Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x-ray reference structures as a prediction benchmark

0559713 - ÚOCHB 2023 RIV US eng J - Článek v odborném periodiku
Vymětal, Jiří - Mertová, Kateřina - Boušová, Kristýna - Šulc, Josef - Tripsianes, K. - Vondrášek, Jiří
Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x-ray reference structures as a prediction benchmark.
Proteins-Structure, Function and Bioinformatics. Roč. 90, č. 12 (2022), s. 2067-2079. ISSN 0887-3585. E-ISSN 1097-0134
Grant CEP: GA MŠMT(CZ) LM2018131; GA MŠMT(CZ) EF16_019/0000729; GA ČR(CZ) GA19-03488S
Výzkumná infrastruktura: e-INFRA CZ - 90140
Institucionální podpora: RVO:61388963
Klíčová slova: 3D structure prediction * fusion proteins * molecular simulations * X-ray crystallography
Obor OECD: Biochemistry and molecular biology
Impakt faktor: 2.9, rok: 2022
Způsob publikování: Open access
https://doi.org/10.1002/prot.26398

Proteins are naturally formed by domains edging their functional and structural properties. A domain out of the context of an entire protein can retain its structure and to some extent also function on its own. These properties rationalize construction of artificial fusion multidomain proteins with unique combination of various functions. Information on the specific functional and structural characteristics of individual domains in the context of new artificial fusion proteins is inevitably encoded in sequential order of composing domains defining their mutual spatial positions. So the challenges in designing new proteins with new domain combinations lie dominantly in structure/function prediction and its context dependency. Despite the enormous body of publications on artificial fusion proteins, the task of their structure/function prediction is complex and nontrivial. The degree of spatial freedom facilitated by a linker between domains and their mutual orientation driven by noncovalent interactions is beyond a simple and straightforward methodology to predict their structure with reasonable accuracy. In the presented manuscript, we tested methodology using available modeling tools and computational methods. We show that the process and methodology of such prediction are not straightforward and must be done with care even when recently introduced AlphaFold II is used. We also addressed a question of benchmarking standards for prediction of multidomain protein structures-x-ray or Nuclear Magnetic Resonance experiments. On the study of six two-domain protein chimeras as well as their composing domains and their x-ray structures selected from PDB, we conclude that the major obstacle for justified prediction is inappropriate sampling of the conformational space by the explored methods. On the other hands, we can still address particular steps of the methodology and improve the process of chimera proteins prediction.
Trvalý link: https://hdl.handle.net/11104/0332921