PROMALS3D web server for accurate multiple protein sequence and structure alignments

Pei, Jimin; Ming, Tang; Grishin, Nick V.

doi:10.1093/nar/gkn322

Cited by 153 publications

(148 citation statements)

References 25 publications

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“…Specifically, we aligned sequences using 10 alternative methods, and for each resulting alignment, we performed maximum likelihood and Bayesian analyses using two different substitution models. Briefly, we aligned sequences using Dialign (66), Kalign2 (67), the E-INS-i, G-INS-i, and L-INS-i strategies from Mafft v6.17 (68), Muscle v3.5 (69), Prank (70), Probalign (71), Probcons (72), and PROMALS3d (73). A data file containing the complete set of sequence alignments is provided in the SI Appendix and Dataset S1.…”

Section: Methodsmentioning

confidence: 99%

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

Hoffmann

Opazo

Storz

2010

Proc. Natl. Acad. Sci. U.S.A.

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Natural selection often promotes evolutionary innovation by coopting preexisting genes for new functions, and this process may be greatly facilitated by gene duplication. Here we report an example of cooptive convergence where paralogous members of the globin gene superfamily independently evolved a specialized O 2 transport function in the two deepest branches of the vertebrate family tree. Specifically, phylogenetic evidence demonstrates that erythroidspecific O 2 transport hemoglobins evolved independently from different ancestral precursor proteins in jawed vertebrates (gnathostomes) and jawless fish (cyclostomes, represented by lamprey and hagfish). A comprehensive phylogenetic analysis of the vertebrate globin gene superfamily revealed that the erythroid hemoglobins of cyclostomes are orthologous to the cytoglobin protein of gnathostome vertebrates, a hexacoordinate globin that has no O 2 transport function and that is predominantly expressed in fibroblasts and related cell types. The phylogeny reconstruction also revealed that vertebrate-specific globins are grouped into four main clades: (i) cyclostome hemoglobin + cytoglobin, (ii) myoglobin + globin E, (iii) globin Y, and (iv) the α-and β-chain hemoglobins of gnathostomes. In the hemoglobins of gnathostomes and cyclostomes, multisubunit quaternary structures provide the basis for cooperative O 2 binding and allosteric regulation by coupling the effects of ligand binding at individual subunits with interactions between subunits. However, differences in numerous structural details belie their independent origins. This example of convergent evolution of protein function provides an impressive demonstration of the ability of natural selection to cobble together complex design solutions by tinkering with different variations of the same basic protein scaffold.cytoglobin | gene family evolution | globin | hagfish | lamprey

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Section: Methodsmentioning

confidence: 99%

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

Hoffmann

Opazo

Storz

2010

Proc. Natl. Acad. Sci. U.S.A.

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“…Protein structural analyses were also performed with the SWISS-MODEL (http://swissmodel.expasy.org/) (31,32) and PROMALS3D (http://prodata.swmed.edu/promals3d/promals3d .php) (40,41) tools. For the original TGD gene prediction numbers, TIGR locus designations, GenBank accession numbers, and scaffold positions, see Table S1 in the supplemental material.…”

Section: Methodsmentioning

confidence: 99%

Nucleus-Specific Importin Alpha Proteins and Nucleoporins Regulate Protein Import and Nuclear Division in the Binucleate Tetrahymena thermophila

Malone

Falkowska

et al. 2008

Eukaryot Cell

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The ciliate Tetrahymena thermophila, having both germ line micronuclei and somatic macronuclei, must possess a specialized nucleocytoplasmic transport system to import proteins into the correct nucleus. To understand how Tetrahymena can target proteins to distinct nuclei, we first characterized FG repeat-containing nucleoporins and found that micro-and macronuclei utilize unique subsets of these proteins. This finding implicates these proteins in the differential permeability of the two nuclei and implies that nuclear pores with discrete specificities are assembled within a single cell. To identify the import machineries that interact with these different pores, we characterized the large families of karyopherin homologs encoded within the genome. Localization studies of 13 putative importin (imp) ␣-and 11 imp ␤-like proteins revealed that imp ␣-like proteins are nucleus specific-nine localized to the germ line micronucleus-but that most imp ␤-like proteins localized to both types of nuclei. These data suggest that micronucleus-specific proteins are transported by specific imp ␣ adapters. The different imp ␣ proteins exhibit substantial sequence divergence and do not appear to be simply redundant in function. Disruption of the IMA10 gene encoding an imp ␣-like protein that accumulates in dividing micronuclei results in nuclear division defects and lethality. Thus, nucleus-specific protein import and nuclear function in Tetrahymena are regulated by diverse, specialized karyopherins.The regulated transport of macromolecules into and out of the nucleus controls many cellular processes. The import of proteins containing nuclear localization signals (NLSs) is facilitated by karyopherin proteins, also known as importins. Karyopherins shuttle their NLS-containing cargo through nuclear pore complexes (NPCs), protein channels that permeate the nuclear membrane. Two classes of karyopherins, imp ␣ and ␤ proteins, collaborate to orchestrate specific nucleocytoplasmic trafficking (reviewed in reference 13). To transport proteins containing a classical NLS (cNLS), imp ␣ binds to the cargo's cNLS and associates with imp ␤ in a ternary complex that docks at an NPC (reviewed in reference 23). The karyopherin-cargo complex is directed through the NPC, primarily through interactions of imp ␤ with NPC proteins (6, 7, 26). Nuclear proteins may, alternatively, contain nonclassical NLSs that mediate direct association with imp ␤ proteins without the imp ␣ adapter.Eukaryotic cells typically encode multiple karyopherins. In yeast and humans, which contain at least 14 and 20 karyopherins, respectively, most are members of the imp ␤ family. Yeast encodes just one imp ␣, whereas humans possess three distinct classes (reviewed in reference 23). The imp ␣ proteins have a characteristic structure consisting of an amino (N)-terminal imp ␤-binding (IBB) domain of ϳ100 amino acids (aa) that is followed by 8 to 10 alpha-helical armadillo (ARM) repeats that span most of the remainder of the protein. The ARM repeats are responsible for recognition ...

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“…Thus, an initial homology model of the C/C dimer of the sapovirus capsid protein was constructed from the atomic structures of vesivirus using the MODELLER 9v10 comparative-modeling program (17). To build the homology model, multiple-sequence alignments of the calicivirus capsid proteins were performed using the PROMALS3D program (18,19); the conserved secondary structural elements as well as the sequence similarities were incorporated to improve the alignment accuracy because of their low sequence similarities (Ͻ30%). Five multiple templates were created initially.…”

Section: Homology Model Building Of Yokote/mc114 Vp1mentioning

confidence: 99%

Antigenic and Cryo-Electron Microscopy Structure Analysis of a Chimeric Sapovirus Capsid

Miyazaki

Taylor

Hansman

et al. 2016

J Virol

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The capsid protein (VP1) of all caliciviruses forms an icosahedral particle with two principal domains, shell (S) and protruding (P) domains, which are connected via a flexible hinge region. The S domain forms a scaffold surrounding the nucleic acid, while the P domains form a homodimer that interacts with receptors. The P domain is further subdivided into two subdomains, termed P1 and P2. The P2 subdomain is likely an insertion in the P1 subdomain; consequently, the P domain is divided into the P1-1, P2, and P1-2 subdomains. In order to investigate capsid antigenicity, N-terminal (N-term)/S/P1-1 and P2/P1-2 were switched between two sapovirus genotypes GI.1 and GI.5. The chimeric VP1 constructs were expressed in insect cells and were shown to self-assemble into virus-like particles (VLPs) morphologically similar to the parental VLPs. Interestingly, the chimeric VLPs had higher levels of cross-reactivities to heterogeneous antisera than the parental VLPs. In order to better understand the antigenicity from a structural perspective, we determined an intermediate-resolution (8.5-Å) cryo-electron microscopy (cryo-EM) structure of a chimeric VLP and developed a VP1 homology model. The cryo-EM structure revealed that the P domain dimers were raised slightly (ϳ5 Å) above the S domain. The VP1 homology model allowed us predict the S domain (67-229) and P1-1 (229 -280), P2 (281-447), and P1-2 (448 -567) subdomains. Our results suggested that the raised P dimers might expose immunoreactive S/P1-1 subdomain epitopes. Consequently, the higher levels of cross-reactivities with the chimeric VLPs resulted from a combination of GI.1 and GI.5 epitopes. IMPORTANCEWe developed sapovirus chimeric VP1 constructs and produced the chimeric VLPs in insect cells. We found that both chimeric VLPs had a higher level of cross-reactivity against heterogeneous VLP antisera than the parental VLPs. The cryo-EM structure of one chimeric VLP (Yokote/Mc114) was solved to 8.5-Å resolution. A homology model of the VP1 indicated for the first time the putative S and P (P1-1, P2, and P1-2) domains. The overall structure of Yokote/Mc114 contained features common among other caliciviruses. We showed that the P2 subdomain was mainly involved in the homodimeric interface, whereas a large gap between the P1 subdomains had fewer interactions. Human sapovirus (genus Sapovirus) is a causative agent of gastroenteritis and a member of the Caliciviridae family. Other genera in the Caliciviridae family include Norovirus, Vesivirus, Lagovirus, and Nebovirus. The genomic organizations of all caliciviruses are similar, with the 5= half encoding the nonstructural proteins and the 3= half encoding structural proteins, including the capsid protein (VP1) and a small unknown structural protein, termed VP2 (reviewed in reference 1). Human sapovirus cannot be grown in cell culture, but expression of the VP1 in insect cells results in the formation of virus-like particles (VLPs) that are morphologically and antigenically similar to the native virions (2). There ar...

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PROMALS3D web server for accurate multiple protein sequence and structure alignments

Cited by 153 publications

References 25 publications

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

Nucleus-Specific Importin Alpha Proteins and Nucleoporins Regulate Protein Import and Nuclear Division in the Binucleate Tetrahymena thermophila

Antigenic and Cryo-Electron Microscopy Structure Analysis of a Chimeric Sapovirus Capsid

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