Instant insight: Sorting perturbed proteins

Ruth Nussinov of the National Cancer Institute at Frederick, US, and colleagues put their case for a more organised way of looking at protein allostery

Allostery is a universal phenomenon: all dynamic proteins are potentially allosteric. Crucial in all cellular pathways, it comes about when a perturbation by a molecule called an effector alters a protein's shape and/or dynamics and leads to a functional change at the substrate binding site. Allosteric perturbation can arise due to small or large molecule binding; changes in pH, temperature, ionic strength, or concentration; or from covalent modifications such as sugar or phosphoryl group linking. Yet, despite how much we know about how allostery occurs, how signals initiating at a perturbation site transmit through a protein is still an open question.

In seven-helix receptor enzymes GDP replacement by GTP involves two allosteric steps

The number, breadth and functional roles of documented protein allostery cases are rising quickly, creating a need to arrange the information into a logical order. Sorting and classifying allosteric mechanisms in this way should be extremely useful in understanding and predicting how the signals are regulated and transmitted in proteins.

Classification assists us in making sense of observations. What are the differences between plants and animals; between mammals, birds, reptiles, fish, and amphibians; between classes of protein structures; drugs; types of interactions and chemical reactions? Sorting objects into distinct categories organises the information, revealing patterns and relationships, and so provides insight. While the importance of classification is clear, how to classify and into which categories is less obvious.

"Our framework is based on six properties, including whether there is conformational change at the substrate site and whether the effector perturbation increases or decreases the affinity of the substrate"

Current classification schemes in signalling class molecules according to their functions. For example, epinephrine - secreted by the central nervous system - is classified as a neurotransmitter; or, when the same molecule is secreted instead by the adrenal medulla in the adrenal gland, as hormone-like. Yet, such classifications account for the molecule's function, not for the molecular mechanism of how the signal transmission initiates and how it is transmitted.

We have presented a unified view of allostery and the first classification framework for allostery mechanisms. Allostery is a vehicle through which function is exerted so the logical approach was to organise mechanisms from a cellular function standpoint. Our framework is based on six properties, including whether there is conformational change at the substrate site and whether the effector perturbation increases or decreases the affinity of the substrate (positive or negative cooperativity respectively).

To illustrate this with an example, consider a textbook mechanism: GDP (guanosine diphosphate) replacement by GTP (guanosine triphosphate) in seven-helix receptor enzymes (see figure). Here classification indicates that two different types of allosteric step are involved. In the first (top), an extracellular ligand binds at an allosteric site causing a conformational change at the GDP binding site (the substrate site) leading to GDP's release. In the second allosteric step (bottom), the empty GDP binding site becomes an allosteric site for GTP binding. GTP binding then causes a protein to dissociate from the system - a negative cooperativity step.

"The aim is to provide a tool to help scientists place allosteric mechanisms in context, allowing a better comprehension of the signalling pathways they affect and how these pathways are regulated."

Textbooks describe series of events, not mechanisms. They cite the event and its consequences: a certain gene knock-out will lead to a certain loss of function. Yet, in disease our goal is to be able to trace back to a particular signalling checkpoint; to identify the source of the functional loss. Further, a disease-related mutation does not have to be in the substrate or the functional sites; but it may block signal propagation. Classifying allostery helps here, since a change in any of the six properties defined in our classification framework could conceivably affect function. A key question is which property would affect it the most.

Eventually, a classification scheme along the lines we propose could allow a systematic compilation and organisation of available allostery cases. The aim is to provide a tool to help scientists place allosteric mechanisms in context, allowing a better comprehension of the signalling pathways they affect and how these pathways are regulated. Ultimately, scientists would be able to predict signalling at the molecular level; it should also be useful for allosteric drug design.

Read more in the opinion article 'Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms' in Molecular BioSystems.

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http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/sorting_perturbed_proteins.asp