Dali server: conservation mapping in 3D
Liisa Holm,Päivi Rosenström +1 more
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TLDR
The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how Conserved residues and ligands cluster together in multiple structure superimpositions.Abstract:
Our web site (http://ekhidna.biocenter.helsinki.fi/dali_server) runs the Dali program for protein structure comparison. The web site consists of three parts: (i) the Dali server compares newly solved structures against structures in the Protein Data Bank (PDB), (ii) the Dali database allows browsing precomputed structural neighbourhoods and (iii) the pairwise comparison generates suboptimal alignments for a pair of structures. Each part has its own query form and a common format for the results page. The inputs are either PDB identifiers or novel structures uploaded by the user. The results pages are hyperlinked to aid interactive analysis. The web interface is simple and easy to use. The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how conserved residues and ligands cluster together in multiple structure superimpositions. In favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis.read more
Citations
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Crystal structure of Cas9 in complex with guide RNA and target DNA
Takashi Yamano,Hiroshi Nishimasu,Hiroshi Nishimasu,Bernd Zetsche,Hisato Hirano,Ian Slaymaker,Yinqing Li,Iana Fedorova,Takanori Nakane,Kira S. Makarova,Eugene V. Koonin,Ryuichiro Ishitani,Feng Zhang,Osamu Nureki +13 more
TL;DR: In this article, the crystal structure of the CRISPR-associated endonuclease Cas9 in complex with sgRNA and its target DNA at 2.5-A resolution was reported.
Journal ArticleDOI
Pore-forming activity and structural autoinhibition of the gasdermin family
Jingjin Ding,Kun Wang,Wang Liu,Yang She,Qi Sun,Jianjin Shi,Hanzi Sun,Da-Cheng Wang,Da-Cheng Wang,Feng Shao +9 more
TL;DR: It is demonstrated that the liposome-leakage and pore-forming activities of the gasdermin-N domain are required for pyroptosis and provide insights into the roles of theGasdermin family in necrosis, immunity and diseases.
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA
Hiroshi Nishimasu,Naoshi Dohmae,Ryuichiro Ishitani,Osamu Nureki,Fei Ran,Patrick D. Hsu,Silvana Konermann,Soraya I. Shehata,Feng Zhang +8 more
TL;DR: The crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, paving the way for the rational design of new, versatile genome-editing technologies.
Journal ArticleDOI
Neuropilin-1 is a host factor for SARS-CoV-2 infection.
James L. Daly,Boris Simonetti,Katja Klein,Kai-En Chen,Maia Kavanagh Williamson,Carlos Antón-Plágaro,Deborah K. Shoemark,Lorena Simón-Gracia,Michael Bauer,Reka Hollandi,Urs F. Greber,Peter Horvath,Peter Horvath,Richard B. Sessions,Ari Helenius,Julian A. Hiscox,Julian A. Hiscox,Tambet Teesalu,David A. Matthews,Andrew D. Davidson,Brett M. Collins,Peter J. Cullen,Yohei Yamauchi,Yohei Yamauchi +23 more
TL;DR: It is shown that neuropilin-1 (NRP1), which is known to bind furin-cleaved substrates, potentiates SARS-CoV-2 infectivity and serves as a host factor for Sars-Cov-2 infection and may potentially provide a therapeutic target for COVID-19.
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Cleavage of DFNA5 by caspase-3 during apoptosis mediates progression to secondary necrotic/pyroptotic cell death.
Corey Rogers,Teresa Fernandes-Alnemri,Lindsey Mayes,Diana Alnemri,Gino Cingolani,Emad S. Alnemri +5 more
TL;DR: This work shows that caspase-3 cleaves the GSDMD-related protein DFNA5 after Asp270 to generate a necroticDFNA5-N fragment that targets the plasma membrane to induce secondary necrosis/pyroptosis, and provides a molecular mechanism forsecondary necrosis.
References
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Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
E. Krissinel,Kim Henrick +1 more
TL;DR: The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.
Journal ArticleDOI
Mapping the Protein Universe
Liisa Holm,Chris Sander +1 more
TL;DR: An exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.
Journal ArticleDOI
Dali: a network tool for protein structure comparison
Liisa Holm,Chris Sander +1 more
Journal ArticleDOI
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
TL;DR: This new version of ConSurf includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release and includes a measure of confidence for the inferred amino acid conservation scores.
Journal ArticleDOI
Surprising similarities in structure comparison
TL;DR: New structural comparison methods, developed in the past two years, increasingly offer this opportunity to structural and molecular biologists in general, and several groups seem to have converged on quite similar approaches with respect to both fast search algorithms and the identification of statistically significant similarities.
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