PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL

Janson, Giacomo; Zhang, Chengxin; Prado, Maria G.; Paiardini, Alessandro

doi:10.1093/bioinformatics/btw638

Cited by 213 publications

(147 citation statements)

References 20 publications

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“…Structure of the CASK L27 domain and its complex with SAP97 have been analyzed using Mistic2 (Colell, Iserte, Simonetti, & Marino‐Buslje, ) to evaluate covariation between residues. Structures were manually explored with Pymol (Janson, Zhang, Prado, & Paiardini, ) or UCSF Chimera (Pettersen et al, ).…”

Section: Methodsmentioning

confidence: 99%

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

et al. 2019

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Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low‐cost next‐generation sequencing gene panel that has been transferred into clinical practice, replacing single disease‐gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease‐gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease‐causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.

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Section: Methodsmentioning

confidence: 99%

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

et al. 2019

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“…There are 94% of most favored, 5.3% of allowed and 0.3% of disallowed Ramachandran plot in the final refinement model. All structural figures were generated using PyMOL 51 .…”

Section: Methodsmentioning

confidence: 99%

Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein

et al. 2019

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Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The epitopes and mechanisms of mAbs targeting non-RBD regions have not been well characterized yet. Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. Structure determination and mutagenesis experiments reveal the epitope and critical residues on the NTD for 7D10 binding and neutralization. Further experiments indicate that the neutralization by 7D10 is not solely dependent on the inhibition of DPP4 binding, but also acts after viral cell attachment, inhibiting the pre-fusion to post-fusion conformational change of the spike. These properties give 7D10 a wide neutralization breadth and help explain its synergistic effects with several RBD-targeting antibodies.

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“…The program Phyre 228 was used to detect template folds for the Nterminal periplasmic domain (PP domain; 20-274) and the best hits (Accuracy = 100%) found were chosen for model construction, and aligned to detect structurally conserved regions (SCRs) using PyMod 2.0. 29,30 A multiple sequence alignment between PA0575 and templates was obtained using the program Muscle. 31 The alignment was then used for the secondary structure prediction (PhD server) 32 and for detection of evolutionary conserved residues.…”

Section: Pa0575 Domains Modelingmentioning

confidence: 99%

A novel bacterial l‐arginine sensor controlling c‐di‐GMP levels in Pseudomonas aeruginosa

et al. 2018

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Nutrients such as amino acids play key roles in shaping the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond taking part to cellular metabolism and to protein synthesis, amino acids are also signaling molecules able to influence group behavior in microorganisms, such as biofilm formation. This lifestyle switch involves complex metabolic reprogramming controlled by local variation of the second messenger 3', 5'-cyclic diguanylic acid (c-di-GMP). The intracellular levels of this dinucleotide are finely tuned by the opposite activity of dedicated diguanylate cyclases (GGDEF signature) and phosphodiesterases (EAL and HD-GYP signatures), which are usually allosterically controlled by a plethora of environmental and metabolic clues. Among the genes putatively involved in controlling c-di-GMP levels in P. aeruginosa, we found that the multidomain transmembrane protein PA0575, bearing the tandem signature GGDEF-EAL, is an l-arginine sensor able to hydrolyse c-di-GMP. Here, we investigate the basis of arginine recognition by integrating bioinformatics, molecular biophysics and microbiology. Although the role of nutrients such as l-arginine in controlling the cellular fate in P. aeruginosa (including biofilm, pathogenicity and virulence) is already well established, we identified the first l-arginine sensor able to link environment sensing, c-di-GMP signaling and biofilm formation in this bacterium.

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PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL

Abstract: alessandro.paiardini@uniroma1.it or giacomo.janson@uniroma1.it

Cited by 213 publications

References 20 publications

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

Characterization of intellectual disability and autism comorbidity through gene panel sequencing

Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein

A novel bacterial l‐arginine sensor controlling c‐di‐GMP levels in Pseudomonas aeruginosa

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