m
`
`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 1 of 31 PageID #:
`9425
`
`iti <i'; :i 'ii hh i! inm ■* . n ain -iiiioii s si* ik min 11 ieliiii iiaLin su issiarii iriiimicin mm iihb . isii
`
`CUuv,___
`
`Biomed
`
`QH
`581.2
`M718
`2002
`
`MOLECULAR BIOLOGY
`
`THE CELL
`
`ALBERTS
`
`JOHNSON
`
`LEWIS
`
`RAFF
`
`ROBERTS
`
`WALTER
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 2 of 31 PageID #:
`Cell Biology Interactive
`Garland
`9426
`Artistic and Scientific Direction: Peter Walter
`Vice President: Denise Schanck
`Narrated by: Julie Theriot
`Managing Editor: Sarah Gibbs
`Production, Design, and Development: Mike Morales
`Senior Editorial Assistant: Kirsten Jenner
`Managing Production Editor: Emma Hunt
`Proofreader and Layout: Emma Hunt
`Production Assistant: Angela Bennett
`Text Editors: Marjorie Singer Anderson and Betsy Dilernia
`Copy Editor: Bruce Goatly
`Word Processors: Fran Dependahl, Misty Landers and Carol Winter
`Designer: Blink Studio, London
`Illustrator: Nigel Orme
`Indexer: Janine Ross and Sherry Granum
`Manufacturing: Nigel Eyre and Marion Morrow
`
`Bruce Alberts received his Ph.D. from Harvard University and is
`President of the National Academy of Sciences and Professor of
`Biochemistry and Biophysics at the University of California, San
`Francisco. Alexander Johnson received his Ph.D. from Harvard
`University and is a Professor of Microbiology and Immunology at
`the University of California, San Francisco. Julian Lewis received
`his D.Phil. from the University of Oxford and is a Principal
`Scientist at the Imperial Cancer Research Fund, London.
`Martin Raff received his M.D. from McGill University and is at the
`Medical Research Council Laboratory for Molecular Cell Biology
`and Cell Biology Unit and in the Biology Department at University
`College London. Keith Roberts received his Ph.D. from the
`University of Cambridge and is Associate Research Director at the
`John Innes Centre, Norwich. Peter Walter received his Ph.D. from
`The Rockefeller University in New York and is Professor and
`Chairman of the Department of Biochemistry and Biophysics at
`the University of California, San Francisco, and an Investigator of
`the Howard Hughes Medical Institute.
`
`© 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis,
`Martin Raff, Keith Roberts, and Peter Walter.
`© 1983, 1989, 1994 by Bruce Alberts, Dennis Bray, Julian Lewis,
`Martin Raff, Keith Roberts, and James D. Watson.
`
`All rights reserved. No part of this book covered by the copyright
`hereon may be reproduced or used in any format in any form or
`by any means—graphic, electronic, or mechanical, including
`photocopying, recording, taping, or information storage and
`retrieval systems—without permission of the publisher.
`
`Library of Congress Cataloging-in-Publicaton Data
`Molecular biology of the cell / Bruce Alberts ... [et al].— 4th ed.
`p. cm
`Includes bibliographical references and index.
`ISBN 0-8153-3218-1 (hardbound) - ISBN 0-8153-4072-9 (pbk.)
`1. Cytology. 2. Molecular biology. I. Alberts, Bruce.
`[DNLM: 1. Cells. 2. Molecular Biology. ]
`QH581.2 .M64 2002
`571.6—dc21
`
`2001054471 CIP
`
`Published by Garland Science, a member of the Taylor & Francis Group,
`29 West 35th Street, New York, NY 10001-2299
`
`Printed in the United States of America
`
`15 14 13 12 11 10 9 8 7 6 5 4 3 2 1
`
`Front cover Human Genome: Reprinted by permission
`from Nature, International Human Genome Sequencing
`Consortium, 409:860-921, 2001 © Macmillan Magazines
`Ltd. Adapted from an image by Francis Collins, NHGRI;
`Jim Kent, UCSC; Ewan Birney, EBI; and Darryl Leja,
`NHGRI; showing a portion of Chromosome 1 from the
`initial sequencing of the human genome.
`
`Back cover In 1967, the British artist Peter Blake created
`a design classic. Nearly 35 years later Nigel Orme
`(illustrator), Richard Denyer (photographer), and the
`authors have together produced an affectionate tribute
`to Mr Blake’s image. With its gallery of icons and
`influences, its assembly created almost as much
`complexity, intrigue and mystery as the original.
`Drosophila, Arabidopsis, Dolly and the assembled
`company tempt you to dip inside where, as in the
`original, “a splendid time is guaranteed for all.”
`(Gunter Blobel, courtesy of The Rockefeller University; Marie
`Curie, Keystone Press Agency Inc; Darwin bust, by permission
`of the President and Council of the Royal Society; Rosalind
`Franklin, courtesy of Cold Spring Harbor Laboratory Archives;
`Dorothy Hodgkin, © The Nobel Foundation, 1964; James Joyce,
`etching by Peter Blake; Robert Johnson, photo booth
`self-portrait early 1930s, © 1986 Delta Haze Corporation all
`rights reserved, used by permission; Albert L. Lehninger,
`(unidentified photographer) courtesy of The Alan Mason
`Chesney Medical Archives of The Johns Hopkins Medical
`Institutions; Linus Pauling, from Ava Helen and Linus Pauling
`Papers, Special Collections, Oregon State University; Nicholas
`Poussin, courtesy ofArtToday.com; Barbara McClintock,
`© David Micklos, 1983; Andrei Sakharov, courtesy of Elena
`Bonner; Frederick Sanger, © The Nobel Foundation, 1958.)
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 3 of 31 PageID #:
`9427
`
`PROTEINS
`
`THE SHAPE AND STRUCTURE OF
`PROTEINS
`
`PROTEIN FUNCTION
`
`When we look at a cell through a microscope or analyze its electrical or bio­
`chemical activity, we are, in essence, observing proteins. Proteins constitute
`most of a cell’s dry mass. They are not only the building blocks from which cells
`are built; they also execute nearly all cell functions. Thus, enzymes provide the
`intricate molecular surfaces in a cell that promote its many chemical reactions.
`Proteins embedded in the plasma membrane form channels and pumps that
`control the passage of small molecules into and out of the cell. Other proteins
`carry messages from one cell to another, or act as signal integrators that relay
`sets of signals inward from the plasma membrane to the cell nucleus. Yet others
`serve as tiny molecular machines with moving parts: kinesin, for example, pro­
`pels organelles through the cytoplasm; topoisomerase can untangle knotted
`DNA molecules. Other specialized proteins act as antibodies, toxins, hormones,
`antifreeze molecules, elastic fibers, ropes, or sources of luminescence. Before we
`can hope to understand how genes work, how muscles contract, how nerves
`conduct electricity, how embryos develop, or how our bodies function, we must
`attain a deep understanding of proteins.
`
`THE SHAPE AND STRUCTURE OF PROTEINS
`From a chemical point of view, proteins are by far the most structurally complex
`and functionally sophisticated molecules known. This is perhaps not surprising,
`once one realizes that the structure and chemistry of each protein has been
`developed and fine-tuned over billions of years of evolutionary history. We start
`this chapter by considering how the location of each amino acid in the long
`string of amino acids that forms a protein determines its three-dimensional
`shape. We will then use this understanding of protein structure at the atomic
`level to describe how the precise shape of each protein molecule determines its
`function in a cell.
`
`The Shape of a Protein Is Specified by Its Amino Acid Sequence
`Recall from Chapter 2 that there are 20 types of amino acids in proteins, each
`with different chemical properties. A protein molecule is made from a long
`chain of these amino acids, each linked to its neighbor through a covalent pep­
`tide bond (Figure 3-1). Proteins are therefore also known as polypeptides. Each
`type of protein has a unique sequence of amino acids, exactly the same from one
`molecule to the next. Many thousands of different proteins are known, each with
`its own particular amino acid sequence.
`
`129
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 4 of 31 PageID #:
`9428
`
`Figure 3-1 A peptide bond. This
`covalent bond forms when the carbon
`atom from the carboxyl group of one
`amino acid shares electrons with the
`nitrogen atom (blue) from the amino
`group of a second amino acid. As
`indicated, a molecule of water is lost in
`this condensation reaction.
`
`PEPTIDE BOND
`FORMATION WITH
`REMOVAL OF WATER
`
`water
`
`peptide bond in glycylalanine
`
`The repeating sequence of atoms along the core of the polypeptide chain is
`referred to as the polypeptide backbone. Attached to this repetitive chain are
`those portions of the amino acids that are not involved in making a peptide
`bond and which give each amino acid its unique properties: the 20 different
`amino acid side chains (Figure 3-2). Some of these side chains are nonpolar and
`hydrophobic (“water-fearing”), others are negatively or positively charged, some
`are reactive, and so on. Their atomic structures are presented in Panel 3-1, and
`a brief list with abbreviations is provided in Figure 3-3.
`As discussed in Chapter 2, atoms behave almost as if they were hard spheres
`with a definite radius (their van derWaals radius). The requirement that no two
`atoms overlap limits greatly the possible bond angles in a polypeptide chain
`(Figure 3-4). This constraint and other steric interactions severely restrict the
`variety of three-dimensional arrangements of atoms (or conformations) that are
`possible. Nevertheless, a long flexible chain, such as a protein, can still fold in an
`enormous number of ways.
`The folding of a protein chain is, however, further constrained by many dif­
`ferent sets of weak noncovalent bonds that form between one part of the chain
`and another. These involve atoms in the polypeptide backbone, as well as atoms
`in the amino acid side chains. The weak bonds are of three types: hydrogen
`bonds, ionic bonds, and van der Waals attractions, as explained in Chapter 2 (see
`p. 57). Individual noncovalent bonds are 30-300 times weaker than the typical
`covalent bonds that create biological molecules. But many weak bonds can act
`in parallel to hold two regions of a polypeptide chain tightly together. The sta­
`bility of each folded shape is therefore determined by the combined strength of
`large numbers of such noncovalent bonds (Figure 3-5).
`A fourth weak force also has a central role in determining the shape of a pro­
`tein. As described in Chapter 2, hydrophobic molecules, including the nonpolar
`side chains of particular amino acids, tend to be forced together in an aqueous
`environment in order to minimize their disruptive effect on the hydrogen-bond­
`ed network of water molecules (see p. 58 and Panel 2-2, pp. 112-113). Therefore,
`an important factor governing the folding of any protein is the distribution of its
`polar and nonpolar amino acids. The nonpolar (hydrophobic) side chains in a
`protein—belonging to such amino acids as phenylalanine, leucine, valine, and
`tryptophan—tend to cluster in the interior of the molecule (just as hydrophobic
`oil droplets coalesce in water to form one large droplet). This enables them to
`
`130 Chapter 3 : PROTEINS
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 5 of 31 PageID #:
`9429
`
`©
`o o
`\ /c
`I
`H CH,
`
`O©
`
`+
`
`/
`
`leucine (Leu)
`
`H H o
`©I I ✓
`H—N—C—C
`
`O©
`
`H CH,
`
`CH
`/ \
`
`CH,
`
`H,C
`
`+
`
`©
`H CH2 o'
`I
`I
`/
`H-=N —C —C
`©|
`|
`%
`H H
`
`O
`
`tyrosine (Tyr)
`
`methionine (Met)
`
`O
`H H
`©1 I A
`H—N—C—C
`\ ©
`o
`
`CH,
`
`IC
`
`H,
`
`h3
`
`ISIc
`
`H
`
`carboxyl terminus
`or C-terminus
`
`c
`
`©
`O
`/
`\
`0
`
`j—c
`H
`
`' peptide bond
`
`Figure 3-2 The
`structural components
`of a protein. A protein
`consists of a polypeptide
`backbone with attached
`side chains. Each type of
`protein differs in its
`sequence and number of
`amino acids; therefore, it is
`the sequence of the
`chemically different side
`chains that makes each
`protein distinct.The two
`ends of a polypeptide chain
`are chemically different; the
`end carrying the free
`amino group (NH3+, also
`written NH2) is the amino
`terminus, or N-terminus,
`and that carrying the free
`carboxyl group (COO-,
`also written COOH) is the
`carboxyl terminus or
`C-terminus.The amino acid
`sequence of a protein is
`always presented in the
`N-to-C direction, reading
`from left to right.
`
`polypeptide backbone
`
`O©
`
`OH
`
`' side chains
`
`CH,
`
`\
`
`H
`
`O
`H
`H H
`ffil
`II
`1 I II
`H —N —C —C- ■N—C
`c
`C-r-N—C
`1
`1
`II
`H
`H H O
`
`- peptide -
`bonds
`
`(ih2
`
`CH
`
`H,C
`
`CH,
`
`polypeptide backbone
`
`(:h2
`CH2
`
`ISIC
`
`H3
`
`ammo terminus
`or N-terminus
`
`SCHEMATIC
`
`SEQUENCE
`
`Met
`
`--- Asp
`
`-----
`
`Leu
`
`Tyr
`
`AMINO ACID
`Aspartic acid
`Asp
`Glutamic acid Glu
`Arg
`Arginine
`Lys
`Lysine
`Histidine
`His
`Asparagine
`Asn
`Glutamine
`Gin
`Ser
`Serine
`Thr
`Threonine
`Tyr
`Tyrosine
`
`D
`E
`R
`K
`H
`N
`Q
`S
`T
`Y
`
`SIDE CHAIN
`negative
`negative
`positive
`positive
`positive
`uncharged polar
`uncharged polar
`uncharged polar
`uncharged polar
`uncharged polar
`
`SIDE CHAIN
`AMINO ACID
`nonpolar
`A
`Alanine
`Ala
`nonpolar
`G
`Gly
`Glycine
`nonpolar
`V
`Valine
`Val
`nonpolar
`L
`Leu
`Leucine
`nonpolar
`1
`Isoleucine
`lie
`nonpolar
`P
`Pro
`Proline
`nonpolar
`F
`Phenylalanine Phe
`Methionine
`Met M nonpolar
`Trp W nonpolar
`Tryptophan
`Cys
`C
`nonpolar
`Cysteine
`
`POLAR AMINO ACIDS
`
`NONPOLAR AMINO ACIDS
`
`Figure 3-3 The 20 amino acids found in proteins. Both three-letter and one-letter abbreviations are listed. As shown,
`there are equal numbers of polar and nonpolar side chains. For their atomic structures, see Panel 3-1 (pp. 132-133).
`
`THE SHAPE AND STRUCTURE OF PROTEINS
`
`31
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 6 of 31 PageID #:
`9430
`PANEL 3-1 The 20 Amino Acids Found in Proteins
`
`THE AMINO ACID
`The general formula of an amino acid is
`- a-carbon atom
`
`amino
`group
`
`■ I l | r rri^i, carboxyl
`H2N — c— cooh group
`
`-side-chain group
`
`OPTICAL ISOMERS The a-carbon atom is asymmetric, which
`allows for two mirror image (or stereo-)
`isomers, l and d.
`
`R is commonly one of 20 different side chains.
`At pH 7 both the amino and carboxyl groups
`are ionized.
`
`H
`© I 0
`H,N—c—COO
`
`,
`
`, ___ ,
`
`J
`
`Proteins consist exclusively of L-amino acids.
`
`histidine
`(His, or H)
`
`H O
`I
`II
`— N—C—C —
`| |
`H CH,
`I
`
`CH
`HN
`/ HC = NH+
`/ \
`These nitrogens have a
`relatively weak affinity for an
`H+ and are only partly positive
`at neutral pH.
`
`BASIC SIDE CHAINS
`lysine
`(Lys, or K)
`
`arginine
`(Arg, or R)
`
`H O
`I
`II
`— N—C—C —
`I
`I
`H CH,
`
`IC
`
`H,
`j -
`CH,
`I ‘
`NH
`I
`C
`/ \
`+H,N
`NH,
`
`I-
`
`H O
`I II
`— N—C—C
`I
`I
`I I
`H CH,
`I '
`CH,
`I
`CH,
`I '
`CH,
`I +
`NH,
`
`This group is
`very basic
`because its
`positive charge
`is stabilized by \
`resonance.
`
`IR
`
`V
`
`FAMILIES OF
`AMINO ACIDS
`
`The common amino acids
`are grouped according to
`whether their side chains
`are
`
`acidic
`basic
`uncharged polar
`nonpolar
`
`These 20 amino acids
`are given both three-letter
`and one-letter abbreviations.
`
`Thus: alanine = Ala = A
`
`Peptide bond: The four atoms in each gray box form a rigid
`planar unit. There is no rotation around the C-N bond.
`
`R
`
`IH
`
`H o
`II
`I
`N--c--c--N--c
`I
`I
`
`H
`
`IR
`
`h2o
`j
`-------A----- -
`
`SH
`
`H
`
`H
`
`\
`/
`
`PEPTIDE BONDS
`Amino acids are commonly joined together by an amide linkage,
`called a peptide bond.
`
`H
`
`H
`
`\
`/
`
`H
`I
`N--c--c
`I
`R
`
`✓
`\
`
`o
`
`OH
`
`+
`
`H
`
`H
`
`\
`/
`
`O
`R
`✓
`N--C- C
`\
`I
`H
`
`OH
`
`Proteins are long polymers
`of amino acids linked by
`peptide bonds, and they
`are always written with the
`N-terminus toward the left.
`The sequence of this tripeptide
`is histidine-cysteine-valine.
`
`amino- or
`N-terminus
`
`O
`H3N —C-----C — N
`
`+
`
`H
`
`CH,
`/C\
`HN CH
`
`HC = NH+
`
`132
`
`carboxyl- or
`C-terminus
`
`These two single bonds allow rotation, so that long chains
`amino acids are very flexible.
`
`of
`
`

`

`\
`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 7 of 31 PageID #:
`9431
`
`ACIDIC SIDE CHAINS
`
`NONPOLAR SIDE CHAINS
`
`valine
`(Val, or V)
`
`H O
`I II
`— N—C—C —
`I I
`H CH/ \
`CH, CH,
`
`isoleucine
`(lie, or I)
`
`H O
`I II
`— N—C—C —
`I I
`H CH
`CH, XCHj
`
`CH,
`
`phenylalanine
`(Phe, or F)
`
`tryptophan
`(Trp, or W)
`
`H O
`
`—N—C—C —
`I I
`H CH,
`
`cysteine
`(Cys, or C)
`
`H O
`I II
`-N —C—C —
`I I
`H CH,
`I “
`SH
`
`alanine
`(Ala, or A)
`
`H O
`I II
`— N—C—C —
`I I
`H CH,
`
`leucine
`(Leu, or L)
`
`H O
`—N —C—C —
`I I
`H CH,
`I ‘
`CH/ \
`CH, CH,
`
`proline
`(Pro, or P)
`
`H O
`—N—C—C —
`/
`CH,
`(actually an CH,
`imino acid)
`
`methionine
`(Met, or M)
`
`H O
`I II
`— N—C—C —
`I I
`H CH,
`
`IC
`
`H,
`I ‘
`S— CH,
`
`glycine
`(Gly, or G)
`
`H O
`I II
`-N —C—C —
`I I
`H H
`
`Disulfide bonds can form between two cysteine side chains in proteins.
`
`----- CH,—S — S —CH,- -
`
`133
`
`glutamic acid
`(Glu, orE)
`
`H O
`I II
`— N —C—C —
`I I
`H CH,
`I '
`CH,
`
`IC
`
`s \
`O cr
`
`aspartic acid
`(Asp, or D)
`
`H O
`I II
`— N —C—C —
`I I
`H CH,
`CS \
`o cr
`
`UNCHARGED POLAR SIDE CHAINS
`
`asparagine
`(Asn, or N)
`
`glutamine
`(Gin, or Q)
`
`Although the amide N is not charged at
`neutral pH, it is polar.
`
`serine
`(Ser, or S)
`
`threonine
`(Thr, orT)
`
`tyrosine
`(Tyr, orY)
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 8 of 31 PageID #:
`9432
`
`peptide bonds
`
`0 +180°
`phi
`Figure 3-4 Steric limitations on the bond angles in a pol/peptide chain. (A) Each amino acid contributes three bonds
`(red) to the backbone of the chain.The peptide bond is planar (gray shading) and does not permit rotation. By contrast, rotation
`can occur about the Ca-C bond, whose angle of rotation is called psi (\|/), and about the N-Ca bond, whose angle of rotation is
`called phi (<j)). By convention, an R group is often used to denote an amino acid side chain (green circles). (B) The conformation of
`the main-chain atoms in a protein is determined by one pair of (j) and \|/ angles for each amino acid; because of steric collisions
`between atoms within each amino acid, most pairs of <f> and \|/ angles do not occur. In this so-called Ramachandran plot, each dot
`represents an observed pair of angles in a protein. (B, from J. Richardson, Adv. Prot. Chem. 34:174-175, 1981. ©Academic Press.)
`
`avoid contact with the water that surrounds them inside a cell. In contrast,
`polar side chains—such as those belonging to arginine, glutamine, and histi­
`dine—tend to arrange themselves near the outside of the molecule, where they
`can form hydrogen bonds with water and with other polar molecules (Figure
`3-6). When polar amino acids are buried within the protein, they are usually
`hydrogen-bonded to other polar amino acids or to the polypeptide backbone
`(Figure 3-7).
`
`Proteins Fold into a Conformation of Lowest Energy
`As a result of all of these interactions, each type of protein has a particular three-
`dimensional structure, which is determined by the order of the amino acids in
`its chain. The final folded structure, or conformation, adopted by any polypep­
`tide chain is generally the one in which the free energy is minimized. Protein
`folding has been studied in a test tube by using highly purified proteins. A pro­
`tein can be unfolded, or denatured, by treatment with certain solvents, which
`disrupt the noncovalent interactions holding the folded chain together. This
`treatment converts the protein into a flexible polypeptide chain that has lost its
`
`Figure 3-5 Three types of noncovalent
`bonds that help proteins fold. Although
`a single one of these bonds is quite weak,
`many of them often form together to
`create a strong bonding arrangement, as in
`the example shown. As in the previous
`figure, R is used as a general designation for
`an amino acid side chain.
`
`134 Chapter 3 : PROTEINS
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 9 of 31 PageID #:
`9433
`
`polar
`side chains
`
`nonpolar
`side chains
`
`Figure 3-6 How a protein folds into a
`compact conformation. The polar
`amino acid side chains tend to gather on
`the outside of the protein, where they can
`interact with water; the nonpolar amino
`acid side chains are buried on the inside
`to form a tightly packed hydrophobic core
`of atoms that are hidden from water. In
`this schematic drawing, the protein
`contains only about 30 amino acids.
`
`core region
`contains
`nonpolar
`side chains
`
`on the outside
`of the molecule
`can form hydrogen
`bonds to water
`
`unfolded polypeptide
`folded conformation in aqueous environment
`natural shape. When the denaturing solvent is removed, the protein often
`refolds spontaneously, or renatures, into its original conformation (Figure 3-8),
`indicating that all the information needed for specifying the three-dimensional
`shape of a protein is contained in its amino acid sequence.
`Each protein normally folds up into a single stable conformation. However,
`the conformation often changes slightly when the protein interacts with other
`molecules in the cell. This change in shape is often crucial to the function of the
`protein, as we see later.
`Although a protein chain can fold into its correct conformation without out­
`side help, protein folding in a living cell is often assisted by special proteins
`called molecular chaperones. These proteins bind to partly folded polypeptide
`chains and help them progress along the most energetically favorable folding
`pathway. Chaperones are vital in the crowded conditions of the cytoplasm, since
`they prevent the temporarily exposed hydrophobic regions in newly synthesized
`protein chains from associating with each other to form protein aggregates (see
`p. 357). However, the final three-dimensional shape of the protein is still speci­
`fied by its amino acid sequence: chaperones simply make the folding process
`more reliable.
`Proteins come in a wide variety of shapes, and they are generally between 50
`and 2000 amino acids long. Large proteins generally consist of several distinct
`protein domains—structural units that fold more or less independently of each
`other, as we discuss below. The detailed structure of any protein is complicated;
`for simplicity a protein’s structure can be depicted in several different ways, each
`emphasizing different features of the protein.
`
`Figure 3-7 Hydrogen bonds in a
`protein molecule. Large numbers of
`hydrogen bonds form between adjacent
`regions of the folded polypeptide chain
`and help stabilize its three-dimensional
`shape. The protein depicted is a portion of
`the enzyme lysozyme, and the hydrogen
`bonds between the three possible pairs of
`partners have been differently colored, as
`indicated. (After C.K. Matthews and
`K.E. van Holde, Biochemistry. Redwood
`City, CA: Benjamin/Cummings, 1996.)
`
`hydrogen bond between
`atoms of two peptide
`bonds
`
`hydrogen bond between
`atoms of a peptide
`bond and an amino
`acid side chain
`
`hydrogen bond between
`two amino acid side
`chains
`
`THE SHAPE AND STRUCTURE OF PROTEINS
`
`135
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 10 of 31 PageID #:
`9434
`Figure 3-8 The refolding of a
`(B)
`denatured protein. (A) This
`experiment demonstrates that the
`conformation of a protein is
`determined solely by its amino acid
`sequence. (B)The structure of urea.
`Urea is very soluble in water and
`unfolds proteins at high
`concentrations, where there is about
`one urea molecule for every six water
`molecules.
`
`OI
`
`Ic
`
`/ \
`h2n nh2
`
`(A)
`
`EXPOSE TO A HIGH
`CONCENTRATION
`OF UREA
`-----------►
`
`purified protein
`isolated from
`cells
`
`denatured
`protein
`
`original conformation
`of protein re-forms
`
`Panel 3-2 (pp. 138-139) presents four different depictions of a protein
`domain called SH2, which has important functions in eucaryotic cells. Con­
`structed from a string of 100 amino acids, the structure is displayed as (A) a
`polypeptide backbone model, (B) a ribbon model, (C) a wire model that includes
`the amino acid side chains, and (D) a space-filling model. Each of the three
`horizontal rows shows the protein in a different orientation, and the image is
`colored in a way that allows the polypeptide chain to be followed from its N-
`terminus (purple) to its C-terminus (red).
`Panel 3-2 shows that a protein’s conformation is amazingly complex, even
`for a structure as small as the SH2 domain. But the description of protein struc­
`tures can be simplified by the recognition that they are built up from several
`common structural motifs, as we discuss next.
`
`The a Helix and the (3 Sheet Are Common Folding Patterns
`When the three-dimensional structures of many different protein molecules are
`compared, it becomes clear that, although the overall conformation of each pro­
`tein is unique, two regular folding patterns are often found in parts of them.
`Both patterns were discovered about 50 years ago from studies of hair and silk.
`The first folding pattern to be discovered, called the a helix, was found in the
`protein a-keratin, which is abundant in skin and its derivatives—such as hair,
`nails, and horns. Within a year of the discovery of the a helix, a second folded
`structure, called a P sheet, was found in the protein fibroin, the major con­
`stituent of silk. These two patterns are particularly common because they result
`from hydrogen-bonding between the N-H and C=0 groups in the polypeptide
`backbone, without involving the side chains of the amino acids. Thus, they can
`be formed by many different amino acid sequences. In each case, the protein
`chain adopts a regular, repeating conformation. These two conformations, as
`well as the abbreviations that are used to denote them in ribbon models of pro­
`teins, are shown in Figure 3-9.
`The core of many proteins contains extensive regions of p sheet. As shown in
`Figure 3-10, these p sheets can form either from neighboring polypeptide chains
`that run in the same orientation (parallel chains) or from a polypeptide chain
`that folds back and forth upon itself, with each section of the chain running in
`the direction opposite to that of its immediate neighbors (antiparallel chains).
`Both types of P sheet produce a very rigid structure, held together by hydrogen
`bonds that connect the peptide bonds in neighboring chains (see Figure 3-9D).
`An a helix is generated when a single polypeptide chain twists around on
`itself to form a rigid cylinder. A hydrogen bond is made between every fourth
`peptide bond, linking the C=0 of one peptide bond to the N-H of another (see
`Figure 3-9A). This gives rise to a regular helix with a complete turn every
`3.6 amino acids. Note that the protein domain illustrated in Panel 3-2 contains
`two a helices, as well as P sheet structures.
`Short regions of a helix are especially abundant in proteins located in cell
`membranes, such as transport proteins and receptors. As we discuss in Chapter
`10, those portions of a transmembrane protein that cross the lipid bilayer usually
`cross as an a helix composed largely of amino acids with nonpolar side chains.
`The polypeptide backbone, which is hydrophilic, is hydrogen-bonded to itself in
`the a helix and shielded from the hydrophobic lipid environment of the mem­
`brane by its protruding nonpolar side chains (see also Figure 3-77).
`
`136 Chapter 3 : PROTEINS
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 11 of 31 PageID #:
`9435
`
`Figure 3-9 The regular conformation of the polypeptide backbone observed in the a helix and
`the p sheet. (A, B, and C) The a helix.The N-H of every peptide bond is hydrogen-bonded to the C=0 of
`a neighboring peptide bond located four peptide bonds away in the same chain. (D, E, and F) The P sheet, in
`this example, adjacent peptide chains run in opposite (antiparallel) directions.The individual polypeptide
`chains (strands) in a P sheet are held together by hydrogen-bonding between peptide bonds in different
`strands, and the amino acid side chains in each strand alternately project above and below the plane of the
`sheet. (A) and (D) show all the atoms in the polypeptide backbone, but the amino acid side chains are
`truncated and denoted by R. In contrast, (B) and (E) show the backbone atoms only, while (C) and (F) display
`the shorthand symbols that are used to represent the a helix and the P sheet in ribbon drawings of proteins
`(see Panel 3-2B).
`
`THE SHAPE AND STRUCTURE OF PROTEINS
`
`137
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 12 of 31 PageID #:
`9436
`PANEL 3-2 Four Different Ways of Depicting a Small Protein Domain: the SH2 Domain.
`(Courtesy of David Lawson.)
`
`(A) Backbone
`
`138
`
`(B) Ribbon
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 13 of 31 PageID #:
`9437
`
`139
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 14 of 31 PageID #:
`9438
`In other proteins, a helices wrap around each other to form a particularly
`stable structure, known as a coiled-coil. This structure can form when the two
`(or in some cases three) a helices have most of their nonpolar (hydrophobic)
`side chains on one side, so that they can twist around each other with these side
`chains facing inward (Figure 3-11). Long rodlike coiled-coils provide the struc­
`tural framework for many elongated proteins. Examples are a-keratin, which
`forms the intracellular fibers that reinforce the outer layer of the skin and its
`appendages, and the myosin molecules responsible for muscle contraction.
`
`The Protein Domain Is a Fundamental Unit of Organization
`Even a small protein molecule is built from thousands of atoms linked together
`by precisely oriented covalent and noncovalent bonds, and it is extremely diffi­
`cult to visualize such a complicated structure without a three-dimensional dis­
`play. For this reason, various graphic and computer-based aids are used. A CD-
`ROM produced to accompany this book contains computer-generated images
`of selected proteins, designed to be displayed and rotated on the screen in a
`variety of formats.
`Biologists distinguish four levels of organization in the structure of a protein.
`The amino acid sequence is known as the primary structure of the protein.
`Stretches of polypeptide chain that form a helices and p sheets constitute the
`protein’s secondary structure. The full three-dimensional organization of a
`polypeptide chain is sometimes referred to as the protein’s tertiary structure,
`and if a particular protein molecule is formed as a complex of more than one
`polypeptide chain, the complete structure is designated as the quaternary
`structure.
`Studies of the conformation, function, and evolution of proteins have also
`revealed the central importance of a unit of organization distinct from the four
`just described. This is the protein domain, a substructure produced by any part
`of a polypeptide chain that can fold independently into a compact, stable struc­
`ture. A domain usually contains between 40 and 350 amino acids, and it is the
`
`140
`
`Chapter 3 : PROTEINS
`
`Figure 3-10 Two types of P sheet
`structures. (A) An antiparallel P sheet
`(see Figure 3-9D). (B) A parallel P sheet.
`Both of these structures are common in
`proteins.
`
`Figure 3-1 I The structure of a
`coiled-coil. (A) A single a helix, with
`successive amino acid side chains labeled
`in a sevenfold sequence, “abcdefg” (from
`bottom to top). Amino acids “a” and “d” in
`such a sequence lie close together on the
`cylinder surface, forming a “stripe” (red)
`that winds slowly around the a helix.
`Proteins that form coiled-coils typically
`have nonpolar amino acids at positions “a”
`and “d.” Consequently, as shown in (B), the
`two a helices can wrap around each other
`with the nonpolar side chains of one a
`helix interacting with the nonpolar side
`chains of the other, while the more
`hydrophilic amino acid side chains are left
`exposed to the aqueous environment.
`(C) The atomic structure of a coiled-coil
`determined by x-ray crystallography.The
`red side chains are nonpolar.
`
`

`

`Case 1:18-cv-01363-CFC Document 79-2 Filed 03/22/19 Page 15 of 31 PageID #:
`9439
`
`Figure 3-12 A protein formed from
`four domains. In the Src protein shown,
`two of the domains form a protein kinase
`enzyme, while the SH2 and SH3 domains
`perform regulatory functions. (A) A ribbon
`model, with ATP substrate in red. (B) A
`spacing-filling model, with ATP substrate in
`red. Note that the site that binds ATP is
`positioned at the interface of the two
`domains that form the kinase.The detailed
`structure of the SH2 domain is illustrated
`in Panel 3-2 (pp. 138-139).
`
`modular unit from which many larger proteins are constructed. The different
`domains of a protein are often associated with different functions. Figure 3-12
`shows an example—the Src protein kinase, which functions in signaling path­
`ways inside vertebrate cells (Src is pronounced “sarc”). This protein has four
`domains: the SH2 and SH3 domains have regulatory roles, while the two
`remaining domains are responsible for the kinase catalytic activity. Later in the
`chapter, we shall return to this protein, in order to explain how proteins can
`form molecular switches that transmit information throughout cells.
`The smallest protein molecules contain only a single domain, whereas larger
`proteins can contain as many as several dozen domains, usually connected to
`each other by short, relatively unstructured lengths of polypeptide chain. Figure
`3-13 presents ribbon models of three differently organized protein domains. As
`these examples illus