Macromolecular complexes

Macromolecular complexes are cellular machines that perform a wide array of vital tasks. Understanding their structure is crucial to understanding their function, and will shed light on how the cell functions in health and disease. Current techniques offer some insights into the structure of these machines, but new and more powerful methods are needed to elucidate them fully.

Macromolecular complexes are naturally occurring machines inside cells. They consist of a handful to several thousand individual components, including proteins, DNA, carbohydrates and lipids, and perform diverse and vital tasks, such as translating the genetic code, converting energy or helping nerve cells communicate.

THE SPLICE OF LIFE

Some well-known complexes help regulate gene expression via effects on RNA and proteins. The spliceosome (Fig. 1; ref 1), for example, removes non-protein-coding snippets from newly formed RNA, then joins the remaining fragments to form functional messenger RNA (mRNA) that can be converted into protein.

The nuclear-pore complex — one of the largest molecular machines — straddles the nuclear membrane, controlling the exit of RNA and the entrance of other molecules including proteins and signalling molecules (Fig. 2; ref 2).

The ribosome (Fig. 1; refs 3,4) binds to and moves along the mRNA template, reading its genetic information and preparing the corresponding amino-acid sequence, which it then stitches together to make protein. Unwanted RNA is broken down by another macromolecular complex, the exosome (Fig. 1; ref 5), and unwanted proteins are recycled by the proteasome.

An interesting group of macromolecular complexes exist within the lipid bilayer membrane that surrounds the cell and its internal compartments. Photosynthetic membrane complexes can be found in plant chloroplasts and bacterial membranes. They convert solar energy into chemical energy6, which can be used to make organic compounds — the building blocks of life.

Another group, found in the plasma membrane of bacteria and the mitochondrial membrane of eukaryotic cells, extracts energy from cellular respiration. During this process, electrons are transferred from organic substrates to molecular oxygen, generating a proton gradient across the membrane, which in turn helps the ATP synthase macromolecular complex to produce chemical energy, providing animal cells with the energy to live.

BRILLIANT DESIGN

X-ray crystallography has revealed the atomic make-up of several stable and plentiful complexes, such as the ribosome, the photosynthetic and respiratory chain complexes, and the proteasome7.

For example, the ribosome3,4 is organized into two subunits that join to read mRNA and then split after the protein is made. The barrel-like proteasome consists of four stacked rings around a central core lined with protein-degrading enzymes. ATP synthase is like a rotary motor powered by the proton flow along the membrane (Fig. 3; ref 8).

A detailed understanding of the structure of these machines is prerequisite to elucidating their function; however, the large size, fragility and scarcity of certain complexes means that high-resolution structural information can be hard to come by. This is made more challenging by the fact that many macromolecular complexes change shape as they perform.

Understanding the structure and function of these intricate machines is central to comprehending the cell, as well as certain disease processes. For example, mitochondrial dysfunction associated with certain neurodegenerative disorders, such as Alzheimer’s and Parkinson’s diseases, might reflect a breakdown of membrane organization.

ORDER NOT CHAOS

It is increasingly clear that macromolecular complexes operate in a controlled, coordinated fashion within the highly ordered environment of the cell. Each macromolecular complex occupies a particular position, with the location and copy number influencing function. It was recently shown, for example, that mitochondrial ATP synthase is not distributed haphazardly through the membrane, but is arranged in long rows of complex dimers that influence the local membrane curvature9.

>> Macromolecular complexes operate in a controlled, coordinated fashion within the highly ordered environment of the cell. Each macromolecular complex occupies a particular position, with the location and copy number influencing function.

Investigating these interactions and processes is a promising but relatively unexplored field that offers opportunities in most areas of chemical, physical, engineering and life sciences. Estimates of the number and location of these macromolecular complexes are now coming into focus.

Many questions and practical challenges remain. Obtaining sufficient quantities of pure, functional macromolecular complexes for biochemical and structural analysis is difficult. The exact molecular components of many of the larger complexes remain a mystery, as do their distribution, dynamic nature and ability to self-assemble. Moreover, it is unclear how these machines interact and operate within the larger context of the cell.

The answers to these problems will help place essential cellular processes onto a quantitative foundation; however, more powerful methods are needed to understand fully the structure and workings of macromolecular complexes.

Mass spectrometry can reveal the molecular composition of certain assemblies, including membrane protein complexes, of up to several hundred thousand atoms. More sensitive techniques for solution and solid-state nuclear magnetic resonance are needed to reveal detailed information about the structure and dynamics of even larger complexes. The recently completed high-brilliance PETRA III synchrotron in Hamburg, Germany, will allow smaller crystals of larger assemblies to be measured more accurately. The new free-electron laser on the same site, scheduled to come on line in 2013, might allow researchers to examine the structure of large, non-crystalline macromolecular complexes with single, ultra-short but extremely powerful X-ray pulses.

A new generation of electron microscopes, operating at near-atomic resolution, will provide a detailed view of large, non-crystalline complexes such as viruses10. In combination with wave-modifying phase plates11 and new direct electron detectors, they will deliver high-quality images of individual macromolecular complexes.

The ability to tag key proteins with fluorescent labels and visualize them through light microscopy, coupled with the detailed three-dimensional views obtained from electron tomography, will make it easier to study the workings of complexes in specific cellular regions, such as the synapse. Modelling studies with ever more powerful computers will enhance and extend structural studies.

LOOKING AHEAD

The study of macromolecular complexes demands new techniques and a cross- disciplinary approach. The knowledge gained will help reveal the workings of these most intricate and complex machines in health and disease. Our detailed understanding of the ribosome, for example, means it is now possible to design antimicrobials with improved antibiotic properties. Like so many machines, these macromolecular complexes are not perfect, so a comprehensive understanding of how they contribute to disease will also aid the design and development of new therapies.

Understanding macromolecular complexes and how they work is a fundamental and fascinating undertaking, but it is also one of the most challenging tasks for the future of basic biomedical research in the Max Planck Society. Scientists from the society have made outstanding contributions to this key area of the molecular life sciences, and are continuously developing new and more powerful methods for investigating the structure and workings of these molecular nanomachines (Wahl, M. C. et al. Cell 136, 701–718, 2009).

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