PDBsum: Structural summaries of PDB entries

Laskowski, Roman A.; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M.

doi:10.1002/pro.3289

Cited by 1,146 publications

(746 citation statements)

References 43 publications

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“…The quantification analysis of the impact of studied mutations on the B30.2 domain secondary structure and structural changes plotting were performed, using the PDBsum web server …”

Section: Methodsmentioning

confidence: 99%

“…The quantification analysis of the impact of studied mutations on the B30.2 domain secondary structure and structural changes plotting were performed, using the PDBsum web server. 32 All software packages were used in the Linux operating system on the computer cluster of the IMB NAS RA and on HPC of Lomonosov Moscow State University. 33…”

Section: A Te Ri a L S A Nd M E Th Odsmentioning

confidence: 99%

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Complex formation dynamics of native and mutated pyrin's B30.2 domain with caspase‐1

Arakelov

Nazaryan

2018

Proteins

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Pyrin protein is the product of the MEFV gene, mutations in which cause manifestation of familial Mediterranean fever (FMF). Functions of pyrin are not completely clear. The secondary structure of the pyrin is represented with four domains and two motifs. Mutations p.M680I, p.M694V, p.M694I, p.K695R, p.V726A, and p.A744S, which are located in the B30.2 domain of pyrin protein, are responsible for manifestation of the most common and severe forms of FMF. All the domains and the motifs of pyrin, are directly or indirectly, involved in the protein-protein interaction with proteins of apoptosis and regulate the cascade of inflammatory reactions, which is impaired due to pyrin mutations. It is well known, that malfunction of the pyrin-caspase-1 complex is the main reason of inflammation during FMF. Complete tertiary structure of pyrin and the effects of mutations in it are experimentally not studied yet. The aim of this study was to identify possible effects of the abovementioned mutations in the B30.2 domain tertiary structure and to determine their potential consequences in formation of the B30.2-caspase-1 complex. Using in silico methods, it was found, that these mutations led to structural rearrangements in B30.2 domain tertiary structure, causing shifts of binding sites and altering the interaction energy between B30.2 and caspase-1.

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“…The quantification analysis of the impact of studied mutations on the B30.2 domain secondary structure and structural changes plotting were performed, using the PDBsum web server …”

Section: Methodsmentioning

confidence: 99%

Section: A Te Ri a L S A Nd M E Th Odsmentioning

confidence: 99%

Complex formation dynamics of native and mutated pyrin's B30.2 domain with caspase‐1

Arakelov

Nazaryan

2018

Proteins

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“…The peptide inhibitors were modeled from the composite omit map and the difference Fourier maps, and were built with O or COOT and further refined with CNS or Refmac until convergence [26][27][28]. Models were validated with the Ramachandran plot using PROCHECK [29]. The final refinement statistics are shown in Table 1.…”

Section: Methodsmentioning

confidence: 99%

“…Surprisingly, for the first time in our studies the C terminal Histag included in cloning was visible in the electron density. More than 90% of residues are within the allowed region of Ramachandran plot as per PROCHECK or PDBSUM [29].…”

Section: Crystal Structure Of Bont/a-lc With Rrkcrllmentioning

confidence: 99%

Structure Based Discovery of Pan Active Botulinum Neurotoxin Inhibitors

Vieni¹,

McGillick²,

Kumaran³

et al. 2018

J Infect Dis Ther

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Clostridium botulinum neurotoxins (BoNTs) released by the bacterium Clostridium botulinum are the most potent toxins causing the fatal disease called botulism. There are seven distinct serotypes of BoNTs (A to G) released by various strains of botulinum. They all have high sequence homology and similar three-dimensional structure. The toxicity of BoNT follows a four-step process-binding, internalization, translocation, and cleavage of its target protein, one of the three components of the SNARE complex (Soluble N-ethylmaleimde-sensitive factor attachment protein receptor) required for membrane docking and neurotransmitter release. Cleavage of one of the three proteins causes blockage of neurotransmitter release leading to flaccid paralysis. Though anyone of the above four steps could be a target for developing antidotes for botulism, the catalytic domain is the most suitable target for post exposure treatment. Of the seven serotypes BoNT/A, B, E and probably F affect humans, with BoNT/A considered to be the most potent. Development of drugs for botulism is focused on serotype specific inhibitors, but pan-active inhibitor acting on several serotypes is preferable since it is difficult to identify the serotype before the treatment, especially since there is at least a 36 h window before botulism can be diagnosed. Using structure-based drug discovery, we have developed three heptapeptides based on the SNARE proteins which inhibit BoNT/A, B and E equally well. Probable reasons for pan-activity of these peptides are discussed.

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“…The I-TASSER pipeline is an online platform that implements the I-TASSER-based algorithms for protein structure and function predictions (Yang et al, 2015;Zhang, Mortuza, He, Wang, & Zhang, 2017). Secondary and tertiary structures were analysed using PDBsum (http://www.ebi.ac.uk/ thorn ton-srv/datab ases/pdbsu m/ (Laskowski, Jablonska, Pravda, Varekova, & Thornton, 2018). Best predicted models were evaluated by means of the stereochemical quality and structural integrity of the model by RAMPAGE at http://mordr ed.bioc.cam.ac.uk/~rappe r/rampa ge.php (Lovell et al, 2003).…”

Section: In Silico Equine Pdia1 Structural Modellingmentioning

confidence: 99%

Structural modelling of the equine protein disulphide isomerase A1 and its quantification in the epididymis and seminal plasma

et al. 2020

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The protein disulphide isomerase A1 (PDIA1) is an important chaperone involved in protein quality control and redox regulation. Also, the ability of PDIA1 to bind to oestrogens suggests that it may play a role in epididymal maturation and male fertility. The goals of this study were to (a) verify the possible interaction between 17β‐estradiol and equine PDIA1 using bioinformatics; (b) identify and quantify PDIA1 protein in equine cauda epididymis throughout peripuberty; and (c) determine whether the amounts of PDIA1 in equine seminal plasma and spermatozoa are associated with fertility. Using in silico analysis, we were able to predict the tertiary structure of equine PDIA1 and to demonstrate the interaction between 17β‐estradiol and the putative binding site in domains b and b’. Colts under 24 months of age had lower relative amounts of PDIA1 in cauda epididymal fluid in comparison with older males (p < .01). No difference was observed in seminal plasma PDIA1 between fertile and subfertile stallions. Our study demonstrates that PDIA1 expression in the epididymis increases during peripuberty. However, in the adult stallion, its quantity in seminal plasma is not associated with fertility.

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PDBsum: Structural summaries of PDB entries

Cited by 1,146 publications

References 43 publications

Complex formation dynamics of native and mutated pyrin's B30.2 domain with caspase‐1

Complex formation dynamics of native and mutated pyrin's B30.2 domain with caspase‐1

Structure Based Discovery of Pan Active Botulinum Neurotoxin Inhibitors

Structural modelling of the equine protein disulphide isomerase A1 and its quantification in the epididymis and seminal plasma

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