Cell Vol 92 291 294 February 6 1998 Copyright 1998 by Cell Press The Cell as a Collection of Protein Machines Preparing the Next Generation of Molecular Biologists Bruce Alberts President National Academy of Sciences 2101 Constitution Avenue NW Washington D C 20418 Professor Department of Biochemistry and Biophysics University of California San Francisco San Francisco California 94143 Introduction We have always underestimated cells Undoubtedly we still do today But at least we are no longer as naive as we were when I was a graduate student in the 1960s Then most of us viewed cells as containing a giant set of second order reactions molecules A and B were thought to diffuse freely randomly colliding with each other to produce molecule AB and likewise for the many other molecules that interact with each other inside a cell This seemed reasonable because as we had learned from studying physical chemistry motions at the scale of molecules are incredibly rapid Consider an enzyme for example If its substrate molecule is present at a concentration of 0 5 mM which is only one substrate molecule for every 105 water molecules the enzyme s active site will randomly collide with about 500 000 molecules of substrate per second And a typical globular protein will be spinning to and fro turning about various axes at rates corresponding to a million rotations per second But as it turns out we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered Proteins make up most of the dry mass of a cell But instead of a cell dominated by randomly colliding individual protein molecules we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules And as it carries out its biological functions each of these protein assemblies interacts with several other large complexes of proteins Indeed the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines each of which is composed of a set of large protein machines Consider as an example the cell cycle dependent degradation of specific proteins that helps to drive a cell through mitosis First a large complex of about 10 proteins the anaphase promoting complex APC selects out a specific protein for polyubiquitination King et al 1996 Zachariae et al 1996 this protein is then targeted to the proteasome s 19S cap complex formed from about 20 different subunits and the cap complex then transfers the targeted protein into the barrel of the large 20S proteasome itself where it is finally converted to small peptides Baumeister et al 1998 this issue Ordered Movements Drive Protein Machines Why do we call the large protein assemblies that underlie cell function protein machines Precisely because like the machines invented by humans to deal efficiently Overview with the macroscopic world these protein assemblies contain highly coordinated moving parts Within each protein assembly intermolecular collisions are not only restricted to a small set of possibilities but reaction C depends on reaction B which in turn depends on reaction A just as it would in a machine of our common experience Alberts 1984 Underlying this highly organized activity are ordered conformational changes in one or more proteins driven by nucleoside triphosphate hydrolysis or by other sources of energy such as an ion gradient Because the conformational changes driven in this way dissipate free energy they generally proceed only in one direction An earlier brief review emphasized how the directionality imparted by nucleoside triphosphate hydrolyses allows allosteric proteins to function in three different ways as motor proteins that move in a polarized fashion along a filament or a nucleic acid strand as proofreading devices or clocks that increase the fidelity of biological reactions by screening out poorly matched partners and as assembly factors that catalyze the formation of protein complexes and are then recycled See figure 1 in Alberts and Miake Lye 1992 Since the time of that review the number of protein assemblies that are recognized to employ such devices has substantially increased In particular the nearly ubiquitous use of energy driven conformational changes to promote the local assembly of protein complexes thereby creating a high degree of order in the cell has become universally recognized A simple generic diagram of such a process is presented in Figure 1 We have also come to realize that protein assemblies can be enormously complex Consider for example the spliceosome Composed of 5 small nuclear RNAs snRNAs and more than 50 proteins this machine is thought to catalyze an ordered sequence of more than 10 RNA rearrangements as it removes an intron from an RNA transcript As cogently described in this issue of Cell by Staley and Guthrie 1998 these steps involve at least eight RNA dependent ATPase proteins and one GTPase each of which is presumed to drive an ordered conformational change in the spliceosome and or in its bound RNA molecule As the example of the spliceosome should make clear the cartoons thus far used to depict protein machines e g Figure 1 vastly underestimate the sophistication of many of these remarkable devices Given the ubiquity of protein machines in biology we should be seriously attempting a comparative analysis of all of the known machines with the aim of classifying them into types and deriving some general principles for future analyses Some of the methodologies that have been derived by the engineers who analyze the machines of our common experience are likely to be relevant For example modern machines comprised of subsystems from different domains i e mechanical electrical fluid thermal are often analyzed by an energy based approach Here a mathematical description of the machine is achieved by considering certain scalar functions that represent the system energy i e kinetic Cell 292 dissipate energy Any particular part of a machine might be modeled as consisting of one or more of these basic constituent elements It seems reasonable to expect that different but analogous approaches could profitably be applied to the protein machines that underlie the workings of all living things Figure 1 How the Energy Derived from Nucleoside Triphosphate Hydrolysis Makes Possible the Localized Assembly of Protein Complexes In this schematic the protein serving as a catalytic