Chemistry
Secondary Structure of Protein
The secondary structure of a protein refers to the local folded structures that form within a polypeptide chain. The two most common types of secondary structures are alpha helices and beta sheets, which are stabilized by hydrogen bonds between the backbone atoms. These structures play a crucial role in determining the overall shape and function of a protein.
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11 Key excerpts on "Secondary Structure of Protein"
eBook - PDF- S Bresler(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
Much of the molecule is irregular in shape and folded into two main parts lying to either side of a cleft at whose surface the active site is located. Even at a resolution of 2.8 Â, sufficient information about the amino acid side chains was available to per-mit the correction of a tentative primary structure proposed on the basis of chemical analysis. The high resolution x-ray analysis of myoglobin, hemoglobin, and six different enzymes demonstrates quite conclusively that ordered secondary structure stabilized by hydrogen bonds plays a major role in defining protein conformation. The import-ance of α-helix in secondary structure was initially overemphasized, however, since myoglobin, with an unusually large helix content of 75 %, remained for many years the only protein whose complete three-dimensional structure was known. Further analysis of protein conformation revealed that polypeptide ^-structure also contributes to the internal order of several compact globular proteins, ranging from the highly organized cross-/}-sheets of carboxypeptidase and subtilisin to the less regular pairing of extended parallel chains in ribonuclease and chymotrypsin. The joint occurrence of a- and /^configuration in a single molecule appears to be quite common, although depending on the protein, one form or the other may predominate. Of course, the absence of hydrogen-bonded secondary structure in a given region of the protein does not necessarily mean that the polypeptide chain can assume a random configuration at that point. It implies simply that the three-dimensional packing is determined by factors other than secondary forces, such as proline residues, disulfide bonds, or hydrophobic interactions, none of which generate regular structure.
eBook - PDFProteins
Concepts in Biochemistry
- Paulo Almeida(Author)
- 2016(Publication Date)
- Garland Science(Publisher)
2.4 THE SECONDARY STRUCTURE IS THE LOCAL SPATIAL ARRANGEMENT OF THE POLYPEPTIDE CHAIN In this section we begin to explore protein structure. Intuitively, most of us think of structure as arising from an organization of elements in space, the connections between those elements appearing from favorable, or attractive, interactions. We will see, however, that the concept of structure is much broader. Although favorable interactions do indeed occur in proteins, structure also arises from constraints . That is, by forbidding some conformations, others become the only possible ones for the polypeptide chain. The Secondary Structure of Proteins is the result of restrictions on possible conformations and the requirement for hydrogen-bond formation. O C α C α N H : O C α C α N H Figure 2.30 The peptide group is a resonance hybrid of two chemical structures, which contribute unequally to the real structure. The Peptide Group is Planar The first restriction that we will encounter is on the peptide group itself. The peptide bond, between the nitrogen atom and the carbonyl carbon, is usually represented as a single bond (N −− C == O). This is misleading. Electrons are delocalized from the nitrogen atom to the carbonyl group by resonance, and the real structure is a hybrid of two resonance forms ( Figure 2.30 ). The two resonance forms do not con-tribute equally to the real structure. The form with an N −− C single bond 50 Chapter 2 PROTEIN STRUCTURE contributes about 60%, whereas the form with an N == C double bond contributes about 40%. Therefore, the peptide bond has approximately 40% double-bond character. As a consequence of the partial double-bond character of the peptide bond, the two C α ’s, the N and its H, and the carbonyl C and its O are all in the same plane. The geometry of the peptide bond is shown in Figure 2.31 . The bond angles are close to 120 ◦ . The atoms inside the rectangle, which constitute the peptide group , are all in the same plane.
eBook - PDF- Ulo Langel, Benjamin F. Cravatt, Astrid Graslund, N.G.H. von Heijne, Matjaz Zorko, Tiit Land, Sherry Niessen(Authors)
- 2009(Publication Date)
- CRC Press(Publisher)
The primary structure: the linear amino acid sequence of the polypeptide chain, including posttranslational modifications and disulfide bonds. 2. The secondary structure: the local structure of the linear segments of the polypeptide backbone atoms without regard to the conformation of the side chains. This level includes two sublevels: the super-secondary structure and the domains. The super-secondary structure means the association of the local secondary structural elements through side-chain interactions. The elements of the super-secondary structure are also called the motifs. A domain is usually a larger part of the protein sequence that can function and exist independently of the rest of the protein chain. 3. The tertiary structure: the three-dimensional arrangement of all the atoms in a polypeptide chain. In the single-chain proteins, this structure is functional. 4. The quaternary structure: the arrangement of the separate polypeptide chains (subunits) into the multi-subunit functional protein. 3.1 THE PRIMARY STRUCTURE The primary structure of a protein is the exact sequence of the amino acids joined by the peptide bond in a given polypeptide. In multichain proteins, each chain is referred to separately. By convention the primary structure is reported using three-letter or one-letter amino-acid coding (see Chapter 1), starting from the aminoter-minal (N) end and finishing at the carboxyl-terminal (C) end. The primary structure also requires specifying the crosslinking cysteines involved in the protein’s disul-fide bonds as well as all the posttranslational modifications in the polypeptide chain (see Chapter 5). Frequently, the modifications include cleavage of the polypeptide chain; therefore, the sequence of the polypeptide does not always correspond to the sequence of its mature mRNA. The linear polypeptide chain folds in a particular arrangement, giving a defined three-dimensional structure.
eBook - PDFProtein Physics
A Course of Lectures
- Alexei V. Finkelstein(Author)
- 2002(Publication Date)
- Academic Press(Publisher)
Part III SECONDARY STRUCTURES OF POLYPEPTIDE CHAINS This Page Intentionally Left Blank LECTURE 7 Having dealt with elementary interactions, in this lecture we will consider the Secondary Structure of Proteins. First of all we will discuss regular secondary structures, that is, α -helices and β -structures. These secondary structures are distinguished by regular arrangements of the main chain with side chains of a variety of conformations. The tertiary structure of a protein is determined by the arrangement of these structures in the globule (Fig. 7.1). We shall consider helices first. They can be right-handed or left-handed (Fig. 7.2) and have different periods and pitches. Right-handed (R) helices come closer to the viewer as they move counterclockwise (which corresponds to positive angle counting in trigonometry), while left-handed (L) helices approach the viewer as they move clockwise. In the polypeptide chain, major helices are stabilized by hydrogen bonds. The bonds are formed between C==O and H –– N groups of the polypeptide backbone, Figure 7.1. The secondary structures of a polypeptide chain ( α -helix and a strand of β -sheet) and the tertiary structure of a protein globule. Usually, taken together, α -and β -structures make up about a half of the chain in a globular protein. 75 76 SECONDARY STRUCTURES OF POLYPEPTIDE CHAINS R L Figure 7.2. Right-handed (R) and left-handed (L) helices. The bottom picture shows positive angle counting in trigonometry; the arrow that is “close” to the viewer moves counterclockwise. Residue number N-end Helices: no 4 13 = 5 16 = 2 7 3 10 N C C N C C N C C N C C N C C N C C C-en d 0 O O O O O O H H H H H H 1 2 3 4 5 Figure 7.3. Hydrogen bonds (shown with arrows) typical of different helices. The chain residues are numbered from the N-to the C-end of the chain. the latter being closer to the C-terminus of the chain.
eBook - PDF- Lizabeth A. Allison(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
. . . . . O O Figure 4.9 Four levels of protein structure. The primary protein structure is the sequence of a chain of amino acids. Secondary structures such as the α -helix and the β -pleated sheet are stabilized by hydrogen bonding between nearby amino acids in the chain. The secondary structure folds into a three-dimensional tertiary structure through noncovalent and covalent interactions. The quaternary structure is a protein consisting of more than one amino acid chain. 4.3 The three-dimensional structure of proteins 91 the first enzyme ever to have its structure solved by X-ray diffraction. Lysozyme is a widespread enzyme found in animal secretions such as tears and in egg white. It catalyzes the breaking of glycosidic bonds between certain residues in components of bacterial cell walls, resulting in lysis of the bacteria. Because of its catalytic properties, lysozyme is C SH HS C C H 2 H 2 H 2 H 2 S S C Figure 4.10 Disulfide bonds in tertiary folding. The backbone structure of α -chymotrypsin, an enzyme involved in digesting proteins in the small intestine, is shown (Protein Data Bank, PDB: 5CHA). Its structure contains five disulfide bonds (red bars). Cysteines are shown in light orange. The inset shows two cysteine side chains on the opposite side of a loop domain. The two thiol groups can undergo a reaction involving the loss of two hydrogens and the formation of a covalent disulfide bond between them. Chymotrypsin is activated by cleavage of the inactive precursor chymotrypsinogen, which is secreted by the pancreas. The three segments of polypeptide chain (green, light blue, and dark blue) produced by proteolytic processing remain linked by disulfide bonds. Source: Based on Protein Data Bank, PDB: 5CHA. (a) Active site (b) (c) Figure 4.11 The structure of the globular protein lysozyme. (a) A ribbon model depicts how the α -helices (coiled ribbons) and β -pleated sheets (flat arrows) present in lysozyme interact to form a globular shape.
eBook - PDF- Bhupendra Pushkar(Author)
- 2020(Publication Date)
- Delve Publishing(Publisher)
Protein Synthesis: Methods and Protocols 14 First and foremost, there is a three – dimensional structure of a protein and this is determined by its amino acid sequence. The second point is that the function of a protein tends to depend on its three – dimensional structure. The third point is that the three – dimensional structure of a protein is unique or somewhat similar to that. The fourth point is that the most important forces which stabilize the specific three – dimensional structure maintained by a provided protein are considered to be non- covalent interactions. Although the structure of proteins is complicated, there are several common patterns that can be recognized. There is a relationship that is possessed by the amino acid sequence and the three – dimensional structure of a protein. This relationship is an intricate puzzle that has yet to be solved in detail. There are polypeptides that have very different amino acid sequences and these are sometimes assumed to be similar structures. Thus, similar amino acid sequences sometimes can obtain very different structures. 1.4. PROTEIN SECONDARY STRUCTURE There are different types of secondary structure which are specifically stable as well as they occur in proteins widely. Among them, there are the most prominent ones which are the α helix and β conformations. Linus Pauling and Robert Corey predicted the existence of these secondary structures in the year 1951. This was the year that was far before the time when the first complete protein structure was elucidated. This was further done by using fundamental chemical principles and a few experimental observations. While considering secondary structure, it can be said that it is useful so as to classify proteins into two major groups. These groups include fibrous proteins and globular proteins. The fibrous proteins have polypeptide chains which are arranged in long strands or sheets. Primary Structure and Three-Dimensional Arrangement of Proteins 15 Figure 1.6.
eBook - PDF- Srinivas Aluru(Author)
- 2005(Publication Date)
- Chapman and Hall/CRC(Publisher)
Hydrogen bonding, electrostatic interactions and van der Waals forces are also very important. From a structural perspective, it is useful to think of protein chains as subdivided into peptide units consisting of the main-chain atoms between successive C α atoms. In protein structures, the atoms in a peptide unit are fixed in a plane with bond lengths and angles similar in all units. Each peptide unit essentially has only two degrees of freedom, given by rotations around its N-C α and C α -C bonds. Phi ( φ ) refers to the angle of rotation around the N-C α bond, and psi ( ψ ) refers to the angle of rotation around the C α -C bond. The entire backbone conformation of a protein can thus be specified with a series of φ and ψ angles. Only certain combinations of φ and ψ angles are observed in protein backbones, due to steric constraints between main-chain and side-chain atoms. As a result of the hydrophobic effect, the interior of water-soluble proteins form a hy-drophobic core. However, a protein backbone is highly polar, and this is unfavorable in the hydrophobic core environment; these main-chain polar groups can be neutralized via the formation of hydrogen bonds. Secondary structure is the “local” ordered structure brought about via hydrogen bonding mainly within the backbone. Regular secondary structures include α -helices and β -sheets (Figure 29.2). A canonical α -helix has 3.6 residues per turn, and is built up from a contiguous amino acid segment via backbone-backbone hydro-gen bond formation between amino acids in positions i and i + 4. The residues taking part in an α -helix have φ angles around − 60 ◦ and ψ angles around − 50 ◦ . Alpha helices vary considerably in length, from four or five amino acids to several hundred as found in fibrous proteins. A β -strand is a more extended structure with 2.0 residues per turn. Values for φ and ψ vary, with typical values of − 140 ◦ and 130 ◦ , respectively.
eBook - PDFBiochemistry
An Integrative Approach
- John T. Tansey(Author)
- 2019(Publication Date)
- Wiley(Publisher)
• Secondary structures are stabilized by hydrogen bonds in the peptide backbone, and can be formed by many different amino acids. • Tertiary structures describe the interaction of different elements of helix and sheet to form a complex structure. • Tertiary structure represents the complete folding of a single polypeptide into a functional protein. • Examples of tertiary motifs include the four-helix bundle and the Greek key motif. • Tertiary structures are stabilized by a combination of many weak forces; these include hydrogen bond- ing, dipole–dipole interactions, salt bridges, disulfide bonds, cation–π interactions, and a phenomenon known as the hydrophobic effect. • Many proteins exhibit quaternary structure interactions between and among different polypeptide chains. WORKED PROBLEM 3.3 Protein structure and disease Sickle cell anemia is a common genetic disorder. The causal mutation in sickle cell anemia is E6V, that is, the substitution of a glutamic acid for valine in the sixth position of the β chain of hemoglobin, a tetrameric protein with the stoichiometry a2β2. In the deoxygenated state, the mutant hemoglobin can polymerize, causing erythrocytes (red blood cells) to form a sickled shape and lyse, leading to the symptoms of this disease. How might this mutation affect all four levels of protein structure? Strategy Examine the information we have been given in the question and think about the four levels of protein structure. How could this alteration in amino acid sequence lead to the observed phenotype and disease? Solution Hemoglobin is a tetrameric protein. The mutation has altered the primary sequence of the β chains of hemoglobin by replacing a negatively charged glutamic acid with a hydrophobic valine residue. It is not apparent from the information provided in the question how this might affect the secondary and tertiary structure of the protein.
eBook - PDF- BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
- 2013(Publication Date)
- Butterworth-Heinemann(Publisher)
The secondary structure(s) are then linked by sections of random coil of irregular structure. extended Other helices can, in principle, occur. Think of either a more extended helix ie greater helices translation along the helix axis per residue, or a more squashed one. Short segments of a more extended helix (the 3.10 helix) are sometimes seen. The fibrous protein of connective tissue, collagen, forms an extended left-handed helix; three of these strands are combined, rope-like, to form a 'super-helix' which is stabilised by inter-chain hydrogen bonds. Proteins 59 Protein a- Keratin Myoglobin Lysozyme Carboxypeptidase Cytochromec % a- helix* 100 77 45 35 15 Table 3.4 Percentage a- helical content of some proteins. *The percentage is the proportion of the total number of amino acids which are found within a- helices. many fibrous proteins have repeated amino acid sequences It is notable that some of the fibrous (ie structural) proteins have primary structures which are 'repeats' of a simple sequence. Thus silk largely consists of a 6-residue repeat: gly-ser-gly-ala-gly-ala, whilst collagen has large amounts of glycine and proline (or hydroxyproline, which is a hydroxylated form of proline). Globular proteins, which constitute the enzymes and proteins which interact with other compounds in cells, have much more varied amino acid sequences. As a consequence, their structures are essentially infinitely varied. myoglobin structure elucidated orientation of polar and hydrophobic sidechains in proteins 3.5 Tertiary structure of proteins The tertiary structure describes the overall shape of the protein. This overall conformation is the consequence of the presence of any secondary structures and how they and the remainder of the chain are positioned. Each protein adopts a unique tertiary structure. This conformation will be the result of the various weak bonds which can arise. It also depends on interaction with the surrounding solvent (usually water).
eBook - PDF- Carl Ivar Branden, John Tooze(Authors)
- 2012(Publication Date)
- Garland Science(Publisher)
(b) Topological diagrams of the b -a -b motif. N N C C C N (a) (b) Figure 2.18 The b -a -b motif can in principle have two “hands.” (a) This connection with the helix above the sheet is found in almost all proteins and is called right-handed because it has the same hand as a right-handed a helix. (b) The left-handed connection with the helix below the sheet. (a) N C (b) N C 29 proteins (see Figure 1.1). Primary structure is the amino acid sequence, or, in other words, the arrangement of amino acids along a linear polypeptide chain. Two different proteins that have significant similarities in their primary structures are said to be homologous to each other, and since their corresponding DNA sequences also are significantly similar, it is generally assumed that the two proteins are evolutionarily related, that they have evolved from a common ancestral gene. Secondary structure occurs mainly as a helices and b strands. The for-mation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or b strands; others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or b strands close to each other. Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary struc-ture as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or sever-al domains. In all cases examined so far it has been found that if there is sig-nificant amino acid sequence homology in two domains in different pro-teins, these domains have similar tertiary structures. Protein molecules that have only one chain are called monomeric pro-teins.
eBook - PDF- M Volkenstein(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
It is obvious that total reversibility of denaturation can be observed for proteins which do not contain groups partici-pating in the denatured state in irreversible chemical reac-tions (e.g., oxidation of SH groups) [101]. Renaturation was established for ribonuclease [135], taka-amylase A [136], and α-amylase [137], The works of Anfinsen et al. have shown that renaturation of proteins with broken disulfide bonds is also possible [138-140]. It can be concluded that denaturation can actually be treated as a thermodynamic conformational transi-tion and that the native structure of protein corresponds to some relative minimum of free energy, if not to an absolute one. 4.9 Primary Structure of the Polypeptide Chain and Spatial Structure of the Globule The problem of the relation between the primary structure of the polypeptide chain and three-dimensional globular struc-ture is one of the most important problems in protein physics. Biological functionality inheres in the native spatial struc-ture of the molecule, but only the primary structure is coded genetically. Should there not be a definite connection be-tween these two kinds of structures, the fundamental ideas of molecular biology would have to be revised. The facts quoted 4.9 Structures of the Polypeptide Chain and the Globule 235 on p. 234 concerning the renaturation of proteins provide the experimental foundation for such a connection, which follows from general theoretical considerations (cf. p. 590). A series of papers reports a comparative analysis of spa-tial protein structures, determined by X-ray diffraction, and their primary structures; the analysis was meant to reveal the amino acid residues forming α-helical regions of the globule and those hindering spiralization. Guzzo [141] divided amino acids into helical and nonhelical ones, using data on he-moglobin and myoglobin (cf. also [142]).
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