THE IMMUNE SYSTEM IN HEALTH AND DISEASE
`
`CHAHLIB A JANEWAY PAUL TRAVIRB
`
`I N I
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`la
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`ll
`
`I.
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`
`ME?“it?
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`E g
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`. 9 I
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`Lassen - Exhibit 1038, p. 1
`
`

`

`
`
`immuno
`iologye
`
`THE IMMUNE SYSTEM IN HEALTH AND DIEEABE
`
`Charles A. Janaway, Jr.
`
`Yale University School of Medicine
`
`Paul Travers
`
`Anthony Nolan Research Institute. London
`
`I
`
`Mark Walpart
`
`Imperial College School of Medicine. London
`
`I
`
`Mark J. Shlomehik
`
`Yale University School of Medioine
`
`
`
`Lassen - Exhibit 1038, p. 2
`
`Lassen - Exhibit 1038, p. 2
`
`

`

`Vice President:
`Text Elmore:
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`
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`
`Q 2001 by Garland Publishing.
`All rights reserved. No part of this publication may be reproduced. stored In a retrieval
`system or transmitted in any form or by any means—electronic. mechanical. photocopying.
`recording. or otherwise—Mlhout the prior written permission oi the copyright holder.
`
`Distributors:
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`
`ISBN 0 8153 3642 X (paperback) Garland
`tSBN o 4430 11393 9 (paperback) Churchill Livingstone
`ISBN 0 4430 7099 7 {paperback} International Student Edition
`
`Library of Congress Cataloging-in—Publiootion Date
`Immunobiology : the immune system in health and disease 1" Charles A. Jar-sway. Jr.
`[at al.].-- 5th ed.
`p. cm.
`Includes blbllographicei references and index.
`ISBN 0-3153-3642-X (plain)
`1. immunology. 2. Immunity. i. Janeway. Chariea it. Title.
`
`QFIIB1 .l454 2001
`613.0?94021
`
`2001016039
`
`This book was produced using Quaanpreea 4.1 t and Adobe Illustrator 9.0
`
`Published by Garland Publishing. a member of the Taylor 5. Francis Group.
`29 West 35m Street. New York. NY 10001-2299.
`
`Printed in the United States of Antenna.
`15141312111098765432
`
`Lassen - Exhibit 1038, p. 3
`
`Lassen - Exhibit 1038, p. 3
`
`

`

`
`
`
`
`PART I
`
`AN INTRODUCTION TO IMMUNOBIOLOGY AND INNATE IMMUNITY
`
`Chapter 1
`
`Basic Concepts in Immunology
`
`Chapter 2
`
`Innate Immunity
`
`PART II
`
`THE RECOGNITION OF ANTIGEN
`
`Chapter 3
`
`Antigen Recognition by B-ceII and T-cell Receptors
`
`Chapter 4
`
`The Generation of Lymphocyte Antigen Receptors
`
`Chapter 5
`
`Antigen Presentation to T Lymphocytes
`
`PART III
`
`THE DEVELOPMENT OF MATURE LYMPHOCYTE RECEPTOR
`REPERTOIRES
`
`Index
`
`Chapter 6
`
`Signaling Through Immune System Receptors
`
`Chapter 7
`
`The Development and Survival of Lymphocytes
`
`PART IV
`
`THE ADAPTIVE IMMUNE RESPONSE
`
`Chapter 8
`
`T Cell-Mediated Immunity
`
`Chapter 9
`
`The Humoral Immune Response
`
`Chapter 10 Adaptive Immunity to Infection
`
`PART V
`
`THE IMMUNE SYSTEM IN HEALTH AND DISEASE
`
`Chapter 11
`
`Failures of Host Defense Mechanisms
`
`Chapter 12 Allergy and Hypersensitivity
`
`Chapter 13 Autoimmunity and Transplantation
`
`Chapter 14 Manipulation of the Immune Response
`
`Afterward Evolution of the Immune System: Past, Present, and Future,
`by Charles A. Janeway, Jr.
`
`Appendix I
`
`Immunologists‘ Toolbox
`
`Appendixll CD Antigens
`
`Appendix III Cytokines and their Receptors
`
`Appendix IV Chemokines and their Receptors
`
`Appendix V
`
`Immunological Constants
`
`Biographies
`
`Glossary
`
`Lassen - Exhibit 1038, p. 4
`
`Lassen - Exhibit 1038, p. 4
`
`

`

`
`II
`
`THE RECOGNITION
`
`OF ANTIGEN
`
`Lassen - Exhibit 1038, p. 5
`
`Lassen - Exhibit 1038, p. 5
`
`

`

`“I
`
`Antigen Recognition by B-cell
`and T-cell Receptors
`
`
`
`
`
`We have learned in Chapter 2 that the body is defended by innate immune
`responses. but these will only work to control pathogens that have certain
`molecular patterns or that induce interferons and other secreted yet non-
`specific defenses. Most crucially. they do not allow memory to form as they
`operate by receptors that are coded in the genome. 'l'hus. innate immunity is
`good for preventing pathogens from growing freely in the body. but it does
`not lead to the most important feature of adaptive immunity. which is long-
`lasting memory of specific pathogen.
`
`the wide range of pathogens an individual will
`To recognize and tight
`encounter, the lymphocytes of the adaptive Immune system have evolved to
`recognize a great variety of different antigens from bacteria. viruses. and
`other disease-causing organisms. The antigen-recognition molecules of B
`cells are the immunoglobulins, or lg. These proteins are produced by B cells
`in a vast range of antigen specificities. each B cell producing immunogiobulin
`of a single specificity [see Sections 1-8 to 140]. Membrane-bound
`immunoglobulin on the B-ceil surface serves as the cell’s receptor for and
`gen. and is known as the B-oeil receptor (BCR). immunogiobulin of the same
`antigen specificity is secreted as antibody by terminally differentiated B
`cells—the plasma cells. The secretion of antibodies. which bind pathogens or
`their toxic products in the extracellular spaces of the body, is the main effector
`function of B cells in adaptive immunity.
`
`Antibodies were the first molecules involved in specific immune recognition to
`be characterized and are still the best understood. The antibody molecule has
`two separate functions: one is to bind specifically to molecules from the
`pathogen that elicited the immune response; the other is to recruit other cells
`and molecules to destroy the pathogen once the antibody is bound to it. For
`example. binding by antibody neutralizes viruses and marks pathogens for
`destruction by phagocytes and Complement. as described in Section 1-14.
`These functions are structurally separated in the antibody molecule. one part
`of which specifically recognizes and binds to the pathogen or antigen whereas
`the other engages different effector mechanisms. The antigen-binding region
`varies extensively between antibody molecules and is thus known as the
`variable region or V region. The variability of antibody molecules allows each
`antibody to bind a different specific antigen. and the total repertoire of anti»
`bodies made by a single individual is large enough to ensure that virtually any
`structure can be recognized. The region of the antibody molecule that engages
`the effector functions ofthe immune system does not vary in the same way and
`is thus known as the constant region or C region. It comes in five main forms.
`which are each specialized for activating different effector mechanisms. The
`membrane-bound B-cell receptor does not have these effector functions. as
`the C region remains inserted in the membrane of the B cell. Its function is as
`a receptor that recognizes and binds antigen by the V regions exposod on
`the surface of the cell. thus transmitting a signal that causes B-cell activation
`leading to clonal expansion and specific antibody production.
`
`Lassen - Exhibit 1038, p. 6
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`Lassen - Exhibit 1038, p. 6
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`

`

`
`
`04
`
`Chapter 3: Antigen Recognition by Scott and T-cell Receptors
`
`
`
`
`
`N terminus
`
`bonds Constant
`
`deullide
`
`region
`
`0 Iennirrus
`
`
`Fig. 3.1 Structure 01 an antibody
`molecule. Panel a illustrates a
`ribbon diagram based on the X-ray
`crystallographic structure of an IgG
`antibody. showing the course of the
`backbones ol the polypeptide chains.
`Three globular regions form a Y. The
`two antigsnbindlng sites are at the tips
`of the arms. which are tethered to the
`trunk of the Y by a flexible hinge region.
`A schematic representation of the
`structure in a is given in panel b.
`illustrating the tour-chain composition
`and the separate domains comprising
`each chain. Panel c shows a simplified
`schematic representation oi an antibody
`molecule that will be used throughout
`this book. Photograph courtesy of
`A. McPherson and L. Harris.
`
`r_
`
`The antigen~recognition molecules of T cells are made solely as membrane“
`bound proteins and only function to signal '1‘ cells for activation. These
`T-cell receptors (TCRs) are related to immunoglobulins both in their protein
`stntcture—having both V and C regions—and in the genetic mechanism that
`produces their great variability (see Section 1-10 and Chapter 4]. However.
`the T-cell receptor diliers from the B-cell receptor in an important way:
`it does not recognize and bind antigen directly. but instead recognizes short
`peptide fragments of pathogen protein antigens. which are bound to MHC
`molecules on the surfaces of other cells.
`
`The MHC molecules are glycoproteins encoded in the large cluster of genes
`known as the major histocompatibility complex (MHC) (see Sections 1~16
`and l-l'r‘]. Their most striking structural feature is a cleft running across
`their outermost surface. in which a variety of peptides can be bound. As We
`shall discuss further in Chapter 5. MHC molecules show great genetic varia—
`tion in the population. and each individual carries up to 12 of the possible
`variants. which increases the range of pathogen-derived peptides that can
`be bound. T-cell receptors recognize features both of the peptide antigen
`and of the MHC molecule to which it is bound. This introduces an extra
`
`dimension to antigen recognition by T cells. known as MHC restriction.
`because any given Tvcell receptor is specific not simply for a foreign peptide
`antigen. but for a unique combination of a peptide and a particular MHC
`molecule. The ability of T—cell receptors to recognize MHC molecules. and
`their selection during T-cell development for the ability to recognize the
`particular MHC molecules expressed by an individual. are topics we shall
`return to in Chapters 5 and 7.
`
`In this chapter we focus on the structure and antigen-binding pr0perties of
`immunoglobulins and T~cell receptors. Although B cells andT cells recognize
`foreign molecules in two distinct fashions. the receptor molecules they use
`for this task are very similar in structure. We will see how this basic structure
`can accommodate great variability in antigen specificity. and how it enables
`immunoglobulins and T-cell receptors to carry out their functions as the
`antigen-recognition moleCules of the adaptive immune response.
`
`Theeshucture ot a "typical,.an't'_l'b'_otly-=molecul_e._
`
`Antibodies are the secreted form of the B-cell receptor. An antibody is identical
`to the B-cell receptor of the cell that secretes it except for a small portion of
`the C-terminus of the heavy-chain constant region. In the case of the B-cell
`receptor the C-terminus is a hydrophobic membrane—anchoring sequence.
`and in the case of antibody it is a hydrophilic sequence that allows secretion.
`Since they are soluble, and secreted in large quantities. antibodies are easily
`obtainable and easily studied. For this reason. most of what we know about
`the B—cell recaptor comes from the study of antibodies.
`
`Antibody molecules are roughly Y-shaped molecules consisting of three
`equal-sized portions. loosely connected by a flexible tether. Three schematic
`representations of antibody structure, which has been determined by X-ray
`crystallography. are shown in Fig. 3.1. The aim of this part ofthe chapter is to
`explain how this structure is formed and how it allows antibody molecules to
`carry out their dual tasks—binding on the one hand to a wide variety of anti—
`gens. and on the other hand to a limited number of effector molecules and
`cells. As we will see. each of these tasks is carried out by separable parts of the
`molecule. The two arms of the Y end in regions that vary between different
`
`Lassen - Exhibit 1038, p. 7
`
`Lassen - Exhibit 1038, p. 7
`
`

`

`The structure oi atypical aiiflbody molecule
`
`
`
`
`antibody molecules, the V regions. These are involved in antigen binding,
`whereas the stern of the Y. or the C region. is far less variable and is the part
`that interacts with effector cells and molecules.
`
`All antibodies are constructed in the same way from paired heavy and light
`polypeptide chains, and the generic term immunoglobulin is used for all such
`proteins. Within this general category, however, five different classes of
`immunoglobulins—IgM, IgD,
`lgG, IgA, and igE—can be distinguished by
`their C regions. which will be described more fully in Chapter 4. More sublle
`differences confined to the V region account for the specificity of antigen
`binding. We will use the IgG antibody molecule as an example to describe the
`general structural features of lmmunoglobulins.
`
`3.1
`
`lgG antibodies consist of tour polypeptide chains.
`
`lgG antibodies are large moleculu, having a molecular might of approximately
`150 kDa. composed of mo different kinds of polypeptide chain. One, of
`approximately 50 kDa, is termed the heavy or H chain, and the other, of 25
`kDa, is termed the light or L chain (Fig. 3.2). Each IgG molecule consists of
`two heavy chains and two light chains. The two heavy chains are linked to
`each other by disulfide bonds and each heavy chain is linked to a light chain
`by a disulfide bond. In any given immunoglobuiin molecule, the mo heavy
`chains and the two light chains are identical, giving an antibody molecule
`two identical antigen-binding sites (see Fig. 3.1), and thus the ability to bind
`simultaneously to two identical structures.
`
`Two types oflight chain, termed lambda [7L] and kappa [it], are found in anti-
`bodies. A given irn munoglobulin either has it chains or it chains, never one of
`each. No functional difference has been found between antibodies having it
`or K light chains, and either type of light chain may be found in antibodies of
`any of the five major classes. The ratio of the two types of light chain varies
`from species to species. In mice, the average it to 1 ratio is 20: 1. whereas in
`humans it
`is 2:1 and in cattle it is 1:20. The reason for this variation
`is unknown. Distortions of this ratio can sometimes be used to detect
`
`the abnormal proliferation of a clone of B cells. These would all express the
`identical light chain, and thus an excess 051 light chains in a person might
`indicate the presence of a B-cell tumor producing 7t chains.
`
`By contrast. the class, and thus the effector function. of an antibody. is defined
`by the structure of its heavy chain. There are five main heavy~chain classes or
`lsotypes, some of which have several subtypes. and these determine the func-
`tional activity of an antibody molecule. The five major classes oflmmunoglob—
`ulin are immtmoglobulln M (13M), immunoglobulin D (IgD), immunoglobulin
`G [IgGL immunoglobulin A (IgA), and immunoglobulin E [lgE}. Their heavy
`chains are denoted by the corresponding lower-case Greek letter to, 5, 7. 0t,
`and E. respectively] . lgG is by far the most abundant immunoglobulin and has
`several subclasses [IgGl, 2, 3, and 4 in humans). Their distinctive functional
`Properties are conferred by the carboxy— terminal part of the heavy chain,
`Where it is not associated with the light chain. We will describe the structure
`and hmctions of the different heavy-chain isotypes in Chapter 4. The general
`Snuctural features of all the isotypes are similar and we will consider IgG. the
`1Mist abundant isotype in plasma. as a typical antibody molecule.
`
`Fig. 3.2 Immumglobulin molecules
`Ire composed of two types of protein
`chain: heavy chains and light chains.
`Each ll‘l'Imunoglobulin molecule ls made
`“9 0! Mo heavy chains {green} and two
`
`light chains (yellow) joined by disuliida
`bonds so that each heavy chain is linked
`to a light chain and the two heavy chains
`are linked together.
`
`
`
`Lassen - Exhibit 1038, p. 8
`
`Lassen - Exhibit 1038, p. 8
`
`

`

`
`
`
`
`CW3: Antlgan Recognition by 3-09]! and T-cell Receptors
`
`3-2
`
`lmmunoglobuiin heavy and light chains are composed of constant
`and variable regions.
`
`The amino acid sequences of many immunoglobulin heavy and light chains
`have been determined and reveal two important features of antibody mole-
`cules. First. each chain consists of a series of similar. although not identical,
`sequences, each about 110 amino acids long. Each of these repeats corre-
`sponds to a discrete, compactly folded region of protein structure known as
`a protein domain. The light chain is made up of two such immunoglobulin
`domains. whereas the heavy chain of the IgG antibody contains four {see Fig
`3.1a]. This suggests that the immunoglobulin chains have evolved by repeated
`duplication of an ancestral gene corresponding to a single domain.
`
`The second important feature revealed by comparisons of amino acid
`sequences is that the amino-terminal sequences of both the heavy and light
`chains vary greatly between different antibodies. The variability in sequence
`is limited to approximately the first 110 amino acids. corresponding to the
`first domain. whereas the remaining domains are constant bemeen
`Immune-globulin chains of the same isotype. The amino-terminal variable or
`V domains of the heavy and light chains NH and V[_, respectively] together
`make up the V region of the antibody and confer on it the ability to bind
`specific antigen. while the constant domains (C domains) of the heavy and
`light chains {CH and CL. respectively) make up the C region (see Fig. 3.1b. c).
`The multiple heavy-chain C domains are numbered from the amino-terminal
`end to the carboxy terminus. for example CHI. C32. and so on.
`
`3-8
`
`The antibody molecule can readily be cleaved Into functionally
`distinct fragments.
`
`The protein domains described above associate to form larger globular
`domains. Thus. when fully folded and assembled. an antibody molecule
`comprises three equal-sized globular portions joined by a flexible stretch of
`polypeptide chain known as the hinge region (see Fig. 3.11:}. Each arm of this
`Y-shaped structure is formed by the association of a light chain with the
`amino-terminal half of a heavy chain. whereas the trunk of the Y is formed by
`the pairing of the carbon-terminal halves of the two heavy chains. The asso-
`ciation of the heavy and light chains is such that the V1.1 and VL domains are
`paired. as are the CH1 and CL domains. The CH3 domains pair with each other
`but the C32 domains do not interact; carbohydrate side chains attached to
`the C32 domains lie between the two heavy chains. The two antigembinding
`sites are formed by the paired VH and V1, domains at the ends of the two arms
`of the Y {see Fig. 3.11)).
`
`Proteolytic enzymes (proteases) that cleave polypeptide sequences have been
`used to dissect the structure of antibody molecules and to determine which
`parts of the molecule are responsible for its various functions. Limited digestion
`with the protease pepsin cleaves antibody molecules into three fragments
`(Fig. 3.3}. Two fragments are identical and contain the antigen-binding activity-
`These are termed the Fab fragments. for Fragment antigen binding. The Fab
`fragments correspond to the two identical arms of the antibody molecule,
`which contain the complete light chains paired with the V" and CHI domains
`of the heavy chains. The other fragment contains no antigen-binding activitl'r
`but was originally observed to crystallize readily. and for this reason was
`named the Fc fragment. for Fragment crystallizabie. This fragment corre-
`sponds to the paired (1.42 and CHS domains and is the part of the antibody
`molecule that interacts with effector molecules and cells. The functional
`differences between heavy-chain isotypes lie mainly in the Fc fragment.
`
`
`
`Lassen - Exhibit 1038, p. 9
`
`Lassen - Exhibit 1038, p. 9
`
`

`

`
`
`
`The structure at a typical antibody mime
`
`
`Flg. 3.3 The Y-shaped Immunoglobu-
`
`Iin molecule can be dissected by
`partial digestion with pretenses.
`Papsln cleaves the immunogiobulin
`molecule into three places. two Fab
`iregmenis and one Fe fragment (upper
`panels). The Feb fragment contains the
`V regions and binds antigen. The Ft:
`iragment is crystallizabie and contains 0
`regions. Pepsin cleaves immunoglobuiin
`to yield one Flair): fragment and many
`small pieces of the Fc fragment, the
`largest of which is called the ch’ trsg-
`ment (lower panels). Home is written
`with a prime because it contains a law
`more amino acids than Fab. including
`the cysteines that form the disuiflde
`bonds.
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`i
`!
`-
`
`
`
`The protein fragments obtained afierproteolysis are determined byud'rere the
`protease cuts the antibody molecule in relation to the disulfide bonds that link
`
`the two heavy chains. These lie in the hinge region heaveen the CH1 and Caz
`domains and, as illustrated in Fig. 3.3, pepsin cleaves the antibody molecule
`on the amino-terminal side of the disulfide bonds. This releases the two arms
`
`
`
`
`
`
`
`
`
`
`
`
`
`
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`
`
`
`
`
`of the antibody as separate Fab fragments, whereas in the Fc fragment the
`Wherry-terminal halves of the heavy chains remain linked.
`
`another protease. pepsin, cuts in the same general region of the antibody
`molecule as pepsin but on the carboxy-terminal side of the disulfide bonds
`(See Fig. 3.3). This produces a fragment, the Ftah’la fragment. in which the
`MD antigen-binding arms of the antibody molecule remain linked. In this
`case the remaining part of the heavy chain is cut into several small fragments.
`The Half}; fragment has exactly the some antigen-binding characteristics as
`the original antibody but is unable to interact with any effector molecule. it is
`thus of potential valuein therapeutic applications of antibodies as well as in
`research into the functional role of the Fc portion.
`
`Genetic engineering techniques also now permit the construction of many
`diiierent antibody-related molecules. One important type is a truncated Feb
`comprising only the V domain of a heavy chain linked by a stretch of
`ii.‘intltetitr peptide to n v domain of a light chain. This is called sings-chain Fv.
`named From Fragment variable. Fv molecules may become valuable theta-
`heath: agents because of their small size, which allows them to penetrate
`tissues readily. They can be coupled to protein toxins to yield inununotorrins
`Wm"! Potential application, for example. in tumor therapy in the case of a Fv
`aIliftiifit: for a tumor antigen [see Chapter 14).
`
`
`
`Lassen - Exhibit 1038, p. 10
`
`Lassen - Exhibit 1038, p. 10
`
`

`

`
`
`Chapter 3: Antigen Matthieu by B-oeil end T-oell Receptors
`
`
`
`3-4 mmmunoglobulin molecule is flexible. especially at the hinge
`
`n.
`
`The hinge region that links the Fe and Fab portions of the antibody molecule
`is in' reality a flexible tether. allowing independent movement of the two Fab
`arms. rather than a rigid hinge. This has been demonstrated by electron
`microscopy of antibodies bound to haptens. These are small molecules of
`various sorts. typically about the size of a tyrosine side chain. They can be
`recognized by antibody but are only able to stimulate production of anti-
`hapten antibodies when linked to a larger protein carrier [see Appendix i.
`Section A-l]. An antigen made of two identical hapten molecules joined by a
`short fletdble region can link turn or more anti-hapten antibodies. forming
`dimers. trimers.
`ten-emote. and so on. which can be seen by electron
`microscopy (Fig. 3.4]. The shapes formed by these complexes demonstrate
`that antibody molecules are flexible at the hinge region. Some flexibility is
`also found at the junction between the V and C domains. allowing bending
`and rotation of the V domain relative to the C domain. For example. in the
`antibody molecule shown in Fig. 3.1a, not only are the Mo hinge regions
`clearly bent difl‘erently. but the angle between the V and C domains in each of
`the two Fab arms is also different. This range of motion has led to the junction
`between the V and C domains being referred to as a 'molecmar ball-
`and-socket joint.’ Flexibility at both the hinge and V—C junction enables the
`binding of both arms of an antibody molecule to sites that are various
`distances apart. for example, sites on bacterial cell-wall polysaccharides.
`Fletdbility at the hinge also enables the antibodies to interact with the
`andbody—bmding proteins that mediate immune effector mechanisms.
`
` Anglebetweenarntsleo"
`
`
`
`Fig. 3.4 Antibody arms are joined by
`I. flexible hinge. An antigen oonehting
`of two hapten molecules {red balls in
`diagrams} that can cross-ilnk two
`antigen-binding sites is used to create
`antigenmntlbody complexes. wrflch can
`be seen in the electron micrograph.
`Linear. triangular. and square tonne are
`seen. with short projeoiions or spikes.
`Limited pepsin digestion removes these
`spikes (not shown in the figure}, which
`therefore correspond to the Fe portion of
`the antibody; the Fieb’}: pieces remain
`cross-linked by antigen. The Interpre-
`tation oi the oomplexes is show In the
`diagrams. The angle between the suns
`ot the embody molecules varies. from
`0' In the antibody dimers. through 80'
`in the triangular tonne, to 90' in the
`square iomts. showing that the
`connections between the arms are
`flexible. Photograph (1:. 300.000}
`courtesy of NM. Green.
`
`
`
`Lassen - Exhibit 1038, p. 11
`
`Lassen - Exhibit 1038, p. 11
`
`

`

`
`
`Thach'ucbtraofatypicaiantlbodymciacule E
`
`35
`
`The contains of an immunoglobulin molecule have similar structures.
`
`As we saw in Section 3-2. immunoglobulin heavy and light chains are
`
`60me of a series of discrete protein domains. These protein domains all
`
`have a similar folded structure. Within this basic three-dimensional struc-
`tore. there are distinct differences between V and C domains. The structural
`
`.gmlarilies and differences can be seen in the diagram of a light chain in Fig.
`1-3.5. Each domain is cooso‘ucted from two [3 sheets. which are elements of
`
`weight structure made up of strands of the polypeptide chain {B strands)
`
`3.... cited together: the sheets are linked by a disulfide bridge and together form
`litmus”? barrel-shaped strttoture. known as a [3 barrel. The distinctive folded
`cture oi'
`the immunoglobulin protein domain is known as the
`
`magnetization fold.
`
`{Both the essential similarity of V and C domains and the critical difi'erence
`
`Wen them are most clearly seen in the bottom panels ofFig. 3.5. where
`-the cylindrical domains are opened out to reveal how the polypeptide chain
`
`fluids to create each of the [5 sheets and how it forms flexible loops as it
`
`.hhanges direction. The main difierence between the V and C domains is that
`‘hevdomain is larger. with an extra loop. We will see in Section 3-6 that the
`sflexihle loops of the V domains form the antigen-binding site of the
`
`. immunoglobulin molecule.
`
`
`
` Fig. 3.5 The atruchire oi immuta-
`
`9lobulin constant and variable
`domains. The upper panels show
`schematically the raiding pattern of the
`constant (C) and variable (V) domains
`of an lmmunoglobulln light chain. Each
`domain is a barrel-shaped structure in
`which strands oi polypeptide chain
`([5 strands) running in opposite directions
`(antiparallai) pack together to form two
`B sheets (shown In yellow and green in
`the diagram of the C domain). which are
`held together by a disulflde bond. The
`way the polypeptide ci'lain folds to give
`the fine] structure can be seen more
`clearly when the sheets are opened
`out. as shown in the lower panels. The
`B strands are lettered sequentially with
`respect to the order at their occurrence
`in the amino acid sequence of the
`domains: the order in each B sheet is
`characteristic of immunoglobulin
`donains. The ii strands C‘ and C" that
`are found in the V domains but not in
`the 0 domains are indicated by a blue
`shaded background. The characteristic
`four-ahead plus three-strand (Ci-region
`type domain) or four-stand plus five-
`slrand (V-reglon type domain) arrange-
`ments are typical lrnmumglohuiin
`superiamily domain bonding blocks.
`found in a whole range of other
`proteins as well as antibodies and
`T-ceil receptors.
`
`Lassen - Exhibit 1038, p. 12
`
`.
`
`‘
`‘
`‘
`
`
`
`Lassen - Exhibit 1038, p. 12
`
`

`

`
`
`
`Chapter 3: Antigen Hamilton by B-celt and T-oall Receptors
`
`
`
`Many of the amino acids that are common to C and V domains of immuno.
`globulin chains lie in the core of the immunoglobulin fold and are critical to
`its stability. For that reason. other proteins having sequences similar to those
`of immunoglobulins are believed to form domains of similar structure. and in
`many cases this has been demonstrated by crystallography. These
`immunoglobulin-like domains are present in many other proteins of the
`immune system. and in proteins involved in cell—cell recognition in the
`nervous system and other tissues. Together with the immunoglobulins and
`the T-cell receptors. they make up the extensive immunuglobufln superfamily.
`
`Summary.
`
`The [36 antibody molecule is made up of four polypeptide chains. comprising
`two identical light chains and two identical heavy chains. and can be thought
`of as forming a flexible Y-s'httped structure. Each of the four chains has a
`variable (V) region at its amino terminus. which contributes to the antigen-
`binding site. and a constant (C) region. which determines the isolype. The
`isotype of the heavy chain determines the functional properties of the
`antibody. The light chains are bound to the heavy chains by many non-
`covalent interactions and by disulfide bonds. and the V regions of the heavy
`and light chains pair in each arm of the Y to generate two identical antigen-
`binding sites. which lie at the tips of the arms of the Y. The possession oftwo
`antigen-binding sites allovvs antibody molecules to cross-link antigens and to
`bind them much more stably. The tmnlt of the Y. or Fc fragment. is composed
`of the coronary-terminal domains orthe heavy chains. lolning the arms of the
`Y to the tnmk are the flexible hinge regions. The Fc fragment and hinge
`regions differ in antibodies of different isotypes.
`thus determining their
`functional properties. However. the overall organization of the domains is
`similar in all isotypes.
`
`Theintermfonpftheanflbodymoleculewlih
`smiles-oer:
`
`We have described the structure of the antibody molecule and how the V
`regions of the heavy and light chains fold and pair to form the antigen-binding
`site. In this part of the chapter we will look at the antigen-binding site in more
`detail. We will discuss the different ways in which antigens can bind to anti-
`body and address the question of how variation in the sequences of the
`antibody V domains determines the specificity for antigen.
`
`3-6
`
`Localized regions of hypervarieble sequence form the antigen-
`bintling site.
`
`The V regions ofany given antibody molecule differ from those ofevery other.
`Sequence variability is not, however. distributed evenly throughout the V
`regions but is concentrated in certain segments of the V region. The distribution
`ofvariable amino acids can be seen clearly in what is termed a variability plot
`(Fig. 3.6). in which the amino acid sequences of many different antibody
`V regions are compared. Three segments of particular variability can be
`identified in both the V“ and VL domains. They are designated hypervariable
`regions and are denoted HVI, HVZ. and HUB. in the light chains these are
`roughly from residues 28 to 35. from 49 to 59. and from 92 to 103. respectively.
`
`
`
`Lassen - Exhibit 1038, p. 13
`
`Lassen - Exhibit 1038, p. 13
`
`

`

`The Interaction oithe antibody molecule with specific antigen
`
`
`
`204030501me
`Residue
`
`6080103120
`Herbie
`
`The most variable part of the domain is in the HVB region. The regions
`between the hypervariable regions. which comprise the rest of the V domain,
`show less variability and are termed the framework regions. There are four
`such regions in each V domain. designated FRI. F112. PBS. and FR4.
`
`The framework regions form the [3 sheets that provide the structural frame
`work of the domain. whereas the hyperveriable sequences correspond to
`three loops at the outer edge of the [3 barrei. which are juxtaposed in the folded
`domain (Fig. 3.7]. Thus. not only is sequence diversity concentrated in
`particular parts of the V domain but it is localized to a particular region on the
`surface of the molecule. When the V1.1 and VL domains are paired in the anti-
`body molecule, the hypervariable loops from each domain are brought
`together. creating a single hypervariable site at the tip of each arm of the
`molecule. This is the binding site for antigen. the antigen-binding site or
`antibody combining site. The three hypervariable loops determine antigen
`specificity by forming a surface complementary to the antigen. and are more
`commonly termed the complementarity-determining regions. or CDRs
`[CURL CDRZ. and CD33). Because (mm from both VH and VL domains con-
`tribute to the antigen-binding site. it is the combination of the heavy and the
`light chain. and not either alone. that determines the final antigen specificity.
`Thus, one way in which the immune system is able to generate antibodies
`of different specificities is by generating different combinations of heavy-
`and light-chain V region