2 Структура и функция белка (1160071), страница 19
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The structures are similar, although the repeat period isshorter for the parallel conformation (0.65 nm, as opposed to 0.7 nm forantiparallel).In some structural situations there are limitations to the kinds ofamino acids that can occur in the /3 structure. When two or morepleated sheets are layered closely together within a protein, the Rgroups of the amino acid residues on the contact surfaces must be relatively small. /3-Keratins such as silk fibroin and the protein of spiderwebs have a very high content of Gly and Ala residues, those with thesmallest R groups. Indeed, in silk fibroin Gly and Ala alternate overlarge parts of the sequence (Fig.
7-9c).Other Secondary Structures Occur in Some ProteinsFigure 7-10 Structure of a /3 turn or /3 bend,(a) Note the hydrogen bond between the peptidegroups of the first and fourth residues involved inthe bend, (b) The trans and cis isomers of a peptide bond involving the imino nitrogen of proline.Over 99.95% of the peptide bonds between aminoacid residues other than Pro are in the trans configuration. About 6% of the peptide bonds involvingthe imino nitrogen of proline, however, are in thecis configuration, and many of these occur at /3turns.The a helix and the /3 conformation are the major repetitive secondarystructures easily recognized in a wide variety of proteins.
Other repetitive structures exist, often in only one or a few specialized proteins. Anexample is the collagen helix (see Fig. 7-14). One other type of secondary structure is common enough to deserve special mention. This is a/3 bend or /3 turn (Fig. 7-10), often found where a polypeptide chainabruptly reverses direction. (These turns often connect the ends of twoadjacent segments of an antiparallel f3 pleated sheet, hence the name.)The structure is a tight turn (—180°) involving four amino acids.
Thepeptide groups flanking the first amino acid are hydrogen bonded tothe peptide groups flanking the fourth. Gly and Pro residues oftenoccur in f3 turns, the former because it is small and flexible; and thelatter because peptide bonds involving the imino nitrogen of prolinereadily assume the cis configuration (Fig. 7-10b), a form that is particularly amenable to a tight turn. /3 Turns are often found near the surface of a protein.Secondary Structure Is Affected by Several FactorsThe a helix and f3 conformation are stable because steric repulsion isminimized and hydrogen bonding is maximized.
As shown by aRamachandran plot, these structures fall within a range of stericallyallowed structures that is relatively restricted. Values of cp and ip forcommon secondary structures are shown in Figure 7-11. Most values ofcf) and \p for amino acid residues, taken from known protein structures,fall into the expected regions, with high concentrations near the a helixand /3 conformation values as expected. The only amino acid oftenfound in a conformation outside these regions is glycine.
Because itshydrogen side chain is small, a Gly residue can take up many conformations that are sterically forbidden for other amino acids.Some amino acids are accommodated in the different types of secondary structures better than others. An overall summary is presentedin Figure 7—12. Some biases, such as the presence of Pro and Gly residues in j8 turns, can be explained readily; other evident biases are notunderstood.Chapter 7 The Three-Dimensional Structure of ProteinsFigure 7-11 A Ramachandran plot. The values of d> and iA for thevarious secondarystructures are overlaidon the plot from Fig.7-5.Antiparallel/3 sheets-180-180SerCysAsnTyrProGly+ 180a-Keratin, collagen, and elastin provide clear examples of the relationship between protein structure and biological function (Table 7-1).These proteins share properties that give strength and/or elasticity tostructures in which they occur.
They have relatively simple structures,and all are insoluble in water, a property conferred by a high concentration of hydrophobic amino acids both in the interior of the proteinand on the surface. These proteins represent an exception to the rulethat hydrophobic groups must be buried. The hydrophobic core of themolecule therefore contributes less to structural stability, and covalentbonds assume an especially important role.Table 7-1 Secondary structures and properties of fibrous proteinsStructureCharacteristicsExamples of occurrencea Helix, cross-linkedby disulfide bondsTough, insoluble protective structures ofvarying hardness andflexibilitySoft, flexible filamentsHigh tensile strength,without stretchTwo-way stretch withelasticitya-Keratin of hair,feathers, and nailsElastin chains crosslinked by desmosineand lysinonorleucine1ji11•ii=ji11,^iijiiiiiFigure 7-12 Relative probabilities that a givenamino acid will occur in the three common typesof secondary structure.Left-handeda helixFibrous Proteins Are Adapted for a Structural Functionj3 ConformationCollagen triple helixj3Bendj3 Sheeta HelixGluMetAlaLeuLysPheGinTrpHeValAspHisRight-handeda helix171Fibroin of silkCollagen of tendons,bone matrixElastin of ligamentsTwo-chain coiled-coilmoleculeCross section of a hairProtofilament -Protofibril-JCells(b)Two-chaincoiled coila Helix -(a)Figure 7—13 (a) Hair a-keratin is an elongated ahelix with somewhat thicker domains near theamino and carboxy termini.
Pairs of these helicesare interwound, probably in a left-handed sense, toform two-chain coiled coils. These then combine inhigher-order structures called protofilaments andprotofibrils, as shown in (b). (About four protofibrils combine to form a filament.) The individualtwo-chain coiled coils in the various substructuresalso appear to be interwound, but the handednessof the interwinding and other structural details areunknown.a-Keratin and collagen have evolved for strength. In vertebrates, a-keratins constitute almost the entire dry weight of hair, wool,feathers, nails, claws, quills, scales, horns, hooves, tortoise shell, andmuch of the outer layer of skin. Collagen is found in connective tissuesuch as tendons, cartilage, the organic matrix of bones, and the corneaof the eye.
The polypeptide chains of both proteins have simple helicalstructures. The a-keratin helix is the right-handed a helix found inmany other proteins (Fig. 7-13). However, the collagen helix is unique.It is left-handed (see Box 7-1) and has three amino acid residues perturn (Fig. 7-14). In both a-keratin and collagen, a few amino acids predominate. a-Keratin is rich in the hydrophobic residues Phe, He, Val,Met, and Ala.
Collagen is 35% Gly, 11% Ala, and 21% Pro and Hyp(hydroxyproline; see Fig. 5-8). The unusual amino acid content of collagen is imposed by structural constraints unique to the collagen helix.The amino acid sequence in collagen is generally a repeating tripeptideunit, Gly-X-Pro or Gly-X-Hyp, where X can be any amino acid. Thefood product gelatin is derived from collagen.
Although it is protein, ithas little nutritional value because collagen lacks significant amountsof many amino acids that are essential in the human diet.In both a-keratin and collagen, strength is amplified by wrappingmultiple helical strands together in a superhelix, much the way stringsare twisted to make a strong rope (Figs. 7-13, 7-14). In both proteinsthe helical path of the supertwists is opposite in sense to the twisting ofthe individual polypeptide helices, a conformation that permits theclosest possible packing of the multiple polypeptide chains. The super-Figure 7-14 Structure of collagen. The collagenhelix is a repeating secondary structure unique tothis protein, (a) The repeating tripeptide sequenceGly-X-Pro or Gly-X-Hyp adopts a left-handedhelical structure with three residues per turn.
Therepeating sequence used to generate this model isGly-Pro-Hyp. (b) Space-filling model of the collagen helix shown in (a), (c) Three of these heliceswrap around one another with a right-handedtwist. The resulting three-stranded molecule is referred to as tropocollagen (see Fig. 7-15). (d) Thethree-stranded collagen superhelix shown from oneend, in a ball-and-stick representation. Glycine residues are shown in red. Glycine, because of its smallsize, is required at the tight junction where thethree chains are in contact.(d)172Chapter 7 The Three-Dimensional Structure of ProteinsBOX 7-2Permanent Waving Is Biochemical Engineeringa-Keratins exposed to moist heat can be stretchedinto the /3 conformation, but on cooling revert tothe a-helical conformation spontaneously.
This isbecause the R groups of a-keratins are larger onaverage than those of /3-keratins and thus are nothelical twisting is probably left-handed in a-keratin (Fig. 7-13) andright-handed in collagen (Fig. 7-14). The tight wrapping of the collagen triple helix provides great tensile strength with no capacity tostretch; Collagen fibers can support up to 10,000 times their ownweight and are said to have greater tensile strength than a steel wireof equal cross section.The strength of these structures is also enhanced by covalentcross-links between polypeptide chains within the multi-helical"ropes" and between adjacent ones. In a-keratin, the cross-links arecontributed by disulflde bonds (Box 7-2). In the hardest and toughesta-keratins, such as those of tortoise shells and rhinoceros horns, up to18% of the residues are cysteines involved in disulfide bonds.
The arrangement of a-keratin to form a hair fiber is shown in Figure 7-13. Incollagen, the cross-links are contributed by an unusual type of covalentlink between two Lys residues that creates a nonstandard amino acidresidue called lysinonorleucine, found only in certain fibrous proteins.H—NXX?N—HCH-CH2-CH2-CH2-CH2—N-CH2—CH2—CH2—CH2—CHO=C\=OXPolypeptidechain173Lys residueminus €-aminogroup (norleucine)LysinonorleucineLysresiduePolypeptidechaincompatible with a stable /3 conformation. Thischaracteristic of a-keratins, as well as their content of disulflde cross-linkages, is the basis of permanent waving. The hair to be waved is first bentaround a form of appropriate shape.
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