Cryogenic (frozen) protein structures are central to understanding the function and development of drugs. Scientists from St. Jude Children’s Research Hospital has developed an algorithm that reveals that freezing proteins can create ‘artifactes’ – errors that cause misleading results. A study recently appeared on AngewandteChemie and highlighted the importance of water networks in protein-ligand interactions. The findings challenge the general notion that assuming well-resolved cryogenic water levels are both accurate and precise.Ligand molecules bind to the receptor protein. When a ligand binds to a protein, the alignment (condition) can change, initiating different types of activity in the cell. Protein-ligand binding and the effect of structural changes are important factors to consider during efforts to improve the drug.
“If you look only at cryogenic data, the information used for drug discovery contains art objects that you would never know existed,” said co-author Marcus Fischer, Ph.D., St. Jude Departments of Chemical Biology and Therapeutics and Structural Biology. “We’ve developed a way to differentiate those artifacts. Using paired comparisons between cryogenic temperatures and room you can identify the protein components that are affected by temperature.”Researchers often use the protein structures obtained by extracting information from a website called the Research Collaboratory for Structural Bioinformatics Protein Data Bank. About 95 percent of those structures are cryogenically scanned, and then modeled within the site for easy use. Drug recipients rarely check raw test data, which is in the form of an electron congestion map. Asking for maps instead of building models provides an unbiased way to highlight dynamic features and cryogenic artifactes.
Flipper algorithm highlights
Fischer and his team developed an algorithm, called Flipper, that looks at raw test data on electron congestion maps. Flipper points to the tops of maps (signals) that would not be visible. These peaks are composed of proteins derived from certain fossils with temperature-sensitive combinations. These remnants can change the related preferences of one region over another, or ‘turn’ into their own, moving between compounds, which is where the algorithm got its name.The researchers used this method to identify fossils that respond to temperature changes and to trace fossils in a barcode-like system for all proteins. This has enabled scientists to determine how fossils inside and outside the ligand binding respond to cold or hot temperatures.
Armed with their new method, the researchers conducted a systematic analysis showing the importance of water networks. Water, one of the most important and abundant molecules on Earth, plays a vital role in the process of fertilization. This is especially true in areas where protein-ligand binding occurs.
“It is the first time we have systematically demonstrated the importance of temperature in water networks in order to refine the ligand binding interface, which is where biology occurs,” Fischer said. “Water is often overlooked in the drug discovery process, but we have shown that in addition to having a significant effect on ligand binding, water also has an effect on the binding site sites, trapping them at different locations depending on temperature.”Flipper and a conformational barcode system that enables comparisons of different ligands at different temperatures are freely available to enable other researchers to identify such patterns in their database.Other authors of this study are Karlo Lopez, California State University; and MurugendraVanarotti and JayaramanSeetharaman of St. Jude.
Source Journal Reference:Timothy R Stachowski, MurugendraVanarotti, JayaramanSeetharaman, Karlo Lopez, Marcus Fischer. Water Networks Repopulate Protein‐Ligand Interfaces With Temperature. AngewandteChemie International Edition, 2022; DOI: 10.1002/anie.202112919
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