Inari Ex. 1033
`Inari Agric. v. Corteva Agriscience
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`chapter
`
`4
`
`THE THREE-DIMENSIONAL
`STRUCTURE OF PROTEINS
`
`4.1 Overview of Protein Structure 116
`4.2
`Protein Secondary Structure 120
`4.3
`Protein Tertiary and Quaternary Structures 125
`4.4
`Protein Denaturation and Folding 147
`
`Perhaps the more remarkable features of [myoglobin] are
`its complexity and its lack of symmetry. The arrangement
`seems to be almost totally lacking in the kind of regulari-
`ties which one instinctively anticipates, and it is more
`complicated than has been predicted by any theory of
`protein structure.
`
`—John Kendrew, article in Nature, 1958
`
`The covalent backbone of a typical protein contains
`
`hundreds of individual bonds. Because free rotation
`is possible around many of these bonds, the protein can
`assume an unlimited number of conformations. How-
`ever, each protein has a specific chemical or structural
`function, strongly suggesting that each has a unique
`three-dimensional structure (Fig. 4–1). By the late
`1920s, several proteins had been crystallized, including
`hemoglobin (Mr 64,500) and the enzyme urease (Mr
`483,000). Given that the ordered array of molecules in
`a crystal can generally form only if the molecular units
`are identical, the simple fact that many proteins can be
`crystallized provides strong evidence that even very
`large proteins are discrete chemical entities with unique
`structures. This conclusion revolutionized thinking
`about proteins and their functions.
`In this chapter, we explore the three-dimensional
`structure of proteins, emphasizing five themes. First,
`the three-dimensional structure of a protein is deter-
`mined by its amino acid sequence. Second, the function
`116
`
`of a protein depends on its structure. Third, an isolated
`protein usually exists in one or a small number of sta-
`ble structural forms. Fourth, the most important forces
`stabilizing the specific structures maintained by a given
`protein are noncovalent interactions. Finally, amid the
`huge number of unique protein structures, we can rec-
`ognize some common structural patterns that help us
`organize our understanding of protein architecture.
`These themes should not be taken to imply that pro-
`teins have static, unchanging three-dimensional struc-
`tures. Protein function often entails an interconversion
`between two or more structural forms. The dynamic as-
`pects of protein structure will be explored in Chapters
`5 and 6.
`The relationship between the amino acid sequence
`of a protein and its three-dimensional structure is an in-
`tricate puzzle that is gradually yielding to techniques
`used in modern biochemistry. An understanding of
`structure, in turn, is essential to the discussion of func-
`tion in succeeding chapters. We can find and understand
`the patterns within the biochemical labyrinth of protein
`structure by applying fundamental principles of chem-
`istry and physics.
`
`4.1 Overview of Protein Structure
`
`The spatial arrangement of atoms in a protein is called
`its conformation. The possible conformations of a pro-
`tein include any structural state that can be achieved
`without breaking covalent bonds. A change in confor-
`mation could occur, for example, by rotation about sin-
`gle bonds. Of the numerous conformations that are
`theoretically possible in a protein containing hundreds
`of single bonds, one or (more commonly) a few gener-
`ally predominate under biological conditions. The need
`for multiple stable conformations reflects the changes
`that must occur in most proteins as they bind to other
`
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`4.1 Overview of Protein Structure
`
`117
`
`can theoretically assume countless different conforma-
`tions, and as a result the unfolded state of a protein is
`characterized by a high degree of conformational en-
`tropy. This entropy, and the hydrogen-bonding interac-
`tions of many groups in the polypeptide chain with sol-
`vent (water), tend to maintain the unfolded state. The
`chemical interactions that counteract these effects and
`stabilize the native conformation include disulfide bonds
`and the weak (noncovalent) interactions described in
`Chapter 2: hydrogen bonds, and hydrophobic and ionic
`interactions. An appreciation of the role of these weak
`interactions is especially important to our understand-
`ing of how polypeptide chains fold into specific sec-
`ondary and tertiary structures, and how they combine
`with other polypeptides to form quaternary structures.
`About 200 to 460 kJ/mol are required to break a sin-
`gle covalent bond, whereas weak interactions can be dis-
`rupted by a mere 4 to 30 kJ/mol. Individual covalent
`bonds that contribute to the native conformations of
`proteins, such as disulfide bonds linking separate parts
`of a single polypeptide chain, are clearly much stronger
`than individual weak interactions. Yet, because they are
`so numerous, it is weak interactions that predominate
`as a stabilizing force in protein structure. In general, the
`protein conformation with the lowest free energy (that
`is, the most stable conformation) is the one with the
`maximum number of weak interactions.
`The stability of a protein is not simply the sum of
`the free energies of formation of the many weak inter-
`actions within it. Every hydrogen-bonding group in a
`folded polypeptide chain was hydrogen-bonded to wa-
`ter prior to folding, and for every hydrogen bond formed
`in a protein, a hydrogen bond (of similar strength) be-
`tween the same group and water was broken. The net
`stability contributed by a given weak interaction, or the
`difference in free energies of the folded and unfolded
`states, may be close to zero. We must therefore look
`elsewhere to explain why the native conformation of a
`protein is favored.
`We find that the contribution of weak interactions
`to protein stability can be understood in terms of the
`properties of water (Chapter 2). Pure water contains a
`network of hydrogen-bonded H2O molecules. No other
`molecule has the hydrogen-bonding potential of water,
`and other molecules present in an aqueous solution dis-
`rupt the hydrogen bonding of water. When water sur-
`rounds a hydrophobic molecule, the optimal arrange-
`ment of hydrogen bonds results in a highly structured
`shell, or solvation layer, of water in the immediate
`vicinity. The increased order of the water molecules in
`the solvation layer correlates with an unfavorable de-
`crease in the entropy of the water. However, when non-
`polar groups are clustered together, there is a decrease
`in the extent of the solvation layer because each group
`no longer presents its entire surface to the solution. The
`result is a favorable increase in entropy. As described in
`
`FIGURE 4–1 Structure of the enzyme chymotrypsin, a globular pro-
`tein. Proteins are large molecules and, as we shall see, each has a
`unique structure. A molecule of glycine (blue) is shown for size com-
`parison. The known three-dimensional structures of proteins are
`archived in the Protein Data Bank, or PDB (www.rcsb.org/pdb). Each
`structure is assigned a unique four-character identifier, or PDB ID.
`Where appropriate, we will provide the PDB IDs for molecular graphic
`images in the figure captions. The image shown here was made using
`data from the PDB file 6GCH. The data from the PDB files provide
`only a series of coordinates detailing the location of atoms and their
`connectivity. Viewing the images requires easy-to-use graphics pro-
`grams such as RasMol and Chime that convert the coordinates into
`an image and allow the viewer to manipulate the structure in three
`dimensions. You will find instructions for downloading Chime with
`the structure tutorials on the textbook website (www.whfreeman.
`com/lehninger). The PDB website has instructions for downloading
`other viewers. We encourage all students to take advantage of the re-
`sources of the PDB and the free molecular graphics programs.
`
`molecules or catalyze reactions. The conformations ex-
`isting under a given set of conditions are usually the
`ones that are thermodynamically the most stable, hav-
`ing the lowest Gibbs free energy (G). Proteins in any of
`their functional, folded conformations are called native
`proteins.
`What principles determine the most stable confor-
`mations of a protein? An understanding of protein con-
`formation can be built stepwise from the discussion of
`primary structure in Chapter 3 through a consideration
`of secondary, tertiary, and quaternary structures. To this
`traditional approach must be added a new emphasis on
`supersecondary structures, a growing set of known and
`classifiable protein folding patterns that provides an im-
`portant organizational context to this complex endeavor.
`We begin by introducing some guiding principles.
`
`A Protein’s Conformation Is Stabilized Largely
`by Weak Interactions
`In the context of protein structure, the term stability
`can be defined as the tendency to maintain a native con-
`formation. Native proteins are only marginally stable;
`the ⌬G separating the folded and unfolded states in typ-
`ical proteins under physiological conditions is in the
`range of only 20 to 65 kJ/mol. A given polypeptide chain
`
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`Chapter 4
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`The Three-Dimensional Structure of Proteins
`
`Chapter 2, this entropy term is the major thermody-
`namic driving force for the association of hydrophobic
`groups in aqueous solution. Hydrophobic amino acid
`side chains therefore tend to be clustered in a protein’s
`interior, away from water.
`Under physiological conditions, the formation of
`hydrogen bonds and ionic interactions in a protein is
`driven largely by this same entropic effect. Polar groups
`can generally form hydrogen bonds with water and
`hence are soluble in water. However, the number of hy-
`drogen bonds per unit mass is generally greater for pure
`water than for any other liquid or solution, and there
`are limits to the solubility of even the most polar mole-
`cules as their presence causes a net decrease in hydro-
`gen bonding per unit mass. Therefore, a solvation shell
`of structured water will also form to some extent around
`polar molecules. Even though the energy of formation
`of an intramolecular hydrogen bond or ionic interaction
`between two polar groups in a macromolecule is largely
`canceled out by the elimination of such interactions be-
`tween the same groups and water, the release of struc-
`tured water when the intramolecular interaction is
`formed provides an entropic driving force for folding.
`Most of the net change in free energy that occurs when
`weak interactions are formed within a protein is there-
`fore derived from the increased entropy in the sur-
`rounding aqueous solution resulting from the burial of
`hydrophobic surfaces. This more than counterbalances
`the large loss of conformational entropy as a polypep-
`tide is constrained into a single folded conformation.
`Hydrophobic interactions are clearly important in
`stabilizing a protein conformation; the interior of a pro-
`tein is generally a densely packed core of hydrophobic
`amino acid side chains. It is also important that any po-
`lar or charged groups in the protein interior have suit-
`able partners for hydrogen bonding or ionic interactions.
`One hydrogen bond seems to contribute little to the
`stability of a native structure, but the presence of
`hydrogen-bonding or charged groups without partners
`in the hydrophobic core of a protein can be so destabi-
`lizing that conformations containing these groups are
`often thermodynamically untenable. The favorable free-
`energy change realized by combining such a group with
`a partner in the surrounding solution can be greater than
`the difference in free energy between the folded and
`unfolded states. In addition, hydrogen bonds between
`groups in proteins form cooperatively. Formation of one
`hydrogen bond facilitates the formation of additional hy-
`drogen bonds. The overall contribution of hydrogen
`bonds and other noncovalent interactions to the stabi-
`lization of protein conformation is still being evaluated.
`The interaction of oppositely charged groups that form
`an ion pair (salt bridge) may also have a stabilizing effect
`on one or more native conformations of some proteins.
`Most of the structural patterns outlined in this chap-
`ter reflect two simple rules: (1) hydrophobic residues
`
`are largely buried in the protein interior, away from wa-
`ter; and (2) the number of hydrogen bonds within the
`protein is maximized. Insoluble proteins and proteins
`within membranes (which we examine in Chapter 11)
`follow somewhat different rules because of their func-
`tion or their environment, but weak interactions are still
`critical structural elements.
`
`The Peptide Bond Is Rigid and Planar
`Protein Architecture—Primary Structure Covalent bonds also
`place important constraints on the conformation of a
`polypeptide. In the late 1930s, Linus Pauling and Robert
`Corey embarked on a series of studies that laid the foun-
`dation for our present understanding of protein struc-
`ture. They began with a careful analysis of the peptide
`bond. The ␣ carbons of adjacent amino acid residues
`are separated by three covalent bonds, arranged as
`C␣OCONOC␣. X-ray diffraction studies of crystals of
`amino acids and of simple dipeptides and tripeptides
`demonstrated that the peptide CON bond is somewhat
`shorter than the CON bond in a simple amine and that
`the atoms associated with the peptide bond are co-
`planar. This indicated a resonance or partial sharing of
`two pairs of electrons between the carbonyl oxygen and
`the amide nitrogen (Fig. 4–2a). The oxygen has a par-
`tial negative charge and the nitrogen a partial positive
`charge, setting up a small electric dipole. The six atoms
`of the peptide group lie in a single plane, with the oxy-
`gen atom of the carbonyl group and the hydrogen atom
`of the amide nitrogen trans to each other. From these
`findings Pauling and Corey concluded that the peptide
`CON bonds are unable to rotate freely because of their
`partial double-bond character. Rotation is permitted
`about the NOC␣ and the C␣OC bonds. The backbone
`of a polypeptide chain can thus be pictured as a series
`of rigid planes with consecutive planes sharing a com-
`mon point of rotation at C␣ (Fig. 4–2b). The rigid pep-
`tide bonds limit the range of conformations that can be
`assumed by a polypeptide chain.
`By convention, the bond angles resulting from ro-
`tations at C␣ are labeled ␾ (phi) for the NOC␣ bond
`and ␺ (psi) for the C␣OC bond. Again by convention,
`both ␾ and ␺ are defined as 180⬚ when the polypeptide
`is in its fully extended conformation and all peptide
`groups are in the same plane (Fig. 4–2b). In principle,
`␾ and ␺ can have any value between ⫺180⬚ and ⫹180⬚,
`but many values are prohibited by steric interference
`between atoms in the polypeptide backbone and amino
`acid side chains. The conformation in which both ␾ and
`␺ are 0⬚ (Fig. 4–2c) is prohibited for this reason; this
`conformation is used merely as a reference point for de-
`scribing the angles of rotation. Allowed values for ␾ and
`␺ are graphically revealed when ␺ is plotted versus ␾ in
`a Ramachandran plot (Fig. 4–3), introduced by G. N.
`Ramachandran.
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`4.1 Overview of Protein Structure
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`119
`
`The carbonyl oxygen has a partial negative
`charge and the amide nitrogen a partial positive
`charge, setting up a small electric dipole.
`Virtually all peptide bonds in proteins occur in
`this trans configuration; an exception is noted in
`Figure 4–8b.
`
`C␣
`
`⫹
`
`N H
`
`⫺
`
`CO
`
`C␣
`
`w
`
`f
`
`f w
`
`Carboxyl
`terminus
`
`␦⫺
`
`CO
`
`C␣
`
`N␦
`
`⫹
`
`H
`
`C␣
`
`C␣
`
`N H
`
`CO
`
`C␣
`
`(a)
`
`(b)
`
`O
`
`1.24 Å
`1.46 Å
`
`1.53 Å
`
`C
`
`Ca
`
`1.32 Å
`
`N
`
`Amino
`terminus
`
`H
`
`R
`
`Ca
`
`f w
`
`N–Ca
`
`Ca–C
`
`C–N
`
`Ca
`
`O
`
`N
`
`Ca
`
`C
`
`O
`
`C
`
`w
`
`N
`
`H
`
`Ca
`
`H
`
`f
`
`R
`
`0
`f (degrees)
`
`⫹180
`
`⫹180
`
`120
`
`60
`
`0
`
`⫺60
`
`⫺120
`
`⫺180
`⫺180
`
`(c)
`
`w (degrees)
`
`FIGURE 4–2 The planar peptide group. (a) Each peptide bond has
`some double-bond character due to resonance and cannot rotate.
`(b) Three bonds separate sequential ␣ carbons in a polypeptide
`chain. The NOC␣ and C␣OC bonds can rotate, with bond angles
`designated ␾ and ␺, respectively. The peptide CON bond is not free
`to rotate. Other single bonds in the backbone may also be
`rotationally hindered, depending on the size and charge of the R
`groups. In the conformation shown, ␾ and ␺ are 180⬚ (or ⫺ 180⬚).
`As one looks out from the ␣ carbon, the ␺ and ␾ angles increase as
`the carbonyl or amide nitrogens (respectively) rotate clockwise.
`(c) By convention, both ␾ and ␺ are defined as 0⬚ when the two
`peptide bonds flanking that ␣ carbon are in the same plane and
`positioned as shown. In a protein, this conformation is prohibited
`by steric overlap between an ␣-carbonyl oxygen and an ␣-amino
`hydrogen atom. To illustrate the bonds between atoms, the balls
`representing each atom are smaller than the van der Waals radii for
`this scale. 1 Å ⫽ 0.1 nm.
`
`FIGURE 4–3 Ramachandran plot for L-Ala residues. The
`conformations of peptides are defined by the values of ␾ and ␺.
`Conformations deemed possible are those that involve little or no
`steric interference, based on calculations using known van der
`Waals radii and bond angles. The areas shaded dark blue reflect
`conformations that involve no steric overlap and thus are fully
`allowed; medium blue indicates conformations allowed at the
`extreme limits for unfavorable atomic contacts; the lightest blue
`area reflects conformations that are permissible if a little flexibility is
`allowed in the bond angles. The asymmetry of the plot results from
`the L stereochemistry of the amino acid residues. The plots for other
`L-amino acid residues with unbranched side chains are nearly
`identical. The allowed ranges for branched amino acid residues
`such as Val, Ile, and Thr are somewhat smaller than for Ala. The Gly
`residue, which is less sterically hindered, exhibits a much broader
`range of allowed conformations. The range for Pro residues is
`greatly restricted because ␾ is limited by the cyclic side chain to the
`range of ⫺35⬚ to ⫺85⬚.
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`The Three-Dimensional Structure of Proteins
`
`ing polar chemical groups such as the CPO and NOH
`groups of the peptide bond. They also had the experi-
`mental results of William Astbury, who in the 1930s had
`conducted pioneering x-ray studies of proteins. Astbury
`demonstrated that the protein that makes up hair and
`porcupine quills (the fibrous protein ␣-keratin) has a
`regular structure that repeats every 5.15 to 5.2 Å. (The
`angstrom, Å, named after the physicist Anders J.
`Ångström, is equal to 0.1 nm. Although not an SI unit,
`it is used universally by structural biologists to describe
`atomic distances.) With this information and their data
`on the peptide bond, and with the help of precisely con-
`structed models, Pauling and Corey set out to deter-
`mine the likely conformations of protein molecules.
`The simplest arrangement the polypeptide chain
`could assume with its rigid peptide bonds (but other
`single bonds free to rotate) is a helical structure, which
`Pauling and Corey called the ␣ helix (Fig. 4–4). In this
`structure the polypeptide backbone is tightly wound
`around an imaginary axis drawn longitudinally through
`the middle of the helix, and the R groups of the amino
`acid residues protrude outward from the helical back-
`bone. The repeating unit is a single turn of the helix,
`which extends about 5.4 Å along the long axis, slightly
`greater than the periodicity Astbury observed on x-ray
`analysis of hair keratin. The amino acid residues in an
`␣ helix have conformations with ␺ ⫽ ⫺45⬚ to ⫺50⬚ and
`␾ ⫽ ⫺60⬚, and each helical turn includes 3.6 amino acid
`residues. The helical twist of the ␣ helix found in all pro-
`teins is right-handed (Box 4–1). The ␣ helix proved to
`be the predominant structure in ␣-keratins. More gen-
`erally, about one-fourth of all amino acid residues in
`polypeptides are found in ␣ helices, the exact fraction
`varying greatly from one protein to the next.
`Why does the ␣ helix form more readily than many
`other possible conformations? The answer is, in part,
`that an ␣ helix makes optimal use of internal hydrogen
`bonds. The structure is stabilized by a hydrogen bond
`between the hydrogen atom attached to the elec-
`tronegative nitrogen atom of a peptide linkage and the
`electronegative carbonyl oxygen atom of the fourth
`amino acid on the amino-terminal side of that peptide
`bond (Fig. 4–4b). Within the ␣ helix, every peptide bond
`(except those close to each end of the helix) partici-
`pates in such hydrogen bonding. Each successive turn
`of the ␣ helix is held to adjacent turns by three to four
`hydrogen bonds. All the hydrogen bonds combined give
`the entire helical structure considerable stability.
`Further model-building experiments have shown
`that an ␣ helix can form in polypeptides consisting of
`either L- or D-amino acids. However, all residues must
`be of one stereoisomeric series; a D-amino acid will dis-
`rupt a regular structure consisting of L-amino acids, and
`vice versa. Naturally occurring L-amino acids can form
`either right- or left-handed ␣ helices, but extended left-
`handed helices have not been observed in proteins.
`
`Linus Pauling, 1901–1994
`
`Robert Corey, 1897–1971
`
`SUMMARY 4.1 Overview of Protein Structure
`
`■ Every protein has a three-dimensional structure
`that reflects its function.
`■ Protein structure is stabilized by multiple weak
`interactions. Hydrophobic interactions are the
`major contributors to stabilizing the globular
`form of most soluble proteins; hydrogen bonds
`and ionic interactions are optimized in the
`specific structures that are thermodynamically
`most stable.
`■ The nature of the covalent bonds in the
`polypeptide backbone places constraints on
`structure. The peptide bond has a partial double-
`bond character that keeps the entire six-atom
`peptide group in a rigid planar configuration.
`The NOC␣ and C␣OC bonds can rotate to
`assume bond angles of ␾ and ␺, respectively.
`
`4.2 Protein Secondary Structure
`The term secondary structure refers to the local con-
`formation of some part of a polypeptide. The discussion
`of secondary structure most usefully focuses on com-
`mon regular folding patterns of the polypeptide back-
`bone. A few types of secondary structure are particu-
`larly stable and occur widely in proteins. The most
`prominent are the ␣ helix and ␤ conformations de-
`scribed below. Using fundamental chemical principles
`and a few experimental observations, Pauling and Corey
`predicted the existence of these secondary structures
`in 1951, several years before the first complete protein
`structure was elucidated.
`
`The ␣ Helix Is a Common Protein
`Secondary Structure
`Protein Architecture— ␣ Helix Pauling and Corey were
`aware of the importance of hydrogen bonds in orient-
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`4.2
`
`Protein Secondary Structure
`
`121
`
`Amino terminus
`
`Carbon
`Hydrogen
`Oxygen
`Nitrogen
`R group
`
`5.4 Å
`(3.6 residues)
`
`Carboxyl terminus
`
`(a)
`
`(b)
`
`(c)
`
`(d)
`
`FIGURE 4–4 Four models of the ␣ helix, showing different aspects
`of its structure. (a) Formation of a right-handed ␣ helix. The planes
`of the rigid peptide bonds are parallel to the long axis of the helix,
`depicted here as a vertical rod. (b) Ball-and-stick model of a right-
`handed ␣ helix, showing the intrachain hydrogen bonds. The repeat
`unit is a single turn of the helix, 3.6 residues. (c) The ␣ helix as viewed
`from one end, looking down the longitudinal axis (derived from PDB
`
`ID 4TNC). Note the positions of the R groups, represented by purple
`spheres. This ball-and-stick model, used to emphasize the helical
`arrangement, gives the false impression that the helix is hollow, be-
`cause the balls do not represent the van der Waals radii of the indi-
`vidual atoms. As the space-filling model (d) shows, the atoms in the
`center of the ␣ helix are in very close contact.
`
`Amino Acid Sequence Affects ␣ Helix Stability
`Not all polypeptides can form a stable ␣ helix. Interac-
`tions between amino acid side chains can stabilize or
`destabilize this structure. For example, if a polypeptide
`chain has a long block of Glu residues, this segment of
`the chain will not form an ␣ helix at pH 7.0. The nega-
`tively charged carboxyl groups of adjacent Glu residues
`repel each other so strongly that they prevent forma-
`tion of the ␣ helix. For the same reason, if there are
`many adjacent Lys and/or Arg residues, which have pos-
`itively charged R groups at pH 7.0, they will also repel
`each other and prevent formation of the ␣ helix. The
`bulk and shape of Asn, Ser, Thr, and Cys residues can
`also destabilize an ␣ helix if they are close together in
`the chain.
`The twist of an ␣ helix ensures that critical inter-
`actions occur between an amino acid side chain and the
`side chain three (and sometimes four) residues away on
`either side of it (Fig. 4–5). Positively charged amino
`acids are often found three residues away from nega-
`tively charged amino acids, permitting the formation of
`an ion pair. Two aromatic amino acid residues are often
`similarly spaced, resulting in a hydrophobic interaction.
`
`FIGURE 4–5 Interactions between R groups of amino acids three
`residues apart in an ␣ helix. An ionic interaction between Asp100 and
`Arg103 in an ␣-helical region of the protein troponin C, a calcium-
`binding protein associated with muscle, is shown in this space-filling
`model (derived from PDB ID 4TNC). The polypeptide backbone (car-
`bons, ␣-amino nitrogens, and ␣-carbonyl oxygens) is shown in gray
`for a helix segment 13 residues long. The only side chains represented
`here are the interacting Asp (red) and Arg (blue) side chains.
`
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`The Three-Dimensional Structure of Proteins
`
`BOX 4–1 WORKING IN BIOCHEMISTRY
`
`Knowing the Right Hand from the Left
`There is a simple method for determining whether a
`helical structure is right-handed or left-handed. Make
`fists of your two hands with thumbs outstretched and
`pointing straight up. Looking at your right hand, think
`of a helix spiraling up your right thumb in the direc-
`tion in which the other four fingers are curled as
`shown (counterclockwise). The resulting helix is
`right-handed. Your left hand will demonstrate a left-
`handed helix, which rotates in the clockwise direction
`as it spirals up your thumb.
`
`A constraint on the formation of the ␣ helix is the
`presence of Pro or Gly residues. In proline, the nitrogen
`atom is part of a rigid ring (see Fig. 4–8b), and rotation
`about the NOC␣ bond is not possible. Thus, a Pro
`residue introduces a destabilizing kink in an ␣ helix. In
`addition, the nitrogen atom of a Pro residue in peptide
`linkage has no substituent hydrogen to participate in hy-
`drogen bonds with other residues. For these reasons,
`proline is only rarely found within an ␣ helix. Glycine
`occurs infrequently in ␣ helices for a different reason:
`it has more conformational flexibility than the other
`amino acid residues. Polymers of glycine tend to take
`up coiled structures quite different from an ␣ helix.
`A final factor affecting the stability of an ␣ helix in
`a polypeptide is the identity of the amino acid residues
`near the ends of the ␣-helical segment. A small electric
`dipole exists in each peptide bond (Fig. 4–2a). These
`dipoles are connected through the hydrogen bonds of
`the helix, resulting in a net dipole extending along the
`helix that increases with helix length (Fig. 4–6). The
`four amino acid residues at each end of the helix do not
`participate fully in the helix hydrogen bonds. The par-
`tial positive and negative charges of the helix dipole ac-
`tually reside on the peptide amino and carbonyl groups
`near the amino-terminal and carboxyl-terminal ends of
`the helix, respectively. For this reason, negatively
`charged amino acids are often found near the amino ter-
`minus of the helical segment, where they have a stabi-
`lizing interaction with the positive charge of the helix
`dipole; a positively charged amino acid at the amino-
`terminal end is destabilizing. The opposite is true at the
`carboxyl-terminal end of the helical segment.
`Thus, five different kinds of constraints affect the
`stability of an ␣ helix: (1) the electrostatic repulsion (or
`attraction) between successive amino acid residues with
`charged R groups, (2) the bulkiness of adjacent R
`groups, (3) the interactions between R groups spaced
`
`three (or four) residues apart, (4) the occurrence of Pro
`and Gly residues, and (5) the interaction between amino
`acid residues at the ends of the helical segment and the
`electric dipole inherent to the ␣ helix. The tendency of
`a given segment of a polypeptide chain to fold up as an
`␣ helix therefore depends on the identity and sequence
`of amino acid residues within the segment.
`
`Amino terminus
`+
`
`d
`+
`
`–
`
`+
`
`+–
`
`–
`
`–
`
`+
`
`+
`
`–
`
`–
`
`+
`
`+
`
`–
`
`+
`
`+
`
`–
`
`+
`
`–
`
`+
`
`–
`
`–
`d–
`Carboxyl terminus
`
`FIGURE 4–6 Helix dipole. The electric dipole of a peptide bond (see
`Fig. 4–2a) is transmitted along an ␣-helical segment through the in-
`trachain hydrogen bonds, resulting in an overall helix dipole. In this
`illustration, the amino and carbonyl constituents of each peptide bond
`are indicated by ⫹ and ⫺ symbols, respectively. Non-hydrogen-
`bonded amino and carbonyl constituents in the peptide bonds near
`each end of the ␣-helical region are shown in red.
`
`PGR2023-00022 Page 00008
`
`

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`4.2
`
`Protein Secondary Structure
`
`123
`
`The ␤ Conformation Organizes Polypeptide Chains
`into Sheets
`Protein Architecture—␤ Sheet Pauling and Corey predicted
`a second type of repetitive structure, the ␤ conforma-
`tion. This is a more extended conformation of polypep-
`tide chains, and its structure has been confirmed by
`x-ray analysis. In the ␤ conformation, the backbone of
`the polypeptide chain is extended into a zigzag rather
`than helical structure (Fig. 4–7). The zigzag polypep-
`tide chains can be arranged side by side to form a struc-
`ture resembling a series of pleats. In this arrangement,
`called a ␤ sheet, hydrogen bonds are formed between
`adjacent segments of polypeptide chain. The individual
`segments that form a ␤ sheet are usually nearby on the
`polypeptide chain, but can also be quite distant from
`each other in the linear sequence of the polypeptide;
`they may even be segments in different polypeptide
`chains. The R groups of adjacent amino acids protrude
`from the zigzag structure in opposite directions, creat-
`ing the alternating pattern seen in the side views in Fig-
`ure 4–7.
`The adjacent polypeptide chains in a ␤ sheet can
`be either parallel or antiparallel (having the same or
`opposite amino-to-carboxyl orientations, respectively).
`The structures are somewhat similar, although the
`repeat period is shorter for the parallel conformation
`(6.5 Å, versus 7 Å for antiparallel) and the hydrogen-
`bonding patterns are different.
`Some protein structures limit the kinds of amino
`acids that can occur in the ␤ sheet. When two or more
`␤ sheets are layered close together within a protein, the
`R groups of the amino acid residues on the touching sur-
`faces must be relatively small. ␤-Keratins such as silk
`fibroin and the fibroin of spider webs have a very high
`content of Gly and Ala residues, the two amino acids
`with the smallest R groups. Indeed, in silk fibroin Gly
`and Ala alternate over large parts of the sequence.
`
`␤ Turns Are Common in Proteins
`Protein Architecture— ␤ Turn In globular proteins, which
`have a compact folded structure, nearly one-third of the
`amino acid residues are in turns or loops where the
`polypeptide chain reverses direction (Fig. 4–8). These
`are the connecting elements that link successive runs
`of ␣ helix or ␤ conformation. Particularly common are
`␤ turns that connect the ends of two adjacent segments
`of an antiparallel ␤ sheet. The structure is a 180⬚ turn
`involving four amino acid residues, with the carbonyl
`oxygen of the first residue forming a hydrogen bond with
`the amino-group hydrogen of the fourth. The peptide
`groups of the central two residues do not participate in
`any
`interresidue hydrogen bonding. Gly and Pro
`residues often occur in ␤ turns, the former because it
`is small and flexible, the latter because peptide bonds
`
`(a) Antiparallel
`
`Top view
`
`Side view
`
`(b) Parallel
`
`Top view
`
`Side view
`
`FIGURE 4–7 The ␤ conformation of polypeptide chains. These top
`and side views reveal the R groups extending out from the ␤ sheet
`and emphasize the pleated shape described by the planes of the pep-
`tide bonds. (An alternative name for this structure is ␤-pleated sheet.)
`Hydrogen-