Alpha-Helix

SAHBs are α-helical surrogates that bind both stable and transient physiologic interactors and have effectively uncovered novel sites of BCL-2 family protein interaction.

From: Methods in Enzymology , 2014

Linkers in Biomacromolecules

Tejas M. Gupte , ... Sivaraj Sivaramakrishnan , in Methods in Enzymology, 2021

1.1 α-helices are a dominant structural element in proteins

α-helices, β-sheets and random coils are the most common elements of secondary structure in proteins. α-helices are formed and maintained by backbone interactions parallel to the primary axis of the helix. These interactions are hydrogen bonds between the carbonyl oxygen and amino nitrogen of the ith and i   +  4th amino acids. The side chains of all residues in the α-helix are directed outwards and away from the helical axis, and the occurrence of polar or charged side chains in the helix can facilitate additional interactions with other side chains in the helix or with other elements outside of the helical structure, imparting further stability (Pauling, Corey, & Branson, 1951). Consequently, α-helices are the most commonly occurring secondary structure, representing 30% of the structure of the average globular protein (Pace & Scholtz, 1998). In globular domains, α-helices can also pack with β-sheets in different arrangements. Among these, orientation of the α-helix along the strands of β-sheets is energetically most favored, followed in stability by a perpendicular orientation of the helical axis to the β-strands (Chou, Némethy, Rumsey, Tuttle, & Scheraga, 1985). α-helices are also the core component of coiled-coil domains and of transmembrane bundles. Coiled-coil domains consist of two to seven α-helices, where the separate helices stabilize each other through hydrophobic patches of side chain interactions following a "knobs-into-holes" motif (Crick, 1953). Multiple α-helices composed primarily of hydrophobic amino acids can also give rise to transmembrane bundles, through protein-protein and protein-lipid interactions (Lee, 2003).

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/S0076687920303487

PROTEINS | Overview☆

L. Skipper , in Encyclopedia of Analytical Science (Third Edition), 2005

Secondary Protein Structure

α-Helices, β-sheets, and triple helices are three types of secondary structures. All are formed and stabilized by noncovalent interactions, mainly hydrogen bonds. Proteins can contain only one or mixtures of secondary structure as well as portions of the protein that contain structures difficult to describe but not less ordered, such as reverse turns and β-bends.

α-Helices are regular right-hand turns of amino acids 3.6 residues long; 5.41   Å. Hydrogen bonding between the first backbone carbonyl oxygen atom and the fourth residue NH group stabilizes the structure; van der Walls interactions across the axis further stabilize the structure. There are some rare exceptions to this general scheme where hydrogen bonding can occur between three residues (310-helix) or between five residues (π-helix). These structures are much less stable than general α-helices and are not normally favored. Any of the 20 amino acids can participate in an α-helix but some are more favored than others. Ala, Glu, Leu, and Met are most often found in helices whereas, Gly, Tyr, Ser, and Pro are less likely to be seen. Proline, for instance, is rarely seen as its backbone nitrogen is bonded to its cyclic side group and cannot participate in hydrogen bonding. When prolines are found in α-helices, they tend to cause the helix to bend due to steric hindrance caused by its side group. They can be found as the first or last residue in the helix where they do not cause bending. The side groups of the other amino acids point out and down relative to the helix. In globular proteins, those that are hydrophobic tend to be on one side of the helix and interact with other amino acids of the protein, and those on the other side are generally hydrophilic and interact with the solvent. For this reason, α-helices of globular proteins are predominantly found on the protein surface and have polar, hydrophobic, and hydrophilic amino acids. On average, α-helices in globular proteins have 11 residues, ∼17   Å long. Some α-helices have mainly hydrophobic residues, which are found buried in the hydrophobic core of a globular protein, or are transmembrane proteins.

β-Sheets are formed by the interactions between parallel regions of a protein chain. These either run in the same direction, parallel; or in the opposite direction, antiparallel. These structures are stabilized by hydrogen bonds between backbone carbonyl oxygen atom and the hydrogen of the amino group. In parallel β-sheets, the distances between the carbon and nitrogen involved in binding on one strand and on the other differ. This means that the hydrogen bonds are at an angle in relation to the protein strand. This is thought to make parallel β-sheets less stable than antiparallel β-sheets. In antiparallel β-sheets, the atoms on opposite strands involved in hydrogen binding are the same distance so that hydrogen bonds are at 90° to the strand. β-Sheets are not flat but have a pleated appearance due to the C i α atoms being successively above and below the plane of the sheet. The side groups are also successively above and below the plane of the sheet and they, therefore, cannot interact with each other. They do have significant interactions with neighboring side chains and with their backbone. Proteins can contain parallel β-sheets, antiparallel β-sheets, or a mixture of both, although mixed proteins account for only 20% of proteins with β-sheets. The strands are typically 5–10 amino acids long and β-sheets contain 2–15 strands. The strands in β-sheets always have a right-handed twist.

α-Helices and β-sheets make up ∼50% of a protein's secondary structure. These structures are connected by looped regions that change the direction of the protein strand. β-Bends connect subsequent strands in a β-sheet, so that they are aligned parallel. Each bend consists of two amino acids, usually Pro because of the flexibility of its C′–N peptide bond and Gly because its side chain gives the least crowding in the tight turn. The structure is stabilized by hydrogen bonding between the residues immediately before and after the bend. Ω-loops are so called as they have the general shape of the letter omega. These are usually 6–16 residues long and connect α-helices and β-sheets. They are predominantly found at the protein surface in globular proteins or connecting membrane α-helices at the cytoplasmic or extracellular face. These structures are often involved in recognition processes. Some of the remaining structure is disordered but nonetheless important, as these regions often confer great flexibility to proteins essential to their function.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B978008101983200493X

Macromolecular Architectures and Soft Nano-Objects

H.G. Börner , J.F. Lutz , in Polymer Science: A Comprehensive Reference, 2012

6.15.3.2.2(i) The α-helix secondary structure

The α-helix secondary structure is considered as the simplest secondary structure motif found in peptides. The folding of a polypeptide into an α-helical structure is the best understood element of the protein folding process and so far the rules are well developed. This is because the α-helix fold is, in contrast to the β-sheet, stable as an isolated peptide chain and does not depend on long-range interactions between residues on neighboring strands. The formation of an α-helix occurs through an initial nucleation step in which a hydrogen bond is formed between an i and i  +   4 residue pair. This entropically unfavorable step restricts the bond angles in three in-between residues. After the energy barrier of nucleation is overcome, helix propagation is thermodynamically favored.

The α-helix motif is adapted by comparatively simple homopeptides such as poly(Z-l-lysine) or poly(Bz-l-glutamate), which are traditionally prepared by ring-opening polymerization of AA NCAs (also known as Leuchs' anhydride). 66–68,70 Due to the simplicity of the fold and the ease of accessibility, the α-helix has been studied by polymer chemist's in more detail so far than sequence-defined peptides. 308,392,393 The α-helix adapted by homopeptides can be described as a structure element of a rather persistent rod, which assembles driven by structural anisotropy and dipole moment. This organization behavior is broadened by peptides with defined monomer sequences. Although the rigid-rod character is preserved, the helices resulting from sequence-defined peptides can be longitudinal polarized, laterally amphiphilic, or can have hydrophobic patches or sticky ends. This allows programming of the interaction capabilities of α-helices and leads to a more complex self-assembly behavior.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780444533494001734

Synthetic and Enzymatic Modifications of the Peptide Backbone

Ganesh S. Jedhe , Paramjit S. Arora , in Methods in Enzymology, 2021

6 Summary

α-Helices constitute the largest class of protein secondary structures, and play a major role in mediating protein-protein interactions (Guharoy & Chakrabarti, 2007; Jones & Thornton, 1996). Significantly, the average length of helical domains in proteins is small and spans two to three helical turns (8–12 residues) (Barlow & Thornton, 1988). Stabilization of short peptide sequences into a defined conformation presents a challenge because short peptides do not contain sufficient stabilizing intrachain interactions. We have developed a hydrogen bond surrogate approach for the synthesis of peptide helices. This approach is based on the helix-coil transition theory, which states that the helix nucleation is slower than the helix propagation in the shorter peptides due to the energetic barrier associated with helix nucleation. The HBS approach provides a preorganized α-helix nucleus consisting of a 13-membered covalent macrocycle to induce a helical conformation in the attached peptide subunit. The significance of HBS methodology is that it allows access to short α-helices with strict conservation of all molecular recognition surfaces required for biomolecular interactions. The α-helical secondary structure in the HBS helices is confirmed using 2D-NMR, CD, and X-ray crystallographic studies. Proteolytically stable derivatives of HBS peptides have been developed by insertion of one β-residue every helical turn (Patgiri et al., 2012; Yoo, Hauser, et al., 2020). The cellular permeability of HBS helices has also been comprehensively studied (Patgiri et al., 2011; Yoo, Barros, et al., 2020). The above studies highlight the potential of HBS helices as rationally designed inhibitors of intracellular protein-protein interactions (Kushal et al., 2013; Patgiri et al., 2011; Yoo, Hauser, et al., 2020).

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/S0076687921001427

Raman optical activity

Ewan W. Blanch , ... Laurence D. Barron , in Chiral Analysis, 2006

16.9.2.1 α-Helical poly(L-lysine)

The α-helix is one of the most common secondary structure motifs found in proteins and polypeptides and comprises a single strand of the polypeptide chain in a helical form with a right handed twist and is stabilized mainly by hydrogen bonds between C=O i and N-H i+4 groups within the same chain. The extended amide III region of the ROA spectrum of α-helical poly(L-lysine) is dominated by the two positive bands that occur at ∼1297 and 1341 cm−1. The band at higher wavenumber is assigned to a hydrated form of α-helix, while the smaller band at lower wavenumber appears to be associated with α-helix in a more hydrophobic environment. Conventional Raman bands at similar wavelengths have been reported in studies of α-helix in polypeptides and filamentous bacteriophages. A Raman study of α-helical poly(L-alanine) by Lee and Krimm [108] provided definitive assignments of several normal modes of vibration in the extended amide III region. These normal modes were shown to transform variously as the A, E 1 and E 2 symmetry species of the point group of a model infinite regular helix. It appears that the ROA bands assigned to α-helix in this region may be related to several of these normal modes identified by Lee and Krimm [108], with the ROA band positions and intensities being a function of the perturbations (which can be geometric, due to various types of hydration or both) to which the helical sequences are subjected.

The relative intensities of these two ROA bands appear to correlate with the exposure of the polypeptide backbone to the solvent within the elements of α-helix. For example, the positive ∼1340 cm−1 α-helix ROA band assigned to hydrated α-helix completely disappears when the polypeptide or protein is dissolved in D2O [78]. This indicates that N-H deformations of the peptide backbone make a significant contribution to the generation of the ∼1340 cm−1 ROA band because the corresponding N–D deformations contribute to normal modes in a spectral region several hundred wavenumbers lower. Furthermore the corresponding sequences in proteins are exposed to solvent, rather than being buried in hydrophobic regions where amide protons can take weeks or longer to exchange. In comparison, although the positive ∼1300 cm−1 α-helix ROA band also changes in D2O, again suggesting some involvement of N-H deformations, in systems containing a significant amount of α-helix in a protected hydrophobic environment quite a lot of intensity is still retained. Further insight into the nature of these hydrated and hydrophobic variants of α-helix is provided by electron spin resonance studies of double spin-labelled alanine rich peptides [109,110] which identified a new and more open conformation of the α-helix. Computer modelling studies indicated that this more open geometry retains the internal hydrogen bonding scheme but changes the C=O … N angles which results in a splaying of the backbone amide carbonyls away from the helix axis and into the surrounding solvent. This more open conformation may, therefore, be the preferred conformation in aqueous solution as it would allow external hydrogen bonding to solvent water molecules. Consequently, an equilibrium would exist between the canonical form of α-helix, which may be responsible for the lower wavelength band ∼1300 cm−1, and this more open form, which may be responsible for the band ∼1340 cm−1. The former would be favored in a hydrophobic environment and the latter would be favored in a hydrophilic, or other hydrogen bonding environment [111].

The small amide I couplet, negative at ∼1626 cm−1 and positive at ∼1656 cm−1 is at a position characteristic of α-helix, though this couplet can be considerably more intense in α-helical proteins. This signature accords with the wavenumber range ∼1645–1655 cm−1 for α-helix bands in conventional Raman spectra [96]. Positive ROA intensity in the range ∼870–950 cm−1 also appears to be a signature of α-helix. The exact position and bandshapes of these ROA signatures vary in different α-helical polypeptides and proteins, possibly indicating heterogeneity within the α-helical sequences or the influence of side chains on the normal vibrational modes responsible. It is well known that the vibrations of nonaromatic side chains can couple with the backbone stretch vibrations in the backbone skeletal stretch region [99].

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780444516695500168

Design and preparation of biomimetic and bioinspired materials

V. Leiro , ... C.C. Barrias , in Bioinspired Materials for Medical Applications, 2017

1.4.2.1 α-Helix

α-Helix is a key secondary structure of natural proteins that consists of a peptide chain coiled into a right-handed spiral conformation and stabilized by hydrogen bonds between the Nsingle bondH and the Cdouble bondO groups in the backbone. Methionine, alanine, leucine, glutamate, and lysine have special propensity to be part of α-helix structures while proline and glycine have poor helix-forming propensities. A particularly abundant α-helix-based structural motif is the coiled coil, in which the α-helix is frequently characterized by a seven residue repeating unit of alternating hydrophobic and hydrophilic residues, often denoted as (abcdefg) n (Fig. 1.4; Banwell et al., 2009; Woolfson, 2010; Woolfson and Ryadnov, 2006; Wagner et al., 2005; Zimenkov et al., 2004; Burkhard et al., 2001; Parry et al., 2008). Coiled coils have been used for drug delivery isolated or incorporated in liposomes and for the design of supramolecular materials. Coiled coils display an inner hydrophobic core that can be explored to carry hydrophobic drugs. Eriksson et al. (2009) studied the potential of loading cisplatin, a hydrophobic chemotherapeutic drug, into a right-handed coiled coil (RHCC). RHCC containing the drug was able to bind and enter cells in vitro. Naturally occurring coiled coils, such as the leucine zipper, led to the recognition of sequence requirements for the assembly of these structures. A generally accepted rule for coiled coil formation is the positioning of hydrophobic (H) and polar (P) residues in the following order (HPPHPPP) n . A two-stranded coiled coil is formed through interhelical hydrophobic interactions of residues in positions a and d, which form the core of this motif.

Fig. 1.4. Representation of coiled coil viewed from the top. Hydrophobic interactions take place within the core residues (a and d) whereas ionic interactions occur between proximal residues (e and g).

The peripheral residues of the coiled coil arrangement are likely to be involved in interfibril interactions. Single point mutations may originate very different materials. For example, Zimenkov et al. reported that the heptad with a histidine residue onto position d assembles in response to pH (Zimenkov et al., 2006). In another study, it was shown that positions b, c, and f have an influence on fibril thickness, with positively charged residues generating long and narrow nanofibers of approximately 4   nm thickness (Dong et al., 2008). Moreover, temperature responsive materials were already designed (Banwell et al., 2009) by interchanging amino acids at this same peripheral region; in one case they incorporated alanine to promote hydrophobic interactions between fibrils and in another by glutamine to foster hydrogen bonding. In both cases physical hydrogels were obtained, with the particularity that glutamine-based gels were formed at low temperature whereas alanine-based gels were achieved at high temperature.

Thermoresponsive coiled-coil peptides were also inserted in liposome membranes to allow greater control over the release of enclosed compounds in response to temperature (Al-Ahmady et al., 2012). In a recent work by More et al. engineered a supercharged coiled coil structure bearing several arginine residues that was successfully complexed with plasmid DNA and encapsulated it in a liposome for gene therapy (More et al., 2014).

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780081007419000012

DNA Sequence Recognition by Proteins

K. Rutherford , G.D. Van Duyne , in Encyclopedia of Biological Chemistry (Second Edition), 2013

α-Helices

The α-helix is the structural element most frequently used for sequence-specific interactions in protein–DNA interfaces. The size of an α-helix matches the width of the DNA major groove, allowing them to fit together tightly while the protein side chains on the helix probe the available base-pair functional groups. The mode of helix docking to the DNA varies widely among different DNA-binding domains that use this element. The maximum number of side-chain–DNA contacts can be achieved when the α-helix docks in the major groove with its axis parallel to the phosphate backbone. However, helices also insert into the major groove in an end-on fashion and with their helical axes parallel to the base pairs. Some examples can be seen in Figures 2(a)–2(d) . Helices can insert into the DNA minor groove as well, as seen with the lactose repressor. However, because the minor groove must be distorted to fit the helix, this type of interaction is not often seen and generally only one or two residues from the helix are inserted.

Figure 2. Examples of DNA-binding motifs bound to specific DNA sequences: (a) helix–turn–helix, (b) basic leucine zipper, (c) basic helix–loop–helix, (d) zinc finger, (e) ribbon–helix–helix, and (f) β-sheet motifs bound to DNA. α-Helices and β-strands that form sequence-specific interactions with the DNA are colored red. Protein structural elements that form nonspecific contacts with the DNA phosphate backbone are colored yellow. Intercalating phenylalanine residues positioned along the TATA-box binding protein's β-sheet edge are colored green. The DNA is shown as a ribbon structure with the sugar-phosphate backbone colored orange and base pairs colored by atom. The Protein Data Bank codes for the examples are given in parentheses.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780123786302002747

Principles and applications of small molecule peptidomimetics

Andrea Trabocchi , in Small Molecule Drug Discovery, 2020

6.5.1 α-Helix mimetics

The α-helix is the most common peptide secondary structure, constituting almost half of the polypeptide structure in proteins. First proposed by Hamilton, a notable entry to α-helix mimetics consisted of molecular templates based on the terphenyl (7) [72] and terpyridyl (8) scaffolds [73] (Fig. 6.16). Successively, Boger described 4-aminobenzoic acid-based oligoamides 9 with the aromatic building block varying in number from 1 to 3 units, respectively [74] (Fig. 6.16). Another entry to helix mimetics composed by aromatic rings was proposed by Koenig and collab. reporting a 1,4-dipiperazinobenzene (10) as a short helix mimetic containing side-chain isosteres at the two piperazines [75] (Fig. 6.16).

Figure 6.16. Representative entries to α-helix mimetics.

 Reproduced from A. Trabocchi, A. Guarna, Peptidomimetics in Organic and Medicinal Chemistry: The Art of Transforming Peptides in Drugs, John Wiley & Sons, UK, 2014 (Chapter 1). Copyright (2014), with permission from John Wiley and Sons.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780128183496000066

De Novo Design of Metallocoiled Coils

E. Oheix , A.F.A. Peacock , in Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, 2015

De Novo Design of CCs

The α-helix is a common protein secondary structure unit. In an ideal α-helix, a network of hydrogen bonds forms between each amide backbone carboxyl oxygen and the i  +   4 amino hydrogen, such that one turn occurs every 3.6 residues. These helices can assemble into CCs, which are characterized by the supercoiling of the helices around each other (often likened to the strands of a rope). The assembly of individual helices is directed by various noncovalent interactions. The interested reader is referred to Ref. [7] for a chronological summary of scientific progress relating to the understanding of CC occurrence, structures, and their artificial design.

De novo CCs are artificial peptide sequences that are designed to maximize these noncovalent interactions and as such can yield highly stable CC scaffolds. For example, Figure 1 compares the native sequence of the well-studied leucine zipper domain of GCN4 8 to that of the man-made CC-pIL-I17N peptide, 9 which both form a parallel homodimeric CC. However, the latter is notably more stable than the former due to the optimization of favorable noncovalent interactions.

Figure 1. Sequence of (a) the GCN4 zipper domain and (b) the CC-pIL-I17N peptide. Underlined residues are those bearing hydrophobic side chains and pointing toward the core of the coiled coil (CC) (a and d positions). Bold residues (e and g positions) can form complementary salt bridges between helices.

CC stabilization is achieved through the formation of favorable side-chain interactions, namely, packing of hydrophobic side chains (such as Leu, Ile, and Val), and complementary electrostatic interactions between side chains (such as Lys and Glu). However, in order to capitalize on these favorable interactions, it is essential that the participating side chains are appropriately orientated. In the 'knobs-into-holes' packing model (of hydrophobic side chains), the most common in soluble CCs, each turn of the helix occurs every 3.6 residues. As a result, the hydrophobic face migrates around the helix, and so in order to maximize the length of the helical interface and thus these stabilizing interactions, supercoiling of the helices occurs (rather than their perfect parallel alignment). 10 CCs are generally constructed from a seven-amino acid heptad repeat, which equates roughly to two helical turns. The residue positions within the heptad are by convention named a-b-c-d-e-f-g, and their relative position can be easily illustrated using a helical wheel diagram; see Figure 2 . Many CCs assemble in aqueous solution to yield an assembly with hydrophobic side chains packed in the central cavity (a and d positions), so as to shield them from the aqueous environment, and form complementary salt bridges between residues across the α-helical interface (e and g positions); see Figure 2(a) and 2(b) .

Figure 2. Helical wheel diagrams (top) and side-view representations (bottom) illustrating the absolute position of residues in a (a) parallel or (b) antiparallel dimeric CC. C- (carboxy-) and N- (amino-) indicate the peptide termini.

Large varieties of CCs exist and can be classified based on their total number of helices, their sequence homology, and their respective orientation ( Figure 2 ). 11 These different CC assemblies will bring different side chains into close proximity, and therefore, careful choice of amino acid residues and their location within the heptad should determine the type of CC assembly formed. For example, the parallel assembly of two helices with different sequences, a parallel heterodimeric CC, can be promoted upon engineering one peptide sequence to include anionic side chains at both the e and the g positions and a second sequence bearing complementary cationic side chains at the analogous (e′ and g′) positions. 12 In a parallel homodimeric CC, the side chains in positions g′ are in close proximity to those in positions e; however, in an antiparallel assembly, these are close to those in position g (see Figure 2(a) and 2(b) ). 10 Therefore, it is possible to control the direction of helix assembly in CCs by careful choice of the primary amino acid sequence. 13

An important driving force for CC formation is the packing of side chains in the central cavity. 14 In a typical two-stranded coiled coil (2SCC), a and d side chains (knobs) from one helix point toward the holes formed between side chains from the second helix. Tight packing is governed by steric factors, and thus, a and d positions must bear suitable hydrophobic side chains. As the oligomerization state of the CC increases, the packing interface is modified and side chains at positions not only e and g but also b, f, and c can contribute as hydrophobic knobs (see Figure 3 ). The positioning of highly branched hydrophobic side chains (such as Ile and Val) at certain positions can prevent the formation of particular oligomers. It was found that the combination of Leu (positions a) and Ile (positions d) tends to form parallel tetramers, whereas the reverse scenario with Ile (positions a) and Leu (positions d) tends to form dimers. 15 Similarly, sequences containing exclusively (positions a and d) Leu or Ile tend to form parallel trimers. 9 However, these are guidelines only as the introduction of an Asn residue at a single a position has been shown to promote dimer over trimer formation, 9 whereas Lys introduced at either a or d position destabilizes higher oligomerization states and favors dimers. 9 The interested reader is directed to Ref. [16] for more information concerning the control of oligomer state based on core packing angles.

Figure 3. Helical-wheel diagram representing examples of CCs with different oligomer states. (a) A classic trimeric 3SCC with a (H-x-x-H-x-x-x) heptad repeat; (b) half of the motif for a hexameric 6SCC involving a (H-x-x-H-H-x-H) heptad repeat in which the hydrophobic interface involves a larger number of residues. In (b), only three helices out of six are represented and gray arcs indicate the interface involved with neighboring unshown helices. H and x, respectively, represent hydrophobic (gray spheres) and nonhydrophobic (white spheres) positions within the a-b-c-d-e-f-g heptad repeat.

Pecoraro et al. designed the TRI and Coil-Ser family of parallel homotrimeric CC scaffolds (3SCC) based on these design features, and analogs of these are frequently referred to as key examples in this report. The TRI sequence consists of four LKALEEK heptad repeats and forms a 3SCC at pH   >   5.5. 17–19 The GRAND and BABY variants are longer (five heptads) and shorter (three heptads), respectively. Other TRI derivatives suitable for metal ion coordination will be introduced in section ' Engineering Metal Sites within CCs and Bundles .'

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780124095472114489

Crystallographic Coordinates and Stereodrawings

LEONARD J. BANASZAK , in Foundations of Structural Biology, 2000

Practicing Stereovision

5.

In an α helix, the C=O bonds all point in the same direction. Does the tetrapeptide MKVA shown in Fig. 3.2 belong to an α helix?

6.

Show schematically the stereochemical arrangement about the Cβ of isoleucine (Fig. 3.3).

7.

Could the two residues –R–F– in Fig. 3.5 be part of an α helix?

8.

Serine side chains in proteins are often oriented so that a hydrogen bond forms between the hydroxyl and the previous carbonyl oxygen. Is that happening in Fig. 3.7?

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780120777006500031