Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function

Vasudeva, Gunjan; Sidhu, Chandni; Kalidas, Nidhi; Ashish, .; Pinnaka, Anil Kumar

doi:10.1016/j.ijbiomac.2021.08.031

Cited by 1 publication

(1 citation statement)

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“…stock of 6-8 mg/ml and its two weight-over-weight half dilutions (~3-4 and ~2 mg/ml). Acquired datasets were corrected for beam position using SAXSTreat program and further processed for buffer subtraction and desmearing using SAXSQuant program as reported before (Kumar et al 2021;Vasudeva, Sidhu, Kalidas, Ashish & Pinnaka 2021). We performed direct desmearing of the datasets on buffer subtracted files using line profile of the beam using SAXSQuant program [detailed in the supplementary section of (Goel et al 2022)].…”

Section: Saxs Data Acquisition and Processingmentioning

confidence: 99%

VISUALIZING GAUSSIAN-CHAIN LIKE STRUCTURAL MODELS OF HUMAN Α-Synuclein IN MONOMERIC PRE-FIBRILLAR STATE: SOLUTION SAXS DATA AND MODELING ANALYSIS

Dey,

Gupta,

Badmalia

et al. 2024

Preprint

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Here, using small angle X-ray scattering (SAXS) data profile as reference, we attempted to visualize conformational ensemble accessible prefibrillar monomeric state of α-synuclein in solution. In agreement with previous reports, our analysis also confirmed that α-synuclein molecules adopted disordered shape profile under non-associating conditions. Chain-ensemble modeling protocol with dummy residues provided two weighted averaged clusters of semi-extended shapes. Further, Ensemble Optimization Method (EOM) computed mole fractions of semi-extended “twisted” conformations which might co-exist in solution. Since these were only Cαtraces of the models, ALPHAFOLD2 server was used to search for all-atom models. Comparison with experimental data showed all predicted models disagreed equally, as individuals. Finally, we employed molecular dynamics simulations and normal mode analysis-based search coupled with SAXS data to seek better agreeing models. Overall, our analysis concludes that a shifting equilibrium of curved models with low α-helical content best-represents non-associating monomeric α-synuclein.

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Section: Saxs Data Acquisition and Processingmentioning

confidence: 99%