MIPT learned how to assemble structures of large membrane proteins, like a mosaic

(ORDO NEWS) — Researchers from MIPT, together with colleagues from the Joint Institute for Nuclear Research in Dubna, have developed a method for obtaining a three-dimensional structure for large membrane protein complexes using small-angle scattering methods.

This will make it possible to better understand their function and, therefore, to control their work, which is extremely important in the development of new drugs. The data obtained by the researchers on the structure of the protein complex, typical for the bacterial world, but not found in mammals and humans, can help in the development of new antibiotics.

The work was published in the top-rated journal Acta Crystallographica sect. D. The “sense organs” of bacteria and archaea are two-component signaling systems. They provide a response to environmental stimuli. An example of a two-component system designed for the perception of light by archaea is the membrane protein complex of sensory rhodopsin 2 and a transducer protein. Sensory rhodopsin 2 is present in the archaeal membrane of Natronomonas pharaonis, it is activated in response to blue light and transmits a signal to its partner, the transducer protein.

The transducer, in turn, with the participation of several more proteins, triggers the work of the bacterial flagellum, which takes the archaea away from blue light. Blue light in the electromagnetic spectrum coexists with ultraviolet light, which has a dangerous mutagenic effect. Activation of sensory rhodopsin 2 triggers the mechanism of “escape” of archaea from blue and, accordingly, ultraviolet light .

Sensory rhodopsin 2 with a transducer form a large-scale protein complex in the cell membrane. This complex turned out to be a convenient object for the development of structural research techniques. These techniques can be further applied to all kinds of membrane proteins, including target proteins of drugs, the understanding of the structure of which is extremely important.

Small-angle scattering is a classic method for obtaining the structural parameters of various proteins. Until recently, this method was used only for water-soluble proteins. Membrane proteins are much more difficult to characterize by small angle scattering.

Typically, small-angle scattering methods produce low-resolution structures that provide an approximate understanding of the behavior of proteins in solution. Therefore, the authors of the study decided to use high-resolution structures for parts of the large complex and add small-angle scattering data to them.

Thus, the scientists connected the parts of a large complex and assembled a three-dimensional model of the protein piece by piece, like a mosaic. Using the method of molecular modeling, they established the mutual orientation of the parts of the complex relative to each other and obtained a full-size high-resolution model of the protein.

Surprisingly, it was possible to obtain a high-resolution structure of a full-size complex using low-resolution methods such as small-angle scattering. Even more surprising was the fact that in the beginning such a structure turned out to be completely wrong.

In nature, proteins embedded in membranes are surrounded by lipids. When studying membrane proteins, the samples undergo a stage of solubilization, during which the membrane part of the protein complexes is surrounded by molecules of surfactants (or detergents). “The detergent belt formed in this way, on the one hand, stabilizes the protein complexes in solution, prevents them from sticking to each other. friend and precipitate.

However, on the other hand, it also makes a significant contribution to the scattering pattern, strong enough to obtain a completely incorrect model of the protein complex, if this detergent belt is not taken into account, ”comments Yuri Rizhao, employee of the Center for Research on Molecular Mechanisms of Aging and Age diseases of the Moscow Institute of Physics and Technology.

This is what happened at the very beginning of this study. The authors obtained an incorrect model of the complex in the so-called Y-state, based on the assumption that the small-angle X-ray scattering pattern is represented exclusively by the target proteins.

When scientists took into account the contribution of the detergent belt and realized how much it influenced the interpretation of the results, it was so amazing. which became an example for choosing the optimal strategy for processing small-angle scattering data for large membrane protein complexes.

“The high-resolution model of a large membrane protein complex was obtained through the combined use of the most powerful methods of structural research: small-angle X-ray and neutron scattering. The combination of these methods with molecular modeling methods made it possible to obtain a completely new high-resolution model for a two-component signaling protein complex, “summarizes Alexander Kuklin, research leader, leading researcher at the Center for Research on Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology.


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