78
3 The Structural Variety and Metabolism of Proteins
acids can be bent by up to 30 0 ; j3-sheets can show
twisting, coiling, bending or bUlging. Because the
different secondary structures of a protein molecule are always tightly packed to a high density,
there is a limited number of possible basic conformations. According to the presence and
arrangement of a-helices and j3-sheets, at least
four classes of proteins or protein domains can be
distinguished: the a-type, the j3-type, the a/j3type in which a and 13 structures alternate, and
the a+j3-type in which both a and 13 structures
are present but mostly separated [33].
In many proteins, the spatial structure has an
internal periodicity, most clearly seen in the fibrillar proteins, the mechanical properties of which
are based on such a regular structure [245]. The
properties of the globular proteins are also determined by their spatial structure and the resulting
spatial arrangement of the amino acid sidechains. Because all the information for the chain
formation of a protein is in the amino acid
sequence, it should be possible to predict the spatial structure from the sequence. However, of the
many analytical procedures developed for this,
none is entirely reliable [68]. Such predictions are
particularly difficult for integrated membrane
proteins; so, for example, the transmembrane
domains are not always clearly delineated from
the parts of the polypeptide chain lying outside of
the membrane [123]. However, on the basis ofthe
known connections between amino acid sequence
and spatial structure, it is possible to presume
with some certainty similarities of spatial structure from sequence comparisons of related proteins. ,This is important for comparative biochemistry because the direct determination of spatial
structure, e.g. by X-ray analysis, is more difficult
and required much more effort than amino acid
sequence analysis, and has so far been achieved
with only about 400 proteins. It should also be
pointed out that such direct analyses provide only
the mean position of the atoms in the protein
crystal, whereas in native proteins the gross
movement of single atoms, side-chains and
domains occurs, as do folding and unfolding
movements; this dynamic situation is of great
importance for allosteric effects, membrane
transport, enzymatic catalysis, electron transport,
and the binding of large and small molecules
[175].
If extensive similarities between both physicochemical and biological properties are found in
the comparison of proteins of different origin,
then similarities of spatial structure can be presumed. Such conclusions are in any case justified
if enzymatically active hybrid molecules are created by combining enzyme subunits from different sources. Functional enzyme chimeras result
between, for example, rabbit aldolase and the
enzyme from Drosophila or Ascaris, the
glyceraldehyde-3-phosphate dehydrogenase of
rabbit and that of Ascaris yeast, and the triosephosphate isomerases of chicken and bacteria. In
all these cases, the amino acid sequences are so
different that the starting enzymes show no
immunological cross-reactivity. If the spatial
structure is sufficiently similar, even enzymes
with different substrate specificities may be
hybridized, for example, the creatinase of rabbit
with the arginine kinase of a holothurian.
3.1.5 Multiple Forms of Proteins
In the 1950s, an increasing number of results indicated that different enzyme species could be present in the same organism, and even in the same
cell, and have the same reaction and substrate
specificity. Markert and M!<111er in 1959 suggested
the name "isozyme" for such multiple enzyme
forms, although linguistically "isoenzyme" is to
be preferred. Multiple forms of non-enzymatic
proteins are termed isoforms. The separation and
identification of multiple proteins can be carried
out by electrophoresis, and also by chromatography, fractionated heat inactivation, etc. The great
biological and medicinal significance of this phenomenon has prompted many extensive reviews
of the subject [182, 195].
The use of the term isoenzyme was at first
independent of the nature of the molecular differences. However, in 1976 the nomenclature commission of the International Union of Biochemistry (IUB) recommended that this term be
applied only when genetic differences are apparent, i.e. for groups 1-3 in their list of multiple
enzyme forms (Table 3.2). It is regrettable that
the same term is now applied both for the products of different loci (groups 1 and 2) and for
products of different alleles of the same locus
(group 3). For allelic variants, Prakash, Lewontin
and Hubby suggested in 1959 the term "allozyme", which would also be better as "alleloenzyme". The allelic polymorphism of the nucleic
acids and the proteins is of great importance for
the theory of molecular evolution and will be
extensively discussed in this connection.
Isoenzymes of group 1 are distinguished only
arbitrarily from other enzymes of similar or overlapping specificity that count as separate enzyme
3 The Structural Variety and Metabolism of Proteins
acids can be bent by up to 30 0 ; j3-sheets can show
twisting, coiling, bending or bUlging. Because the
different secondary structures of a protein molecule are always tightly packed to a high density,
there is a limited number of possible basic conformations. According to the presence and
arrangement of a-helices and j3-sheets, at least
four classes of proteins or protein domains can be
distinguished: the a-type, the j3-type, the a/j3type in which a and 13 structures alternate, and
the a+j3-type in which both a and 13 structures
are present but mostly separated [33].
In many proteins, the spatial structure has an
internal periodicity, most clearly seen in the fibrillar proteins, the mechanical properties of which
are based on such a regular structure [245]. The
properties of the globular proteins are also determined by their spatial structure and the resulting
spatial arrangement of the amino acid sidechains. Because all the information for the chain
formation of a protein is in the amino acid
sequence, it should be possible to predict the spatial structure from the sequence. However, of the
many analytical procedures developed for this,
none is entirely reliable [68]. Such predictions are
particularly difficult for integrated membrane
proteins; so, for example, the transmembrane
domains are not always clearly delineated from
the parts of the polypeptide chain lying outside of
the membrane [123]. However, on the basis ofthe
known connections between amino acid sequence
and spatial structure, it is possible to presume
with some certainty similarities of spatial structure from sequence comparisons of related proteins. ,This is important for comparative biochemistry because the direct determination of spatial
structure, e.g. by X-ray analysis, is more difficult
and required much more effort than amino acid
sequence analysis, and has so far been achieved
with only about 400 proteins. It should also be
pointed out that such direct analyses provide only
the mean position of the atoms in the protein
crystal, whereas in native proteins the gross
movement of single atoms, side-chains and
domains occurs, as do folding and unfolding
movements; this dynamic situation is of great
importance for allosteric effects, membrane
transport, enzymatic catalysis, electron transport,
and the binding of large and small molecules
[175].
If extensive similarities between both physicochemical and biological properties are found in
the comparison of proteins of different origin,
then similarities of spatial structure can be presumed. Such conclusions are in any case justified
if enzymatically active hybrid molecules are created by combining enzyme subunits from different sources. Functional enzyme chimeras result
between, for example, rabbit aldolase and the
enzyme from Drosophila or Ascaris, the
glyceraldehyde-3-phosphate dehydrogenase of
rabbit and that of Ascaris yeast, and the triosephosphate isomerases of chicken and bacteria. In
all these cases, the amino acid sequences are so
different that the starting enzymes show no
immunological cross-reactivity. If the spatial
structure is sufficiently similar, even enzymes
with different substrate specificities may be
hybridized, for example, the creatinase of rabbit
with the arginine kinase of a holothurian.
3.1.5 Multiple Forms of Proteins
In the 1950s, an increasing number of results indicated that different enzyme species could be present in the same organism, and even in the same
cell, and have the same reaction and substrate
specificity. Markert and M!<111er in 1959 suggested
the name "isozyme" for such multiple enzyme
forms, although linguistically "isoenzyme" is to
be preferred. Multiple forms of non-enzymatic
proteins are termed isoforms. The separation and
identification of multiple proteins can be carried
out by electrophoresis, and also by chromatography, fractionated heat inactivation, etc. The great
biological and medicinal significance of this phenomenon has prompted many extensive reviews
of the subject [182, 195].
The use of the term isoenzyme was at first
independent of the nature of the molecular differences. However, in 1976 the nomenclature commission of the International Union of Biochemistry (IUB) recommended that this term be
applied only when genetic differences are apparent, i.e. for groups 1-3 in their list of multiple
enzyme forms (Table 3.2). It is regrettable that
the same term is now applied both for the products of different loci (groups 1 and 2) and for
products of different alleles of the same locus
(group 3). For allelic variants, Prakash, Lewontin
and Hubby suggested in 1959 the term "allozyme", which would also be better as "alleloenzyme". The allelic polymorphism of the nucleic
acids and the proteins is of great importance for
the theory of molecular evolution and will be
extensively discussed in this connection.
Isoenzymes of group 1 are distinguished only
arbitrarily from other enzymes of similar or overlapping specificity that count as separate enzyme