Molecular machines and networking

We began the 20th century with very little knowledge of the molecules of life. For the first 50 years, researchers focused largely on trying to understand molecules' make up, wondering how molecules were able to do such mysterious things as pass on hereditary information.

In 1953, James Watson and Francis Crick, 1962 Nobel laureates, discov- ered the double helical structure of DNA and deduced the chemistry of how the subunits, the nucleotides, on each intertwined strand interacted. This discovery led to the understanding of the genetic code. In that same year the first crystal structure of a protein was solved, the oxygen storing muscle protein myoglobin, and researchers gained insights into how proteins achieved the chemistry of life.

For the next 50 years researchers gained a wealth of detailed informa- tion on individual biological molecules and came to understand that the biological function is achieved by the coordi- nated functions of many proteins. Indeed most of life's processes are carried out by what can be called "molecular machines" that are made of dozens of proteins that act in concert to carry out multiple functions such as read the genetic code from the genome and transcribe it by creating the messenger RNA molecule; read the messenger RNA containing the code to construct a protein and synthesize it; repair a DNA molecule damaged by radiation or chemicals; or form a "motor" that can create force and movement as in muscle. All of these complex processes must be performed in a highly coordinated and regulated manner. This coordi- nation is achieved through signaling networks that involve multiple proteins as well as small signal molecules. The language of these signaling networks is largely conformational—the proteins respond to signals in the cells such as a change in concentration of a small signal molecule by binding that molecule and undergoing a conformational change. This change allows it to interact with the next protein in the signaling network, thus transmitting the message. And in this fashion the signal can be passed along through many partners. It also can be amplified.

A major challenge for the 21st century is to unlock the secrets of molecular machines and networks. At Los Alamos, researchers are approaching this challenge by studying "second messenger" signaling. A second messenger is a small signal molecule, in some cases a simple ion like a calcium ion that is released inside a cell when a "first messenger" signal is received at the surface of the cell. A well-known first messenger signal is the binding of a hormone, like adrenaline, to a cell surface receptor in response to a fright–this message must be translated into the molecular action needed for a response, such as fleeing. To achieve flight, the brain must signal the cells in our bodies to make energy, so they can then turn on the molecular machines, our muscles, that will help us escape.

Capturing the interactions in the signaling networks and machines that keep us healthy and functioning is a great challenge. Protein complexes are often dynamic and transitory and are not well suited for study by a single technique that must trap the complex in a particular physical state. Los Alamos researchers have approached the problem by using hybrid experimental data and computational modeling. The experi- mental data came from many different sources, such as crystallography and nuclear magnetic resonance for the structures of individual protein components; fluorescence and cross-linking data for distances between components; neutron scattering for the shapes and position of components; and mutagenesis data for the proximity of different amino acids on different components combine and with computational methods develop models that best fit all of the known data.

In this manner, researchers have developed a model for the molecular switch that controls muscle contraction that now can be further tested and refined. Muscle is made of assemblies of protein molecules that form thick and thin filaments. The filaments sliding past each other via the action of "cross-bridges" between the filaments give rise to contraction and movement. The cross-bridge interactions are controlled by calcium-ion signals that affect molecular switches sitting on the thin filaments. The Los Alamos model for these molecular switches shows them to be made from two intertwined protein molecules, called troponin C and troponin I. When troponin C sees a calcium-ion signal, it undergoes a conformational change that causes it to "grab" part of the troponin I molecule that, in the absence of the calcium-ion signal, binds to the thin filament protein actin. This action releases troponin I's inhibitory effect on the cross-bridge formation and triggers the contraction.