SCIENCE

Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes—those enigmatic jumbles of molecules that are the protein factories of living cells. The research, published today in the journal Nature, could aid in development of new antibiotics used to fight multidrug resistant superbugs such as MRSA (methicillin-resistant Staphylococcus aureus infections) found in many U.S. hospitals. The work may also be important for combating engineered strains of anthrax and plague.

In the context of synthetic biology, understanding the ribosome could be key to developing nanofactories that produce designer biomolecules and polymers.

In the paper, "Head swivel on the ribosome facilitates translocation via intra-subunit tRNA hybrid sites," Los Alamos National Laboratory researchers Karissa Sanbonmatsu and Paul Whitford and José N. Onuchic at the University of California-San Diego join Christian Spahn, Andreas Ratje, and others from the Institute for Medical Physics and Biophysics, Berlin, Germany, to describe for the first time how a complicated swivel movement within a bacterial ribosome accommodates synthesis of proteins.

Ribosomes are composed of long chemical chains, called ribonucleic acids (RNA), and proteins. Each ribosome has two interlocked subunits, one large and one small, which behave as a single molecular machine. Because of its makeup, each ribosome resembles a tangle of threads or a handful of rubber bands tossed together. Despite the ribosome's outwardly disjointed appearance, researchers have found that the two subunits ratchet, un-ratchet, and swivel during protein synthesis to allow introduction of helper chemicals called transfer RNAs (tRNAs) into its folds to manufacture new chains of protein molecules. The proteins are used to create new cells or perform necessary functions within the host cell or organism.

Ribosomes build proteins by linking chemical segments fashioned from instructions delivered via messenger RNA, which is DNA's molecular cousin. Each segment, or amino acid, corresponds to a trio of bases in the message that, in turn, complement trios encoded in transfer RNA. Each base in the trio corresponds to a single chemical complement found on the RNA. In order for protein synthesis to occur, the tRNA must bind to the ribosome at two distinct sites—one to decode the information and another to link the new amino acid to the emerging protein.