Validation and quality assessment of macromolecular structures using complex network analysis

Pražnikar, Jure; Tomić, Miloš; Turk, Dušan

doi:10.1107/s2053273318094494

Cited by 6 publications

(10 citation statements)

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“…The extent of change of the contacts was analyzed by packing analysis of the structures using graph nodes described recently 56 . Here we calculated graphs of intra residue interactions within a 4.6 Å radius using only nonhydrogen atoms and disregarding two neighboring residues in the chain.…”

Section: Methodsmentioning

confidence: 99%

Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis

et al. 2020

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To achieve productive binding, enzymes and substrates must align their geometries to complement each other along an entire substrate binding site, which may require enzyme flexibility. In pursuit of novel drug targets for the human pathogen S. aureus, we studied peptidoglycan N-acetylglucosaminidases, whose structures are composed of two domains forming a V-shaped active site cleft. Combined insights from crystal structures supported by site-directed mutagenesis, modeling, and molecular dynamics enabled us to elucidate the substrate binding mechanism of SagB and AtlA-gl. This mechanism requires domain sliding from the open form observed in their crystal structures, leading to polysaccharide substrate binding in the closed form, which can enzymatically process the bound substrate. We suggest that these two hydrolases must exhibit unusual extents of flexibility to cleave the rigid structure of a bacterial cell wall.

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Section: Methodsmentioning

confidence: 99%

Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis

et al. 2020

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“…Due to this, 3D predictive models generated from this project, like the one we provided for AUH26_00140, should be further validated for accuracy. Procheck and other free webbased programs check the stereochemical quality of a model's structure, such as deviations from ideal bonding angles and bond length, and produce a Ramachandran plot identifying outliers and clashing contacts which is a standard part of structure analysis before deposition (Praznikar et al, 2019). Further, after completion of the project, selected HPs and identified similarly sequenced proteins with established annotation should undergo additional comparisons to support re-annotation conclusions.…”

Section: Further Computational Analysis Expands the Hpcp For Advancedmentioning

confidence: 99%

An Educational Bioinformatics Project to Improve Genome Annotation

2020

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Scientific advancement is hindered without proper genome annotation because biologists lack a complete understanding of cellular protein functions. In bacterial cells, hypothetical proteins (HPs) are open reading frames with unknown functions. HPs result from either an outdated database or insufficient experimental evidence (i.e., indeterminate annotation). While automated annotation reviews help keep genome annotation up to date, often manual reviews are needed to verify proper annotation. Students can provide the manual review necessary to improve genome annotation. This paper outlines an innovative classroom project that determines if HPs have outdated or indeterminate annotation. The Hypothetical Protein Characterization Project uses multiple well-documented, freely available, web-based, bioinformatics resources that analyze an amino acid sequence to (1) detect sequence similarities to other proteins, (2) identify domains, (3) predict tertiary structure including active site characterization and potential binding ligands, and (4) determine cellular location. Enough evidence can be generated from these analyses to support re-annotation of HPs or prioritize HPs for experimental examinations such as structural determination via X-ray crystallography. Additionally, this paper details several approaches for selecting HPs to characterize using the Hypothetical Protein Characterization Project. These approaches include student- and instructor-directed random selection, selection using differential gene expression from mRNA expression data, and selection based on phylogenetic relations. This paper also provides additional resources to support instructional use of the Hypothetical Protein Characterization Project, such as example assignment instructions with grading rubrics, links to training videos in YouTube, and several step-by-step example projects to demonstrate and interpret the range of achievable results that students might encounter. Educational use of the Hypothetical Protein Characterization Project provides students with an opportunity to learn and apply knowledge of bioinformatic programs to address scientific questions. The project is highly customizable in that HP selection and analysis can be specifically formulated based on the scope and purpose of each student’s investigations. Programs used for HP analysis can be easily adapted to course learning objectives. The project can be used in both online and in-seat instruction for a wide variety of undergraduate and graduate classes as well as undergraduate capstone, honor’s, and experiential learning projects.

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“…In proteins, some regions and strands may be intrinsically disordered such that they cannot be resolved by x-ray diffraction irrespective on the resolution and the overall quality of the experimental data. For this reason, the Z-score has been used as a measure of local model accuracy [46,47]. The Z-score is given by Z = (R − R res )/σ res [46][47][48], where R res and σ res are respectively the expected R-factor and the standard deviation of the R-factor values, calculated with the same amino acid in structures within the same resolution range.…”

Section: N-sh2 Domain Loops Are Characterized By Structural Disordermentioning

confidence: 99%

“…For this reason, the Z-score has been used as a measure of local model accuracy [46,47]. The Z-score is given by Z = (R − R res )/σ res [46][47][48], where R res and σ res are respectively the expected R-factor and the standard deviation of the R-factor values, calculated with the same amino acid in structures within the same resolution range. For instance, for the case of 2SHP with a resolution of 1.95 Å, the R-factor of each residue is compared with the expected R-factor and standard deviation detected from the same kind of residue in all structures of the database with resolution between 1.8 and 2.0 Å [48].…”

Section: N-sh2 Domain Loops Are Characterized By Structural Disordermentioning

confidence: 99%

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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Anselmi

Hub

2020

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SHP2 is a critical regulator of signal transduction implicated in developmental disorders and cancer. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as a key "allosteric switch" for SHP2 activation. We critically review structural data and use extensive molecular simulations to test the "allosteric switch" model of activation. We find that the binding cleft in N-SH2 is constitutively flexible and open in solution, and that a closed cleft found in certain structures has been imposed by crystal contacts. The free energy cost for N-SH2 release is only marginally influenced by the binding cleft. We conclude that not the N-SH2 binding cleft but instead the opening of a central β-sheet of N-SH2 is the key allosteric switch triggering SHP2 activation.

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Validation and quality assessment of macromolecular structures using complex network analysis

Cited by 6 publications

References 0 publications

Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis

Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis

An Educational Bioinformatics Project to Improve Genome Annotation

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

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