20.500.12556/RUL-125376 Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes Background: The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly contribute to the precision and accuracy of structural models obtained using computational approaches. To obtain such restraints, chemical cross-linking coupled with mass spectrometry (XL-MS) is commonly used. However, the use of XL-MS in the modeling of protein complexes comprised of identical subunits (homo-oligomers) is often hindered by the inherent ambiguity of intra- and inter-subunit connection assignment. Results: We present a comprehensive evaluation of (1) different methods for inter-residue distance calculations, and (2) different approaches for the scoring of spatial restraints. Our results show that using Solvent Accessible Surface distances (SASDs) instead of Euclidean distances (EUCs) greatly reduces the assignation ambiguity and delivers better modeling precision. Furthermore, ambiguous connections should be considered as inter-subunit only when the intra-subunit alternative exceeds the distance threshold. Modeling performance can also be improved if symmetry, characteristic for most homo-oligomers, is explicitly defined in the scoring function. Conclusions: Our findings provide guidelines for proper evaluation of chemical cross-linking-based spatial restraints in modeling homo-oligomeric protein complexes, which could facilitate structural characterization of this important group of proteins. chemical cross-linking homo-oligomers cross-link assignation ambiguity solvent accessible surface distances modeling prečno povezovanje homo-oligomeri nedoločljivost prečnih povezav topilu dostopne razdalje modeliranje true false true Angleški jezik Slovenski jezik Članek v reviji 2021-03-12 13:58:02 2021-03-12 13:58:04 2022-09-05 03:50:29 0000-00-00 00:00:00 2019 0 0 12 str. art. 464 Vol. 20 2019 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 577.112 1471-2105 10.1186/s12859-019-3032-x 1538315971 2433556 RAZ_Gaber_Aljaz_2019.pdf RAZ_Gaber_Aljaz_2019.pdf 1 64C870DC41270E34BA41DDD50B2D60EE 3b9ad562b9dc5cf26d8d5e7aa232c1f8a54f18eea2579ddacab9138737fa6ecc b312dbf0-a1bb-11eb-a523-00155dcfd717 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=141079 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3032-x 1 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=141078 Fakulteta za kemijo in kemijsko tehnologijo 0 0 0