Chemistry
Beta Pleated Sheet
A beta pleated sheet is a secondary structure found in proteins, characterized by its accordion-like arrangement of amino acid chains. The chains are aligned side by side with hydrogen bonds forming between them, creating a stable and rigid structure. This arrangement contributes to the overall stability and function of the protein.
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11 Key excerpts on "Beta Pleated Sheet"
- Frank H. Stillinger(Author)
- 2015(Publication Date)
- Princeton University Press(Publisher)
Residue-identifying side groups in beta-sheet secondary structures protrude alternately from one side of the beta sheet to the other. These protrusions are amplified somewhat because the strands, and thus the sheets themselves, have a pleated texture. As a result of these side-group Protein Folding Phenomena 449 FIGURE XI.8. Beta-sheet patterns of lateral hydrogen bonds between neighboring backbone strands whose directions are indicated by arrows. (a) Close-by pairs of oppositely directed hydrogen bonds connecting antiparallel strands. (b) Se-quence of hydrogen bonds between parallel strands. Adapted with permission of the publisher from Pauling, 1960, Figures 12-19 and 12-20. Copyright © 1960 by Cornell University. H H H H H C α C α C α C β N N C C O O H H H H H C α C α C α C β N N C C O O (b) (a) locations, it is possible for all residues on one side of the sheet to be polar while those on the other side are nonpolar (Table XI.2). Consequently, the beta sheet would simultaneously possess both hydrophilic and hydrophobic surfaces. This is a feature that can play an important role in estab-lishing the native structure of the protein involved. The hydrogen bond patterns for antiparallel or parallel beta strands do not require the overall shape of a beta sheet (beyond its pleated texture) to be close to planar. Various distortions from overall planarity are possible and are the norm in experimentally observed native structures. Pre-sumably, such flexibility incurs relatively little energy or free energy cost and can be an important contributor to the ability of the protein to conduct its biological role. A protein’s “tertiary structure” specifies the overall spatial deployment of its constituent back-bone secondary structures and of the residues along the backbone that connect those secondary structures.
eBook - PDF- H. Stephen Stoker(Author)
- 2015(Publication Date)
- Cengage Learning EMEA(Publisher)
Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 9-11 Secondary Structure of Proteins 377 contain more than one chain (interchain bonds). ◀ In molecules where the b pleated sheet involves a single molecule, several U-turns in the protein chain arrangement are needed in order to form the structure. C-terminal end N-terminal end This “U-turn structure” is the most frequently encountered type of b pleated sheet structure. Figure 9-7a shows a representation of the b pleated sheet structure that occurs when portions of two different peptide chains are aligned parallel to each other (interchain bonds). The term pleated sheet arises from the repeated zigzag pattern in the structure (Figure 9-7b). ◀ Further features of the b pleated sheet secondary protein structure are: 1. The hydrogen bonds between C O and N ! H entities lie in the plane of the sheet (Figure 9-7a). 2. The amino acid R groups are found above and below the plane of the sheet and within a given backbone segment alternating between the top and bottom positions (Figure 9-7b). Unstructured Segments Very few proteins have entirely a helix or b pleated sheet structures. Instead, only cer-tain portions of the molecules of most proteins are in these conformations. It is also possible to have both a helix and b pleated sheet structures within the same protein (see Figure 9-8). Helical structure and pleated sheet structure are found only in the portions of a protein where the amino acid R groups present are relatively small; large R groups tend to disrupt both of these types of secondary structure. Carbon Nitrogen Hydrogen Oxygen Side group C O C O H N C O N H N C O H N H C O N H C O N H C O N H Arrangement of protein backbone with no detail shown. a Backbone arrangement with hydrogen-bonding interactions shown. b Backbone atomic detail shown, as well as hydrogen-bonding interactions.
eBook - PDF- Carl Ivar Branden, John Tooze(Authors)
- 2012(Publication Date)
- Garland Science(Publisher)
The b sheets that are formed from several such b strands are “ pleated ” with C a atoms successively a little above and below the plane of the b sheet. The side chains follow this pattern such that within a b strand they also point alternately above and below the b sheet. Beta strands can interact in two ways to form a pleated sheet. Either the amino acids in the aligned b strands can all run in the same biochemical direction, amino terminal to carboxy terminal, in which case the sheet is described as parallel, or the amino acids in successive strands can have alter-nating directions, amino terminal to carboxy terminal followed by carboxy terminal to amino terminal, followed by amino terminal to carboxy terminal, and so on, in which case the sheet is called antiparallel. Each of the two forms has a distinctive pattern of hydrogen-bonding. The antiparallel b sheet (Figure 2.5) has narrowly spaced hydrogen bond pairs that alternate with widely spaced pairs. Parallel b sheets (Figure 2.6) have evenly spaced hydro-gen bonds that bridge the b strands at an angle. Within both types of b sheets all possible main-chain hydrogen bonds are formed, except for the two flank-ing strands of the b sheet that have only one neighboring b strand. Figure 2.6 Parallel b sheet. (a) Schematic diagram showing the hydrogen bond pattern in a parallel b sheet. (b) Ball-and-stick version of (a). The same color scheme is used as in Figure 2.5c. (c) Schematic diagram illustrating the pleat of a parallel b sheet. (b) (c) N N C C C α C α C C O O N N N H H C α C α C C O O N N H H C α C α C C O N H C α C α C C O O N N N H H C α C α C C O O N N H H C α C α C C O N H C α C α C C O O N N N H H C α C α C C O O N N H H C α C α C C O N H C α C α C C O O N N N H H C α C α C C O O N N H H C α C α C C O N H (a) 20 Beta strands can also combine into mixed b sheets with some b strand pairs parallel and some antiparallel.
eBook - PDF- Lizabeth A. Allison(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
The structure involves extended amino acid chains in a protein that interact by hydrogen bonding. The chains are packed side by side to create a pleated, accordion-like appearance with a repeat distance of 7.0 Å. Two segments of a polypeptide chain (or two individual polypeptide chains) can form two different types of β -structures. If both segments are aligned in the N-terminal to C-terminal direction, or in the C-terminal to N-terminal direction, the β -structure is said to be parallel. If one segment is N-terminal to C-terminal and the other is C-terminal to N-terminal, the β -structure is termed antiparallel. 3 Turns: Connecting the α -helices and β -pleated sheets elements in protein are “turns.” Turns are relatively short loops of amino acids that do not exhibit a defined secondary structure themselves but are essential for the overall folding of a protein. Other disor-dered or irregular structures in proteins are normally confined to the N- and C-terminals or more rarely to loop regions within a protein or linker region connecting one or more domains. Such disordered regions are described later in this chapter. Tertiary structure The folded three-dimensional shape of a polypeptide is its tertiary structure (Figure 4.9). This spatial arrangement of amino acid residues that are widely separated in the pri-mary sequence is stabilized by covalent and noncovalent bonds. Most interactions are 90 Ch 4 Protein Structure and Folding noncovalent. The principal covalent bonds within and between polypeptides are disulfide (S–S) bonds , or “disulfide bridges,” between cysteines (Figure 4.10). Disulfide bonds are only broken at high temperature, at acidic pH, or in the presence of reducing agents. The noncovalent bonds are primarily hydrophobic interactions, charge-pair interactions, and hydrogen bonds. Predictably, hydrophobic amino acids cluster together in the interior of a polypeptide, or at the interface between polypeptides, so they can avoid contact with water.
eBook - ePubFundamentals of Biochemistry, Integrated E-Text with E-Student Companion
Life at the Molecular Level
- Donald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
- 2017(Publication Date)
- Wiley(Publisher)
β sheet has a two-residue repeat with a repeat distance of 7.0 Å.Pleated appearance of a β sheet. Dashed lines indicate hydrogen bonds. The R groups (purple) on each polypeptide chain alternately extend to opposite sides of the sheet and are in register on adjacent chains. [Illustration, Irving Geis. Image from the Irving Geis Collection/Howard Hughes Medical Institute. Rights owned by HHMI. Reproduction by permission only.]FIG. 6-10How many residues are in this β sheet? How many interchain hydrogen bonds?β Sheets in proteins contain 2 to as many as 22 polypeptide strands, with an average of 6 strands. Each strand may contain up to 15 residues, the average being 6 residues. A seven-stranded antiparallel β sheet is shown inFig. 6-11.Space-filling model of a β sheet. The backbone atoms are colored according to type with C green, N blue, O red, and H white. The R groups are represented by large magenta spheres. This seven-stranded antiparallel β sheet, which is shown with its polypeptide strands approximately horizontal, is from the jack bean protein concanavalin A. [Based on an X-ray structure by Gerald Edelman, The Rockefeller University. PDBid 2CNA.]FIG. 6-11Parallel β sheets containing fewer than five strands are rare. This observation suggests that parallel β sheets are less stable than antiparallel β sheets, possibly because the hydrogen bonds of parallel sheets are distorted compared to those of the antiparallel sheets (Fig. 6-9 ). β Sheets containing mixtures of parallel and antiparallel strands frequently occur.β Sheets almost invariably exhibit a pronounced right-handed twist when viewed along their polypeptide strands (Fig. 6-12). Conformational energy calculations indicate that the twist is a consequence of interactions between chiral l-amino acid residues in the extended polypeptide chains. The twist distorts and weakens the β sheet’s interchain hydrogen bonds. The geometry of a particular β
eBook - PDFProteins
Concepts in Biochemistry
- Paulo Almeida(Author)
- 2016(Publication Date)
- Garland Science(Publisher)
In parallel β -sheets, two strands run side by side in a parallel orientation—that is, the polypeptide chain runs from N → C in both strands ( Figure 2.46 ). The hydrogen bonds between N −− H · · · O == C are somewhat distorted from the ideal orientation, which makes them slightly weaker. The pitch is 6.5 Å. In antiparallel β -sheets the two strands run in opposite directions ( Figure 2.47 ). The hydro-gen bonds N −− H · · · O == C between the amide groups are satisfied in an ideal orientation. The pitch is 7.0 Å. In both cases, because of the kinked, up-and-down structure of the β -strands, the sheet is not flat but pleated. The side chains protrude outward, above and below the sheet (not shown in Figures 2.46 and 2.47). Each strand has a right-handed twist, which causes further devia-tion from a flat structure. In the representation of Figure 2.48 an arrow indicates the C-terminus and the blunt end indicates the N-terminus. C N N C O O H H C N N C O O H H C N N C O O H H C N N C O O H H C N N C O O H H C N N C O O H H Pitch = 6.5 Å N C N C Figure 2.46 The parallel β -pleated sheet viewed from top. Note that the H α and the R groups were omitted for clarity. 60 Chapter 2 PROTEIN STRUCTURE Figure 2.47 The antiparallel β -pleated sheet viewed from top. The H α and the R groups were omitted for clarity. C N N C O C O C O C O O C O C O C O H N H N H N H H N H N H N H C N N C O O H H C N N C O O H H Pitch = 7.0 Å N C N C Circular Dichroism is a Simple Method to Identify α -Helices and β -Sheets In organic chemistry you learned that chiral molecules are optically active: they change the plane of polarization of light. Light is an electro-magnetic perturbation, periodic in time and space. In plane-polarized light, the electrical component of light is a vector that oscillates in a plane. The interaction of this electrical field with the electrons in a molecule is what gives rise to optical activity. Circular dichroism (CD) is one of the expressions of optical activity.
eBook - ePub- Wei Wang, Christopher J. Roberts, Wei Wang, Christopher J. Roberts(Authors)
- 2010(Publication Date)
- Wiley(Publisher)
The contacts involved in beta structure are more disbursed and cannot assemble as rapidly as adjacent interactions within individual helices because the segments forming β-strands are discontinuous. This is not to say that all helices form equally rapidly, as was noted above in the discussion of sequence effects. The antiparallel arrangement may form more rapidly when a short turn, particularly a well-defined turn, separates the strands, whereas parallel configurations are necessarily separated by long stretches of residues not involved in the sheet. Proteins with such arrangements often receive assistance from chaperones to fold in vivo. For example, rhodanese contains a parallel beta sheet in which the strand sequences are separated by helical segments. Refolding experiments show that rhodanese aggregates readily following dilution from denaturants, despite a significant retention of the secondary structure. Inclusion of several chaperones is necessary to prevent aggregation and facilitate its refolding. 59 The results of this study indicate that both extended structure and an MG-like state exist, which must be stabilized during the folding process to avoid aggregation. The inference then is that the sequences involved in sheet formation are protected from aggregation by chaperones until they are oriented properly with respect to each other. Antiparallel sheets composed of strands with long intervening sequences are akin to parallel configurations in this regard, indicating a longer time may be needed for their formation. This difference in kinetics may provide an explanation for why alpha to beta conversion is observed in aggregation. When alpha helices are destabilized, beta strands that exist may become amenable to rapid intermolecular association since they are no longer protected by intramolecular structural elements
eBook - PDF- Charis Ghelis(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
In the last section of Chapter 4, recent information on structural fluctua-tions of protein structure is presented. It is an important aspect in the under-standing of the folding of a protein and of the expression of its biological activity. Structura l Characteristic s of Folde d Protein s 2.1. D E F I N I T I O N O F T H E L E V E L S O F P R O T E I N S T R U C T U R E The terminology introduced by Linderstrom-Lang (1952) is generally used to define three levels of protein structure designated as primary, secondary, and tertiary structure. The primary structure is defined by the amino acid sequence of the polypeptide chain which is maintained by covalent links called the peptide bonds and does not describe the spatial arrangement. However, stereoisomerism ( L and D forms) is included in this level of structure. The secondary structure refers to the local spatial arrangement of the back-bone without regard to the conformation of the side chains or the overall arrangement of the whole chain. The tertiary structure refers to the spatial arrangement of the entire chain, including the side chain of the amino acids and results from side chain interactions. Thus, the spatial arrangement of the polypeptide chain is frequently described as the secondary and the tertiary structures. However, the distinction between these two levels of structure is not always evident. Historically, after the discovery of helical structures by Pauling and Corey (1951a,b,c,d, 1952, 1953a,b), Pauling (1940), and Pauling et al (1953, 1962), it was commonly thought that the polypeptide chain first folds into regular structures (mainly α helix) which are stabilized by peptide hydrogen bonds that give the secondary structure, and that these structures then fold and are stabilized by side-chain interactions to form the tertiary structure thus 37 2 38 I. Characteristic s of Folde d Protein s yielding the compact overall shape of the molecule.
- R Fraser(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
For example the unit 246 10. THE BETA CONFORMATION height and the interchain and intersheet distances all differ between forms I and II of [Cys(Cbz)] n and the distance between chains in the sheet changes with hydration of the side chain in [Lys(HCl)] n (Fig. 10.9). The unit height and interchain distance do not show any significant correlation. In a number of cases the X-ray diffraction data from homopolypeptides indicate that the unit cell contains two sheets which are crystallographi-cally different, as, for example, in [Asp(nPr)] w . This departure from equivalence is presumably dictated by the requirements of obtaining optimum side-chain packing between the sheets. In sequential poly-peptides that contain an even number of residues in the repeating unit there exists the possibility that the arrangement of chains in the sheet, and of sheets in the crystal, is such as to produce two distinct types of sheet-sheet contacts which alternate regularly throughout the crystal (Fig. 10.8, bottom left). This arrangement, which is believed to be present in B. mori silk fibroin (Marsh et al, 1955b), also appears to be present in [Ala-Gly] n (Fraser et al, 1965a), [Ala-Gly-Ala-Gly-Ser-Gly] n (Fraser et al, 1966), and [Cys(Bzl)-Gly] n (Fraser et al, 1965h). Sequential polypeptides are in many ways better models than homopolypeptides for the β conformation in proteins due to the variety of side-chain compositions in the natural material. A striking feature of the data obtained so far is that the X-ray diffraction data can be indexed on a pseudocell in which the cell sides in the plane of the sheet have lengths appropriate to a homopolypeptide rather than a sequential polypeptide. This can be interpreted as indicating that the equivalence of the atoms in the main-chain framework of the pleated sheet is little affected by the type of side chain.
- Moti Lal, P J Lillford, V M Naik(Authors)
- 2000(Publication Date)
- ICP(Publisher)
The sequence -[(AG) 3 EG(GA)jEG]- was also crystallised and investigated. This structure helps establish which of two structural aspects is dominant: (1) the alanyl-alanyl hydrophobic interactions, or, (2) they-turn rather than the P-turn in the fold. The results indicate that the y-tum is preferred in these chain-folded, stacked pleated-sheet apP-sheet structures. 1. Introduction The controlled biosynthetic production of sequence-designed artificial proteins is an emerging area of macromolecular science and technology. In general, we seek to understand the factors governing the relationship between amino acid sequence and spatial architecture of protein molecules. This contribution is a review of recent results on the controlled creation of chain-folded antiparallel (ap) (S-sheet crystalline protein structures based on repetitive amino sequences that relate to the silk-like p-proteins. 1 5 It had been reported by Keith, Lotz and coworkers, 6 9 that sequential polypeptides in the P-conformation could be crystallised in the form of chain-folded lamellae with thickness of the order of 5 nm. In addition, it is generally accepted that adjacent re-entry, chain-folded lamellae is a common crystalline form in linear polymers that are sufficiently flexible to form hairpin-like folds. It is also well-known, from crystallography of globular proteins, that the polypeptide chains can 2 make sharp folds (turns), with either one or two amide units (two or three amino acid C a atoms) in the turn; known as |J- or 7-tums, respectively. Some of the perceived advantages creating such chain-folded lamellae would be as follows. (1) A regular chain-folding structure would contain two (P-strand and chain turn) of the three prominent and recognisable protein conformations (the third being the a-helix). Thus, the results would be pertinent to protein structure and folding in general.
eBook - PDF- A.K. Konopka, M. James C. Crabbe, A.K. Konopka, M. James C. Crabbe(Authors)
- 2004(Publication Date)
- CRC Press(Publisher)
It is also a remarkable coincidence (some would say further evidence of divine intervention) that the ‘‘ ladder ’’ of bonds can be formed when the juxtaposed chains run either parallel or antiparallel. (See Reid and Franchini [5] for a comprehensive survey of these constraints for protein design.) 1.4. Packed Layers The units of globular protein are secondary structures that pack together to form a hydrophobic core. Provided the protein main-chain atoms are tied up in one of the two secondary structure types, a core can be constructed using any mix of a or h building blocks. The incorporation of a h -sheet, however, imposes a long-range constraint across the structure. The h -sheet has free hydrogen bonds on its two edges that consequently prevent the sheet from terminating in the core. This divides the core into two and, if considered more generally, imposes a layered structure onto the further arrangement of secondary structures in the protein. (See Figure 2 for ex-amples.) (See Refs. 6 and 7 for further consideration of protein structure along these lines.) F IGURE 2 Protein structures with one secondary structure type. (a) An all-h protein (immunoglobulin) with two packed h -sheets. (b) An all-a protein (globin) showing packed a -helices. Taylor 226 Seldom are more than four layers seen in proteins, and because these can be composed of only one of two secondary structures (i.e., no mixed layers), the possibilities are few enough to enumerate. Two layers: BB; AB; AA Three layers: BBB; ABB, BAB; AAB, ABA; AAA Four layers: BBBB; ABBB, BABB; AABB, BAAB, ABAB, ABBA; AAAB, AABA; AAAA (These combinations allow for reversals, because proteins do not distinguish top from bottom.) This gives 19 possible combinations, but this is something of an overestimate, because adjacent layers of a -helices are not always distinct.
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