Homology-based loop modeling yields more complete crystallographic protein structures

Beusekom, Bart van; Joosten, Krista; Hekkelman, Maarten L.; Joosten, Robbie P.; Perrakis, Anastassis

doi:10.1107/s2052252518010552

Cited by 31 publications

(21 citation statements)

References 44 publications

(50 reference statements)

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“…The data were phased using PHASER using pdb 4OUE as a molecular replacement model and refined using REFMAC [ 37 ] and Coot [ 38 ] within the CCP4 software environment [ 39 ]. The PDB REDO server [ 40 ] was used to optimize the refinement parameters and the model was validated using the Molprobity server [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

Fucosidases from the human gut symbiont Ruminococcus gnavus

Rebello

Crost

et al. 2020

Cell. Mol. Life Sci.

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The availability and repartition of fucosylated glycans within the gastrointestinal tract contributes to the adaptation of gut bacteria species to ecological niches. To access this source of nutrients, gut bacteria encode α-l-fucosidases (fucosidases) which catalyze the hydrolysis of terminal α-l-fucosidic linkages. We determined the substrate and linkage specificities of fucosidases from the human gut symbiont Ruminococcus gnavus. Sequence similarity network identified strain-specific fucosidases in R. gnavus ATCC 29149 and E1 strains that were further validated enzymatically against a range of defined oligosaccharides and glycoconjugates. Using a combination of glycan microarrays, mass spectrometry, isothermal titration calorimetry, crystallographic and saturation transfer difference NMR approaches, we identified a fucosidase with the capacity to recognize sialic acid-terminated fucosylated glycans (sialyl Lewis X/A epitopes) and hydrolyze α1-3/4 fucosyl linkages in these substrates without the need to remove sialic acid. Molecular dynamics simulation and docking showed that 3′-Sialyl Lewis X (sLeX) could be accommodated within the binding site of the enzyme. This specificity may contribute to the adaptation of R. gnavus strains to the infant and adult gut and has potential applications in diagnostic glycomic assays for diabetes and certain cancers.

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Section: Methodsmentioning

confidence: 99%

Fucosidases from the human gut symbiont Ruminococcus gnavus

Rebello

Crost

et al. 2020

Cell. Mol. Life Sci.

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“…Pathogenicity of the p.L381P renin variant was predicted using the following in silico tools: PolyPhen-2 29 , Sorting Intolerant From Tolerant (SIFT) 30 , Site Directed Mutator (SDM) 31 and Mutation Taster 32 . The effect of the L381P mutation was predicted with the standalone version of FoldX 33 using as starting point the re-refined coordinates of PDB entry 4AMT in the PDB-REDO databank 34 . This model was prepared using the RepairPDB command of FoldX and subsequently subjected to 5 BuildModel runs, resulting in an average free energy difference between the wild-type and the mutant of 3.1 Kcal/mol (consistent with a destabilizing mutation).…”

Section: Methodsmentioning

confidence: 99%

Autosomal Dominant Tubulointerstitial Kidney Disease with Adult Onset due to a Novel Renin Mutation Mapping in the Mature Protein

Schaeffer

Izzi

Vettori

et al. 2019

Sci Rep

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Autosomal dominant tubulointerstitial kidney disease (ADTKD) is a genetically heterogeneous renal disorder leading to progressive loss of renal function. ADTKD- REN is due to rare mutations in renin, all localized in the protein leader peptide and affecting its co-translational insertion in the endoplasmic reticulum (ER). Through exome sequencing in an adult-onset ADTKD family we identified a new renin variant, p.L381P, mapping in the mature protein. To assess its pathogenicity, we combined genetic data, computational and predictive analysis and functional studies. The L381P substitution affects an evolutionary conserved residue, co-segregates with renal disease, is not found in population databases and is predicted to be deleterious by in silico tools and by structural modelling. Expression of the L381P variant leads to its ER retention and induction of the Unfolded Protein Response in cell models and to defective pronephros development in zebrafish. Our work shows that REN mutations outside of renin leader peptide can cause ADTKD and delineates an adult form of ADTKD- REN , a condition which has usually its onset in childhood. This has implications for the molecular diagnosis and the estimated prevalence of the disease and points at ER homeostasis as a common pathway affected in ADTKD- REN , and possibly more generally in ADTKD.

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“…None of the three models pass these criteria. The Ramachandran plot Z-score (Rama-Z; Hooft et al, 1997;van Beusekom et al, 2018;Sobolev et al, 2020) provides a convenient numerical estimate of the protein main-chain conformation validity. The rule-of-thumb interpretation of the Ramachandran plot Z-score (Sobolev et al, 2020) can be summarized as |Rama-Z| > 3 is poor, indicating improbable backbone geometry, 2 < |Rama-Z| < 3 is unlikely yet possible and |Rama-Z| < 2 is a good, normal backbone.…”

Section: Test-model Selection Preparation Refinement Setup and Analmentioning

confidence: 99%

Real-space quantum-based refinement for cryo-EM: Q|R#3

Wang

Kruse

Sobolev

et al. 2020

Acta Cryst Sect D Struct Biol

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Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.

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Homology-based loop modeling yields more complete crystallographic protein structures

Abstract: Thousands of regions missing from existing protein structure models are completed using new methods based on homology.

Cited by 31 publications

References 44 publications

Fucosidases from the human gut symbiont Ruminococcus gnavus

Fucosidases from the human gut symbiont Ruminococcus gnavus

Autosomal Dominant Tubulointerstitial Kidney Disease with Adult Onset due to a Novel Renin Mutation Mapping in the Mature Protein

Real-space quantum-based refinement for cryo-EM: Q|R#3

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