scholarly journals 3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

2021 ◽  
Vol 12 (2) ◽  
pp. 85
Author(s):  
Tina Zarkiyani ◽  
I Made Budiarsa ◽  
Astija Astija ◽  
Mursito S Bialangi
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Columba Livia ◽  
Dimensional Structure ◽  
Structural Quality ◽  
Three Dimensional Structure ◽  
3 Dimensional ◽  
Access Code ◽  
Development And Differentiation

The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.

scholarly journals Prediksi Struktur Tiga Dimensi Protein β-NGF (Nerve Growth Factor) Burung Merpati (Columba livia)

2020 ◽  
Vol 20 (2) ◽  
pp. 106
Author(s):  
Nur Alam ◽  
I Made Budiarsa ◽  
Dewi Tureni
Keyword(s):  
Nerve Growth Factor ◽  
Growth Factor ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Columba Livia ◽  
Dimensional Structure ◽  
Avian Embryo ◽  
Nerve Growth ◽  
Three Dimensional Structure ◽  
Access Code

Protein β-NGF berperan dalam kelangsungan hidup sel neuron dan diferensiasi embrio aves yang diekspresikan oleh gen NGF. Informasi protein β-NGF telah diidentifikasi pada ayam dan masih terbatas dilaporkan pada merpati. Tujuan penelitian adalah memprediksi struktur tiga dimensi protein β-NGF merpati untuk menambah informasi karakter proteinnya. Protein target diperoleh dari server UniProt dengan kode akses B4ZE95. Prediksi struktur tiga dimensi dan karakterisasi protein β-NGF menggunakan server SWISS-MODEL dan program Chimera. Hasil analisis menunjukkan bahwa protein β-NGF merpati dan template memiliki nilai identity sebesar 89,91%, QMEAN 0,51 serta GMQE sebesar 0,44. Struktur tiga dimensi protein B4ZE95 memiliki  asam amino hidrofobik (Ile, Leu, Trp, Phe, Val, Ala, Gly, Met, Cys); karboksil (Glu, Ser, Asp); amina (Lys, Thr) dengan 83 ikatan hidrogen.Kata kunci: columba livia, chimera, protein β-NGF, swiss-model Three Dimensional Protein Structure Prediction of β-NGF(Nerve Growth Factor) on Pigeon (Columba livia)ABSTRACTThe β-NGF protein plays a role in the survival of neuron cells and differentiation of avian embryo which is expressed by NGF gene. Information of β -NGF protein was identified in chicken and it is still limited reported in pigeon. The purpose of this study is to predict the three-dimensional structure of pigeon β-NGF protein to add information about its protein character. The target protein is obtained from UniProt server with access code B4ZE95. The prediction of three-dimensional structure and characterization of β-NGF protein were carried out using SWISS-MODEL server and Chimera program. The analysis showed that pigeon β-NGF protein and template had identity of 89,91%, QMEAN 0,51 and GMQE of 0,44. The three-dimensional structure of the B4ZE95 protein has hydrophobic amino acids namely (Ile, Leu, Trp, Phe, Val, Ala, Gly, Met, Cys); carboxyl namely (Glu, Ser, Asp); amine namely (Lys, Thr) with 83 hydrogen bonds.Keywords: columba livia, chimera, protein β-NGF, swiss model

Controlled chemical assembly of enzyme in cell lysate enabled by genetic-encoded nonstandard Amino Acid

2021 ◽  
Author(s):  
Jing Zhang ◽  
Ru Wang ◽  
Zhiyuan Luo ◽  
Dongmei Jia ◽  
Haoming Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Biological Materials ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Cell Lysate ◽  
Ordered Nanostructures

Enzyme proteins are nanometer-sized molecules with a three-dimensional structure that can be manipulated and assembled into highly ordered nanostructures, which allows access to advanced biological materials. Here, genetically-encoded nonstandard amino...

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 fromVicia villosa

FEBS Letters ◽  
1997 ◽  
Vol 412 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Eduardo Osinaga ◽  
Diana Tello ◽  
Carlos Batthyany ◽  
Mario Bianchet ◽  
Gisele Tavares ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Isolectin B4

scholarly journals Isocitrate dehydrogenase from bovine heart: primary structure of subunit 3/4

1995 ◽  
Vol 310 (2) ◽  
pp. 507-516 ◽  
Author(s):  
Y Zeng ◽  
C Weiss ◽  
T T Yao ◽  
J Huang ◽  
L Siconolfi-Baez ◽  
...  
Keyword(s):  
Amino Acid ◽  
Isocitrate Dehydrogenase ◽  
Three Dimensional ◽  
Alpha Subunit ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Three Dimensional Structure ◽  
Catalytic Function ◽  
N Terminus ◽  
Enzyme Subunits

Bovine NAD(+)-dependent isocitrate dehydrogenase was shown previously to contain four subunits of approx. 40 kDa (subunits 1-4) possessing different peptide maps and electrophoretic properties [Rushbrook and Harvey (1978) Biochemistry 17, 5339-5346]. In this study the heterogeneity is confirmed using enzyme purified by updated methods and from single animals, ruling out allelic variability. Subunits 1 and 2 were differentiated from each other and from subunits 3 and 4 by N-terminal amino acid sequencing. Subunits 3 and 4 (subunits 3/4) were identical in sequence over 30 residues. The N-terminal residues of subunits 1 and 2 were homologous but not identical with the beta- and gamma-subunits respectively of the comparable pig heart enzyme. Subunits 3/4 were identical over 30 residues with the N-terminus of the pig heart alpha-subunit. Full-length sequence, including that for mitochondrial import, is presented for a protein with the processed N-terminus of subunits 3/4, deduced from cloned cDNA obtained utilizing the N-terminal sequence information. The derived amino acid sequence for the mature protein contains 339 amino acids and has a molecular mass of 36,685 Da. Complete identity with N-terminal and Cys-containing peptides totalling 92 residues from the alpha-subunit of the pig heart enzyme [Huang and Colman (1990) Biochemistry 29, 8266-8273] suggests that maintenance of a particular three-dimensional structure in this subunit is crucial to the function of the enzyme. An electrophoretic heterogeneity within the pig heart alpha-subunit, similar to that shown by bovine subunits 3/4, was demonstrated. One reordering of the Cys-containing peptides of the pig heart alpha-subunit is indicated. Sequence comparison with the distantly related NADP(+)-dependent enzyme from Escherichia coli, for which the three-dimensional structure is known [Stoddard, Dean and Koshland (1993) Biochemistry 32, 9310-9316] shows strong conservation of residues binding isocitrate, Mg2+ and the NAD+ moiety of NADP+, consistent with a catalytic function.

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