Structural biologists, let’s mind our colors

Saladi, Shyam; Maggiolo, Ailiena O.; Radford, Kate; Clemons, William M.

doi:10.1101/2020.09.22.308593

Cited by 4 publications

(2 citation statements)

References 14 publications

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“…Ab initio structure prediction was employed for other STI1‐domains using RobettaTR (transform restrained) 93 with the full‐length protein sequences of each protein, with the specific STI1 region of interest visualized. Images were rendered using PyMOL 2.4 (http://www.pymol.org) with a viridis coloring scheme 94 . Helical wheel diagrams were rendered in R using a fork (https://github.com/smsaladi/heliquest) of the HELIQUEST source code 95 …”

Section: Methodsmentioning

confidence: 99%

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The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove

2021

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STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.

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Section: Methodsmentioning

confidence: 99%

“…Images were rendered using PyMOL 2.4 (www.pymol.org) with a viridis coloring scheme. 94 Helical wheel diagrams were rendered in R using a fork (https://github.com/smsaladi/heliquest) of the HELIQUEST source code. 95…”

Section: Molecular Visualizationmentioning

confidence: 99%

The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove

2021

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Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3

Fry

Najdrová

Maggiolo

et al. 2022

Nat Struct Mol Biol

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Comprehensive Mutational Landscape Analysis of Monkeypox Virus Proteome

Ozaktas,

Dizkirici,

Carbone

et al. 2024

Preprint

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We present a comprehensive computational analysis of the single point mutational landscapes of the Monkeypox virus (MPXV) proteome. We reconstructed full single-point mutational landscapes of 171 MPXV proteins using two advanced mutational effect predictors, ESCOTT and iGEMME, selected for their superior performance on viral proteins, assessed by benchmarking against the experimental data in the ProteinGym (v1.0.0) dataset. A recent MPXV strain sequenced in July 2024 was used as the reference genome. Multiple sequence alignments and protein structures were generated using Colabfold v1.5.5, and the predicted structures were evaluated with pLDDT metric, secondary structure predictions, and comparisons with available experimental data, ensuring high confidence in the structural models. To prioritize the most mutation-sensitive proteins within the large MPXV proteome as prime candidates for drug or vaccine development, we introduced a novel, interpretable metric: Average Gene Mutation Sensitivity (AGMS). Among the top 20 identified proteins, several were membrane-associated proteins, expected to be important for viral interactions with the hosts. This analysis provides a valuable resource for assessing the impact of new MPXV variants and guiding therapeutic strategies. This pioneering study underscores the significance of understanding MPXV evolution in the context of the ongoing global health crisis and offers a robust computational framework to support this effort.

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Structural biologists, let’s mind our colors

Cited by 4 publications

References 14 publications

The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove

The STI1‐domain is a flexible alpha‐helical fold with a hydrophobic groove

Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3

Comprehensive Mutational Landscape Analysis of Monkeypox Virus Proteome

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