Protein Structure:
The properties of a protein are determined by its covalently-linked amino
acid sequence, otherwise known as its primary structure. Depending on
the nature and arrangement of the amino acids present, different parts of
the molecule form secondary structure such as the alpa helices or beta
sheets shown below. Further folding and reorganization within the
molecule results in higher order or tertiary structure.
Secondary
and
tertiary
structure
represents
the
most
thermodynamically stable conformation (or shape) for the molecule in
solution, and results from non-covalent interactions (ionic bonds,
hydrogen bonds, hydrophobic interactions) between the various amino
acid side-chains within the molecule and with the water molecules
surrounding it. Different regions of the protein, often with distinct
functions, may form structuraly distinct domains. Structurally related
domains are found in different proteins which perform similar functions.
The exposed surface of the protein may also be involved in interactions
with other molecules, including proteins. Protein-protein interactions, for
example between sub-units of enzyme complexes or polymeric structural
proteins, results in the highest level of organization, or quaternary
structure.
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Protein-protein interactions:
Protein molecules in solution are in constant motion and frequently collide with one
another. Molecules whose shapes closely match can potentially form more stable
associations, mediated by non-covalent bonds which can only form at close range. In
water these non-covalent bonds are at least an order of magnitude weaker than the
covalent peptide bonds which hold amino acids together, and are easily disrupted by
other solutes or heat. Many of these bonds must form in order to overcome the forces
(exerted by thermal motions) which tend to seperate the molecules involved.
In the example below protein-A has a surface which closely matches a surface on
protein-D, allowing the formation of a greater number of non-covalent bonds than
between protein-A and protein-B. Protein-A does not stable associate with protein-B
or protein-C.
Many enzymes, such as the cyclin dependant kinase cdk2 / cyclinA , are composed of
two or more sub-units which stably associate in this way.
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Non-covalent bonds:
The non-covalent interactions involved in organising the structure of protein
molecules fall chiefly into four categories:
o
o
o
o
ionic bonds
hydrogen bonds
van der Waals forces
hydrophobic interactions
ionic bonds
hydrogen bonds
Ionic bonds involve interactions between
the oppositely charged groups of a molecule
- for example the positively charged amino
side chains of lysine and argenine, and the
negatively charged carboxyl groups of
glutamic and aspartic acid.
Hydrogen bonds are formed by "sharing" of
a hydrogen atom between to two
electronegative atoms such as N and O.
van der Waals attractions
hydrophobic interactions
van der Waals forces are very weak
attractions (or repulsions) which occur
between atoms at close range.
The hydrophobic amino acids of a protein
will tend to cluster together, not as a result
of attraction, but as a result of their
repulsion by the hydrogen bonded water
network in which the protein is dissolved.
Hydrophobic regions of a protein will
preferentially locate away from the surface
of the molecule.
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Post-translational regulation:
Post-translational modification of a protein can have a profound effect on its structure,
and consequently affect its activity or function. Phosphorylation (the covalent
attachment of a phosphate group to either serine, threonine or tyrosine) is the most
common modification, and is catalysed by enzymes known as protein kinases. The
human genome is thought to encode thousands of different protein kinases, which
function to regulate virtually all aspects of a cells behaviour, including chromatin
structure (histone phosphorylation), gene expression (transcription factor activity),
cell proliferation (growth factor receptors, cyclin dependent kinases, MAP kinases),
metabolic activities, etc.
The additional negative charge of a phosphate group (or groups) alters the balance of
non-covalent interactions which determine secondary, tertiary or even quaternary
structure. The resulting change in conformation of the protein may cause (i) activation
or inactivation of a biological function, or (ii) association or dissociation of sub-units.
In the example below, phosphorylation of a serine residue in an inactive enzyme
molecule results in a conformational change which exposes the catalytic site and
acivates the enzyme.
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Examples:
The transcription factor AP1 is a heterodimer formed from the
proto-oncogenes c-fos (shown in red) and c-jun (shown in blue).
In order to bind to DNA, and activate transcription, the two
subunits associate by virtue of hydrophobic interactions,
involving a structural motif known as a leucine zipper repeated leucine residues in alpha-helical regions of each
protein.
The protein kinase cdk2 / cyclin A is a heterodimer formed
from a catalytic subunit (shown in blue) and a regulatory subunit (shown in green).
Catalytic activation of cdk2 is dependent on conformational
changes which expose the substrate binding cleft, and involves
(i) phosphorylation and (ii) cyclinA association.
The PDGF receptor tyrosine kinase becomes phosphorylated on
tyrosine residues when activated by ligand (PDGF) binding.
The phospho-tyrosines (shown in red) are located in specific
regions of the PDGF receptor (shown in green).
Receptor phosphotyosines serve to recruit other molecules such
as phospholipase C which possess SH2 domains (shown in
blue). These effector molecules function to regulate cell activity
in response to receptor activation.
A collection 3D molecular models is available which includes these and other
examples proteins where biological activity depends on protein-protein interactions
and / or changes in conformation resulting from phosphorylation and cofactor
binding.
3. Protein Structure and Function
Proteins are the most versatile macromolecules in living systems and serve crucial
functions in essentially all biological processes. They function as catalysts, they
transport and store other molecules such as oxygen, they provide mechanical support
and immune protection, they generate movement, they transmit nerve impulses, and
they control growth and differentiation. Indeed, much of this text will focus on
understanding what proteins do and how they perform these functions.
Several key properties enable proteins to participate in such a wide range of functions.
1. Proteins are linear polymers built of monomer units called amino acids. The
construction of a vast array of macromolecules from a limited number of monomer
building blocks is a recurring theme in biochemistry. Does protein function depend on
the linear sequence of amino acids? The function of a protein is directly dependent on
its threedimensional structure (Figure 3.1). Remarkably, proteins spontaneously fold
up into three-dimensional structures that are determined by the sequence of amino
acids in the protein polymer. Thus, proteins are the embodiment of the transition from
the one-dimensional world of sequences to the three-dimensional world of molecules
capable of diverse activities.
2. Proteins contain a wide range of functional groups. These functional groups
include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of
basic groups. When combined in various sequences, this array of functional groups
accounts for the broad spectrum of protein function. For instance, the chemical
reactivity associated with these groups is essential to the function of enzymes, the
proteins that catalyze specific chemical reactions in biological systems (see Chapters
8 10).
3. Proteins can interact with one another and with other biological macromolecules
to form complex assemblies. The proteins within these assemblies can act
synergistically to generate capabilities not afforded by the individual component
proteins (Figure 3.2). These assemblies include macro-molecular machines that carry
out the accurate replication of DNA, the transmission of signals within cells, and
many other essential processes.
4. Some proteins are quite rigid, whereas others display limited flexibility. Rigid units
can function as structural elements in the cytoskeleton (the internal scaffolding within
cells) or in connective tissue. Parts of proteins with limited flexibility may act as
hinges, springs, and levers that are crucial to protein function, to the assembly of
proteins with one another and with other molecules into complex units, and to the
transmission of information within and between cells (Figure 3.3).