Volume 342 No.6252 21/280ecember1989 $5.75
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`RETURN TO
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`INTERNATIONALWEEKLY JOURNAL OF SCIENCE
`
`DRAINAGE PATTERNS
`
`MANTLE PLUMES AND CONTINENTAL
`
`Pfier Ex. 109
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`nature
`
`21/28 December 1989
`Vol. 342 Issue no. 6252
`
`DRAINAGE PATTERNS 4 The Rio Pelotas in southern Brazil,
`
`along the border between the Santa
`Catarina and Rio Grande do Sul states.
`This river flows west. away from the
`Atlantic, down the flank of a dome of
`basaltic lavas uplifted by a mantle
`plume. See page 873.
`
`
`HUME; A111} commu.
`
`
`THIS WEEK
`
`Volcano predicted
`A ten-year study of the Poas vol-
`cano in Costa Rica provides the
`first unambiguous evidence that
`small changes in gravity can be
`precursors to a volcanic eruption,
`and may be of predictive value.
`Pages 902 and 862.
`
`Setback on male gene
`Genetic evidence strongly sug—
`, gests that the development of
`testes can be determined by a
`region of the Y chromosome that
`,
`‘ does not contain ZFY. thought to
`’ be the testis-determining gene
`(page 937) but which now seems
`in fact to determine spermato—
`genesis (page 940). See also
`News and Views page 860.
`
`Antibody construction
`The hypothesis that a few key
`. conserved residues in the hyper-
`variable
`regions of
`antibody
`genes determine the main chain
`conformation of
`these hyper-
`variable loops is supported by
`Zggctural predictions. see page
`Arresting enzyme
`Self fertilization in many flower-
`ing plants is prevented by self-
`incompatibllity genes with many
`alleles, but it has not been known
`how they work. One of these
`genes was recently isolated from '
`tobacco and is now shown to have
`strong similarity to ribonuclease.
`Ribonuclease
`activity can be
`demonstrated in proteins
`ex-
`tracted from the plant style where
`they presumably act on the pollen
`tube cells to arrest growth. Page
`955.
`
`Rules for waves
`Experiments performed in a wave
`tank show that the moderating
`effect of rain on wave motions is
`exerted by the suppression of
`short-wavelength gravity waves,
`and the accompanying reduction
`in the breaking of long waves.
`The finding affects the validity of
`some remote sensing data, sea
`surface radar imaging and radar-
`based wind
`speed measure-
`ments, page 893.
`Lunar flnd
`Evidence from a thin section of
`the Antarctic meteorite Elephant
`Moraine 87521 shows it to be of
`lunar origin. But unlike previously
`discovered lunar meteorites, it is
`made up of material from a mare
`region, rather than from the high-
`lands. Page 889.
`Signal splicing
`Alternative splicing of the mRNA
`for the 02 dopamine receptor,
`the target of antischlzophrenia
`drugs, gives rise to two forms of
`the receptor, one of which con—
`tains an additional 29 amino-
`acid fragment in a putative signal
`transduction loop. Pages 923,
`926 and 865.
`
`Membrane fusion arrest
`When cells enter mitosis. all
`intracellular membrane traffic is
`halted. Experiments with endo-
`cytic vesicles in vitro suggest that
`the cell-cycle
`control protein
`kinase cdc2 is responsible for
`this inhibition. Page 942.
`
`Enzyme chaperone
`Chaperonins, a ubiquitous class
`of proteins thought to play a part
`in the post-translational folding
`and assembly of other proteins,
`Nitrate source
`facilitate the reconstitution of the
`green-
`The
`‘ozone-unfriendly’
`enzyme
`ribulose bisphosphate
`house gas N20 may be produced
`carboxylase (Rubisco) in a step-
`wise fashion from an unfolded
`in the ocean primarily by produc-
`tion of nitrate (denitrification)
`state in vitro. Page 884.
`not. as was thought, by oxidation
`Guide to Authors
`of
`ammonium (nitrification).
`Facing page 958.
`Page 895.
`l‘Jairire‘m (ISSN 0028-0836) is published weekly on Thursday, exce t the last week in December.
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`
`NATURE SAYS
`
`We must not forget Sakharov I Gorbachev has problem
`
`841
`
`
`NATURE REPORTS
`
`Moscow’s farewell to Sakharov I DNA fingerprinting trial fails I
`Animal rights I India plans Antarctic base I Patents I Shuttle
`rescue I Cancer drugs restricted I Selling student places
`CORRESPONDENCE
`848
`
`Journals and databanks I Explosives I Embryos I Etc.
`
`842
`
`
`COMMENTARY
`
`The overdose ofdrugs in Japan
`M Fuk ushima
`Reflections on the discovery of fission
`R Peierls
`
`NEWS AND VIEWS
`
`Making authors toe the line
`John Maddox
`Plate tectonics: Helium line in the Banda arc
`Eli A Silver
`Cell biology: Mitosis and membranes
`Graham Warren
`Ecology: Answers that lie in the soil
`Peter D Moore
`Synthetic chemistry: Chemists get topological
`Roland Pease
`Mammalian sex determination: Thumbs down for zinc finger?
`Paul S Burgoyne
`Volcano prediction: Measures of little gravity
`Robert I Tilling
`Immunology: Making antigen-receptor genes
`Gary Rathbun, Frederick W Alt & George D Yancopoulos
`Daedalus: Lifeless prose
`
`SCIENTIFIC CORRESPONDENCE
`
`D, receptor, a missing exon K A Eidnc, P L Taylor. J Zabavnik.
`P T K Saunders & J D Inglis l Exxon Valdez bird toll
`J F Piatt & C J Lensink
`Bacterial zipper R Giraldo, C Nieto, M-E Fernandez-
`Tresguerres & R Diaz I Which Haldane? R Passmore
`
`BOOK REVIEWS
`
`No Ghost in the Machine: Modern Science and the Brain,
`the Mind and the Soul by R Correrill John Morton
`For lnstructionand Recreation: A Centenary History
`of the Museums Association by G Lewis Carole Scott
`I The Metabolic Basis of Inherited Disease C R Scriver,
`A L Bequdet, WS Sly & D Valle eds Richard W E Watts
`Mathematical Biology by] D Murray M B Usher
`Prochloron: A Microbial Enigma R A Lewin
`& L Cheng eds T Cavalie r-Smith I Cold Fusion: The Making
`of a Scientific Controversy by F D Pear David Lindlcy
`Empires ofTime: Calendars, Clocks, and Cultures
`by A A veni Owen Gingerich
`The Experimental Foundation of Particle Physics
`by R N Cahn D H Perkins I One and Two Dimensional
`NMR Spectroscopy by Arra-ur-Rahman P J Hore
`
`ARTICLES
`
`The role of mantle plumes in the development of continental
`drainage patterns
`K G Cox
`Conformationsol‘ immunoglobulin hypervariable regions
`C Chothia. A M Lesk, A Tramontano, M Levitt, S J Smith-Gill,
`G Air. S Sheriff, E A Padlan. D Davies, W R Tulip, P M Colman,
`S Spinelli. P M Alzari & RJ Poljak
`
`
`
`850
`
`852
`
`855
`
`856
`
`857
`
`858
`
`859
`
`880
`
`862
`
`863
`864
`
`865
`
`866
`
`867
`
`868
`869
`
`870
`
`871
`
`872
`
`873
`
`877>
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`Pfizer Ex. 1009
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`Pfizer Ex. 1009
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`

`

`MacLennan
`Blockage 0? 043 T-ceil development by TCR yd transgenes
`M BonneVIlle, I Ishlda, P Mombaerts, M Katsukl, S Verbeek, A
`Berns & S Tonegawa
`A protein binding to the JK recombination sequence of immuno-
`globulin genes contains a sequence related to the integrase motif
`N Matsunami, Y Hamaguchi, Y Yamamoto, K Kuze,
`K Kangawa, H Matsuo, M Kawaichi & T Honjo
`Genetic evidence that ZFY is not the testis-determining factor
`M s Palmer, A H Sinclair, P Berta, N A Ellis, P N Goodfellow,
`N E Abbas & M Fellous
`ny gene expression patterns are not compatible with a primary
`role m mouse sex determination
`P Koopman. J Gubbay, J Collignon & R Lovell-Badge
`Inhibition ofendocytic vesicle fusion in vitra by the cell-cycle
`control protein kinase cdc2
`T'Tuon-llkoskl ' MiA Felix, MPOICB & IGruenberg
`Dissectionol' functional domains ofthe pituitary-speCIfic
`transcription factor (FHF'I
`_
`L E Them” J'I‘ Castrillo, D Wu & M Kan"
`A highly divergent HIV-2 related isolate
`U DFmCh' M AdfimSk" R Kreutz, A Seipp, H Ki'ihnel &
`H Rubsamen-Walgmann
`Isolation and characterization of the G-actin—myosin head
`lex
`comp
`,
`P Chaussepied & A A Kasprzak
`Sensitivity to cyclosporin A is mediated by cyclophilin in
`Neurospora crassa and Saccharomyces cerevisiae
`M Tropschug. l B Barthelmess & W Neupert
`Style self-incompatibility gene products ofNicotiana alata
`are rlhonucleases
`‘
`B A McClure. V Haring. P R Ebert, MA Anderson,
`.
`R J Simpson, .FSakiyama & A E Clarke
`Changes in spinal cord reflexes after cross-anastomoms ol‘
`gunk??? :nd zuscle “CI-1:95 m the adult rat (Erratum)
`B C
`a on
`P D_ Wa
`_
`_
`An optical yield that Increases With temperature In a
`pgotfihgmically Induced enantiomeric Isomenzauon
`0" c
`n
`_
`_
`_
`YInoue, T Yokoyama, N Yamasaki & ATal
`'I he Winter solstice phenomenon at Newgrange, Ireland: acCIdent
`orgsign? (Correction)
`58
`
`T
`ay
`9
`-See News and Views
`
`NEXT WEEK IN NATURE
`.
`.
`.
`The next Issue, dated 4 January 1990 includes items on: The year’s
`
`934
`
`931
`
`940
`
`942
`
`945
`
`948
`
`950
`
`953
`
`955
`
`958
`
`958
`
`889
`
`890
`
`893
`
`'
`
`895
`
`897
`
`900
`
`902
`
`906
`
`908
`
`913
`
`916
`
`918
`
`920
`
`923
`
`'
`
`1
`
`
`
`Mechanism ofantigen-driven selection in germinal centres
`Y-J Liu, D E Joshua, GTWilliams. C A Smith, J Gordon & I C M
`
`929
`
`931
`
`Reconstitution of active dimeric ribulose bisphosphate
`cal-boxylase from an unfolded state depends on two chaperonin
`Proteins and Mg-ATP
`p Goloubinoff. J T Christeller. A A Gatenby & G H Lorimer
`884
`
`LETTERS TO NATURE
`'
`,
`.
`,
`,
`figugrlbasalt breccia identified among Antarctic meteorites
`“
`e ancy
`.
`,
`Nc¥lg033|efihefl copper oXIde compounds wnh Blo
`or
`I ayers
`,
`,
`.
`.
`Y gORU’a’: mma’lHPTLakag“ 5:512:23 I:h'gak" H Asa“°'
`5“ 333:“ in 52%;! mm
`’3 “e
`M A‘l‘simplispdr 1; 13Thorpe
`Nitrification rates and lsN abundances ofN20 and N0; in the
`western North Pacific
`N Yoshida H Morimoto M Hirano I Koike S Matsuo E Wada
`T 5.aino & A Hat!ori
`‘
`'
`'
`'
`Evidence for a change in the periodicity oftropical climate cycles
`at 2.4 Myr from whole-core magnetic susceptibility measurements
`J Bloemendal & P deMenocal
`Thermal entrainment by deflected mantle plumes
`. M A Richards & R W Griffiths
`Gravity changes as a precursor to volcanic eruption of Paris
`volcano, Costa Rica
`H Rymer & G Brown
`.
`.
`.
`.
`A helium Isotope transect along the lndonesran archipelago
`D R Hilton & H Craig
`Leakage ofhelium from the Pannonian basin
`D J Martel J Deak P Dovenyi F Horwith R K O‘Nions
`E R Oxburgh L Stegena & M étute
`‘
`Boron isotopeievidence for the involvement of non-marine
`.
`. t
`.
`th
`.
`.
`f th B k
`1111
`d
`'ts
`3:332;ng 55:33; E :1 $65215. ore ep05i
`Wavelength sensitivity in blindsight
`P Sioerig & A Cowey
`Arachidonic acid induces a prolonged inhibition ofglutamate
`uptake into glial cells
`B Barbour, M Szatkowski, N Ingledew & D Attwell
`Molecular cloning, expression and regional distribution of rat
`ciliary neurotrophic factor
`K A Stockli, F Lottspeich, M Sendtner. P Masiakowski.
`P Carroll R Ginz D Lindh0|m & H Thoenen
`Alternative splicing directs the expression oftwo Dz dopamine
`receptor isoforms
`-
`c war 2
`2233355,: Sol‘wloff, M-P Marlres, J-F Riou, L] Emorine
`anniversaries l Extendingthegenetic alphabet I Marine bacteria
`Multiple D2 dopamine receptors produced by
`alternative RNA splicing
`i
`.
`.
`926
`EJRbéfifergaJr‘ L D Mchttle, C R Gerfen, L C Mahan &
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`NATURE - VOL 342 ‘ 21/28 DECEMBER 1989
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`NATURE ~ VOL 342 - 21/28 DECEMBER 198!
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`

`1:5. Ollier, C. D, Tectonics and Landforms [Longman New York, 1981),
`26, Fitch, F. J & Miller, J. A Spec, Pub/s geol, Soc. S Afr 13. 247-266 (1984)
`27 Cox, K G J. Petrol 21, 629765011980).
`2H England, P. C, & Molnar. P. Geology (in the press).
`29. Petri. S & Fulfarb. V. J, Geologia do Brasil (Editora da Umversidade de 850 Paulo, 1983).
`30. Tankard, A.
`.l. er al. Crustal Evolution of Southern Africa (Springer, New Vork, 1982).
`31. Craddock. C led) Antarctic Geascrenoe onrversrty of Wisconsin Press. Madison. 1982)
`
`32. King, L, C. South African Scenery 2nd edn (Oliver and Boyd, Edinburgh. 1951).
`33, King, L. C, The Morphology of the Earth (Oliver and Boyd. Edinburgh, 1962).
`34. Partridge, T. C, [L Maud, R R. S Afr geol. J so. 179-208 (1987).
`35. Cahen, L, Snelling, N. J., DelnaIJ. & Vail, J. R. The Geochrono/ogy and Evolution orArnca (Clarendon.
`Oxford. 1984).
`36, Brown. R. W. 6thlnt. Conf. Fission Track Dating Abstr Vol. Université de Franche-Comté,Besan<;on,
`1988).
`
`
`
`ARTICLES
`
`Conformations of immunoglobulin
`hypervariable regions
`
`Cyrus Chothia‘l, Arthur M. Lesk”, Anna Tramontanoi, Michael Levitt“,
`Sandra J. Smith-Gill“, Gillian Air“, Steven Sheriift’", Eduardo A. Padlan’“,
`David Davies#, William R. Tulip", Peter M. Colman”, Silvia Spinelli“,
`i’edro M. Alzari“ & Roberto J. Poljak“
`"‘ MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
`3: European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 1022.09, D6900 Heidelberg, FRG
`§ Department of Cell Biology, Stanford University Medical School, Stanford. California 94305, USA
`+ Christopher Ingold Laboratory. University College London, 20 Gordon Street, London WClH OAJ, UK
`ll National Institute of Cancer and # National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda,
`Maryland 20892, USA
`fl Department of Microbiology, University of Alabama, Birmingham, Alabama 35294, USA
`tt CSIRO Division of Biotechnology, 343 Royal Parade, Parkville 3052, Australia
`5:: Unite d'lmmunologie Structurale, Département d'lmmunologie, Institut Pasteur. 25 rue du Dr Roux, 75724 Paris, France
`
`On the basis of comparative studies of known
`antibody structures and sequences it has been
`argued that there is a small repertoire of main-
`chain conformations for at least five of the six
`
`hypervariable regions of antibodies, and that the
`particular conformation adopted is determined by
`a few key conserved residues. These hypotheses
`are now supported by reasonably successful pre-
`dictions of the structures of most hypervariable
`regions of various antibodies, as revealed by
`comparison with their subsequently determined
`structures.
`
`THE relationships between the amino-acid sequences of
`immunoglobulins and the structures of their antigen-binding
`sites are important for understanding the molecular mechanisms
`of the generation and maturation of the immune response and
`for designing engineered antibodies. Antigen-binding sites are
`formed by six loops of polypeptide, the hypervariable regions;
`three from the variable domain ofthe light chain (VL) and three
`from the variable domain of the heavy chain (VH), denoted L1,
`L2, L3, and H1, H2, H3, respectively (Fig. la). Within the
`domains, the loops are connected to a B-shcct framework whose
`structure is conserved "3. The specificity and affinity of the bind-
`ing sites are governed by the structures of the six hypervariable
`regions”.
`Two models can be proposed for the relationship between
`the amino-acid sequence and structure ofthe binding-site loops.
`In one model, different sequences produce different conforma-
`tions for both the main chain and side chains of the loops.
`Because hypervariable regions have different sequences in
`different antibodies, this model implies that each region adopts
`a diiferent conformation in different antibodies. In the other
`
`
`** Present address: The Squibb institute for Medical Research, PO Box 4000,
`Princeton, New Jersey 08543-4000. USA.
`
`NATURE - VOL 342 ~ 21/28 DECEMBER 1989
`
`model, antibodies have only a few main-chain conformations
`or “canonical structures’ for each hypervariable region. Most
`sequence variations would only modify the surface provided by
`the side chains on a canonical main—chain structure. Sequence
`changes at a few specific sets of positions would switch the main
`chain [0 a different canonical conformation.
`
`Canonical structure model
`Experimental evidence indicates that the canonical structure
`model describes the relationship between amino-acid sequence
`and structure for at least five of the six hypervariable regions”.
`Kabat er al.5 found conserved residues at sites within certain
`sets of hypervariable regions and suggested that they had a
`structural role. Padlan and Davies“, and more recently de la
`Paz er al.7, showed that some of the hypervariable regions
`in the immunoglobulins of known structure have the same
`main-chain conformation in spite of several differences in
`sequence.
`
`Chothia and Lesk" identified the residues that through pack-
`ing, hydrogen bonding, or the ability to assume unusual values
`of the torsion angles 45,
`ll: or w, are primarily responsible for
`the main—chain conformations of the hypervariable regions in
`the structures then known—the Fab fragments of NEW (ref.
`10), McPC603 (ref. 1|), KOL (ref. 12) and J539 (ref. 13) and
`the VL domains of REI
`(ref. 14) and RHE (ref. 15). The
`conformations are determined by the interactions of a few
`residues at specific sites in the hypervariable regions and, for
`certain loops, in the framework regions. Hypervariable regions
`that have the same conformations in different immunoglobulins
`have the same or very similar residues at these sites (Fig. 1 and
`Table 1). Examination of the amino-acid sequence of the anti-
`body D1.3 showed that its hypervariable regions are the same
`size as those in known structures and contain the same or similar
`residues at the sites responsible for known conformation59. On
`the basis ofthese observations the atomic structure ofthe VL-VH
`dimer of D1.3 was predicted before its experimental determina-
`tion. Comparison ofthis predicted structure with the preliminary
`crystal structure showed that the conformations of four of the
`hypervariable regions had been predicted correctly; the confor-
`mation of L3 was significantly different from that predicted, and
`877
`
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`

`ARTICLES
`
`
`TABLE 1 Sequences and conformations of VK and VH hypervariable regions of known structure
`L1 Regions‘i
`Canonical
`Structure
`
`29
`3F
`V
`V
`V
`i
`i
`i
`V
`L
`L
`
`30
`
`S
`N
`R
`|
`H
`G
`S
`L
`V
`
`Blabcdef32 2253371
`****
`
`SIALY
`firereiieViAMY
`———-————Y|AMY
`K—————-VIALY
`N—i—«———Y|ALY
`N—————————NIALF
`T—.———v-—AIALY
`NSGN KNFiSLF
`H5-
`(3
`TY VSLF
`
`Protein
`
`26
`
`27
`
`28
`
`1
`
`2
`
`3
`4
`
`J539
`HyHEL»5
`NQlO
`RE!
`01.3
`HyHEL-iO
`NC41
`McPCGOB
`4-4-20
`
`S
`S
`S
`5
`S
`S
`S
`S
`5
`
`S
`S
`S
`Q
`G
`Q
`0
`E
`Q
`
`S
`S
`S
`D
`N
`S
`D
`S
`S
`
`'otal no. of sequences known for L1 regions: human, 95; mouse. 299.
`Canonical structure
`1
`2
`3
`4
`Human sequences that fit (96)
`—
`60
`5
`5
`Mouse sequences that tit (%)
`15
`25
`20
`10
`
`64
`il<
`
`ccsccceG<
`
`3
`
`A00
`
`___._.__—__...*
`
`50
`
`51
`
`52
`
`E
`G
`E
`Y
`o
`Y
`W
`D
`K
`
`A
`A
`i
`T
`T
`A
`A
`T
`V
`
`S
`S
`S
`T
`s
`S
`S
`S
`8
`
`Protein
`
`REI
`McPC603
`J539
`D13
`HyHEL—S
`HyHEL-1O
`NC41
`N010
`4-4.20
`
`L2 Regions
`Canonical
`Structure
`
`1
`
`Total no. of sequences known for L2 regions; human, 69: mouse. 183.
`Canonical structure
`1
`Human sequences that fit (Va)
`95
`Mouse sequences that fit (96)
`95
`
`L3 Regions
`Canonical
`Structure
`
`1
`
`2
`3
`
`Protein
`
`RE
`McPCGO3
`D1.3
`Hyi-EL-lo
`NC41
`4-4-20
`N010
`1539
`HyHEL-5
`
`91
`
`92
`
`93
`
`94
`
`Y
`D
`F
`S
`H
`5
`W
`w
`w
`
`Q
`H
`W
`N
`Y
`T
`S
`r
`G
`
`S
`S
`S
`s
`S
`H
`S
`Y
`R
`
`L
`Y
`T
`W
`P
`V
`N
`i3
`N
`
`9596
`l“
`FY
`PL
`PR
`PY
`PW
`PW
`PL
`LI
`t
`p,
`
`90
`4
`Q
`N
`H
`Q
`Q
`Q
`Q.
`Q
`t
`o
`
`Total no. of sequences known for L3 regions: human, 52; mouse, 152.
`Canonical structure
`1
`2
`3
`Human sequences that fit (96)
`90
`—
`2
`Mouse sequences that fit (%)
`80
`10
`1
`
`“m
`
`Hl had a very different fold from that predicted". (We report
`below that the refined conformation of D13 corresponds more
`closely to the predicted structure.)
`An examination ofthe library of the known immunoglobulin
`sequences shows that many immunoglobulins have hyper-
`variable regions that are the same size as those in the known
`structures and contain the same or closély related residues at
`the sites responsible for the known conformationss. These
`observations indicate that for at least five of the hypervariable
`regions there is only a small repertoire of canonical main-chain
`conformations and that the conformation actually present can
`often be predicted from the sequence by the presence of specific
`residues.
`
`for
`structure model
`canonical
`the
`accuracy of
`The
`immunoglobulin binding sites depends on (1) the correct deter~
`878
`
`mination of the sets of residues responsible for the observed
`conformations and (2) changes in the identity of residues at
`other sites not significantly affecting the conformations of the
`canonical structures. The model can be tested, refined and
`extended by using it to predict the atomic structures of binding
`sites in immunoglobulins before their structures have been deter-
`mined by X-ray crystallography
`We have now tested the canonical structure model by using
`it to predict the structures of four immunoglobulins before their
`structures
`had
`been
`experimentally
`determined. These
`immunoglobulins are HyHEL-S (ref. 16), HyHEL-IO (ref. 17),
`NC41 (ref. 18) and NQlO (S.S., P.M.A. and R.J.P., manuscript
`in preparation). The analysis of the amino-acid sequences of
`these immunoglobulins indicated that 19 of their 24 hypervari-
`able regions should have conformations close to known canoni—
`
`NATURE - VOL 342 - 21/28 DECEMBER 1989
`
`Pfizer Ex. 1009
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`

`

`AR l'ICLES
`
`
`H1 Regionsi
`Canonical
`Structure
`
`1
`
`1'
`
`Protein
`
`McPC603
`KOL
`1539
`01.3
`HyHEL-S
`NC41
`N010
`4-4-20
`NEW
`HyHEL-lo
`
`26
`it
`G
`G
`G
`G
`G
`G
`G
`G
`G
`G
`
`27
`*
`F
`F
`F
`F
`Y
`Y
`F
`F
`S
`D
`
`28
`
`T
`I
`D
`S
`T
`T
`T
`T
`T
`S
`
`29
`at
`F
`F
`F
`L
`F
`F
`F
`F
`F
`l
`
`S
`, S
`S
`T
`S
`T
`S
`S
`S
`T
`
`Total no. of sequences known for H1 regions: human. 50; mouse, 321.
`Canonical structure
`1
`Human sequences that fit (%)
`50
`Mouse sequences that fit (%)
`80
`
`H2 Regions§
`Canonical
`Structure
`
`Protein
`
`523
`
`1
`
`2
`
`3
`
`4
`
`NEW
`01.3
`HyHEL-lO .
`
`HyHEL—S
`NC41
`
`KOL
`J539
`NQiO
`
`McPC603
`44120
`
`—
`
`—
`3k
`P
`T
`
`D
`P
`S
`
`N
`N
`
`b
`
`—
`
`—
`
`—
`—
`
`—
`—~
`—
`
`K
`K
`
`c
`
`—
`
`—
`
`—
`—
`
`—
`——
`—
`
`G
`P
`
`53
`
`54
`
`Y
`G
`Y
`
`G
`N
`
`D
`D
`G
`
`N
`Y
`
`H
`D
`S
`
`S
`T
`1*)
`G
`S
`S
`(1:)
`K
`N
`
`30
`
`31
`
`32
`
`34
`*
`M
`M
`M
`V
`I
`M
`M
`M
`Y
`W
`
`94
`1!
`Fl
`R
`R
`R
`R
`R
`R
`G
`R
`N
`
`F
`Y
`Y
`Y
`Y
`Y
`F
`Y
`D
`D
`
`D
`S
`K
`G
`D
`N
`S
`D
`N
`D
`
`55
`i.
`G
`G
`G
`(t)
`G
`G
`
`S
`G
`S
`iv
`Y
`Y
`
`71
`
`e
`A
`L
`r
`R
`R
`R
`in
`
`R
`
`Total no. of sequences known for H2 regions: human, 54: mouse, 248.
`Canonical structure
`1
`2
`3
`’
`4
`Human sequences that fit (96)
`15
`1
`40
`15
`Mouse sequences that fit (96)
`15
`40
`5
`2O
`
`The residues listed here (single-letter code) are those that form the hypervariable regions and those in the framework regions that are important for the observed conformations
`of these regionsa. The hypervariable regions are taken as those outside the framework B-sheeta. Except for H2, they are similar to, but not identical with the regions that show
`high sequence variations and which Kabat et al.26 use to define hypervariable regions. The sequences are grouped so that those that have the same main-chain conformation.
`or canonical structure, are adjacent. The canonical structure numbers used below refer to the conformations shown in Fig. 1. The residues in the hypervariable and framework
`regions that are mainly responsible lor these conformationsB are indicated by an asterisk. The classification and sequence requirements of the H2 conformations have been
`revised in the light of work described here and elsewhere“. For each hypervariable region the number of human and mouse sequences listed by Kabat et 3126 are given, We
`also give the percentage of these sequences that are the same size as the known canonical structures and have the same residues at the positions marked by an asterisk.
`i Canonical structure ‘4 is illustrated in Fig. 4. Although the size of the known L1 structures varies between 6 and 13 residues, they have closely related folds with residues
`26—19 and 32 packed against the framework in the same conformations, The remaining residues form a turn or loop on the surface (Figs 1 and 4). The ends of the long loops
`have some flexibility. There are another 25% of the human sequences and 20% of the mouse sequences that have one more residue than structure 2, or one fewer than structure
`4, and whose sequences satisfy the requirements listed above. It is expected that these differ only in the conformations of the tips of the surface loops.
`IThe H1 nypervariable regions with canonical structure 1 have very similar conformations: the r.m.s. differences in the coordinates of their main‘chain atoms are 0.3—0.8 A.
`The H1 regions in NEW and l-IyHEL-lO only partly satisfy the sequence requirements for structure 1 and have a distorted version of its conformation.
`§The H2 region here comprises residues 523755. The region with high sequence variation is 50—65 (ref. 26).
`In the known structures the main—chain conformation of 50—52
`and 56—63 do not differ significantly3 (Fig. 1b). (*1 The residues at positions 55 or 54 in the canonical structures 2, 3 and 4 have residues with positive values for as and ll],
`and usually. but not in all cases. Gly, Asn or Asp is found at these sites. For a sequence to match that of canonical structure 2, 3 or 4 the presence of these residues at sites
`54 or 55 is required.
`
`cal structures. We then compared the predicted structures of
`these hypervariable regions with the subsequently determined
`structures. Another immunoglobulin structure, 4-4-20 (ref. 19)
`has recently been reported. We did not have the opportunity to
`predict the structure of4-4—20 before its experimental determina-
`tion, and we discuss here only how its hypervariable regions
`have the conformations expected from the known canonical
`structures. Also, we report that the refined conformation of D1,}
`(ref. 20) corresponds more closely to the predicted structure.
`
`MOdel building p'ocedure
`Thc main-chain conformations of the hypervariablc regions in
`the VK and VH domains of known structure are shown in Fig.
`1. The residues responsible for these conformations are listed
`NATURE . VOL 342 . 21/28 DECEMBER 1989
`
`in Table 1. Each hypervariable region in the immunoglobulins
`of unknown structure was examined to determine (1) Whether
`it has the same size as any homologous hypervariable region of
`known structure and (2) whether its sequence contains the set
`of residues responsible for a known conformation. Except for
`L3 in HyHEL-S, all the light-chain regions correspond to a
`known canonical structure, as do all the H1 regions and the H2
`region in HyHELJO (Table 1). The conformation predicted for
`the H2 regions in NC41 and HyHEL-S was based on the analysis
`of the H2 region in the preliminary structure of .1539 (ref. 8).
`in all three of these antibodies the H2 region is a four-residue
`turn with Gly at the fourth position and the predicted conforma-
`tion is that almost always found for such turns“. (Below we
`present a more accurate analysis of H2 regions.) For H3 regions
`in HyHEL-S, HyHEL-lO, NC41 and N010, no prediction of
`879
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`

`ARTICLES
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`
`conformation could be made on the basis ofthe known canonical
`structures.
`
`The sequences of the VL and VH domains were compared to
`see which of the known framework structures have sequences
`close to those ofthe unknown structures. From the comparisons
`
`of the hypervaria