{"entity": "researcher", "timestamp": "2026-08-22T07:48:14.765Z", "family": "Atilgan", "given": "Canan", "initials": "C", "orcid": "0000-0003-0557-6044", "affiliations": ["Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, T\u00fcrkiye."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4bec0a4bd6741e49add40deafb4ca6f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4bec0a4bd6741e49add40deafb4ca6f"}}, "publications": [{"entity": "publication", "iuid": "ea07ead46c5c4bc4a9ba9a7fe944b6de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea07ead46c5c4bc4a9ba9a7fe944b6de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea07ead46c5c4bc4a9ba9a7fe944b6de"}}, "title": "Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations.", "authors": [{"family": "Liu", "given": "Goksin", "initials": "G", "orcid": "0000-0002-8409-1311", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b77d918c4ae7485b9ae390c44b8d4f27.json"}}, {"family": "Ekmen", "given": "Erhan", "initials": "E", "orcid": "0000-0003-2340-625X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4c7f2d6beef4578a7363d1925c913ad.json"}}, {"family": "Jalalypour", "given": "Farzaneh", "initials": "F", "orcid": "0000-0001-5092-1914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a67015ef36ea44869b6a202771cc0e4d.json"}}, {"family": "Mertens", "given": "Haydyn D T", "initials": "HDT", "orcid": "0000-0002-5664-744X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8286016d8da043458627cb5332517f91.json"}}, {"family": "Jeffries", "given": "Cy M", "initials": "CM", "orcid": "0000-0002-8718-7343", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16e851b6446e47019f2e88ba146462d9.json"}}, {"family": "Svergun", "given": "Dmitri", "initials": "D", "orcid": "0000-0003-0830-5696", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1fc37bb2b8434b1082bc9a16cd96eda7.json"}}, {"family": "Atilgan", "given": "Ali Rana", "initials": "AR", "orcid": "0000-0003-0604-6301", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02ffb37e6f904e3bbc1800975315baee.json"}}, {"family": "Atilgan", "given": "Canan", "initials": "C", "orcid": "0000-0003-0557-6044", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4bec0a4bd6741e49add40deafb4ca6f.json"}}, {"family": "Sayers", "given": "Zehra", "initials": "Z", "orcid": "0000-0003-3653-4736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd5f76a3d8b4ddab667fb7a727b5bca.json"}}], "type": "journal article", "published": "2023-02-28", "journal": {"title": "J Chem Phys", "issn": "1089-7690", "volume": "158", "issue": "8", "pages": "085101", "issn-l": "0021-9606"}, "abstract": "This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment. While we show that these changes fall within the detectable range for SAXS as evidenced by differences observed in the theoretical scattering patterns calculated from the crystal structure models of apo and holo forms, detection of conformational changes due to the point mutation D52A and changes in ionic strength (IS) from SAXS scattering profiles have been challenging. Here, to reach conclusions, statistical analyses with SAXS profiles and results from different techniques were combined in a complementary fashion. The SAXS data complemented by size exclusion chromatography point to multiple and/or alternative conformations at physiological IS, whereas they are well-explained by single crystallographic structures in low IS buffers. By fitting the SAXS data with unique conformations sampled by a series of MD simulations under conditions mimicking the buffers, we quantify the populations of the occupied substates. We also find that the D52A mutant that we predicted by coarse-grained computational modeling to allosterically control the iron binding site in FbpA, responds to the environmental changes in our experiments with conformational selection scenarios that differ from those of the wild type.", "doi": "10.1063/5.0136558", "pmid": "36859088", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-21T12:00:03.728Z", "modified": "2026-08-21T12:00:04.165Z"}, {"entity": "publication", "iuid": "28e7852d485f40448d9c5d8bb1575294", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/28e7852d485f40448d9c5d8bb1575294.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/28e7852d485f40448d9c5d8bb1575294"}}, "title": "Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS.", "authors": [{"family": "Ilter", "given": "Metehan", "initials": "M"}, {"family": "Kasmer", "given": "Ramazan", "initials": "R"}, {"family": "Jalalypour", "given": "Farzaneh", "initials": "F"}, {"family": "Atilgan", "given": "Canan", "initials": "C", "orcid": "0000-0003-0557-6044", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4bec0a4bd6741e49add40deafb4ca6f.json"}}, {"family": "Topcu", "given": "Ozan", "initials": "O"}, {"family": "Karakas", "given": "Nihal", "initials": "N"}, {"family": "Sensoy", "given": "Ozge", "initials": "O", "orcid": "0000-0001-5950-3436", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de69a65feb3749418e7e127bd40220bd.json"}}], "type": "journal article", "published": "2022-12-02", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "11", "issn-l": "2050-084X"}, "abstract": "Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.", "doi": "10.7554/eLife.79747", "pmid": "36458814", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9762712"}, {"db": "pii", "key": "79747"}], "notes": [], "created": "2026-08-21T13:07:58.980Z", "modified": "2026-08-21T13:07:59.046Z"}]}