Tools for comparative protein structure modeling and analysis

Eswar, Narayanan; John, Bino; Mirkovic, Nebojsa; Fiser, András; Ilyin, Valentin A.; Pieper, Ursula; Stuart, Ashley C.; Martí‐Renom, Marc A.; Madhusudhan, M.S.; Yerkovich, Bozidar; Šali, Andrej

doi:10.1093/nar/gkg543

Cited by 432 publications

(364 citation statements)

References 38 publications

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“…Our pipeline workflow incorporates the NCBI tools platform (24), including the BLAST program for similarity searching of sequence databases. T-COFFEE (25) was used for alignment of the test sequence with the template, followed by iterations of the MODELLER-9.11 program (26) to generate the final model structure. The Chimera program (27) was used for the viewing of models and generation of images.…”

Section: Methodsmentioning

confidence: 99%

New Hyperekplexia Mutations Provide Insight into Glycine Receptor Assembly, Trafficking, and Activation Mechanisms

Bode

Wood

Mullins

et al. 2013

Journal of Biological Chemistry

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Background: Hyperekplexia mutations have provided much information about glycine receptor structure and function. Results: We identified and characterized nine new mutations. Dominant mutations resulted in spontaneous activation, whereas recessive mutations precluded surface expression. Conclusion: These data provide insight into glycine receptor activation mechanisms and surface expression determinants. Significance: The results enhance our understanding of hyperekplexia pathology and glycine receptor structure-function.

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Section: Methodsmentioning

confidence: 99%

New Hyperekplexia Mutations Provide Insight into Glycine Receptor Assembly, Trafficking, and Activation Mechanisms

Bode

Wood

Mullins

et al. 2013

Journal of Biological Chemistry

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“…The PALES (38) software was used to fit the measured H N -N RDCs to those back-calculated from the crystal structure of the holo-(histidine) HisJ complex (PDB 1HSL) and models of D1 and D2 built from the apo-and holo-HisJ structures. Of note, the deposited holo-HisJ structure (1HSL) contains four point mutations (N5K, S22A, E107A, and S184A) that were corrected to match the HisJ sequence from E. coli K12 (GenBank TM accession number BAA16155.1) using MODELLER (39) CSPs upon ligand binding were examined on a per residue basis using a combined chemical shift difference, where applicable, according to Mulder et al (40) for backbone atoms, where R i denotes the scaling factor of nucleus i. The scaling factors used were R N ϭ 6.4, R CЈ ϭ 3.0, R C ␣ , and R C ␤ ϭ 3.2 as shown in Equation 3.…”

Section: Methodsmentioning

confidence: 99%

Role of the Two Structural Domains from the Periplasmic Escherichia coli Histidine-binding Protein HisJ

Chu

DeWolf

Vogel

2013

Journal of Biological Chemistry

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“…Structure modelling of cpnSET was carried out using the virus SET structure as a template (Eswar et al, 2003;Manzur et al, 2003) and peptide docking analysis onto cpnSET was performed using AutoDock (Morris et al, 1996).…”

Section: Methodsmentioning

confidence: 99%

Chlamydial SET domain protein functions as a histone methyltransferase

et al. 2007

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SET domain genes have been identified in numbers of bacterial genomes based on similarity to SET domains of eukaryotic histone methyltransferases. Herein, a Chlamydophila pneumoniae SET domain gene was clarified to be coincidently expressed with hctA and hctB genes encoding chlamydial histone H1-like proteins, Hc1 and Hc2, respectively. The SET domain protein (cpnSET) is localized in chlamydial cells and interacts with Hc1 and Hc2 through the C-terminal SET domain. As expected from conservation of catalytic sites in cpnSET, it functions as a protein methyltransferase to murine histone H3 and Hc1. However, little is known about protein methylation in the molecular pathogenesis of chlamydial infection. cpnSET may play an important role in chlamydial cell maturation due to modification of chlamydial histone H1-like proteins. INTRODUCTIONChlamydophila pneumoniae is an obligatory intracellular eubacterium that causes acute respiratory diseases and may be involved in chronic inflammatory processes, such as atherosclerosis (Rosenfeld et al., 2000), asthma (Hahn et al., 1991) and Alzheimer's disease (Itzhaki et al., 2004). Persistence of chlamydial infection has been thought to be important for chronic diseases and has been characterized using model animals and activation stimuli such as cytokines and antibiotics (Beatty et al., 1993;Belland et al., 2003;Malinverni et al., 1995;Mehta et al., 1998). However, molecular-level relationships between chronic disease progression and persistent infection are not yet clear.Chlamydiae exhibit a unique life cycle in which they alternate morphologies between elementary bodies (EBs) and reticulate bodies (RBs). EBs are transcriptionally inactive electron-dense particles that are internalized into host cells by inducing phagocytosis. EB differentiation into RBs occurs with the development of phagosomes into inclusions. Transcriptionally active RBs multiply by binary fission with nutrients acquired from the host cell. At the end of the developmental cycle, RBs are converted into EBs and released from host cells for the next infection. Besides the developmental cycle, during persistent infection caused by exposure to interferon gamma (IFN-c) or antibiotics, RBs differentiate into aberrantly large and non-multiplying RBs (Belland et al., 2003). However, little is known about the switching mechanism whereby vegetative RBs convert into infectious EBs or aberrant RBs. Understanding this molecular system should be helpful for the prevention of persistent chlamydial infection.Two eukaryotic histone H1-like proteins of chlamydiae, Hc1 and Hc2, are present mainly in EBs, where those proteins bind DNA and promote genomic DNA condensation (Barry et al., 1992;Hackstadt et al., 1991;Perara et al., 1992;Tao et al., 1991). Recently a small regulatory RNA gene was identified as a suppressor of the lethal phenotype of hctA overexpression in Escherichia coli and it was shown to negatively regulate Hc1 synthesis at an early stage of infection (Grieshaber et al., 2006 HEp-2 cells (ATCC CCL-23) were used ...

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Tools for comparative protein structure modeling and analysis

Cited by 432 publications

References 38 publications

New Hyperekplexia Mutations Provide Insight into Glycine Receptor Assembly, Trafficking, and Activation Mechanisms

New Hyperekplexia Mutations Provide Insight into Glycine Receptor Assembly, Trafficking, and Activation Mechanisms

Role of the Two Structural Domains from the Periplasmic Escherichia coli Histidine-binding Protein HisJ

Chlamydial SET domain protein functions as a histone methyltransferase

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