Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues (N T ) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (R g ) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments.The R g values are well-described by the standard Flory scaling law,with ν ≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence of R g on chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case for α-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone, cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.

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“…with q-dependent structure factors (f (q)), which were reported elsewhere. 86 In Eq. 4, N tot is the total number of beads in a given IDP.…”

Section: Methodsmentioning

confidence: 99%

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Baul

Chakraborty

Mugnai

et al. 2018

Preprint

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“…The dimension of the beads can be tuned to find a proper balance between accuracy and computational efficiency (Niebling et al, 2014). The beads can also be placed in different positions: examples include the atom's centre of mass, the centre of electron-density distribution or, in the case of protein residues, the C atom (Tong et al, 2016). Given M beads and their associated scattering factors F (q), the Debye equation becomes…”

Section: Coarse-grain Form Factorsmentioning

confidence: 99%

Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data

2019

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The use of small-angle X-ray scattering (SAXS) in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speeded up by using a coarse-grain representation of the structure. Following the work of Niebling, Bjö rling & Westenhoff [J. Appl. Cryst. (2014), 47, 1190-1198], the Martini bead form factors for nucleic acids have been derived and then implemented, together with those previously determined for proteins, in the publicly available PLUMED library. A hybrid multi-resolution strategy has also been implemented to perform SAXS restrained simulations at atomic resolution by calculating the virtual positions of the Martini beads on the fly and using them for the calculation of SAXS. The accuracy and efficiency of the method are demonstrated by refining the structure of two protein-nucleic acid complexes. Instrumental for this result is the use of metainference, which allows the consideration and alleviation of the approximations at play in the present SAXS calculations. research papers J. Appl. Cryst. (2019). 52, 394-402 Cristina Paissoni et al. Martini bead form factors for nucleic acids 395

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“…It should be noted that if the SAXS profiles at high-q regions (say, q>0.4 Å -1 where q is the amplitude of X-ray momentum transfer during the scattering) are required, the Fast-SAXS-pro method has been improved due to recent optimization of form factors at high-q values (Tong et al, 2016). The goodness of fit between the theoretical ( I cal ) and experimental ( I exp ) SAXS profiles is assessed by…”

Section: Methods and Detailsmentioning

confidence: 99%

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking

Huang

Ravikumar

Parisien

et al. 2016

Journal of Structural Biology

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Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.3 Å and 4.2 Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT—using either rigid-body or MD-based flexible docking—is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes.

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Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

Cited by 22 publications

References 75 publications

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking

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