Journal Article

PUBDB-2024-07772

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins

Yu, M. ; Gruzinov, A. Y. ; Ruan, H. ; Scheidt, T. ; Chowdhury, A. ; Giofrè, S. ; Mohammed, A. S. A. ; Caria, J. ; Sauter, P. F. ; Svergun, D. I. (Corresponding author)EMBL* ; Lemke, E. A. (Corresponding author)

2024
National Acad. of Sciences Washington, DC

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Please use a persistent id in citations: doi:10.1073/pnas.2415220121  doi:10.3204/PUBDB-2024-07772

Abstract: Intrinsically disordered proteins (IDPs) adopt ensembles of rapidly fluctuating heterogeneous conformations, influencing their binding capabilities and supramolecular transitions. The primary conformational descriptors for understanding IDP ensembles—the radius of gyration (RG), measured by small-angle X-ray scattering (SAXS), and the root mean square (rms) end-to-end distance (RE), probed by fluorescent resonance energy transfer (FRET)—are often reported to produce inconsistent results regarding IDP expansion as a function of denaturant concentration in the buffer. This ongoing debate surrounding the FRET-SAXS discrepancy raises questions about the overall reliability of either method for quantitatively studying IDP properties. To address this discrepancy, we introduce a genetically encoded anomalous SAXS (ASAXS) ruler, enabling simultaneous and direct measurements of RG and RE without assuming a specific structural model. This ruler utilizes a genetically encoded noncanonical amino acid with two bromine atoms, providing an anomalous X-ray scattering signal for precise distance measurements. Through this approach, we experimentally demonstrate that the ratio between RE and RG varies under different denaturing conditions, highlighting the intrinsic properties of IDPs as the primary source of the observed SAXS-FRET discrepancy rather than shortcomings in either of the two established methods. The developed genetically encoded ASAXS ruler emerges as a versatile tool for both IDPs and folded proteins, providing a unified approach for obtaining complementary and site-specific conformational information in scattering experiments, thereby contributing to a deeper understanding of protein functions.

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Contributing Institute(s):

1. EMBL-User (EMBL-User)
2. EMBL (EMBL)

Research Program(s):

1. 6G3 - PETRA III (DESY) (POF4-6G3) (POF4-6G3)
2. DFG project G:(GEPRIS)432343117 - Eine genetisch kodierte ASAXS Methode zur Messung der Eigenschaften von Intrinsisch ungeordneten Proteinen (432343117) (432343117)
3. DFG project 464588647 - SFB 1551: Polymerkonzepte zum Verstehen zellulärer Funktionen (464588647) (464588647)
4. iNEXT-Discovery - Infrastructure for transnational access and discovery in structural biology (871037) (871037)

Experiment(s):

1. PETRA Beamline P12 (PETRA III)

Appears in the scientific report 2024

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Database coverage:
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