scholarly journals Molecular Modeling of Cathepsin B protein in different Leishmania strains

2018 ◽  
Vol 8 (6-s) ◽  
pp. 224-226
Author(s):  
Jayprakash Mahato
Keyword(s):  
Protein Kinase ◽  
Cathepsin B ◽  
Phosphorylation Site ◽  
Three Dimensional ◽  
Cysteine Proteases ◽  
Glycosylation Site ◽  
Mammalian Host ◽  
Disulfide Bonding ◽  
Intracellular Protein Degradation ◽  
Kinase Phosphorylation

Cathepsin B like cysteine proteases representing a major component of the lysosomal proteolytic repertoire plays an important role in intracellular protein degradation. Comparative models of cathepsin B (CatB) protein of six different Leishmania strains were developed using MODELLER. The modeled three-dimensional (3-D) structure has the correct stereochemistry as gauged from the Ramachandran plot and good 3-D structure compatibility as assessed by PROCHECK and the DOPE score (DS2.1, Accelrys). The modeled proteins were energy minimized and validated using standard dynamic cascade protocol (DS 2.1). Seven different disulfide bonding sites are predicted in CatB protein of Leishmania. Two domains were identified and different motifs are present in catB protein of Leishmania like aspargine glycosylation site, protein kinase phosphorylation site, Protein kinase C activation site, N-myristoylation site. Considering that cathepsin B is essential for survival of Leishmania, including for virulence to the mammalian host, it may be viewed as an attractive drug target. Keyword: Molecular Modelling, Leishmania, Discover Studio, Protein Binding.   

Four distinct and unusual linker proteins in a mitotically dividing nucleus are derived from a 71-kilodalton polyprotein, lack p34cdc2 sites, and contain protein kinase A sites

1994 ◽  
Vol 14 (1) ◽  
pp. 10-20
Author(s):  
M Wu ◽  
C D Allis ◽  
M T Sweet ◽  
R G Cook ◽  
T H Thatcher ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinase A ◽  
Phosphorylation Site ◽  
High Mobility ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Associated Proteins ◽  
Kinase Phosphorylation ◽  
Kinase A

Tetrahymena thermophila micronuclei contain four linker-associated proteins, alpha, beta, gamma, and delta. Synthetic oligonucleotides based on N-terminal protein sequences of beta and gamma were used to clone the micronuclear linker histone (MLH) gene. The MLH gene is single copy and is transcribed into a 2.4-kb message encoding all four linker-associated proteins. The message is translated into a polypeptide (Mic LH) that is processed at the sequence decreases RTK to give proteins whose amino acid sequences differ markedly from each other, from the sequence of macronuclear H1, and from sequences of typical H1s of other organisms. This represents the first example of multiple chromatin proteins derived from a single polyprotein. The delta protein consists largely of two high-mobility-group (HMG) boxes. An evolutionary analysis of HMG boxes indicates that the delta HMG boxes are similar to the HMG boxes of tsHMG, a protein that appears in elongating mouse spermatids when they condense and cease transcription, suggesting that delta could play a similar role in the micronucleus. The micronucleus divides mitotically, while the macronucleus divides amitotically. Surprisingly, macronuclear H1 but not Mic LH contains sequences resembling p34cdc2 kinase phosphorylation sites, while each of the Mic LH-derived proteins contains a typical protein kinase A phosphorylation site in its carboxy terminus.

Complete Nucleotide Sequence Analysis of Outer Membrane Efflux Protein Gene of 1347bp ORF from Riemerella anatipestifer

2013 ◽  
Vol 647 ◽  
pp. 408-412
Author(s):  
Dan Dan Shen ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Protein Kinase ◽  
Outer Membrane ◽  
Protein Gene ◽  
Cell Attachment ◽  
Phosphorylation Site ◽  
Nucleotide Sequence Analysis ◽  
Phosphorylation Sites ◽  
Reading Frame ◽  
Riemerella Anatipestifer ◽  
Kinase Phosphorylation

A 1347bp complete open reading frame of the Riemerella anatipestifer outer membrane efflux protein﹙GenBank No.CP003388﹚was analyzed by bioinformatics software. The gene encoded a protein of 448 amino acids, Molecular weight was 50811.1. The formula of the outer membrane efflux protein gene is C2265H3639N609O689S12. There was no transmembrane region and signal peptide. six N-glycosylation sites, one cAMP- and cGMP-dependent protein kinase phosphorylation site, eight Protein kinase C phosphorylation sites, ten Casein kinase II phosphorylation sites, four Tyrosine kinase phosphorylation sites, five N-myristoylation sites, one Cell attachment sequence. The sequence of Riemerella anatipestifer outer membrane efflux protein shared high homology with other members of flavobacterium. These results will lay the foundation for further study.

Bioinformatics Analysis of OmpA/MotB Protein Encoded by OmpA/MotB Gene(ORF 648bp) of Riemerella anatipestifer

2013 ◽  
Vol 647 ◽  
pp. 304-309
Author(s):  
Xu Pan ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Jia Wang
Keyword(s):  
Protein Kinase ◽  
Phosphorylation Site ◽  
Evolutionary Relationship ◽  
Antigenic Determinants ◽  
Phosphorylation Sites ◽  
Dependent Protein ◽  
Relative Molecular Weight ◽  
Kinase Phosphorylation ◽  
Camp And Cgmp ◽  
Protein Kinase Phosphorylation Site

The OmpA/MotB gene from RA by our lab was sequenced. And the molecular characteristic of this gene was analyzed with bioinformatics software. The results indicated that this gene encodes an estimated 215 protein, contains the conserved domain of the OmpA-like protein. The relative molecular weight of the protein was 23.34525kDa, and there is no signal peptide and transmembrane region of the protein. One cAMP-and cGMP-dependent protein kinase phosphorylation site, six Protein kinase C phosphorylation sites, five Casein kinase II phosphorylation sites, five N-myristoylation sites and antigenic determinants were searched in the protein. Most of the total proteins were located in the Outer membrane and cytoplasmic. Phylogenetic tree of the amino acids sequences showed this gene has a close evolutionary relationship with Elizabethkingia anopheles Ag1 and Weeksella virosa DSM16922, indicating that the RA OmpA/MotB protein may have some similar functions with them. These results provided rational data to elucidate biological function and physiological features of the protein.

scholarly journals Four distinct and unusual linker proteins in a mitotically dividing nucleus are derived from a 71-kilodalton polyprotein, lack p34cdc2 sites, and contain protein kinase A sites.

1994 ◽  
Vol 14 (1) ◽  
pp. 10-20 ◽  
Author(s):  
M Wu ◽  
C D Allis ◽  
M T Sweet ◽  
R G Cook ◽  
T H Thatcher ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinase A ◽  
Phosphorylation Site ◽  
High Mobility ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Associated Proteins ◽  
Kinase Phosphorylation ◽  
Kinase A

Tetrahymena thermophila micronuclei contain four linker-associated proteins, alpha, beta, gamma, and delta. Synthetic oligonucleotides based on N-terminal protein sequences of beta and gamma were used to clone the micronuclear linker histone (MLH) gene. The MLH gene is single copy and is transcribed into a 2.4-kb message encoding all four linker-associated proteins. The message is translated into a polypeptide (Mic LH) that is processed at the sequence decreases RTK to give proteins whose amino acid sequences differ markedly from each other, from the sequence of macronuclear H1, and from sequences of typical H1s of other organisms. This represents the first example of multiple chromatin proteins derived from a single polyprotein. The delta protein consists largely of two high-mobility-group (HMG) boxes. An evolutionary analysis of HMG boxes indicates that the delta HMG boxes are similar to the HMG boxes of tsHMG, a protein that appears in elongating mouse spermatids when they condense and cease transcription, suggesting that delta could play a similar role in the micronucleus. The micronucleus divides mitotically, while the macronucleus divides amitotically. Surprisingly, macronuclear H1 but not Mic LH contains sequences resembling p34cdc2 kinase phosphorylation sites, while each of the Mic LH-derived proteins contains a typical protein kinase A phosphorylation site in its carboxy terminus.

scholarly journals A three-dimensional model of the Cdc2 protein kinase: localization of cyclin- and Suc1-binding regions and phosphorylation sites

1993 ◽  
Vol 13 (8) ◽  
pp. 5122-5131
Author(s):  
M J Marcote ◽  
D R Knighton ◽  
G Basi ◽  
J M Sowadski ◽  
P Brambilla ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Binding Sites ◽  
Phosphorylation Site ◽  
Three Dimensional ◽  
Cyclin A ◽  
Sequence Motif ◽  
Three Dimensional Model ◽  
Alanine Scanning Mutagenesis ◽  
Catalytic Core ◽  
Peptide Recognition

The Cdc2 protein kinase requires cyclin binding for activity and also binds to a small protein, Suc1. Charged-to-alanine scanning mutagenesis of Cdc2 was used previously to localize cyclin A- and B- and Suc1-binding sites (B. Ducommun, P. Brambilla, and G. Draetta, Mol. Cell. Biol. 11:6177-6184, 1991). Those sites were mapped by building a Cdc2 model based on the crystallographic coordinates of the catalytic subunit of cyclic AMP-dependent protein kinase (cAPK) (D. R. Knighton, J. Zheng, L. F. Ten Eyck, V. A. Ashford, N.-H. Xuong, S. S. Taylor, and J. M. Sowadski, Science 253:407-414, 1991). On the basis of this model, additional mutations were made and tested for cyclin A and Suc1 binding and for kinase activity. Mutations that interfere with cyclin A binding are localized primarily on the small lobe near its interface with the cleft and include an acidic patch on the B helix and R-50 in the highly conserved PSTAIRE sequence. Two residues in the large lobe, R-151 and T-161, influence cyclin binding, and both are at the surface of the cleft near its interface with the PSTAIRE motif. Cyclin-dependent phosphorylation of T-161 in Cdc2 is essential for activation, and the model provides insights into the importance of this site. T-161 is equivalent to T-197, a stable phosphorylation site in cAPK. On the basis of the model, cyclin binding very likely alters the surface surrounding T-161 to allow for T-161 phosphorylation. The two major ligands to T-197 in cAPK are conserved as R-127 and R-151 in Cdc2. The equivalent of the third ligand, H-87, is T-47 in the PSTAIRE sequence motif. Once phosphorylated, T-161 is predicted to play a major structural role in Cdc2, comparable to that of T-197 in cAPK, by assembling the active conformation required for peptide recognition. The inhibitory phosphorylation at Y-15 also comes close to the cleft interface and on the basis of this model would disrupt the cleft interface and the adjacent peptide recognition site rather than prevent ATP binding. In contrast to cyclin A, both lobes influence Suc1 binding; however, the Suc1-binding sites are far from the active site. Several mutants map to the surface in cAPK, which is masked in part by the N-terminal 40 residues that lie outside the conserved catalytic core. The other Suc1-binding site maps to the large lobe near a 25-residue insert and includes R-215.

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