Johns Hopkins biologists have developed a powerful new technique for studying how some proteins turn on and off.
"Scientists have known for years that many proteins have regulatory sites, regions where another compound can bind to turn the protein's activity on or off," says Ernesto Freire, professor of biology in the Krieger School of Arts and Sciences. "Proteins also have active sites, regions they use to perform their functions. But those two regions are often distant from each other on the protein, and we needed to figure out how they were connected."
To put it another way, scientists had found proteins with light switches and light sockets. But the wires connecting switch to socket were vanishing into the incredibly complex maze of spirals, sheets and folds that make up a protein.
Freire's research team has created a new approach to the problem and incorporated it into a computer algorithm known as Core_Bind. They've had one early success with it and have begun to use it on a protein that may be linked to cancers. Core_Bind may help scientists better understand how proteins involved in a wide variety of important processes throughout the body are controlled, probe what happens when these controls malfunction and design drugs to prevent malfunction or artificially trigger the switch.
Proteins' maddeningly intricate and all too permutable chains of peptides and amino acids were at the heart of the challenge of creating their new approach.
"Proteins are flexible molecules; they can take on many different configurations," Freire says. "Each configuration has a different energy level, and the ones with the lowest energy levels are the most stable. We decided to use a statistical representation of these different configurations to identify those that are the most likely."
Core_Bind puts the thousands of parts of a protein through many possible configurations and estimates the energy level and corresponding probability of each. It then repeats the calculations including the compound that binds to the protein to turn it on or off. By comparing the low-energy results from each group of calculations (the forms of the proteins most likely to appear in nature), they can track the path used to transmit the activation or inactivation signal and reveal the connections between switch and socket.
For their test run of the new technique, Freire's lab studied the interaction between an antibody and the target it specifically binds to, a protein known as a lysozyme. Another research group had documented the structure of the antibody and lysozyme joined together. Freire's group entered the structures of the antibody and the lysozyme into Core_Bind and used it to predict the structural effects of joining the two together. Then they checked their predictions against the other group's observations and published the successful results in August in The Proceedings of the National Academy of Sciences.
Currently, Freire and two postdoctoral associates, Jonathon Stillman and Irene Luque, are using Core_Bind to study tyrosine kinases, a family of proteins involved in cell growth and differentiation. These proteins are known to have regulatory sites in their structures that turn their activity on and off. In some forms of cancers, the regulation of these proteins is lost. Core_Bind should provide new insight into how these regulatory sites work and help scientists develop new approaches to treating the cancer.