MAFFT-DASH: integrated protein sequence and structural alignment

Rozewicki, John; Li, Songling; Amada, Karlou Mar; Standley, Daron M.; Katoh, Kazutaka

doi:10.1093/nar/gkz342

Cited by 509 publications

(478 citation statements)

References 33 publications

Supporting

Mentioning

448

Contrasting

Unclassified

Order By: Relevance

“…Other coronaviruses (subgenus Sarbecovirus ) were downloaded from GenBank (Extended Data Table S3) and compared to those obtained here. We constructed a multiple sequence alignment of their complete genomes and individual genes using MAFFT v7.273 14 . Maximum likelihood phylogenies were estimated using PhyML v3.1 15 , utilizing the GTR+I+Γ model of nucleotide substitution with 1,000 bootstrap replicates.…”

Section: Methodsmentioning

confidence: 99%

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Lam

Shum

Zhu

et al. 2020

Preprint

231

234

View full text Add to dashboard Cite

27The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel 28 coronavirus, provisionally termed 2019-nCoV. This outbreak has been tentatively associated 29 with a seafood market in Wuhan, China, where the sale of wild animals may be the source of 30 zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, the identity of 31 any intermediate host facilitating transfer to humans is unknown. Here, we report the 32 identification of 2019-nCoV related coronaviruses in pangolins (Manis javanica) seized in 33 anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin 34 associated CoVs that belong to two sub-lineages of 2019-nCoV related coronaviruses, 35 including one very closely related to 2019-nCoV in the receptor-binding domain. The 36 discovery of multiple lineages of pangolin coronavirus and their similarity to 2019-nCoV 37 suggests that pangolins should be considered as possible intermediate hosts for this novel 38 human virus and should be removed from wet markets to prevent zoonotic transmission.

show abstract

Section: Methodsmentioning

confidence: 99%

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Lam

Shum

Zhu

et al. 2020

Preprint

231

234

View full text Add to dashboard Cite

show abstract

“…The homologous protein sequences were aligned with the program MAFFT [59]. The protein disorder probability was calculated using the disEMBL [60] server with loops and coils defined by dictionary of secondary structure of proteins [61].…”

Section: Methodsmentioning

confidence: 99%

Structural role of essential light chains in the apicomplexan glideosome

Pažický

Dhamotharan

Kaszuba

et al. 2019

Preprint

View full text Add to dashboard Cite

28Apicomplexan parasites, such as Plasmodium falciparum and Toxoplasma gondii, traverse 29 the host tissues and invade the host cells exhibiting a specific type of motility called gliding. 30The molecular mechanism of gliding lies in the actin-myosin motor localized to the 31 intermembrane space between the plasma membrane and inner membrane complex (IMC) of 32 the parasites. Myosin A (MyoA) is a part of the glideosome, a large multi-protein complex, 33 which is anchored in the outer membrane of the IMC. MyoA is bound to the proximal essential 34 light chain (ELC) and distal myosin light chain (MLC1), which further interact with the 35 glideosome associated proteins GAP40, GAP45 and GAP50. Whereas structures of several 36 individual glideosome components and small dimeric complexes have been solved, structural 37 information concerning the interaction of larger glideosome subunits and their role in 38 glideosome function still remains to be elucidated. Here, we present structures of a T. gondii 39 trimeric glideosome sub complex composed of a myosin A light chain domain with bound 40 MLC1 and TgELC1 or TgELC2. Regardless of the differences between the secondary 41 structure content observed for free P. falciparum PfELC and T. gondii TgELC1 or TgELC2, 42 the proteins interact with a conserved region of TgMyoA to form structurally conserved 43 complexes. Upon interaction, the essential light chains undergo contraction and induce 44 α-helical structure in the myosin A C-terminus, stiffening the myosin lever arm. The complex 45 formation is further stabilized through binding of a single calcium ion to T. gondii ELCs. Our 46 work provides an important step towards the structural understanding of the entire glideosome 47 and uncovering the role of its members in parasite motility and invasion. 48 49 50 3 51 Author summary 52 Apicomplexans, such as Toxoplasma gondii or the malaria agent Plasmodium falciparum, are 53 small unicellular parasites that cause serious diseases in humans and other animals. These 54 parasites move and infect the host cells by a unique type of motility called gliding. Gliding is 55 empowered by an actin-myosin molecular motor located at the periphery of the parasites. 56 Myosin interacts with additional proteins such as essential light chains to form the glideosome, 57 a large protein assembly that anchors myosin in the inner membrane complex. Unfortunately, 58 our understanding of the glideosome is insufficient because we lack the necessary structural 59 information. Here we describe the first structures of trimeric glideosome sub complexes of T. 60 gondii myosin A bound to two different light chain combinations, which show that T. gondii and 61 P. falciparum form structurally conserved complexes. With an additional calcium-free complex 62 structure, we demonstrate that calcium binding does not change the formation of the 63 complexes, although it provides them with substantial stability. With additional data, we 64 propose that the role of the essential light chains is to enhance myosin perfor...

show abstract

“…For the maximum likelihood approach, sequences were first aligned using MAFFT with default settings (Rozewicki, et al 2019). Gap rich sites and poorly-aligned sequences were trimmed with TrimAl (Capella-Gutiérrez, et al 2009).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic inference identifies two eumetazoan TRPM clades and an 8^th family of TRP channel, TRP soromelastatin (TRPS)

Himmel

Gray

Cox

2019

Preprint

View full text Add to dashboard Cite

1TRP melastatins (TRPMs) are most well-known as cold and menthol sensors, but are in fact 2 broadly critical for life, from ion homeostasis to reproduction. Yet the evolutionary relationship 3 between TRPM channels remains largely unresolved, particularly with respect to the placement 4 of several highly divergent members. To characterize the evolution of TRPM and like channels, 5 we performed a large-scale phylogenetic analysis of >1,300 TRPM-like sequences from 14 phyla 6

show abstract

MAFFT-DASH: integrated protein sequence and structural alignment

Cited by 509 publications

References 33 publications

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Structural role of essential light chains in the apicomplexan glideosome

Phylogenetic inference identifies two eumetazoan TRPM clades and an 8^th family of TRP channel, TRP soromelastatin (TRPS)

Contact Info

Product

Resources

About

MAFFT-DASH: integrated protein sequence and structural alignment

Cited by 509 publications

References 33 publications

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

Structural role of essential light chains in the apicomplexan glideosome

Phylogenetic inference identifies two eumetazoan TRPM clades and an 8th family of TRP channel, TRP soromelastatin (TRPS)

Contact Info

Product

Resources

About

Phylogenetic inference identifies two eumetazoan TRPM clades and an 8^th family of TRP channel, TRP soromelastatin (TRPS)