Unit 3. Basic of Biopolymers (3) Control of Protein Function

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Transcript Unit 3. Basic of Biopolymers (3) Control of Protein Function

Spectroscopy of Biopolymers
Unit 3. Basic of Biopolymers (3)
Control of Protein Function
Major Mechanisms of Protein Regulation
• Controlled by localization of the gene product or
the species it interacts.
• Controlled by the covalent or noncovalent binding
of effector molecules.
• Controlled by the amount and lifetime of the
active protein.
Proteins can be targeted to
specific compartments and
Protein is only present in its active form in the specific
compartment where it is needed, or when bound in a
complex with other macromolecules that participate in its
Localization Specification
targeted to cellular compartments by signal sequences or by
attachment of a lipid tail that inserts into membranes.
directed to a complex of interacting proteins by a structural
interaction domain
Localization is a dynamic process and a given protein may
be targeted to different compartments at different stages of
the cell cycle
Interaction domain
A protein domain that recognizes another
protein, usually via a specific recognition motif.
Interaction domains The name of the particular example shown for
each family is given below each structure, along with the function and
specificity of the domain.
Control by pH & Redox environment
• Protein function is modulated by
the environment in which the
protein operates
• Changes in redox environment
can greatly affect protein
structure and function
• Changes in pH can drastically
alter protein structure and
Cathepsin D conformational
switching by pH
At neutral pH
Avtive siteis
blocked by the
At low pH
The active site
is opened by
reorientation of
the N-terminal
Protein activity can be regulated by
binding of an effector and by covalent
• Protein activity can also be controlled by the
binding of effector molecules, which often work
by inducing conformational changes that
produce inactive or active forms of the protein.
Effector Ligand
• Effector ligand: a ligand that induces a change
in the properties of a protein.
• Effectors may be as small as a proton or as
large as another macromolecule.
• Effectors may bind noncovalently or may modify
the covalent structure of the protein, reversibly
or irreversibly.
• Effectors that regulate activity by binding to the
active site usually take the form of inhibitors that
compete with the substrate for binding.
Competitive Binding and Cooperativity
• cooperative binding: interaction between two
sites on a protein such that the binding of a
ligand to the first one affects the properties of the
second one.
•positive cooperativity
the first ligand molecule to bind is bound weakly, but its
binding alters the conformation of the protein in such a
way that binding of the second and subsequent ligand
molecules is promoted.
•negative cooperativity
the first ligand binding weakens and thereby effectively
Cooperative Ligand Binding
1. Protein function can
be controlled by
effector ligands that
bind competitively to
ligand-binding or
active sites
2. Cooperative binding
by effector ligands
amplifies their effects
Effector Binding and Allostery
Effector molecules can cause conformational
changes at distant sites
allostery: the property of being able to exist in two
structural states of differing activity. The
equilibrium between these states is modulated by
ligand binding.
•allosteric activator: a ligand that binds to a protein and
induces a conformational change that increases the
protein’s activity.
•allosteric inhibitor: a ligand that binds to a protein and
induces a conformational change that decreases the
conformational change
activates aspartate
Iron binding regulates the repressor of the diphtheria toxin gene
Comparison of the structures of the aporepressor DtxR (red, left, PDB 1dpr)
and the ternary complex (right) of repressor (green), metal ion (Fe2+, orange)
and DNA (grey) (PDB 1fst). Iron binding induces a conformational change that
moves the recognition helices (X) in the DtxR dimer closer together, providing
an optimal fit between these helices and the major groove of DNA. In addition,
metal-ion binding changes the conformation of the amino terminus of the first
turn of the amino-terminal helix (N) of each monomer. Without this
conformational change, leucine 4 in this helix would clash with a phosphate
group of the DNA backbone. Thus, DtxR only binds to DNA when metal ion is
bound to the repressor.
Effector Binding
• Binding of effector molecules can be covalent
or can lead to covalent changes in a protein.
Examples :
• Phosphorylation on the hydroxyl group of the side
chains of serine, threonine or tyrosine residues
• side-chain methylation,
• covalent attachment of carbohydrates and lipids,
• amino-terminal acetylation and
• limited proteolytic cleavage, in which proteases cut
the polypeptide chain in one or more places.
Protein activity may be regulated by
protein quantity and lifetime
• The activity of a protein can also be regulated by
controlling its amount and lifetime in the cell.
• The amount of protein can be set by the level of
• At the level of the protein, quantities are
controlled by the lifetime of the molecule, which
is determined by its rate of degradation.
• there are several specific mechanisms for targeting
protein molecules to degradative machinery in the
cell, including covalent attachment of the small
protein ubiquitin.
Nobel Prize in Chemistry 2004
"for the discovery of ubiquitin-mediated protein degradation"
• Aaron Ciechanover
Technion – Israel Institute of Technology
• Avram Hershko
Technion – Israel Institute of Technology
• Irwin Rose
University of California Irvine
Pathway for degradation of
ubiquitinated proteins A
substrate protein with an exposed
lysine side chain near the amino
terminus is targeted by binding of a
multienzyme ubiquitinating
complex which recognizes the
amino-terminal amino acid of the
substrate. The complex attaches
polyubiquitin chains to the
substrate in an ATP-dependent
reaction. The polyubiquitinated
substrate is then targeted to the
proteasome, whose cap
recognizes the ubiquitin tag. After
the substrate is chopped up into
peptide fragments (which may then
be degraded further by other
The eukaryotic proteasome
Proteins targeted for destruction (green)
are fed into the multiprotein complex called
the proteasome. In prokaryotes, these
machines of destruction consist simply of a
tunnel-like enzymatic core; in eukaryotes
they have an additional cap (here shown in
purple) at either or both ends. The core is
formed by four stacked rings surrounding a
central channel that acts as a degradation
chamber. The caps recognize and bind to
proteins targeted by the cell for destruction.
On entry into the proteasome, proteins are
unfolded in a process that uses the energy
released by ATP hydrolysis and injected
into the central core, where they are
enzymatically degraded into small
fragments. http://doegenomestolife.org.
Ubiquitin and protein degradation
Ubiquitin Structure
complex of the vps23 uev with ubiquitin
A single protein may be subject to
many regulatory influences
Coordination and
integration of regulatory
signals is achieved largely
through signal
transduction networks that
set the balance of
activities and thereby the
balance of metabolism
and cell growth and
protein kinases that
control progression through the cell cycle
are regulated by a number of different