The Croonian lecture 2006. Structure of the living cell

Abstract

The smallest viable unit of life is a single cell. To understand life, we need to visualize the structure of the cell as well as all cellular components and their complexes. This is a formidable task that requires sophisticated tools. These have developed from the rudimentary early microscopes of 350 years ago to a toolbox that includes electron microscopes, synchrotrons, high magnetic fields and vast computing power. This lecture briefly reviews the development of biophysical tools and illustrates how they begin to unravel the 'molecular logic of the living state'.

Figure 1

Illustration of the dimensions of some life-related systems on a logarithmic scale (powers of 10). The range visible by some of the different methods mentioned in the text is indicated by horizontal arrows. X-rays and NMR can be used to look at human anatomy in hospitals using tomographic methods, so these are shown as having the capacity to view a very wide range of dimensions. Their application at the nanometre level and below is, however, the only aspect dealt with in the text. FRET refers to ‘fluorescence resonance energy transfer’ and AFM to ‘atomic force microscopy’.

Figure 2

An illustration of advances in structural cell biology (a and b) and structural molecular biology (c and d). (a) Drawings of ‘animalcules’ seen by van Leeuwenhoek in a single lens microscope (figure 3 in the reference Leeuwenhoek 1683). (b) Visualization of the actin network (orange colour) and cytoplasmic complexes (light blue colour) in a Dictyostelium cell, embedded in vitrified ice and viewed by electron microscopy (Baumeister 2004). (c) A photograph of the first model of a protein, myoglobin, derived from X-ray diffraction data. The polypeptide chains are white and the haem group is shown as a grey disc (Kendrew et al. 1958). (d) The large subunit of the ribosome (PDB accession code 1ffk) is composed of two strands of RNA (shown as grey and brown wire models) and many different protein chains, shown in blue. Several of the proteins were not seen in this crystallographic structure but can be detected using cryo-electron microscopy. The dimension bars are approximate. Note that the resolution of the myoglobin model, approximately 0.5 nm, was only enough to show the general path of the polypeptide. The much larger ribosome, obtained some 40 years later was obtained at a resolution of around 0.25 nm (Ban et al. 2000), sufficient to observe individual amino acids and bases. (a–c) are reproduced with permission. (d) was produced using the computer visualization program Rastop (http://www.geneinfinity.org/rastop/manual/index.html).

Figure 3

(a) A representation of a cell showing some intracellular organelles such as mitochondria (blue-green) and the nucleus (pink); (b) a side view of the same cell showing some of the actin cytoskeleton (green) and focal adhesions (brown) that form a bridge between the extracellular matrix (blue hatching) and the actin cytoskeleton; (c) the cell extends in a directed way by generating actin filaments that extend by the addition of actin monomers; (d) new focal adhesions form at the front and old ones dissolve at the rear of the cell; (e) a schematic of some of the modular proteins that make up a focal adhesions; A, actin; P, paxillin; T, talin; Fl, filamin; Fak, focal adhesion kinase; V, vinculin; PTP, phosphatases; Pk, PIP kinase; Iα and Iβ, α and β subunits of integrin; Fn, part of fibronectin, a large protein in the extracellular matrix.

Figure 4

The structures of some of the modular protein units identified in figure 3e. The symbols generally correspond to those used in the SMART module database (http://smart.embl-heidelberg.de/). The structures were drawn using the graphics program Rastop (http:www.geneinfinity.org/rastop/); they can be seen to consist of a series of helices and strands. The LIM domain contains two zinc ions, coloured in magenta. PDB (http://www.rcsb.org/pdb/) accession codes, for the coordinates used to generate the protein representations, are shown for each structure. The structures were produced using Rastop (http://www.geneinfinity.org/rastop/manual/index.html).

Figure 5

An illustration of two of the conformational states available to integrins. These correspond to an ‘off’ state on the left and an ‘on’ state, also shown in figure 3e. The large movements mainly arise from a rearrangement of the various modular units, but there is also a significant movement of a helical segment in the vWA domain in going from on state to the other (Luo & Springer 2006). The ‘on’ state can be stabilized by talin (cloverleaf structure) binding to the beta tail (red; Wegener et al. in press).