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CHEMISTRY OF
METALLOPROTEINS
WILEY SERIES IN PROTEIN AND PEPTIDE SCIENCE
Flexible Viruses: Structural Disorder in Viral Proteins • Vladimir Uversky and Sonia
Longhi
JOSEPH J. STEPHANOS
ANTHONY W. ADDISON
Copyright 2014 by John Wiley & Sons, Inc. All rights reserved
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form
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Library of Congress Cataloging-in-Publication Data:
Stephanos, Joseph J., author.
Chemistry of metalloproteins: problems and solutions in bioinorganic chemistry/by Joseph J.
Stephanos, Anthony W. Addison.
p.; cm. – (Wiley series in protein and peptide science)
Includes bibliographical references and index.
ISBN 978-1-118-47044-2 (paperback)
I. Addison, A. W., author. II. Title. III. Series: Wiley series in protein and peptide science.
[DNLM: 1. Metalloproteins–chemistry–Examination Questions. QU 18.2]
QP551
5720.6076–dc23
2013041995
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
CONTENTS
Preface ix
1 Introduction 1
Proteins: Formation, Structures, and Metalloproteins, 4
References, 28
3 Nonredox Metalloenzymes 71
Carboxypeptidases, 75
Carbonic Anhydrase, 84
Alcohol Dehydrogenase, 88
References, 91
4 Copper Proteins 95
Introduction, 95
Electronic Spectra of Copper Ions, 96
ESR Spectra of Copper Ions, 105
Copper Proteins, 117
Plastocyanin, 119
Azurin and Stellacyanin, 127
Superoxide Dismutase, 131
v
vi CONTENTS
Hemocyanin, 135
Ascorbic Oxidase, 139
References, 142
7 Chlorophyll 407
References, 421
Index 423
PREFACE
This book is an attempt to reveal the chemical concepts that rule the biological action
of metalloproteins. The emphasis is on building up an understanding of basic ideas
and familiarization with basic techniques. Enough background information is pro-
vided to introduce the field from both chemical and biological areas. It is hoped that
the book may be of interest to workers in biological sciences, and so, primarily for this
purpose, a brief survey of relevant properties of transition metals is presented.
The book is intended for undergraduates and postgraduates taking courses in
coordination chemistry and students in biology and medicine. It should also be a value
to research workers who would like an introduction to this area of inorganic
chemistry. It is very suitable for self-study; the range covered is so extensive that
the book can serve as a student’s companion throughout his or her university career.
At the same time, teachers can turn to it for ideas and inspirations.
The book is divided into seven chapters and covers a full range of topics in
bioinorganic chemistry. It is well-illustrated and each chapter contains suggestions for
further reading, providing access to important review articles and papers of relevance.
A reference list is also included, so that the interested reader can readily consult the
literature cited in the text.
It is hoped that the present book will provide the basis for a more advanced study in
this field.
JOSEPH J. STEPHANOS
ANTHONY W. ADDISON
ix
1
INTRODUCTION
• A physiological deficiency appears when the element is removed from the diet.
• The deficiency is relieved by the addition of that element to the diet.
• A specific biological function is associated with the element.
1
2 INTRODUCTION
FIGURE 1-1 Distribution of elements essential for life (Cotton and Wilkinson, 1980).
INTRODUCTION 3
This section is designed to introduce the chemistry of proteins. The text broadly
includes where and how the proteins are formed, along with the structure and
formation of metalloproteins.
Following the introduction of organelles and their functions within the cell, the
discussion will be concerned with the general structure of deoxyribonucleic acid
(DNA) and how the nucleus maintains its control of cell growth, division, and
formation of [messenger, transfer, and ribosomal ribonucleic acid (mRNA, tRNA,
PROTEINS: FORMATION, STRUCTURES, AND METALLOPROTEINS 5
rRNA)]. This is followed by how mRNA and tRNA master the formation of
proteins within a cell. Then, primary, secondary, tertiary, and quaternary structures
of the formed proteins and the factors that control each of these structures are
discussed.
Specific points about the ligation of various metal ions to different amino acids
within the proteins are made, and the binding stabilities of various metal ions toward
different amino acids are arranged.
The general formulas, side chains, and corresponding names of the common
natural α-amino acids, the formation of the peptide chain from the amino acids, and
the physiological roles of proteins are described.
The chemistry of the prosthetic and cofactors is explored. Enough basic bio-
chemistry is presented to enable the student to understand the discussions that follow.
Structure of DNA
• The order in which they appear on the chain makes up the molecular message
(Fig. 1-4).
• The DNA molecule is also capable of duplicating itself and dividing.
8 INTRODUCTION
How does the nucleus maintain its control of cell growth and division?
• During ordinary cell division called mitosis, two new cells result from a single
parent.
• Each daughter has the same number of chromosomes as the parent.
• If DNA is the molecular stuff of the chromosome, it must be able to reproduce itself.
• The DNA double helix rewinds and separates into two single strands (Fig. 1-6).
• As the unwinding occurs, the single strands act as templates for synthesis of new
complementary strands.
• When the parent DNA double helix has completed its unwinding, two new
DNA double-stranded molecules are formed.
• The process by which new DNA is formed is called replication.
Protein Synthesis
• The order of the N bases on the DNA molecule determines the order of amino
acids in the protein molecule.
• While DNA is in the nucleus, the proteins are synthesized on ribosomes outside
the nucleus as follows:
FIGURE 1-6 DNA double helix rewinds and separates into two single strands.
PROTEINS: FORMATION, STRUCTURES, AND METALLOPROTEINS 11
As the DNA double helix unwinds, the N base segment becomes exposed.
The DNA molecule serves as template for the synthesis of mRNA molecule.
The synthesis of mRNA is analogous to the replication synthesis of DNA
(Fig. 1-7).
mRNA has structure similar to DNA but contains:
• Ribose instead of deoxyribose
• N-base uracil instead of thymine:
• After the tRNA has discharged its amino acid passenger, it moves out into the
cytoplasm, finds another amino acid, and returns to the ribosome surface.
Give the general formula, side chain, and corresponding name of the common
natural α -amino acids.
(continued )
14 INTRODUCTION
How can the peptide chain be formed from the amino acids?
Define: primary, secondary, tertiary, and quaternary structures. And what are
the factors that control each of these structures?
The groups of four gray-shaded atoms are coplanar. Free rotation occurs
about the bond connecting the carbon with the carbonyl and the nitrogen.
Therefore, the extended polypeptide chain is a semirigid structure with two-
thirds of the atoms of the backbone held in a fixed plane.
Examples of secondary structures:
(a) random coil
(b) α–helix (Fig. 1-9)
(c) β–pleated (Fig. 1-10), associated as (i) parallel and (ii) antiparallel
(d) reverse turns (Fig. 1-11)
(e) omega loops (Fig. 1-12)
Both reverse turns and omega loops appear at the outer surface of the
molecules.
• A Tertiary structure refers to the folding of the already secondary structured
amino acids to form a three-dimensional (3D) structure. The overall 3D
architecture of the polypeptide backbone:
Fibrous proteins: coils (Fig. 1-13).
Globular proteins: compact, ellipsoidal, spherical, until denatured. The
folded tertiary, globular, structure of myoglobins is imposed over the
helical secondary structure. Structures from X-ray diffraction are shown
in Fig. 1-14.
Synthetic polypeptides have random or simply repetitive structures.
PROTEINS: FORMATION, STRUCTURES, AND METALLOPROTEINS 17