In
molecular biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
, ultrasensitivity describes an output response that is more sensitive to stimulus change than the hyperbolic
Michaelis-Menten response. Ultrasensitivity is one of the
biochemical switches in the cell cycle A series of biochemical switches control transitions between and within the various phases of the cell cycle. The cell cycle is a series of complex, ordered, sequential events that control how a single cell divides into two cells, and involves sever ...
and has been implicated in a number of important cellular events, including exiting G2 cell cycle arrests in ''
Xenopus laevis
The African clawed frog (''Xenopus laevis'', also known as the xenopus, African clawed toad, African claw-toed frog or the ''platanna'') is a species of African aquatic frog of the family Pipidae. Its name is derived from the three short claws ...
'' oocytes, a stage to which the cell or organism would not want to return.
Ultrasensitivity is a cellular system which triggers entry into a different cellular state. Ultrasensitivity gives a small response to first input signal, but an increase in the input signal produces higher and higher levels of output. This acts to filter out noise, as small stimuli and threshold concentrations of the stimulus (input signal) is necessary for the trigger which allows the system to get activated quickly. Ultrasensitive responses are represented by sigmoidal graphs, which resemble
cooperativity
Cooperativity is a phenomenon displayed by systems involving identical or near-identical elements, which act dependently of each other, relative to a hypothetical standard non-interacting system in which the individual elements are acting indepen ...
. The quantification of ultrasensitivity is often performed approximately by the
Hill equation:
:
Where Hill's coefficient (n) may represent quantitative measure of ultrasensitive response.
Historical development
Zero-order ultrasensitivity was first described by Albert Goldbeter and
Daniel Koshland, Jr in 1981 in a paper in the
Proceedings of the National Academy of Sciences
''Proceedings of the National Academy of Sciences of the United States of America'' (often abbreviated ''PNAS'' or ''PNAS USA'') is a peer-reviewed multidisciplinary scientific journal. It is the official journal of the National Academy of Sci ...
.
They showed using
mathematical modeling
A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, b ...
that modification of enzymes operating outside of first order kinetics required only small changes in the concentration of the effector to produce larger changes in the amount of modified protein. This amplification provided added sensitivity in biological control, and implicated the importance of this in many biological systems.
Many biological processes are binary (ON-OFF), such as cell fate decisions, metabolic states, and signaling pathways. Ultrasensitivity is a switch that helps decision-making in such biological processes. For example, in apoptotic process, a model showed that a positive feedback of inhibition of caspase 3 (Casp3) and Casp9 by inhibitors of apoptosis can bring about ultrasensitivity (bistability). This positive feedback cooperates with Casp3-mediated feedback cleavage of Casp9 to generate irreversibility in caspase activation (switch ON), which leads to cell apoptosis. Another model also showed similar but different positive feedback controls in Bcl-2 family proteins in apoptotic process.
Recently, Jeyeraman et al. have proposed that the phenomenon of ultrasensitivity may be further subdivided into three sub-regimes, separated by sharp stimulus threshold values: OFF, OFF-ON-OFF, and ON. Based on their model, they proposed that this sub-regime of ultrasensitivity, OFF-ON-OFF, is like a switch-like adaption which can be accomplished by coupling N phosphorylation–dephosphorylation cycles unidirectionally, without any explicit feedback loops.
Other recent work has emphasized that not only is the topology of networks important for creating ultrasensitivity responses, but that their composition (enzymes vs. transcription factors) strongly affects whether they will exhibit robust ultrasensitivity. Mathematical modeling suggests for a broad array of network topologies that a combination of enzymes and transcription factors tends to provide more robust ultrasensitivity than that seen in networks composed entirely of transcription factors or composed entirely of enzymes.
Mechanisms
Ultrasensitivity can be achieved through several mechanisms:
#Multistep mechanisms (examples: cooperativity)
and multisite phosphorylation
#Buffering mechanisms (examples: decoy phosphorylation sites)
or stoichiometric inhibitors
#Changes in localisation (such as translocation across the nuclear envelope)
#Saturation mechanisms (also known as zero-order ultrasensitivity)
#Positive feedback
#Allovalency
#Non-Zero-Order Ultrasensitivity in Membrane Proteins
#Dissipative Allostery
Multistep Mechanisms
Multipstep ultrasensitivity occurs when a single effector acts on several steps in a cascade.
Successive cascade signals can result in higher levels of noise being introduced into the signal that can interfere with the final output. This is especially relevant for large cascades, such as the flagellar regulatory system in which the master regulator signal is transmitted through multiple intermediate regulators before activating transcription. Cascade ultrasensitivity can reduce noise and therefore require less input for activation.
Additionally, multiple phosphorylation events are an example of ultrasensitivity. Recent modeling has shown that multiple phosphorylation sites on membrane proteins could serve to locally saturate enzyme activity. Proteins at the membrane are greatly reduced in mobility compared to those in the cytoplasm, this means that a membrane tethered enzyme acting upon a membrane protein will take longer to diffuse away. With the addition of multiple phosphorylation sites upon the membrane substrate, the enzyme can - by a combination of increased local concentration of enzyme and increased substrates - quickly reach saturation.
Buffering Mechanisms
Buffering Mechanisms such as molecular
titration
Titration (also known as titrimetry and volumetric analysis) is a common laboratory method of quantitative chemical analysis to determine the concentration of an identified analyte (a substance to be analyzed). A reagent, termed the ''titrant'' ...
can generate ultrasensitivity. ''
In vitro
''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology an ...
'', this can be observed for the simple mechanism:
:
A + B <=> AB
Where the monomeric form of A is active and it can be inactivated by binding B to form the heterodimer AB. When the concentration of
( =
+
B is much greater than the
, this system exhibits a threshold determined by the concentration of
. At concentrations of
( =
+
B, lower than
, B acts as a buffer to free A and nearly all A will be found as AB. However, at the equivalence point, when
≈
,
can no longer buffer the increase in
, so a small increase in
causes a large increase in A.
The strength of the ultrasensitivity of
to changes in
is determined by
/
.
Ultrasensitivity occurs when this ratio is greater than one and is increased as the ratio increases. Above the equivalence point,
and A are again linearly related.
''
In vivo
Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and ...
'', the synthesis of A and B as well as the degradation of all three components complicates generation of ultrasensitivity. If the synthesis rates of A and B are equal this system still exhibits ultrasensitivity at the equivalence point.
One example of a buffering mechanism is protein sequestration, which is a common mechanism found in signalling and regulatory networks. In 2009, Buchler and Cross constructed a synthetic genetic network that was regulated by protein sequestration of a transcriptional activator by a dominant-negative inhibitor. They showed that this system results in a flexibile ultrasensitive response in gene expression. It is flexible in that the degree of ultrasensitivity can be altered by changing expression levels of the dominant-negative inhibitor. Figure 1 in their article illustrates how an active transcription factor can be sequestered by an inhibitor into the inactive complex AB that is unable to bind DNA. This type of mechanism results in an "all-or-none" response, or ultransensitivy, when the concentration of the regulatory protein increases to the point of depleting the inhibitor. Robust buffering against a response exists below this concentration threshold, and when it is reached any small increase in input is amplified into a large change in output.
Changes in localization
Translocation
Signal transduction is regulated in various ways and one of the ways is translocation. Regulated translocation generates ultrasensitive response in mainly three ways:
#Regulated translocation increases the local concentration of the signaling protein. When concentration of the signaling protein is high enough to partially saturate the enzyme that inactivates it, ultrasensitive response is generated.
#Translocation of multiple components of the signaling cascade, where stimulus (input signal) causes translocation of both signaling protein and its activator in the same subcellular compartment and thereby generates ultrasensitive response which increases speed and accuracy of the signal.
#Translocation to the compartment which contains stoichiometric inhibitors.
Translocation is one way of regulating signal transduction, and it can generate ultrasensitive switch-like responses or multistep-feedback loop mechanisms. A switch-like response will occur if translocation raises the local concentration of a signaling protein. For example,
epidermal growth factor
Epidermal growth factor (EGF) is a protein that stimulates cell growth and differentiation by binding to its receptor, EGFR. Human EGF is 6-k Da and has 53 amino acid residues and three intramolecular disulfide bonds.
EGF was originally descr ...
(EGF) receptors can be internalized through clathrin-independent endocytosis (CIE) and/or clathrin-dependent endocytosis (CDE) in ligand concentration-dependent manner. The distribution of receptors into the two pathways was shown to be EGF concentration-dependent. In the presence of low concentrations of EGF, the receptor was exclusively internalized via CDE, whereas at high concentrations, receptors were equally distributed between CDE and CIE.
Saturation mechanisms (Zero-order ultrasensitivity)
Zero-order ultrasensitivity takes place under saturating conditions.
For example, consider an enzymatic step with a kinase, phosphatase, and substrate. Steady state levels of the phosphorylated substrate have an ultrasensitive response when there is enough substrate to saturate all available kinases and phosphatases.
Under these conditions, small changes in the ratio of kinase to phosphatase activity can dramatically change the number of phosphorylated substrate (For a graph illustrating this behavior, see
). This enhancement in sensitivity of steady state phosphorylated substrate to Km, or the ratio of kinase to phosphatase activity, is termed zero-order to distinguish it from the first order behavior described by Michaelis-Menten dynamics, wherein the steady state concentration responds in a more gradual fashion than the switch-like behavior exhibited in ultrasensitivity.
Using the notation from Goldbeter & Koshland,
let W be a certain substrate protein and let W' be a covalently modified version of W. The conversion of W to W' is catalyzed by some enzyme
E1 and the reverse conversion of W' to W is catalyzed by a second enzyme
E2 according to following equations:
:
The concentrations of all necessary components (such as ATP) are assumed to be constant and represented in the kinetic constants.
Using the chemical equations above, the reaction
rate equation
In chemistry, the rate law or rate equation for a reaction is an equation that links the initial or forward reaction rate with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reacti ...
s for each component are:
: