SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

Guex, Nicolas; Peitsch, Manuel C.

doi:10.1002/elps.1150181505

Cited by 10,321 publications

(7,403 citation statements)

References 33 publications

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“…In this context, we made a model of a homodimer of βNAC NAC domain (TβNAC, Supplemental Fig. 3) using the SWISS-MODEL online server (Guex and Peitsch, 1997;Schwede et al, 2003;Arnold et al, 2006) and the NAC α -NAC β heterodimer as the template structure. We assessed packing quality of this TβNAC model using the atomic empirical mean force potential implemented in the program ANOLEA (Melo and Feytmans, 1998) and using the program Protein & Cell PROCHECK (Laskowski et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

et al. 2010

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Nascent polypeptide associated complex (NAC) and its two isolated subunits, αNAC and βNAC, play important roles in nascent peptide targeting. We determined a 1.9 Å resolution crystal structure of the interaction core of NAC heterodimer and a 2.4 Å resolution crystal structure of αNAC NAC domain homodimer. These structures provide detailed information of NAC heterodimerization and αNAC homodimerization. We found that the NAC domains of αNAC and βNAC share very similar folding despite of their relative low identity of amino acid sequences. Furthermore, different electric charge distributions of the two subunits at the NAC interface provide an explanation to the observation that the heterodimer of NAC complex is more stable than the single subunit homodimer. In addition, we successfully built a βNAC NAC domain homodimer model based on homologous modeling, suggesting that NAC domain dimerization is a general property of the NAC family. These 3D structures allow further studies on structurefunction relationship of NAC.

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Section: Discussionmentioning

confidence: 99%

Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

et al. 2010

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“…These template structures were prepared by removing all but one catalytic dimer, by removing all ligands and crystallographic ions and solvent, and by removing atoms to convert modified residues to their parent residues. An alignment with the template structures was generated for each MLSA using SWISS‐PDB Viewer (Guex & Peitsch, 1997) with the MLSA threaded to the superimposed templates. Spatially restrained homology models based on these alignments were generated using Modeller 9.15 (Sali & Overington, 1994) with the positions of the alpha carbons constrained to maintain backbone symmetry across the two chains of the dimer.…”

Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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“…The three-dimensional structure of the basal inactive form of SHP-2 was obtained through Protein Data bank code 2SHP (Hof et al, 1998) with the use of DeepView Swiss-PdbViewer 3.7 (Guex and Peitsch, 1997).…”

Section: Molecular Modelingmentioning

confidence: 99%

Isolation of a distinct class of gain-of-function SHP-2 mutants with oncogenic RAS-like transforming activity from solid tumors

Miyamoto

Takahashi

et al. 2008

Oncogene

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SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

Cited by 10,321 publications

References 33 publications

Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Isolation of a distinct class of gain-of-function SHP-2 mutants with oncogenic RAS-like transforming activity from solid tumors

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