Structure and Molecular Dynamic Regulation of FKBP35 from Plasmodium knowlesi by Structural Homology Modeling and Electron Microscopy

Silvester, Jovi; Linda, Herman Umbau Anak; Lee, Ping Chin; Ying, Lau Tiek; Budiman, Cahyo

doi:10.3923/jbs.2017.369.380

Cited by 4 publications

(3 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This indicated that the cleavage of Pk-FKBP35 by chymotrypsin was not in the region responsible for catalysis. The domain linker of Pk-FKBP35 was indeed found not to play any role in catalysis (Silvester et al, 2017). Similarly, the TPR domain, which was apparently sensitive toward chymotrypsin, was not involved in the catalytic activity of Pk-FKBP35.…”

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 94%

“…Earlier, the linker of the catalytic and TPR domains of Pk-FKBP35 structurally is a flexible loop with high solvent accessibility. A fragment between Ser113 and Gln120 of the linker was found to have the highest flexibility and therefore predicted to be susceptible against protease (Silvester, Lindang, Chin, Ying, & Budiman, 2017). Similarly, a multidomain FKBP22, which consisted of N-chaperone and C-catalytic domains, were also cleaved by chymotrypsin at the domain linkers (Budiman et al, 2012).…”

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 99%

“…Further digestion might also occurred in the catalytic domain, yet, at a much lower rate than the TPR domain. Structurally, the catalytic domain folded into a more globular structure, while the TPR domain folded into a more elongated structure (Silvester et al, 2017;Alag et al, 2009), which made this domain is theoretically more prone to proteolytic degradation. Unfortunately, the N-terminal sequencings on E and F bands were unsuccessful (Table 1), which might be due to various fragments accumulated in these bands.…”

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 99%

See 2 more Smart Citations

REASSESSMENT OF THE CATALYTIC ACTIVITY AND SUBSTRATE SPECIFICITY OF FKBP35 FROM Plasmodium knowlesi USING PROTEASE-FREE ASSAY

Budiman¹,

Goh²,

Lee³

et al. 2020

BIJB

Self Cite

View full text Add to dashboard Cite

FK506-binding protein35 of Plasmodium knowlesi (Pk-FKBP35) is a member of peptidyl prolyl cis-trans isomerase (PPIase) and is considered as a promising avenue of antimalarial drug target development. This protein is organized into the N-terminal domain responsible for PPIase catalytic activity followed and the tetratricopeptide repeat domain for its dimerization. The protease-coupling and protease-free assays are known to be the common methods for investigating the catalytic properties of PPIase. Earlier, the protease-coupling assay was used to confirm the catalytic activity of Pk-FKBP35 in accelerating cis-trans isomerization of the peptide substrate. This report is aimed to re-assess the catalytic and substrate specificity of Pk-FKBP35 using an alternative method of a protease-free assay. The result indicated that while Pk-FKBP35 theoretically contained many possible cleavage sites of chymotrypsin, experimentally, the catalytic domain was relatively stable from chymotrypsin. Furthermore, under protease-free assay, Pk-FKBP35 also demonstrated remarkable PPIase catalytic activity with kcat/KM of 4.5 + 0.13 × 105 M−1 s−1, while the kcat/KM of active site mutant of D55A is 0.81 + 0.05 × 105 M−1 s−1. These values were considered comparable to kcat/KM obtained from the protease-coupling assay. Interestingly, the substrate specificities of Pk-FKBP35 obtained from both methods are also similar, with the preference of Pk-FKBP35 towards Xaa at P1 position was Leu>Phe>Lys>Trp>Val>Ile>His>Asp>Ala>Gln>Glu. Altogether, we proposed that protease-free and protease-coupling assays arereliable for Pk-FKBP35.

show abstract

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 94%

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 99%

Section: Stability Of Pk-fkbp35 Towards Chymotrypsinmentioning

confidence: 99%

See 1 more Smart Citation

REASSESSMENT OF THE CATALYTIC ACTIVITY AND SUBSTRATE SPECIFICITY OF FKBP35 FROM Plasmodium knowlesi USING PROTEASE-FREE ASSAY

Budiman¹,

Goh²,

Lee³

et al. 2020

BIJB

Self Cite

View full text Add to dashboard Cite

show abstract

DNA Binding Activity of Marine Shrimp LvProfilin

Laoong-u-thai¹,

Wanna²,

Kaikaew³

2021

j.asep

View full text Add to dashboard Cite

Shrimp farming is an important business in Thailand and worldwide. The study of molecular biology and biochemical pathway of the key molecules controlling muscle growth is an essential to improve shrimp livestock. Profilin is a pivotal protein in muscle formation, especially actin protein. Its nuclear function has been reported in many species for gene regulation. Here in this work, we characterized the function of LvProfilin, a marine shrimp profilin from Litopenaeus vannamei, both in silico and in vitro. The phylogenetic tree of LvProfilin among organisms and its 3D protein structure showed that LvProfilin was highly conserved among shrimp and arthropods. The homology modeling of its 3D structure revealed 3 alpha-helices and 6 beta-strands similar to most eukaryotic profilins. To interpret its possible function, the gene expression of LvProfilin in various tissues was performed. We found that this gene was expressed in various tissues. This result may imply that LvProfilin could share a common function in all tissues. Nuclear activity has been a promising function of LvProfilin. We performed a DNA/RNA binding prediction analysis using DRNApred. The result indicated that Lysine-90 and Threonine-91 were the putative DNA-binding sites with the probability of 63.12% and 54.16%, respectively. Its binding activity was confirmed in vitro which bound stronger to single strand DNA than double strand DNA. To our best knowledge, this is the first report of DNA binding activity of profilin in invertebrates.

show abstract

Thermal Stability Properties of A 35-KDa FK506-binding Protein of Plasmodium knowlesi

Sari¹,

Budiman²

2019

Asian J. of Biological Sciences

View full text Add to dashboard Cite

Structure and Molecular Dynamic Regulation of FKBP35 from Plasmodium knowlesi by Structural Homology Modeling and Electron Microscopy

Cited by 4 publications

References 48 publications

REASSESSMENT OF THE CATALYTIC ACTIVITY AND SUBSTRATE SPECIFICITY OF FKBP35 FROM Plasmodium knowlesi USING PROTEASE-FREE ASSAY

REASSESSMENT OF THE CATALYTIC ACTIVITY AND SUBSTRATE SPECIFICITY OF FKBP35 FROM Plasmodium knowlesi USING PROTEASE-FREE ASSAY

DNA Binding Activity of Marine Shrimp LvProfilin

Thermal Stability Properties of A 35-KDa FK506-binding Protein of Plasmodium knowlesi

Contact Info

Product

Resources

About