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Handbook
of
Biochemistry
and
Molecular Biology
CRC Handbook
of
Biochemistry
and
Molecular Biology
3rd Edition
Proteins
Volume II
Editor
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Handbook
of
Biochemistry
and
Molecular Biology
3rd Edition
Proteins
Volume II
Editor
Gerald D. Fasman, Ph. D.
Rosenfield Professor of Biochemistry
Graduate Department of Biochemistry
Brandeis University
Waltham, Massachusetts
Gerald D. Fasman
Editor
MEMBERS
1. M. Klotz
Alton Meister
Professor, Department of Chemistry
Professor, Department of Biochemistry
Northwestern University
Cornell University Medical College
Evanston, Illinois 60201
New York, New York 10021
Robert Langridge
Professor, Department of Biochemistry Kivie Moldave
Princeton University Professor, Department of Biochemistry
Princeton, New Jersey 08540 California College of Medicine
University of California
Philip Leder Irvine, California 92664
Chief, Laboratory of Molecular Genetics
National Institute of Child Health D. C. Phillips
and Human Development Professor, Laboratory of Molecular
National Institutes of Health Biophysics
Bethesda, Maryland 20014 Department of Zoology
Oxford University
I. Robert Lehman Oxford
Professor, Department Biochemistry England
School of Medicine
Stanford University William D. Phillips
Stanford, California 94305 The Lord Rank Research Centre
Ranks Hove, McDougall Ltd.
Lawrence Levine Lincoln Road, High Wycombe
Professor, Graduate Department of Bucks
Biochemistry England
Brandeis University
Waltham, Massachusetts 02154
G. N. Ramachandran
John Lowenstein Professor, Molecular Biophysics Unit
Professor, Graduate Department of Indian Institute of Science
Biochemistry Bangalore
Brandeis University India
Waltham, Massachusetts 02154
Michael Sela
Emanuel Margoliash Professor, Department of Chemical
Professor, Department of Biological Immunology
Sciences The Weizmann Institute of Science
Northwestern University Rehovot
Evanston, Illinois 60201 Israel
ADVISORY BOARD (continued)
Colin F. Chignell
Donald M. Kirschenbaum
Section of Molecular Pharmacology
Department of Biochemistry
Pulmonary Branch
State University of New York
National Heart and Lung Institute
Brooklyn, New York 11203
National Institutes of Health
Bethesda, Maryland 20014
Walter Kisiel
Waldo E. Cohn Department of Biochemistry
Biology Division University of Washington
Oak Ridge National Laboratory Seattle, Washington 98195
Oak Ridge, Tennessee 37830
Irving M. KJotz
Dennis A. Darnall Biochemistry Division
Department of Chemistry Department of Chemistry
New Mexico State University Northwestern University
Las Cruses, New Mexico 88003 Evanston, Illinois 60201
The rapid pace at which new data is currently accumulated in science presents one of
the significant problems of today - the problem of rapid retrieval of information. The
fields of biochemistry and molecular biology are two areas in which the information
explosion is manifest. Such data is of interest in the disciplines of medicine, modern
biology, genetics, immunology, biophysics, etc., to name but a few related areas. It was
this need which first prompted CRC Press, with Dr. Herbert A. Sober as Editor, to
publish the first two editions of a modern Handbook o f Biochemistry, which made
available unique, in depth compilations of critically evaluated data to graduate students,
post-doctoral fellows, and research workers in selected areas of biochemistry.
This third edition of the Handbook demonstrates the wealth of new information
which has become available since 1970. The title has been changed to include molecular
biology; as the fields of biochemistry and molecular biology exist today, it becomes more
difficult to differentiate between them. As a result of this philosophy, this edition has
been greatly expanded. Also, previous data has been revised and obsolete material has
been eliminated. As before, however, all areas of interest have not been covered in this
edition. Elementary data, readily available elsewhere, has not been included. We have
attempted to stress the areas of today’s principal research frontiers and consequently
certain areas of important biochemical interest are relatively neglected, but hopefully not
totally ignored.
This third edition is over double the size of the second edition. Tables used from the
second edition without change are so marked, but their number is small. Most of the
tables from the second edition have been extensively revised, and over half of the data is
new material. In addition, a far more extensive index has been compiled to facilitate the
use of the Handbook. To make more facile use of the Handbook because of the increased
size, it has been divided into four sections. Each section will have one or more volumes.
The four sections are titled:
By means of this division of the data, we can continuously update the Handbook by
publishing new data as they become available.
The Editor wishes to thank the numerous contributors, Dr. Herbert A. Sober, who
assisted the Editor generously, and the Advisory Board for their counsel and cooperation.
Without their efforts this edition would not have been possible. Special acknowledgments
are due to the editorial staff of CRC Press, Inc., particularly Ms. Susan Cubar Benovich,
Ms. Sandy Pearlman, and Mrs. Gayle Tavens, for their perspicacity and invaluable assistance
in the editing of the manuscript. The editor alone, however, is responsible for the
scope and the organization of the tables.
We invite comments and criticisms regarding format and selection of subject matter, as
well as specific suggestions for new data (and their sources) which might be included in
subsequent editions. We hope that errors and omissions in the data that appear in the
Handbook will be brought to the attention of the Editor and the publisher.
Gerald D. F asm an
Editor
August 1975
PR EFACE TO AMINO ACIDS, PEPTIDES, POLYPEPTIDES,
AND PROTEINS, VOLUME II
The section of the Handbook o f Biochemistry and Molecular Biology on Amino Acids,
Peptides, Polypeptides, and Proteins is divided into three volumes. The second volume
contains information mainly on Proteins.
Data on cleavage, chemical modification and hydrolysis of proteins are contained
herein. Physical-chemical data on proteins, such as refractive index increments, molecular
extinction coefficients, pK values, viscosity data, dimensions of the amide group, and
protein conformation are listed. Molecular parameters of plasma proteins, glycoproteins,
histones, muscle proteins, and many other proteins are tabulated. Properties of lectins,
protein ligands, proteinase inhibitors, and proteoglycans are listed.
The third volume will contain additional material on proteins and the first volume
contains information on amino acids, amino acid derivatives, etc.
Although the data, for which the editor alone is responsible is far from complete, it is
hoped that these volumes will be of assistance to those working in the field of
biochemistry and molecular biology.
Gerald D. Fasman
Editor
January 1976
THE EDITOR
NOMENCLATURE
Biochemical Nomenclature .......................................................................................................................3
Nomenclature of Labeled C o m p o u n d s.....................................................................................................16
The Citation of Bibliographic References in Biochemical J o u r n a l s ................................................ 17
IUPAC Tentative Rules for the Nomenclature of Organic Chemistry Section E.
Fundamental S tereochem istry............................................................................................................ 21
A One-letter Notation for Amino Acid S e q u e n c e s .................................................................................59
Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains . . 63
Rules for Naming Synthetic Modification of Natural P e p t i d e s ........................................................ 79
The Nomenclature of Multiple Forms of E n z y m e s ............................................................................ 84
Nomenclature of Iron-sulfur proteins .................................................................................................... 89
Enzyme Nomenclature ............................................................................................................................ 91
Recommendations for the Nomenclature of Human Immunoglobulins.............................................. 173
The Nomenclature of Peptide H o rm o n e s...............................................................................................175
Nomenclature for Human Immunoglobulins ...................................................................................... 179
Notation for Human Immunoglobulin Subclasses .............................................................................. 184
Notation for Genetic Factors of Human Immunoglobulins ............................................................ 186
An Extension of the Nomenclature for Im m unoglobulins............................ ....................................191
Tentative Nomenclature for Blood Coagulation Factors ...................................................................195
PROTEINS
Cyanogen Bromide Cleavage of Peptides and Proteins .................................................................... 199
Cyanogen Bromide Cleavage of Peptides and Proteins —Collagen ................................................ 202
Specificity of Reagents Commonly Used to Chemically Modify Proteins .................................... 203
Hydrolysis of Proteins .......................................................................................................................... 206
Acid Hydrolysis of Proteins .................................................................................................................. 208
Index to Physical-chemical Data of Proteins .................................................................................... 222
Molecular Parameters of Purified Human Plasma P ro te in s ............................................................ . 242
The Proteins of Blood Coagulation ........................................................................................ ... 254
G ly c o p ro te in s.......................................................................................................................................... 257
Metalloproteins and Metalloenzymes .................................................................................................. 276
Characterization of H is to n e s ................................................................................................ 293
Table of Histone Sequences .................................................................................................................. 295
Enzymes Found in Normal Human Urine .......................................................................................... 301
Properties of U ro k in a s e .......................................................................................................................... 302
Amino Acid Composition of Urokinase .............................................................................................. 302
Carbohydrate and Protein Composition of T-H Glycoprotein .......................................................... 303
Amino Acid Composition of T-H G ly c o p ro te in ................................................................ 303
Amino Acid Composition of Human Retinol-binding Protein .......................................................... 303
Retinol-binding P r o t e i n .......................................................................................................................... 304
Tamm-Horsfall M u c o p ro te in .................................................................................................................. 304
02 M icroglobulin....................................................................................................................................305
Amino Acid Sequence of β2 M icroglobulin.......................................................................................... 305
Molecular Parameters of the Contractile Proteins .............................................................................. 306
Proteins in Nonmuscle C e l l s .................................................................................................................. 307
Subunit Constitution of P r o t e i n s .......................................................................................................... 325
Refractive Index Increments of P r o t e i n s .............................................................................................. 372
Molar Absorptivity and A Values for Proteins at Selected Wavelengths of the
Ultraviolet and Visible R e g io n .................................................... 383
Properties of Purified Lectins .................... ........................................................................................546
Ligand Binding to Plasma A lb u m in .................................................................................... . . . . 554
Introduction to Proteinase I n h i b i t o r s ................ ................................................................................583
Specificities and Some Properties of Plant Proteinase Inhibitors .....................................................586
Amino Acid Composition of Plant Proteinase Inhibitors ................................................................ 605
Amino Acid Sequence of Plant Proteinase In h ib ito rs .................................... ................................... 611
Specificities and Some Properties of Animal Proteinase Inhibitors ................................................ 618
Amino Acid Composition of Animal Proteinase Inhibitors ............................................................ 649
Amino Acid Sequences of Animal Proteinase Inhibitors ................................................ ... 656
Specificities and Some Properties of Microbial Proteinase Inhibitors ............................................ 661
Amino Acid Composition of Microbial Proteinase Inhibitors ........................................................ 664
Amino Acid Sequence of a Microbial Proteinase Inhibitor ............................................................ 665
Carbohydrate Composition of Selected Proteinase Inhibitors ........................................................ 666
Endo-7 -glutamin: e-Lysine Transferases, Enzymes which Cross-link P r o t e i n s .................................. 669
Connective Tissue Polysaccharides (Glycosaminoglycans, Mucopolysaccharides) .......................... 686
Protein pK Values .................................................................................................................................. 689
Enzymatic Activities of Subcellular F ra c tio n s...................................................................................... 697
Intrinsic Viscosity of Proteins in Native and Denatured S t a t e s ........................................................ 721
Methods for the Immobilization of E n z y m e s ...................................................................................... 722
Dimensions of the Amino Acid Group, Amino Acid Side Chains, and the Peptide Linkage . . . 742
Protein Structures .................................................................................................................................. 760
INDEX .............................................................................................................................................................7 6 9
Nomenclature
3
BIOCHEMICAL NOMENCLATURE
IV. Physiochemical Quantities and Units (IUPAC)a J. Am. Chem. Soc., 82, 5517 (1960) [Revised 1970: Pure Appl.
Chem., 21,1 (1970)]
V. Nomenclature of Inorganic Chemistry (IUPAC) J. Am. Chem. Soc., 82, 5523a [Revised 1971: Pure Appl. Chem.,
28, No. 1 (1971)]a
VI. Drugs and Related Compounds or Preparations
1. U.S. Adopted Names (USAN) No. 10 (1972) and Supplement [U.S. Pharmacopeial Convention, Inc., 12601
Twinbrook Parkway, Rockville, Md.]
2. International Nonproprietary Names (INN) [WHO, Geneva]
CBN RECOMMENDATIONS APPEAR IN THE FOLLOWING PLACESa
Arch. Biochim.
Biochem. Biophys. Eur. J. J. Biol. Pure Appl. Biochimie Molek. Z Phys.
Biophys. Biochem. J. Biochemistry Acta Biochem. Chem. ChemA (Bull. Soc.)c BiolA Chem.e
II,I(Revised) 128,269* 112,17* 165,1* 5,1* 243,5809* N 37,285 (R) 51,3* 350,523*
II, 2f 136,13 113,5 8,2227 164,453 10,1 31,285(R) 51,819 351,663
Amendments 147,4 127,613 10,4994 248,387 25,2
11,3 125,673 10,3983 244,223 21,455 247,613
11,4 127,741 10,4827 286,217 25,397 247,2633
}
Amendments 151,507 14,1803
ABBREVIATIONS
Abbreviations are distinguished from symbols as follows (taken from Reference Al):
[Abbreviations are thus distinguished from symbols in that they (a) are for
semi-systematic or trivial names, (b) are brief rather than systematic, (c) are usually
formed from three or four capital letters, and (d) are not used —as are symbols —as units
of larger structures. ATP, FAD, etc., are abbreviations. Gly, Ser, Ado, Glc, etc., are
symbols (as are Na, K, Ca, 0 , S, etc.); they are sometimes useful as abbreviations in
figures, tables, etc., where space is limited, but are usually not permitted in text. The use
of abbreviations is permitted when necessary but is never required.]
2. Coenzymes, vitamins
3. Miscellaneous
4. Nucleic Acids
SYMBOLS
Symbols are distinguished from abbreviations in that they are designed to represent
specific parts of larger molecules, just as the symbols for the elements are used in
depicting molecules, and are thus rather systematic in construction and use. Symbols are
not designed to be used as abbreviations and should not be used as such in text, but they
may often serve this purpose when space is limited (as in a figure or table). Symbols are
always written with a single capital letter, all subsequent letters being lower-case (e.g., Ca,
Cl, Me, Ac, Gly, Rib, Ado), regardless of their position in a sequence, a sentence, or as a
superscript or subscript.
Some abbreviations expressed in symbols (see also Section II F below), as examples of
the use of symbols:
Dimethylsulfoxide Me, SO a
Tetranitromethane (N 02)4C b
Guanidine hydrochloride Gdn · H Q c
Guanidinium chloride GdmCl
Cetyltrimethylammonium bromide CtMe3 NBr d
Ethyl methanesulfonate MeS03Et
Methylnitronitrosoguanidine MeN20 3Gdn
-nitrosourea -Nur e
-nitrosamine -Nam *
-fluorene -Fin
Aminofluorene NH2Fln
Acetylaminofluorene AcNHFlnS
Acetoxyacetylaminofluorene Ac(AcO)NFln
iV-Acetylneuraminic acid AcNeu b
aReplaces DMSO.
b Replaces TNM.
cReplaces Gu, Gd, and G.
dReplaces CTAB (similarly for other ammonium
compounds).
eReplaces NU.
^Replaces NA.
^Replaces AAF.
hNot NANA.
8 Handbook o f Biochemistry and Molecular Biology
-P 03 H2 (or its 10ns) -P(or P-) (“p ” in Nucleic Acids; see IV)
-P02 H-(or its ion) -/’-(hyphen in Nucleic Acids; see IV)
-P02 H-PO3 H2 (or ions) -P-P or -PP or PP- (cf. PPj in Abbreviations)
Examples :a
aNote that symbols are hyphenated even where names are not.
b Recommended by OBN.
Symbol Symbol
Name Symbol
0-Alanine 0Ala
Alloisoleucine alle
2- Aminoadipic acid Aad
3- Aminoadipic acid 0Aad
2-Aminobutyric acid Abu
6-Aminocaproic acid3 eAhx a
2- Aminopimelic acid Apm
2,4-Diaminobutyric acid A2bu b
2,2'-Diaminopimelic A2p m b
2,3-Diaminopropionic acid A2pr b
A-Ethylglycine, etc. EtGly, etc.
Hydroxylysine Hyl
tf//o-Hydroxylysine aUyl
3- Hvdroxyproline 3H ypc
4- Hydroxyproline 4Hypc
jV-Methylglycine (sarcosine) MeGly or Sar
A-Methylisoleucine Melle
Af-Methylvaline, etc. MeVal, etc.
Norleucine Nle
Norvaline Nva
Ornithine Orn
Groups substituted for hydrogen or for hydroxyl may be indicated either by their
structural formulae, or by symbols, or by combinations of both, e.g.,
OMe Me
I I1
4-Methyl aspartate Asp or Asp or Asp(OMe) O-Methyltyrosinf Tyr or Tyr or Tyr (Me)
OMe lile
Ac Et
I1 I1
A^-Acetyllysine Lyks or Lys or Lys(Ac) 5-Ethylcyteine Cys or Cys or Cys( Lt)
1
Ac Lt
P
I1 Me
I
r 1
O-Phosphoserine Ser or Ser or Ser( ) yV-Methylhistidine* (see 3.3) His or His or His(rMe)
P (/c/cmethylhistidine) T(lle
similarly \'or N " substitution (prosmethylhistidine)
jV-Glycylsarcosine Gly - Gly or Gly-(Me-)Gly or Gly-Sar
~ rI
Me
Ac
1 A c \
W-Glycyl-A'-acetylglycine Gly ___l _ Gly or Gly-(Ac-)Gly or ^ >Gly
Gly G \y ^
Gly
y , iV-Digl ycy1gl ycine Gly T Gly or Gly2 > Gly or ^ >Gly
G ly /^
*The prolonged and well-entrenched ambiguity in the nomenclature of the N -1 being the
biochemist’s N -3 and vice versa) led to a new trivial system for designating these substances:
The imidazole N nearer the alanine residue is designated pros (symbol it ) and the one farther
tele (symbol r), to give the following names and symbols: prosmethylhistidine or
7r-methylhistidine, His(wMe); te/emethylhistidine or r-methylhistidine, His(rMe).
Glyeylglycine Gly-Gly
Λ'-α-Glutamylglycine Glu-Gly J ^ | I
yV-7 -Glutamylglycine Glu or Glu or Glu ·---- Gly
I-------Gly
Lfy
i.o
iv T
!_
_I
Not Glu or Glu CysGly
1
Cys-Gly I
I----------- 1 I
Λ ’ -α-Glutamyllysine G lu------1 or Glu-----* I— ' Lys or Glu-elys
Lys I---------- 1
11
1. Homodetic: Gramicidin S
cyc/o-Val-Orn-Leu-DPhe-Pro-Val-Orn-Leu-DPhe-Pro
Val-Orn-Leu-DPhe-Pro-Val-Orn-Leu-DPhe-Pro
2. Heterodetic:
Oxytocin Cys-Tyr-Ile-Asn-GIn-Cys-Pro-Leu-Gly-NLL
I________________ i
I I
Thr-Gly-Gly-Gly—I or H Thr-Gly-Gly-Gly—j
aPreferred.
bNot BOC or rBOC.
cThe use of D for di and T for tri (or tetra) is discouraged. Recognized symbols with numerical subscripts are
recommended.
dfMet is approved for formylmethionine.
eMalNEt is recommended for Af-ethylmaleimide (not NEM).
fMtc and Ptc have been used to denote methyl- and phenylthiohydantoins (e.g., Ptc-Leu). Since this incorrectly
implies the substitution of an amino acid by a “phenyl (or methyl) thiohydantoyl” group, the correct
representation, ,CS-Leu7NPh oriPhNCS-Leu-t or, in text, Leu>PhNCS, is recommended.
gNot THP or Thp (see Footnote c).
hNot TFA (see Footnote c).
‘Or trityl.