Protein Machines

Under the present paradigm of modern biochemistry, the cell can be regarded as a factory-like system. It is crowded with a variety of specialized molecular machines of nanometer size (Fig. 8.1a), most of which are proteins either as single polypeptides or as complex assemblies of protein "parts" (Alberts 1998). Very often, their functions involve the conversion of chemical energy (stored or supplied) into mechanical work through changes in their conformation, ttus, from the cell nucleus to the extracellular matrix there are "bionanomachines" involved in mechanical processes as diverse as replication, transcription, translation, protein folding, protein and nucleic acid unfolding, protein degradation, nucleic acid and protein translocation, organelle transport, cell adhesion, membrane fusion, or cell crawling (Howard 2001; Bustamante et al. 2004).

Although the "machine" metaphor is a useful first approximation to describe these cellular structures and there are striking parallels between artificial and natural machines, it does not hold for two important aspects. Indeed, these are issues that prevent us from learning about the behavior of natural machines by analogy to artificial ones. First, since bionanomachines are products of evolution, rather than being "designed" by engineers, their structure has been shaped by natural selection instead of human planning. Second, in contrast to macroscopic machines (i.e., conventional machines, excluding the artificial nanomachines) that are mainly affected by gravity and inertia, bionanomachines are mainly dominated by the so-called thermal

"forces", owing to their smaller mass (strictly speaking, in the current view of phys--►

Fig. 8.1. Single-molecule manipulation (SMM): relevant parameters and scales, a Spatial resolution of SMM techniques (red) and size of representative biological structures (black), b Force ranges of SMM techniques (red), physicochemical forces at the molecular level (blacksquares), and force ranges of typical biological machines and interactions (black lines), c Temporal resolution of SMM techniques (red) and the time duration of characteristic biological processes (black), d Pulling speed range of SMM techniques (red) and representative speed range of protein machines measured in vitro (grey) and in vivo (black). AFM atomic force microscopy, OToptical tweezers, BFPbiomembraneforce probe,MNmicroneedles,MTmagnetic tweezers, FFflowfield

ics there are only four fundamental forces in nature from which the other "forces" derive: strong nuclear, weak nuclear, electromagnetic, and gravitational). Since thermal forces are ubiquitous and random in nature (Fig. 8.1b), at room temperature, bionanomachines in their aqueous environment experience a constant "bombardment" by the numerous water molecules that surround them, ttese forces are in the femtonewton (10~15 N) range and result in what is called Brownian motion (a phenomenon originally described by the botanist Robert Brown, in 1827, and later explained in physical terms by Albert Einstein, in 1905). ttis unfamiliar environment confers on them the particular properties that dominate their behavior. It is through this thermal agitation of their molecular structure that proteins reach the high-energy transition states that are essential in biochemical reactions (thermal energy is k-g,T=4.1 pN nm=0.6 kcal moL1, at room temperature; fcg is the Boltzmann constant and Tis the absolute temperature). To understand life inside the cell, it is essential to know how these protein machines move their parts and change shape in response to the mechanical and thermal forces present in their nanoenviron-ment. tte energies involved in protein conformational changes (the "signals" in our experiments) are just above thermal energy levels (the "noise"), typically ranging from 1 k%T (thermal energy) to 25 k%T (ATP hydrolysis), such that the structures are stable enough to prevail at physiological temperatures. Owing to these natural fluctuations, the behavior of these machines is stochastic and typically very "noisy." In contrast, artificial machines use much higher energy values than thermal energy to work rapidly, accurately, and deterministically.

Like the other major biological macromolecules (DNA, RNA, and polysaccharides), proteins can be thought of as polymers (more specifically, they are heteropolymers or copolymers), i.e., articulated chains of atoms, that interact in a few, well-defined ways. It would be necessary to apply quantum mechanics to provide a quantitative description of the properties of the atoms involved, but fortunately most of the basic properties of these biomolecules can be understood qualitatively using a small set of simplified rules such as entropic elasticity, steric repulsion, van der Waals forces, electrostatic interactions, and hydrogen bonding, tte central concept here is that two types of bonds exist: covalent bonds, connecting monomeric units into a primary structure; and noncovalent interactions, which stabilize their tertiary structure and permit structural (conformational) changes upon binding to other biomolecules. Proteins are synthesized as flexible chains that typically fold spontaneously into a unique and compact 3D structure, the so-called native conformation. ttus, through the course of evolution random molecular fluctuations have been harnessed into self-organized protein structures, ttese protein "folds" are impressive examples of self-organization (a key feature of biological systems), which is also responsible for the spontaneous assembly into the functional complexes we call bionanomachines.

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