Embedding function in protein assemblies
Most cellular functions are carried out by assemblies of multiple proteins referred to as protein complexes. Although we often explain how protein complexes function by analogy with engineered devices, there are fundamental differences. First, unlike man made machines, protein complexes self-assemble from their constituent components. Second, the concerted motion of atoms in an assembly may not be analogous to that of rigid cogs moving relative to each other. Finally, as proteins operate at the thermal energy scale, reliable operation is a challenge.
Self-assembly state of matter
One fundamental characteristic of protein complexes is that they self-assemble from their constituent components. Self-assembly of hundreds of different complexes occurs in the cytoplasm, a mixture of thousands of different protein species. This makes accurate assembly a formidable discriminatory task, as each growing complex needs to distinguish its few constituent proteins. What are the states of matter of a mixture of thousands of proteins? Is self-assembly a robust phase? What are the generic properties of assemblies that allow them to self-assemble accurately?
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Coarse graining assembly function
The function of an assembly is determined by the motion of its atomic structure. Different molecular forces underlay the motion of the large number of atoms in an assembly (10^5 for the ATP synthase). This makes the dimensionality of assemblies function formidably large. Surprisingly, very simple mechano-chemical descriptions of assemblies, with two or three degrees of freedom, have been greatly succesful in biophysics. How do such simple descriptions emerge from the high dimensional structural description of assemblies? Can we describe protein assemblies as a “special” kind of evolved elastic material?
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