoterTranscriptionpreinitiationcomplex▲ FIGURE 3-9 The mRNA transcription-initiation machinery.The core RNA polymerase, general transcription factors, amediator complex containing about 20 subunits, and otherprotein complexes not depicted here assemble at a promoter inDNA.
The polymerase carries out transcription of DNA; theassociated proteins are required for initial binding of polymeraseto a specific promoter, thereby initiating transcription.Studies on myoglobin and hemoglobin, the oxygen-carryingproteins in muscle and blood, respectively, provided early evidence that function derives from three-dimensional structure, which in turn is specified by amino acid sequence.X-ray crystallographic analysis showed that the threedimensional structures of myoglobin and the and subunits of hemoglobin are remarkably similar.
Subsequent sequencing of myoglobin and the hemoglobin subunitsrevealed that many identical or chemically similar residuesare found in identical positions throughout the primarystructures of both proteins.Similar comparisons between other proteins conclusivelyconfirmed the relation between the amino acid sequence,three-dimensional structure, and function of proteins.
Thisprinciple is now commonly employed to predict, on thebasis of sequence comparisons with proteins of knownstructure and function, the structure and function of proteins that have not been isolated (Chapter 9). This use ofsequence comparisons has expanded substantially in recentyears as the genomes of more and more organisms havebeen sequenced.The molecular revolution in biology during the lastdecades of the twentieth century also created a new schemeααVertebrateHEMOGLOBINαβMYOGLOBINDicotMonocothemoglobin LEGHEMOGLOBIN hemoglobinAnnelidInsectNematodeββHemoglobinProtozoanAlgalFungalBacterialAncestraloxygen-bindingprotein▲ FIGURE 3-10 Evolution of the globin protein family.
(Left)A primitive monomeric oxygen-binding globin is thought to be theancestor of modern-day blood hemoglobins, muscle myoglobins,and plant leghemoglobins. Sequence comparisons have revealedthat evolution of the globin proteins parallels the evolution ofanimals and plants. Major junctions occurred with the divergenceof plant globins from animal globins and of myoglobin fromhemoglobin. Later gene duplication gave rise to the and Leghemoglobinβ subunitof hemoglobinMyoglobinsubunits of hemoglobin. (Right) Hemoglobin is a tetramer of two and two subunits. The structural similarity of these subunitswith leghemoglobin and myoglobin, both of which aremonomers, is evident.
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