Deciphering Another Secret of Life
Posted on by Dr. Francis Collins
In 1953, Francis Crick famously told the surprised customers at the Eagle and Child pub in London that he and Jim Watson had discovered the secret of life. When NIH’s Marshall Nirenberg and his colleagues cracked the genetic code in 1961, it was called the solution to life’s greatest secret. Similarly, when the complete human genome sequence was revealed for the first time in 2003, commentators (including me) referred to this as the moment where the book of life for humans was revealed. But there are many more secrets of life that still need to be unlocked, including figuring out the biochemical rules of a protein shape-shifting phenomenon called allostery [1].
Among those taking on this ambitious challenge is a recipient of a 2018 NIH Director’s New Innovator Award, Srivatsan Raman of the University of Wisconsin-Madison. If successful, such efforts could revolutionize biology by helping us better understand how allosteric proteins reconfigure themselves in the right shapes at the right times to regulate cell signaling, metabolism, and many other important biological processes.
What exactly is an allosteric protein? Proteins have active, or orthosteric, sites that turn the proteins off or on when specific molecules bind to them. Some proteins also have less obvious regulatory, or allosteric, sites that indirectly affect the proteins’ activity when outside molecules bind to them. In many instances, allosteric binding triggers a change in the shape of the protein.
Allosteric proteins include oxygen-carrying hemoglobin and a variety of enzymes crucial to human health and development. In his work, Raman will start by studying a relatively simple bacterial protein, consisting of less than 200 amino acids, to understand the basics of how allostery works over time and space.
Raman, who is a synthetic biologist, got the idea for this project a few years ago while tinkering in the lab to modify an allosteric protein to bind new molecules. As part of the process, he and his team used a new technology called deep mutational scanning to study the functional consequences of removing individual amino acids from the protein [2].
The screen took them on a wild ride of unexpected functional changes, and a new research opportunity called out to him. He could combine this scanning technology with artificial intelligence and other cutting-edge imaging and computational tools to probe allosteric proteins more systematically in hopes of deciphering the basic molecular rules of allostery.
With the New Innovator Award, Raman’s group will first create a vast number of protein mutants to learn how best to determine the allosteric signaling pathway(s) within a protein. They want to dissect out the properties of each amino acid and determine which connect into a binding site and precisely how those linkages are formed. The researchers also want to know how the amino acids tend to configure into an inactive state and how that structure changes into an active state.
Based on these initial studies, the researchers will take the next step and use their dataset to predict where allosteric pathways are found in individual proteins. They will also try to figure out if allosteric signals are sent in one direction only or whether they can be bidirectional.
The experiments will be challenging, but Raman is confident that they will serve to build a more unified view of how allostery works. In fact, he hopes the data generated—and there will be a massive amount—will reveal novel sites to control or exploit allosteric signaling. Such information will not only expand fundamental biological understanding, but will accelerate efforts to discover new therapies for diseases, such as cancer, in which disruption of allosteric proteins plays a crucial role.
References:
[1] Allostery: an illustrated definition for the ‘second secret of life.’ Fenton AW. Trends Biochem Sci. 2008 Sep;33(9):420-425.
[2] Engineering an allosteric transcription factor to respond to new ligands. Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S. Nat Methods. 2016 Feb;13(2):177-183.
Links:
Drug hunters explore allostery’s advantages. Jarvis LM, Chemical & Engineering News. 2019 March 10
Allostery: An Overview of Its History, Concepts, Methods, and Applications. Liu J, Nussinov R. PLoS Comput Biol. 2016 Jun 2;12(6):e1004966.
Srivatsan Raman (University of Wisconsin-Madison)
Raman Project Information (NIH RePORTER)
NIH Director’s New Innovator Award (Common Fund/NIH)
NIH Support: National Institute of General Medical Sciences; Common Fund
Great Article. Very well written and informative. Thank you.
In 1971, reading What’s Life and discussing point to point, judged important by Prof. Leloir, it was clear that biochemical techniques would make it trivial to understand the molecular basis of genetics so much so that the translation of triplets into amino acids became available as well as signs of starting and stopping the translations. However, the technical biochemistry and area of knowledge could last forever as a mystery. Allosterism is a small part of what allows us to consider proteins as the interacting macromolecules. The ensembles of proteins in the membranes, constituting signal transduction systems would not be “allosteric” like hemoglobin or regulatory proteins of metabolism but, show very clearly the delicacy and power of macromolecular interactions. Other examples show the same. I remain faithful to the biochemistry that must be guided always starting from the general aspect observed and going to the particular aspects.
I like to read about emergence where, as matter goes from micro- to macro-states, new and often unpredictable properties arise. Physicists like Sean Carroll and biologists like Harold Morowitz as well as philosophers write about emergence or how the universe becomes more complex and organized while being driven by entropy. Oddly, I have not come across the term emergence when reading about allostery. It would certainly enlighten the discussion.
One aspect of emergence can be found in the so-called neutral mutations that have been and remain a controversial topic in evolution even for very important biologists. By definition they would be mutations that do not affect the activity and / or function of a protein and thus would have no evolutionary role. However, when the characteristics of proteins as interacting macromolecules are highlighted, it is possible to envisage situations in which interaction with their substrates and regulators is not affected by mutations (neutral for this aspect) but emerge from new interactions not predicted by those studying the proteins as parts whose structure is deterministically linked to its function. A non-perceived function in a protein known and studied in isolation may emerge from new interaction even if the function observed alone is preserved. These observations indicate the importance of being guided by general references to understand the molecular level. Understand physiology first to present its molecular basis.
Rosalind Franklin, whose X-ray diffraction images provided the framework for the double helix model, continues to be overlooked for her contributions to our current understanding of DNA structure and function.
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