Lodish H. - Molecular Cell Biology (5ed, Freeman, 2003) (794361), страница 29
Текст из файла (страница 29)
A heme molecule (red) noncovalentlyassociated with each globin polypeptide is the actual oxygenbinding moiety in these proteins. [(Left) Adapted from R. C.Hardison, 1996, Proc. Natl. Acad. Sci. USA 93:5675.]68CHAPTER 3 • Protein Structure and Functionof biological classification based on similarities and differences in the amino acid sequences of proteins. Proteins thathave a common ancestor are referred to as homologs.
Themain evidence for homology among proteins, and hencetheir common ancestry, is similarity in their sequences orstructures. We can therefore describe homologous proteinsas belonging to a “family” and can trace their lineage fromcomparisons of their sequences. The folded three-dimensional structures of homologous proteins are similar even ifparts of their primary structure show little evidence ofhomology.The kinship among homologous proteins is most easilyvisualized by a tree diagram based on sequence analyses. Forexample, the amino acid sequences of globins from bacteria,plants, and animals suggest that they evolved from an ancestral monomeric, oxygen-binding protein (Figure 3-10).With the passage of time, the gene for this ancestral proteinslowly changed, initially diverging into lineages leading toanimal and plant globins.
Subsequent changes gave rise tomyoglobin, a monomeric oxygen-storing protein in muscle,and to the and subunits of the tetrameric hemoglobinmolecule (22) of the circulatory system.KEY CONCEPTS OF SECTION 3.1Hierarchical Structure of ProteinsA protein is a linear polymer of amino acids linkedtogether by peptide bonds. Various, mostly noncovalent,interactions between amino acids in the linear sequencestabilize a specific folded three-dimensional structure (conformation) for each protein.■The helix, strand and sheet, and turn are the mostprevalent elements of protein secondary structure, whichis stabilized by hydrogen bonds between atoms of the peptide backbone.■Certain combinations of secondary structures give riseto different motifs, which are found in a variety of proteins and are often associated with specific functions (seeFigure 3-6).■Protein tertiary structure results from hydrophobic interactions between nonpolar side groups and hydrogenbonds between polar side groups that stabilize folding ofthe secondary structure into a compact overall arrangement, or conformation.■■ Large proteins often contain distinct domains, independently folded regions of tertiary structure with characteristicstructural or functional properties or both (see Figure 3-7).The incorporation of domains as modules in differentproteins in the course of evolution has generated diversityin protein structure and function.■Quaternary structure encompasses the number and organization of subunits in multimeric proteins.■Cells contain large macromolecular assemblies in whichall the necessary participants in complex cellular processes(e.g., DNA, RNA, and protein synthesis; photosynthesis;signal transduction) are integrated to form molecular machines (see Table 3-1).■■ The sequence of a protein determines its three-dimensionalstructure, which determines its function.
In short, functionderives from structure; structure derives from sequence.Homologous proteins, which have similar sequences,structures, and functions, evolved from a common ancestor.■3.2 Folding, Modification,and Degradation of ProteinsA polypeptide chain is synthesized by a complex process calledtranslation in which the assembly of amino acids in a particular sequence is dictated by messenger RNA (mRNA). The intricacies of translation are considered in Chapter 4. Here, wedescribe how the cell promotes the proper folding of a nascent polypeptide chain and, in many cases, modifies residuesor cleaves the polypeptide backbone to generate the final protein.
In addition, the cell has error-checking processes thateliminate incorrectly synthesized or folded proteins. Incorrectly folded proteins usually lack biological activity and, insome cases, may actually be associated with disease. Proteinmisfolding is suppressed by two distinct mechanisms. First,cells have systems that reduce the chances for misfolded proteins to form. Second, any misfolded proteins that do form,as well as cytosolic proteins no longer needed by a cell, are degraded by a specialized cellular garbage-disposal system.The Information for Protein Folding Is Encodedin the SequenceAny polypeptide chain containing n residues could, in principle, fold into 8n conformations. This value is based on thefact that only eight bond angles are stereochemically allowedin the polypeptide backbone.
In general, however, all molecules of any protein species adopt a single conformation,called the native state; for the vast majority of proteins, thenative state is the most stably folded form of the molecule.What guides proteins to their native folded state? The answer to this question initially came from in vitro studies onprotein refolding. Thermal energy from heat, extremes of pHthat alter the charges on amino acid side chains, and chemicals such as urea or guanidine hydrochloride at concentrations of 6–8 M can disrupt the weak noncovalent interactionsthat stabilize the native conformation of a protein.
Thedenaturation resulting from such treatment causes a proteinto lose both its native conformation and its biological activity.Many proteins that are completely unfolded in 8 M ureaand -mercaptoethanol (which reduces disulfide bonds) spontaneously renature (refold) into their native states when the denaturing reagents are removed by dialysis. Because no cofactors3.2 • Folding, Modification, and Degradation of Proteins69class of proteins found in all organisms from bacteria to humans.
Chaperones are located in every cellular compartment,bind a wide range of proteins, and function in the generalprotein-folding mechanism of cells. Two general families ofchaperones are reconized:or other proteins are required, in vitro protein folding is a selfdirected process. In other words, sufficient information mustbe contained in the protein’s primary sequence to direct correct refolding. The observed similarity in the folded, threedimensional structures of proteins with similar amino acidsequences, noted in Section 3.1, provided other evidence thatthe primary sequence also determines protein folding in vivo.■ Molecular chaperones, which bind and stabilize unfolded or partly folded proteins, thereby preventing theseproteins from aggregating and being degradedFolding of Proteins in Vivo Is Promotedby Chaperones■Although protein folding occurs in vitro, only a minority ofunfolded molecules undergo complete folding into the nativeconformation within a few minutes.
Clearly, cells require afaster, more efficient mechanism for folding proteins intotheir correct shapes; otherwise, cells would waste much energy in the synthesis of nonfunctional proteins and in thedegradation of misfolded or unfolded proteins. Indeed, morethan 95 percent of the proteins present within cells have beenshown to be in their native conformation, despite high protein concentrations (200–300 mg/ml), which favor the precipitation of proteins in vitro.The explanation for the cell’s remarkable efficiency inpromoting protein folding probably lies in chaperones, aMolecular chaperones consist of Hsp70 and its homologs:Hsp70 in the cytosol and mitochondrial matrix, BiP in the endoplasmic reticulum, and DnaK in bacteria.
First identifiedby their rapid appearance after a cell has been stressed by heatshock, Hsp70 and its homologs are the major chaperones inall organisms. (Hsc70 is a constitutively expressed homolog ofHsp70.) When bound to ATP, Hsp70-like proteins assume anopen form in which an exposed hydrophobic pocket transiently binds to exposed hydrophobic regions of the unfoldedtarget protein.
Hydrolysis of the bound ATP causes molecular chaperones to assume a closed form in which a target protein can undergo folding. The exchange of ATP for ADPreleases the target protein (Figure 3-11a, top). This cycle isChaperonins, which directly facilitate the folding ofproteins(a)(b)RibosomeProteinPartiallyfoldedproteinATPProperlyfoldedproteinGroEL "tight"conformationADP+PiProteinProperlyfoldedproteinATPGroESGroEL▲ FIGURE 3-11 Chaperone- and chaperonin-mediatedprotein folding. (a) Many proteins fold into their proper threedimensional structures with the assistance of Hsp70-like proteins(top). These molecular chaperones transiently bind to a nascentpolypeptide as it emerges from a ribosome. Proper folding ofother proteins (bottom) depends on chaperonins such as theprokaryotic GroEL, a hollow, barrel-shaped complex of 14identical 60,000-MW subunits arranged in two stacked rings.GroEL "relaxed"conformationOne end of GroEL is transiently blocked by the cochaperonin GroES, an assembly of 10,000-MW subunits.(b) In the absence of ATP or presence of ADP, GroEL existsin a “tight” conformational state that binds partly folded ormisfolded proteins.
Binding of ATP shifts GroEL to a moreopen, “relaxed” state, which releases the folded protein.See text for details. [Part (b) from A. Roseman et al., 1996, Cell87:241; courtesy of H. Saibil.]MEDIA CONNECTIONSHsp 70-ATPADPFocus Animation: Chaperone-Mediated FoldingPi70CHAPTER 3 • Protein Structure and Functionspeeded by the co-chaperone Hsp40 in eukaryotes. In bacteria,an additional protein called GrpE also interacts with DnaK,promoting the exchange of ATP for the bacterial co-chaperoneDnaJ and possibly its dissociation.
![](https://s.studizba.com/z.php?f=/templates/si/i/noavatar.png&w=100&h=100&t=1"){kind=avatar}
